Biochemistry

An introduction
Contents

1 Cells and water 1

1.1 Biochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
1.1.2 Starting materials: the chemical elements of life . . . . . . . . . . . . . . . . . . . . . . . 2
1.1.3 Biomolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.1.4 Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.5 Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.1.6 Lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.1.7 Nucleic acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.1.8 Relationship to other “molecular-scale” biological sciences . . . . . . . . . . . . . . . . . . 7
1.1.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.1.10 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.1.11 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.1.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.2 Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.2.1 Anatomy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.2.2 Subcellular components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.2.3 Structures outside the cell membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
1.2.4 Cellular processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
1.2.5 Multicellularity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
1.2.6 Origins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.2.7 History of research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
1.2.8 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.2.9 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
1.2.10 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.3 Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
1.3.1 Chemical and physical properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
1.3.2 Taste and odor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
1.3.3 Distribution in nature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
1.3.4 On Earth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
1.3.5 Effects on life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
1.3.6 Effects on human civilization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

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1.3.7 Law, politics, and crisis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

1.3.8 In culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
1.3.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
1.3.10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
1.3.11 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
1.3.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

2 Structural Biochemistry 39

3 Nucleic acids 40
3.1 Nucleic acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.1.1 Occurrence and nomenclature[7] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
[15]
3.1.2 Molecular composition and size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.1.3 Topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.1.4 Nucleic acid sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.1.5 Types of nucleic acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.1.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
3.1.7 Notes and references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
3.1.8 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.1.9 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.2 RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.2.1 Comparison with DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
3.2.2 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.2.3 Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.2.4 Types of RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.2.5 Key discoveries in RNA biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
3.2.6 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.2.7 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.2.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.2.9 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.3 DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.3.1 Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.3.2 Chemical modifications and altered DNA packaging . . . . . . . . . . . . . . . . . . . . . 57
3.3.3 Biological functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
3.3.4 Interactions with proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
3.3.5 Genetic recombination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
3.3.6 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
3.3.7 Uses in technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.3.8 History of DNA research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.3.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.3.10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
3.3.11 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
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3.3.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

4 Proteins and amino acids 75

4.1 Protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.1.1 Biochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.1.2 Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
4.1.3 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
4.1.4 Cellular functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
4.1.5 Methods of study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
4.1.6 Nutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.1.7 History and etymology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
4.1.8 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
4.1.9 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
4.1.10 Textbooks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
4.1.11 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
4.2 Amino acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
4.2.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
4.2.2 General structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
4.2.3 Occurrence and functions in biochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . 90
4.2.4 Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.2.5 Uses in industry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.2.6 Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.2.7 Physicochemical properties of amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4.2.8 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4.2.9 References and notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
4.2.10 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
4.2.11 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
4.3 Properties of the twenty amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
4.3.1 Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
4.3.2 Non-specific abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
4.3.3 Chemical properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
4.3.4 Life based on alternative proteinogenic sets . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.3.5 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.3.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.4 Myoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
4.4.1 Meat color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.4.2 Role in disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.4.3 Structure and bonding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.4.4 Synthetic analogues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.4.5 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
4.4.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
4.4.7 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
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4.4.8 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

4.5 Hemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
4.5.1 Research history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
4.5.2 Genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
4.5.3 Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.5.4 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.5.5 Iron’s oxidation state in oxyhemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
4.5.6 Cooperativity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
4.5.7 Binding for ligands other than oxygen . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
4.5.8 Types in humans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
4.5.9 Degradation in vertebrate animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
4.5.10 Role in disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
4.5.11 Diagnostic uses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.5.12 Analogues in non-vertebrate organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.5.13 Other oxygen-binding proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
4.5.14 Presence in nonerythroid cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.5.15 In history, art and music . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.5.16 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.5.17 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.5.18 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
4.5.19 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

5 Enzyme mechanisms 121

5.1 Enzyme catalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.1.1 Induced fit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.1.2 Mechanisms of an alternative reaction route . . . . . . . . . . . . . . . . . . . . . . . . . 122
5.1.3 Examples of catalytic mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
5.1.4 Enzyme diffusivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.1.5 Reaction Similarity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.1.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.1.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
5.1.8 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

6 Enzyme kinetics 128

6.1 Enzyme kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
6.1.1 General principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
6.1.2 Enzyme assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
6.1.3 Single-substrate reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
6.1.4 Multi-substrate reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
6.1.5 Non-Michaelis–Menten kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
6.1.6 Pre-steady-state kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
6.1.7 Chemical mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
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6.1.8 Enzyme inhibition and activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

6.1.9 Mechanisms of catalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.1.10 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.1.11 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.1.12 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
6.1.13 Footnotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.1.14 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.1.15 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
6.1.16 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

7 Lipids and membranes 141

7.1 Lipid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
7.1.1 Categories of lipids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
7.1.2 Biological functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
7.1.3 Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
7.1.4 Nutrition and health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
7.1.5 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
7.1.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
7.1.7 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
7.2 Biological membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
7.2.1 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
7.2.2 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.2.3 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.2.4 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.3 Membrane protein . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.3.1 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
7.3.2 Topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
7.3.3 3D Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
7.3.4 Membrane proteins in genomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
7.3.5 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
7.3.6 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
7.3.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
7.4 Cell membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
7.4.1 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
7.4.2 Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
7.4.3 Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
7.4.4 Composition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
7.4.5 Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
7.4.6 Permeability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
7.4.7 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
7.4.8 Notes and references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
7.4.9 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
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8 Carbohydrate structure 161

8.1 Carbohydrate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
8.1.1 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
8.1.2 Monosaccharides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
8.1.3 Disaccharides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
8.1.4 Nutrition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
8.1.5 Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
8.1.6 Carbohydrate chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
8.1.7 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
8.1.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
8.1.9 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
8.2 Polysaccharide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
8.2.1 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
8.2.2 Storage polysaccharides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
8.2.3 Structural polysaccharides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
8.2.4 Acidic polysaccharides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
8.2.5 Bacterial capsular polysaccharides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
8.2.6 Chemical identification tests for polysaccharides . . . . . . . . . . . . . . . . . . . . . . . 170
8.2.7 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
8.2.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
8.2.9 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170

9 Intermediary metabolism 171

10 Metabolism 172
10.1 Overview of metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
10.1.1 Key biochemicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
10.1.2 Catabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
10.1.3 Energy transformations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
10.1.4 Anabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
10.1.5 Xenobiotics and redox metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
10.1.6 Thermodynamics of living organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
10.1.7 Regulation and control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
10.1.8 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
10.1.9 Investigation and manipulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
10.1.10 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
10.1.11 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
10.1.12 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
10.1.13 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
10.1.14 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188

11 Carbohydrate metabolism 190

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11.1 Glycolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190

11.1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
11.1.2 Elucidation of the pathway . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
11.1.3 Sequence of reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
11.1.4 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
11.1.5 Post-glycolysis processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
11.1.6 Intermediates for other pathways = . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
11.1.7 Glycolysis in disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
11.1.8 Interactive pathway map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
11.1.9 Alternative nomenclature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
11.1.10 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
11.1.11 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
11.1.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
11.2 Gluconeogenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
11.2.1 Precursors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
11.2.2 Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
11.2.3 Pathway . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
11.2.4 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
11.2.5 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
11.2.6 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
11.3 Glycogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
11.3.1 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
11.3.2 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
11.3.3 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
11.3.4 Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
11.3.5 Clinical relevance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
11.3.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
11.3.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
11.3.8 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
11.4 Pentose phosphate pathway . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
11.4.1 Outcome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
11.4.2 Phases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
11.4.3 Erythrocytes and the pentose phosphate pathway . . . . . . . . . . . . . . . . . . . . . . . 208
11.4.4 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
11.4.5 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
11.4.6 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208

12 Citric acid cycle 209

12.1 Citric acid cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
12.1.1 Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
12.1.2 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
12.1.3 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
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12.1.4 Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210

12.1.5 Products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
12.1.6 Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210
12.1.7 Variation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
12.1.8 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
12.1.9 Major metabolic pathways converging on the TCA cycle . . . . . . . . . . . . . . . . . . 212
12.1.10 Citric acid cycle intermediates serve as substrates for biosynthetic processes . . . . . . . . 212
12.1.11 Interactive pathway map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
12.1.12 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
12.1.13 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
12.1.14 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217

13 Oxidative phosphorylation 218

13.1 Oxidative phosphorylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
13.1.1 Overview of energy transfer by chemiosmosis . . . . . . . . . . . . . . . . . . . . . . . . 218
13.1.2 Electron and proton transfer molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
13.1.3 Eukaryotic electron transport chains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
13.1.4 Prokaryotic electron transport chains . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
13.1.5 ATP synthase (complex V) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
13.1.6 Reactive oxygen species . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
13.1.7 Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
13.1.8 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
13.1.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
13.1.10 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
13.1.11 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
13.1.12 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
13.1.13 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230

14 Photosynthesis 231
14.1 Photosynthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
14.1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
14.1.2 Photosynthetic membranes and organelles . . . . . . . . . . . . . . . . . . . . . . . . . . 233
14.1.3 Light-dependent reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
14.1.4 Light-independent reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
14.1.5 Order and kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
14.1.6 Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
14.1.7 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
14.1.8 Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 238
14.1.9 Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
14.1.10 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
14.1.11 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
14.1.12 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
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14.1.13 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243

15 Lipid metabolism 244

15.1 Fatty acid synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
15.1.1 Straight-chain fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
15.1.2 Branched-chain fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
15.1.3 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
15.1.4 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
15.1.5 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
15.2 Lipogenesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
15.2.1 Fatty acid synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
15.2.2 Fatty acid esterification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
15.2.3 In industry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
15.2.4 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
15.3 Acetyl-CoA carboxylase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
15.3.1 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
15.3.2 Mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
15.3.3 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
15.3.4 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
15.3.5 Clinical implications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
15.3.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
15.3.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
15.3.8 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
15.4 Fatty acid degradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
15.4.1 Lipolysis and release . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
15.4.2 Activation and transport into mitochondria . . . . . . . . . . . . . . . . . . . . . . . . . . 254
15.4.3 β-oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
15.4.4 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
15.4.5 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
15.5 Beta oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
15.5.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
15.5.2 Activation and membrane transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
15.5.3 General mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
15.5.4 Even-numbered saturated fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
15.5.5 Odd-numbered saturated fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
15.5.6 Unsaturated fatty acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
15.5.7 Peroxisomal beta-oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
15.5.8 Energy yield . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
15.5.9 History and discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
15.5.10 Clinical significance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
15.5.11 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
15.5.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
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15.5.13 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258

16 Nitrogen metabolism 259

16.1 Nitrogen fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
16.1.1 Biological nitrogen fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
16.1.2 Industrial nitrogen fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
16.1.3 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
16.1.4 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
16.1.5 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
16.2 Amino acid synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
16.2.1 Nitrogen fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
16.2.2 Transamination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
16.2.3 From intermediates of the citric acid cycle and other pathways . . . . . . . . . . . . . . . 264
16.2.4 Regulation by feedback inhibition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
16.2.5 Amino acids as precursors to other biomolecules . . . . . . . . . . . . . . . . . . . . . . 268
16.2.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
16.2.7 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
16.3 Nucleotide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
16.3.1 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
16.3.2 Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
16.3.3 Unnatural base pair (UBP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
16.3.4 Length unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
16.3.5 Abbreviation codes for degenerate bases . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
16.3.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
16.3.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
16.3.8 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
16.4 Urea cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
16.4.1 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
16.4.2 Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
16.4.3 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
16.4.4 Pathology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
16.4.5 Additional images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
16.4.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
16.4.7 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

17 Integration of metabolism 276

17.1 Hormone . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
17.1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
17.1.2 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
17.1.3 Receptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
17.1.4 Effects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
17.1.5 Chemical classes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
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17.1.6 Therapeutic use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278

17.1.7 Hormone-behavior interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
17.1.8 Comparison with neurotransmitters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
17.1.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
17.1.10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
17.1.11 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
17.2 Signal transduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
17.2.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
17.2.2 Environmental stimuli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
17.2.3 Receptors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
17.2.4 Cellular responses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
17.2.5 Major pathways . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
17.2.6 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
17.2.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
17.2.8 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
17.3 Diabetes mellitus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
17.3.1 Signs and symptoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
17.3.2 Causes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
17.3.3 Pathophysiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
17.3.4 Diagnosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
17.3.5 Prevention . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
17.3.6 Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
17.3.7 Epidemiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
17.3.8 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
17.3.9 Society and culture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
17.3.10 Other animals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
17.3.11 Research . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
17.3.12 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
17.3.13 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
17.3.14 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298

18 Informational Macromolecules 299

19 DNA synthesis and repair 300

19.1 DNA replication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
19.1.1 Background on DNA structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
19.1.2 DNA polymerase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 301
19.1.3 Replication process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
19.1.4 Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
19.1.5 Polymerase chain reaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
19.1.6 Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
19.1.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
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19.2 DNA repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308

19.2.1 DNA damage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
19.2.2 DNA repair mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
19.2.3 Global response to DNA damage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
19.2.4 DNA repair and aging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
19.2.5 Medicine and DNA repair modulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316
19.2.6 DNA repair and cancer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316
19.2.7 DNA repair and evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
19.2.8 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
19.2.9 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
19.2.10 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
19.3 Oncogenes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
19.3.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
19.3.2 Proto-oncogene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
19.3.3 Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
19.3.4 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
19.3.5 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
19.3.6 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325

20 RNA synthesis and processing 326

20.1 Transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
20.1.1 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
20.1.2 Major steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
20.1.3 Inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
20.1.4 Transcription factories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
20.1.5 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
20.1.6 Measuring and detecting transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
20.1.7 Reverse transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
20.1.8 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330
20.1.9 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330
20.1.10 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
20.2 Regulation of gene expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
20.2.1 Regulated stages of gene expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
20.2.2 Modification of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
20.2.3 Regulation of transcription . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
20.2.4 Post-transcriptional regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
20.2.5 Regulation of translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
20.2.6 Examples of gene regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
20.2.7 Circuitry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
20.2.8 Study methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
20.2.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
20.2.10 Notes and references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
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20.2.11 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336

20.2.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336

21 Protein synthesis and modifications 337

21.1 Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
21.1.1 Basic mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
21.1.2 Genetic code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
21.1.3 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
21.1.4 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
21.1.5 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
21.1.6 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
21.2 Posttranslational modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
21.2.1 PTMs involving addition of functional groups . . . . . . . . . . . . . . . . . . . . . . . . 341
21.2.2 Other proteins or peptides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
21.2.3 Chemical modification of amino acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
21.2.4 Structural changes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
21.2.5 Post-translational modification statistics . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
21.2.6 Case examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
21.2.7 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
21.2.8 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
21.2.9 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
21.3 Glycosaminoglycans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
21.3.1 Production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
21.3.2 Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
21.3.3 Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
21.3.4 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
21.3.5 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
21.3.6 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
21.4 Proteolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
21.4.1 Post-translational proteolytic processing . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
21.4.2 Protein degradation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
21.4.3 Proteolysis in cellular regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
21.4.4 Regulatory domains in proteolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
21.4.5 Proteolysis and diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
21.4.6 Non-enzymatic proteolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
21.4.7 Laboratory applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
21.4.8 Venoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
21.4.9 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
21.4.10 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
21.4.11 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
21.4.12 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
21.5 Proteasome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
xiv CONTENTS

21.5.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352

21.5.2 Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
21.5.3 Structure and organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
21.5.4 Assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
21.5.5 The protein degradation process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
21.5.6 Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
21.5.7 Cell cycle control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
21.5.8 Response to cellular stress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
21.5.9 Role in the immune system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360
21.5.10 Proteasome inhibitors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360
21.5.11 Clinical significance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
21.5.12 See also . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
21.5.13 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
21.5.14 Further reading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
21.5.15 External links . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367

22 Text and image sources, contributors, and licenses 368

22.1 Text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368
22.2 Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
22.3 Content license . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Chapter 1

Cells and water

1.1 Biochemistry vestigate soil and fertilizers, and try to discover ways to
improve crop cultivation, crop storage and pest control.
For the journal, see Biochemistry (journal).
“Biological Chemistry” redirects here. For the journal
formerly named Biological Chemistry Hoppe-Seyler, see
1.1.1 History
Biological Chemistry (journal).
Main article: History of biochemistry
It once was generally believed that life and its materi-
Biochemistry, sometimes called biological chemistry,
is the study of chemical processes within and relating
to living organisms.[1] By controlling information flow
through biochemical signaling and the flow of chemical
energy through metabolism, biochemical processes give
rise to the complexity of life. Over the last 40 years,
biochemistry has become so successful at explaining liv-
ing processes that now almost all areas of the life sci-
ences from botany to medicine are engaged in biochem-
ical research.[2] Today, the main focus of pure biochem-
istry is in understanding how biological molecules give
rise to the processes that occur within living cells, which
in turn relates greatly to the study and understanding of
whole organisms.
Biochemistry is closely related to molecular biology, the
study of the molecular mechanisms by which genetic in-
formation encoded in DNA is able to result in the pro-
cesses of life. Depending on the exact definition of the
terms used, molecular biology can be thought of as a
branch of biochemistry, or biochemistry as a tool with
which to investigate and study molecular biology.
Much of biochemistry deals with the structures, functions
and interactions of biological macromolecules, such as
proteins, nucleic acids, carbohydrates and lipids, which Gerty Cori and Carl Cori jointly won the Nobel Prize in 1947 for
their discovery of the Cori cycle at RPMI.
provide the structure of cells and perform many of the
functions associated with life. The chemistry of the cell
also depends on the reactions of smaller molecules and als had some essential property or substance (often re-
ions. These can be inorganic, for example water and ferred to as the "vital principle") distinct from any found
metal ions, or organic, for example the amino acids which in non-living matter, and it was thought that only living
are used to synthesize proteins. The mechanisms by beings could produce the molecules of life.[3] Then, in
which cells harness energy from their environment via 1828, Friedrich Wöhler published a paper on the synthe-
chemical reactions are known as metabolism. The find- sis of urea, proving that organic compounds can be cre-
ings of biochemistry are applied primarily in medicine, ated artificially.[4]
nutrition, and agriculture. In medicine, biochemists in- The beginning of biochemistry may have been the discov-
vestigate the causes and cures of disease. In nutrition, ery of the first enzyme, diastase (today called amylase),
they study how to maintain health and study the effects in 1833 by Anselme Payen.[5] Eduard Buchner con-
of nutritional deficiencies. In agriculture, biochemists in- tributed the first demonstration of a complex biochem-

1
2 CHAPTER 1. CELLS AND WATER

ical process outside a cell in 1896: alcoholic fermenta- 1.1.3 Biomolecules

tion in cell extracts of yeast.[6] Although the term “bio-
chemistry” seems to have been first used in 1882, it The four main classes of molecules in biochemistry
is generally accepted that the formal coinage of bio- (often called biomolecules) are carbohydrates, lipids,
chemistry occurred in 1903 by Carl Neuberg, a German proteins, and nucleic acids. Many biological molecules
chemist.[7] Since then, biochemistry has advanced, es- are polymers: in this terminology, monomers are rela-
pecially since the mid-20th century, with the develop- tively small micromolecules that are linked together to
ment of new techniques such as chromatography, X-ray create large macromolecules known as polymers. When
diffraction, dual polarisation interferometry, NMR spec- monomers are linked together to synthesize a biological
troscopy, radioisotopic labeling, electron microscopy, polymer, they undergo a process called dehydration syn-
and molecular dynamics simulations. These techniques thesis. Different macromolecules can assemble in larger
allowed for the discovery and detailed analysis of many complexes, often needed for biological activity.
molecules and metabolic pathways of the cell, such as
glycolysis and the Krebs cycle (citric acid cycle).
Carbohydrates
Another significant historic event in biochemistry is the
discovery of the gene and its role in the transfer of in- Main articles: Carbohydrate, Monosaccharide,
formation in the cell. This part of biochemistry is of- Disaccharide and Polysaccharide
ten called molecular biology.[8] In the 1950s, James D. Carbohydrates are made from monomers called
Watson, Francis Crick, Rosalind Franklin, and Maurice
Wilkins were instrumental in solving DNA structure
and suggesting its relationship with genetic transfer of
information.[9] In 1958, George Beadle and Edward
Tatum received the Nobel Prize for work in fungi show-
ing that one gene produces one enzyme.[10] In 1988,
Colin Pitchfork was the first person convicted of mur-
der with DNA evidence, which led to growth of forensic
science.[11] More recently, Andrew Z. Fire and Craig C.
Mello received the 2006 Nobel Prize for discovering the
role of RNA interference (RNAi), in the silencing of gene
A molecule of sucrose (glucose + fructose), a disaccharide.
expression.[12]
monosaccharides. Some of these monosaccharides
include glucose (C6 H12 O6 ), fructose (C6 H12 O6 ), and
deoxyribose (C5 H10 O4 ). When two monosaccharides
1.1.2 Starting materials: the chemical ele- undergo dehydration synthesis, water is produced, as two
ments of life hydrogen atoms and one oxygen atom are lost from the
two monosaccharides’ hydroxyl group.
Main articles: Composition of the human body and
Dietary mineral Lipids

Around two dozen of the 92 naturally occurring chemical Main articles: Lipid, Glycerol and Fatty acid
elements are essential to various kinds of biological life. Lipids are usually made from one molecule of glycerol
Most rare elements on Earth are not needed by life (ex-
ceptions being selenium and iodine), while a few com-
mon ones (aluminum and titanium) are not used. Most
organisms share element needs, but there are a few dif-
ferences between plants and animals. For example ocean
algae use bromine but land plants and animals seem to
need none. All animals require sodium, but some plants
do not. Plants need boron and silicon, but animals may
not (or may need ultra-small amounts).
Just six elements—carbon, hydrogen, nitrogen, oxygen, A triglyceride with a glycerol molecule on the left and three fatty
calcium, and phosphorus—make up almost 99% of the acids coming off it.
mass of a human body (see composition of the human
body for a complete list). In addition to the six major combined with other molecules. In triglycerides, the main
elements that compose most of the human body, humans group of bulk lipids, there is one molecule of glycerol and
require smaller amounts of possibly 18 more.[13] three fatty acids. Fatty acids are considered the monomer
1.1. BIOCHEMISTRY 3

in that case, and may be saturated (no double bonds in the Thymine
carbon chain) or unsaturated (one or more double bonds Adenine
in the carbon chain). 5′ end O− O
O
NH 2 3′ end
P
Lipids, especially phospholipids, are also used in various −O
O
N
N
HN
N
OH

pharmaceutical products, either as co-solubilisers (e.g., in O N

N O O

parenteral infusions) or else as drug carrier components O O−

(e.g., in a liposome or transfersome). O P

O NH 2 O
N
P O
O
O
−O
N HN N
O N
N
O
O H2N

Proteins O O−
Phosphate- O O H2N
N
P O
O
deoxyribose O P O
O
−
Main articles: Protein and Amino acid backbone
O N
NH N N

N
Proteins are very large molecules – macro-biopolymers O
O

O O−
H2N P
O O
O
O P
N O
−O O N
NH N

O N
N O O
NH 2

O O−
OH P
3′ end Cytosine −O
O

Guanine 5′ end

The structure of deoxyribonucleic acid (DNA), the picture shows

the monomers being put together.

Nucleic acids are the molecules that make up DNA, an

extremely important substance that all cellular organ-
isms use to store their genetic information. The most
The general structure of an α-amino acid, with the amino group common nucleic acids are deoxyribonucleic acid (DNA)
on the left and the carboxyl group on the right. and ribonucleic acid (RNA). Their monomers are called
nucleotides. A nucleotide consists of a phosphate group,
– made from monomers called amino acids. There are 20 a ribose sugar, and a nitrogenous base. The phosphate
standard amino acids, each containing a carboxyl group, group and the sugar of each nucleotide bond with each
an amino group, and a side-chain (known as an “R” other to form the backbone of the nucleic acid, while
group). The “R” group is what makes each amino acid the sequence of nitrogenous bases stores the informa-
different, and the properties of the side-chains greatly in- tion. The most common nitrogenous bases are adenine,
fluence the overall three-dimensional conformation of a cytosine, guanine, thymine, and uracil. The nitrogenous
protein. When amino acids combine, they form a special bases of each strand of a nucleic acid will form hydrogen
bond called a peptide bond through dehydration synthe- bonds with certain other nitrogenous bases in a comple-
sis, and become a polypeptide, or protein. mentary strand of nucleic acid (similar to a zipper). Ade-
In order to determine whether two proteins are related, or nine binds with thymine and uracil; Thymine binds only
in other words to decide whether they are homologous or with adenine; and cytosine and guanine can bind only with
not, scientists use sequence-comparison methods. Meth- one another.
ods like Sequence Alignments and Structural Alignments
are powerful tools that help scientists identify homologies
between related molecules.[14]
The relevance of finding homologies among proteins goes
1.1.4 Carbohydrates
beyond forming an evolutionary pattern of protein fam-
ilies. By finding how similar two protein sequences are, Main article: Carbohydrate
we acquire knowledge about their structure and therefore
their function. The function of carbohydrates includes energy storage
and providing structure. Sugars are carbohydrates, but
not all carbohydrates are sugars. There are more car-
Nucleic acids bohydrates on Earth than any other known type of
biomolecule; they are used to store energy and genetic
Main articles: Nucleic acid, DNA, RNA and Nucleotides information, as well as play important roles in cell to cell
interactions and communications.
4 CHAPTER 1. CELLS AND WATER

Monosaccharides molecule, consisting of two monosaccharides, is called a

disaccharide and is conjoined together by a glycosidic or
ether bond. The reverse reaction can also occur, using a
molecule of water to split up a disaccharide and break the
glycosidic bond; this is termed hydrolysis. The most well-
known disaccharide is sucrose, ordinary sugar (in scien-
tific contexts, called table sugar or cane sugar to differen-
tiate it from other sugars). Sucrose consists of a glucose
molecule and a fructose molecule joined together. An-
other important disaccharide is lactose, consisting of a
glucose molecule and a galactose molecule. As most hu-
mans age, the production of lactase, the enzyme that hy-
Glucose
drolyzes lactose back into glucose and galactose, typically
decreases. This results in lactase deficiency, also called
lactose intolerance.
The simplest type of carbohydrate is a monosaccharide,
which between other properties contains carbon, hydro- Sugar polymers are characterized by having reducing or
gen, and oxygen, mostly in a ratio of 1:2:1 (generalized non-reducing ends. A reducing end of a carbohydrate is
formula CnH₂nOn, where n is at least 3). Glucose, one a carbon atom that can be in equilibrium with the open-
of the most important carbohydrates, is an example of chain aldehyde or keto form. If the joining of monomers
a monosaccharide. So is fructose, the sugar commonly takes place at such a carbon atom, the free hydroxy group
associated with the sweet taste of fruits.[15][a] Some car- of the pyranose or furanose form is exchanged with an
bohydrates (especially after condensation to oligo- and OH-side-chain of another sugar, yielding a full acetal.
polysaccharides) contain less carbon relative to H and O, This prevents opening of the chain to the aldehyde or
which still are present in 2:1 (H:O) ratio. Monosaccha- keto form and renders the modified residue non-reducing.
rides can be grouped into aldoses (having an aldehyde Lactose contains a reducing end at its glucose moiety,
group at the end of the chain, e.g. glucose) and ketoses whereas the galactose moiety form a full acetal with the
(having a keto group in their chain; e.g. fructose). Both C4-OH group of glucose. Saccharose does not have a re-
aldoses and ketoses occur in an equilibrium (starting with ducing end because of full acetal formation between the
chain lengths of C4) cyclic forms. These are generated by aldehyde carbon of glucose (C1) and the keto carbon of
bond formation between one of the hydroxyl groups of fructose (C2).
the sugar chain with the carbon of the aldehyde or keto
group to form a hemiacetal bond. This leads to saturated
five-membered (in furanoses) or six-membered (in pyra- Oligosaccharides and polysaccharides
noses) heterocyclic rings containing one O as heteroatom.

Disaccharides

CH2OH
CH2OH
H O H O H
H
OH H O H HO Cellulose as polymer of β-D-glucose
HO CH2OH
When a few (around three to six) monosaccharides are
H OH OH H joined, it is called an oligosaccharide (oligo- meaning
“few”). These molecules tend to be used as markers
Sucrose: ordinary table sugar and probably the most familiar and signals, as well as having some other uses. Many
carbohydrate. monosaccharides joined together make a polysaccharide.
They can be joined together in one long linear chain,
Two monosaccharides can be joined using dehydration or they may be branched. Two of the most common
synthesis, in which a hydrogen atom is removed from polysaccharides are cellulose and glycogen, both consist-
the end of one molecule and a hydroxyl group (—OH) ing of repeating glucose monomers.
is removed from the other; the remaining residues are
then attached at the sites from which the atoms were • Cellulose is made by plants and is an important struc-
removed. The H—OH or H2 O is then released as a tural component of their cell walls. Humans can nei-
molecule of water, hence the term dehydration. The new ther manufacture nor digest it.
1.1. BIOCHEMISTRY 5

• Glycogen, on the other hand, is an animal carbohy- glucose provides an organism with far more energy than
drate; humans and other animals use it as a form of any oxygen-independent metabolic feature, and this is
energy storage. thought to be the reason why complex life appeared only
after Earth’s atmosphere accumulated large amounts of
oxygen.
Use of carbohydrates as an energy source

Main article: Carbohydrate metabolism Gluconeogenesis Main article: Gluconeogenesis

Glucose is the major energy source in most life forms. In vertebrates, vigorously contracting skeletal muscles
For instance, polysaccharides are broken down into (during weightlifting or sprinting, for example) do not re-
their monomers (glycogen phosphorylase removes glu- ceive enough oxygen to meet the energy demand, and so
cose residues from glycogen). Disaccharides like lactose they shift to anaerobic metabolism, converting glucose to
or sucrose are cleaved into their two component monosac- lactate. The liver regenerates the glucose, using a process
charides. called gluconeogenesis. This process is not quite the op-
posite of glycolysis, and actually requires three times the
amount of energy gained from glycolysis (six molecules
Glycolysis (anaerobic) Glucose is mainly metabolized of ATP are used, compared to the two gained in gly-
by a very important ten-step pathway called glycolysis, colysis). Analogous to the above reactions, the glucose
the net result of which is to break down one molecule of produced can then undergo glycolysis in tissues that need
glucose into two molecules of pyruvate; this also produces energy, be stored as glycogen (or starch in plants), or be
a net two molecules of ATP, the energy currency of cells, converted to other monosaccharides or joined into di- or
along with two reducing equivalents as converting NAD+ oligosaccharides. The combined pathways of glycolysis
to NADH. This does not require oxygen; if no oxygen is during exercise, lactate’s crossing via the bloodstream to
available (or the cell cannot use oxygen), the NAD is re- the liver, subsequent gluconeogenesis and release of glu-
stored by converting the pyruvate to lactate (lactic acid) cose into the bloodstream is called the Cori cycle.[17]
(e.g., in humans) or to ethanol plus carbon dioxide (e.g.,
in yeast). Other monosaccharides like galactose and fruc-
tose can be converted into intermediates of the glycolytic 1.1.5 Proteins
pathway.[16]
Main article: Protein
Like carbohydrates, some proteins perform largely struc-
Aerobic In aerobic cells with sufficient oxygen, as in
most human cells, the pyruvate is further metabolized.
It is irreversibly converted to acetyl-CoA, giving off one
carbon atom as the waste product carbon dioxide, gen-
erating another reducing equivalent as NADH. The two
molecules acetyl-CoA (from one molecule of glucose)
then enter the citric acid cycle, producing two more
molecules of ATP, six more NADH molecules and two
reduced (ubi)quinones (via FADH2 as enzyme-bound co-
factor), and releasing the remaining carbon atoms as car-
bon dioxide. The produced NADH and quinol molecules
then feed into the enzyme complexes of the respiratory
chain, an electron transport system transferring the elec-
trons ultimately to oxygen and conserving the released en-
ergy in the form of a proton gradient over a membrane
(inner mitochondrial membrane in eukaryotes). Thus,
oxygen is reduced to water and the original electron ac-
ceptors NAD+ and quinone are regenerated. This is why
humans breathe in oxygen and breathe out carbon diox-
ide. The energy released from transferring the electrons
from high-energy states in NADH and quinol is conserved A schematic of hemoglobin. The red and blue ribbons represent
first as proton gradient and converted to ATP via ATP the protein globin; the green structures are the heme groups.
synthase. This generates an additional 28 molecules of
ATP (24 from the 8 NADH + 4 from the 2 quinols), to- tural roles. For instance, movements of the proteins actin
taling to 32 molecules of ATP conserved per degraded and myosin ultimately are responsible for the contraction
glucose (two from glycolysis + two from the citrate cy- of skeletal muscle. One property many proteins have is
cle). It is clear that using oxygen to completely oxidize that they specifically bind to a certain molecule or class of
6 CHAPTER 1. CELLS AND WATER

molecules—they may be extremely selective in what they will tend to curl up in a coil called an α-helix or into a
bind. Antibodies are an example of proteins that attach to sheet called a β-sheet; some α-helixes can be seen in the
one specific type of molecule. In fact, the enzyme-linked hemoglobin schematic above. Tertiary structure is the en-
immunosorbent assay (ELISA), which uses antibodies, is tire three-dimensional shape of the protein. This shape is
one of the most sensitive tests modern medicine uses to determined by the sequence of amino acids. In fact, a
detect various biomolecules. Probably the most impor- single change can change the entire structure. The alpha
tant proteins, however, are the enzymes. These molecules chain of hemoglobin contains 146 amino acid residues;
recognize specific reactant molecules called substrates; substitution of the glutamate residue at position 6 with
they then catalyze the reaction between them. By low- a valine residue changes the behavior of hemoglobin
ering the activation energy, the enzyme speeds up that so much that it results in sickle-cell disease. Finally,
reaction by a rate of 1011 or more: a reaction that would quaternary structure is concerned with the structure of
normally take over 3,000 years to complete spontaneously a protein with multiple peptide subunits, like hemoglobin
might take less than a second with an enzyme. The en- with its four subunits. Not all proteins have more than
zyme itself is not used up in the process, and is free to one subunit.[19]
catalyze the same reaction with a new set of substrates.
Ingested proteins are usually broken up into single amino
Using various modifiers, the activity of the enzyme can acids or dipeptides in the small intestine, and then ab-
be regulated, enabling control of the biochemistry of the sorbed. They can then be joined to make new proteins.
cell as a whole. Intermediate products of glycolysis, the citric acid cycle,
In essence, proteins are chains of amino acids. An amino and the pentose phosphate pathway can be used to make
acid consists of a carbon atom bound to four groups. One all twenty amino acids, and most bacteria and plants pos-
is an amino group, —NH2 , and one is a carboxylic acid sess all the necessary enzymes to synthesize them. Hu-
group, —COOH (although these exist as —NH3 + and mans and other mammals, however, can synthesize only
—COO− under physiologic conditions). The third is a half of them. They cannot synthesize isoleucine, leucine,
simple hydrogen atom. The fourth is commonly denoted lysine, methionine, phenylalanine, threonine, tryptophan,
"—R” and is different for each amino acid. There are and valine. These are the essential amino acids, since
20 standard amino acids. Some of these have functions it is essential to ingest them. Mammals do possess
by themselves or in a modified form; for instance, gluta- the enzymes to synthesize alanine, asparagine, aspartate,
mate functions as an important neurotransmitter. Also if cysteine, glutamate, glutamine, glycine, proline, serine,
a glycine amino acid undergoes methylation to a pseudo and tyrosine, the nonessential amino acids. While they
alanine amino acid, it is an indication of cancer metasta- can synthesize arginine and histidine, they cannot pro-
sis. duce it in sufficient amounts for young, growing animals,
and so these are often considered essential amino acids.
If the amino group is removed from an amino acid, it
leaves behind a carbon skeleton called an α-keto acid. En-
zymes called transaminases can easily transfer the amino
group from one amino acid (making it an α-keto acid) to
another α-keto acid (making it an amino acid). This is
Generic amino acids (1) in neutral form, (2) as they exist physi- important in the biosynthesis of amino acids, as for many
ologically, and (3) joined together as a dipeptide. of the pathways, intermediates from other biochemical
pathways are converted to the α-keto acid skeleton, and
Amino acids can be joined via a peptide bond. In this de- then an amino group is added, often via transamination.
hydration synthesis, a water molecule is removed and the The amino [20]
acids may then be linked together to make a
peptide bond connects the nitrogen of one amino acid’s protein.
amino group to the carbon of the other’s carboxylic acid A similar process is used to break down proteins. It is
group. The resulting molecule is called a dipeptide, and first hydrolyzed into its component amino acids. Free
short stretches of amino acids (usually, fewer than thirty) ammonia (NH3 ), existing as the ammonium ion (NH4 + )
are called peptides or polypeptides. Longer stretches in blood, is toxic to life forms. A suitable method for
merit the title proteins. As an example, the important excreting it must therefore exist. Different tactics have
blood serum protein albumin contains 585 amino acid evolved in different animals, depending on the animals’
residues.[18] needs. Unicellular organisms, of course, simply release
The structure of proteins is traditionally described in a hi- the ammonia into the environment. Likewise, bony fish
erarchy of four levels. The primary structure of a protein can release the ammonia into the water where it is quickly
simply consists of its linear sequence of amino acids; for diluted. In general, mammals [21]
convert the ammonia into
instance, “alanine-glycine-tryptophan-serine-glutamate- urea, via the urea cycle.
asparagine-glycine-lysine-…". Secondary structure is
concerned with local morphology (morphology being the
study of structure). Some combinations of amino acids
1.1. BIOCHEMISTRY 7

1.1.6 Lipids or deoxyribonucleic acid contains 2-deoxyriboses). Also,

the nitrogenous bases possible in the two nucleic acids are
Main article: Lipid different: adenine, cytosine, and guanine occur in both
RNA and DNA, while thymine occurs only in DNA and
uracil occurs in RNA.[24]
The term lipid composes a diverse range of molecules and
to some extent is a catchall for relatively water-insoluble
or nonpolar compounds of biological origin, includ- 1.1.8 Relationship to other “molecular-
ing waxes, fatty acids, fatty-acid derived phospholipids,
sphingolipids, glycolipids, and terpenoids (e.g., retinoids
scale” biological sciences
and steroids). Some lipids are linear aliphatic molecules,
while others have ring structures. Some are aromatic,
while others are not. Some are flexible, while others are
rigid.[22]
Most lipids have some polar character in addition to being
largely nonpolar. In general, the bulk of their structure
is nonpolar or hydrophobic (“water-fearing”), meaning
that it does not interact well with polar solvents like wa-
ter. Another part of their structure is polar or hydrophilic
(“water-loving”) and will tend to associate with polar sol-
vents like water. This makes them amphiphilic molecules
(having both hydrophobic and hydrophilic portions). In
the case of cholesterol, the polar group is a mere -OH
(hydroxyl or alcohol). In the case of phospholipids, the
polar groups are considerably larger and more polar, as
described below.
Lipids are an integral part of our daily diet. Most oils
and milk products that we use for cooking and eating
like butter, cheese, ghee etc., are composed of fats. Schematic relationship between biochemistry, genetics, and
Vegetable oils are rich in various polyunsaturated fatty molecular biology
acids (PUFA). Lipid-containing foods undergo digestion
within the body and are broken into fatty acids and glyc- Researchers in biochemistry use specific techniques na-
erol, which are the final degradation products of fats and tive to biochemistry, but increasingly combine these with
lipids. techniques and ideas developed in the fields of genetics,
molecular biology and biophysics. There has never been
a hard-line among these disciplines in terms of content
1.1.7 Nucleic acids and technique. Today, the terms molecular biology and
biochemistry are nearly interchangeable. The following
Main article: Nucleic acid figure is a schematic that depicts one possible view of the
relationship between the fields:
A nucleic acid is a complex, high-molecular-weight bio-
chemical macromolecule composed of nucleotide chains • Biochemistry is the study of the chemical substances
that convey genetic information.[23] The most common and vital processes occurring in living organisms.
nucleic acids are deoxyribonucleic acid (DNA) and ri- Biochemists focus heavily on the role, function, and
bonucleic acid (RNA). Nucleic acids are found in all liv- structure of biomolecules. The study of the chem-
ing cells and viruses. Aside from the genetic material of istry behind biological processes and the synthesis
the cell, nucleic acids often play a role as second messen- of biologically active molecules are examples of bio-
gers, as well as forming the base molecule for adenosine chemistry.
triphosphate (ATP), the primary energy-carrier molecule • Genetics is the study of the effect of genetic dif-
found in all living organisms. ferences on organisms. Often this can be inferred
Nucleic acid, so called because of its prevalence in cellu- by the absence of a normal component (e.g., one
lar nuclei, is the generic name of the family of biopoly- gene). The study of "mutants" – organisms with a
mers. The monomers are called nucleotides, and each changed gene that leads to the organism being dif-
consists of three components: a nitrogenous heterocyclic ferent with respect to the so-called "wild type" or
base (either a purine or a pyrimidine), a pentose sugar, normal phenotype. Genetic interactions (epistasis)
and a phosphate group. Different nucleic acid types dif- can often confound simple interpretations of such
fer in the specific sugar found in their chain (e.g., DNA “knock-out” or “knock-in” studies.
8 CHAPTER 1. CELLS AND WATER

• Molecular biology is the study of molecular under- 1.1.10 Notes

pinnings of the process of replication, transcrip-
tion and translation of the genetic material. The a. ^ Fructose is not the only sugar found in fruits. Glu-
central dogma of molecular biology where genetic cose and sucrose are also found in varying quantities in
material is transcribed into RNA and then translated various fruits, and indeed sometimes exceed the fructose
into protein, despite being an oversimplified picture present. For example, 32% of the edible portion of date is
of molecular biology, still provides a good start- glucose, compared with 23.70% fructose and 8.20% su-
ing point for understanding the field. This picture, crose. However, peaches contain more sucrose (6.66%)
however, is undergoing revision in light of emerging than they do fructose (0.93%) or glucose (1.47%).[26]
novel roles for RNA.[25]

• Chemical biology seeks to develop new tools based 1.1.11 References

on small molecules that allow minimal perturbation
of biological systems while providing detailed in- [1] “Biochemistry”. acs.org.
formation about their function. Further, chemical
biology employs biological systems to create non- [2] “scientific term 'biochemistry'".
natural hybrids between biomolecules and synthetic [3] Fiske, John (1890). Outlines of Cosmic Philosophy Based
devices (for example emptied viral capsids that can on the Doctrines of Evolution, with Criticisms on the Pos-
deliver gene therapy or drug molecules). itive Philosophy, Volume 1. Boston and New York:
Houghton, Mifflin. pp. 419–20. Retrieved 16 February
2015.
1.1.9 See also
[4] Kauffman, G.B.; Chooljian, S.H. (2001). “Friedrich
Wöhler (1800–1882), on the bicentennial of his
Main article: Outline of biochemistry
birth”. The Chemical Educator 6 (2): 121–133.
doi:10.1007/s00897010444a.

[5] Hunter (2000), p. 75.

Lists
[6] Hunter (2000), pp. 96–98.
• Important publications in biochemistry (chemistry)
[7] Ben-Menahem, Ari (2009). Historical Encyclopedia of
• List of biochemistry topics Natural and Mathematical Sciences. Springer. p. 2982.
ISBN 978-3-540-68831-0.
• List of biochemists
[8] Tropp (2012), p. 2.
• List of biomolecules
[9] Tropp (2012), pp. 19–20.

See also [10] Krebs, Jocelyn E.; Goldstein, Elliott S.; Lewin, Benjamin;
Kilpatrick, Stephen T. (2012). Essential Genes. Jones &
Bartlett Publishers. p. 32. ISBN 978-1-4496-1265-8.
• Chemical ecology
[11] Butler, John M. (2009). Fundamentals of Forensic DNA
• Computational biomodeling Typing. Academic Press. p. 5. ISBN 978-0-08-096176-
7.
• EC number
[12] Sen, Chandan K.; Roy, Sashwati (2007). “miRNA:
• Hypothetical types of biochemistry
Licensed to kill the messenger”. DNA Cell Biology
• International Union of Biochemistry and Molecular 26 (4): 193–194. doi:10.1089/dna.2006.0567. PMID
17465885.
Biology
[13] Ultratrace minerals. Authors: Nielsen, Forrest H. USDA,
• Metabolome ARS Source: Modern nutrition in health and disease / ed-
• Metabolomics itors, Maurice E. Shils ... et al.. Baltimore : Williams &
Wilkins, c1999., p. 283-303. Issue Date: 1999 URI:
• Molecular medicine
[14] Fariselli, Piero; Rossi, Ivan; Capriotti, Emidio; Casadio,
• Plant biochemistry Rita (2007). “The WWWH of remote homolog detection:
the state of the art”. Briefings in Bioinformatics 8 (2): 78–
• Proteolysis 87. doi:10.1093/bib/bbl032. PMID 17003074.

• Small molecule [15] Whiting, G.C (1970). “Sugars”. In A.C. Hulme. The Bio-
chemistry of Fruits and their Products. Volume 1. London
• Structural biology & New York: Academic Press. pp. 1–31.
1.2. CELLS 9

[16] Fromm and Hargrove (2012), pp. 163–180. 1.2 Cells

[17] Fromm and Hargrove (2012), pp. 183–194.
[18] Metzler, David Everett; Metzler, Carol M. (2001).
This article is about the term in biology. For other uses,
Biochemistry: The Chemical Reactions of Living Cells 1. see Cell (disambiguation).
Academic Press. p. 58. ISBN 978-0-12-492540-3.
[19] Fromm and Hargrove (2012), pp. 35–51.
[20] Fromm and Hargrove (2012), pp. 279–292.
[21] Sherwood, Lauralee; Klandorf, Hillar; Yancey, Paul H.
(2012). Animal Physiology: From Genes to Organisms.
Cengage Learning. p. 558. ISBN 978-0-8400-6865-1.
[22] Fromm and Hargrove (2012), pp. 22–27.
[23] Voet, D. and Voet, J, G. (2011). Biochemistry (4th ed.).
John Wiley & Sons Inc.: Hoboken, NJ
[24] Tropp (2012), pp. 5–9.
[25] Ulveling, Damien; Francastel, Claire; Hubé, Flo- Structure of an animal cell
rent (2011). “When one is better than two: RNA
with dual functions”. Biochimie 93 (4): 633–644.
doi:10.1016/j.biochi.2010.11.004. PMID 21111023. The cell (from Latin cella, meaning “small room”[1] ) is
the basic structural, functional, and biological unit of all
[26] Whiting, G.C. (1970), p.5 known living organisms. Cells are the smallest unit of life
that can replicate independently, and are often called the
Cited literature “building blocks of life”. The study of cells is called cell
biology.
• Fromm, Herbert J.; Hargrove, Mark (2012). Essen- Cells consist of cytoplasm enclosed within a membrane,
tials of Biochemistry. Springer. ISBN 978-3-642- which contains many biomolecules such as proteins
19623-2. and nucleic acids.[2] Organisms can be classified as
• Hunter, Graeme K. (2000). Vital Forces: The Dis- unicellular (consisting of a single cell; including bacteria)
covery of the Molecular Basis of Life. Academic or multicellular (including plants and animals). While
Press. ISBN 978-0-12-361811-5. the number of cells in plants and animals varies from
species to species, humans contain about 100 trillion
• Tropp, Burton E. (2012). Molecular Biology (4th (1014 ) cells.[3] Most plant and animal cells are visible only
ed.). Jones & Bartlett Learning. ISBN 978-1-4496- under the microscope, with dimensions between 1 and
0091-4. 100 micrometres.[4]
The cell was discovered by Robert Hooke in 1665, who
1.1.12 External links named the biological unit for its resemblance to cells in-
habited by Christian monks in a monastery.[5][6] Cell the-
• The Virtual Library of Biochemistry and Cell Biol- ory, first developed in 1839 by Matthias Jakob Schleiden
ogy and Theodor Schwann, states that all organisms are com-
posed of one or more cells, that cells are the fundamen-
• Biochemistry, 5th ed. Full text of Berg, Tymoczko,
tal unit of structure and function in all living organisms,
and Stryer, courtesy of NCBI.
that all cells come from preexisting cells, and that all cells
• Biochemistry, 2nd ed. Full text of Garrett and Gr- contain the hereditary information necessary for regulat-
isham. ing cell functions and for transmitting information to the
next generation of cells.[7] Cells emerged on Earth at least
• Biochemistry Animation (Narrated Flash anima- 3.5 billion years ago.[8][9][10]
tions.)
• SystemsX.ch - The Swiss Initiative in Systems Biol-
ogy
1.2.1 Anatomy
• Biochemistry Online Resources – Lists of Biochem-
istry departments, websites, journals, books and re-
Cells are of two types, eukaryotic, which contain a
views, employment opportunities and events.
nucleus, and prokaryotic, which do not. Prokaryotes are
• Full text of Biochemistry by Kevin and Indira, an single-celled organisms, while eukaryotes can be either
introductory biochemistry textbook. single-celled or multicellular.
10 CHAPTER 1. CELLS AND WATER

Prokaryotic cells found in the cytoplasm. Prokaryotes can carry

extrachromosomal DNA elements called plasmids,
Main article: Prokaryote which are usually circular. Linear bacterial plasmids
Prokaryotic cells were the first form of life on Earth, have been identified in several species of spirochete
bacteria, including members of the genus Borrelia
notably Borrelia burgdorferi, which causes Lyme
disease.[13] Though not forming a nucleus, the DNA
is condensed in a nucleoid. Plasmids encode addi-
tional genes, such as antibiotic resistance genes.

Eukaryotic cells

Main article: Eukaryote

Plants, animals, fungi, slime moulds, protozoa, and al-

Diagram of a typical prokaryotic cell

characterised by having vital biological processes in-

cluding cell signaling and being self-sustaining. They
are simpler and smaller than eukaryotic cells, and
lack membrane-bound organelles such as the nucleus.
Prokaryotes include two of the domains of life, bacteria
and archaea. The DNA of a prokaryotic cell consists of
a single chromosome that is in direct contact with the
cytoplasm. The nuclear region in the cytoplasm is called Structure of a typical animal cell
the nucleoid. Most prokaryotes are the smallest of all or-
ganisms ranging from 0.5 to 2.0 µm in diameter.[12]
A prokaryotic cell has three architectural regions:

• On the outside, flagella and pili project from the

cell’s surface. These are structures (not present in all
prokaryotes) made of proteins that facilitate move-
ment and communication between cells.

• Enclosing the cell is the cell envelope – generally

consisting of a cell wall covering a plasma mem-
brane though some bacteria also have a further cov-
ering layer called a capsule. The envelope gives
rigidity to the cell and separates the interior of the
cell from its environment, serving as a protective fil-
ter. Though most prokaryotes have a cell wall, there
Structure of a typical plant cell
are exceptions such as Mycoplasma (bacteria) and
Thermoplasma (archaea). The cell wall consists of
peptidoglycan in bacteria, and acts as an additionalgae are all eukaryotic. These cells are about fifteen times
wider than a typical prokaryote and can be as much as a
barrier against exterior forces. It also prevents the
cell from expanding and bursting (cytolysis) from thousand times greater in volume. The main distinguish-
osmotic pressure due to a hypotonic environment. ing feature of eukaryotes as compared to prokaryotes is
Some eukaryotic cells (plant cells and fungal cells)compartmentalization: the presence of membrane-bound
also have a cell wall. organelles (compartments) in which specific metabolic
activities take place. Most important among these is a
• Inside the cell is the cytoplasmic region that con- cell nucleus, an organelle that houses the cell’s DNA. This
tains the genome (DNA), ribosomes and various nucleus gives the eukaryote its name, which means “true
sorts of inclusions. The genetic material is freely kernel (nucleus)". Other differences include:
1.2. CELLS 11

• The plasma membrane resembles that of prokary- build various proteins such as enzymes, the cell’s primary
otes in function, with minor differences in the setup. machinery. There are also other kinds of biomolecules in
Cell walls may or may not be present. cells. This article lists these primary components of the
cell, then briefly describes their function.
• The eukaryotic DNA is organized in one or more
linear molecules, called chromosomes, which are as-
sociated with histone proteins. All chromosomal Membrane
DNA is stored in the cell nucleus, separated from
the cytoplasm by a membrane. Some eukaryotic Main article: Cell membrane
organelles such as mitochondria also contain some
DNA. The cell membrane, or plasma membrane, is a biological
membrane that surrounds the cytoplasm of a cell. In ani-
• Many eukaryotic cells are ciliated with primary cilia.
Primary cilia play important roles in chemosensa- mals, the plasma membrane is the outer boundary of the
tion, mechanosensation, and thermosensation. Cilia cell, while in plants and prokaryotes it is usually covered
may thus be “viewed as a sensory cellular antennae by a cell wall. This membrane serves to separate and pro-
that coordinates a large number of cellular signal-tect a cell from its surrounding environment and is made
ing pathways, sometimes coupling the signaling to mostly from a double layer of phospholipids, which are
amphiphilic (partly hydrophobic and partly hydrophilic).
ciliary motility or alternatively to cell division and
differentiation.”[14] Hence, the layer is called a phospholipid bilayer, or some-
times a fluid mosaic membrane. Embedded within this
• Eukaryotes can move using motile cilia or flagella. membrane is a variety of protein molecules that act as
Eukaryotic flagella are less complex than those of channels and pumps that move different molecules into
prokaryotes. and out of the cell. The membrane is said to be 'semi-
permeable', in that it can either let a substance (molecule
or ion) pass through freely, pass through to a limited ex-
1.2.2 Subcellular components tent or not pass through at all. Cell surface membranes
also contain receptor proteins that allow cells to detect
external signaling molecules such as hormones.

Cytoskeleton

Main article: Cytoskeleton

The cytoskeleton acts to organize and maintain the

Illustration depicting major structures inside a eukaryotic animal

cell
A fluorescent image of an endothelial cell. Nuclei are stained
All cells, whether prokaryotic or eukaryotic, have a blue, mitochondria are stained red, and microfilaments are
membrane that envelops the cell, regulates what moves stained green.
in and out (selectively permeable), and maintains the
electric potential of the cell. Inside the membrane, a cell’s shape; anchors organelles in place; helps during
salty cytoplasm takes up most of the cell’s volume. All endocytosis, the uptake of external materials by a cell,
cells (except red blood cells which lack a cell nucleus and cytokinesis, the separation of daughter cells after
and most organelles to accommodate maximum space cell division; and moves parts of the cell in processes
for hemoglobin) possess DNA, the hereditary material of of growth and mobility. The eukaryotic cytoskeleton
genes, and RNA, containing the information necessary to is composed of microfilaments, intermediate filaments
12 CHAPTER 1. CELLS AND WATER

and microtubules. There are a great number of pro- Organelles are parts of the cell which are adapted and/or
teins associated with them, each controlling a cell’s struc- specialized for carrying out one or more vital functions,
ture by directing, bundling, and aligning filaments. The analogous to the organs of the human body (such as the
prokaryotic cytoskeleton is less well-studied but is in- heart, lung, and kidney, with each organ performing a dif-
volved in the maintenance of cell shape, polarity and ferent function). Both eukaryotic and prokaryotic cells
cytokinesis.[15] The subunit protein of microfilaments is have organelles, but prokaryotic organelles are generally
a small, monomeric protein called actin. The subunit of simpler and are not membrane-bound.
microtubules is a dimeric molecule called tubulin. In- There are several types of organelles in a cell. Some
termediate filaments are heteropolymers whose subunits
(such as the nucleus and golgi apparatus) are typically
vary among the cell types in different tissues. But some solitary, while others (such as mitochondria, chloroplasts,
of the subunit protein of intermediate filaments include
peroxisomes and lysosomes) can be numerous (hundreds
vimentin, desmin, lamin (lamins A, B and C), keratin to thousands). The cytosol is the gelatinous fluid that fills
(multiple acidic and basic keratins), neurofilament pro-
the cell and surrounds the organelles.
teins (NF - L, NF - M).

Genetic material

Two different kinds of genetic material exist:

deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). Cells use DNA for their long-term information
storage. The biological information contained in an
organism is encoded in its DNA sequence. RNA is used
for information transport (e.g., mRNA) and enzymatic
functions (e.g., ribosomal RNA). Transfer RNA (tRNA)
molecules are used to add amino acids during protein
translation.
Prokaryotic genetic material is organized in a simple
circular DNA molecule (the bacterial chromosome) in
the nucleoid region of the cytoplasm. Eukaryotic ge-
Human cancer cells with nuclei (specifically the DNA) stained
netic material is divided into different, linear molecules blue. The central and rightmost cell are in interphase, so the
called chromosomes inside a discrete nucleus, usually entire nuclei are labeled. The cell on the left is going through
with additional genetic material in some organelles like mitosis and its DNA has condensed.
mitochondria and chloroplasts (see endosymbiotic the-
ory). Eukaryotic
A human cell has genetic material contained in the cell
nucleus (the nuclear genome) and in the mitochondria • Cell nucleus: A cell’s information center, the cell
(the mitochondrial genome). In humans the nuclear nucleus is the most conspicuous organelle found in
genome is divided into 46 linear DNA molecules called a eukaryotic cell. It houses the cell’s chromosomes,
chromosomes, including 22 homologous chromosome and is the place where almost all DNA replication
pairs and a pair of sex chromosomes. The mitochon- and RNA synthesis (transcription) occur. The nu-
drial genome is a circular DNA molecule distinct from cleus is spherical and separated from the cytoplasm
the nuclear DNA. Although the mitochondrial DNA is by a double membrane called the nuclear envelope.
very small compared to nuclear chromosomes, it codes The nuclear envelope isolates and protects a cell’s
for 13 proteins involved in mitochondrial energy produc- DNA from various molecules that could acciden-
tion and specific tRNAs. tally damage its structure or interfere with its pro-
cessing. During processing, DNA is transcribed, or
Foreign genetic material (most commonly DNA) can also copied into a special RNA, called messenger RNA
be artificially introduced into the cell by a process called (mRNA). This mRNA is then transported out of the
transfection. This can be transient, if the DNA is not in- nucleus, where it is translated into a specific pro-
serted into the cell’s genome, or stable, if it is. Certain tein molecule. The nucleolus is a specialized re-
viruses also insert their genetic material into the genome. gion within the nucleus where ribosome subunits are
assembled. In prokaryotes, DNA processing takes
place in the cytoplasm.
Organelles
• Mitochondria and Chloroplasts: generate energy
Main article: Organelle for the cell. Mitochondria are self-replicating or-
ganelles that occur in various numbers, shapes,
1.2. CELLS 13

and sizes in the cytoplasm of all eukaryotic cells. transport through the ER and the Golgi apparatus.
Respiration occurs in the cell mitochondria, which Centrosomes are composed of two centrioles, which
generate the cell’s energy by oxidative phosphoryla- separate during cell division and help in the forma-
tion, using oxygen to release energy stored in cellular tion of the mitotic spindle. A single centrosome is
nutrients (typically pertaining to glucose) to gener- present in the animal cells. They are also found in
ate ATP. Mitochondria multiply by binary fission, some fungi and algae cells.
like prokaryotes. Chloroplasts can only be found in
plants and algae, and they capture the sun’s energy • Vacuoles: Vacuoles sequester waste products and
to make carbohydrates through photosynthesis. in plant cells store water. They are often described
as liquid filled space and are surrounded by a mem-
brane. Some cells, most notably Amoeba, have con-
tractile vacuoles, which can pump water out of the
cell if there is too much water. The vacuoles of plant
cells and fungal cells are usually larger than those of
animal cells.

Eukaryotic and prokaryotic

• Ribosomes: The ribosome is a large complex of

RNA and protein molecules. They each consist of
two subunits, and act as an assembly line where
RNA from the nucleus is used to synthesise proteins
from amino acids. Ribosomes can be found either
floating freely or bound to a membrane (the rough
endoplasmatic reticulum in eukaryotes, or the cell
membrane in prokaryotes).[16]

1.2.3 Structures outside the cell membrane

Diagram of an endomembrane system Many cells also have structures which exist wholly or par-
tially outside the cell membrane. These structures are no-
table because they are not protected from the external en-
• Endoplasmic reticulum: The endoplasmic reticu-
vironment by the semipermeable cell membrane. In or-
lum (ER) is a transport network for molecules tar-
der to assemble these structures, their components must
geted for certain modifications and specific destina-
be carried across the cell membrane by export processes.
tions, as compared to molecules that float freely in
the cytoplasm. The ER has two forms: the rough
ER, which has ribosomes on its surface that secrete Cell wall
proteins into the ER, and the smooth ER, which
lacks ribosomes. The smooth ER plays a role in cal- Many types of prokaryotic and eukaryotic cells have a cell
cium sequestration and release. wall. The cell wall acts to protect the cell mechanically
• Golgi apparatus: The primary function of the and chemically from its environment, and is an additional
Golgi apparatus is to process and package the layer of protection to the cell membrane. Different types
macromolecules such as proteins and lipids that are of cell have cell walls made up of different materials; plant
synthesized by the cell. cell walls are primarily made up of cellulose, fungi cell
walls are made up of chitin and bacteria cell walls are
• Lysosomes and Peroxisomes: Lysosomes contain made up of peptidoglycan.
digestive enzymes (acid hydrolases). They digest
excess or worn-out organelles, food particles, and
engulfed viruses or bacteria. Peroxisomes have en- Prokaryotic
zymes that rid the cell of toxic peroxides. The cell
could not house these destructive enzymes if they Capsule A gelatinous capsule is present in some bacte-
were not contained in a membrane-bound system. ria outside the cell membrane and cell wall. The capsule
may be polysaccharide as in pneumococci, meningococci
• Centrosome – the cytoskeleton organiser: The or polypeptide as Bacillus anthracis or hyaluronic acid as
centrosome produces the microtubules of a cell – a in streptococci. Capsules are not marked by normal stain-
key component of the cytoskeleton. It directs the ing protocols and can be detected by India ink or methyl
14 CHAPTER 1. CELLS AND WATER

blue; which allows for higher contrast between the cells

for observation.[17]:87

Flagella Flagella are organelles for cellular mobility.

The bacterial flagellum stretches from cytoplasm through
the cell membrane(s) and extrudes through the cell wall.
They are long and thick thread-like appendages, protein
in nature. A different type of flagellum is found in ar-
chaea and a different type is found in eukaryotes.

Fimbria A fimbria also known as a pilus is a short,

thin, hair-like filament found on the surface of bacte-
ria. Fimbriae, or pili are formed of a protein called pilin
(antigenic) and are responsible for attachment of bacteria
to specific receptors of human cell (cell adhesion). There
are special types of specific pili involved in bacterial con-
jugation.
Bacteria divide by binary fission, while eukaryotes divide by
mitosis or meiosis.
1.2.4 Cellular processes
DNA replication, or the process of duplicating a cell’s
Growth and metabolism
genome, always happens when a cell divides through mi-
tosis or binary fission. This occurs during the S phase of
Main articles: Cell growth and Metabolism
the cell cycle.
In meiosis, the DNA is replicated only once, while the
Between successive cell divisions, cells grow through the
cell divides twice. DNA replication only occurs before
functioning of cellular metabolism. Cell metabolism
meiosis I. DNA replication does not occur when the cells
is the process by which individual cells process nu-
divide the second time, in meiosis II.[18] Replication, like
trient molecules. Metabolism has two distinct divi-
all cellular activities, requires specialized proteins for car-
sions: catabolism, in which the cell breaks down com-
rying out the job.
plex molecules to produce energy and reducing power,
and anabolism, in which the cell uses energy and reduc-
ing power to construct complex molecules and perform
Protein synthesis
other biological functions. Complex sugars consumed
by the organism can be broken down into simpler sugar
Main article: Protein biosynthesis
molecules called monosaccharides such as glucose. Once
inside the cell, glucose is broken down to make adeno-
sine triphosphate (ATP), a molecule that possesses read- Cells are capable of synthesizing new proteins, which are
ily available energy, through two different pathways. essential for the modulation and maintenance of cellu-
lar activities. This process involves the formation of new
protein molecules from amino acid building blocks based
Replication on information encoded in DNA/RNA. Protein synthesis
generally consists of two major steps: transcription and
Main article: Cell division translation.
Transcription is the process where genetic information in
Cell division involves a single cell (called a mother cell) DNA is used to produce a complementary RNA strand.
dividing into two daughter cells. This leads to growth in This RNA strand is then processed to give messenger
multicellular organisms (the growth of tissue) and to pro- RNA (mRNA), which is free to migrate through the cell.
creation (vegetative reproduction) in unicellular organ- mRNA molecules bind to protein-RNA complexes called
isms. Prokaryotic cells divide by binary fission, while ribosomes located in the cytosol, where they are trans-
eukaryotic cells usually undergo a process of nuclear di- lated into polypeptide sequences. The ribosome medi-
vision, called mitosis, followed by division of the cell, ates the formation of a polypeptide sequence based on the
called cytokinesis. A diploid cell may also undergo mRNA sequence. The mRNA sequence directly relates
meiosis to produce haploid cells, usually four. Haploid to the polypeptide sequence by binding to transfer RNA
cells serve as gametes in multicellular organisms, fusing (tRNA) adapter molecules in binding pockets within the
to form new diploid cells. ribosome. The new polypeptide then folds into a func-
1.2. CELLS 15

adhesion, motor and other proteins.[19] The process is di-

vided into three steps – protrusion of the leading edge of
the cell, adhesion of the leading edge and de-adhesion at
the cell body and rear, and cytoskeletal contraction to pull
the cell forward. Each step is driven by physical forces
generated by unique segments of the cytoskeleton.[20][21]

1.2.5 Multicellularity

Main article: Multicellular organism

Cell specialization

An overview of protein synthesis.

Within the nucleus of the cell (light blue), genes (DNA, dark
blue) are transcribed into RNA. This RNA is then subject to post-
transcriptional modification and control, resulting in a mature
mRNA (red) that is then transported out of the nucleus and into
the cytoplasm (peach), where it undergoes translation into a pro-
tein. mRNA is translated by ribosomes (purple) that match the
three-base codons of the mRNA to the three-base anti-codons of
the appropriate tRNA. Newly synthesized proteins (black) are of-
ten further modified, such as by binding to an effector molecule
(orange), to become fully active.

tional three-dimensional protein molecule. Staining of a Caenorhabditis elegans which highlights the nuclei
of its cells.

Movement or motility Multicellular organisms are organisms that consist of

more than one cell, in contrast to single-celled organ-
Main article: Motility isms.[22]
In complex multicellular organisms, cells specialize into
Unicellular organisms can move in order to find food or different cell types that are adapted to particular func-
escape predators. Common mechanisms of motion in- tions. In mammals, major cell types include skin cells,
clude flagella and cilia. muscle cells, neurons, blood cells, fibroblasts, stem cells,
In multicellular organisms, cells can move during pro- and others. Cell types differ both in appearance and func-
cesses such as wound healing, the immune response and tion, yet are genetically identical. Cells are able to be of
cancer metastasis. For example, in wound healing in an- the same genotype but of different cell type due to the
imals, white blood cells move to the wound site to kill differential expression of the genes they contain.
the microorganisms that cause infection. Cell motility Most distinct cell types arise from a single totipotent cell,
involves many receptors, crosslinking, bundling, binding, called a zygote, that differentiates into hundreds of dif-
16 CHAPTER 1. CELLS AND WATER

ferent cell types during the course of development. Dif-

ferentiation of cells is driven by different environmental
cues (such as cell–cell interaction) and intrinsic differ-
ences (such as those caused by the uneven distribution of
molecules during division).

Origin of multicellularity

Multicellularity has evolved independently at

least 25 times,[23] including in some prokaryotes,
like cyanobacteria, myxobacteria, actinomycetes,
Magnetoglobus multicellularis or Methanosarcina. How-
ever, complex multicellular organisms evolved only in Stromatolites are left behind by cyanobacteria, also called blue-
six eukaryotic groups: animals, fungi, brown algae, red green algae. They are the oldest known fossils of life on Earth.
algae, green algae, and plants.[24] It evolved repeatedly This one-billion-year-old fossil is from Glacier National Park in
the United States.
for plants (Chloroplastida), once or twice for animals,
once for brown algae, and perhaps several times for
fungi, slime molds, and red algae.[25] Multicellularity Cells emerged at least 3.5 billion years ago.[8][9][10] The
may have evolved from colonies of interdependent current belief is that these cells were heterotrophs. The
organisms, from cellularization, or from organisms in early cell membranes were probably more simple and
symbiotic relationships. permeable than modern ones, with only a single fatty
The first evidence of multicellularity is from acid chain per lipid. Lipids are known to spontaneously
cyanobacteria-like organisms that lived between 3 and form bilayered vesicles in water, and could have preceded
3.5 billion years ago.[23] Other early fossils of multicellu- RNA, but the first cell membranes could also have been
lar organisms include the contested Grypania spiralis and produced by catalytic RNA, or even have required struc-
the fossils of the black shales of the Palaeoproterozoic tural proteins before they could form.[28]
Francevillian Group Fossil B Formation in Gabon.[26]
The evolution of multicellularity from unicellular ances- Origin of eukaryotic cells
tors has been replicated in the laboratory, in evolution
experiments using predation as the selective pressure.[23] Further information: Evolution of sexual reproduction

The eukaryotic cell seems to have evolved from a

1.2.6 Origins
symbiotic community of prokaryotic cells. DNA-bearing
organelles like the mitochondria and the chloroplasts
Main article: Evolutionary history of life
are descended from ancient symbiotic oxygen-breathing
proteobacteria and cyanobacteria, respectively, which
The origin of cells has to do with the origin of life, which were endosymbiosed by an ancestral archaean prokary-
began the history of life on Earth. ote.
There is still considerable debate about whether or-
Origin of the first cell ganelles like the hydrogenosome predated the origin of
mitochondria, or vice versa: see the hydrogen hypothesis
Further information: Abiogenesis and Evolution of cells for the origin of eukaryotic cells.

There are several theories about the origin of small 1.2.7 History of research
molecules that led to life on the early Earth. They may
have been carried to Earth on meteorites (see Murchison • 1632–1723: Antonie van Leeuwenhoek teaches
meteorite), created at deep-sea vents, or synthesized by himself to make lenses, constructs basic optical mi-
lightning in a reducing atmosphere (see Miller–Urey ex- croscopes and draws protozoa, such as Vorticella
periment). There is little experimental data defining what from rain water, and bacteria from his own mouth.
the first self-replicating forms were. RNA is thought to
be the earliest self-replicating molecule, as it is capable of • 1665: Robert Hooke discovers cells in cork, then
both storing genetic information and catalyzing chemical in living plant tissue using an early compound mi-
reactions (see RNA world hypothesis), but some other croscope. He coins the term cell (from Latin cella,
entity with the potential to self-replicate could have pre- meaning “small room”[1] ) in his book Micrographia
[27]
ceded RNA, such as clay or peptide nucleic acid. (1665).[29]
1.2. CELLS 17

• 1839: Theodor Schwann and Matthias Jakob Schlei- blocks” move to shape developing embryos. It is also com-
den elucidate the principle that plants and animals mon to describe small molecules such as amino acids as
are made of cells, concluding that cells are a com- "molecular building blocks".
mon unit of structure and development, and thus [3] Lodish (2007). Molecular Cell Biology,6e. W.H.Freeman
founding the cell theory. and Company. ISBN 0-7167-7601-4.
• 1855: Rudolf Virchow states that new cells come [4] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
from pre-existing cells by cell division (omnis cellula (2006). Biology: Exploring Life. Boston, Massachusetts:
ex cellula). Pearson Prentice Hall. ISBN 0-13-250882-6.

• 1859: The belief that life forms can occur spon- [5] Karp, Gerald (19 October 2009). Cell and Molecular Biol-
taneously (generatio spontanea) is contradicted by ogy: Concepts and Experiments. John Wiley & Sons. p. 2.
ISBN 9780470483374. Hooke called the pores cells be-
Louis Pasteur (1822–1895) (although Francesco
cause they re- minded him of the cells inhabited by monks
Redi had performed an experiment in 1668 that sug- living in a monastery.
gested the same conclusion).
[6] Alan Chong Tero (1990). Achiever’s Biology. Allied Pub-
• 1931: Ernst Ruska builds the first transmission elec- lishers. p. 36. ISBN 9788184243697. In 1665, an En-
tron microscope (TEM) at the University of Berlin. glishman, Robert Hooke observed a thin slice of” cork
By 1935, he has built an EM with twice the resolu- under a simple microscope. (A simple microscope is a
tion of a light microscope, revealing previously un- microscope with only one biconvex lens, rather like a
resolvable organelles. magnifying glass). He saw many small box like struc-
tures. These reminded him of small rooms called “cells”
• 1953: Watson and Crick made their first announce- in which Christian monks lived and meditated.
ment on the double helix structure of DNA on
[7] Maton, Anthea; Hopkins, Jean Johnson, Susan LaHart,
February 28. David Quon Warner, Maryanna Wright, Jill D (1997).
Cells Building Blocks of Life. New Jersey: Prentice Hall.
• 1981: Lynn Margulis published Symbiosis in Cell
ISBN 0-13-423476-6.
Evolution detailing the endosymbiotic theory.
[8] Schopf, JW, Kudryavtsev, AB, Czaja, AD, and Tripathi,
AB. (2007). Evidence of Archean life: Stromatolites and
1.2.8 See also microfossils. Precambrian Research 158:141-155.

• Topic outline of cell biology [9] Schopf, JW (2006). Fossil evidence of Archaean life. Phi-
los Trans R Soc Lond B Biol Sci 29;361(1470):869-85.
• Cell culture [10] Peter Hamilton Raven; George Brooks Johnson (2002).
Biology. McGraw-Hill Education. p. 68. ISBN 978-0-
• Cellular component
07-112261-0. Retrieved 7 July 2013.
• Cellular model [11] Campbell Biology—Concepts and Connections. Pearson
Education. 2009. p. 320.
• Cytorrhysis
[12] Microbiology : Principles and Explorations By Jacquelyn
• Cytotoxicity G. Black
• Lipid raft [13] European Bioinformatics Institute, Karyn’s Genomes:
Borrelia burgdorferi, part of 2can on the EBI-EMBL
• Plasmolysis database. Retrieved 5 August 2012
• Stem cell [14] Satir, Peter; Christensen, ST; Søren T. Christensen
(2008-03-26). “Structure and function of mam-
• Syncytium malian cilia”. Histochemistry and Cell Biology
(Springer Berlin/Heidelberg) 129 (6): 687–693.
• Vault (organelle)
doi:10.1007/s00418-008-0416-9. PMC 2386530. PMID
18365235. 1432-119X. Retrieved 2009-09-12.
1.2.9 References [15] Michie K, Löwe J (2006). “Dynamic filaments of the
bacterial cytoskeleton”. Annu Rev Biochem 75: 467–
[1] “Cell”. Online Etymology Dictionary. Retrieved 31 De- 92. doi:10.1146/annurev.biochem.75.103004.142452.
cember 2012. PMID 16756499.
[2] Cell Movements and the Shaping of the Vertebrate Body [16] Ménétret JF, Schaletzky J, Clemons WM, CW; Akey
in Chapter 21 of Molecular Biology of the Cell fourth edi- et al. (December 2007). “Ribosome binding of a
tion, edited by Bruce Alberts (2002) published by Garland single copy of the SecY complex: implications for
Science. protein translocation”. Mol. Cell 28 (6): 1083–92.
The Alberts text discusses how the “cellular building doi:10.1016/j.molcel.2007.10.034. PMID 18158904.
18 CHAPTER 1. CELLS AND WATER

[17] Prokaryotes. Newnes. Apr 11, 1996. ISBN 1.2.10 External links
9780080984735.
• MBInfo - Descriptions on Cellular Functions and
[18] Campbell Biology—Concepts and Connections. Pearson Processes
Education. 2009. p. 138.
• MBInfo - Cellular Organization
[19] Revathi Ananthakrishnan1 *, Allen Ehrlicher2 ✉. “The
Forces Behind Cell Movement”. Biolsci.org. Retrieved • Inside the Cell - a science education booklet by
2009-04-17. National Institutes of Health, in PDF and ePub.
[20] Alberts B, Johnson A, Lewis J. et al. Molecular Biology • Cells Alive!
of the Cell, 4e. Garland Science. 2002
• Cell Biology in “The Biology Project” of University
[21] Ananthakrishnan, R; Ehrlicher, A (2007). “The Forces of Arizona.
Behind Cell Movement”. Int J Biol Sci 3: 303–317.
doi:10.7150/ijbs.3.303. • Centre of the Cell online

[22] Becker, Wayne M. et al. (2009). The world of the cell. • The Image & Video Library of The American So-
Pearson Benjamin Cummings. p. 480. ISBN 978-0-321- ciety for Cell Biology, a collection of peer-reviewed
55418-5. still images, video clips and digital books that illus-
trate the structure, function and biology of the cell.
[23] Grosberg RK, Strathmann RR. The evolution of multicel-
lularity: A minor major transition? Annu Rev Ecol Evol • HighMag Blog, still images of cells from recent re-
Syst. 2007;38:621–654. search articles.
[24] http://public.wsu.edu/~{}lange-m/Documnets/ • New Microscope Produces Dazzling 3D Movies of
Teaching2011/Popper2011.pdf Live Cells, March 4, 2011 - Howard Hughes Medi-
[25] Bonner, John Tyler (1998). “The Origins of Multicellu-
cal Institute.
larity” (PDF, 0.2 MB). Integrative Biology: Issues, News, • WormWeb.org: Interactive Visualization of the C.
and Reviews 1 (1): 27–36. doi:10.1002/(SICI)1520-
elegans Cell lineage - Visualize the entire cell lineage
6602(1998)1:1<27::AID-INBI4>3.0.CO;2-6. ISSN
1093-4391.
tree of the nematode C. elegans

[26] El Albani, Abderrazak; A, Bengtson S, Canfield DE,

Bekker A, Macchiarelli R, Mazurier A, Hammarlund EU,
Textbooks
Boulvais P, Dupuy JJ, Fontaine C, Fürsich FT, Gauthier-
Lafaye F, Janvier P, Javaux E, Ossa FO, Pierson- • Alberts B, Johnson A, Lewis J, Raff M, Roberts K,
Wickmann AC, Riboulleau A, Sardini P, Vachard D, Walter P (2002). Molecular Biology of the Cell (4th
Whitehouse M, Meunier A. (1 July 2010). “Large colo- ed.). Garland. ISBN 0-8153-3218-1.
nial organisms with coordinated growth in oxygenated
environments 2.1 Gyr ago”. Nature 466 (7302): 100– • Lodish H, Berk A, Matsudaira P, Kaiser CA,
104. doi:10.1038/nature09166. ISSN 0028-0836. PMID Krieger M, Scott MP, Zipurksy SL, Darnell J
20596019. (2004). Molecular Cell Biology (5th ed.). WH Free-
man: New York, NY. ISBN 978-0-7167-4366-8.
[27] Orgel LE (1998). “The origin of life--a review of facts
and speculations”. Trends Biochem Sci 23 (12): 491–5. • Cooper GM (2000). The cell: a molecular approach
doi:10.1016/S0968-0004(98)01300-0. PMID 9868373. (2nd ed.). Washington, D.C: ASM Press. ISBN 0-
87893-102-3.
[28] Griffiths G (December 2007). “Cell evolution and the
problem of membrane topology”. Nature reviews. Molec-
ular cell biology 8 (12): 1018–24. doi:10.1038/nrm2287.
PMID 17971839. 1.3 Water
[29] "... I could exceedingly plainly perceive it to be all perfo- This article is about general aspects of water. For a
rated and porous, much like a Honey-comb, but that the
detailed discussion of its physical and chemical proper-
pores of it were not regular [..] these pores, or cells, [..]
ties, see Properties of water. For other uses, see Water
were indeed the first microscopical pores I ever saw, and
perhaps, that were ever seen, for I had not met with any (disambiguation).
Writer or Person, that had made any mention of them be-
fore this. . .” – Hooke describing his observations on a
Water (chemical formula: H2 O) is a transparent fluid
thin slice of cork. Robert Hooke which forms the world’s streams, lakes, oceans and rain,
and is the major constituent of the fluids of living things.
• This article incorporates public domain material As a chemical compound, a water molecule contains one
from the NCBI document “Science Primer”. oxygen and two hydrogen atoms that are connected by
1.3. WATER 19

sanitation.[4] There is a clear correlation between access

to safe water and gross domestic product per capita.[5]
However, some observers have estimated that by 2025
more than half of the world population will be facing
water-based vulnerability.[6] A report, issued in Novem-
ber 2009, suggests that by 2030, in some developing re-
gions of the world, water demand will exceed supply by
50%.[7] Water plays an important role in the world econ-
omy, as it functions as a solvent for a wide variety of
chemical substances and facilitates industrial cooling and
transportation. Approximately 70% of the freshwater
Water in three states: liquid, solid (ice), and gas (invisible water used by humans goes to agriculture.[8]
vapor in the air). Clouds are accumulations of water droplets,
condensed from vapor-saturated air.
1.3.1 Chemical and physical properties

Main articles: Properties of water, Water (data page) and

Water model
Water is the chemical substance with chemical formula

Video demonstrating states of water present in domestic life.

covalent bonds. Water is a liquid at standard ambient

temperature and pressure, but it often co-exists on Earth
with its solid state, ice; and gaseous state, steam (water
vapor). It also exists as snow, fog, dew and cloud.
Water covers 71% of the Earth’s surface.[1] It is vital for
all known forms of life. On Earth, 96.5% of the planet’s
water is found in seas and oceans, 1.7% in groundwater,
1.7% in glaciers and the ice caps of Antarctica and Green-
land, a small fraction in other large water bodies, and
0.001% in the air as vapor, clouds (formed of ice and liq-
uid water suspended in air), and precipitation.[2][3] Only Model of hydrogen bonds (1) between molecules of water.
2.5% of the Earth’s water is freshwater, and 98.8% of that
water is in ice (excepting ice in clouds) and groundwater.
Less than 0.3% of all freshwater is in rivers, lakes, and the
atmosphere, and an even smaller amount of the Earth’s
freshwater (0.003%) is contained within biological bod-
ies and manufactured products.[2]
Water on Earth moves continually through the water cy-
cle of evaporation and transpiration (evapotranspiration),
condensation, precipitation, and runoff, usually reaching
the sea. Evaporation and transpiration contribute to the
precipitation over land. Water used in the production of
a good or service is known as virtual water.
Safe drinking water is essential to humans and other
lifeforms even though it provides no calories or organic
nutrients. Access to safe drinking water has improved Impact from a water drop causes an upward “rebound” jet sur-
over the last decades in almost every part of the world, rounded by circular capillary waves.
but approximately one billion people still lack access to
safe water and over 2.5 billion lack access to adequate H
20 CHAPTER 1. CELLS AND WATER

Snowflakes by Wilson Bentley, 1902.

Capillary action of water compared to mercury.

• Water is transparent in the visible electromagnetic

spectrum. Thus aquatic plants can live in water
because sunlight can reach them. Infrared light is
strongly absorbed by the hydrogen-oxygen or OH
bonds.

• Since the water molecule is not linear and the oxy-

gen atom has a higher electronegativity than hydro-
gen atoms, the oxygen atom carries a slight negative
charge, whereas the hydrogen atoms are slightly pos-
itive. As a result, water is a polar molecule with an
electrical dipole moment. Water also can form an
unusually large number of intermolecular hydrogen
Dew drops adhering to a spider web. bonds (four) for a molecule of its size. These factors
lead to strong attractive forces between molecules of
water, giving rise to water’s high surface tension[10]
2O: one molecule of water has two hydrogen atoms and capillary forces. The capillary action refers to
covalently bonded to a single oxygen atom. the tendency of water to move up a narrow tube
Water appears in nature in all three common states of against the force of gravity. This property is relied
matter (solid, liquid, and gas) and may take many dif- upon by all vascular plants, such as trees.[11]
ferent forms on Earth: water vapor and clouds in the
sky, seawater in the oceans, icebergs in the polar oceans, • Water is a good polar solvent and is often referred
glaciers in the mountains, fresh and salt water lakes, to as the universal solvent. Substances that dis-
rivers, and aquifers in the ground. solve in water, e.g., salts, sugars, acids, alkalis, and
some gases – especially oxygen and carbon diox-
The major chemical and physical properties of water are:
ide (carbonation) – are known as hydrophilic (water-
loving) substances, while those that are immiscible
• Water is a liquid at standard temperature and pres- with water (e.g., fats and oils), are known as
sure. It is tasteless and odorless. The intrinsic colour hydrophobic (water-fearing) substances.
of water and ice is a very slight blue hue, although
both appear colorless in small quantities. Water • All of the components in cells (proteins, DNA and
vapour is essentially invisible as a gas.[9] polysaccharides) are dissolved in water, deriving
1.3. WATER 21

their structure and activity from their interactions gradually formed in the low temperature water; the
with the water. random orientations of the water molecules in the
liquid are maintained by the thermal motion, and
• Pure water has a low electrical conductivity, but this below 3.98 °C there is not enough thermal energy to
increases with the dissolution of a small amount of maintain this randomness. As water is cooled there
ionic material such as sodium chloride. are two competing effects: 1) decreasing volume,
and 2) increase overall volume of the liquid as the
• The boiling point of water (and all other liquids) is molecules begin to orient into the organized struc-
dependent on the barometric pressure. For exam- ture of ice. Between 3.98 °C and 0 °C, the second
ple, on the top of Mount Everest water boils at 68 °C effect will cancel the first effect so the net effect is an
(154 °F), compared to 100 °C (212 °F) at sea level increase of volume with decreasing temperature.[13]
at a similar latitude (since latitude modifies atmo- Water expands to occupy a 9% greater volume as
spheric pressure slightly). Conversely, water deep ice, which accounts for the fact that ice floats on liq-
in the ocean near geothermal vents can reach tem- uid water, as in icebergs.
peratures of hundreds of degrees and remain liquid.
• Water is miscible with many liquids, such as ethanol,
• At 4181.3 J/(kg·K), water has a high specific heat ca- in all proportions, forming a single homogeneous
pacity, as well as a high heat of vaporization (40.65 liquid. On the other hand, water and most oils are
kJ·mol−1 ), both of which are a result of the extensive immiscible, usually forming layers with the least
hydrogen bonding between its molecules. These two dense liquid as the top layer, and the most dense
unusual properties allow water to moderate Earth’s layer at the bottom.
climate by buffering large fluctuations in tempera-
ture. • Water forms an azeotrope with many other solvents.

• The density of liquid water is 1,000 kg/m3 (62.43 • Water can be split by electrolysis into hydrogen and
lb/cu ft) at 4 °C. Ice has a density of 917 kg/m3 oxygen. The energy required to split water into
(57.25 lb/cu ft). hydrogen and oxygen by electrolysis or any other
means is greater than the energy that can be col-
lected when the hydrogen and oxygen recombine.[14]

• As an oxide of hydrogen, water is formed when hy-

drogen or hydrogen-containing compounds burn or
react with oxygen or oxygen-containing compounds.
Water is not a fuel, it is an end-product of the com-
bustion of hydrogen.

• Elements which are more electropositive than hy-

drogen such as lithium, sodium, calcium, potassium
DANGEROUS WHEN
WET and caesium displace hydrogen from water, form-
ing hydroxides. Being a flammable gas, the hydro-
gen given off is dangerous and the reaction of water
with the more electropositive of these elements may

4
be violently explosive.

1.3.2 Taste and odor

ADR label for transporting goods dangerously reactive with wa- Pure H2 O is tasteless and odorless.
ter Water can dissolve many different substances, giving it
varying tastes and odors. Humans, and other animals,
• The maximum density of water occurs at 3.98 °C have developed senses that enable them to evaluate the
[12]
(39.16 °F). Most known pure substances become potability of water by avoiding water that is too salty or
more dense as they cool, however water has the putrid.
anomalous property of becoming less dense when The taste of spring water and mineral water, often adver-
it is cooled to its solid form, ice. During cooling tised in marketing of consumer products, derives from the
water becomes more dense until reaching 3.98 °C. minerals dissolved in it. The advertised purity of spring
Below this temperature, the open structure of ice is and mineral water refers to absence of toxins, pollutants,
22 CHAPTER 1. CELLS AND WATER

and microbes, not to the absence of naturally occurring • Earth’s atmosphere: ~0.40% over full atmosphere,
minerals. typically 1–4% at surface; as well as that of the
Moon in trace amounts[22]

1.3.3 Distribution in nature • Atmosphere of Mars: 0.03%[23]

• Atmosphere of Ceres[24]
In the universe
• Atmosphere of Jupiter: 0.0004%[25] – in ices only;
and that of its moon Europa[26]
• Atmosphere of Saturn – in ices only; and that of
its moons Titan (stratospheric), Enceladus: 91%[27]
and Dione (exosphere)
• Atmosphere of Uranus - in trace amounts below 50
bar[28]
• Atmosphere of Neptune - found in the deeper
layers[29]
• Extrasolar planet atmospheres: including those
of HD 189733 b[30] and HD 209458 b,[31] Tau
Boötis b,[32] HAT-P-11b,[33][34] XO-1b, WASP-
Band 5 ALMA receiver is an instrument specifically designed to 12b, WASP-17b, and WASP-19b.[35]
detect water in the Universe.[15]
• Stellar atmospheres: not limited to cooler stars and
even detected in giant hot stars such as Betelgeuse,
Much of the universe’s water is produced as a byprod-
Mu Cephei, Antares and Arcturus.[34][36]
uct of star formation. When stars are born, their birth is
accompanied by a strong outward wind of gas and dust. • Circumstellar disks: including those of more than
When this outflow of material eventually impacts the sur- half of T Tauri stars such as AA Tauri[34] as well
rounding gas, the shock waves that are created compress as TW Hydrae,[37][38] IRC +10216[39] and APM
and heat the gas. The water observed is quickly produced 08279+5255,[17][18] VY Canis Majoris and S Per-
in this warm dense gas.[16] sei.[36]
On 22 July 2011 a report described the discovery of a gi-
gantic cloud of water vapor containing “140 trillion times Liquid water Liquid water is known to be present
more water than all of Earth’s oceans combined” around on Earth, covering 71% of its surface. Scientists be-
a quasar located 12 billion light years from Earth. Ac- lieve liquid water is present in the Saturnian moons
cording to the researchers, the “discovery shows that wa- of Enceladus, as a 10-kilometre thick ocean approxi-
ter has been prevalent in the universe for nearly its entire mately 30-40 kilometres below Enceladus’ south polar
existence”.[17][18] surface,[40][41] and Titan, as a subsurface layer, possibly
Water has been detected in interstellar clouds within our mixed with ammonia.[42] Jupiter’s moon Europa has sur-
galaxy, the Milky Way. Water probably exists in abun- face characteristics which suggest a subsurface liquid wa-
dance in other galaxies, too, because its components, hy- ter ocean.[43] Liquid water may also exist on Jupiter’s
drogen and oxygen, are among the most abundant ele- moon Ganymede as a layer sandwiched between high
ments in the universe. Based on models of the formation pressure ice and rock.[44]
and evolution of the Solar System and that of other star
systems, most other planetary systems are likely to have
Water ice Water is present as ice on:
similar ingredients.

• Mars: under the regolith and at the poles

Water vapor Water is present as vapor in:
• Earth-Moon system: mainly as ice sheets on
Earth and in Lunar craters and volcanic rocks[45]
• Atmosphere of the Sun: in detectable trace NASA reported the detection of water molecules by
amounts[19] NASA’s Moon Mineralogy Mapper aboard the In-
dian Space Research Organization’s Chandrayaan-1
• Atmosphere of Mercury: 3.4%, and large amounts spacecraft in September 2009.[46]
of water in Mercury’s exosphere[20]
• Jupiter’s moons: Europa's surface and also that of
• Atmosphere of Venus: 0.002%[21] Ganymede
1.3. WATER 23

The existence of liquid water, and to a lesser extent its

gaseous and solid forms, on Earth are vital to the exis-
tence of life on Earth as we know it. The Earth is located
in the habitable zone of the solar system; if it were slightly
closer to or farther from the Sun (about 5%, or about 8
million kilometers), the conditions which allow the three
forms to be present simultaneously would be far less likely
to exist.[50][51]
Earth’s gravity allows it to hold an atmosphere. Water
vapor and carbon dioxide in the atmosphere provide a
temperature buffer (greenhouse effect) which helps main-
tain a relatively steady surface temperature. If Earth were
smaller, a thinner atmosphere would allow temperature
extremes, thus preventing the accumulation of water ex-
cept in polar ice caps (as on Mars).
The surface temperature of Earth has been relatively con-
stant through geologic time despite varying levels of in-
coming solar radiation (insolation), indicating that a dy-
namic process governs Earth’s temperature via a combi-
nation of greenhouse gases and surface or atmospheric
albedo. This proposal is known as the Gaia hypothesis.
The state of water on a planet depends on ambient pres-
sure, which is determined by the planet’s gravity. If a
Turquoise water with a bit of Sun. planet is sufficiently massive, the water on it may be solid
even at high temperatures, because of the high pressure
caused by gravity, as it was observed on exoplanets Gliese
• Saturn: in the planet’s ring system[47] and on the sur- 436 b[52] and GJ 1214 b.[53]
face and mantle of Titan and Enceladus

• Pluto-Charon system[47] 1.3.4 On Earth

• Comets and related (Kuiper belt and Oort cloud ob- Main articles: Hydrology and Water distribution on Earth
jects). Hydrology is the study of the movement, distribu-

And may also be present on:

• Mercury’s poles[48]

• Ceres

• Tethys

Exotic forms Water and other volatiles probably com-

prise much of the internal structures of Uranus and
Neptune and the water in the deeper layers may be in the
form of ionic water in which the molecules break down
into a soup of hydrogen and oxygen ions, and deeper
down as superionic water in which the oxygen crystallises
but the hydrogen ions float around freely within the oxy-
gen lattice.[49]

Water covers 71% of the Earth’s surface; the oceans contain

Water and habitable zone 96.5% of the Earth’s water. The Antarctic ice sheet, which con-
tains 61% of all fresh water on Earth, is visible at the bottom.
Further information: Water distribution on Earth Condensed atmospheric water can be seen as clouds, contribut-
ing to the Earth’s albedo.
24 CHAPTER 1. CELLS AND WATER

tion, and quality of water throughout the Earth. The the air and transpiration from land plants and ani-
study of the distribution of water is hydrography. The mals into air.
study of the distribution and movement of groundwa-
ter is hydrogeology, of glaciers is glaciology, of in- • precipitation, from water vapor condensing from the
land waters is limnology and distribution of oceans is air and falling to earth or ocean.
oceanography. Ecological processes with hydrology are • runoff from the land usually reaching the sea.
in focus of ecohydrology.
The collective mass of water found on, under, and over Most water vapor over the oceans returns to the oceans,
the surface of a planet is called the hydrosphere. Earth’s but winds carry water vapor over land at the same rate
approximate water volume (the total water supply of the as runoff into the sea, about 47 Tt per year. Over land,
world) is 1,338,000,000 km3 (321,000,000 mi3 ).[2] evaporation and transpiration contribute another 72 Tt
Liquid water is found in bodies of water, such as an ocean, per year. Precipitation, at a rate of 119 Tt per year over
sea, lake, river, stream, canal, pond, or puddle. The ma- land, has several forms: most commonly rain, snow, and
jority of water on Earth is sea water. Water is also present hail, with some contribution from fog and dew.[54] Dew
in the atmosphere in solid, liquid, and vapor states. It also is small drops of water that are condensed when a high
exists as groundwater in aquifers. density of water vapor meets a cool surface. Dew usually
forms in the morning when the temperature is the low-
Water is important in many geological processes. est, just before sunrise and when the temperature of the
Groundwater is present in most rocks, and the pressure of earth’s surface starts to increase.[55] Condensed water in
this groundwater affects patterns of faulting. Water in the the air may also refract sunlight to produce rainbows.
mantle is responsible for the melt that produces volcanoes
Water runoff often collects over watersheds flowing into
at subduction zones. On the surface of the Earth, water
rivers. A mathematical model used to simulate river or
is important in both chemical and physical weathering
stream flow and calculate water quality parameters is a
processes. Water, and to a lesser but still significant
hydrological transport model. Some water is diverted to
extent, ice, are also responsible for a large amount of
irrigation for agriculture. Rivers and seas offer opportu-
sediment transport that occurs on the surface of the earth.
nity for travel and commerce. Through erosion, runoff
Deposition of transported sediment forms many types of
shapes the environment creating river valleys and deltas
sedimentary rocks, which make up the geologic record of
Earth history. which provide rich soil and level ground for the establish-
ment of population centers. A flood occurs when an area
of land, usually low-lying, is covered with water. It is
Water cycle when a river overflows its banks or flood comes from the
sea. A drought is an extended period of months or years
Main article: Water cycle when a region notes a deficiency in its water supply. This
The water cycle (known scientifically as the hydro- occurs when a region receives consistently below average
precipitation.

Fresh water storage

Water cycle

logic cycle) refers to the continuous exchange of water

within the hydrosphere, between the atmosphere, soil wa-
ter, surface water, groundwater, and plants.
Water moves perpetually through each of these regions in
the water cycle consisting of following transfer processes:

• evaporation from oceans and other water bodies into

1.3. WATER 25

The Bay of Fundy at high tide (left) and low tide (right)
Main article: Water resources

Some runoff water is trapped for periods of time, for ex-

ample in lakes. At high altitude, during winter, and in the
far north and south, snow collects in ice caps, snow pack
and glaciers. Water also infiltrates the ground and goes
into aquifers. This groundwater later flows back to the
surface in springs, or more spectacularly in hot springs
and geysers. Groundwater is also extracted artificially in
wells. This water storage is important, since clean, fresh
water is essential to human and other land-based life. In
many parts of the world, it is in short supply.
An oasis is an isolated water source with vegetation in a desert.
Sea water and tides
Plants, algae, many bacteria
Main articles: Seawater and Tides
(Autotrophs)

Sea water contains about 3.5% salt on average, plus

smaller amounts of other substances. The physical prop-
erties of sea water differ from fresh water in some im-
portant respects. It freezes at a lower temperature (about
−1.9 °C) and its density increases with decreasing tem-
perature to the freezing point, instead of reaching maxi- Organic Carbon dioxide
mum density at a temperature above freezing. The salin- compounds
Water
ity of water in major seas varies from about 0.7% in the
Oxygen
Baltic Sea to 4.0% in the Red Sea.
Tides are the cyclic rising and falling of local sea levels
caused by the tidal forces of the Moon and the Sun acting
on the oceans. Tides cause changes in the depth of the
marine and estuarine water bodies and produce oscillat- Animals, fungi,
ing currents known as tidal streams. The changing tide many bacteria
produced at a given location is the result of the chang- (Heterotrophs)
ing positions of the Moon and Sun relative to the Earth
coupled with the effects of Earth rotation and the local
bathymetry. The strip of seashore that is submerged at
high tide and exposed at low tide, the intertidal zone, is Overview of photosynthesis and respiration. Water (at right),
an important ecological product of ocean tides. together with carbon dioxide (CO2 ), form oxygen and organic
compounds (at left), which can be respired to water and (CO2 ).

1.3.5 Effects on life

energy use or other purposes). Without water, these par-
From a biological standpoint, water has many distinct ticular metabolic processes could not exist.
properties that are critical for the proliferation of life. It
carries out this role by allowing organic compounds to re- Water is fundamental to photosynthesis and respiration.
act in ways that ultimately allow replication. All known Photosynthetic cells use the sun’s energy to split off wa-
forms of life depend on water. Water is vital both as a ter’s hydrogen from oxygen. Hydrogen is combined with
solvent in which many of the body’s solutes dissolve and CO2 (absorbed from air or water) to form glucose and
as an essential part of many metabolic processes within release oxygen. All living cells use such fuels and oxi-
the body. Metabolism is the sum total of anabolism dize the hydrogen and carbon to capture the sun’s energy
and catabolism. In anabolism, water is removed from and reform water and CO2 in the process (cellular respi-
molecules (through energy requiring enzymatic chem- ration).
ical reactions) in order to grow larger molecules (e.g. Water is also central to acid-base neutrality and enzyme
starches, triglycerides and proteins for storage of fuels function. An acid, a hydrogen ion (H+ , that is, a proton)
and information). In catabolism, water is used to break donor, can be neutralized by a base, a proton acceptor
bonds in order to generate smaller molecules (e.g. glu- such as a hydroxide ion (OH− ) to form water. Water is
cose, fatty acids and amino acids to be used for fuels for considered to be neutral, with a pH (the negative log of the
26 CHAPTER 1. CELLS AND WATER

hydrogen ion concentration) of 7. Acids have pH values Aquatic vertebrates must obtain oxygen to survive, and
less than 7 while bases have values greater than 7. they do so in various ways. Fish have gills instead of
lungs, although some species of fish, such as the lungfish,
have both. Marine mammals, such as dolphins, whales,
Aquatic life forms otters, and seals need to surface periodically to breathe
air. Some amphibians are able to absorb oxygen through
Main articles: Hydrobiology and Aquatic plant their skin. Invertebrates exhibit a wide range of modi-
Earth surface waters are filled with life. The earliest life fications to survive in poorly oxygenated waters includ-
ing breathing tubes (see insect and mollusc siphons) and
gills (Carcinus). However as invertebrate life evolved in
an aquatic habitat most have little or no specialisation for
respiration in water.

1.3.6 Effects on human civilization

Water fountain

Some of the biodiversity of a coral reef Civilization has historically flourished around rivers and
major waterways; Mesopotamia, the so-called cradle of
civilization, was situated between the major rivers Tigris
and Euphrates; the ancient society of the Egyptians de-
pended entirely upon the Nile. Large metropolises like
Rotterdam, London, Montreal, Paris, New York City,
Buenos Aires, Shanghai, Tokyo, Chicago, and Hong
Kong owe their success in part to their easy accessibil-
ity via water and the resultant expansion of trade. Islands
with safe water ports, like Singapore, have flourished for
the same reason. In places such as North Africa and the
Middle East, where water is more scarce, access to clean
drinking water was and is a major factor in human devel-
opment.

Some marine diatoms – a key phytoplankton group

Health and pollution
forms appeared in water; nearly all fish live exclusively
in water, and there are many types of marine mammals, Water fit for human consumption is called drinking water
such as dolphins and whales. Some kinds of animals, such or potable water. Water that is not potable may be made
as amphibians, spend portions of their lives in water and potable by filtration or distillation, or by a range of other
portions on land. Plants such as kelp and algae grow in the methods.
water and are the basis for some underwater ecosystems. Water that is not fit for drinking but is not harmful for
Plankton is generally the foundation of the ocean food humans when used for swimming or bathing is called by
chain. various names other than potable or drinking water, and is
1.3. WATER 27

in reserve in the earth (about 1% of our drinking water

supply, which is replenished in aquifers around every 1
to 10 years), that is a non-renewable resource, and it is,
rather, the distribution of potable and irrigation water
which is scarce, rather than the actual amount of it that
exists on the earth. Water-poor countries use importa-
tion of goods as the primary method of importing water
(to leave enough for local human consumption), since the
manufacturing process uses around 10 to 100 times prod-
ucts’ masses in water.
In the developing world, 90% of all wastewater still goes
untreated into local rivers and streams.[58] Some 50 coun-
tries, with roughly a third of the world’s population, also
suffer from medium or high water stress, and 17 of these
An environmental science program - a student from Iowa State extract more water annually than is recharged through
University sampling water
their natural water cycles.[59] The strain not only affects
surface freshwater bodies like rivers and lakes, but it also
degrades groundwater resources.
sometimes called safe water, or “safe for bathing”. Chlo-
rine is a skin and mucous membrane irritant that is used to
make water safe for bathing or drinking. Its use is highly Human uses
technical and is usually monitored by government regu-
lations (typically 1 part per million (ppm) for drinking Further information: Water supply
water, and 1–2 ppm of chlorine not yet reacted with im-
purities for bathing water). Water for bathing may be
maintained in satisfactory microbiological condition us-
ing chemical disinfectants such as chlorine or ozone or by
the use of ultraviolet light.
In the USA, non-potable forms of wastewater generated
by humans may be referred to as greywater, which is
treatable and thus easily able to be made potable again,
and blackwater, which generally contains sewage and
other forms of waste which require further treatment in
order to be made reusable. Greywater composes 50–80%
of residential wastewater generated by a household’s san-
itation equipment (sinks, showers and kitchen runoff, but
not toilets, which generate blackwater.) These terms may
have different meanings in other countries and cultures.
This natural resource is becoming scarcer in certain
places, and its availability is a major social and economic
concern. Currently, about a billion people around the Water distribution in subsurface drip irrigation
world routinely drink unhealthy water. Most countries
accepted the goal of halving by 2015 the number of peo-
ple worldwide who do not have access to safe water and
sanitation during the 2003 G8 Evian summit.[56] Even
if this difficult goal is met, it will still leave more than
an estimated half a billion people without access to safe
drinking water and over a billion without access to ade-
quate sanitation. Poor water quality and bad sanitation
are deadly; some five million deaths a year are caused by
polluted drinking water. The World Health Organization
estimates that safe water could prevent 1.4 million child
deaths from diarrhea each year.[57]
Water, however, is not a finite resource, but rather re-
circulated as potable water in precipitation in quantities
many degrees of magnitude higher than human consump-
tion. Therefore, it is the relatively small quantity of water Irrigation of field crops
28 CHAPTER 1. CELLS AND WATER

Agriculture The most important use of water in 4 °C (39 °F).[67]

agriculture is for irrigation, which is a key component The Kelvin temperature scale of the SI system is based
to produce enough food. Irrigation takes up to 90% of on the triple point of water, defined as exactly 273.16 K
water withdrawn in some developing countries[60] and or 0.01 °C. The scale is an absolute temperature scale
significant proportions in more economically developed with the same increment as the Celsius temperature scale,
countries (United States, 30% of freshwater usage is for which was originally defined according the boiling point
irrigation).[61] (set to 100 °C) and melting point (set to 0 °C) of water.
Fifty years ago, the common perception was that water Natural water consists mainly of the isotopes hydrogen-1
was an infinite resource. At this time, there were fewer and oxygen-16, but there is also a small quantity of heav-
than half the current number of people on the planet. ier isotopes such as hydrogen-2 (deuterium). The amount
People were not as wealthy as today, consumed fewer of deuterium oxides or heavy water is very small, but it
calories and ate less meat, so less water was needed to pro- still affects the properties of water. Water from rivers
duce their food. They required a third of the volume of and lakes tends to contain less deuterium than seawater.
water we presently take from rivers. Today, the competi- Therefore, standard water is defined in the Vienna Stan-
tion for the fixed amount of water resources is much more dard Mean Ocean Water specification.
intense, giving rise to the concept of peak water.[62] This
is because there are now nearly seven billion people on
the planet, their consumption of water-thirsty meat and For drinking Main article: Drinking water
vegetables is rising, and there is increasing competition The human body contains from 55% to 78% water, de-
for water from industry, urbanisation and biofuel crops.
In future, even more water will be needed to produce food
because the Earth’s population is forecast to rise to 9 bil-
lion by 2050.[63]
An assessment of water management in agriculture was
conducted in 2007 by the International Water Manage-
ment Institute in Sri Lanka to see if the world had suffi-
cient water to provide food for its growing population.[64]
It assessed the current availability of water for agricul-
ture on a global scale and mapped out locations suffering
from water scarcity. It found that a fifth of the world’s
people, more than 1.2 billion, live in areas of physical
water scarcity, where there is not enough water to meet
all demands. A further 1.6 billion people live in areas ex-
periencing economic water scarcity, where the lack of in- A young girl drinking bottled water
vestment in water or insufficient human capacity make it
impossible for authorities to satisfy the demand for water.
The report found that it would be possible to produce the
food required in future, but that continuation of today’s
food production and environmental trends would lead to
crises in many parts of the world. To avoid a global water
crisis, farmers will have to strive to increase productivity
to meet growing demands for food, while industry and
cities find ways to use water more efficiently.[65] Everyone has clean water (95-100% of pop.)
Most people have clean water (75-94.9% of pop.)
At least 1 in every 4 people don't have clean water (<74.9% of pop.)
No data available

As a scientific standard On 7 April 1795, the gram

was defined in France to be equal to “the absolute weight Water availability: fraction of population using improved water
of a volume of pure water equal to a cube of one hun- sources by country
dredth of a meter, and at the temperature of melting
ice.”[66] For practical purposes though, a metallic ref- pending on body size.[68] To function properly, the body
erence standard was required, one thousand times more requires between one and seven liters of water per day
massive, the kilogram. Work was therefore commis- to avoid dehydration; the precise amount depends on the
sioned to determine precisely the mass of one liter of wa- level of activity, temperature, humidity, and other fac-
ter. In spite of the fact that the decreed definition of the tors. Most of this is ingested through foods or beverages
gram specified water at 0 °C — a highly reproducible tem- other than drinking straight water. It is not clear how
perature — the scientists chose to redefine the standard much water intake is needed by healthy people, though
and to perform their measurements at the temperature of most specialists agree that approximately 2 liters (6 to 7
highest water density, which was measured at the time as glasses) of water daily is the minimum to maintain proper
1.3. WATER 29

hydration.[69] Medical literature favors a lower consump- sweating, and by exhalation of water vapor in the breath.
tion, typically 1 liter of water for an average male, exclud- With physical exertion and heat exposure, water loss will
ing extra requirements due to fluid loss from exercise or increase and daily fluid needs may increase as well.
warm weather.[70] Humans require water with few impurities. Common
For those who have healthy kidneys, it is rather difficult impurities include metal salts and oxides, including cop-
to drink too much water, but (especially in warm humid per, iron, calcium and lead,[84] and/or harmful bacteria,
weather and while exercising) it is dangerous to drink too such as Vibrio. Some solutes are acceptable and even
little. People can drink far more water than necessary desirable for taste enhancement and to provide needed
while exercising, however, putting them at risk of water electrolytes.[85]
intoxication (hyperhydration), which can be fatal.[71][72] The single largest (by volume) freshwater resource suit-
The popular claim that “a person should consume eight able for drinking is Lake Baikal in Siberia.[86]
glasses of water per day” seems to have no real basis in
science.[73] Studies have shown that extra water intake,
especially up to 500 ml at mealtime was conducive to Washing The propensity of water to form solutions and
weight loss.[74][75][76][77][78][79] Adequate fluid intake is emulsions is useful in various washing processes. Many
helpful in preventing constipation.[80] industrial processes rely on reactions using chemicals dis-
solved in water, suspension of solids in water slurries or
using water to dissolve and extract substances. Washing
is also an important component of several aspects of per-
sonal body hygiene.

Transportation Main article: Ship transport

The use of water for transportation of materials through

rivers and canals as well as the international shipping lanes
is an important part of the world economy.

Chemical uses Water is widely used in chemical re-

actions as a solvent or reactant and less commonly as a
solute or catalyst. In inorganic reactions, water is a com-
mon solvent, dissolving many ionic compounds. In or-
ganic reactions, it is not usually used as a reaction sol-
vent, because it does not dissolve the reactants well and is
Hazard symbol for non-potable water amphoteric (acidic and basic) and nucleophilic. Never-
theless, these properties are sometimes desirable. Also,
An original recommendation for water intake in 1945 acceleration of Diels-Alder reactions by water has been
by the Food and Nutrition Board of the United States observed. Supercritical water has recently been a topic
National Research Council read: “An ordinary standard of research. Oxygen-saturated supercritical water com-
for diverse persons is 1 milliliter for each calorie of busts organic pollutants efficiently.
food. Most of this quantity is contained in prepared
foods.”[81] The latest dietary reference intake report by Heat exchange Water and steam are a common fluid
the United States National Research Council in general used for heat exchange, due to its availability and high
recommended (including food sources): 3.7 liters for heat capacity, both for cooling and heating. Cool water
men and 2.7 liters of water total for women.[82] may even be naturally available from a lake or the sea. It’s
Specifically, pregnant and breastfeeding women need ad- especially effective to transport heat through vaporization
ditional fluids to stay hydrated. The Institute of Medicine and condensation of water because of its large latent heat
(U.S.) recommends that, on average, men consume 3.0 of vaporization. A disadvantage is that metals commonly
liters and women 2.2 liters; pregnant women should in- found in industries such as steel and copper are oxidized
crease intake to 2.4 liters (10 cups) and breastfeeding faster by untreated water and steam. In almost all thermal
women should get 3 liters (12 cups), since an especially power stations, water is used as the working fluid (used
large amount of fluid is lost during nursing.[83] Also noted in a closed loop between boiler, steam turbine and con-
is that normally, about 20% of water intake comes from denser), and the coolant (used to exchange the waste heat
food, while the rest comes from drinking water and bev- to a water body or carry it away by evaporation in a
erages (caffeinated included). Water is excreted from the cooling tower). In the United States, cooling power plants
body in multiple forms; through urine and feces, through is the largest use of water.[61]
30 CHAPTER 1. CELLS AND WATER

In the nuclear power industry, water can also be used as

a neutron moderator. In most nuclear reactors, water is
both a coolant and a moderator. This provides something
of a passive safety measure, as removing the water from
the reactor also slows the nuclear reaction down. However
other methods are favored for stopping a reaction and it
is preferred to keep the nuclear core covered with water
so as to ensure adequate cooling.

Grand Anse Beach, St. George’s, Grenada, West Indies

water to be calming, and fountains and other water fea-

tures are popular decorations. Some keep fish and other
life in aquariums or ponds for show, fun, and companion-
ship. Humans also use water for snow sports i.e. skiing,
sledding, snowmobiling or snowboarding, which require
the water to be frozen.

Water is used for fighting wildfires.

Fire extinction Water has a high heat of vaporization

and is relatively inert, which makes it a good fire extin-
guishing fluid. The evaporation of water carries heat away
from the fire. It is dangerous to use water on fires in-
volving oils and organic solvents, because many organic
materials float on water and the water tends to spread the
burning liquid.
Use of water in fire fighting should also take into account
the hazards of a steam explosion, which may occur when
water is used on very hot fires in confined spaces, and of
a hydrogen explosion, when substances which react with
water, such as certain metals or hot carbon such as coal,
charcoal, or coke graphite, decompose the water, produc-
ing water gas.
The power of such explosions was seen in the Chernobyl
disaster, although the water involved did not come from
fire-fighting at that time but the reactor’s own water cool-
ing system. A steam explosion occurred when the ex-
treme overheating of the core caused water to flash into
steam. A hydrogen explosion may have occurred as a re-
sult of reaction between steam and hot zirconium.

Recreation Main article: Water sport (recreation) A water-carrier in India, 1882. In many places where running
water is not available, water has to be transported by people.
Humans use water for many recreational purposes, as well
as for exercising and for sports. Some of these include Water industry The water industry provides drinking
swimming, waterskiing, boating, surfing and diving. In water and wastewater services (including sewage treat-
addition, some sports, like ice hockey and ice skating, are ment) to households and industry. Water supply facil-
played on ice. Lakesides, beaches and water parks are ities include water wells, cisterns for rainwater harvest-
popular places for people to go to relax and enjoy recre- ing, water supply networks, and water purification facili-
ation. Many find the sound and appearance of flowing ties, water tanks, water towers, water pipes including old
1.3. WATER 31

resources.
Polluting water may be the biggest single misuse of wa-
ter; to the extent that a pollutant limits other uses of the
water, it becomes a waste of the resource, regardless of
benefits to the polluter. Like other types of pollution, this
does not enter standard accounting of market costs, be-
ing conceived as externalities for which the market can-
not account. Thus other people pay the price of water
pollution, while the private firms’ profits are not redis-
tributed to the local population, victims of this pollution.
Pharmaceuticals consumed by humans often end up in the
waterways and can have detrimental effects on aquatic life
if they bioaccumulate and if they are not biodegradable.
A manual water pump in China Wastewater facilities are storm sewers and wastewater
treatment plants. Another way to remove pollution from
surface runoff water is bioswale.

Industrial applications Water is used in power gen-

eration. Hydroelectricity is electricity obtained from
hydropower. Hydroelectric power comes from water
driving a water turbine connected to a generator. Hydro-
electricity is a low-cost, non-polluting, renewable energy
source. The energy is supplied by the motion of water.
Typically a dam is constructed on a river, creating an ar-
tificial lake behind it. Water flowing out of the lake is
forced through turbines that turn generators.

Water purification facility

aqueducts. Atmospheric water generators are in develop-

ment.
Drinking water is often collected at springs, extracted
from artificial borings (wells) in the ground, or pumped
from lakes and rivers. Building more wells in adequate
places is thus a possible way to produce more water, as-
suming the aquifers can supply an adequate flow. Other
water sources include rainwater collection. Water may
require purification for human consumption. This may
involve removal of undissolved substances, dissolved sub-
stances and harmful microbes. Popular methods are
filtering with sand which only removes undissolved mate-
rial, while chlorination and boiling kill harmful microbes. Three Gorges Dam is the largest hydro-electric power
Distillation does all three functions. More advanced tech- station.
niques exist, such as reverse osmosis. Desalination of
abundant seawater is a more expensive solution used in Pressurized water is used in water blasting and water jet
coastal arid climates. cutters. Also, very high pressure water guns are used for
The distribution of drinking water is done through precise cutting. It works very well, is relatively safe, and
municipal water systems, tanker delivery or as bottled wa- is not harmful to the environment. It is also used in the
ter. Governments in many countries have programs to cooling of machinery to prevent overheating, or prevent
distribute water to the needy at no charge. saw blades from overheating.
Reducing usage by using drinking (potable) water only Water is also used in many industrial processes and ma-
for human consumption is another option. In some cities chines, such as the steam turbine and heat exchanger, in
such as Hong Kong, sea water is extensively used for addition to its use as a chemical solvent. Discharge of un-
flushing toilets citywide in order to conserve fresh water treated water from industrial uses is pollution. Pollution
32 CHAPTER 1. CELLS AND WATER

includes discharged solutes (chemical pollution) and dis- mg/l (USA).[90]

charged coolant water (thermal pollution). Industry re- According to a report published by the Water Footprint
quires pure water for many applications and utilizes a va- organization in 2010, a single kilogram of beef requires
riety of purification techniques both in water supply and 15 thousand litres of water; however, the authors also
discharge. make clear that this is a global average and circumstan-
tial factors determine the amount of water used in beef
production.[91]

1.3.7 Law, politics, and crisis

Main articles: Water law, Water right and Water crisis
Water politics is politics affected by water and water re-

Water can be used to cook foods such as noodles.

Food processing Boiling, steaming, and simmering are

popular cooking methods that often require immersing
food in water or its gaseous state, steam. Water is also
used for dishwashing. Water also plays many critical roles
within the field of food science. It is important for a food
scientist to understand the roles that water plays within An estimate of the share of people in developing countries with
food processing to ensure the success of their products. access to potable water 1970–2000
Solutes such as salts and sugars found in water affect the
physical properties of water. The boiling and freezing sources. For this reason, water is a strategic resource in
points of water are affected by solutes, as well as air pres- the globe and an important element in many political con-
sure, which is in turn is affected by altitude. Water boils flicts. It causes health impacts and damage to biodiver-
at lower temperatures with the lower air pressure that oc- sity.
curs at higher elevations. One mole of sucrose (sugar) 1.6 billion people have gained access to a safe water
per kilogram of water raises the boiling point of water by source since 1990.[92] The proportion of people in de-
0.51 °C (0.918 °F), and one mole of salt per kg raises the veloping countries with access to safe water is calculated
boiling point by 1.02 °C (1.836 °F); similarly, increasing to have improved from 30% in 1970[93] to 71% in 1990,
the number of dissolved particles lowers water’s freezing 79% in 2000 and 84% in 2004. This trend is projected
point.[87] to continue.[4] To halve, by 2015, the proportion of peo-
Solutes in water also affect water activity that affects ple without sustainable access to safe drinking water is
one of the Millennium Development Goals. This goal is
many chemical reactions and the growth of microbes in
food. Water activity can be described as a ratio of the projected to be reached.
[88]

vapor pressure of water in a solution to the vapor pressure A 2006 United Nations report stated that “there is enough
of pure water.[87] Solutes in water lower water activity— water for everyone”, but that access to it is hampered
this is important to know because most bacterial growth by mismanagement and corruption.[94] In addition, global
ceases at low levels of water activity.[88] Not only does initiatives to improve the efficiency of aid delivery, such
microbial growth affect the safety of food, but also the as the Paris Declaration on Aid Effectiveness, have not
preservation and shelf life of food. been taken up by water sector donors as effectively as they
Water hardness is also a critical factor in food processing have in education and health, potentially leaving multi-
and may be altered or treated by using a chemical ion ple donors working on overlapping projects[95] and recipient
exchange system. It can dramatically affect the quality governments without empowerment to act.
of a product, as well as playing a role in sanitation. Water The authors of the 2007 Comprehensive Assessment of
hardness is classified based on concentration of calcium Water Management in Agriculture cited poor governance
carbonate the water contains. Water is classified as soft as one reason for some forms of water scarcity. Water
if it contains less than 100 mg/l (UK)[89] or less than 60 governance is the set of formal and informal processes
1.3. WATER 33

through which decisions related to water management are body using clean water (wudu), unless water is unavail-
made. Good water governance is primarily about know- able (see Tayammum). In Shinto, water is used in almost
ing what processes work best in a particular physical and all rituals to cleanse a person or an area (e.g., in the ritual
socioeconomic context. Mistakes have sometimes been of misogi).
made by trying to apply 'blueprints’ that work in the de-
veloped world to developing world locations and con-
texts. The Mekong river is one example; a review by Philosophy
the International Water Management Institute of policies
in six countries that rely on the Mekong river for water The Ancient Greek philosopher Empedocles held that
found that thorough and transparent cost-benefit analyses water is one of the four classical elements along with fire,
and environmental impact assessments were rarely under- earth and air, and was regarded as the ylem, or basic sub-
taken. They also discovered that Cambodia’s draft water stance of the universe. Thales, who was portrayed by
law was much more complex than it needed to be.[96] Aristotle as an astronomer and an engineer, theorized that
the earth, which is denser than water, emerged from the
The UN World Water Development Report (WWDR, water. Thales, a monist, believed further that all things
2003) from the World Water Assessment Program in- are made from water. Plato believed the shape of water
dicates that, in the next 20 years, the quantity of water is an icosahedron which accounts for why it is able to flow
available to everyone is predicted to decrease by 30%. easily compared to the cube-shaped earth.[97]
40% of the world’s inhabitants currently have insufficient
fresh water for minimal hygiene. More than 2.2 million In the theory of the four bodily humors, water was associ-
people died in 2000 from waterborne diseases (related to ated with phlegm, as being cold and moist. The classical
the consumption of contaminated water) or drought. In element of water was also one of the five elements in tra-
2004, the UK charity WaterAid reported that a child dies ditional Chinese philosophy, along with earth, fire, wood,
every 15 seconds from easily preventable water-related and metal.
diseases; often this means lack of sewage disposal; see Water is also taken as a role model in some parts of tra-
toilet. ditional and popular Asian philosophy. James Legge’s
Organizations concerned with water protection include 1891 translation of the Dao De Jing states “The high-
the International Water Association (IWA), WaterAid, est excellence is like (that of) water. The excellence of
Water 1st, and the American Water Resources Associ- water appears in its benefiting all things, and in its oc-
ation. The International Water Management Institute un- cupying, without striving (to the contrary), the low place
dertakes projects with the aim of using effective water which all men dislike. Hence (its way) is near to (that
management to reduce poverty. Water related conven- of) the Tao” and “There is nothing in the world more soft
tions are United Nations Convention to Combat Deserti- and weak than water, and yet for attacking things that are
fication (UNCCD), International Convention for the Pre- firm and strong there is nothing that can take precedence
vention of Pollution from Ships, United Nations Con- of it—for there is nothing (so effectual) for which it can
vention on the Law of the Sea and Ramsar Convention. be changed.”[98] Guanzi in “Shui di” chapter further
World Day for Water takes place on 22 March and World elaborates on symbolism of water, proclaiming that “man
Ocean Day on 8 June. is water” and attributing natural qualities of the people of
different Chinese regions to the character of local water
resources.[99]
1.3.8 In culture
1.3.9 See also
Religion
Main article: Outline of water
Main article: Water and religion

Water is considered a purifier in most religions. • The water (data page) is a collection of the chemical
Faiths that incorporate ritual washing (ablution) include and physical properties of water.
Christianity, Hinduism, Islam, Judaism, the Rastafari
movement, Shinto, Taoism, and Wicca. Immersion (or Water is described in many terms and contexts:
aspersion or affusion) of a person in water is a central
sacrament of Christianity (where it is called baptism); it • according to state
is also a part of the practice of other religions, includ-
ing Islam (Ghusl), Judaism (mikvah) and Sikhism (Amrit • solid – ice
Sanskar). In addition, a ritual bath in pure water is per- • liquid – water
formed for the dead in many religions including Islam and
Judaism. In Islam, the five daily prayers can be done in • gaseous – water vapor
most cases after completing washing certain parts of the • plasma
34 CHAPTER 1. CELLS AND WATER

• purified water, laboratory-grade, analytical-

grade or reagent-grade water – water which
has been highly purified for specific uses in sci-
ence or engineering. Often broadly classified
as Type I, Type II, or Type III, this category
of water includes, but is not limited to, the fol-
lowing:
• deionized water
• distilled water
• double distilled water
Liquid water and ice structures • reverse osmosis plant water
• tap water
• according to meteorology: • according to other features
• hydrometeor • distilled water, double distilled water,
• precipitation deionized water – contains no minerals
• hard water – from underground, contains more
minerals
• heavy water – made from heavy atoms of hy-
• • levitating particles drogen – deuterium. It is in nature in normal
water in very low concentration. It was used
• clouds in construction of first nuclear reactors.
• fog • hydrates – water bound into other chemical
• mist substances
• ascending particles (drifted by wind) • soft water – contains fewer minerals
• spindrift • tritiated water
• stirred snow • water of crystallization – water incorporated
into crystalline structures
• according to occurrence
• according to civil engineering
• brackish water • drinking water
• brine • stormwater or surface water
• connate water • wastewater
• dead water – strange phenomenon which can
• according to religion
occur when a layer of fresh or brackish wa-
ter rests on top of denser salt water, without • holy water
the two layers mixing. It is dangerous for ship
traveling.
Other topics
• fresh water
• groundwater • Aquaphobia (fear of water)
• meltwater • Dihydrogen monoxide hoax
• meteoric water • Drought
• mineral water – contains many minerals • Mirage
• seawater
• Mpemba effect
• surface water
• Oral rehydration therapy
• according to uses • Ripple effect

• bottled water • Thirst

• drinking water or potable water – useful for • Water Pasteurization Indicator
everyday drinking, without fouling, it con-
• Water pinch analysis
tains balanced minerals that are not harmful
to health (see below) • Willard Water
1.3. WATER 35

1.3.10 References [17] Clavin, Whitney; Buis, Alan (22 July 2011).
“Astronomers Find Largest, Most Distant Reservoir
[1] “CIA - The world factbook”. Central Intelligence Agency. of Water”. NASA. Retrieved 25 July 2011.
Retrieved 20 December 2008.
[18] Staff (22 July 2011). “Astronomers Find Largest, Oldest
[2] Gleick, P.H., ed. (1993). Water in Crisis: A Guide to the Mass of Water in Universe”. Space.com. Retrieved 23
World’s Freshwater Resources. Oxford University Press. July 2011.
p. 13, Table 2.1 “Water reserves on the earth”.
[19] Solanki, S. K.; Livingston, W.; Ayres, T.
[3] Water Vapor in the Climate System, Special Report, (1994). “New Light on the Heart of Dark-
[AGU], December 1995 (linked 4/2007). Vital Water ness of the Solar Chromosphere”. Science 263
UNEP. (5143): 64–66. Bibcode:1994Sci...263...64S.
[4] “MDG Report 2008” (PDF). Retrieved 25 July 2010. doi:10.1126/science.263.5143.64. PMID 17748350.

[5] “Public Services”, Gapminder video [20] “MESSENGER Scientists 'Astonished' to Find Water in
Mercury’s Thin Atmosphere”. Planetary Society. 3 July
[6] Kulshreshtha, S.N (1998). “A Global Outlook for Water 2008. Archived from the original on 16 October 2010.
Resources to the Year 2025”. Water Resources Manage- Retrieved 5 July 2008.
ment 12 (3): 167–184. doi:10.1023/A:1007957229865.
[21] Bertaux, Jean-Loup; Vandaele, Ann-Carine; Ko-
[7] “Charting Our Water Future: Economic frameworks to rablev, Oleg; Villard, E.; Fedorova, A.; Fussen, D.;
inform decision-making” (PDF). Retrieved 25 July 2010. Quémerais, E.; Belyaev, D. et al. (2007). “A warm
layer in Venus’ cryosphere and high-altitude measure-
[8] Baroni, L.; Cenci, L.; Tettamanti, M.; Berati, M.
ments of HF, HCl, H2O and HDO”. Nature 450
(2007). “Evaluating the environmental impact of vari-
(7170): 646–649. Bibcode:2007Natur.450..646B.
ous dietary patterns combined with different food pro-
doi:10.1038/nature05974. PMID 18046397.
duction systems”. European Journal of Clinical Nutrition
61 (2): 279–286. doi:10.1038/sj.ejcn.1602522. PMID
[22] Sridharan, R.; S.M. Ahmed, Tirtha Pratim Dasa, P.
17035955.
Sreelathaa, P. Pradeepkumara, Neha Naika, and Gogu-
[9] Braun, Charles L.; Sergei N. Smirnov (1993). lapati Supriya (2010). "'Direct' evidence for water
“Why is water blue?". J. Chem. Educ. 70 (H2O) in the sunlit lunar ambience from CHACE on
(8): 612. Bibcode:1993JChEd..70..612B. MIP of Chandrayaan I”. Planetary and Space Sci-
doi:10.1021/ed070p612. ence 58 (6): 947. Bibcode:2010P&SS...58..947S.
doi:10.1016/j.pss.2010.02.013.
[10] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
(2006). Biology: Exploring Life. Boston, Massachusetts: [23] Donald Rapp (28 November 2012). Use of Extraterrestrial
Pearson Prentice Hall. ISBN 0-13-250882-6. Resources for Human Space Missions to Moon or Mars.
Springer. pp. 78–. ISBN 978-3-642-32762-9.
[11] Capillary Action – Liquid, Water, Force, and Surface –
JRank Articles [24] Küppers, M.; O'Rourke, L.; Bockelée-Morvan, D.; Za-
kharov, V.; Lee, S.; Von Allmen, P.; Carry, B.; Teyssier,
[12] Kotz, J. C., Treichel, P., & Weaver, G. C. (2005). D.; Marston, A.; Müller, T.; Crovisier, J.; Barucci, M.
Chemistry & Chemical Reactivity. Thomson Brooks/Cole. A.; Moreno, R. (23 January 2014). “Localized sources
ISBN 0-534-39597-X. of water vapour on the dwarf planet (1) Ceres”. Nature
[13] Ben-Naim, Ariel; Ben-Naim, Roberta et al. (2011). 505 (7484): 525–527. Bibcode:2014Natur.505..525K.
Alice’s Adventures in Water-land. Singapore. doi:10.1038/nature12918. ISSN 0028-0836. PMID
doi:10.1142/8068. ISBN 978-981-4338-96-7. 24451541.

[14] Ball, Philip (14 September 2007). “Burning water and [25] Atreya, Sushil K.; Wong, Ah-San (2005). “Coupled
other myths”. Nature News. Retrieved 14 September Clouds and Chemistry of the Giant Planets — A
2007. Case for Multiprobes” (PDF). Space Science Reviews
116: 121–136. Bibcode:2005SSRv..116..121A.
[15] “ALMA Greatly Improves Capacity to Search for Water doi:10.1007/s11214-005-1951-5. ISSN 0032-0633.
in Universe”. Retrieved 20 July 2015.
[26] Cook, Jia-Rui C.; Gutro, Rob; Brown, Dwayne; Harring-
[16] Melnick, Gary, Harvard-Smithsonian Center for Astro- ton, J.D.; Fohn, Joe (12 December 2013). “Hubble Sees
physics and Neufeld, David, Johns Hopkins University Evidence of Water Vapor at Jupiter Moon”. NASA. Re-
quoted in: “Discover of Water Vapor Near Orion Nebula trieved 12 December 2013.
Suggests Possible Origin of H20 in Solar System (sic)".
The Harvard University Gazette. 23 April 1998. “Space [27] Hansen; C. J. et al. (2006). “Enceladus’
Cloud Holds Enough Water to Fill Earth’s Oceans 1 Mil- Water Vapor Plume”. Science 311 (5766):
lion Times”. Headlines@Hopkins, JHU. 9 April 1998. 1422–5. Bibcode:2006Sci...311.1422H.
“Water, Water Everywhere: Radio telescope finds water doi:10.1126/science.1121254. PMID 16527971.
is common in universe”. The Harvard University Gazette.
25 February 1999.(linked 4/2007) [28] Encrenaz 2003, p. 92.
36 CHAPTER 1. CELLS AND WATER

[29] Hubbard, W. B. (1997). “Neptune’s Deep [48] NASA, "MESSENGER Finds New Evidence for Water
Chemistry”. Science 275 (5304): 1279–1280. Ice at Mercury’s Poles", 29 November 2012.
doi:10.1126/science.275.5304.1279. PMID 9064785.
[49] Weird water lurking inside giant planets, New Scientist, 1
[30] Water Found on Distant Planet 12 July 2007 By Laura September 2010, Magazine issue 2776.
Blue, Time
[50] Ehlers, E.; Krafft, T, ed. (2001). “J. C. I. Dooge. “Inte-
[31] Water Found in Extrasolar Planet’s Atmosphere – grated Management of Water Resources"". Understand-
Space.com ing the Earth System: compartments, processes, and inter-
actions. Springer. p. 116.
[32] Near-IR Direct Detection of Water Vapor in Tau Boo
b: Alexandra C. Lockwood, John A. Johnson, Chad F. [51] “Habitable Zone”. The Encyclopedia of Astrobiology, As-
Bender, John S. Carr, Travis Barman, Alexander J.W. tronomy and Spaceflight.
Richert, Geoffrey A. Blake
[52] Shiga, David (6 May 2007). “Strange alien world made of
[33] Clavin, Whitney; Chou, Felicia; Weaver, Donna; Villard; “hot ice"". New Scientist. Retrieved 28 March 2010.
Johnson, Michele (24 September 2014). “NASA Tele-
scopes Find Clear Skies and Water Vapor on Exoplanet”. [53] Aguilar, David A. (16 December 2009). “Astronomers
NASA. Retrieved 24 September 2014. Find Super-Earth Using Amateur, Off-the-Shelf Technol-
ogy”. Harvard-Smithsonian Center for Astrophysics. Re-
[34] Arnold Hanslmeier (29 September 2010). Water in the trieved 28 March 2010.
Universe. Springer Science & Business Media. pp. 159–.
ISBN 978-90-481-9984-6. [54] Gleick, P.H., ed. (1993). Water in Crisis: A Guide to the
World’s Freshwater Resources. Oxford University Press.
[35] Staff (3 December 2013). “Hubble Traces Subtle Signals p. 15, Table 2.3.
of Water on Hazy Worlds”. NASA. Retrieved 4 Decem-
ber 2013. [55] Ben-Naim, A. and Ben-Naim, R., P.H. (2011). Alice’s
Adventures in Water-land. World Scientific Publishing. p.
[36] http://lup.lub.lu.se/luur/download?func=downloadFile& 31. doi:10.1142/8068. ISBN 978-981-4338-96-7.
recordOId=2969749&fileOId=2969772
[56] “G8 “Action plan” decided upon at the 2003 Evian sum-
[37] Herschel Finds Oceans of Water in Disk of Nearby Star mit”. G8.fr. 2 June 2003. Retrieved 25 July 2010.
[38] Herschel Finds Oceans of Water in Disk of Nearby Star [57] “World Health Organization. Safe Water and Global
[39] Lloyd, Robin. “Water Vapor, Possible Comets, Found Or- Health”. Who.int. 25 June 2008. Retrieved 25 July 2010.
biting Star”, 11 July 2001, Space.com. Retrieved 15 De-
[58] UNEP International Environment (2002). Environmen-
cember 2006.
tally Sound Technology for Wastewater and Stormwater
[40] Platt, Jane; Bell, Brian (3 April 2014). “NASA Space As- Management: An International Source Book. IWA Pub-
sets Detect Ocean inside Saturn Moon”. NASA. Retrieved lishing. ISBN 1-84339-008-6. OCLC 49204666.
3 April 2014.
[59] Ravindranath, Nijavalli H.; Jayant A. Sathaye (2002). Cli-
[41] Iess, L.; Stevenson, D.J.; Parisi, M.; Hemingway, D.; Ja- mate Change and Developing Countries. Springer. ISBN
cobson, R.A.; Lunine, J.I.; Nimmo, F.; Armstrong, J.w.; 1-4020-0104-5. OCLC 231965991.
Asmar, S.w.; Ducci, M.; Tortora, P. (4 April 2014).
[60] “WBCSD Water Facts & Trends”. Retrieved 25 July
“The Gravity Field and Interior Structure of Enceladus”.
2010.
Science 344 (6179): 78–80. Bibcode:2014Sci...344...78I.
doi:10.1126/science.1250551. Retrieved 3 April 2014. [61] Water Use in the United States, National Atlas.gov
[42] http://www.lpi.usra.edu/meetings/lpsc2013/pdf/2454. [62] Gleick, P.H.; Palaniappan, M. (2010). “Peak Wa-
pdf ter” (PDF). Proceedings National Academy of Sci-
[43] Tritt, Charles S. (2002). “Possibility of Life on Europa”. ence (National Academy of Science) 107 (125):
Milwaukee School of Engineering. Retrieved 10 August 11155–11162. Bibcode:2010PNAS..10711155G.
2007. doi:10.1073/pnas.1004812107. Retrieved 11 October
2011.
[44] Jupiter’s moon Ganymede may have 'club sandwich' layers
of ocean | Reuters [63] United Nations Press Release POP/952, 13 March 2007.
World population will increase by 2.5 billion by 2050
[45] Versteckt in Glasperlen: Auf dem Mond gibt es Wasser –
Wissenschaft – Der Spiegel – Nachrichten [64] Molden, D. (Ed). Water for food, Water for life: A Com-
prehensive Assessment of Water Management in Agricul-
[46] Water Molecules Found on the Moon, NASA, 24 Septem- ture. Earthscan/IWMI, 2007.
ber 2009
[65] Chartres, C. and Varma, S. Out of water. From Abun-
[47] Sparrow, Giles (2006). The Solar System. Thunder Bay dance to Scarcity and How to Solve the World’s Water Prob-
Press. ISBN 1-59223-579-4. lems FT Press (USA), 2010
1.3. WATER 37

[66] Décret relatif aux poids et aux mesures. 18 germinal an 3 review”. The American Journal of Clinical Nutrition
(7 April 1795). Decree relating to the weights and mea- 98 (2): 282–99. doi:10.3945/ajcn.112.055061. PMID
surements (in French). quartier-rural.org 23803882.

[67] here L'Histoire Du Mètre, La Détermination De L'Unité [80] Water, Constipation, Dehydration, and Other Fluids
De Poids. histoire.du.metre.free.fr
[81] Food and Nutrition Board, National Academy of Sciences.
[68] Re: What percentage of the human body is composed of Recommended Dietary Allowances. National Research
water? Jeffrey Utz, M.D., The MadSci Network Council, Reprint and Circular Series, No. 122. 1945. pp.
3–18.
[69] “Healthy Water Living”. BBC. Retrieved 1 February
2007. [82] “Are you consuming enough water? recommendations
from the United States National Research Council”. water
[70] Rhoades RA, Tanner GA (2003). Medical Physiology
softener critic. Retrieved 21 July 2014.
(2nd ed.). Baltimore: Lippincott Williams & Wilkins.
ISBN 0-7817-1936-4. OCLC 50554808. [83] “Water: How much should you drink every day?". May-
oclinic.com. Retrieved 25 July 2010.
[71] Noakes TD, Goodwin N, Rayner BL et al. (1985).
“Water intoxication: a possible complication during en- [84] Conquering Chemistry 4th Ed. Published 2008
durance exercise”. Med Sci Sports Exerc 17 (3): 370–
375. doi:10.1249/00005768-198506000-00012. PMID [85] Maton, Anthea; Jean Hopkins; Charles William
4021781. McLaughlin; Susan Johnson; Maryanna Quon Warner;
David LaHart; Jill D. Wright (1993). Human Biology and
[72] Noakes TD, Goodwin N, Rayner BL, Branken T, Taylor Health. Englewood Cliffs, New Jersey, USA: Prentice
RK (2005). “Water intoxication: a possible compli- Hall. ISBN 0-13-981176-1. OCLC 32308337.
cation during endurance exercise, 1985”. Wilderness
Environ Med 16 (4): 221–7. doi:10.1580/1080- [86] Unesco (2006). Water: a shared responsibility. Berghahn
6032(2005)16[221:WIAPCD]2.0.CO;2. PMID Books. p. 125. ISBN 1-84545-177-5.
16366205.
[87] Vaclavik, Vickie A. and Christian, Elizabeth W (2007).
[73] “Drink at least eight glasses of water a day.” Really? Is Essentials of Food Science. Springer. ISBN 0-387-69939-
there scientific evidence for “8 × 8"? by Heinz Valdin, 2.
Department of Physiology, Dartmouth Medical School,
Lebanon, New Hampshire [88] DeMan, John M (1999). Principles of Food Chemistry.
Springer. ISBN 0-8342-1234-X.
[74] Stookey JD, Constant F, Popkin BM, Gardner CD
(November 2008). “Drinking water is associated with [89] “Map showing the rate of hardness in mg/l as Calcium car-
weight loss in overweight dieting women independent bonate in England and Wales” (PDF). DEFRA/ Drinking
of diet and activity”. Obesity 16 (11): 2481–8. Water Inspectorate. 2009.
doi:10.1038/oby.2008.409. PMID 18787524.
[90] “Water hardness”. US Geological Service. 8 April 2014.
[75] http://www.sciencedaily.com/releases/2010/08/
100823142929.htm[] [91] M.M. Mekonnen; A.Y. Hoekstra (December 2010). “The
green, blue and grey wate r footprint of farm animals and
[76] Dubnov-Raz G, Constantini NW, Yariv H, Nice S, animal products, Value of Water Research Report Series
Shapira N (October 2011). “Influence of water drink- No. 48 - Volume 1: Main report” (PDF). The green,
ing on resting energy expenditure in overweight chil- blue and grey wate r footprint of farm animals and ani-
dren”. International Journal of Obesity 35 (10): 1295– mal products, Value of Water Research Report Series No.
300. doi:10.1038/ijo.2011.130. PMID 21750519. 48 - Volume 1: Main report. UNESCO-IHE Institute for
Water Education. Retrieved 30 January 2014.
[77] Dennis EA, Dengo AL, Comber DL et al. (Febru-
ary 2010). “Water consumption increases weight [92] The Millennium Development Goals Report, United Na-
loss during a hypocaloric diet intervention in middle- tions, 2008
aged and older adults”. Obesity 18 (2): 300–7.
doi:10.1038/oby.2009.235. PMC 2859815. PMID [93] Lomborg, Björn (2001). The Skeptical Environmentalist
19661958. (PDF). Cambridge University Press. p. 22. ISBN 0-521-
01068-3.
[78] Vij VA, Joshi AS (September 2013). “Effect of 'water
induced thermogenesis’ on body weight, body mass in- [94] UNESCO, (2006), Water, a shared responsibility. The
dex and body composition of overweight subjects”. Jour- United Nations World Water Development Report 2.
nal of Clinical and Diagnostic Research 7 (9): 1894–
6. doi:10.7860/JCDR/2013/5862.3344. PMC 3809630. [95] Welle, Katharina; Evans, Barbara; Tucker, Josephine and
PMID 24179891. Nicol, Alan (2008) Is water lagging behind on Aid Effec-
tiveness?
[79] Muckelbauer R, Sarganas G, Grüneis A, Müller-
Nordhorn J (August 2013). “Association between water [96] Water governance, Water Issue Brief, Issue 5, 2010,
consumption and body weight outcomes: a systematic IWMI
38 CHAPTER 1. CELLS AND WATER

[97] Lindberg, D. (2008). The beginnings of western science:

The European scientific tradition in philosophical, reli-
gious, and institutional context, prehistory to A.D. 1450.
(2nd ed.). Chicago: University of Chicago Press.

[98] “Internet Sacred Text Archive Home”. Sacred-texts.com.

Retrieved 25 July 2010.

[99] Guanzi : Shui Di - Chinese Text Project

1.3.11 Further reading

• Debenedetti, PG., and HE Stanley, “Supercooled
and Glassy Water”, Physics Today 56 (6), p. 40–46
(2003). Downloadable PDF (1.9 MB)
• Franks, F (Ed), Water, A comprehensive treatise,
Plenum Press, New York, 1972–1982
• Gleick, PH., (editor), The World’s Water: The Bien-
nial Report on Freshwater Resources. Island Press,
Washington, D.C. (published every two years, be-
ginning in 1998.) The World’s Water, Island Press
• Jones, OA., JN Lester and N Voulvoulis, Pharma-
ceuticals: a threat to drinking water? TRENDS in
Biotechnology 23(4): 163, 2005
• Journal of Contemporary Water Research & Edu-
cation
• Postel,S., Last Oasis: Facing Water Scarcity. W.W.
Norton and Company, New York. 1992
• Reisner,M., Cadillac Desert: The American West
and Its Disappearing Water. Penguin Books, New
York. 1986.
• United Nations World Water Development Report.
Produced every three years. UN World Water De-
velopment Report

1.3.12 External links

• OECD Water statistics
• The World’s Water Data Page
• FAO Comprehensive Water Database, AQUASTAT
• The Water Conflict Chronology: Water Conflict
Database
• US Geological Survey Water for Schools informa-
tion
• Portal to The World Bank’s strategy, work and asso-
ciated publications on water resources
• America Water Resources Association
• America Water Resources Association
• Water structure and science
Chapter 2

Structural Biochemistry

39
Chapter 3

Nucleic acids

3.1 Nucleic acid

Cytosine Cytosine
Nucleobases

Guanine Guanine

Base pair
Adenine Adenine

Uracil Thymine

helix of
sugar-phosphates

Nucleobases Nucleobases
of RNA of DNA
RNA DNA
Ribonucleic acid Deoxyribonucleic acid

A comparison of the two principal nucleic acids: RNA (left) and

DNA (right), showing the helices and nucleobases each employs.

Nucleic acids are biopolymers, or large biomolecules,

essential for all known forms of life. Nucleic acids,
which include DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid), are made from monomers known as
nucleotides. Each nucleotide has three components: a 5- The Swiss scientist Friedrich Miescher discovered nucleic acids
carbon sugar, a phosphate group, and a nitrogenous base. (DNA) in 1869.[1] Later, he raised the idea that they could be
If the sugar is deoxyribose, the polymer is DNA. If the involved in heredity.[2]
sugar is ribose, the polymer is RNA.
Together with proteins, nucleic acids are the most impor- 3.1.1 Occurrence and nomenclature[7]
tant biological macromolecules; each are found in abun-
dance in all living things, where they function in encod- The term nucleic acid is the overall name for DNA and
ing, transmitting and expressing genetic information—in RNA, members of a family of biopolymers,[8] and is syn-
other words, information is conveyed through the nucleic onymous with polynucleotide. Nucleic acids were named
acid sequence, or the order of nucleotides within a DNA for their initial discovery within the nucleus, and for
or RNA molecule. Strings of nucleotides strung together the presence of phosphate groups (related to phosphoric
in a specific sequence are the mechanism for storing and acid).[9] Although first discovered within the nucleus of
transmitting hereditary, or genetic information via pro- eukaryotic cells, nucleic acids are now known to be found
tein synthesis. in all life forms as well as some nonliving entities, includ-
Nucleic acids were discovered by Friedrich Miescher in ing within bacteria, archaea, mitochondria, chloroplasts,
1869.[3] Experimental studies of nucleic acids constitute viruses and viroids.[10] All living cells contain both DNA
a major part of modern biological and medical research, and RNA (except some cells such as mature red blood
and form a foundation for genome and forensic science, cells), while viruses contain either DNA or RNA, but
as well as the biotechnology and pharmaceutical indus- usually not both.[11] The basic component of biologi-
tries.[4][5][6] cal nucleic acids is the nucleotide, each of which con-

40
3.1. NUCLEIC ACID 41

tains a pentose sugar (ribose or deoxyribose), a phosphate 3.1.3 Topology

group, and a nucleobase.[12] Nucleic acids are also gener-
ated within the laboratory, through the use of enzymes[13] Double-stranded nucleic acids are made up of comple-
(DNA and RNA polymerases) and by solid-phase chem- mentary sequences, in which extensive Watson-Crick
ical synthesis. The chemical methods also enable the base pairing results in a highly repeated and quite uni-
generation of altered nucleic acids that are not found in form double-helical three-dimensional structure.[21] In
nature,[14] for example peptide nucleic acids. contrast, single-stranded RNA and DNA molecules are
not constrained to a regular double helix, and can adopt
highly complex three-dimensional structures that are
based on short stretches of intramolecular base-paired se-
quences that include both Watson-Crick and noncanoni-
3.1.2 Molecular composition and size[15] cal base pairs, as well as a wide range of complex tertiary
interactions.[22]
Nucleic acids are generally very large molecules. In-
Nucleic acid molecules are usually unbranched, and
deed, DNA molecules are probably the largest individual
may occur as linear and circular molecules. For ex-
molecules known. Well-studied biological nucleic acid
ample, bacterial chromosomes, plasmids, mitochondrial
molecules range in size from 21 nucleotides (small in-
DNA and chloroplast DNA are usually circular double-
terfering RNA) to large chromosomes (human chromo-
stranded DNA molecules, while chromosomes of the
some 1 is a single molecule that contains 247 million base
eukaryotic nucleus are usually linear double-stranded
pairs[16] ).
DNA molecules.[11] Most RNA molecules are linear,
In most cases, naturally occurring DNA molecules single-stranded molecules, but both circular and branched
are double-stranded and RNA molecules are single- molecules can result from RNA splicing reactions.[7]
stranded.[17] There are numerous exceptions, however—
some viruses have genomes made of double-stranded
RNA and other viruses have single-stranded DNA 3.1.4 Nucleic acid sequences
genomes,[18] and, in some circumstances, nucleic acid
structures with three or four strands can form.[19] Main article: Nucleic acid sequence
Nucleic acids are linear polymers (chains) of nucleotides.
Each nucleotide consists of three components: a purine One DNA or RNA molecule differs from another pri-
or pyrimidine nucleobase (sometimes termed nitrogenous marily in the sequence of nucleotides. Nucleotide se-
base or simply base), a pentose sugar, and a phosphate quences are of great importance in biology since they
group. The substructure consisting of a nucleobase plus carry the ultimate instructions that encode all biological
sugar is termed a nucleoside. Nucleic acid types differ in molecules, molecular assemblies, subcellular and cellu-
the structure of the sugar in their nucleotides–DNA con- lar structures, organs and organisms, and directly enable
tains 2'-deoxyribose while RNA contains ribose (where cognition, memory and behavior (See: Genetics). Enor-
the only difference is the presence of a hydroxyl group). mous efforts have gone into the development of exper-
Also, the nucleobases found in the two nucleic acid types imental methods to determine the nucleotide sequence
are different: adenine, cytosine, and guanine are found in of biological DNA and RNA molecules,[23][24] and today
both RNA and DNA, while thymine occurs in DNA and hundreds of millions of nucleotides are sequenced daily
uracil occurs in RNA. at genome centers and smaller laboratories worldwide.
The sugars and phosphates in nucleic acids are connected In addition to maintaining the GenBank nucleic acid se-
to each other in an alternating chain (sugar-phosphate quence database, the National Center for Biotechnology
backbone) through phosphodiester linkages.[15] In Information (NCBI, http://www.ncbi.nlm.nih.gov) pro-
conventional nomenclature, the carbons to which the vides analysis and retrieval resources for the data in Gen-
phosphate groups attach are the 3'-end and the 5'-end car- Bank and other biological data made available through
bons of the sugar. This gives nucleic acids directionality, the NCBI Web site [25]
and the ends of nucleic acid molecules are referred to
as 5'-end and 3'-end. The nucleobases are joined to the
sugars via an N-glycosidic linkage involving a nucleobase 3.1.5 Types of nucleic acids
ring nitrogen (N-1 for pyrimidines and N-9 for purines)
and the 1' carbon of the pentose sugar ring. Deoxyribonucleic acid
Non-standard nucleosides are also found in both RNA
and DNA and usually arise from modification of the stan- Main article: DNA
dard nucleosides within the DNA molecule or the pri-
mary (initial) RNA transcript. Transfer RNA (tRNA) Deoxyribonucleic acid (DNA) is a nucleic acid contain-
molecules contain a particularly large number of modi- ing the genetic instructions used in the development and
fied nucleosides.[20] functioning of all known living organisms . The DNA
42 CHAPTER 3. NUCLEIC ACIDS

segments carrying this genetic information are called nucleic acid and threose nucleic acid. Each of these is
genes. Likewise, other DNA sequences have structural distinguished from naturally occurring DNA or RNA by
purposes, or are involved in regulating the use of this ge- changes to the backbone of the molecule.
netic information. Along with RNA and proteins, DNA is
one of the three major macromolecules that are essential
for all known forms of life. DNA consists of two long 3.1.6 See also
polymers of simple units called nucleotides, with back-
bones made of sugars and phosphate groups joined by • History of biochemistry
ester bonds. These two strands run in opposite directions
• History of molecular biology
to each other and are, therefore, anti-parallel. Attached
to each sugar is one of four types of molecules called • History of RNA biology
nucleobases (informally, bases). It is the sequence of
these four nucleobases along the backbone that encodes • Nucleic acid simulations
information. This information is read using the genetic
code, which specifies the sequence of the amino acids • Molecular biology
within proteins. The code is read by copying stretches • Nucleic acid structure
of DNA into the related nucleic acid RNA in a process
called transcription. Within cells DNA is organized into • Nucleic acid methods
long structures called chromosomes. During cell divi-
sion these chromosomes are duplicated in the process of • Nucleic acid thermodynamics
DNA replication, providing each cell its own complete set
• Oligonucleotide synthesis
of chromosomes. Eukaryotic organisms (animals, plants,
fungi, and protists) store most of their DNA inside the • Quantification of nucleic acids
cell nucleus and some of their DNA in organelles, such
as mitochondria or chloroplasts.[1] In contrast, prokary-
otes (bacteria and archaea) store their DNA only in the 3.1.7 Notes and references
cytoplasm. Within the chromosomes, chromatin proteins
such as histones compact and organize DNA. These com- [1] He called them nuclein.
pact structures guide the interactions between DNA and
other proteins, helping control which parts of the DNA [2] Bill Bryson, A Short History of Nearly Everything, Broad-
way Books, 2005, p. 500.
are transcribed.
[3] Dahm, R (January 2008). “Discovering DNA: Friedrich
Miescher and the early years of nucleic acid research”.
Ribonucleic acid Human Genetics 122 (6): 565–81. doi:10.1007/s00439-
007-0433-0. ISSN 0340-6717. PMID 17901982.
Main article: RNA
[4] International Human Genome Sequencing Consortium
(2001). “Initial sequencing and analysis of the hu-
Ribonucleic acid (RNA) functions in converting genetic man genome.” (PDF). Nature 409 (6822): 860–921.
information from genes into the amino acid sequences of doi:10.1038/35057062. PMID 11237011.
proteins. The three universal types of RNA include trans-
fer RNA (tRNA), messenger RNA (mRNA), and riboso- [5] Venter, JC et al. (2001). “The sequence of the
mal RNA (rRNA). Messenger RNA acts to carry genetic human genome.” (PDF). Science 291 (5507):
1304–1351. Bibcode:2001Sci...291.1304V.
sequence information between DNA and ribosomes, di-
doi:10.1126/science.1058040. PMID 11181995.
recting protein synthesis. Ribosomal RNA is a major
component of the ribosome, and catalyzes peptide bond [6] Budowle B, van Daal A (April 2009). “Extracting evi-
formation. Transfer RNA serves as the carrier molecule dence from forensic DNA analyses: future molecular bi-
for amino acids to be used in protein synthesis, and is ology directions”. BioTechniques 46 (5): 339–40, 342–
responsible for decoding the mRNA. In addition, many 50. doi:10.2144/000113136. PMID 19480629.
other classes of RNA are now known.
[7] Alberts, Bruce (2008). Molecular biology of the cell. New
York: Garland Science. ISBN 0-8153-4105-9.
Artificial nucleic acid analogs [8] Elson D (1965). “Metabolism of nucleic acids (macro-
molecular DNA and RNA)". Annu. Rev. Biochem.
Main article: Nucleic acid analogues 34: 449–86. doi:10.1146/annurev.bi.34.070165.002313.
PMID 14321176.
Artificial nucleic acid analogs have been designed and [9] National Institute of Health (September 28, 2007).
synthesized by chemists, and include peptide nucleic acid, “Discovering DNA: Friedrich Miescher and the early
morpholino- and locked nucleic acid, as well as glycol years of nucleic acid research.”. nih.gov.
3.2. RNA 43

[10] Aparadh, V. T. and B. A. Karadge (2012). “Infrared [25] “Database resources of the National Center for Biotech-
Spectroscopic Studies in Some Cleome species” (PDF). nology Information”. Nucleic Acid Research 42: D7–17.
ISSN 2319-8877. 2014. doi:10.1093/nar/gkt1146. PMC 3965057. PMID
24259429.
[11] Brock, Thomas D.; Madigan, Michael T. (2009). Brock
biology of microorganisms. Pearson / Benjamin Cum-
mings. ISBN 0-321-53615-0.
3.1.8 Bibliography
[12] Hardinger, Steven; University of California, Los Angeles
(2011). “Knowing Nucleic Acids” (PDF). ucla.edu. • Wolfram Saenger, Principles of Nucleic Acid Struc-
ture, 1984, Springer-Verlag New York Inc.
[13] Mullis, Kary B. The Polymerase Chain Reaction (No-
bel Lecture). 1993. (retrieved December 1, 2010)
• Bruce Alberts, Alexander Johnson, Julian Lewis,
http://nobelprize.org/nobel_prizes/chemistry/laureates/
Martin Raff, Keith Roberts, and Peter Walter Molec-
1993/mullis-lecture.html
ular Biology of the Cell, 2007, ISBN 978-0-8153-
[14] Verma S, Eckstein F (1998). “Modified oligonucleotides: 4105-5. Fourth edition is available online through
synthesis and strategy for users”. Annu. Rev. Biochem. the NCBI Bookshelf: link
67: 99–134. doi:10.1146/annurev.biochem.67.1.99.
PMID 9759484. • Jeremy M Berg, John L Tymoczko, and Lubert
Stryer, Biochemistry 5th edition, 2002, W H Free-
[15] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L.
(2007). Biochemistry. San Francisco: W.H. Freeman.
man. Available online through the NCBI Bookshelf:
ISBN 0-7167-6766-X. link

[16] Gregory SG, Barlow KF, McLay KE et al. (May • Astrid Sigel, Helmut Sigel and Roland K. O. Sigel,
2006). “The DNA sequence and biological an- ed. (2012). Interplay between Metal Ions and
notation of human chromosome 1”. Nature 441 Nucleic Acids. Metal Ions in Life Sciences 10.
(7091): 315–21. Bibcode:2006Natur.441..315G. Springer. doi:10.1007/978-94-007-2172-2. ISBN
doi:10.1038/nature04727. PMID 16710414. 978-94-007-2171-5.
[17] Todorov TI, Morris MD; National Institutes of Health
(April 23, 2002). “Comparison of RNA, single-stranded
DNA and double-stranded DNA behavior during capillary 3.1.9 External links
electrophoresis in semidilute polymer solutions”. nih.gov.
• Interview with Aaron Klug, Nobel Laureate for
[18] Dr. Margaret Hunt; University of South Carolina (2010).
structural elucidation of biologically important
“RN Virus Replication Strategies”. sc.edu.
nucleic-acid protein complexes provided by the
[19] McGlynn Peter, Robert G. Lloyd (June 10, 1999). “RecG Vega Science Trust.
helicase activity at three- and four-strand DNA struc-
tures”. oxfordjournals.org. ISSN 1362-4962. • Nucleic Acids Research (Journal)
[20] Rich A, RajBhandary UL (1976). “Transfer • Nucleic Acids Book (free online book on the chem-
RNA: molecular structure, sequence, and prop- istry and biology of nucleic acids)
erties”. Annu. Rev. Biochem. 45: 805–60.
doi:10.1146/annurev.bi.45.070176.004105. PMID
60910.
3.2 RNA
[21] Watson JD, Crick FH (April 1953). “Molecular
structure of nucleic acids; a structure for deoxyri-
bose nucleic acid”. Nature 171 (4356): 737–8. For other uses, see RNA (disambiguation).
Bibcode:1953Natur.171..737W. doi:10.1038/171737a0. Ribonucleic acid (RNA) is a polymeric molecule im-
PMID 13054692. plicated in various biological roles in coding, decoding,
regulation, and expression of genes. RNA and DNA are
[22] Ferré-D'Amaré AR, Doudna JA (1999). “RNA
nucleic acids, and, along with proteins and carbohydrates,
folds: insights from recent crystal structures”.
Annu Rev Biophys Biomol Struct 28: 57–73.
constitute the three major macromolecules essential for
doi:10.1146/annurev.biophys.28.1.57. PMID 10410795. all known forms of life. Like DNA, RNA is assembled
as a chain of nucleotides, but unlike DNA it is more of-
[23] Gilbert, Walter G. 1980. DNA Sequencing and Gene ten found in nature as a single-strand folded onto itself,
Structure (Nobel Lecture) http://nobelprize.org/nobel_ rather than a paired double-strand. Cellular organisms
prizes/chemistry/laureates/1980/gilbert-lecture.html use messenger RNA (mRNA) to convey genetic infor-
[24] Sanger, Frederick. 1980. Determination of Nu- mation (using the letters G, U, A, and C to denote the
cleotide Sequences in DNA (Nobel Lecture) nitrogenous bases guanine, uracil, adenine, and cytosine)
http://nobelprize.org/nobel_prizes/chemistry/laureates/ that directs synthesis of specific proteins. Many viruses
1980/sanger-lecture.html encode their genetic information using an RNA genome.
44 CHAPTER 3. NUCLEIC ACIDS

A hairpin loop from a pre-mRNA. Highlighted are the

nucleobases (green) and the ribose-phosphate backbone (blue).
Note that this is a single strand of RNA that folds back upon it-
self.

Some RNA molecules play an active role within cells by

catalyzing biological reactions, controlling gene expres-
sion, or sensing and communicating responses to cellular
signals. One of these active processes is protein synthe- Bases in an RNA molecule.
sis, a universal function whereby mRNA molecules direct
the assembly of proteins on ribosomes. This process uses RNA can, by complementary base pairing, form in-
transfer RNA (tRNA) molecules to deliver amino acids trastrand double helixes, as in tRNA.
to the ribosome, where ribosomal RNA (rRNA) links
amino acids together to form proteins. • While DNA contains deoxyribose, RNA contains
ribose (in deoxyribose there is no hydroxyl group at-
tached to the pentose ring in the 2' position). These
3.2.1 Comparison with DNA hydroxyl groups make RNA less stable than DNA
because it is more prone to hydrolysis.
The chemical structure of RNA is very similar to that of • The complementary base to adenine is not thymine,
DNA, but differs in three main ways: as it is in DNA, but rather uracil, which is an
unmethylated form of thymine.[1]
• Unlike double-stranded DNA, RNA is a single-
stranded molecule in many of its biological roles and Like DNA, most biologically active RNAs, including
has a much shorter chain of nucleotides. However, mRNA, tRNA, rRNA, snRNAs, and other non-coding
3.2. RNA 45

attached to the 3' position of one ribose and the 5' po-
sition of the next. The phosphate groups have a neg-
ative charge each at physiological pH, making RNA a
charged molecule (polyanion). The bases form hydrogen
bonds between cytosine and guanine, between adenine
and uracil and between guanine and uracil.[5] However,
other interactions are possible, such as a group of adenine
bases binding to each other in a bulge,[6] or the GNRA
tetraloop that has a guanine–adenine base-pair.[5]

Three-dimensional representation of the 50S ribosomal subunit.

RNA is in ochre, protein in blue. The active site is in the middle
(red).

RNAs, contain self-complementary sequences that allow

parts of the RNA to fold[2] and pair with itself to form
double helices. Analysis of these RNAs has revealed that
they are highly structured. Unlike DNA, their structures
do not consist of long double helices, but rather collec-
tions of short helices packed together into structures akin
to proteins. In this fashion, RNAs can achieve chemical
Chemical structure of RNA
catalysis, like enzymes.[3] For instance, determination of
the structure of the ribosome—an enzyme that catalyzes
An important structural feature of RNA that distin-
peptide bond formation—revealed that its active site is
[4] guishes it from DNA is the presence of a hydroxyl group
composed entirely of RNA.
at the 2' position of the ribose sugar. The presence of this
functional group causes the helix to adopt the A-form ge-
3.2.2 Structure ometry rather than the B-form most commonly observed
in DNA.[7] This results in a very deep and narrow ma-
jor groove and a shallow and wide minor groove.[8] A
second consequence of the presence of the 2'-hydroxyl
group is that in conformationally flexible regions of an
RNA molecule (that is, not involved in formation of a
double helix), it can chemically attack the adjacent phos-
phodiester bond to cleave the backbone.[9]

Watson-Crick base pairs in a siRNA (hydrogen atoms are not

shown)

Each nucleotide in RNA contains a ribose sugar, with car-

bons numbered 1' through 5'. A base is attached to the
1' position, in general, adenine (A), cytosine (C), guanine
(G), or uracil (U). Adenine and guanine are purines, cy-
tosine and uracil are pyrimidines. A phosphate group is Secondary structure of a telomerase RNA.
46 CHAPTER 3. NUCLEIC ACIDS

RNA is transcribed with only four bases (adenine, cy- Primary transcript RNAs are often modified by enzymes
tosine, guanine and uracil),[10] but these bases and at- after transcription. For example, a poly(A) tail and a 5'
tached sugars can be modified in numerous ways as the cap are added to eukaryotic pre-mRNA and introns are
RNAs mature. Pseudouridine (Ψ), in which the linkage removed by the spliceosome.
between uracil and ribose is changed from a C–N bond There are also a number of RNA-dependent RNA poly-
to a C–C bond, and ribothymidine (T) are found in vari- merases that use RNA as their template for synthesis of
ous places (the most notable ones being in the TΨC loop a new strand of RNA. For instance, a number of RNA
of tRNA).[11] Another notable modified base is hypox- viruses (such as poliovirus) use this type of enzyme to
anthine, a deaminated adenine base whose nucleoside is
replicate their genetic material.[21] Also, RNA-dependent
called inosine (I). Inosine plays a key role in the wobble RNA polymerase is part of the RNA interference path-
hypothesis of the genetic code.[12]
way in many organisms.[22]
There are more than 100 other naturally occurring mod-
ified nucleosides,[13] The greatest structural diversity of
modifications can be found in tRNA,[14] while pseu- 3.2.4 Types of RNA
douridine and nucleosides with 2'-O-methylribose often
present in rRNA are the most common.[15] The specific See also: List of RNAs
roles of many of these modifications in RNA are not fully
understood. However, it is notable that, in ribosomal
RNA, many of the post-transcriptional modifications oc-
Overview
cur in highly functional regions, such as the peptidyl trans-
ferase center and the subunit interface, implying that they
are important for normal function.[16]
The functional form of single-stranded RNA molecules,
just like proteins, frequently requires a specific tertiary
structure. The scaffold for this structure is provided by
secondary structural elements that are hydrogen bonds
within the molecule. This leads to several recogniz-
able “domains” of secondary structure like hairpin loops,
bulges, and internal loops.[17] Since RNA is charged,
metal ions such as Mg2+ are needed to stabilise many sec-
ondary and tertiary structures.[18]
The naturally occurring enantiomer of RNA is D-RNA
composed of D-ribonucleotides. All chirality centers are
located in the D-ribose. By the use of L-ribose or rather
L-ribonucleotides, L-RNA can be synthesized. L-RNA is
much more stable against degradation by RNase.[19]
Like other structured biopolymers such as proteins, one
can define topology of a folded RNA molecule. This is
often done based on arrangement of intra-chain contacts
within a folded RNA, termed as circuit topology.

3.2.3 Synthesis

Synthesis of RNA is usually catalyzed by an enzyme—

RNA polymerase—using DNA as a template, a process
known as transcription. Initiation of transcription begins
with the binding of the enzyme to a promoter sequence
in the DNA (usually found “upstream” of a gene). The Structure of a hammerhead ribozyme, a ribozyme that cuts RNA
DNA double helix is unwound by the helicase activity of
the enzyme. The enzyme then progresses along the tem- Messenger RNA (mRNA) is the RNA that carries infor-
plate strand in the 3’ to 5’ direction, synthesizing a com- mation from DNA to the ribosome, the sites of protein
plementary RNA molecule with elongation occurring in synthesis (translation) in the cell. The coding sequence
the 5’ to 3’ direction. The DNA sequence also dictates of the mRNA determines the amino acid sequence in the
where termination of RNA synthesis will occur.[20] protein that is produced.[23] However, many RNAs do not
3.2. RNA 47

code for protein (about 97% of the transcriptional output Regulatory RNAs
is non-protein-coding in eukaryotes[24][25][26][27] ).
Several types of RNA can downregulate gene expression
These so-called non-coding RNAs (“ncRNA”) can be en-
by being complementary to a part of an mRNA or a gene’s
coded by their own genes (RNA genes), but can also de-
[28] DNA.[31][32] MicroRNAs (miRNA; 21-22 nt) are found
rive from mRNA introns. The most prominent exam-
in eukaryotes and act through RNA interference (RNAi),
ples of non-coding RNAs are transfer RNA (tRNA) and
where an effector complex of miRNA and enzymes can
ribosomal RNA (rRNA), both of which are involved in
[1] cleave complementary mRNA, block the mRNA from
the process of translation. There are also non-coding
being translated, or accelerate its degradation.[33][34]
RNAs involved in gene regulation, RNA processing and
other roles. Certain RNAs are able to catalyse chem- While small interfering RNAs (siRNA; 20-25 nt) are
ical reactions such as cutting and ligating other RNA often produced by breakdown of viral RNA, there are
molecules,[29] and the catalysis of peptide bond forma- also endogenous sources of siRNAs.[35][36] siRNAs act
tion in the ribosome;[4] these are known as ribozymes. through RNA interference in a fashion similar to miR-
NAs. Some miRNAs and siRNAs can cause genes they
target to be methylated, thereby decreasing or increasing
transcription of those genes.[37][38][39] Animals have
Piwi-interacting RNAs (piRNA; 29-30 nt) that are active
In translation
in germline cells and are thought to be a defense against
transposons and play a role in gametogenesis.[40][41]
Messenger RNA (mRNA) carries information about a
Many prokaryotes have CRISPR RNAs, a regulatory sys-
protein sequence to the ribosomes, the protein synthe-
tem similar to RNA interference.[42] Antisense RNAs are
sis factories in the cell. It is coded so that every three
widespread; most downregulate a gene, but a few are
nucleotides (a codon) correspond to one amino acid. In
activators of transcription.[43] One way antisense RNA
eukaryotic cells, once precursor mRNA (pre-mRNA) has
can act is by binding to an mRNA, forming double-
been transcribed from DNA, it is processed to mature
stranded RNA that is enzymatically degraded.[44] There
mRNA. This removes its introns—non-coding sections
are many long noncoding RNAs that regulate genes in
of the pre-mRNA. The mRNA is then exported from
eukaryotes,[45] one such RNA is Xist, which coats one X
the nucleus to the cytoplasm, where it is bound to ribo-
chromosome in female mammals and inactivates it.[46]
somes and translated into its corresponding protein form
with the help of tRNA. In prokaryotic cells, which do An mRNA may contain regulatory elements itself, such
not have nucleus and cytoplasm compartments, mRNA as riboswitches, in the 5' untranslated region or 3' un-
can bind to ribosomes while it is being transcribed from translated region; these cis-regulatory elements regulate
DNA. After a certain amount of time the message de- the activity of that mRNA.[47] The untranslated regions
grades into its component nucleotides with the assistance can also contain elements that regulate other genes.[48]
of ribonucleases.[23]
Transfer RNA (tRNA) is a small RNA chain of about In RNA processing
80 nucleotides that transfers a specific amino acid to a
growing polypeptide chain at the ribosomal site of protein
synthesis during translation. It has sites for amino acid
attachment and an anticodon region for codon recognition
that binds to a specific sequence on the messenger RNA
chain through hydrogen bonding.[28]
Ribosomal RNA (rRNA) is the catalytic component of
the ribosomes. Eukaryotic ribosomes contain four dif-
ferent rRNA molecules: 18S, 5.8S, 28S and 5S rRNA.
Three of the rRNA molecules are synthesized in the
nucleolus, and one is synthesized elsewhere. In the cy-
toplasm, ribosomal RNA and protein combine to form Uridine to pseudouridine is a common RNA modification.
a nucleoprotein called a ribosome. The ribosome binds
mRNA and carries out protein synthesis. Several ribo- Many RNAs are involved in modifying other RNAs.
somes may be attached to a single mRNA at any time.[23]Introns are spliced out of pre-mRNA by spliceosomes,
Nearly all the RNA found in a typical eukaryotic cell is
which contain several small nuclear RNAs (snRNA),[1]
rRNA. or the introns can be ribozymes that are spliced by
Transfer-messenger RNA (tmRNA) is found in many themselves.[49] RNA can also be altered by having its nu-
bacteria and plastids. It tags proteins encoded by mR- cleotides modified to other nucleotides than A, C, G and
NAs that lack stop codons for degradation and prevents U. In eukaryotes, modifications of RNA nucleotides are
the ribosome from stalling.[30] in general directed by small nucleolar RNAs (snoRNA;
48 CHAPTER 3. NUCLEIC ACIDS

60-300 nt),[28] found in the nucleolus and cajal bodies.

snoRNAs associate with enzymes and guide them to a
spot on an RNA by basepairing to that RNA. These en-
zymes then perform the nucleotide modification. rRNAs
and tRNAs are extensively modified, but snRNAs and
mRNAs can also be the target of base modification.[50][51]
RNA can also be methylated.[52][53]

RNA genomes

Like DNA, RNA can carry genetic information. RNA

viruses have genomes composed of RNA that encodes a
number of proteins. The viral genome is replicated by Robert W. Holley, left, poses with his research team.
some of those proteins, while other proteins protect the
genome as the virus particle moves to a new host cell.
Viroids are another group of pathogens, but they consist
only of RNA, do not encode any protein and are repli-
cated by a host plant cell’s polymerase.[54] two separate strands of RNA to form the first crystal
of RNA whose structure could be determined by X-ray
In reverse transcription crystallography.[64]
The sequence of the 77 nucleotides of a yeast tRNA was
Reverse transcribing viruses replicate their genomes found by Robert W. Holley in 1965,[65] winning Holley
by reverse transcribing DNA copies from their RNA; the 1968 Nobel Prize in Medicine (shared with Har Gob-
these DNA copies are then transcribed to new RNA. ind Khorana and Marshall Nirenberg). In 1967, Carl
Retrotransposons also spread by copying DNA and RNA Woese hypothesized that RNA might be catalytic and
from one another,[55] and telomerase contains an RNA suggested that the earliest forms of life (self-replicating
that is used as template for building the ends of eukary- molecules) could have relied on RNA both to carry ge-
otic chromosomes.[56] netic information and to catalyze biochemical reactions—
an RNA world.[66][67]
Double-stranded RNA During the early 1970s, retroviruses and reverse tran-
scriptase were discovered, showing for the first time that
Double-stranded RNA (dsRNA) is RNA with two com- enzymes could copy RNA into DNA (the opposite of
plementary strands, similar to the DNA found in all the usual route for transmission of genetic information).
cells. dsRNA forms the genetic material of some viruses For this work, David Baltimore, Renato Dulbecco and
(double-stranded RNA viruses). Double-stranded RNA Howard Temin were awarded a Nobel Prize in 1975. In
such as viral RNA or siRNA can trigger RNA inter- 1976, Walter Fiers and his team determined the first com-
ference in eukaryotes, as well as interferon response in plete nucleotide sequence of an RNA virus genome, that
vertebrates.[57][58][59][60] of bacteriophage MS2.[68]
In 1977, introns and RNA splicing were discovered in
both mammalian viruses and in cellular genes, resulting
3.2.5 Key discoveries in RNA biology
in a 1993 Nobel to Philip Sharp and Richard Roberts.
Further information: History of RNA biology Catalytic RNA molecules (ribozymes) were discovered
Research on RNA has led to many important biolog- in the early 1980s, leading to a 1989 Nobel award to
ical discoveries and numerous Nobel Prizes. Nucleic Thomas Cech and Sidney Altman. In 1990, it was found
acids were discovered in 1868 by Friedrich Miescher, in Petunia that introduced genes can silence similar genes
who called the material 'nuclein' since it was found in of the plant’s own, now known to be a result of RNA in-
the nucleus.[61] It was later discovered that prokaryotic terference.[69][70]
cells, which do not have a nucleus, also contain nucleic At about the same time, 22 nt long RNAs, now called
acids. The role of RNA in protein synthesis was sus- microRNAs, were found to have a role in the development
pected already in 1939.[62] Severo Ochoa won the 1959 of C. elegans.[71] Studies on RNA interference gleaned a
Nobel Prize in Medicine (shared with Arthur Kornberg) Nobel Prize for Andrew Fire and Craig Mello in 2006,
after he discovered an enzyme that can synthesize RNA and another Nobel was awarded for studies on the tran-
in the laboratory.[63] However, the enzyme discovered by scription of RNA to Roger Kornberg in the same year.
Ochoa (polynucleotide phosphorylase) was later shown The discovery of gene regulatory RNAs has led to at-
to be responsible for RNA degradation, not RNA syn- tempts to develop drugs made of RNA, such as siRNA,
thesis. In 1956 Alex Rich and David Davies hybridized to silence genes.[72]
3.2. RNA 49

3.2.6 Evolution [9] Mikkola S; Stenman E; Nurmi K; Yousefi-Salakdeh E;

Strömberg R; Lönnberg H (1999). “The mechanism of
In March 2015, complex DNA and RNA organic com- the metal ion promoted cleavage of RNA phosphodiester
pounds of life, including uracil, cytosine and thymine, bonds involves a general acid catalysis by the metal aquo
were reportedly formed in the laboratory under outer ion on the departure of the leaving group”. Perkin trans-
actions 2 (8): 1619–26. doi:10.1039/a903691a.
space conditions, using starting chemicals, such as
pyrimidine, found in meteorites. Pyrimidine, like [10] Jankowski JAZ; Polak JM (1996). Clinical gene analysis
polycyclic aromatic hydrocarbons (PAHs), the most and manipulation: Tools, techniques and troubleshooting.
carbon-rich chemical found in the Universe, may have Cambridge University Press. p. 14. ISBN 0-521-47896-
been formed in red giants or in interstellar dust and gas 0. OCLC 33838261.
clouds, according to the scientists.[73]
[11] Yu Q; Morrow CD (2001). “Identification of crit-
ical elements in the tRNA acceptor stem and TΨC
loop necessary for human immunodeficiency virus
3.2.7 See also type 1 infectivity”. J Virol 75 (10): 4902–6.
doi:10.1128/JVI.75.10.4902-4906.2001. PMC 114245.
• Biomolecular structure PMID 11312362.

• DNA, RNA and proteins: The three essential [12] Elliott MS; Trewyn RW (1983). “Inosine biosynthesis in
macromolecules of life transfer RNA by an enzymatic insertion of hypoxanthine”.
J. Biol. Chem. 259 (4): 2407–10. PMID 6365911.
• DNA
[13] Cantara, WA; Crain, PF; Rozenski, J; McCloskey, JA;
Harris, KA; Zhang, X; Vendeix, FA; Fabris, D; Agris,
PF (January 2011). “The RNA Modification Database,
3.2.8 References
RNAMDB: 2011 update”. Nucleic Acids Research 39
(Database issue): D195–201. doi:10.1093/nar/gkq1028.
[1] Berg JM; Tymoczko JL; Stryer L (2002). Biochemistry
PMC 3013656. PMID 21071406.
(5th ed.). WH Freeman and Company. pp. 118–19,
781–808. ISBN 0-7167-4684-0. OCLC 179705944 [14] Söll D; RajBhandary U (1995). TRNA: Structure, biosyn-
48055706 59502128. thesis, and function. ASM Press. p. 165. ISBN 1-55581-
073-X. OCLC 183036381 30663724.
[2] I. Tinoco & C. Bustamante (1999). “How
RNA folds”. J. Mol. Biol. 293 (2): 271–281. [15] Kiss T (2001). “Small nucleolar RNA-guided
doi:10.1006/jmbi.1999.3001. PMID 10550208. post-transcriptional modification of cellular
RNAs”. The EMBO Journal 20 (14): 3617–22.
[3] Higgs PG (2000). “RNA secondary structure: doi:10.1093/emboj/20.14.3617. PMC 125535. PMID
physical and computational aspects”. Quar- 11447102.
terly Reviews of Biophysics 33 (3): 199–253.
doi:10.1017/S0033583500003620. PMID 11191843. [16] King TH; Liu B; McCully RR; Fournier MJ (2002). “Ri-
bosome structure and activity are altered in cells lack-
[4] Nissen P; Hansen J; Ban N; Moore PB; Steitz TA ing snoRNPs that form pseudouridines in the peptidyl
(2000). “The structural basis of ribosome ac- transferase center”. Molecular Cell 11 (2): 425–35.
tivity in peptide bond synthesis”. Science 289 doi:10.1016/S1097-2765(03)00040-6. PMID 12620230.
(5481): 920–30. Bibcode:2000Sci...289..920N.
doi:10.1126/science.289.5481.920. PMID 10937990. [17] Mathews DH; Disney MD; Childs JL; Schroeder SJ;
Zuker M; Turner DH (2004). “Incorporating chem-
[5] Lee JC; Gutell RR (2004). “Diversity of base-pair con- ical modification constraints into a dynamic program-
formations and their occurrence in rRNA structure and ming algorithm for prediction of RNA secondary
RNA structural motifs”. J. Mol. Biol. 344 (5): 1225–49. structure”. Proc. Natl. Acad. Sci. USA
doi:10.1016/j.jmb.2004.09.072. PMID 15561141. 101 (19): 7287–92. Bibcode:2004PNAS..101.7287M.
doi:10.1073/pnas.0401799101. PMC 409911. PMID
[6] Barciszewski J; Frederic B; Clark C (1999). RNA bio- 15123812.
chemistry and biotechnology. Springer. pp. 73–87. ISBN
0-7923-5862-7. OCLC 52403776. [18] Tan ZJ; Chen SJ (2008). “Salt dependence
of nucleic acid hairpin stability”. Biophys. J.
[7] Salazar M; Fedoroff OY; Miller JM; Ribeiro NS; Reid 95 (2): 738–52. Bibcode:2008BpJ....95..738T.
BR (1992). “The DNA strand in DNAoRNA hybrid du- doi:10.1529/biophysj.108.131524. PMC 2440479.
plexes is neither B-form nor A-form in solution”. Bio- PMID 18424500.
chemistry 32 (16): 4207–15. doi:10.1021/bi00067a007.
PMID 7682844. [19] Vater A; Klussmann S (January 2015). “Turning mirror-
image oligonucleotides into drugs: the evolution of
[8] Hermann T; Patel DJ (2000). “RNA bulges as architec- Spiegelmer therapeutics”. Drug Discovery Today 20
tural and recognition motifs”. Structure 8 (3): R47–R54. (1): 147–155. doi:10.1016/j.drudis.2014.09.004. PMID
doi:10.1016/S0969-2126(00)00110-6. PMID 10745015. 25236655.
50 CHAPTER 3. NUCLEIC ACIDS

[20] Nudler E; Gottesman ME (2002). “Transcription termi- [33] Wu L; Belasco JG (January 2008). “Let me count
nation and anti-termination in E. coli”. Genes to Cells the ways: mechanisms of gene regulation by miR-
7 (8): 755–68. doi:10.1046/j.1365-2443.2002.00563.x. NAs and siRNAs”. Mol. Cell 29 (1): 1–7.
PMID 12167155. doi:10.1016/j.molcel.2007.12.010. PMID 18206964.

[21] Jeffrey L Hansen; Alexander M Long; Steve C Schultz [34] Matzke MA; Matzke AJM (2004). “Planting the
(1997). “Structure of the RNA-dependent RNA poly- seeds of a new paradigm”. PLoS Biology 2 (5):
merase of poliovirus”. Structure 5 (8): 1109–22. e133. doi:10.1371/journal.pbio.0020133. PMC 406394.
doi:10.1016/S0969-2126(97)00261-X. PMID 9309225. PMID 15138502.
[22] Ahlquist P (2002). “RNA-Dependent RNA Poly-
[35] Vazquez F; Vaucheret H; Rajagopalan R; Lepers C; Gas-
merases, Viruses, and RNA Silencing”. Science
ciolli V; Mallory AC; Hilbert J; Bartel DP; Crété P
296 (5571): 1270–73. Bibcode:2002Sci...296.1270A.
(2004). “Endogenous trans-acting siRNAs regulate the
doi:10.1126/science.1069132. PMID 12016304.
accumulation of Arabidopsis mRNAs”. Molecular Cell 16
[23] Cooper GC; Hausman RE (2004). The Cell: A Molecular (1): 69–79. doi:10.1016/j.molcel.2004.09.028. PMID
Approach (3rd ed.). Sinauer. pp. 261–76, 297, 339– 15469823.
44. ISBN 0-87893-214-3. OCLC 174924833 52121379
52359301 56050609. [36] Watanabe T, Totoki Y, Toyoda A et al. (May
2008). “Endogenous siRNAs from naturally formed dsR-
[24] Mattick JS; Gagen MJ (1 September 2001). “The evo- NAs regulate transcripts in mouse oocytes”. Nature
lution of controlled multitasked gene networks: the role 453 (7194): 539–43. Bibcode:2008Natur.453..539W.
of introns and other noncoding RNAs in the development doi:10.1038/nature06908. PMID 18404146.
of complex organisms”. Mol. Biol. Evol. 18 (9): 1611–
30. doi:10.1093/oxfordjournals.molbev.a003951. PMID [37] Sontheimer EJ; Carthew RW (July 2005). “Silence from
11504843. within: endogenous siRNAs and miRNAs”. Cell 122 (1):
9–12. doi:10.1016/j.cell.2005.06.030. PMID 16009127.
[25] Mattick, JS (2001). “Noncoding RNAs: the architects
of eukaryotic complexity”. EMBO Reports 2 (11): 986– [38] Doran G (2007). “RNAi – Is one suffix sufficient?". Jour-
91. doi:10.1093/embo-reports/kve230. PMC 1084129. nal of RNAi and Gene Silencing 3 (1): 217–19.
PMID 11713189.
[39] Pushparaj PN; Aarthi JJ; Kumar SD; Manikandan
[26] Mattick JS (October 2003). “Challenging the dogma: the
J (2008). “RNAi and RNAa — The Yin and
hidden layer of non-protein-coding RNAs in complex or-
Yang of RNAome”. Bioinformation 2 (6): 235–7.
ganisms” (PDF). BioEssays : News and Reviews in Molec-
doi:10.6026/97320630002235. PMC 2258431. PMID
ular, Cellular and Developmental Biology 25 (10): 930–9.
18317570.
doi:10.1002/bies.10332. PMID 14505360.

[27] Mattick JS (October 2004). “The hidden genetic pro- [40] Horwich MD; Li C; Matranga C; Vagin V; Farley G;
gram of complex organisms”. Scientific American 291 (4): Wang P; Zamore PD (2007). “The Drosophila RNA
60–7. doi:10.1038/scientificamerican1004-60. PMID methyltransferase, DmHen1, modifies germline piRNAs
15487671. and single-stranded siRNAs in RISC”. Current Biology 17
(14): 1265–72. doi:10.1016/j.cub.2007.06.030. PMID
[28] Wirta W (2006). Mining the transcriptome – methods and 17604629.
applications. Stockholm: School of Biotechnology, Royal
Institute of Technology. ISBN 91-7178-436-5. OCLC [41] Girard A; Sachidanandam R; Hannon GJ; Carmell
185406288. MA (2006). “A germline-specific class of small
RNAs binds mammalian Piwi proteins”. Nature 442
[29] Rossi JJ (2004). “Ribozyme diagnostics comes (7099): 199–202. Bibcode:2006Natur.442..199G.
of age”. Chemistry & Biology 11 (7): 894–95. doi:10.1038/nature04917. PMID 16751776.
doi:10.1016/j.chembiol.2004.07.002. PMID 15271347.
[42] Horvath P; Barrangou R (2010). “CRISPR/Cas, the
[30] Gueneau de Novoa P, Williams KP; Williams (2004).
Immune System of Bacteria and Archaea”. Science
“The tmRNA website: reductive evolution of tmRNA
327 (5962): 167–70. Bibcode:2010Sci...327..167H.
in plastids and other endosymbionts”. Nucleic Acids Res
doi:10.1126/science.1179555. PMID 20056882.
32 (Database issue): D104–8. doi:10.1093/nar/gkh102.
PMC 308836. PMID 14681369. [43] Wagner EG; Altuvia S; Romby P (2002). “Antisense
[31] Carthew, RW; Sontheimer, EJ. “Origins and RNAs in bacteria and their genetic elements”. Adv Genet.
Mechanisms of miRNAs and siRNAs.”. Cell. Advances in Genetics 46: 361–98. doi:10.1016/S0065-
doi:10.1016/j.cell.2009.01.035. PMC 2675692. 2660(02)46013-0. ISBN 9780120176465. PMID
PMID 19239886. Retrieved 2009-02-20. 11931231.

[32] Liang, Kung-Hao; Yeh, Chau-Ting. “A gene expression [44] Gilbert SF (2003). Developmental Biology (7th
restriction network mediated by sense and antisense Alu ed.). Sinauer. pp. 101–3. ISBN 0-87893-258-5.
sequences located on protein-coding messenger RNAs.”. OCLC 154656422 154663147 174530692 177000492
BMC Genomics. doi:10.1186/1471-2164-14-325. PMC 177316159 51544170 54743254 59197768 61404850
3655826. PMID 23663499. Retrieved 2013-05-11. 66754122.
3.2. RNA 51

[45] Amaral PP; Mattick JS (October 2008). “Noncoding [56] Podlevsky JD; Bley CJ; Omana RV; Qi X; Chen JJ
RNA in development”. Mammalian genome : official (2008). “The telomerase database”. Nucleic Acids Res 36
journal of the International Mammalian Genome Soci- (Database issue): D339–43. doi:10.1093/nar/gkm700.
ety 19 (7–8): 454–92. doi:10.1007/s00335-008-9136-7. PMC 2238860. PMID 18073191.
PMID 18839252.
[57] Blevins, T.; Rajeswaran, R.; Shivaprasad, PV.; Bek-
[46] Heard E; Mongelard F; Arnaud D; Chureau C; nazariants, D.; Si-Ammour, A.; Park, HS.; Vazquez, F.;
Vourc'h C; Avner P (1999). “Human XIST yeast Robertson, D.; Meins, F. (2006). “Four plant Dicers
artificial chromosome transgenes show partial X mediate viral small RNA biogenesis and DNA virus in-
inactivation center function in mouse embryonic duced silencing”. Nucleic Acids Res 34 (21): 6233–
stem cells”. Proc. Natl. Acad. Sci. USA 96 46. doi:10.1093/nar/gkl886. PMC 1669714. PMID
(12): 6841–46. Bibcode:1999PNAS...96.6841H. 17090584.
doi:10.1073/pnas.96.12.6841. PMC 22003. PMID
10359800. [58] Jana S; Chakraborty C; Nandi S; Deb JK (2004). “RNA
interference: potential therapeutic targets”. Appl. Micro-
[47] Batey RT (2006). “Structures of regulatory elements in biol. Biotechnol. 65 (6): 649–57. doi:10.1007/s00253-
mRNAs”. Curr. Opin. Struct. Biol. 16 (3): 299–306. 004-1732-1. PMID 15372214.
doi:10.1016/j.sbi.2006.05.001. PMID 16707260.
[59] Schultz U; Kaspers B; Staeheli P (2004). “The interferon
[48] Scotto L; Assoian RK (June 1993). “A GC-rich domain system of non-mammalian vertebrates”. Dev. Comp. Im-
with bifunctional effects on mRNA and protein levels: im- munol. 28 (5): 499–508. doi:10.1016/j.dci.2003.09.009.
plications for control of transforming growth factor beta PMID 15062646.
1 expression”. Mol. Cell. Biol. 13 (6): 3588–97. PMC
359828. PMID 8497272. [60] Whitehead, K. A.; Dahlman, J. E.; Langer, R. S.;
Anderson, D. G. (2011). “Silencing or Stimulation?
[49] Steitz TA; Steitz JA (1993). “A general two- SiRNA Delivery and the Immune System”. Annual Re-
metal-ion mechanism for catalytic RNA”. view of Chemical and Biomolecular Engineering 2: 77–
Proc. Natl. Acad. Sci. U.S.A. 90 (14): 96. doi:10.1146/annurev-chembioeng-061010-114133.
6498–502. Bibcode:1993PNAS...90.6498S. PMID 22432611.
doi:10.1073/pnas.90.14.6498. PMC 46959. PMID
8341661. [61] Dahm R (2005). “Friedrich Miescher and the discov-
ery of DNA”. Developmental Biology 278 (2): 274–88.
[50] Xie J; Zhang M; Zhou T; Hua X; Tang L; Wu W (2007). doi:10.1016/j.ydbio.2004.11.028. PMID 15680349.
“Sno/scaRNAbase: a curated database for small nucleolar
RNAs and cajal body-specific RNAs”. Nucleic Acids Res [62] Caspersson T; Schultz J (1939). “Pentose nucleotides
35 (Database issue): D183–7. doi:10.1093/nar/gkl873. in the cytoplasm of growing tissues”. Nature 143
PMC 1669756. PMID 17099227. (3623): 602–3. Bibcode:1939Natur.143..602C.
doi:10.1038/143602c0.
[51] Omer AD; Ziesche S; Decatur WA; Fournier MJ;
Dennis PP (2003). “RNA-modifying machines in [63] Ochoa S (1959). “Enzymatic synthesis of ribonucleic
archaea”. Molecular Microbiology 48 (3): 617– acid” (PDF). Nobel Lecture.
29. doi:10.1046/j.1365-2958.2003.03483.x. PMID
12694609. [64] Rich A; Davies, D (1956). “A New Two-Stranded Heli-
cal Structure: Polyadenylic Acid and Polyuridylic Acid”.
[52] Cavaillé J; Nicoloso M; Bachellerie JP (1996). “Tar- Journal of the American Chemical Society 78 (14): 3548–
geted ribose methylation of RNA in vivo directed by tai- 3549. doi:10.1021/ja01595a086.
lored antisense RNA guides”. Nature 383 (6602): 732–5.
Bibcode:1996Natur.383..732C. doi:10.1038/383732a0. [65] Holley RW et al. (1965). “Structure of
PMID 8878486. a ribonucleic acid”. Science 147 (3664):
1462–65. Bibcode:1965Sci...147.1462H.
[53] Kiss-László Z; Henry Y; Bachellerie JP; Caizergues- doi:10.1126/science.147.3664.1462. PMID 14263761.
Ferrer M; Kiss T (1996). “Site-specific ribose methylation
of preribosomal RNA: a novel function for small nucleo- [66] Siebert S (2006). “Common sequence structure prop-
lar RNAs”. Cell 85 (7): 1077–88. doi:10.1016/S0092- erties and stable regions in RNA secondary structures”
8674(00)81308-2. PMID 8674114. (PDF). Dissertation, Albert-Ludwigs-Universität, Freiburg
im Breisgau. p. 1.
[54] Daròs JA; Elena SF; Flores R (2006). “Viroids: an Ari-
adne’s thread into the RNA labyrinth”. EMBO Rep 7 (6): [67] Szathmáry E (1999). “The origin of the genetic code:
593–8. doi:10.1038/sj.embor.7400706. PMC 1479586. amino acids as cofactors in an RNA world”. Trends Genet
PMID 16741503. 15 (6): 223–9. doi:10.1016/S0168-9525(99)01730-8.
PMID 10354582.
[55] Kalendar R; Vicient CM; Peleg O; Anamthawat-Jonsson
K; Bolshoy A; Schulman AH (2004). “Large retrotranspo- [68] Fiers W et al. (1976). “Complete nucleotide-sequence
son derivatives: abundant, conserved but nonautonomous of bacteriophage MS2-RNA: primary and secondary
retroelements of barley and related genomes”. Genet- structure of replicase gene”. Nature 260 (5551): 500–7.
ics 166 (3): 1437–50. doi:10.1534/genetics.166.3.1437. Bibcode:1976Natur.260..500F. doi:10.1038/260500a0.
PMC 1470764. PMID 15082561. PMID 1264203.
52 CHAPTER 3. NUCLEIC ACIDS

[69] Napoli C; Lemieux C; Jorgensen R (1990). “Introduction

of a chimeric chalcone synthase gene into petu-
nia results in reversible co-suppression of homolo-
gous genes in trans”. Plant Cell 2 (4): 279–
89. doi:10.1105/tpc.2.4.279. PMC 159885. PMID
12354959.

[70] Dafny-Yelin M; Chung SM; Frankman EL; Tzfira T

(December 2007). “pSAT RNA interference vectors:
a modular series for multiple gene down-regulation
in plants”. Plant Physiol. 145 (4): 1272–81.
doi:10.1104/pp.107.106062. PMC 2151715. PMID
17766396.

[71] Ruvkun G (2001). “Glimpses of a tiny RNA world”. Sci-

ence 294 (5543): 797–99. doi:10.1126/science.1066315.
PMID 11679654.

[72] Fichou Y; Férec C (2006). “The potential

of oligonucleotides for therapeutic applica-
tions”. Trends in Biotechnology 24 (12): 563–70. The structure of the DNA double helix. The atoms in the structure
doi:10.1016/j.tibtech.2006.10.003. PMID 17045686. are colour-coded by element and the detailed structure of two
base pairs are shown in the bottom right.
[73] Marlaire, Ruth (3 March 2015). “NASA Ames Repro-
duces the Building Blocks of Life in Laboratory”. NASA.
Retrieved 5 March 2015.

3.2.9 External links

• RNA World website Link collection (structures, se-
quences, tools, journals)

• Nucleic Acid Database Images of DNA, RNA and

complexes.

• RNA Calculators

3.3 DNA
For a non-technical introduction to the topic, see
Introduction to genetics. For other uses, see DNA (dis-
ambiguation).
Deoxyribonucleic acid ( i /diˌɒksiˌraɪbɵ.njuːˌkleɪ.ɨk
ˈæsɪd/; DNA) is a molecule that carries most of the
genetic instructions used in the development, function-
ing and reproduction of all known living organisms and
many viruses. DNA is a nucleic acid; alongside proteins
and carbohydrates, nucleic acids compose the three ma-
jor macromolecules essential for all known forms of life.
Most DNA molecules consist of two biopolymer strands
coiled around each other to form a double helix. The
two DNA strands are known as polynucleotides since
they are composed of simpler units called nucleotides.
Each nucleotide is composed of a nitrogen-containing
nucleobase—either cytosine (C), guanine (G), adenine The structure of part of a DNA double helix
(A), or thymine (T)—as well as a monosaccharide sugar
called deoxyribose and a phosphate group. The nu-
cleotides are joined to one another in a chain by covalent phosphate of the next, resulting in an alternating sugar-
bonds between the sugar of one nucleotide and the phosphate backbone. According to base pairing rules (A
3.3. DNA 53

with T, and C with G), hydrogen bonds bind the nitroge- Thymine
nous bases of the two separate polynucleotide strands to Adenine
make double-stranded DNA. The total amount of related 5′ end O− O
NH 2 3′ end
DNA base pairs on Earth is estimated at 5.0 x 1037 , and O
P
O
N OH
−O HN
weighs 50 billion tonnes.[1] In comparison, the total mass O N
N N

of the biosphere has been estimated to be as much as 4 N O O

TtC (trillion tons of carbon).[2] O NH 2 O

O
P
O−

O
O N
P O
DNA stores biological information. The DNA backbone −O
O
N HN N

is resistant to cleavage, and both strands of the double- O N

N
O
O H2N
stranded structure store the same biological information. O O−
Phosphate- O P
Biological information is replicated as the two strands are O
O H2N
N
O

deoxyribose O P O

separated. A significant portion of DNA (more than 98% backbone

− O
NH N N
O N
for humans) is non-coding, meaning that these sections do O
N
O

not serve as patterns for protein sequences. H2N

O O−
O P O
O
O P
The two strands of DNA run in opposite directions to −O O
N
N
N
O

NH
each other and are therefore anti-parallel. Attached to O N
N O O
each sugar is one of four types of nucleobases (informally, NH 2

O O−

bases). It is the sequence of these four nucleobases along Cytosine

OH P
O
3′ end −O
the backbone that encodes biological information. Un- Guanine 5′ end
der the genetic code, RNA strands are translated to spec-
ify the sequence of amino acids within proteins. These
Chemical structure of DNA; hydrogen bonds shown as dotted
RNA strands are initially created using DNA strands as a
lines
template in a process called transcription.
Within cells, DNA is organized into long structures
called chromosomes. During cell division these chro-
by Miescher in 1869 at the University of Tübingen, a
mosomes are duplicated in the process of DNA replica-
substance he called nuclein, and the double helix struc-
tion, providing each cell its own complete set of chro-
ture of DNA was first discovered in 1953 by Watson and
mosomes. Eukaryotic organisms (animals, plants, fungi,
Crick at the University of Cambridge, using experimental
and protists) store most of their DNA inside the cell
data collected by Rosalind Franklin and Maurice Wilkins.
nucleus and some of their DNA in organelles, such as
The structure of DNA of all species comprises two he-
mitochondria or chloroplasts.[3] In contrast, prokaryotes
lical chains each coiled round the same axis, and each
(bacteria and archaea) store their DNA only in the
with a pitch of 34 ångströms (3.4 nanometres) and a ra-
cytoplasm. Within the chromosomes, chromatin proteins
dius of 10 ångströms (1.0 nanometre).[8] According to an-
such as histones compact and organize DNA. These com-
other study, when measured in a particular solution, the
pact structures guide the interactions between DNA and
DNA chain measured 22 to 26 ångströms wide (2.2 to
other proteins, helping control which parts of the DNA
2.6 nanometres), and one nucleotide unit measured 3.3
are transcribed.
Å (0.33 nm) long.[9] Although each individual repeat-
First isolated by Friedrich Miescher in 1869 and with its ing unit is very small, DNA polymers can be very large
molecular structure first identified by James Watson and molecules containing millions of nucleotides. For in-
Francis Crick in 1953, DNA is used by researchers as a stance, the DNA in the largest human chromosome, chro-
molecular tool to explore physical laws and theories, such mosome number 1, consists of approximately 220 million
as the ergodic theorem and the theory of elasticity. The base pairs[10] and would be 85 mm long if straightened.
unique material properties of DNA have made it an at-
In living organisms DNA does not usually exist as a sin-
tractive molecule for material scientists and engineers in-
gle molecule, but instead as a pair of molecules that are
terested in micro- and nano-fabrication. Among notable
held tightly together.[11][12] These two long strands en-
advances in this field are DNA origami and DNA-based
twine like vines, in the shape of a double helix. The nu-
hybrid materials.[4]
cleotide repeats contain both the segment of the backbone
The obsolete synonym "desoxyribonucleic acid" may of the molecule, which holds the chain together, and a
occasionally be encountered, for example, in pre-1953 nucleobase, which interacts with the other DNA strand
genetics. in the helix. A nucleobase linked to a sugar is called a
nucleoside and a base linked to a sugar and one or more
phosphate groups is called a nucleotide. A polymer com-
3.3.1 Properties prising multiple linked nucleotides (as in DNA) is called
a polynucleotide.[13]
DNA is a long polymer made from repeating units called The backbone of the DNA strand is made from alternat-
nucleotides.[5][6][7] DNA was first identified and isolated ing phosphate and sugar residues.[14] The sugar in DNA
54 CHAPTER 3. NUCLEIC ACIDS

is 2-deoxyribose, which is a pentose (five-carbon) sugar. The four bases found in DNA are adenine (abbreviated
The sugars are joined together by phosphate groups that A), cytosine (C), guanine (G) and thymine (T). These
form phosphodiester bonds between the third and fifth four bases are attached to the sugar/phosphate to form the
carbon atoms of adjacent sugar rings. These asymmetric complete nucleotide, as shown for adenosine monophos-
bonds mean a strand of DNA has a direction. In a dou- phate.
ble helix the direction of the nucleotides in one strand is
opposite to their direction in the other strand: the strands
are antiparallel. The asymmetric ends of DNA strands
are called the 5′ (five prime) and 3′ (three prime) ends, Nucleobase classification
with the 5′ end having a terminal phosphate group and
the 3′ end a terminal hydroxyl group. One major dif-
ference between DNA and RNA is the sugar, with the The nucleobases are classified into two types: the
2-deoxyribose in DNA being replaced by the alternative purines, A and G, being fused five- and six-membered
pentose sugar ribose in RNA.[12] heterocyclic compounds, and the pyrimidines, the six-
membered rings C and T.[12] A fifth pyrimidine nucle-
obase, uracil (U), usually takes the place of thymine in
RNA and differs from thymine by lacking a methyl group
on its ring. In addition to RNA and DNA a large num-
ber of artificial nucleic acid analogues have also been cre-
ated to study the properties of nucleic acids, or for use in
biotechnology.[17]
Uracil is not usually found in DNA, occurring only as a
breakdown product of cytosine. However, in a number
of bacteriophages – Bacillus subtilis bacteriophages PBS1
and PBS2 and Yersinia bacteriophage piR1-37 – thymine
has been replaced by uracil.[18] Another phage - Staphy-
lococcal phage S6 - has been identified with a genome
where thymine has been replaced by uracil.[19]
Base J (beta-d-glucopyranosyloxymethyluracil), a modi-
fied form of uracil, is also found in a number of organ-
isms: the flagellates Diplonema and Euglena, and all the
kinetoplastid genera[20] Biosynthesis of J occurs in two
steps: in the first step a specific thymidine in DNA is con-
verted into hydroxymethyldeoxyuridine; in the second
HOMedU is glycosylated to form J.[21] Proteins that bind
specifically to this base have been identified.[22][23][24]
These proteins appear to be distant relatives of the Tet1
oncogene that is involved in the pathogenesis of acute
myeloid leukemia.[25] J appears to act as a termination
signal for RNA polymerase II.[26][27]

A section of DNA. The bases lie horizontally between the two

spiraling strands.[15] (animated version).

The DNA double helix is stabilized primarily by two

forces: hydrogen bonds between nucleotides and base-
stacking interactions among aromatic nucleobases.[16] In
the aqueous environment of the cell, the conjugated π
Major and minor grooves of DNA. Minor groove is a binding site
bonds of nucleotide bases align perpendicular to the axis
for the dye Hoechst 33258.
of the DNA molecule, minimizing their interaction with
the solvation shell and therefore, the Gibbs free energy.
3.3. DNA 55

Grooves (dsDNA) is maintained largely by the intrastrand base

stacking interactions, which are strongest for G,C stacks.
Twin helical strands form the DNA backbone. Another The two strands can come apart – a process known as
double helix may be found tracing the spaces, or grooves, melting – to form two single-stranded DNA molecules
between the strands. These voids are adjacent to the base (ssDNA) molecules. Melting occurs at high tempera-
pairs and may provide a binding site. As the strands ture, low salt and high pH (low pH also melts DNA, but
are not symmetrically located with respect to each other, since DNA is unstable due to acid depurination, low pH
the grooves are unequally sized. One groove, the major is rarely used).
groove, is 22 Å wide and the other, the minor groove, The stability of the dsDNA form depends not only on
is 12 Å wide.[28] The width of the major groove means the GC-content (% G,C basepairs) but also on sequence
that the edges of the bases are more accessible in the ma- (since stacking is sequence specific) and also length
jor groove than in the minor groove. As a result, pro- (longer molecules are more stable). The stability can be
teins such as transcription factors that can bind to spe- measured in various ways; a common way is the “melting
cific sequences in double-stranded DNA usually make temperature”, which is the temperature at which 50% of
contact with the sides of the bases exposed in the major the ds molecules are converted to ss molecules; melting
groove.[29] This situation varies in unusual conformations temperature is dependent on ionic strength and the con-
of DNA within the cell (see below), but the major and mi- centration of DNA. As a result, it is both the percent-
nor grooves are always named to reflect the differences in age of GC base pairs and the overall length of a DNA
size that would be seen if the DNA is twisted back into double helix that determines the strength of the associa-
the ordinary B form. tion between the two strands of DNA. Long DNA he-
lices with a high GC-content have stronger-interacting
strands, while short helices with high AT content have
Base pairing
weaker-interacting strands.[31] In biology, parts of the
DNA double helix that need to separate easily, such as
Further information: Base pair
the TATAAT Pribnow box in some promoters, tend to
have a high AT content, making the strands easier to pull
In a DNA double helix, each type of nucleobase on one apart.[32]
strand bonds with just one type of nucleobase on the other
In the laboratory, the strength of this interaction can
strand. This is called complementary base pairing. Here,
be measured by finding the temperature necessary to
purines form hydrogen bonds to pyrimidines, with ade-
break the hydrogen bonds, their melting temperature
nine bonding only to thymine in two hydrogen bonds,
(also called Tm value). When all the base pairs in a DNA
and cytosine bonding only to guanine in three hydrogen
double helix melt, the strands separate and exist in solu-
bonds. This arrangement of two nucleotides binding to-
tion as two entirely independent molecules. These single-
gether across the double helix is called a base pair. As
stranded DNA molecules (ssDNA) have no single com-
hydrogen bonds are not covalent, they can be broken and
mon shape, but some conformations are more stable than
rejoined relatively easily. The two strands of DNA in a
others.[33]
double helix can therefore be pulled apart like a zipper,
either by a mechanical force or high temperature.[30] As
a result of this complementarity, all the information in Sense and antisense
the double-stranded sequence of a DNA helix is dupli-
cated on each strand, which is vital in DNA replication. Further information: Sense (molecular biology)
Indeed, this reversible and specific interaction between
complementary base pairs is critical for all the functions
of DNA in living organisms.[6] A DNA sequence is called “sense” if its sequence is the
same as that of a messenger RNA copy that is translated
Top, a GC base pair with three hydrogen bonds. Bottom, into protein.[34] The sequence on the opposite strand is
an AT base pair with two hydrogen bonds. Non-covalent called the “antisense” sequence. Both sense and antisense
hydrogen bonds between the pairs are shown as dashed sequences can exist on different parts of the same strand
lines. of DNA (i.e. both strands can contain both sense and an-
tisense sequences). In both prokaryotes and eukaryotes,
The two types of base pairs form different numbers of hy- antisense RNA sequences are produced, but the functions
drogen bonds, AT forming two hydrogen bonds, and GC of these RNAs are not entirely clear.[35] One proposal is
forming three hydrogen bonds (see figures, right). DNA that antisense RNAs are involved in regulating gene ex-
with high GC-content is more stable than DNA with low pression through RNA-RNA base pairing.[36]
GC-content. A few DNA sequences in prokaryotes and eukaryotes,
As noted above, most DNA molecules are actually two and more in plasmids and viruses, blur the distinction be-
polymer strands, bound together in a helical fashion tween sense and antisense strands by having overlapping
by noncovalent bonds; this double stranded structure genes.[37] In these cases, some DNA sequences do double
56 CHAPTER 3. NUCLEIC ACIDS

duty, encoding one protein when read along one strand, The first published reports of A-DNA X-ray diffrac-
and a second protein when read in the opposite direc- tion patterns—and also B-DNA—used analyses based
tion along the other strand. In bacteria, this overlap may on Patterson transforms that provided only a limited
be involved in the regulation of gene transcription,[38] amount of structural information for oriented fibers of
while in viruses, overlapping genes increase the amount DNA.[44][45] An alternate analysis was then proposed by
of information that can be encoded within the small viral Wilkins et al., in 1953, for the in vivo B-DNA X-ray
genome.[39] diffraction/scattering patterns of highly hydrated DNA
fibers in terms of squares of Bessel functions.[46] In the
same journal, James Watson and Francis Crick presented
Supercoiling their molecular modeling analysis of the DNA X-ray
diffraction patterns to suggest that the structure was a
Further information: DNA supercoil double-helix.[8]
Although the “B-DNA form” is most common under the
DNA can be twisted like a rope in a process called DNA conditions found in cells,[47] it is not a well-defined con-
supercoiling. With DNA in its “relaxed” state, a strand formation but a family of related DNA conformations[48]
usually circles the axis of the double helix once every 10.4 that occur at the high hydration levels present in living
base pairs, but if the DNA is twisted the strands become cells. Their corresponding X-ray diffraction and scatter-
more tightly or more loosely wound.[40] If the DNA is ing patterns are characteristic of molecular paracrystals
twisted in the direction of the helix, this is positive super- with a significant degree of disorder.[49][50]
coiling, and the bases are held more tightly together. If
they are twisted in the opposite direction, this is negative Compared to B-DNA, the A-DNA form is a wider right-
supercoiling, and the bases come apart more easily. In handed spiral, with a shallow, wide minor groove and
nature, most DNA has slight negative supercoiling that is a narrower, deeper major groove. The A form oc-
introduced by enzymes called topoisomerases.[41] These curs under non-physiological conditions in partially de-
enzymes are also needed to relieve the twisting stresses hydrated samples of DNA, while in the cell it may be
introduced into DNA strands during processes such as produced in hybrid pairings of DNA and RNA strands,
transcription and DNA replication.[42] as well as in enzyme-DNA complexes.[51][52] Segments
of DNA where the bases have been chemically modified
by methylation may undergo a larger change in conforma-
tion and adopt the Z form. Here, the strands turn about
the helical axis in a left-handed spiral, the opposite of the
more common B form.[53] These unusual structures can
be recognized by specific Z-DNA binding proteins and
may be involved in the regulation of transcription.[54]

Alternative DNA chemistry

For a number of years exobiologists have proposed the

existence of a shadow biosphere, a postulated micro-
bial biosphere of Earth that uses radically different bio-
From left to right, the structures of A, B and Z DNA chemical and molecular processes than currently known
life. One of the proposals was the existence of life-
forms that use arsenic instead of phosphorus in DNA.
A report in 2010 of the possibility in the bacterium
Alternate DNA structures GFAJ-1, was announced,[55][55][56] though the research
was disputed,[56][57] and evidence suggests the bacterium
Further information: Molecular Structure of Nucleic actively prevents the incorporation of arsenic into the
Acids: A Structure for Deoxyribose Nucleic Acid, DNA backbone and other biomolecules.[58]
Molecular models of DNA, and DNA structure

DNA exists in many possible conformations that in- Quadruplex structures

clude A-DNA, B-DNA, and Z-DNA forms, although,
only B-DNA and Z-DNA have been directly observed Further information: G-quadruplex
in functional organisms.[14] The conformation that DNA
adopts depends on the hydration level, DNA sequence, At the ends of the linear chromosomes are specialized
the amount and direction of supercoiling, chemical modi- regions of DNA called telomeres. The main function of
fications of the bases, the type and concentration of metal these regions is to allow the cell to replicate chromosome
ions, as well as the presence of polyamines in solution.[43] ends using the enzyme telomerase, as the enzymes that
3.3. DNA 57

normally replicate DNA cannot copy the extreme 3′ ends Branched DNA
of chromosomes.[59] These specialized chromosome caps
also help protect the DNA ends, and stop the DNA re- Further information: Branched DNA and DNA nan-
pair systems in the cell from treating them as damage otechnology
to be corrected.[60] In human cells, telomeres are usually
lengths of single-stranded DNA containing several thou-
In DNA fraying occurs when non-complementary regions
sand repeats of a simple TTAGGG sequence.[61]
exist at the end of an otherwise complementary double-
strand of DNA. However, branched DNA can occur if a
third strand of DNA is introduced and contains adjoin-
ing regions able to hybridize with the frayed regions of
the pre-existing double-strand. Although the simplest ex-
ample of branched DNA involves only three strands of
DNA, complexes involving additional strands and mul-
tiple branches are also possible.[66] Branched DNA can
be used in nanotechnology to construct geometric shapes,
see the section on uses in technology below.

3.3.2 Chemical modifications and altered

DNA packaging

Structure of cytosine with and without the 5-methyl

group. Deamination converts 5-methylcytosine into
thymine.

DNA quadruplex formed by telomere repeats. The looped con-

formation of the DNA backbone is very different from the typical Base modifications and DNA packaging
DNA helix.[62]
Further information: DNA methylation, Chromatin
remodeling
These guanine-rich sequences may stabilize chromosome
ends by forming structures of stacked sets of four-base The expression of genes is influenced by how the DNA
units, rather than the usual base pairs found in other DNA is packaged in chromosomes, in a structure called
molecules. Here, four guanine bases form a flat plate chromatin. Base modifications can be involved in pack-
and these flat four-base units then stack on top of each aging, with regions that have low or no gene expression
other, to form a stable G-quadruplex structure.[63] These
usually containing high levels of methylation of cytosine
structures are stabilized by hydrogen bonding between bases. DNA packaging and its influence on gene ex-
the edges of the bases and chelation of a metal ion in the
pression can also occur by covalent modifications of the
centre of each four-base unit.[64] Other structures can alsohistone protein core around which DNA is wrapped in the
be formed, with the central set of four bases coming from
chromatin structure or else by remodeling carried out by
either a single strand folded around the bases, or several chromatin remodeling complexes (see Chromatin remod-
different parallel strands, each contributing one base to
eling). There is, further, crosstalk between DNA methy-
the central structure. lation and histone modification, so they can coordinately
In addition to these stacked structures, telomeres also affect chromatin and gene expression.[67]
form large loop structures called telomere loops, or T- For one example, cytosine methylation, produces 5-
loops. Here, the single-stranded DNA curls around in a methylcytosine, which is important for X-chromosome
long circle stabilized by telomere-binding proteins.[65] At inactivation.[68] The average level of methylation varies
the very end of the T-loop, the single-stranded telomere between organisms – the worm Caenorhabditis ele-
DNA is held onto a region of double-stranded DNA by gans lacks cytosine methylation, while vertebrates have
the telomere strand disrupting the double-helical DNA higher levels, with up to 1% of their DNA con-
and base pairing to one of the two strands. This triple- taining 5-methylcytosine.[69] Despite the importance
stranded structure is called a displacement loop or D- of 5-methylcytosine, it can deaminate to leave a
loop.[63] thymine base, so methylated cytosines are particularly
Branched DNA can form networks containing multiple prone to mutations.[70] Other base modifications in-
branches. clude adenine methylation in bacteria, the presence
of 5-hydroxymethylcytosine in the brain,[71] and the
58 CHAPTER 3. NUCLEIC ACIDS

glycosylation of uracil to produce the “J-base” in due to normal cellular processes that produce reactive
kinetoplastids.[72][73] oxygen species, the hydrolytic activities of cellular wa-
ter, etc., also occur frequently. Although most of these
damages are repaired, in any cell some DNA damage
Damage may remain despite the action of repair processes. These
remaining DNA damages accumulate with age in mam-
Further information: DNA damage (naturally occurring), malian postmitotic tissues. This accumulation appears to
Mutation, DNA damage theory of aging be an important underlying cause of aging.[81][82][83]
DNA can be damaged by many sorts of mutagens,
Many mutagens fit into the space between two adja-
cent base pairs, this is called intercalation. Most in-
tercalators are aromatic and planar molecules; exam-
ples include ethidium bromide, acridines, daunomycin,
and doxorubicin. For an intercalator to fit between
base pairs, the bases must separate, distorting the DNA
strands by unwinding of the double helix. This inhibits
both transcription and DNA replication, causing toxi-
city and mutations.[84] As a result, DNA intercalators
may be carcinogens, and in the case of thalidomide, a
teratogen.[85] Others such as benzo[a]pyrene diol epox-
ide and aflatoxin form DNA adducts that induce errors in
replication.[86] Nevertheless, due to their ability to inhibit
DNA transcription and replication, other similar toxins
are also used in chemotherapy to inhibit rapidly growing
cancer cells.[87]

3.3.3 Biological functions

Cell DNA

A covalent adduct between a metabolically activated form of

benzo[a]pyrene, the major mutagen in tobacco smoke, and
DNA[74]

which change the DNA sequence. Mutagens include Nucleus Chromosome

oxidizing agents, alkylating agents and also high-energy
electromagnetic radiation such as ultraviolet light and X- Location of eukaryote nuclear DNA within the chromosomes.
rays. The type of DNA damage produced depends on
the type of mutagen. For example, UV light can dam- DNA usually occurs as linear chromosomes in
age DNA by producing thymine dimers, which are cross- eukaryotes, and circular chromosomes in prokaryotes.
links between pyrimidine bases.[75] On the other hand, The set of chromosomes in a cell makes up its genome;
oxidants such as free radicals or hydrogen peroxide pro- the human genome has approximately 3 billion base
duce multiple forms of damage, including base mod- pairs of DNA arranged into 46 chromosomes.[88] The
ifications, particularly of guanosine, and double-strand information carried by DNA is held in the sequence of
breaks.[76] A typical human cell contains about 150,000 pieces of DNA called genes. Transmission of genetic
bases that have suffered oxidative damage.[77] Of these information in genes is achieved via complementary
oxidative lesions, the most dangerous are double-strand base pairing. For example, in transcription, when a cell
breaks, as these are difficult to repair and can produce uses the information in a gene, the DNA sequence is
point mutations, insertions and deletions from the DNA copied into a complementary RNA sequence through
sequence, as well as chromosomal translocations.[78] the attraction between the DNA and the correct RNA
These mutations can cause cancer. Because of inher- nucleotides. Usually, this RNA copy is then used to
ent limitations in the DNA repair mechanisms, if hu- make a matching protein sequence in a process called
mans lived long enough, they would all eventually develop translation, which depends on the same interaction
cancer.[79][80] DNA damages that are naturally occurring, between RNA nucleotides. In alternative fashion, a cell
3.3. DNA 59

may simply copy its genetic information in a process tain few genes, but are important for the function and
called DNA replication. The details of these functions stability of chromosomes.[60][94] An abundant form of
are covered in other articles; here the focus is on the noncoding DNA in humans are pseudogenes, which are
interactions between DNA and other molecules that copies of genes that have been disabled by mutation.[95]
mediate the function of the genome. These sequences are usually just molecular fossils, al-
though they can occasionally serve as raw genetic material
for the creation of new genes through the process of gene
Genes and genomes duplication and divergence.[96]
Further information: Cell nucleus, Chromatin,
Chromosome, Gene, Noncoding DNA

Genomic DNA is tightly and orderly packed in the pro- Transcription and translation
cess called DNA condensation to fit the small available
volumes of the cell. In eukaryotes, DNA is located in Further information: Genetic code, Transcription (ge-
the cell nucleus, as well as small amounts in mitochondria netics), Protein biosynthesis
and chloroplasts. In prokaryotes, the DNA is held within
an irregularly shaped body in the cytoplasm called the
nucleoid.[89] The genetic information in a genome is held A gene is a sequence of DNA that contains genetic infor-
within genes, and the complete set of this information in mation and can influence the phenotype of an organism.
an organism is called its genotype. A gene is a unit of Within a gene, the sequence of bases along a DNA strand
heredity and is a region of DNA that influences a par- defines a messenger RNA sequence, which then defines
ticular characteristic in an organism. Genes contain an one or more protein sequences. The relationship be-
open reading frame that can be transcribed, as well as tween the nucleotide sequences of genes and the amino-
regulatory sequences such as promoters and enhancers, acid sequences of proteins is determined by the rules of
which control the transcription of the open reading frame.translation, known collectively as the genetic code. The
genetic code consists of three-letter 'words’ called codons
In many species, only a small fraction of the total se- formed from a sequence of three nucleotides (e.g. ACT,
quence of the genome encodes protein. For example, only CAG, TTT).
about 1.5% of the human genome consists of protein-
coding exons, with over 50% of human DNA consisting In transcription, the codons of a gene are copied into mes-
of non-coding repetitive sequences.[90] The reasons for senger RNA by RNA polymerase. This RNA copy is then
the presence of so much noncoding DNA in eukaryotic decoded by a ribosome that reads the RNA sequence by
genomes and the extraordinary differences in genome base-pairing the messenger RNA to transfer RNA, which
size, or C-value, among species represent a long-standing carries amino acids. Since there are 4 bases in3 3-letter
puzzle known as the "C-value enigma".[91] However, combinations, there are 64 possible codons (4 combi-
some DNA sequences that do not code protein may still nations). These encode the twenty standard amino acids,
encode functional non-coding RNA molecules, which are giving most amino acids more than one possible codon.
involved in the regulation of gene expression.[92] There are also three 'stop' or 'nonsense' codons signifying
the end of the coding region; these are the TAA, TGA,
and TAG codons.

DNA primase

DNA-ligase RNA primer

DNA-Polymerase (Polα)

3’
Lagging
strand 3’

5’
Okazaki fragment
5’ 5’
Leading
strand
Topoisomerase
3’
DNA Polymerase (Polδ)
Helicase
Single strand,
Binding proteins

DNA replication. The double helix is unwound by a helicase

and topoisomerase. Next, one DNA polymerase produces the
leading strand copy. Another DNA polymerase binds to the
T7 RNA polymerase (blue) producing a mRNA (green) from a lagging strand. This enzyme makes discontinuous segments
DNA template (orange).[93] (called Okazaki fragments) before DNA ligase joins them to-
gether.
Some noncoding DNA sequences play structural roles in
chromosomes. Telomeres and centromeres typically con-
60 CHAPTER 3. NUCLEIC ACIDS

Replication Structural proteins that bind DNA are well-understood

examples of non-specific DNA-protein interactions.
Further information: DNA replication Within chromosomes, DNA is held in complexes with
structural proteins. These proteins organize the DNA
into a compact structure called chromatin. In eukary-
Cell division is essential for an organism to grow, but,
otes this structure involves DNA binding to a complex of
when a cell divides, it must replicate the DNA in its
small basic proteins called histones, while in prokaryotes
genome so that the two daughter cells have the same ge-
multiple types of proteins are involved.[105][106] The his-
netic information as their parent. The double-stranded
tones form a disk-shaped complex called a nucleosome,
structure of DNA provides a simple mechanism for DNA
which contains two complete turns of double-stranded
replication. Here, the two strands are separated and then
DNA wrapped around its surface. These non-specific in-
each strand’s complementary DNA sequence is recreated
teractions are formed through basic residues in the his-
by an enzyme called DNA polymerase. This enzyme
tones making ionic bonds to the acidic sugar-phosphate
makes the complementary strand by finding the correct
backbone of the DNA, and are therefore largely in-
base through complementary base pairing, and bonding
dependent of the base sequence.[107] Chemical mod-
it onto the original strand. As DNA polymerases can
ifications of these basic amino acid residues include
only extend a DNA strand in a 5′ to 3′ direction, differ-
methylation, phosphorylation and acetylation.[108] These
ent mechanisms are used to copy the antiparallel strands
chemical changes alter the strength of the interaction be-
of the double helix.[97] In this way, the base on the old
tween the DNA and the histones, making the DNA more
strand dictates which base appears on the new strand, and
or less accessible to transcription factors and changing
the cell ends up with a perfect copy of its DNA.
the rate of transcription.[109] Other non-specific DNA-
binding proteins in chromatin include the high-mobility
Extracellular nucleic acids group proteins, which bind to bent or distorted DNA.[110]
These proteins are important in bending arrays of nucle-
osomes and arranging them into the larger structures that
Naked extracellular DNA (eDNA), most of it released
make up chromosomes.[111]
by cell death, is nearly ubiquitous in the environment.
Its concentration in soil may be as high as 2 μg/L, and A distinct group of DNA-binding proteins are the DNA-
its concentration in natural aquatic environments may be binding proteins that specifically bind single-stranded
as high at 88 μg/L.[98] Various possible functions have DNA. In humans, replication protein A is the best-
been proposed for eDNA: it may be involved in horizontal understood member of this family and is used in pro-
gene transfer;[99] it may provide nutrients;[100] and it may cesses where the double helix is separated, including
act as a buffer to recruit or titrate ions or antibiotics.[101] DNA replication, recombination and DNA repair.[112]
Extracellular DNA acts as a functional extracellular ma- These binding proteins seem to stabilize single-stranded
trix component in the biofilms of a number of bacterial DNA and protect it from forming stem-loops or being
species. It may act as a recognition factor to regulate degraded by nucleases.
the attachment and dispersal of specific cell types in the In contrast, other proteins have evolved to bind to par-
biofilm;[102] it may contribute to biofilm formation;[103] ticular DNA sequences. The most intensively studied of
and it may contribute to the biofilm’s physical strength these are the various transcription factors, which are pro-
and resistance to biological stress.[104] teins that regulate transcription. Each transcription fac-
tor binds to one particular set of DNA sequences and
activates or inhibits the transcription of genes that have
3.3.4 Interactions with proteins these sequences close to their promoters. The transcrip-
tion factors do this in two ways. Firstly, they can bind
All the functions of DNA depend on interactions with the RNA polymerase responsible for transcription, either
proteins. These protein interactions can be non-specific, directly or through other mediator proteins; this locates
or the protein can bind specifically to a single DNA se- the polymerase at the promoter and allows it to begin
quence. Enzymes can also bind to DNA and of these, the transcription.[114] Alternatively, transcription factors can
polymerases that copy the DNA base sequence in tran- bind enzymes that modify the histones at the promoter.
scription and DNA replication are particularly important. This changes the accessibility of the DNA template to
the polymerase.[115]

DNA-binding proteins As these DNA targets can occur throughout an organ-

ism’s genome, changes in the activity of one type of tran-
Further information: DNA-binding protein scription factor can affect thousands of genes.[116] Conse-
Interaction of DNA (shown in orange) with histones quently, these proteins are often the targets of the signal
(shown in blue). These proteins’ basic amino acids bind transduction processes that control responses to environ-
to the acidic phosphate groups on DNA. mental changes or cellular differentiation and develop-
ment. The specificity of these transcription factors’ inter-
3.3. DNA 61

cleotides from the ends of DNA strands are called

exonucleases, while endonucleases cut within strands.
The most frequently used nucleases in molecular biology
are the restriction endonucleases, which cut DNA at spe-
cific sequences. For instance, the EcoRV enzyme shown
to the left recognizes the 6-base sequence 5′-GATATC-
3′ and makes a cut at the vertical line. In nature, these
enzymes protect bacteria against phage infection by di-
gesting the phage DNA when it enters the bacterial cell,
acting as part of the restriction modification system.[118]
In technology, these sequence-specific nucleases are used
in molecular cloning and DNA fingerprinting.
Enzymes called DNA ligases can rejoin cut or broken
DNA strands.[119] Ligases are particularly important in
lagging strand DNA replication, as they join together the
short segments of DNA produced at the replication fork
into a complete copy of the DNA template. They are also
used in DNA repair and genetic recombination.[119]

Topoisomerases and helicases Topoisomerases are

enzymes with both nuclease and ligase activity. These
proteins change the amount of supercoiling in DNA.
Some of these enzymes work by cutting the DNA he-
lix and allowing one section to rotate, thereby reduc-
ing its level of supercoiling; the enzyme then seals the
DNA break.[41] Other types of these enzymes are capa-
The lambda repressor helix-turn-helix transcription factor bound
ble of cutting one DNA helix and then passing a sec-
to its DNA target[113]
ond strand of DNA through this break, before rejoin-
ing the helix.[120] Topoisomerases are required for many
actions with DNA come from the proteins making mul- processes involving DNA, such as DNA replication and
[42]
tiple contacts to the edges of the DNA bases, allowing transcription.
them to “read” the DNA sequence. Most of these base- Helicases are proteins that are a type of molecular mo-
interactions are made in the major groove, where the tor. They use the chemical energy in nucleoside triphos-
bases are most accessible.[29] phates, predominantly ATP, to break hydrogen bonds be-
tween bases and unwind the DNA double helix into sin-
gle strands.[121] These enzymes are essential for most pro-
cesses where enzymes need to access the DNA bases.

Polymerases Polymerases are enzymes that synthe-

size polynucleotide chains from nucleoside triphosphates.
The sequence of their products are created based on
existing polynucleotide chains—which are called tem-
plates. These enzymes function by repeatedly adding a
nucleotide to the 3′ hydroxyl group at the end of the grow-
ing polynucleotide chain. As a consequence, all poly-
merases work in a 5′ to 3′ direction.[122] In the active site
of these enzymes, the incoming nucleoside triphosphate
The restriction enzyme EcoRV (green) in a complex with its sub- base-pairs to the template: this allows polymerases to
strate DNA[117] accurately synthesize the complementary strand of their
template. Polymerases are classified according to the type
of template that they use.
DNA-modifying enzymes In DNA replication, DNA-dependent DNA polymerases
make copies of DNA polynucleotide chains. In order to
Nucleases and ligases Nucleases are enzymes that preserve biological information, it is essential that the se-
cut DNA strands by catalyzing the hydrolysis of the quence of bases in each copy are precisely complemen-
phosphodiester bonds. Nucleases that hydrolyse nu- tary to the sequence of bases in the template strand. Many
62 CHAPTER 3. NUCLEIC ACIDS

DNA polymerases have a proofreading activity. Here, of different chromosomes is important for the ability
the polymerase recognizes the occasional mistakes in the of DNA to function as a stable repository for informa-
synthesis reaction by the lack of base pairing between the tion, as one of the few times chromosomes interact is in
mismatched nucleotides. If a mismatch is detected, a 3′ chromosomal crossover which occurs during sexual re-
to 5′ exonuclease activity is activated and the incorrect production, when genetic recombination occurs. Chro-
base removed.[123] In most organisms, DNA polymerases mosomal crossover is when two DNA helices break, swap
function in a large complex called the replisome that con- a section and then rejoin.
tains multiple accessory subunits, such as the DNA clamp Recombination allows chromosomes to exchange genetic
or helicases.[124]
information and produces new combinations of genes,
RNA-dependent DNA polymerases are a specialized which increases the efficiency of natural selection and can
class of polymerases that copy the sequence of an RNA be important in the rapid evolution of new proteins.[129]
strand into DNA. They include reverse transcriptase, Genetic recombination can also be involved in DNA re-
which is a viral enzyme involved in the infection of cells pair, particularly in the cell’s response to double-strand
by retroviruses, and telomerase, which is required for the breaks.[130]
replication of telomeres.[59][125] Telomerase is an unusual The most common form of chromosomal crossover is
polymerase because it contains its own RNA template as homologous recombination, where the two chromosomes
part of its structure.[60] involved share very similar sequences. Non-homologous
Transcription is carried out by a DNA-dependent RNA recombination can be damaging to cells, as it can pro-
polymerase that copies the sequence of a DNA strand into duce chromosomal translocations and genetic abnormali-
RNA. To begin transcribing a gene, the RNA polymerase ties. The recombination reaction is catalyzed by enzymes
binds to a sequence of DNA called a promoter and sepa- known as recombinases, such as RAD51.[131] The first
rates the DNA strands. It then copies the gene sequence step in recombination is a double-stranded break caused
into a messenger RNA transcript until it reaches a region by either an endonuclease or damage to the DNA.[132]
of DNA called the terminator, where it halts and detaches A series of steps catalyzed in part by the recombinase
from the DNA. As with human DNA-dependent DNA then leads to joining of the two helices by at least one
polymerases, RNA polymerase II, the enzyme that tran- Holliday junction, in which a segment of a single strand
scribes most of the genes in the human genome, operates in each helix is annealed to the complementary strand
as part of a large protein complex with multiple regula- in the other helix. The Holliday junction is a tetrahe-
tory and accessory subunits.[126] dral junction structure that can be moved along the pair
of chromosomes, swapping one strand for another. The
recombination reaction is then halted by cleavage of the
3.3.5 Genetic recombination junction and re-ligation of the released DNA.[133]

Structure of the Holliday junction intermediate in genetic

recombination. The four separate DNA strands are
3.3.6 Evolution
coloured red, blue, green and yellow.[127]
Further information: Genetic recombination
Further information: RNA world hypothesis
A DNA helix usually does not interact with other seg-

A G C C G M DNA contains the genetic information that allows all

modern living things to function, grow and reproduce.
G A T T A F However, it is unclear how long in the 4-billion-year
history of life DNA has performed this function, as it has
been proposed that the earliest forms of life may have
used RNA as their genetic material.[134][135] RNA may
have acted as the central part of early cell metabolism
A G T T A C1 as it can both transmit genetic information and carry
out catalysis as part of ribozymes.[136] This ancient RNA
world where nucleic acid would have been used for both
G A C C G C2 catalysis and genetics may have influenced the evolution
of the current genetic code based on four nucleotide
Recombination involves the breakage and rejoining of two chro- bases. This would occur, since the number of differ-
mosomes (M and F) to produce two re-arranged chromosomes ent bases in such an organism is a trade-off between a
(C1 and C2). small number of bases increasing replication accuracy
and a large number of bases increasing the catalytic
ments of DNA, and in human cells the different chromo- efficiency of ribozymes.[137] However, there is no di-
somes even occupy separate areas in the nucleus called rect evidence of ancient genetic systems, as recovery of
“chromosome territories”.[128] This physical separation DNA from most fossils is impossible because DNA sur-
3.3. DNA 63

vives in the environment for less than one million years, and first used in forensic science to convict Colin Pitch-
and slowly degrades into short fragments in solution.[138] fork in the 1988 Enderby murders case.[153]
Claims for older DNA have been made, most notably a The development of forensic science, and the ability to
report of the isolation of a viable bacterium from a salt now obtain genetic matching on minute samples of blood,
crystal 250 million years old,[139] but these claims are skin, saliva or hair has led to a re-examination of a num-
controversial.[140][141] ber of cases. Evidence can now be uncovered that was not
Building blocks of DNA (adenine, guanine and related scientifically possible at the time of the original exami-
organic molecules) may have been formed extraterrestri- nation. Combined with the removal of the double jeop-
ally in outer space.[142][143][144] Complex DNA and RNA ardy law in some places, this can allow cases to be re-
organic compounds of life, including uracil, cytosine and opened where previous trials have failed to produce suf-
thymine, have also been formed in the laboratory un- ficient evidence to convince a jury. People charged with
der conditions mimicking those found in outer space, serious crimes may be required to provide a sample of
using starting chemicals, such as pyrimidine, found in DNA for matching purposes. The most obvious defence
meteorites. Pyrimidine, like polycyclic aromatic hydro- to DNA matches obtained forensically is to claim that
carbons (PAHs), the most carbon-rich chemical found in cross-contamination of evidence has taken place. This
the universe, may have been formed in red giants or in has resulted in meticulous strict handling procedures with
interstellar dust and gas clouds.[145] new cases of serious crime. DNA profiling is also used to
identify victims of mass casualty incidents.[154] As well as
positively identifying bodies or body parts in serious ac-
3.3.7 Uses in technology cidents, DNA profiling is being successfully used to iden-
tify individual victims in mass war graves – matching to
Genetic engineering family members.
DNA profiling is also used in parental testing in order to
Further information: Molecular biology, nucleic acid determine if someone is the biologicalparent or grandpar-
methods and genetic engineering ent of a child with the probability of parentage is typically
99.99% when the alleged parent is biologically related to
Methods have been developed to purify DNA from or- the child. Normal DNA sequencing methods happen af-
ganisms, such as phenol-chloroform extraction, and to ter birth but there are new methods to test paternity while
[155]
manipulate it in the laboratory, such as restriction digests the mother is still pregnant.
and the polymerase chain reaction. Modern biology and
biochemistry make intensive use of these techniques in
recombinant DNA technology. Recombinant DNA is a Bioinformatics
man-made DNA sequence that has been assembled from
other DNA sequences. They can be transformed into or- Further information: Bioinformatics
ganisms in the form of plasmids or in the appropriate for-
mat, by using a viral vector.[146] The genetically modi-
Bioinformatics involves the development of techniques to
fied organisms produced can be used to produce prod-
store, data mine, search and manipulate biological data,
ucts such as recombinant proteins, used in medical re-
including DNA nucleic acid sequence data. These have
search,[147] or be grown in agriculture.[148][149]
led to widely applied advances in computer science, es-
pecially string searching algorithms, machine learning
and database theory.[156] String searching or matching
DNA profiling
algorithms, which find an occurrence of a sequence of
letters inside a larger sequence of letters, were devel-
Further information: DNA profiling oped to search for specific sequences of nucleotides.[157]
The DNA sequence may be aligned with other DNA
Forensic scientists can use DNA in blood, semen, skin, sequences to identify homologous sequences and locate
saliva or hair found at a crime scene to identify a matching the specific mutations that make them distinct. These
DNA of an individual, such as a perpetrator. This process techniques, especially multiple sequence alignment, are
is formally termed DNA profiling, but may also be called used in studying phylogenetic relationships and pro-
"genetic fingerprinting". In DNA profiling, the lengths of tein function.[158] Data sets representing entire genomes’
variable sections of repetitive DNA, such as short tandem worth of DNA sequences, such as those produced by the
repeats and minisatellites, are compared between people. Human Genome Project, are difficult to use without the
This method is usually an extremely reliable technique for annotations that identify the locations of genes and regu-
identifying a matching DNA.[150] However, identification latory elements on each chromosome. Regions of DNA
can be complicated if the scene is contaminated with sequence that have the characteristic patterns associated
DNA from several people.[151] DNA profiling was devel- with protein- or RNA-coding genes can be identified by
oped in 1984 by British geneticist Sir Alec Jeffreys,[152] gene finding algorithms, which allow researchers to pre-
64 CHAPTER 3. NUCLEIC ACIDS

dict the presence of particular gene products and their DNA evidence is being used to try to identify the Ten
possible functions in an organism even before they have Lost Tribes of Israel.[165][166]
been isolated experimentally.[159] Entire genomes may
also be compared, which can shed light on the evolution-
ary history of particular organism and permit the exami- Information storage
nation of complex evolutionary events.
Main article: DNA digital data storage

DNA nanotechnology
In a paper published in Nature in January 2013, scientists
from the European Bioinformatics Institute and Agilent
Technologies proposed a mechanism to use DNA’s abil-
ity to code information as a means of digital data stor-
age. The group was able to encode 739 kilobytes of
data into DNA code, synthesize the actual DNA, then
sequence the DNA and decode the information back to
its original form, with a reported 100% accuracy. The
encoded information consisted of text files and audio
files. A prior experiment was published in August 2012.
It was conducted by researchers at Harvard University,
where the text of a 54,000-word book was encoded in
DNA.[167][168]
The DNA structure at left (schematic shown) will self-assemble
into the structure visualized by atomic force microscopy at right.
DNA nanotechnology is the field that seeks to design nanoscale
structures using the molecular recognition properties of DNA 3.3.8 History of DNA research
molecules. Image from Strong, 2004.
Further information: History of molecular biology
Further information: DNA nanotechnology DNA was first isolated by the Swiss physician Friedrich

DNA nanotechnology uses the unique molecular recogni-

tion properties of DNA and other nucleic acids to create
self-assembling branched DNA complexes with useful
properties.[160] DNA is thus used as a structural material
rather than as a carrier of biological information. This has
led to the creation of two-dimensional periodic lattices
(both tile-based and using the "DNA origami" method)
as well as three-dimensional structures in the shapes of
polyhedra.[161] Nanomechanical devices and algorithmic
self-assembly have also been demonstrated,[162] and these
DNA structures have been used to template the arrange-
ment of other molecules such as gold nanoparticles and
streptavidin proteins.[163]

James Watson and Francis Crick (right), co-originators of the

History and anthropology double-helix model, with Maclyn McCarty (left).

Further information: Phylogenetics and Genetic geneal- Miescher who, in 1869, discovered a microscopic
ogy substance in the pus of discarded surgical bandages.
As it resided in the nuclei of cells, he called it
Because DNA collects mutations over time, which are “nuclein”.[169][170] In 1878, Albrecht Kossel isolated the
then inherited, it contains historical information, and, by non-protein component of “nuclein”, nucleic acid, and
comparing DNA sequences, geneticists can infer the evo- later isolated its five primary nucleobases.[171][172] In
lutionary history of organisms, their phylogeny.[164] This 1919, Phoebus Levene identified the base, sugar and
field of phylogenetics is a powerful tool in evolutionary phosphate nucleotide unit.[173] Levene suggested that
biology. If DNA sequences within a species are com- DNA consisted of a string of nucleotide units linked to-
pared, population geneticists can learn the history of par- gether through the phosphate groups. Levene thought
ticular populations. This can be used in studies ranging the chain was short and the bases repeated in a fixed or-
from ecological genetics to anthropology; For example, der. In 1937, William Astbury produced the first X-ray
3.3. DNA 65

issue of Nature.[182] Of these, Franklin and Gosling’s pa-

per was the first publication of their own X-ray diffraction
data and original analysis method that partially supported
the Watson and Crick model;[45][183] this issue also con-
tained an article on DNA structure by Maurice Wilkins
and two of his colleagues, whose analysis and in vivo B-
DNA X-ray patterns also supported the presence in vivo
of the double-helical DNA configurations as proposed by
Crick and Watson for their double-helix molecular model
of DNA in the previous two pages of Nature.[46] In 1962,
after Franklin’s death, Watson, Crick, and Wilkins jointly
received the Nobel Prize in Physiology or Medicine.[184]
Nobel Prizes were awarded only to living recipients at the
time. A debate continues about who should receive credit
for the discovery.[185]
In an influential presentation in 1957, Crick laid out the
central dogma of molecular biology, which foretold the
relationship between DNA, RNA, and proteins, and ar-
ticulated the “adaptor hypothesis”.[186] Final confirma-
tion of the replication mechanism that was implied by
the double-helical structure followed in 1958 through the
Meselson–Stahl experiment.[187] Further work by Crick
and coworkers showed that the genetic code was based on
Pencil sketch of the DNA double helix by Francis Crick in 1953 non-overlapping triplets of bases, called codons, allowing
Har Gobind Khorana, Robert W. Holley and Marshall
Warren Nirenberg to decipher the genetic code.[188]
diffraction patterns that showed that DNA had a regular These findings represent the birth of molecular biology.
structure.[174]
In 1927, Nikolai Koltsov proposed that inherited traits
would be inherited via a “giant hereditary molecule”
3.3.9 See also
made up of “two mirror strands that would replicate
• Autosome
in a semi-conservative fashion using each strand as a
template”.[175][176] In 1928, Frederick Griffith in his • Crystallography
experiment discovered that traits of the “smooth” form
of Pneumococcus could be transferred to the “rough” • DNA-encoded chemical library
form of the same bacteria by mixing killed “smooth”
• DNA microarray
bacteria with the live “rough” form.[177][178] This sys-
tem provided the first clear suggestion that DNA carries • DNA sequencing
genetic information—the Avery–MacLeod–McCarty ex-
periment—when Oswald Avery, along with coworkers • DNA, RNA and proteins: The three essential
Colin MacLeod and Maclyn McCarty, identified DNA macromolecules of life
[179]
as the transforming principle in 1943. DNA’s role
in heredity was confirmed in 1952, when Alfred Her- • Genetic disorder
shey and Martha Chase in the Hershey–Chase experi- • Haplotype
ment showed that DNA is the genetic material of the T2
phage.[180] • Nucleic acid modeling
In 1953, James Watson and Francis Crick suggested what • Meiosis
is now accepted as the first correct double-helix model
of DNA structure in the journal Nature.[8] Their double- • Nucleic acid double helix
helix, molecular model of DNA was then based on a sin-
gle X-ray diffraction image (labeled as "Photo 51")[181] • Nucleic acid notation
taken by Rosalind Franklin and Raymond Gosling in May • Pangenesis
1952, as well as the information that the DNA bases are
paired—also obtained through private communications • Phosphoramidite
from Erwin Chargaff in the previous years.
• Southern blot
Experimental evidence supporting the Watson and Crick
model was published in a series of five articles in the same • X-ray scattering techniques
66 CHAPTER 3. NUCLEIC ACIDS

• Xeno nucleic acid [14] Ghosh A, Bansal M (2003). “A glossary of DNA struc-
tures from A to Z”. Acta Crystallogr D 59 (4): 620–6.
• Proteopedia DNA doi:10.1107/S0907444903003251. PMID 12657780.

[15] Created from PDB 1D65

• RNA
[16] Yakovchuk P, Protozanova E, Frank-Kamenetskii MD
(2006). “Base-stacking and base-pairing contributions
3.3.10 References into thermal stability of the DNA double helix”. Nu-
cleic Acids Res. 34 (2): 564–74. doi:10.1093/nar/gkj454.
[1] Nuwer, Rachel (18 July 2015). “Counting All the DNA on PMC 1360284. PMID 16449200.
Earth”. The New York Times (New York: The New York
Times Company). ISSN 0362-4331. Retrieved 2015-07- [17] Verma S, Eckstein F (1998). “Modified oligonucleotides:
18. synthesis and strategy for users”. Annu. Rev. Biochem.
67: 99–134. doi:10.1146/annurev.biochem.67.1.99.
[2] “The Biosphere: Diversity of Life”. Aspen Global Change PMID 9759484.
Institute. Basalt, CO. Retrieved 2015-07-19.
[18] Kiljunen S, Hakala K, Pinta E, Huttunen S, Pluta P,
[3] Russell, Peter (2001). iGenetics. New York: Benjamin Gador A, Lönnberg H, Skurnik M (2005). “Yersin-
Cummings. ISBN 0-8053-4553-1. iophage phiR1-37 is a tailed bacteriophage having a
270 kb DNA genome with thymidine replaced by
[4] Mashaghi A, Katan A (2013). “A physicist’s view of deoxyuridine”. Microbiology 151 (12): 4093–4102.
DNA”. De Physicus 24e (3): 59–61. arXiv:1311.2545v1. doi:10.1099/mic.0.28265-0. PMID 16339954.
Bibcode:2013arXiv1311.2545M.
[19] Uchiyama J, Takemura-Uchiyama I, Sakaguchi Y, Gamoh
[5] Saenger, Wolfram (1984). Principles of Nucleic Acid K, Kato SI, Daibata M, Ujihara T, Misawa N, Matsuzaki
Structure. New York: Springer-Verlag. ISBN 0-387- S (2014) Intragenus generalized transduction in Staphylo-
90762-9. coccus spp. by a novel giant phage. ISME J. 2014 Mar 6.
doi:10.1038/ismej.2014.29
[6] Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff,
Martin; Roberts, Keith; Walters, Peter (2002). Molecu- [20] Simpson L (1998). “A base called J”.
lar Biology of the Cell; Fourth Edition. New York and Proc Natl Acad Sci USA 95 (5): 2037–
London: Garland Science. ISBN 0-8153-3218-1. OCLC 2038. Bibcode:1998PNAS...95.2037S.
145080076 48122761 57023651 69932405. doi:10.1073/pnas.95.5.2037. PMC 33841. PMID
9482833.
[7] Butler, John M. (2001). Forensic DNA Typing. El-
sevier. ISBN 978-0-12-147951-0. OCLC 223032110 [21] Borst P, Sabatini R (2008). “Base J: dis-
45406517. pp. 14–15. covery, biosynthesis, and possible functions”.
Annual review of microbiology 62: 235–51.
[8] Watson JD, Crick FH (1953). “A Structure for Deoxyri- doi:10.1146/annurev.micro.62.081307.162750. PMID
bose Nucleic Acid” (PDF). Nature 171 (4356): 737–738. 18729733.
Bibcode:1953Natur.171..737W. doi:10.1038/171737a0.
PMID 13054692. [22] Cross M, Kieft R, Sabatini R, Wilm M, de Kort M,
van der Marel GA, van Boom JH, van Leeuwen F,
[9] Mandelkern M, Elias JG, Eden D, Crothers DM (1981). Borst P (1999). “The modified base J is the target
“The dimensions of DNA in solution”. J Mol Biol 152 (1): for a novel DNA-binding protein in kinetoplastid pro-
153–61. doi:10.1016/0022-2836(81)90099-1. PMID tozoans”. The EMBO Journal 18 (22): 6573–6581.
7338906. doi:10.1093/emboj/18.22.6573. PMC 1171720. PMID
10562569.
[10] Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck
D, Dunham A et al. (2006). “The DNA sequence and [23] DiPaolo C, Kieft R, Cross M, Sabatini R (2005).
biological annotation of human chromosome 1”. Nature “Regulation of trypanosome DNA glycosylation by a
441 (7091): 315–21. Bibcode:2006Natur.441..315G. SWI2/SNF2-like protein”. Mol Cell 17 (3): 441–451.
doi:10.1038/nature04727. PMID 16710414. doi:10.1016/j.molcel.2004.12.022. PMID 15694344.

[11] Watson JD, Crick FH (1953). “A Structure for Deoxyri- [24] Vainio S, Genest PA, ter Riet B, van Luenen H,
bose Nucleic Acid” (PDF). Nature 171 (4356): 737–738. Borst P (2009). “Evidence that J-binding protein
Bibcode:1953Natur.171..737W. doi:10.1038/171737a0. 2 is a thymidine hydroxylase catalyzing the first
PMID 13054692. Retrieved 4 May 2009. step in the biosynthesis of DNA base J”. Molec-
ular and biochemical parasitology 164 (2): 157–
[12] Berg J., Tymoczko J. and Stryer L. (2002) Biochemistry. 61. doi:10.1016/j.molbiopara.2008.12.001. PMID
W. H. Freeman and Company ISBN 0-7167-4955-6 19114062.

[13] Abbreviations and Symbols for Nucleic Acids, Polynu- [25] Iyer LM, Tahiliani M, Rao A, Aravind L (2009).
cleotides and their Constituents IUPAC-IUB Commission “Prediction of novel families of enzymes involved in
on Biochemical Nomenclature (CBN). Retrieved 3 Jan- oxidative and other complex modifications of bases
uary 2006. in nucleic acids”. Cell Cycle 8 (11): 1698–1710.
3.3. DNA 67

doi:10.4161/cc.8.11.8580. PMC 2995806. PMID [37] Makalowska I, Lin CF, Makalowski W (2005). “Over-
19411852. lapping genes in vertebrate genomes”. Comput Biol Chem
29 (1): 1–12. doi:10.1016/j.compbiolchem.2004.12.006.
[26] van Luenen HG, Farris C, Jan S, Genest PA, Tripathi P, PMID 15680581.
Velds A, Kerkhoven RM, Nieuwland M, Haydock A, Ra-
masamy G, Vainio S, Heidebrecht T, Perrakis A, Pagie L, [38] Johnson ZI, Chisholm SW (2004). “Properties of over-
van Steensel B, Myler PJ, Borst P (2012). “Leishmania”. lapping genes are conserved across microbial genomes”.
Cell 150 (5): 909–921. doi:10.1016/j.cell.2012.07.030. Genome Res 14 (11): 2268–72. doi:10.1101/gr.2433104.
PMC 3684241. PMID 22939620. PMC 525685. PMID 15520290.

[27] Hazelbaker DZ, Buratowski S (2012). “Transcription: [39] Lamb RA, Horvath CM (1991). “Diversity of coding
base J blocks the way”. Curr Biol 22 (22): R960–2. strategies in influenza viruses”. Trends Genet 7 (8): 261–
doi:10.1016/j.cub.2012.10.010. PMC 3648658. PMID 6. doi:10.1016/0168-9525(91)90326-L. PMID 1771674.
23174300.
[40] Benham CJ, Mielke SP (2005). “DNA me-
[28] Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura chanics”. Annu Rev Biomed Eng 7: 21–53.
K, Dickerson RE (1980). “Crystal structure analysis of a doi:10.1146/annurev.bioeng.6.062403.132016. PMID
complete turn of B-DNA”. Nature 287 (5784): 755–8. 16004565.
Bibcode:1980Natur.287..755W. doi:10.1038/287755a0.
[41] Champoux JJ (2001). “DNA topoisomerases: struc-
PMID 7432492.
ture, function, and mechanism”. Annu Rev Biochem
[29] Pabo CO, Sauer RT (1984). “Protein-DNA 70: 369–413. doi:10.1146/annurev.biochem.70.1.369.
recognition”. Annu Rev Biochem 53: 293–321. PMID 11395412.
doi:10.1146/annurev.bi.53.070184.001453. PMID
[42] Wang JC (2002). “Cellular roles of DNA topoisomerases:
6236744.
a molecular perspective”. Nature Reviews Molecular Cell
Biology 3 (6): 430–40. doi:10.1038/nrm831. PMID
[30] Clausen-Schaumann H, Rief M, Tolksdorf C,
12042765.
Gaub HE (2000). “Mechanical stability of single
DNA molecules”. Biophys J 78 (4): 1997–2007. [43] Basu HS, Feuerstein BG, Zarling DA, Shafer RH, Mar-
Bibcode:2000BpJ....78.1997C. doi:10.1016/S0006- ton LJ (1988). “Recognition of Z-RNA and Z-DNA de-
3495(00)76747-6. PMC 1300792. PMID 10733978. terminants by polyamines in solution: experimental and
theoretical studies”. J Biomol Struct Dyn 6 (2): 299–
[31] Chalikian TV, Völker J, Plum GE, Breslauer KJ (1999).
309. doi:10.1080/07391102.1988.10507714. PMID
“A more unified picture for the thermodynamics of nu-
2482766.
cleic acid duplex melting: A characterization by calori-
metric and volumetric techniques”. Proc Natl Acad Sci [44] Franklin RE, Gosling RG (6 March 1953). “The Struc-
USA 96 (14): 7853–8. Bibcode:1999PNAS...96.7853C. ture of Sodium Thymonucleate Fibres I. The Influence of
doi:10.1073/pnas.96.14.7853. PMC 22151. PMID Water Content” (PDF). Acta Crystallogr 6 (8–9): 673–7.
10393911. doi:10.1107/S0365110X53001939. Archived from the
original (PDF) on 2007-06-12.
[32] deHaseth PL, Helmann JD (1995). “Open complex Franklin RE, Gosling RG (1953). “The structure of
formation by Escherichia coli RNA polymerase: the sodium thymonucleate fibres. II. The cylindrically sym-
mechanism of polymerase-induced strand separation of metrical Patterson function”. Acta Crystallogr 6 (8–9):
double helical DNA”. Mol Microbiol 16 (5): 817– 678–85. doi:10.1107/S0365110X53001940.
24. doi:10.1111/j.1365-2958.1995.tb02309.x. PMID
7476180. [45] Franklin RE, Gosling RG (1953). “Molecular Con-
figuration in Sodium Thymonucleate. Franklin R.
[33] Isaksson J, Acharya S, Barman J, Cheruku P, Chat- and Gosling R.G” (PDF). Nature 171 (4356): 740–1.
topadhyaya J (2004). “Single-stranded adenine-rich DNA Bibcode:1953Natur.171..740F. doi:10.1038/171740a0.
and RNA retain structural characteristics of their respec- PMID 13054694.
tive double-stranded conformations and show directional
differences in stacking pattern”. Biochemistry 43 (51): [46] Wilkins MH, Stokes AR, Wilson HR (1953). “Molecular
15996–6010. doi:10.1021/bi048221v. PMID 15609994. Structure of Deoxypentose Nucleic Acids” (PDF). Nature
171 (4356): 738–740. Bibcode:1953Natur.171..738W.
[34] Designation of the two strands of DNA JCBN/NC-IUB doi:10.1038/171738a0. PMID 13054693.
Newsletter 1989. Retrieved 7 May 2008
[47] Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL
[35] Hüttenhofer A, Schattner P, Polacek N (2005). “Non- (1980). “Polymorphism of DNA double helices”. J.
coding RNAs: hope or hype?". Trends Genet 21 (5): 289– Mol. Biol. 143 (1): 49–72. doi:10.1016/0022-
97. doi:10.1016/j.tig.2005.03.007. PMID 15851066. 2836(80)90124-2. PMID 7441761.

[36] Munroe SH (2004). “Diversity of antisense regulation in [48] Baianu, I.C. (1980). “Structural Order and Partial Dis-
eukaryotes: multiple mechanisms, emerging patterns”. J order in Biological systems”. Bull. Math. Biol. 42 (4):
Cell Biochem 93 (4): 664–71. doi:10.1002/jcb.20252. 137–141. doi:10.1016/s0092-8240(80)80083-8. http:
PMID 15389973. //cogprints.org/3822/
68 CHAPTER 3. NUCLEIC ACIDS

[49] Hosemann R., Bagchi R.N., Direct analysis of diffrac- [63] Burge S, Parkinson GN, Hazel P, Todd AK, Nei-
tion by matter, North-Holland Publs., Amsterdam – New dle S (2006). “Quadruplex DNA: sequence, topol-
York, 1962. ogy and structure”. Nucleic Acids Res 34 (19): 5402–
15. doi:10.1093/nar/gkl655. PMC 1636468. PMID
[50] Baianu, I.C. (1978). “X-ray scattering by partially 17012276.
disordered membrane systems”. Acta Crystallogr A
34 (5): 751–753. Bibcode:1978AcCrA..34..751B. [64] Parkinson GN, Lee MP, Neidle S (2002). “Crys-
doi:10.1107/S0567739478001540. tal structure of parallel quadruplexes from human
telomeric DNA”. Nature 417 (6891): 876–80.
[51] Wahl MC, Sundaralingam M (1997). “Crystal struc- Bibcode:2002Natur.417..876P. doi:10.1038/nature755.
tures of A-DNA duplexes”. Biopolymers 44 (1): 45– PMID 12050675.
63. doi:10.1002/(SICI)1097-0282(1997)44:1<45::AID-
BIP4>3.0.CO;2-#. PMID 9097733. [65] Griffith JD, Comeau L, Rosenfield S, Stansel RM, Bianchi
A, Moss H, de Lange T (1999). “Mammalian telom-
[52] Lu XJ, Shakked Z, Olson WK (2000). “A-form confor- eres end in a large duplex loop”. Cell 97 (4): 503–14.
mational motifs in ligand-bound DNA structures”. J. Mol. doi:10.1016/S0092-8674(00)80760-6. PMID 10338214.
Biol. 300 (4): 819–40. doi:10.1006/jmbi.2000.3690.
PMID 10891271. [66] Seeman NC (2005). “DNA enables nanoscale control of
the structure of matter”. Q. Rev. Biophys. 38 (4): 363–
[53] Rothenburg S, Koch-Nolte F, Haag F (2001). “DNA
71. doi:10.1017/S0033583505004087. PMC 3478329.
methylation and Z-DNA formation as mediators of
PMID 16515737.
quantitative differences in the expression of alleles".
Immunol Rev 184: 286–98. doi:10.1034/j.1600- [67] Hu Q, Rosenfeld MG (2012). “Epigenetic regulation of
065x.2001.1840125.x. PMID 12086319. human embryonic stem cells”. Frontiers in Genetics 3:
238. doi:10.3389/fgene.2012.00238. PMC 3488762.
[54] Oh DB, Kim YG, Rich A (2002). “Z-DNA-binding
PMID 23133442.
proteins can act as potent effectors of gene expres-
sion in vivo”. Proc. Natl. Acad. Sci. U.S.A. [68] Klose RJ, Bird AP (2006). “Genomic DNA methyla-
99 (26): 16666–71. Bibcode:2002PNAS...9916666O. tion: the mark and its mediators”. Trends Biochem Sci
doi:10.1073/pnas.262672699. PMC 139201. PMID 31 (2): 89–97. doi:10.1016/j.tibs.2005.12.008. PMID
12486233. 16403636.
[55] Palmer, Jason (2 December 2010). “Arsenic-loving bac- [69] Bird A (2002). “DNA methylation patterns and
teria may help in hunt for alien life”. BBC News. Retrieved epigenetic memory”. Genes Dev 16 (1): 6–21.
2 December 2010. doi:10.1101/gad.947102. PMID 11782440.
[56] Bortman, Henry (2 December 2010). “Arsenic-
[70] Walsh CP, Xu GL (2006). “Cytosine methylation and
Eating Bacteria Opens New Possibilities for Alien Life”.
DNA repair”. Curr Top Microbiol Immunol. Current
Space.Com web site (Space.com). Retrieved 2 December
Topics in Microbiology and Immunology 301: 283–315.
2010.
doi:10.1007/3-540-31390-7_11. ISBN 3-540-29114-8.
[57] Katsnelson, Alla (2 December 2010). “Arsenic-eating PMID 16570853.
microbe may redefine chemistry of life”. Nature News.
[71] Kriaucionis S, Heintz N (2009). “The nuclear
doi:10.1038/news.2010.645.
DNA base 5-hydroxymethylcytosine is present
[58] <Please add first missing authors to populate meta- in Purkinje neurons and the brain”. Science 324
data.>, Cressey (3 October 2012). "'Arsenic-life' Bac- (5929): 929–30. Bibcode:2009Sci...324..929K.
terium Prefers Phosphorus after all”. Nature News. doi:10.1126/science.1169786. PMC 3263819. PMID
doi:10.1038/news.2012.11520. 19372393.

[59] Greider CW, Blackburn EH (1985). “Identification [72] Ratel D, Ravanat JL, Berger F, Wion D (2006). “N6-
of a specific telomere terminal transferase activity in methyladenine: the other methylated base of DNA”.
Tetrahymena extracts”. Cell 43 (2 Pt 1): 405–13. BioEssays 28 (3): 309–15. doi:10.1002/bies.20342.
doi:10.1016/0092-8674(85)90170-9. PMID 3907856. PMC 2754416. PMID 16479578.

[60] Nugent CI, Lundblad V (1998). “The telomerase reverse [73] Gommers-Ampt JH, Van Leeuwen F, de Beer AL,
transcriptase: components and regulation”. Genes Dev Vliegenthart JF, Dizdaroglu M, Kowalak JA, Crain PF,
12 (8): 1073–85. doi:10.1101/gad.12.8.1073. PMID Borst P (1993). “beta-D-glucosyl-hydroxymethyluracil:
9553037. a novel modified base present in the DNA of the par-
asitic protozoan T. brucei”. Cell 75 (6): 1129–36.
[61] Wright WE, Tesmer VM, Huffman KE, Levene SD, Shay doi:10.1016/0092-8674(93)90322-H. PMID 8261512.
JW (1997). “Normal human chromosomes have long G-
rich telomeric overhangs at one end”. Genes Dev 11 (21): [74] Created from PDB 1JDG
2801–9. doi:10.1101/gad.11.21.2801. PMC 316649.
PMID 9353250. [75] Douki T, Reynaud-Angelin A, Cadet J, Sage E (2003).
“Bipyrimidine photoproducts rather than oxidative le-
[62] Created from NDB UD0017 sions are the main type of DNA damage involved in
3.3. DNA 69

the genotoxic effect of solar UVA radiation”. Biochem- [87] Braña MF, Cacho M, Gradillas A, de Pascual-
istry 42 (30): 9221–6. doi:10.1021/bi034593c. PMID Teresa B, Ramos A (2001). “Intercalators as anti-
12885257. cancer drugs”. Curr Pharm Des 7 (17): 1745–80.
doi:10.2174/1381612013397113. PMID 11562309.
[76] Cadet J, Delatour T, Douki T, Gasparutto D, Pouget
JP, Ravanat JL, Sauvaigo S (1999). “Hydroxyl radicals [88] Venter JC, Adams MD, Myers EW, Li PW,
and DNA base damage”. Mutat Res 424 (1–2): 9–21. Mural RJ, Sutton GG et al. (2001). “The se-
doi:10.1016/S0027-5107(99)00004-4. PMID 10064846. quence of the human genome”. Science 291
(5507): 1304–51. Bibcode:2001Sci...291.1304V.
[77] Beckman KB, Ames BN (1997). “Oxidative decay doi:10.1126/science.1058040. PMID 11181995.
of DNA”. J. Biol. Chem. 272 (32): 19633–6.
doi:10.1074/jbc.272.32.19633. PMID 9289489. [89] Thanbichler M, Wang SC, Shapiro L (2005). “The bacte-
rial nucleoid: a highly organized and dynamic structure”.
[78] Valerie K, Povirk LF (2003). “Regulation and mecha- J Cell Biochem 96 (3): 506–21. doi:10.1002/jcb.20519.
nisms of mammalian double-strand break repair”. Onco- PMID 15988757.
gene 22 (37): 5792–812. doi:10.1038/sj.onc.1206679.
[90] Wolfsberg TG, McEntyre J, Schuler GD (2001). “Guide
PMID 12947387.
to the draft human genome”. Nature 409 (6822): 824–6.
[79] Johnson, George (28 December 2010). “Unearthing Pre- doi:10.1038/35057000. PMID 11236998.
historic Tumors, and Debate”. The New York Times. If we [91] Gregory TR (2005). “The C-value enigma in plants
lived long enough, sooner or later we all would get cancer. and animals: a review of parallels and an appeal
for partnership”. Annals of Botany 95 (1): 133–46.
[80] Alberts, B, Johnson A, Lewis J et al. (2002). “The Pre-
doi:10.1093/aob/mci009. PMID 15596463.
ventable Causes of Cancer”. Molecular biology of the cell
(4th ed.). New York: Garland Science. ISBN 0-8153- [92] Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R,
4072-9. A certain irreducible background incidence of Gingeras TR, Margulies EH et al. (2007). “Identification
cancer is to be expected regardless of circumstances: mu- and analysis of functional elements in 1% of the hu-
tations can never be absolutely avoided, because they are man genome by the ENCODE pilot project”. Nature
an inescapable consequence of fundamental limitations on 447 (7146): 799–816. Bibcode:2007Natur.447..799B.
the accuracy of DNA replication, as discussed in Chapter doi:10.1038/nature05874. PMC 2212820. PMID
5. If a human could live long enough, it is inevitable that 17571346.
at least one of his or her cells would eventually accumulate
a set of mutations sufficient for cancer to develop. [93] Created from PDB 1MSW

[81] Bernstein H, Payne CM, Bernstein C, Garewal H, [94] Pidoux AL, Allshire RC (2005). “The role of het-
Dvorak K (2008). Cancer and aging as conse- erochromatin in centromere function”. Philosophical
quences of un-repaired DNA damage. In: New Re- Transactions of the Royal Society B 360 (1455): 569–
search on DNA Damages (Editors: Honoka Kimura 79. doi:10.1098/rstb.2004.1611. PMC 1569473. PMID
and Aoi Suzuki) Nova Science Publishers, Inc., New 15905142.
York, Chapter 1, pp. 1–47. open access, but read
[95] Harrison PM, Hegyi H, Balasubramanian S, Luscombe
only https://www.novapublishers.com/catalog/product_
NM, Bertone P, Echols N, Johnson T, Gerstein M
info.php?products_id=43247 ISBN 1604565810 ISBN
(2002). “Molecular Fossils in the Human Genome:
978-1604565812
Identification and Analysis of the Pseudogenes in Chro-
[82] Hoeijmakers JH (October 2009). “DNA damage, aging, mosomes 21 and 22”. Genome Res 12 (2): 272–
and cancer”. N. Engl. J. Med. 361 (15): 1475–85. 80. doi:10.1101/gr.207102. PMC 155275. PMID
doi:10.1056/NEJMra0804615. PMID 19812404. 11827946.

[96] Harrison PM, Gerstein M (2002). “Studying genomes

[83] Freitas AA, de Magalhães JP (2011). “A review and ap-
through the aeons: protein families, pseudogenes and
praisal of the DNA damage theory of ageing”. Mutat. Res.
proteome evolution”. J Mol Biol 318 (5): 1155–74.
728 (1–2): 12–22. doi:10.1016/j.mrrev.2011.05.001.
doi:10.1016/S0022-2836(02)00109-2. PMID 12083509.
PMID 21600302.
[97] Albà M (2001). “Replicative DNA polymerases”.
[84] Ferguson LR, Denny WA (1991). “The genetic tox- Genome Biol 2 (1): reviews3002.1–reviews3002.4.
icology of acridines”. Mutat Res 258 (2): 123–60. doi:10.1186/gb-2001-2-1-reviews3002. PMC 150442.
doi:10.1016/0165-1110(91)90006-H. PMID 1881402. PMID 11178285.
[85] Stephens TD, Bunde CJ, Fillmore BJ (2000). “Mecha- [98] Tani, Katsuji; Nasu, Masao (2010). “Roles of Extracel-
nism of action in thalidomide teratogenesis”. Biochem lular DNA in Bacterial Ecosystems”. In Kikuchi, Yo;
Pharmacol 59 (12): 1489–99. doi:10.1016/S0006- Rykova, Elena Y. Extracellular Nucleic Acids. Springer.
2952(99)00388-3. PMID 10799645. pp. 25–38. ISBN 978-3-642-12616-1.

[86] Jeffrey AM (1985). “DNA modification by chemi- [99] Vlassov, V. V.; Laktionov, P. P.; Rykova, E. Y. (2007).
cal carcinogens”. Pharmacol Ther 28 (2): 237–72. “Extracellular nucleic acids”. Bioessays 29: 654–667.
doi:10.1016/0163-7258(85)90013-0. PMID 3936066. doi:10.1002/bies.20604.
 70 CHAPTER 3. NUCLEIC ACIDS

[100] Finkel, S. E.; Kolter, R. (2001). “DNA as a nutrient: novel [113] Created from PDB 1LMB
role for bacterial competence gene homologs”. J. Bac-
teriol. 183: 6288–6293. doi:10.1128/JB.183.21.6288- [114] Myers LC, Kornberg RD (2000). “Mediator of tran-
6293.2001. scriptional regulation”. Annu Rev Biochem 69: 729–
49. doi:10.1146/annurev.biochem.69.1.729. PMID
[101] Mulcahy, H.; Charron-Mazenod, L.; Lewenza, 10966474.
S. (2008). “Extracellular DNA chelates cations
and induces antibiotic resistance in Pseudomonas [115] Spiegelman BM, Heinrich R (2004). “Biological con-
aeruginosa biofilms”. PLoSPathog 4: e1000213. trol through regulated transcriptional coactivators”. Cell
doi:10.1371/journal.ppat.1000213. 119 (2): 157–67. doi:10.1016/j.cell.2004.09.037. PMID
15479634.
[102] Berne, C.; Kysela, D. T.; Brun, Y. V. (2010). “A bacte-
rial extracellular DNA inhibits settling of motile progeny
[116] Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren
cells within a biofilm”. Mol. Microbiol. 77: 815–829.
B (2003). “A global transcriptional regulatory role for c-
doi:10.1111/j.1365-2958.2010.07267.x.
Myc in Burkitt’s lymphoma cells”. Proc Natl Acad Sci USA
[103] Whitchurch, C. B.; Tolker-Nielsen, T.; Ragas, P. C.; 100 (14): 8164–9. Bibcode:2003PNAS..100.8164L.
Mattick, J. S. (2002). “Extracellular DNA required for doi:10.1073/pnas.1332764100. PMC 166200. PMID
bacterial biofilm formation” (PDF). Science 295: 1487. 12808131.
doi:10.1126/science.295.5559.1487.
[117] Created from PDB 1RVA
[104] Hu, W.; Li, L.; Sharma, S.; Wang, J.; McHardy, I.; Lux,
R.; Yang, Z.; He, X.; Gimzewski, J. K.; Li, Y.; Shi, W. [118] Bickle TA, Krüger DH (1993). “Biology of DNA re-
(2012). “DNA Builds and Strengthens the Extracellular striction”. Microbiol Rev 57 (2): 434–50. PMC 372918.
Matrix in Myxococcus xanthus Biofilms by Interacting PMID 8336674.
with Exopolysaccharides”. PLoS ONE 7 (12): e51905.
doi:10.1371/journal.pone.0051905. [119] Doherty AJ, Suh SW (2000). “Structural and mecha-
nistic conservation in DNA ligases”. Nucleic Acids Res
[105] Sandman K, Pereira SL, Reeve JN (1998). “Diversity 28 (21): 4051–8. doi:10.1093/nar/28.21.4051. PMC
of prokaryotic chromosomal proteins and the origin of 113121. PMID 11058099.
the nucleosome”. Cell Mol Life Sci 54 (12): 1350–64.
doi:10.1007/s000180050259. PMID 9893710. [120] Schoeffler AJ, Berger JM (2005). “Recent advances in un-
derstanding structure-function relationships in the type II
[106] Dame RT (2005). “The role of nucleoid-associated
topoisomerase mechanism”. Biochem Soc Trans 33 (Pt 6):
proteins in the organization and compaction of bac-
1465–70. doi:10.1042/BST20051465. PMID 16246147.
terial chromatin”. Mol. Microbiol. 56 (4): 858–
70. doi:10.1111/j.1365-2958.2005.04598.x. PMID
[121] Tuteja N, Tuteja R (2004). “Unraveling DNA heli-
15853876.
cases. Motif, structure, mechanism and function”. Eur
[107] Luger K, Mäder AW, Richmond RK, Sargent DF, J Biochem 271 (10): 1849–63. doi:10.1111/j.1432-
Richmond TJ (1997). “Crystal structure of the nu- 1033.2004.04094.x. PMID 15128295.
cleosome core particle at 2.8 A resolution”. Nature
389 (6648): 251–60. Bibcode:1997Natur.389..251L. [122] Joyce CM, Steitz TA (1995). “Polymerase structures and
doi:10.1038/38444. PMID 9305837. function: variations on a theme?". J Bacteriol 177 (22):
6321–9. PMC 177480. PMID 7592405.
[108] Jenuwein T, Allis CD (2001). “Translating the
histone code”. Science 293 (5532): 1074–80. [123] Hubscher U, Maga G, Spadari S (2002). “Eukary-
doi:10.1126/science.1063127. PMID 11498575. otic DNA polymerases”. Annu Rev Biochem 71: 133–
63. doi:10.1146/annurev.biochem.71.090501.150041.
[109] Ito T (2003). “Nucleosome assembly and remodelling”. PMID 12045093.
Curr Top Microbiol Immunol. Current Topics in Micro-
biology and Immunology 274: 1–22. doi:10.1007/978- [124] Johnson A, O'Donnell M (2005). “Cellular DNA
3-642-55747-7_1. ISBN 978-3-540-44208-0. PMID replicases: components and dynamics at the repli-
12596902. cation fork”. Annu Rev Biochem 74: 283–315.
doi:10.1146/annurev.biochem.73.011303.073859.
[110] Thomas JO (2001). “HMG1 and 2: architectural DNA-
PMID 15952889.
binding proteins”. Biochem Soc Trans 29 (Pt 4): 395–401.
doi:10.1042/BST0290395. PMID 11497996.
[125] Tarrago-Litvak L, Andréola ML, Nevinsky GA, Sarih-
[111] Grosschedl R, Giese K, Pagel J (1994). “HMG domain Cottin L, Litvak S (1 May 1994). “The reverse transcrip-
proteins: architectural elements in the assembly of nu- tase of HIV-1: from enzymology to therapeutic interven-
cleoprotein structures”. Trends Genet 10 (3): 94–100. tion”. FASEB J 8 (8): 497–503. PMID 7514143.
doi:10.1016/0168-9525(94)90232-1. PMID 8178371.
[126] Martinez E (2002). “Multi-protein complexes in eukary-
[112] Iftode C, Daniely Y, Borowiec JA (1999). “Repli- otic gene transcription”. Plant Mol Biol 50 (6): 925–47.
cation protein A (RPA): the eukaryotic SSB”. doi:10.1023/A:1021258713850. PMID 12516863.
Crit Rev Biochem Mol Biol 34 (3): 141–80.
doi:10.1080/10409239991209255. PMID 10473346. [127] Created from PDB 1M6G
 3.3. DNA 71

[128] Cremer T, Cremer C (2001). “Chromosome territo- [141] Nickle DC, Learn GH, Rain MW, Mullins JI, Mit-
ries, nuclear architecture and gene regulation in mam- tler JE (2002). “Curiously modern DNA for a “250
malian cells”. Nature Reviews Genetics 2 (4): 292–301. million-year-old” bacterium”. J Mol Evol 54 (1): 134–7.
doi:10.1038/35066075. PMID 11283701. doi:10.1007/s00239-001-0025-x. PMID 11734907.

[129] Pál C, Papp B, Lercher MJ (2006). “An integrated view [142] Callahan MP, Smith KE, Cleaves HJ, Ruzicka J, Stern
of protein evolution”. Nature Reviews Genetics 7 (5): 337– JC, Glavin DP, House CH, Dworkin JP (August 2011).
48. doi:10.1038/nrg1838. PMID 16619049. “Carbonaceous meteorites contain a wide range of ex-
traterrestrial nucleobases”. Proc. Natl. Acad. Sci. U.S.A.
[130] O'Driscoll M, Jeggo PA (2006). “The role of double- 108 (34): 13995–8. doi:10.1073/pnas.1106493108.
strand break repair – insights from human genetics”. Na- PMC 3161613. PMID 21836052.
ture Reviews Genetics 7 (1): 45–54. doi:10.1038/nrg1746.
PMID 16369571. [143] Steigerwald, John (8 August 2011). “NASA Researchers:
DNA Building Blocks Can Be Made in Space”. NASA.
[131] Vispé S, Defais M (1997). “Mammalian Rad51 protein: Retrieved 10 August 2011.
a RecA homologue with pleiotropic functions”. Biochimie
[144] ScienceDaily Staff (9 August 2011). “DNA Building
79 (9–10): 587–92. doi:10.1016/S0300-9084(97)82007-
Blocks Can Be Made in Space, NASA Evidence Sug-
X. PMID 9466696.
gests”. ScienceDaily. Retrieved 9 August 2011.
[132] Neale MJ, Keeney S (2006). “Clarifying the mechanics [145] Marlaire, Ruth (3 March 2015). “NASA Ames Repro-
of DNA strand exchange in meiotic recombination”. Na- duces the Building Blocks of Life in Laboratory”. NASA.
ture 442 (7099): 153–8. Bibcode:2006Natur.442..153N. Retrieved 5 March 2015.
doi:10.1038/nature04885. PMID 16838012.
[146] Goff SP, Berg P (1976). “Construction of hybrid viruses
[133] Dickman MJ, Ingleston SM, Sedelnikova SE, Rafferty containing SV40 and lambda phage DNA segments and
JB, Lloyd RG, Grasby JA, Hornby DP (2002). “The their propagation in cultured monkey cells”. Cell 9 (4
RuvABC resolvasome”. Eur J Biochem 269 (22): 5492– PT 2): 695–705. doi:10.1016/0092-8674(76)90133-1.
501. doi:10.1046/j.1432-1033.2002.03250.x. PMID PMID 189942.
12423347.
[147] Houdebine LM (2007). “Transgenic animal models in
[134] Joyce GF (2002). “The antiquity of RNA- biomedical research”. Methods Mol Biol 360: 163–202.
based evolution”. Nature 418 (6894): 214–21. doi:10.1385/1-59745-165-7:163. ISBN 1-59745-165-7.
Bibcode:2002Natur.418..214J. doi:10.1038/418214a. PMID 17172731.
PMID 12110897.
[148] Daniell H, Dhingra A (2002). “Multigene engineer-
[135] Orgel LE (2004). “Prebiotic chemistry and the origin ing: dawn of an exciting new era in biotechnology”.
of the RNA world”. Crit Rev Biochem Mol Biol 39 Current Opinion in Biotechnology 13 (2): 136–41.
(2): 99–123. doi:10.1080/10409230490460765. PMID doi:10.1016/S0958-1669(02)00297-5. PMC 3481857.
15217990. PMID 11950565.

[136] Davenport RJ (2001). “Ribozymes. Making copies [149] Job D (2002). “Plant biotechnology in agriculture”.
in the RNA world”. Science 292 (5520): 1278. Biochimie 84 (11): 1105–10. doi:10.1016/S0300-
doi:10.1126/science.292.5520.1278a. PMID 11360970. 9084(02)00013-5. PMID 12595138.

[137] Szathmáry E (1992). “What is the optimum size [150] Collins A, Morton NE (1994). “Likelihood ratios
for the genetic alphabet?". Proc Natl Acad Sci for DNA identification”. Proc Natl Acad Sci USA
USA 89 (7): 2614–8. Bibcode:1992PNAS...89.2614S. 91 (13): 6007–11. Bibcode:1994PNAS...91.6007C.
doi:10.1073/pnas.89.7.2614. PMC 48712. PMID doi:10.1073/pnas.91.13.6007. PMC 44126. PMID
1372984. 8016106.

[151] Weir BS, Triggs CM, Starling L, Stowell LI, Walsh KA,
[138] Lindahl T (1993). “Instability and decay of the pri-
Buckleton J (1997). “Interpreting DNA mixtures”. J
mary structure of DNA”. Nature 362 (6422): 709–15.
Forensic Sci 42 (2): 213–22. PMID 9068179.
Bibcode:1993Natur.362..709L. doi:10.1038/362709a0.
PMID 8469282. [152] Jeffreys AJ, Wilson V, Thein SL (1985). “Individual-
specific 'fingerprints’ of human DNA”. Nature
[139] Vreeland RH, Rosenzweig WD, Powers DW (2000). 316 (6023): 76–9. Bibcode:1985Natur.316...76J.
“Isolation of a 250 million-year-old halotolerant bac- doi:10.1038/316076a0. PMID 2989708.
terium from a primary salt crystal”. Nature 407 (6806):
897–900. doi:10.1038/35038060. PMID 11057666. [153] Colin Pitchfork — first murder conviction on DNA evi-
dence also clears the prime suspect Forensic Science Ser-
[140] Hebsgaard MB, Phillips MJ, Willerslev E (2005). “Ge- vice Accessed 23 December 2006
ologically ancient DNA: fact or artefact?". Trends Mi-
crobiol 13 (5): 212–20. doi:10.1016/j.tim.2005.03.010. [154] “DNA Identification in Mass Fatality Incidents”. National
PMID 15866038. Institute of Justice. September 2006.
 72 CHAPTER 3. NUCLEIC ACIDS

[155] “Paternity Blood Tests That Work Early in a Pregnancy” [168] Naik, Gautam (24 January 2013). “Storing Digital Data in
New York Times June 20, 2012 DNA”. Wall Street Journal. Retrieved 24 January 2013.

[156] Baldi, Pierre; Brunak, Soren (2001). Bioinformatics: The [169] Miescher, Friedrich (1871) “Ueber die chemische Zusam-
Machine Learning Approach. MIT Press. ISBN 978-0- mensetzung der Eiterzellen” (On the chemical composi-
262-02506-5. OCLC 45951728. tion of pus cells), Medicinisch-chemische Untersuchungen,
4 : 441–460. From p. 456: “Ich habe mich daher später
[157] Gusfield, Dan. Algorithms on Strings, Trees, and Se- mit meinen Versuchen an die ganzen Kerne gehalten, die
quences: Computer Science and Computational Biology. Trennung der Körper, die ich einstweilen ohne weiteres
Cambridge University Press, 15 January 1997. ISBN 978- Präjudiz als lösliches und unlösliches Nuclein bezeichnen
0-521-58519-4. will, einem günstigeren Material überlassend.” (Therefore,
in my experiments I subsequently limited myself to the
[158] Sjölander K (2004). “Phylogenomic infer- whole nucleus, leaving to a more favorable material the
ence of protein molecular function: advances separation of the substances, that for the present, without
and challenges”. Bioinformatics 20 (2): 170–9. further prejudice, I will designate as soluble and insoluble
doi:10.1093/bioinformatics/bth021. PMID 14734307. nuclear material (“Nuclein”).)
[159] Mount DM (2004). Bioinformatics: Sequence and [170] Dahm R (2008). “Discovering DNA: Friedrich Miescher
Genome Analysis (2 ed.). Cold Spring Harbor, NY: Cold and the early years of nucleic acid research”. Hum.
Spring Harbor Laboratory Press. ISBN 0-87969-712-1. Genet. 122 (6): 565–81. doi:10.1007/s00439-007-0433-
OCLC 55106399. 0. PMID 17901982.
[160] Rothemund PW (2006). “Folding DNA to cre- [171] See:
ate nanoscale shapes and patterns”. Nature 440
(7082): 297–302. Bibcode:2006Natur.440..297R. • Albrect Kossel (1879) “Ueber Nucleïn der Hefe”
doi:10.1038/nature04586. PMID 16541064. (On nuclein in yeast) Zeitschrift für physiologische
Chemie, 3 : 284-291.
[161] Andersen ES, Dong M, Nielsen MM, Jahn K, Subra-
mani R, Mamdouh W, Golas MM, Sander B, Stark • Albrect Kossel (1880) “Ueber Nucleïn der Hefe II”
H, Oliveira CL, Pedersen JS, Birkedal V, Besenbacher (On nuclein in yeast, Part 2) Zeitschrift für physiol-
F, Gothelf KV, Kjems J (2009). “Self-assembly of ogische Chemie, 4 : 290-295.
a nanoscale DNA box with a controllable lid”. Na- • Albrect Kossel (1881) “Ueber die Verbreitung des
ture 459 (7243): 73–6. Bibcode:2009Natur.459...73A. Hypoxanthins im Thier- und Pflanzenreich” (On the
doi:10.1038/nature07971. PMID 19424153. distribution of hypoxanthins in the animal and plant
kingdoms) Zeitschrift für physiologische Chemie, 5 :
[162] Ishitsuka Y, Ha T (2009). “DNA nanotechnol-
267-271.
ogy: a nanomachine goes live”. Nat Nanotech-
nol 4 (5): 281–2. Bibcode:2009NatNa...4..281I. • Albrect Kossel, Untersuchungen über die Nucleine
doi:10.1038/nnano.2009.101. PMID 19421208. und ihre Spaltungsprodukte [Investigations into nu-
clein and its cleavage products] (Strassburg, Ger-
[163] Aldaye FA, Palmer AL, Sleiman HF (2008). “As- many: K.J. Trübne, 1881), 19 pages.
sembling materials with DNA as the guide”. Science
• Albrect Kossel (1882) “Ueber Xanthin und Hypox-
321 (5897): 1795–9. Bibcode:2008Sci...321.1795A.
anthin” (On xanthin and hypoxanthin), Zeitschrift
doi:10.1126/science.1154533. PMID 18818351.
für physiologische Chemie, 6 : 422-431.
[164] Wray GA (2002). “Dating branches on the • Albrect Kossel (1883) “Zur Chemie des Zellkerns”
Tree of Life using DNA”. Genome Biol 3 (1): (On the chemistry of the cell nucleus), Zeitschrift
reviews0001.1–reviews0001.7. doi:10.1046/j.1525- für physiologische Chemie, 7 : 7-22.
142X.1999.99010.x. PMC 150454. PMID 11806830.
• Albrect Kossel (1886) “Weitere Beiträge zur
[165] Lost Tribes of Israel, NOVA, PBS airdate: 22 February Chemie des Zellkerns” (Further contributions to
2000. Transcript available from PBS.org. Retrieved 4 the chemistry of the cell nucleus), Zeitschrift für
March 2006. Physiologische Chemie, 10 : 248-264. Available
on-line at: Max Planck Institute for the History
[166] Kleiman, Yaakov. “The Cohanim/DNA Connection: The of Science, Berlin, Germany. On p. 264, Kos-
fascinating story of how DNA studies confirm an ancient sel remarked presciently: “Der Erforschung der
biblical tradition”. aish.com (13 January 2000). Retrieved quantitativen Verhältnisse der vier stickstoffreichen
4 March 2006. Basen, der Abhängigkeit ihrer Menge von den phys-
iologischen Zuständen der Zelle, verspricht wichtige
[167] Goldman N, Bertone P, Chen S, Dessimoz C, LeP- Aufschlüsse über die elementaren physiologisch-
roust EM, Sipos B, Birney E (23 January 2013). chemischen Vorgänge.” (The study of the quantita-
“Towards practical, high-capacity, low-maintenance in- tive relations of the four nitrogenous bases — [and]
formation storage in synthesized DNA”. Nature of the dependence of their quantity on the physio-
494 (7435): 77–80. Bibcode:2013Natur.494...77G. logical states of the cell — promises important in-
doi:10.1038/nature11875. PMC 3672958. PMID sights into the fundamental physiological-chemical
23354052. processes.)
 3.3. DNA 73

[172] Jones ME (September 1953). “Albrecht Kossel, A Bio- [179] Avery OT, Macleod CM, McCarty M (1944). “Studies
graphical Sketch”. Yale Journal of Biology and Medicine on the Chemical Nature of the Substance Inducing Trans-
(National Center for Biotechnology Information) 26 (1): formation of Pneumococcal Types: Induction of Trans-
80–97. PMC 2599350. PMID 13103145. formation by a Desoxyribonucleic Acid Fraction Isolated
from Pneumococcus Type Iii”. J Exp Med 79 (2): 137–
[173] Levene P, (1 December 1919). “The structure of yeast 158. doi:10.1084/jem.79.2.137. PMC 2135445. PMID
nucleic acid”. J Biol Chem 40 (2): 415–24. 19871359.
[174] See: [180] Hershey AD, Chase M (1952). “Independent Func-
tions of Viral Protein and Nucleic Acid in Growth
• W. T. Astbury and Florence O. Bell (1938) “Some of Bacteriophage”. J Gen Physiol 36 (1): 39–
recent developments in the X-ray study of proteins 56. doi:10.1085/jgp.36.1.39. PMC 2147348. PMID
and related structures,” Cold Spring Harbor Sym- 12981234.
posia on Quantitative Biology, 6 : 109-121. Avail-
able on-line at: University of Leeds. [181] The B-DNA X-ray pattern on the right of this linked
• Astbury, W. T., (1947) “X-ray studies of nucleic image was obtained by Rosalind Franklin and Raymond
acids,” Symposia of the Society for Experimental Bi- Gosling in May 1952 at high hydration levels of DNA and
ology, 1 : 66-76. Available on-line at: Oregon State it has been labeled as “Photo 51”
University. [182] Nature Archives Double Helix of DNA: 50 Years
[175] Koltsov proposed that a cell’s genetic information was en- [183] “Original X-ray diffraction image”. Osuli-
coded in a long chain of amino acids. See: brary.oregonstate.edu. Retrieved 6 February 2011.
• Н. К. Кольцов, "Физико-химические основы [184] The Nobel Prize in Physiology or Medicine 1962 Nobel-
морфологии" (The physical-chemical basis of prize .org Accessed 22 December 06
morphology) -- speech given at the 3rd All-Union
Meeting of Zoologist, Anatomists, and Histologists [185] Maddox B (23 January 2003). “The double he-
at Leningrad, U.S.S.R., December 12, 1927. lix and the 'wronged heroine'" (PDF). Nature 421
(6921): 407–408. Bibcode:2003Natur.421..407M.
• Reprinted in: Успехи экспериментальной
doi:10.1038/nature01399. PMID 12540909.
биологии (Advances in Experimental Biology),
series B, 7 (1) : ?-? (1928). [186] Crick, F.H.C. On degenerate templates and the adap-
• Reprinted in German as: Nikolaj K. Koltzoff tor hypothesis (PDF). genome.wellcome.ac.uk (Lecture,
(1928) “Physikalisch-chemische Grundlagen der 1955). Retrieved 22 December 2006.
Morphologie” (The physical-chemical basis of mor-
[187] Meselson M, Stahl FW (1958). “The replication
phology), Biologisches Zentralblatt, 48 (6) : 345-
of DNA in Escherichia coli”. Proc Natl Acad Sci
369.
USA 44 (7): 671–82. Bibcode:1958PNAS...44..671M.
• In 1934, Koltsov contended that the proteins that doi:10.1073/pnas.44.7.671. PMC 528642. PMID
contain a cell’s genetic information replicate. See: 16590258.
N. K. Koltzoff (October 5, 1934) “The struc-
ture of the chromosomes in the salivary glands of [188] The Nobel Prize in Physiology or Medicine 1968 Nobel-
Drosophila,” Science, 80 (2075) : 312-313. From prize.org Accessed 22 December 06
page 313: “I think that the size of the chromosomes
in the salivary glands [of Drosophila] is determined
through the multiplication of genonemes. By this 3.3.11 Further reading
term I designate the axial thread of the chromo-
some, in which the geneticists locate the linear com- • Berry, Andrew; Watson, James. (2003). DNA: the
bination of genes; … In the normal chromosome secret of life. New York: Alfred A. Knopf. ISBN
there is usually only one genoneme; before cell- 0-375-41546-7.
division this genoneme has become divided into two
strands.” • Calladine, Chris R.; Drew, Horace R.; Luisi, Ben
F. and Travers, Andrew A. (2003). Understanding
[176] Soyfer VN (2001). “The consequences of political dicta- DNA: the molecule & how it works. Amsterdam: El-
torship for Russian science”. Nature Reviews Genetics 2
sevier Academic Press. ISBN 0-12-155089-3.
(9): 723–729. doi:10.1038/35088598. PMID 11533721.
• Dennis, Carina; Julie Clayton (2003). 50 years of
[177] Griffith F (January 1928). “The significance of pneu-
DNA. Basingstoke: Palgrave Macmillan. ISBN 1-
mococcal types”. The Journal of Hygiene (London) 27
(2): 113–59. doi:10.1017/S0022172400031879. PMC 4039-1479-6.
2167760. PMID 20474956.
• Judson, Horace F. 1979. The Eighth Day of Cre-
[178] Lorenz MG, Wackernagel W (1994). “Bacterial gene ation: Makers of the Revolution in Biology. Touch-
transfer by natural genetic transformation in the environ- stone Books, ISBN 0-671-22540-5. 2nd edition:
ment”. Microbiol. Rev. 58 (3): 563–602. PMC 372978. Cold Spring Harbor Laboratory Press, 1996 paper-
PMID 7968924. back: ISBN 0-87969-478-5.
74 CHAPTER 3. NUCLEIC ACIDS

• Olby, Robert C. (1994). The path to the double helix: • Genetic Education Modules for Teachers—DNA
the discovery of DNA. New York: Dover Publica- from the Beginning Study Guide
tions. ISBN 0-486-68117-3., first published in Oc-
tober 1974 by MacMillan, with foreword by Francis • PDB Molecule of the Month pdb23_1
Crick;the definitive DNA textbook,revised in 1994 • Rosalind Franklin’s contributions to the study of
with a 9-page postscript DNA
• Micklas, David. 2003. DNA Science: A First Course. • U.S. National DNA Day—watch videos and partic-
Cold Spring Harbor Press: ISBN 978-0-87969-636- ipate in real-time chat with top scientists
8
• Clue to chemistry of heredity found The New York
• Ridley, Matt (2006). Francis Crick: discoverer of Times June 1953. First American newspaper cov-
the genetic code. Ashland, OH: Eminent Lives, Atlas erage of the discovery of the DNA structure
Books. ISBN 0-06-082333-X.
• Olby R (2003). “Quiet debut for the
• Olby, Robert C. (2009). Francis Crick: A Biogra- double helix”. Nature 421 (6921):
phy. Plainview, N.Y: Cold Spring Harbor Labora- 402–5. Bibcode:2003Natur.421..402O.
tory Press. ISBN 0-87969-798-9. doi:10.1038/nature01397. PMID 12540907.
• Rosenfeld, Israel. 2010. DNA: A Graphic Guide to
• DNA from the Beginning Another DNA Learn-
the Molecule that Shook the World. Columbia Uni-
ing Center site on DNA, genes, and heredity from
versity Press: ISBN 978-0-231-14271-7
Mendel to the human genome project.
• Schultz, Mark and Zander Cannon. 2009. The Stuff
• The Register of Francis Crick Personal Papers 1938
of Life: A Graphic Guide to Genetics and DNA. Hill
– 2007 at Mandeville Special Collections Library,
and Wang: ISBN 0-8090-8947-5
University of California, San Diego
• Stent, Gunther Siegmund; Watson, James. (1980).
• Seven-page, handwritten letter that Crick sent to
The double helix: a personal account of the discovery
his 12-year-old son Michael in 1953 describing the
of the structure of DNA. New York: Norton. ISBN
structure of DNA. See Crick’s medal goes under the
0-393-95075-1.
hammer, Nature, 5 April 2013.
• Watson, James. 2004. DNA: The Secret of Life.
• 3D map of DNA reveals hidden loops that al-
Random House: ISBN 978-0-09-945184-6
low genes to work together (11 December 2014),
• Wilkins, Maurice (2003). The third man of the Science (Daily News)
double helix the autobiography of Maurice Wilkins.
Cambridge, Eng: University Press. ISBN 0-19-
860665-6.

3.3.12 External links

• DNA at DMOZ
• DNA binding site prediction on protein
• DNA the Double Helix Game From the official No-
bel Prize web site
• DNA under electron microscope
• Dolan DNA Learning Center
• Double Helix: 50 years of DNA, Nature
• Proteopedia DNA
• Proteopedia Forms_of_DNA
• ENCODE threads explorer ENCODE Home page.
Nature (journal)
• Double Helix 1953–2003 National Centre for
Biotechnology Education
Chapter 4

Proteins and amino acids

4.1 Protein polypeptide. A protein contains at least one long polypep-

tide. Short polypeptides, containing less than about 20-
This article is about a class of molecules. For protein 30 residues, are rarely considered to be proteins and are
as a nutrient, see Protein (nutrient). For other uses, see commonly called peptides, or sometimes oligopeptides.
Protein (disambiguation). The individual amino acid residues are bonded together
by peptide bonds and adjacent amino acid residues. The
sequence of amino acid residues in a protein is defined
by the sequence of a gene, which is encoded in the
genetic code. In general, the genetic code specifies 20
standard amino acids; however, in certain organisms the
genetic code can include selenocysteine and—in certain
archaea—pyrrolysine. Shortly after or even during syn-
thesis, the residues in a protein are often chemically mod-
ified by posttranslational modification, which alters the
physical and chemical properties, folding, stability, ac-
tivity, and ultimately, the function of the proteins. Some-
times proteins have non-peptide groups attached, which
can be called prosthetic groups or cofactors. Proteins can
also work together to achieve a particular function, and
they often associate to form stable protein complexes.
Once formed, proteins only exist for a certain period of
time and are then degraded and recycled by the cell’s ma-
chinery through the process of protein turnover. A pro-
tein’s lifespan is measured in terms of its half-life and
covers a wide range. They can exist for minutes or years
with an average lifespan of 1–2 days in mammalian cells.
A representation of the 3D structure of the protein myoglobin Abnormal and or misfolded proteins are degraded more
showing turquoise alpha helices. This protein was the first to rapidly either due to being targeted for destruction or due
have its structure solved by X-ray crystallography. Towards the
to being unstable.
right-center among the coils, a prosthetic group called a heme
group (shown in gray) with a bound oxygen molecule (red). Like other biological macromolecules such as
polysaccharides and nucleic acids, proteins are es-
Proteins (/ˈproʊˌtiːnz/ or /ˈproʊti.ɨnz/) are large sential parts of organisms and participate in virtually
biomolecules, or macromolecules, consisting of one every process within cells. Many proteins are enzymes
or more long chains of amino acid residues. Proteins that catalyze biochemical reactions and are vital to
perform a vast array of functions within living organisms, metabolism. Proteins also have structural or mechanical
including catalyzing metabolic reactions, DNA replica- functions, such as actin and myosin in muscle and the
tion, responding to stimuli, and transporting molecules proteins in the cytoskeleton, which form a system of
from one location to another. Proteins differ from one scaffolding that maintains cell shape. Other proteins
another primarily in their sequence of amino acids, are important in cell signaling, immune responses, cell
which is dictated by the nucleotide sequence of their adhesion, and the cell cycle. Proteins are also necessary
genes, and which usually results in protein folding into a in animals’ diets, since animals cannot synthesize all the
specific three-dimensional structure that determines its amino acids they need and must obtain essential amino
activity. acids from food. Through the process of digestion,
animals break down ingested protein into free amino
A linear chain of amino acid residues is called a

75
76 CHAPTER 4. PROTEINS AND AMINO ACIDS

acids that are then used in metabolism. are linked by peptide bonds. Once linked in the protein
Proteins may be purified from other cellular components chain, an individual amino acid is called a residue, and
using a variety of techniques such as ultracentrifugation, the linked series of carbon, nitrogen, and oxygen[3]atoms
precipitation, electrophoresis, and chromatography; the are known as the main chain or protein backbone.
advent of genetic engineering has made possible a num- The peptide bond has two resonance forms that contribute
ber of methods to facilitate purification. Methods com- some double-bond character and inhibit rotation around
monly used to study protein structure and function in- its axis, so that the alpha carbons are roughly coplanar.
clude immunohistochemistry, site-directed mutagenesis, The other two dihedral angles in the peptide bond deter-
X-ray crystallography, nuclear magnetic resonance and mine the local shape assumed by the protein backbone.[4]
mass spectrometry. The end of the protein with a free carboxyl group is
known as the C-terminus or carboxy terminus, whereas
the end with a free amino group is known as the N-
4.1.1 Biochemistry terminus or amino terminus. The words protein, polypep-
tide, and peptide are a little ambiguous and can over-
lap in meaning. Protein is generally used to refer to the
complete biological molecule in a stable conformation,
whereas peptide is generally reserved for a short amino
acid oligomers often lacking a stable three-dimensional
structure. However, the boundary between the two is
not well defined and usually lies near 20–30 residues.[5]
Polypeptide can refer to any single linear chain of amino
acids, usually regardless of length, but often implies an
absence of a defined conformation.

4.1.2 Synthesis

Biosynthesis

Chemical structure of the peptide bond (bottom) and the three-

dimensional structure of a peptide bond between an alanine and
an adjacent amino acid (top/inset)

Resonance structures of the peptide bond that links individual

amino acids to form a protein polymer

Main articles: Biochemistry, Amino acid and Peptide

bond
A ribosome produces a protein using mRNA as template
Most proteins consist of linear polymers built from series
of up to 20 different L-α-amino acids. All proteinogenic
GTGCATCTGACTCCTGAGGAGAAG DNA
amino acids possess common structural features, includ- CACGTAGACTGAGGACTCCTCTTC
ing an α-carbon to which an amino group, a carboxyl (transcription)
group, and a variable side chain are bonded. Only proline GUGCAUCUGACUCCUGAGGAGAAG RNA
differs from this basic structure as it contains an unusual
(translation)
ring to the N-end amine group, which forces the CO–
NH amide moiety into a fixed conformation.[1] The side V H L T P E E K protein
chains of the standard amino acids, detailed in the list of
standard amino acids, have a great variety of chemical The DNA sequence of a gene encodes the amino acid sequence
structures and properties; it is the combined effect of all of a protein
of the amino acid side chains in a protein that ultimately
determines its three-dimensional structure and its chem- Main article: Protein biosynthesis
ical reactivity.[2] The amino acids in a polypeptide chain
4.1. PROTEIN 77

Proteins are assembled from amino acids using informa- generally not for commercial applications. Chemical syn-
tion encoded in genes. Each protein has its own unique thesis is inefficient for polypeptides longer than about 300
amino acid sequence that is specified by the nucleotide amino acids, and the synthesized proteins may not readily
sequence of the gene encoding this protein. The genetic assume their native tertiary structure. Most chemical syn-
code is a set of three-nucleotide sets called codons and thesis methods proceed from C-terminus to N-terminus,
each three-nucleotide combination designates an amino opposite the biological reaction.[11]
acid, for example AUG (adenine-uracil-guanine) is the
code for methionine. Because DNA contains four nu-
cleotides, the total number of possible codons is 64; 4.1.3 Structure
hence, there is some redundancy in the genetic code, with
some amino acids specified by more than one codon.[6]
Genes encoded in DNA are first transcribed into pre-
messenger RNA (mRNA) by proteins such as RNA poly-
merase. Most organisms then process the pre-mRNA
(also known as a primary transcript) using various forms
of Post-transcriptional modification to form the mature
mRNA, which is then used as a template for protein syn-
thesis by the ribosome. In prokaryotes the mRNA may
either be used as soon as it is produced, or be bound by
a ribosome after having moved away from the nucleoid. The crystal structure of the chaperonin. Chaperonins assist pro-
tein folding.
In contrast, eukaryotes make mRNA in the cell nucleus
and then translocate it across the nuclear membrane into
the cytoplasm, where protein synthesis then takes place.
The rate of protein synthesis is higher in prokaryotes
than eukaryotes and can reach up to 20 amino acids per
second.[7]
The process of synthesizing a protein from an mRNA
template is known as translation. The mRNA is loaded
onto the ribosome and is read three nucleotides at a time
by matching each codon to its base pairing anticodon
Three possible representations of the three-dimensional structure
located on a transfer RNA molecule, which carries the
of the protein triose phosphate isomerase. Left: All-atom rep-
amino acid corresponding to the codon it recognizes. resentation colored by atom type. Middle: Simplified represen-
The enzyme aminoacyl tRNA synthetase “charges” the tation illustrating the backbone conformation, colored by sec-
tRNA molecules with the correct amino acids. The grow- ondary structure. Right: Solvent-accessible surface representa-
ing polypeptide is often termed the nascent chain. Pro- tion colored by residue type (acidic residues red, basic residues
teins are always biosynthesized from N-terminus to C- blue, polar residues green, nonpolar residues white).
terminus.[6]
The size of a synthesized protein can be measured by Main article: Protein structure
the number of amino acids it contains and by its to- Further information: Protein structure prediction
tal molecular mass, which is normally reported in units
of daltons (synonymous with atomic mass units), or the Most proteins fold into unique 3-dimensional structures.
derivative unit kilodalton (kDa). Yeast proteins are on The shape into which a protein naturally folds is known as
average 466 amino acids long and 53 kDa in mass.[5] The its native conformation.[12] Although many proteins can
largest known proteins are the titins, a component of the fold unassisted, simply through the chemical properties
muscle sarcomere, with a molecular mass of almost 3,000 of their amino acids, others require the aid of molec-
kDa and a total length of almost 27,000 amino acids.[8] ular chaperones to fold into their native states.[13] Bio-
chemists often refer to four distinct aspects of a protein’s
structure:[14]
Chemical synthesis
• Primary structure: the amino acid sequence. A pro-
Short proteins can also be synthesized chemically by a tein is a polyamide.
family of methods known as peptide synthesis, which rely
on organic synthesis techniques such as chemical ligation • Secondary structure: regularly repeating local struc-
to produce peptides in high yield.[9] Chemical synthesis tures stabilized by hydrogen bonds. The most
allows for the introduction of non-natural amino acids common examples are the alpha helix, beta sheet
into polypeptide chains, such as attachment of fluorescent and turns. Because secondary structures are local,
probes to amino acid side chains.[10] These methods are many regions of different secondary structure can
useful in laboratory biochemistry and cell biology, though be present in the same protein molecule.
78 CHAPTER 4. PROTEINS AND AMINO ACIDS

• Tertiary structure: the overall shape of a single pro- Structure determination

tein molecule; the spatial relationship of the sec-
ondary structures to one another. Tertiary struc- Discovering the tertiary structure of a protein, or the qua-
ture is generally stabilized by nonlocal interactions, ternary structure of its complexes, can provide important
most commonly the formation of a hydrophobic clues about how the protein performs its function. Com-
core, but also through salt bridges, hydrogen bonds, mon experimental methods of structure determination
disulfide bonds, and even posttranslational modifica- include X-ray crystallography and NMR spectroscopy,
tions. The term “tertiary structure” is often used as both of which can produce information at atomic resolu-
synonymous with the term fold. The tertiary struc- tion. However, NMR experiments are able to provide in-
ture is what controls the basic function of the pro- formation from which a subset of distances between pairs
tein. of atoms can be estimated, and the final possible confor-
mations for a protein are determined by solving a distance
geometry problem. Dual polarisation interferometry is a
• Quaternary structure: the structure formed by sev- quantitative analytical method for measuring the overall
eral protein molecules (polypeptide chains), usually protein conformation and conformational changes due to
called protein subunits in this context, which func- interactions or other stimulus. Circular dichroism is an-
tion as a single protein complex. other laboratory technique for determining internal beta
sheet/ helical composition of proteins. Cryoelectron mi-
croscopy is used to produce lower-resolution structural
information about very large protein complexes, includ-
Proteins are not entirely rigid molecules. In addition to
ing assembled viruses;[18] a variant known as electron
these levels of structure, proteins may shift between sev-
crystallography can also produce high-resolution infor-
eral related structures while they perform their functions.
mation in some cases, especially for two-dimensional
In the context of these functional rearrangements, these
crystals of membrane proteins.[19] Solved structures are
tertiary or quaternary structures are usually referred to as
usually deposited in the Protein Data Bank (PDB), a
"conformations", and transitions between them are called
freely available resource from which structural data about
conformational changes. Such changes are often induced
thousands of proteins can be obtained in the form of
by the binding of a substrate molecule to an enzyme’s
Cartesian coordinates for each atom in the protein.[20]
active site, or the physical region of the protein that par-
ticipates in chemical catalysis. In solution proteins also Many more gene sequences are known than protein struc-
undergo variation in structure through thermal vibration tures. Further, the set of solved structures is biased to-
and the collision with other molecules.[15] ward proteins that can be easily subjected to the condi-
tions required in X-ray crystallography, one of the major
structure determination methods. In particular, globular
proteins are comparatively easy to crystallize in prepa-
ration for X-ray crystallography. Membrane proteins,
by contrast, are difficult to crystallize and are underrep-
resented in the PDB.[21] Structural genomics initiatives
have attempted to remedy these deficiencies by system-
Molecular surface of several proteins showing their compara- atically solving representative structures of major fold
tive sizes. From left to right are: immunoglobulin G (IgG, an classes. Protein structure prediction methods attempt to
antibody), hemoglobin, insulin (a hormone), adenylate kinase provide a means of generating a plausible structure for
(an enzyme), and glutamine synthetase (an enzyme). proteins whose structures have not been experimentally
determined.[22]

Proteins can be informally divided into three main

classes, which correlate with typical tertiary structures: 4.1.4 Cellular functions
globular proteins, fibrous proteins, and membrane pro-
teins. Almost all globular proteins are soluble and many
Proteins are the chief actors within the cell, said to be
are enzymes. Fibrous proteins are often structural, such
carrying out the duties specified by the information en-
coded in genes.[5] With the exception of certain types of
as collagen, the major component of connective tissue, or
keratin, the protein component of hair and nails. Mem- RNA, most other biological molecules are relatively in-
brane proteins often serve as receptors or provide chan-
ert elements upon which proteins act. Proteins make up
nels for polar or charged molecules to pass through thehalf the dry weight of an Escherichia coli cell, whereas
cell membrane.[16] other macromolecules such as DNA and RNA make up
[23]
A special case of intramolecular hydrogen bonds only 3% and 20%, respectively. The set of proteins
within proteins, poorly shielded from water attack and expressed in a particular cell or cell type is known as its
hence promoting their own dehydration, are called proteome.
dehydrons.[17] The chief characteristic of proteins that also allows their
4.1. PROTEIN 79

Enzymes

Main article: Enzyme

The best-known role of proteins in the cell is as enzymes,

which catalyze chemical reactions. Enzymes are usually
highly specific and accelerate only one or a few chem-
ical reactions. Enzymes carry out most of the reac-
tions involved in metabolism, as well as manipulating
DNA in processes such as DNA replication, DNA re-
pair, and transcription. Some enzymes act on other pro-
teins to add or remove chemical groups in a process
The enzyme hexokinase is shown as a conventional ball-and-stick known as posttranslational modification. About 4,000 re-
molecular model. To scale in the top right-hand corner are two actions are known to be catalyzed by enzymes.[28] The
of its substrates, ATP and glucose. rate acceleration conferred by enzymatic catalysis is often
enormous—as much as 1017 -fold increase in rate over the
uncatalyzed reaction in the case of orotate decarboxylase
(78 million years without the enzyme, 18 milliseconds
with the enzyme).[29]
diverse set of functions is their ability to bind other
molecules specifically and tightly. The region of the pro- The molecules bound and acted upon by enzymes are
tein responsible for binding another molecule is known called substrates. Although enzymes can consist of hun-
as the binding site and is often a depression or “pocket” dreds of amino acids, it is usually only a small fraction
on the molecular surface. This binding ability is medi- of the residues that come in contact with the substrate,
ated by the tertiary structure of the protein, which de- and an even smaller fraction—three to four residues on
fines the binding site pocket, and by the chemical prop- average—that are directly involved in catalysis.[30] The
erties of the surrounding amino acids’ side chains. Pro- region of the enzyme that binds the substrate and con-
tein binding can be extraordinarily tight and specific; for tains the catalytic residues is known as the active site.
example, the ribonuclease inhibitor protein binds to hu- Dirigent proteins are members of a class of proteins
man angiogenin with a sub-femtomolar dissociation con- which dictate the stereochemistry of a compound synthe-
stant (<10−15 M) but does not bind at all to its amphibian sized by other enzymes.
homolog onconase (>1 M). Extremely minor chemical
changes such as the addition of a single methyl group to a
binding partner can sometimes suffice to nearly eliminate
Cell signaling and ligand binding
binding; for example, the aminoacyl tRNA synthetase
specific to the amino acid valine discriminates against the
very similar side chain of the amino acid isoleucine.[24] Many proteins are involved in the process of cell sig-
naling and signal transduction. Some proteins, such as
Proteins can bind to other proteins as well as to small- insulin, are extracellular proteins that transmit a signal
molecule substrates. When proteins bind specifically to from the cell in which they were synthesized to other cells
other copies of the same molecule, they can oligomerize in distant tissues. Others are membrane proteins that act
to form fibrils; this process occurs often in structural pro- as receptors whose main function is to bind a signaling
teins that consist of globular monomers that self-associate molecule and induce a biochemical response in the cell.
to form rigid fibers. Protein–protein interactions also reg- Many receptors have a binding site exposed on the cell
ulate enzymatic activity, control progression through the surface and an effector domain within the cell, which may
cell cycle, and allow the assembly of large protein com- have enzymatic activity or may undergo a conformational
plexes that carry out many closely related reactions with change detected by other proteins within the cell.[31]
a common biological function. Proteins can also bind to,
or even be integrated into, cell membranes. The abil- Antibodies are protein components of an adaptive im-
ity of binding partners to induce conformational changes mune system whose main function is to bind antigens, or
in proteins allows the construction of enormously com- foreign substances in the body, and target them for de-
plex signaling networks.[25] Importantly, as interactions struction. Antibodies can be secreted into the extracel-
between proteins are reversible, and depend heavily on lular environment or anchored in the membranes of spe-
the availability of different groups of partner proteins to cialized B cells known as plasma cells. Whereas enzymes
form aggregates that are capable to carry out discrete sets are limited in their binding affinity for their substrates by
of function, study of the interactions between specific the necessity of conducting their reaction, antibodies have
proteins is a key to understand important aspects of cellu- no such constraints. An antibody’s binding affinity to its
lar function, and ultimately the properties that distinguish target is extraordinarily high.[32]
particular cell types.[26][27] Many ligand transport proteins bind particular small
80 CHAPTER 4. PROTEINS AND AMINO ACIDS

proteins are fibrous proteins; for example, collagen and

elastin are critical components of connective tissue such
as cartilage, and keratin is found in hard or filamen-
tous structures such as hair, nails, feathers, hooves, and
some animal shells.[36] Some globular proteins can also
play structural functions, for example, actin and tubulin
are globular and soluble as monomers, but polymerize
to form long, stiff fibers that make up the cytoskeleton,
which allows the cell to maintain its shape and size.
Other proteins that serve structural functions are motor
proteins such as myosin, kinesin, and dynein, which are
capable of generating mechanical forces. These proteins
are crucial for cellular motility of single celled organisms
and the sperm of many multicellular organisms which re-
produce sexually. They also generate the forces exerted
by contracting muscles[37] and play essential roles in in-
tracellular transport.

4.1.5 Methods of study

Main article: Protein methods

Ribbon diagram of a mouse antibody against cholera that binds The activities and structures of proteins may be examined
a carbohydrate antigen in vitro, in vivo, and in silico. In vitro studies of purified
proteins in controlled environments are useful for learn-
ing how a protein carries out its function: for example,
biomolecules and transport them to other locations in the enzyme kinetics studies explore the chemical mechanism
body of a multicellular organism. These proteins must of an enzyme’s catalytic activity and its relative affinity for
have a high binding affinity when their ligand is present various possible substrate molecules. By contrast, in vivo
in high concentrations, but must also release the ligand experiments can provide information about the physio-
when it is present at low concentrations in the target tis- logical role of a protein in the context of a cell or even
sues. The canonical example of a ligand-binding protein a whole organism. In silico studies use computational
is haemoglobin, which transports oxygen from the lungs methods to study proteins.
to other organs and tissues in all vertebrates and has close
homologs in every biological kingdom.[33] Lectins are
sugar-binding proteins which are highly specific for their Protein purification
sugar moieties. Lectins typically play a role in biological
recognition phenomena involving cells and proteins.[34] Main article: Protein purification
Receptors and hormones are highly specific binding pro-
teins.
To perform in vitro analysis, a protein must be purified
Transmembrane proteins can also serve as ligand trans- away from other cellular components. This process usu-
port proteins that alter the permeability of the cell mem- ally begins with cell lysis, in which a cell’s membrane is
brane to small molecules and ions. The membrane alone disrupted and its internal contents released into a solu-
has a hydrophobic core through which polar or charged tion known as a crude lysate. The resulting mixture can
molecules cannot diffuse. Membrane proteins contain in- be purified using ultracentrifugation, which fractionates
ternal channels that allow such molecules to enter and exit the various cellular components into fractions containing
the cell. Many ion channel proteins are specialized to se- soluble proteins; membrane lipids and proteins; cellular
lect for only a particular ion; for example, potassium and organelles, and nucleic acids. Precipitation by a method
sodium channels often discriminate for only one of the known as salting out can concentrate the proteins from
two ions.[35] this lysate. Various types of chromatography are then
used to isolate the protein or proteins of interest based
on properties such as molecular weight, net charge and
Structural proteins binding affinity.[38] The level of purification can be moni-
tored using various types of gel electrophoresis if the de-
Structural proteins confer stiffness and rigidity to sired protein’s molecular weight and isoelectric point are
otherwise-fluid biological components. Most structural known, by spectroscopy if the protein has distinguishable
4.1. PROTEIN 81

spectroscopic features, or by enzyme assays if the pro- orescent protein (GFP).[41] The fused protein’s position
tein has enzymatic activity. Additionally, proteins can be within the cell can be cleanly and efficiently visualized
isolated according their charge using electrofocusing.[39] using microscopy,[42] as shown in the figure opposite.
For natural proteins, a series of purification steps may be Other methods for elucidating the cellular location of pro-
necessary to obtain protein sufficiently pure for labora- teins requires the use of known compartmental mark-
tory applications. To simplify this process, genetic engi- ers for regions such as the ER, the Golgi, lysosomes or
neering is often used to add chemical features to proteins vacuoles, mitochondria, chloroplasts, plasma membrane,
that make them easier to purify without affecting their etc. With the use of fluorescently tagged versions of these
structure or activity. Here, a “tag” consisting of a specific markers or of antibodies to known markers, it becomes
amino acid sequence, often a series of histidine residues much simpler to identify the localization of a protein of
(a "His-tag"), is attached to one terminus of the protein. interest. For example, indirect immunofluorescence will
As a result, when the lysate is passed over a chromatogra- allow for fluorescence colocalization and demonstration
phy column containing nickel, the histidine residues lig- of location. Fluorescent dyes are used to label cellular
ate the nickel and attach to the column while the untagged compartments for a similar purpose.[43]
components of the lysate pass unimpeded. A number of Other possibilities exist, as well. For example,
different tags have been developed to help researchers pu- immunohistochemistry usually utilizes an antibody to one
rify specific proteins from complex mixtures.[40] or more proteins of interest that are conjugated to en-
zymes yielding either luminescent or chromogenic signals
Cellular localization that can be compared between samples, allowing for lo-
calization information. Another applicable technique is
cofractionation in sucrose (or other material) gradients
using isopycnic centrifugation.[44] While this technique
does not prove colocalization of a compartment of known
density and the protein of interest, it does increase the
likelihood, and is more amenable to large-scale studies.
Finally, the gold-standard method of cellular localization
is immunoelectron microscopy. This technique also uses
an antibody to the protein of interest, along with classical
electron microscopy techniques. The sample is prepared
for normal electron microscopic examination, and then
treated with an antibody to the protein of interest that is
conjugated to an extremely electro-dense material, usu-
ally gold. This allows for the localization of both ultra-
structural details as well as the protein of interest.[45]
Through another genetic engineering application known
as site-directed mutagenesis, researchers can alter the
protein sequence and hence its structure, cellular localiza-
tion, and susceptibility to regulation. This technique even
allows the incorporation of unnatural amino acids into
proteins, using modified tRNAs,[46] and may allow the
rational design of new proteins with novel properties.[47]

Proteomics
Proteins in different cellular compartments and structures tagged
with green fluorescent protein (here, white)
Main article: Proteomics
The study of proteins in vivo is often concerned with the
synthesis and localization of the protein within the cell. The total complement of proteins present at a time in a
Although many intracellular proteins are synthesized in cell or cell type is known as its proteome, and the study of
the cytoplasm and membrane-bound or secreted proteins such large-scale data sets defines the field of proteomics,
in the endoplasmic reticulum, the specifics of how pro- named by analogy to the related field of genomics. Key
teins are targeted to specific organelles or cellular struc- experimental techniques in proteomics include 2D elec-
tures is often unclear. A useful technique for assessing trophoresis,[48] which allows the separation of a large
cellular localization uses genetic engineering to express in number of proteins, mass spectrometry,[49] which allows
a cell a fusion protein or chimera consisting of the natural rapid high-throughput identification of proteins and se-
protein of interest linked to a "reporter" such as green flu- quencing of peptides (most often after in-gel digestion),
82 CHAPTER 4. PROTEINS AND AMINO ACIDS

protein microarrays,[50] which allow the detection of the Structure prediction and simulation Main articles:
relative levels of a large number of proteins present in a Protein structure prediction and List of protein structure
cell, and two-hybrid screening, which allows the system- prediction software
atic exploration of protein–protein interactions.[51] The
total complement of biologically possible such interac- Complementary to the field of structural genomics, pro-
tions is known as the interactome.[52] A systematic at- tein structure prediction seeks to develop efficient ways
tempt to determine the structures of proteins representing to provide plausible models for proteins whose struc-
every possible fold is known as structural genomics.[53] tures have not yet been determined experimentally.[54]
The most successful type of structure prediction, known
as homology modeling, relies on the existence of a “tem-
Bioinformatics plate” structure with sequence similarity to the protein
being modeled; structural genomics’ goal is to provide
Main article: Bioinformatics sufficient representation in solved structures to model
most of those that remain.[55] Although producing accu-
rate models remains a challenge when only distantly re-
A vast array of computational methods have been devel-
lated template structures are available, it has been sug-
oped to analyze the structure, function, and evolution of
gested that sequence alignment is the bottleneck in this
proteins.
process, as quite accurate models can be produced if a
The development of such tools has been driven by the “perfect” sequence alignment is known.[56] Many struc-
large amount of genomic and proteomic data available ture prediction methods have served to inform the emerg-
for a variety of organisms, including the human genome. ing field of protein engineering, in which novel pro-
It is simply impossible to study all proteins experimen- tein folds have already been designed.[57] A more com-
tally, hence only a few are subjected to laboratory ex- plex computational problem is the prediction of inter-
periments while computational tools are used to extrap- molecular interactions, such as in molecular docking and
olate to similar proteins. Such homologous proteins can protein–protein interaction prediction.[58]
be efficiently identified in distantly related organisms by
The processes of protein folding and binding can be sim-
sequence alignment. Genome and gene sequences can
ulated using such technique as molecular mechanics, in
be searched by a variety of tools for certain proper-
particular, molecular dynamics and Monte Carlo, which
ties. Sequence profiling tools can find restriction enzyme
increasingly take advantage of parallel and distributed
sites, open reading frames in nucleotide sequences, and
computing (Folding@home project;[59] molecular mod-
predict secondary structures. Phylogenetic trees can be
eling on GPU). The folding of small alpha-helical pro-
constructed and evolutionary hypotheses developed using
tein domains such as the villin headpiece[60] and the
special software like ClustalW regarding the ancestry of
HIV accessory protein[61] have been successfully simu-
modern organisms and the genes they express. The field
lated in silico, and hybrid methods that combine stan-
of bioinformatics is now indispensable for the analysis of
dard molecular dynamics with quantum mechanics cal-
genes and proteins.
culations have allowed exploration of the electronic states
of rhodopsins.[62]

4.1.6 Nutrition
Further information: Protein (nutrient)

Most microorganisms and plants can biosynthesize all

20 standard amino acids, while animals (including hu-
mans) must obtain some of the amino acids from the
diet.[23] The amino acids that an organism cannot synthe-
size on its own are referred to as essential amino acids.
Key enzymes that synthesize certain amino acids are not
present in animals — such as aspartokinase, which cat-
alyzes the first step in the synthesis of lysine, methionine,
and threonine from aspartate. If amino acids are present
in the environment, microorganisms can conserve energy
by taking up the amino acids from their surroundings and
downregulating their biosynthetic pathways.
Constituent amino-acids can be analyzed to predict secondary,
tertiary and quaternary protein structure, in this case hemoglobin In animals, amino acids are obtained through the con-
containing heme units sumption of foods containing protein. Ingested pro-
4.1. PROTEIN 83

teins are then broken down into amino acids through The difficulty in purifying proteins in large quantities
digestion, which typically involves denaturation of the made them very difficult for early protein biochemists to
protein through exposure to acid and hydrolysis by en- study. Hence, early studies focused on proteins that could
zymes called proteases. Some ingested amino acids are be purified in large quantities, e.g., those of blood, egg
used for protein biosynthesis, while others are converted white, various toxins, and digestive/metabolic enzymes
to glucose through gluconeogenesis, or fed into the citric obtained from slaughterhouses. In the 1950s, the Armour
acid cycle. This use of protein as a fuel is particularly im- Hot Dog Co. purified 1 kg of pure bovine pancreatic
portant under starvation conditions as it allows the body’s ribonuclease A and made it freely available to scientists;
own proteins to be used to support life, particularly those this gesture helped ribonuclease A become a major target
found in muscle.[63] Amino acids are also an important for biochemical study for the following decades.[67]
dietary source of nitrogen.

4.1.7 History and etymology

Further information: History of molecular biology

Proteins were recognized as a distinct class of biologi-

cal molecules in the eighteenth century by Antoine Four-
croy and others, distinguished by the molecules’ ability
to coagulate or flocculate under treatments with heat or
acid.[64] Noted examples at the time included albumin
from egg whites, blood serum albumin, fibrin, and wheat
gluten. John Kendrew with model of myoglobin in progress
Proteins were first described by the Dutch chemist
Gerardus Johannes Mulder and named by the Swedish Linus Pauling is credited with the successful predic-
chemist Jöns Jacob Berzelius in 1838.[65][66] Mulder car- tion of regular protein secondary structures based on
ried out elemental analysis of common proteins and hydrogen bonding, an idea first put forth by William Ast-
found that nearly all proteins had the same empirical for- bury in 1933.[72] Later work by Walter Kauzmann on
mula, C400 H620 N100 O120 P1 S1 .[67] He came to the erro- denaturation,[73][74] based partly on previous studies by
neous conclusion that they might be composed of a sin- Kaj Linderstrøm-Lang,[75] contributed an understanding
gle type of (very large) molecule. The term “protein” of protein folding and structure mediated by hydrophobic
to describe these molecules was proposed by Mulder’s interactions.
associate Berzelius; protein is derived from the Greek The first protein to be sequenced was insulin, by
word πρώτειος (proteios), meaning “primary”,[68] “in the Frederick Sanger, in 1949. Sanger correctly determined
lead”, or “standing in front”.[69] Mulder went on to iden-the amino acid sequence of insulin, thus conclusively
tify the products of protein degradation such as the aminodemonstrating that proteins consisted of linear polymers
acid leucine for which he found a (nearly correct) molec- of amino acids rather than branched chains, colloids, or
ular weight of 131 Da.[67] cyclols.[76] He won the Nobel Prize for this achievement
Early nutritional scientists such as the German Carl von in 1958.
Voit believed that protein was the most important nutri- The first protein structures to be solved were hemoglobin
ent for maintaining the structure of the body, because it and myoglobin, by Max Perutz and Sir John Cowdery
was generally believed that “flesh makes flesh.”[70] Karl Kendrew, respectively, in 1958.[77][78] As of 2014, the
Heinrich Ritthausen extended known protein forms with Protein Data Bank has over 90,000 atomic-resolution
the identification of glutamic acid. At the Connecticut structures of proteins.[79] In more recent times, cryo-
Agricultural Experiment Station a detailed review of electron microscopy of large macromolecular assem-
the vegetable proteins was compiled by Thomas Burr blies[80] and computational protein structure prediction of
Osborne. Working with Lafayette Mendel and apply- small protein domains[81] are two methods approaching
ing Liebig’s law of the minimum in feeding laboratory atomic resolution.
rats, the nutritionally essential amino acids were estab-
lished. The work was continued and communicated by
William Cumming Rose. The understanding of pro- 4.1.8 See also
teins as polypeptides came through the work of Franz
Hofmeister and Hermann Emil Fischer. The central role • DNA-binding protein
of proteins as enzymes in living organisms was not fully
appreciated until 1926, when James B. Sumner showed • DNA, RNA and proteins: The three essential
that the enzyme urease was in fact a protein.[71] macromolecules of life
84 CHAPTER 4. PROTEINS AND AMINO ACIDS

• Intein [12] Murray et al., p. 36.

• List of proteins [13] Murray et al., p. 37.

• Protein design [14] Murray et al., pp. 30–34.

• Proteopathy [15] van Holde and Mathews, pp. 368–75.

• Proteopedia [16] van Holde and Mathews, pp. 165–85.

• Proteolysis [17] Fernández A, Scott R (2003). “Dehydron: a structurally

encoded signal for protein interaction”. Biophysical Jour-
• Intrinsically disordered proteins nal 85 (3): 1914–28. Bibcode:2003BpJ....85.1914F.
doi:10.1016/S0006-3495(03)74619-0. PMC 1303363.
• Protein sequence space PMID 12944304.
• Protein superfamily [18] Branden and Tooze, pp. 340–41.

• Protein structure [19] Gonen T, Cheng Y, Sliz P, Hiroaki Y, Fujiyoshi Y, Har-

rison SC, Walz T (2005). “Lipid-protein interactions in
• Protein fold double-layered two-dimensional AQP0 crystals”. Nature
438 (7068): 633–38. Bibcode:2005Natur.438..633G.
doi:10.1038/nature04321. PMC 1350984. PMID
4.1.9 References 16319884.

[1] Nelson DL, Cox MM (2005). Lehninger’s Principles of [20] Standley DM, Kinjo AR, Kinoshita K, Nakamura
Biochemistry (4th ed.). New York, New York: W. H. H (2008). “Protein structure databases with new
Freeman and Company. web services for structural biology and biomedical re-
search”. Briefings in Bioinformatics 9 (4): 276–85.
[2] Gutteridge A, Thornton JM (2005). “Understanding na- doi:10.1093/bib/bbn015. PMID 18430752.
ture’s catalytic toolkit”. Trends in Biochemical Sciences
30 (11): 622–29. doi:10.1016/j.tibs.2005.09.006. PMID [21] Walian P, Cross TA, Jap BK (2004). “Structural genomics
16214343. of membrane proteins”. Genome Biology 5 (4): 215.
doi:10.1186/gb-2004-5-4-215. PMC 395774. PMID
[3] Murray et al., p. 19. 15059248.
[4] Murray et al., p. 31.
[22] Sleator RD. (2012). “Prediction of protein functions”.
[5] Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Methods in Molecular Biology. Methods in Molecular Bi-
Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell ology 815: 15–24. doi:10.1007/978-1-61779-424-7_2.
Biology (5th ed.). New York, New York: WH Freeman ISBN 978-1-61779-423-0. PMID 22130980.
and Company.
[23] Voet D, Voet JG. (2004). Biochemistry Vol 1 3rd ed. Wi-
[6] van Holde and Mathews, pp. 1002–42. ley: Hoboken, NJ.

[7] Dobson CM (2000). “The nature and significance of pro- [24] Sankaranarayanan R, Moras D (2001). “The fidelity of the
tein folding”. In Pain RH (ed.). Mechanisms of Protein translation of the genetic code”. Acta Biochimica Polonica
Folding. Oxford, Oxfordshire: Oxford University Press. 48 (2): 323–35. PMID 11732604.
pp. 1–28. ISBN 0-19-963789-X.
[25] van Holde and Mathews, pp. 830–49.
[8] Fulton A, Isaacs W (1991). “Titin, a huge, elastic sar-
comeric protein with a probable role in morphogenesis”. [26] Copland JA, Sheffield-Moore M, Koldzic-Zivanovic N,
BioEssays 13 (4): 157–61. doi:10.1002/bies.950130403. Gentry S, Lamprou G, Tzortzatou-Stathopoulou F,
PMID 1859393. Zoumpourlis V, Urban RJ, Vlahopoulos SA (2009).
“Sex steroid receptors in skeletal differentiation and ep-
[9] Bruckdorfer T, Marder O, Albericio F (2004). “From ithelial neoplasia: is tissue-specific intervention pos-
production of peptides in milligram amounts for re- sible?". BioEssays: news and reviews in molecular,
search to multi-tons quantities for drugs of the future”. cellular and developmental biology 31 (6): 629–41.
Current Pharmaceutical Biotechnology 5 (1): 29–43. doi:10.1002/bies.200800138. PMID 19382224.
doi:10.2174/1389201043489620. PMID 14965208.
[27] Samarin S, Nusrat A (2009). “Regulation of epithelial
[10] Schwarzer D, Cole P (2005). “Protein semisynthesis apical junctional complex by Rho family GTPases”. Fron-
and expressed protein ligation: chasing a protein’s tail”. tiers in bioscience: a journal and virtual library 14 (14):
Current Opinion in Chemical Biology 9 (6): 561–69. 1129–42. doi:10.2741/3298. PMID 19273120.
doi:10.1016/j.cbpa.2005.09.018. PMID 16226484.
[28] Bairoch A (2000). “The ENZYME database in
[11] Kent SB (2009). “Total chemical synthesis of pro- 2000” (PDF). Nucleic Acids Research 28 (1): 304–
teins”. Chemical Society Reviews 38 (2): 338–51. 305. doi:10.1093/nar/28.1.304. PMC 102465. PMID
doi:10.1039/b700141j. PMID 19169452. 10592255.
4.1. PROTEIN 85

[29] Radzicka A, Wolfenden R (1995). “A [46] Hohsaka T, Sisido M (2002). “Incorporation of non-
proficient enzyme”. Science 267 (5194): natural amino acids into proteins”. Current Opinion in
90–93. Bibcode:1995Sci...267...90R. Chemical Biology 6 (6): 809–15. doi:10.1016/S1367-
doi:10.1126/science.7809611. PMID 7809611. 5931(02)00376-9. PMID 12470735.
[30] EBI External Services (2010-01-20). “The Catalytic [47] Cedrone F, Ménez A, Quéméneur E (2000). “Tai-
Site Atlas at The European Bioinformatics Institute”. loring new enzyme functions by rational redesign”.
Ebi.ac.uk. Retrieved 2011-01-16. Current Opinion in Structural Biology 10 (4): 405–
10. doi:10.1016/S0959-440X(00)00106-8. PMID
[31] Branden and Tooze, pp. 251–81.
10981626.
[32] van Holde and Mathews, pp. 247–50.
[48] Görg A, Weiss W, Dunn MJ (2004). “Cur-
[33] van Holde and Mathews, pp. 220–29. rent two-dimensional electrophoresis technology
for proteomics”. Proteomics 4 (12): 3665–85.
[34] Rüdiger H, Siebert HC, Solís D, Jiménez-Barbero J, doi:10.1002/pmic.200401031. PMID 15543535.
Romero A, von der Lieth CW, Diaz-Mariño T, Gabius HJ
(2000). “Medicinal chemistry based on the sugar code: [49] Conrotto P, Souchelnytskyi S (2008). “Proteomic ap-
fundamentals of lectinology and experimental strategies proaches in biological and medical sciences: principles
with lectins as targets”. Current Medicinal Chemistry 7 and applications”. Experimental Oncology 30 (3): 171–
(4): 389–416. doi:10.2174/0929867003375164. PMID 80. PMID 18806738.
10702616.
[50] Joos T, Bachmann J (2009). “Protein microarrays: po-
[35] Branden and Tooze, pp. 232–34. tentials and limitations”. Frontiers in Bioscience 14 (14):
4376–85. doi:10.2741/3534. PMID 19273356.
[36] van Holde and Mathews, pp. 178–81.
[51] Koegl M, Uetz P (2007). “Improving yeast two-hybrid
[37] van Holde and Mathews, pp. 258–64; 272. screening systems”. Briefings in Functional Genomics
[38] Murray et al., pp. 21–24. & Proteomics 6 (4): 302–12. doi:10.1093/bfgp/elm035.
PMID 18218650.
[39] Hey J, Posch A, Cohen A, Liu N, Harbers A (2008).
“Fractionation of complex protein mixtures by liquid- [52] Plewczyński D, Ginalski K (2009). “The interac-
phase isoelectric focusing”. Methods in Molecular Bi- tome: predicting the protein–protein interactions in cells”.
ology. Methods in Molecular Biology™ 424: 225– Cellular & Molecular Biology Letters 14 (1): 1–22.
39. doi:10.1007/978-1-60327-064-9_19. ISBN 978-1- doi:10.2478/s11658-008-0024-7. PMID 18839074.
58829-722-8. PMID 18369866.
[53] Zhang C, Kim SH (2003). “Overview of structural ge-
[40] Terpe K (2003). “Overview of tag protein fusions: from nomics: from structure to function”. Current Opinion
molecular and biochemical fundamentals to commercial in Chemical Biology 7 (1): 28–32. doi:10.1016/S1367-
systems”. Applied Microbiology and Biotechnology 60 5931(02)00015-7. PMID 12547423.
(5): 523–33. doi:10.1007/s00253-002-1158-6. PMID
[54] Zhang Y (2008). “Progress and challenges in protein
12536251.
structure prediction”. Current Opinion in Structural Bi-
[41] Stepanenko OV, Verkhusha VV, Kuznetsova IM, ology 18 (3): 342–48. doi:10.1016/j.sbi.2008.02.004.
Uversky VN, Turoverov KK (2008). “Fluorescent PMC 2680823. PMID 18436442.
proteins as biomarkers and biosensors: throwing
[55] Xiang Z (2006). “Advances in homology protein struc-
color lights on molecular and cellular processes”.
ture modeling”. Current Protein and Peptide Science 7
Current Protein & Peptide Science 9 (4): 338–69.
(3): 217–27. doi:10.2174/138920306777452312. PMC
doi:10.2174/138920308785132668. PMC 2904242.
1839925. PMID 16787261.
PMID 18691124.
[56] Zhang Y, Skolnick J (2005). “The protein struc-
[42] Yuste R (2005). “Fluorescence microscopy today”. Na-
ture prediction problem could be solved us-
ture Methods 2 (12): 902–904. doi:10.1038/nmeth1205-
ing the current PDB library”. Proceedings of
902. PMID 16299474.
the National Academy of Sciences U.S.A. 102
[43] Margolin W (2000). “Green fluorescent protein as (4): 1029–34. Bibcode:2005PNAS..102.1029Z.
a reporter for macromolecular localization in bacterial doi:10.1073/pnas.0407152101. PMC 545829. PMID
cells”. Methods (San Diego, Calif.) 20 (1): 62–72. 15653774.
doi:10.1006/meth.1999.0906. PMID 10610805.
[57] Kuhlman B, Dantas G, Ireton GC, Varani G, Stod-
[44] Walker JH, Wilson K (2000). Principles and Techniques dard BL, Baker D (2003). “Design of a novel glob-
of Practical Biochemistry. Cambridge, UK: Cambridge ular protein fold with atomic-level accuracy”. Science
University Press. pp. 287–89. ISBN 0-521-65873-X. 302 (5649): 1364–68. Bibcode:2003Sci...302.1364K.
doi:10.1126/science.1089427. PMID 14631033.
[45] Mayhew TM, Lucocq JM (2008). “Developments in
cell biology for quantitative immunoelectron microscopy [58] Ritchie DW (2008). “Recent progress and fu-
based on thin sections: a review”. Histochemistry and ture directions in protein–protein docking”. Cur-
Cell Biology 130 (2): 299–313. doi:10.1007/s00418-008- rent Protein and Peptide Science 9 (1): 1–15.
0451-6. PMC 2491712. PMID 18553098. doi:10.2174/138920308783565741. PMID 18336319.
86 CHAPTER 4. PROTEINS AND AMINO ACIDS

[59] Scheraga HA, Khalili M, Liwo A (2007). “Protein- 37 (5): 235–40. Bibcode:1951PNAS...37..235P.
folding dynamics: overview of molecular simulation doi:10.1073/pnas.37.5.235. PMC 1063348. PMID
techniques”. Annual Review of Physical Chem- 14834145.
istry 58: 57–83. Bibcode:2007ARPC...58...57S.
doi:10.1146/annurev.physchem.58.032806.104614. [73] Kauzmann W (1956). “Structural factors in protein denat-
PMID 17034338. uration”. Journal of Cellular Physiology. Supplement 47
(Suppl 1): 113–31. doi:10.1002/jcp.1030470410. PMID
[60] Zagrovic B, Snow CD, Shirts MR, Pande VS (2002). 13332017.
“Simulation of folding of a small alpha-helical pro-
tein in atomistic detail using worldwide-distributed [74] Kauzmann W (1959). “Some factors in the interpre-
computing”. Journal of Molecular Biology 323 (5): tation of protein denaturation”. Advances in Protein
927–37. doi:10.1016/S0022-2836(02)00997-X. PMID Chemistry. Advances in Protein Chemistry 14: 1–63.
12417204. doi:10.1016/S0065-3233(08)60608-7. ISBN 978-0-12-
034214-3. PMID 14404936.
[61] Herges T, Wenzel W (2005). "In silico folding of a three
helix protein and characterization of its free-energy land- [75] Kalman SM, Linderstrom-Lang K, Ottesen M, Richards
scape in an all-atom force field”. Physical Review Let- FM (1955). “Degradation of ribonuclease by subtil-
ters 94 (1): 018101. Bibcode:2005PhRvL..94a8101H. isin”. Biochimica et Biophysica Acta 16 (2): 297–99.
doi:10.1103/PhysRevLett.94.018101. PMID 15698135. doi:10.1016/0006-3002(55)90224-9. PMID 14363272.

[62] Hoffmann M, Wanko M, Strodel P, König PH, Frauen- [76] Sanger F (1949). “The terminal peptides of insulin”. Bio-
heim T, Schulten K, Thiel W, Tajkhorshid E, Elstner M chemical Journal 45 (5): 563–74. PMC 1275055. PMID
(2006). “Color tuning in rhodopsins: the mechanism for 15396627.
the spectral shift between bacteriorhodopsin and sensory
rhodopsin II”. Journal of the American Chemical Soci- [77] Muirhead H, Perutz M (1963). “Structure of hemoglobin.
ety 128 (33): 10808–18. doi:10.1021/ja062082i. PMID A three-dimensional fourier synthesis of reduced hu-
16910676. man hemoglobin at 5.5 Å resolution”. Nature 199
(4894): 633–38. Bibcode:1963Natur.199..633M.
[63] Brosnan J (June 2003). “Interorgan amino acid transport doi:10.1038/199633a0. PMID 14074546.
and its regulation”. Journal of Nutrition 133 (6 Suppl 1):
2068S–72S. PMID 12771367. [78] Kendrew J, Bodo G, Dintzis H, Parrish R, Wyckoff H,
Phillips D (1958). “A three-dimensional model of the
[64] Thomas Burr Osborne (1909): The Vegetable Proteins, myoglobin molecule obtained by X-ray analysis”. Nature
History pp 1 to 6, from archive.org 181 (4610): 662–66. Bibcode:1958Natur.181..662K.
doi:10.1038/181662a0. PMID 13517261.
[65] Bulletin des Sciences Physiques et Naturelles en Néer-
lande (1838). pg 104. SUR LA COMPOSITION DE [79] “RCSB Protein Data Bank”. Retrieved 2014-04-05.
QUELQUES SUBSTANCES ANIMALES
[80] Zhou ZH (2008). “Towards atomic resolution struc-
[66] Hartley, Harold. “Origin of the Word ‘Protein.’” Nature tural determination by single-particle cryo-electron mi-
168, no. 4267 (August 11, 1951): 244–244. doi:10.1038/ croscopy”. Current Opinion in Structural Biology 18 (2):
168244a0. 218–28. doi:10.1016/j.sbi.2008.03.004. PMC 2714865.
PMID 18403197.
[67] Perrett D (2007). “From 'protein' to the beginnings of
clinical proteomics”. Proteomics: Clinical Applications [81] Keskin O, Tuncbag N, Gursoy A (2008). “Char-
1 (8): 720–38. doi:10.1002/prca.200700525. PMID acterization and prediction of protein interfaces to
21136729. infer protein-protein interaction networks”. Cur-
rent Pharmaceutical Biotechnology 9 (2): 67–76.
[68] New Oxford Dictionary of English doi:10.2174/138920108783955191. PMID 18393863.
[69] Reynolds JA, Tanford C (2003). Nature’s Robots: A His-
tory of Proteins (Oxford Paperbacks). New York, New
York: Oxford University Press. p. 15. ISBN 0-19- 4.1.10 Textbooks
860694-X.
• Branden C, Tooze J (1999). Introduction to Protein
[70] Bischoff TLW, Voit, C (1860). Die Gesetze der Er- Structure. New York: Garland Pub. ISBN 0-8153-
naehrung des Pflanzenfressers durch neue Untersuchungen 2305-0.
festgestellt (in German). Leipzig, Heidelberg.
• Murray RF, Harper HW, Granner DK, Mayes PA,
[71] Sumner JB (1926). “The isolation and crystallization of
Rodwell VW (2006). Harper’s Illustrated Biochem-
the enzyme urease. Preliminary paper” (PDF). Journal of
Biological Chemistry 69 (2): 435–41. istry. New York: Lange Medical Books/McGraw-
Hill. ISBN 0-07-146197-3.
[72] Pauling L, Corey RB, Branson HR (1951). “The
structure of proteins: two hydrogen-bonded helical • Van Holde KE, Mathews CK (1996). Biochemistry.
configurations of the polypeptide chain” (PDF). Pro- Menlo Park, California: Benjamin/Cummings Pub.
ceedings of the National Academy of Sciences U.S.A. Co., Inc. ISBN 0-8053-3931-0.
4.2. AMINO ACID 87

4.1.11 External links

Databases and projects

• The Protein Naming Utility

• Human Protein Atlas

• NCBI Entrez Protein database

• NCBI Protein Structure database

• Human Protein Reference Database

The generic structure of an alpha amino acid in its un-ionized
form
• Human Proteinpedia

• Folding@Home (Stanford University)

• Comparative Toxicogenomics Database cu-

rates protein–chemical interactions, as well as
gene/protein–disease relationships and chemical-
disease relationships.

• Bioinformatic Harvester A Meta search engine (29

databases) for gene and protein information.

• Protein Databank in Europe (see also PDBeQuips,

short articles and tutorials on interesting PDB struc-
tures)

• Research Collaboratory for Structural Bioinformat-

ics (see also Molecule of the Month, presenting short
accounts on selected proteins from the PDB)

• Proteopedia – Life in 3D: rotatable, zoomable 3D

model with wiki annotations for every known pro-
tein molecular structure.
The 21 proteinogenic α-amino acids found in eukaryotes,
• UniProt the Universal Protein Resource grouped according to their side-chains’ pKa values and charges
carried at physiological pH 7.4
• neXtProt – Exploring the universe of human pro-
teins: human-centric protein knowledge resource
4.2 Amino acid
• Multi-Omics Profiling Expression Database:
MOPED human and model organism protein/gene
This article is about the class of chemicals. For the struc-
knowledge and expression data
tures and properties of the standard proteinogenic amino
acids, see Proteinogenic amino acid.
Amino acids (/əˈmiːnoʊ, ˈæmənoʊ, əˈmaɪnoʊ/) are
Tutorials and educational websites biologically important organic compounds composed of
amine (-NH2 ) and carboxylic acid (-COOH) functional
• “An Introduction to Proteins” from HOPES (Hunt- groups, along with a side-chain specific to each amino
ington’s Disease Outreach Project for Education at acid.[1][2][3] The key elements of an amino acid are
Stanford) carbon, hydrogen, oxygen, and nitrogen, though other
elements are found in the side-chains of certain amino
• Proteins: Biogenesis to Degradation – The Virtual acids. About 500 amino acids are known and can be
Library of Biochemistry and Cell Biology classified in many ways.[4] They can be classified accord-
88 CHAPTER 4. PROTEINS AND AMINO ACIDS

ing to the core structural functional groups’ locations as Because of their biological significance, amino acids
alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino are important in nutrition and are commonly used in
acids; other categories relate to polarity, pH level, and nutritional supplements, fertilizers, and food technol-
side-chain group type (aliphatic, acyclic, aromatic, con- ogy. Industrial uses include the production of drugs,
taining hydroxyl or sulfur, etc.). In the form of proteins, biodegradable plastics, and chiral catalysts.
amino acids comprise the second-largest component (wa-
ter is the largest) of human muscles, cells and other
tissues.[5] Outside proteins, amino acids perform critical 4.2.1 History
roles in processes such as neurotransmitter transport and
biosynthesis. The first few amino acids were discovered in the early
19th century. In 1806, French chemists Louis-Nicolas
In biochemistry, amino acids having both the amine
Vauquelin and Pierre Jean Robiquet isolated a compound
and the carboxylic acid groups attached to the first
in asparagus that was subsequently named asparagine,
(alpha-) carbon atom have particular importance. They
the first amino acid to be discovered.[21][22] Cystine was
are known as 2-, alpha-, or α-amino acids (generic
discovered in 1810,[23] although its monomer, cysteine,
formula H2 NCHRCOOH in most cases,[6] where R is
remained undiscovered until 1884.[22][24] Glycine and
an organic substituent known as a "side-chain");[7] of-
leucine were discovered in 1820.[25] The last of the 20
ten the term “amino acid” is used to refer specif-
common amino acids to be discovered was threonine
ically to these. They include the 23 proteinogenic
in 1935 by William Cumming Rose, who also deter-
(“protein-building”) amino acids,[8][9][10] which combine
mined the essential amino acids and established the min-
into peptide chains (“polypeptides”) to form the building-
imum daily requirements of all amino acids for optimal
blocks of a vast array of proteins.[11] These are all L-
growth.[26][27]
stereoisomers ("left-handed" isomers), although a few
D-amino acids (“right-handed”) occur in bacterial en- Usage of the term amino acid in the English language is
velopes and some antibiotics.[12] Twenty of the pro- from 1898.[28] Proteins were found to yield amino acids
teinogenic amino acids are encoded directly by triplet after enzymatic digestion or acid hydrolysis. In 1902,
codons in the genetic code and are known as “stan- Emil Fischer and Franz Hofmeister proposed that pro-
dard” amino acids. The other three (“non-standard” teins are the result of the formation of bonds between
or “non-canonical”) are selenocysteine (present in many the amino group of one amino acid with the carboxyl
noneukaryotes as well as most eukaryotes, but not coded group of another, in a linear structure that Fischer termed
directly by DNA), pyrrolysine (found only in some archea "peptide".[29]
and one bacterium) and N-formylmethionine (which is
often the initial amino acid of proteins in bacteria, mito-
chondria, and chloroplasts). Pyrrolysine and selenocys- 4.2.2 General structure
teine are encoded via variant codons; for example, se-
lenocysteine is encoded by stop codon and SECIS ele- Further information: Alpha carbon
ment.[13][14][15] Codon–tRNA combinations not found in
nature can also be used to “expand” the genetic code and In the structure shown at the top of the page, R represents
create novel proteins known as alloproteins incorporating a side-chain specific to each amino acid. The carbon atom
non-proteinogenic amino acids.[16][17][18] next to the carboxyl group (which is therefore numbered
Many important proteinogenic and non-proteinogenic 2 in the carbon chain starting from that functional group)
amino acids also play critical non-protein roles within is called the α–carbon. Amino acids containing an amino
the body. For example, in the human brain, gluta- group bonded directly to the alpha carbon are referred
mate (standard glutamic acid) and gamma-amino-butyric to as alpha amino acids.[30] These includes amino acids
acid (“GABA”, non-standard gamma-amino acid) are, re- such as proline which contain secondary amines, which
spectively, the main excitatory and inhibitory neurotrans- formerly were often referred to as “imino acids”.[31][32][33]
mitters;[19] hydroxyproline (a major component of the
connective tissue collagen) is synthesised from proline;
the standard amino acid glycine is used to synthesise por- Isomerism
phyrins used in red blood cells; and the non-standard
carnitine is used in lipid transport. The alpha amino acids are the most common form found
in nature, but only when occurring in the L-isomer. The
Nine proteinogenic amino acids are called “essential” alpha carbon is a chiral carbon atom, with the excep-
for humans because they cannot be created from other tion of glycine which has two indistinguishable hydrogen
compounds by the human body and, so, must be taken in atoms on the alpha carbon.[34] Therefore, all alpha amino
as food. Others may be conditionally essential for certain acids but glycine can exist in either of two enantiomers,
ages or medical conditions. Essential amino acids may called L or D amino acids, which are mirror images of
also differ between species.[20] each other (see also Chirality). While L-amino acids
represent all of the amino acids found in proteins dur-
4.2. AMINO ACID 89

1
COO
α 2
H3N C H
β 3
CH2
γ 4
CH2
δ 5
The two enantiomers of alanine, D-alanine and L-alanine CH2
ε 6
ing translation in the ribosome, D-amino acids are found
CH2
in some proteins produced by enzyme posttranslational
modifications after translation and translocation to the en- NH3
doplasmic reticulum, as in exotic sea-dwelling organisms
such as cone snails.[35] They are also abundant compo-
Lysine with the carbon atoms in the side-chain labeled
nents of the peptidoglycan cell walls of bacteria,[36] and
D-serine may act as a neurotransmitter in the brain.[37] D-
amino acids are used in racemic crystallography to create are non-linear; these are leucine, isoleucine, and valine.
centrosymmetric crystals, which (depending on the pro- Proline is the only proteinogenic amino acid whose side-
tein) may allow for easier and more robust protein struc- group links to the α-amino group and, thus, is also the
ture determination.[38] The L and D convention for amino only proteinogenic amino acid containing a secondary
acid configuration refers not to the optical activity of the amine at this position.[34] In chemical terms, proline is,
amino acid itself but rather to the optical activity of the therefore, an imino acid, since it lacks a primary amino
isomer of glyceraldehyde from which that amino acid can, group,[41] although it is still classed as an amino acid in
in theory, be synthesized (D-glyceraldehyde is dextroro- the current biochemical nomenclature,[42] and may also
tatory; L-glyceraldehyde is levorotatory). In alternative be called an “N-alkylated alpha-amino acid”.[43]
fashion, the (S) and (R) designators are used to indicate
the absolute stereochemistry. Almost all of the amino
acids in proteins are (S) at the α carbon, with cysteine Zwitterions
being (R) and glycine non-chiral.[39] Cysteine is unusual
since it has a sulfur atom at the second position in its side-
chain, which has a larger atomic mass than the groups 1 2
attached to the first carbon, which is attached to the α- H H
carbon in the other standard amino acids, thus the (R) O O
instead of (S). α α
H2N C C H3N C C
OH O
R R
Side chains

In amino acids that have a carbon chain attached to the

α–carbon (such as lysine, shown to the right) the car- An amino acid in its (1) un-ionized and (2) zwitterionic forms
bons are labeled in order as α, β, γ, δ, and so on.[40] In
some amino acids, the amine group is attached to the β The α-carboxylic acid group of amino acids is a weak
or γ-carbon, and these are therefore referred to as beta or acid, meaning that it releases a hydron (such as a proton)
gamma amino acids. at moderate pH values. In other words, carboxylic acid
groups (−CO2 H) can be deprotonated to become nega-
Amino acids are usually classified by the properties of tive carboxylates (−CO2 − ). The negatively charged car-
their side-chain into four groups. The side-chain can boxylate ion predominates at pH values greater than the
make an amino acid a weak acid or a weak base, and pKa of the carboxylic acid group (mean for the 20 com-
a hydrophile if the side-chain is polar or a hydrophobe mon amino acids is about 2.2, see the table of amino acid
if it is nonpolar.[34] The chemical structures of the 22 structures above). In a complementary fashion, the α-
standard amino acids, along with their chemical prop- amine of amino acids is a weak base, meaning that it ac-
erties, are described more fully in the article on these cepts a proton at moderate pH values. In other words,
proteinogenic amino acids. α-amino groups (NH2 −) can be protonated to become
The phrase "branched-chain amino acids" or BCAA positive α-ammonium groups (+ NH3 −). The positively
refers to the amino acids having aliphatic side-chains that charged α-ammonium group predominates at pH values
90 CHAPTER 4. PROTEINS AND AMINO ACIDS

less than the pKa of the α-ammonium group (mean for for Asp, Glu with negative side-chains, pI = ½(pKa1 +
the 20 common α-amino acids is about 9.4). pKaR), where pKaR is the side-chain pKa. Cysteine also
Because all amino acids contain amine and car- has potentially negative side-chain with pKaR = 8.14, so
boxylic acid functional groups, they share amphiprotic pI should be calculated as for Asp and Glu, even though
properties.[34] Below pH 2.2, the predominant form will the side-chain is not significantly charged at neutral pH.
have a neutral carboxylic acid group and a positive α- For His, Lys, and Arg with positive side-chains, pI =
ammonium ion (net charge +1), and above pH 9.4, a neg- ½(pKaR + pKa2 ). Amino acids have zero mobility in
ative carboxylate and neutral α-amino group (net charge electrophoresis at their isoelectric point, although this be-
haviour is more usually exploited for peptides and pro-
−1). But at pH between 2.2 and 9.4, an amino acid
usually contains both a negative carboxylate and a pos- teins than single amino acids. Zwitterions have minimum
solubility at their isoelectric point and some amino acids
itive α-ammonium group, as shown in structure (2) on
the right, so has net zero charge. This molecular state is (in particular, with non-polar side-chains) can be isolated
by precipitation from water by adjusting the pH to the
known as a zwitterion, from the German Zwitter mean-
ing hermaphrodite or hybrid. [44]
The fully neutral form required isoelectric point.
(structure (1) on the right) is a very minor species in aque-
ous solution throughout the pH range (less than 1 part in 4.2.3 Occurrence and functions in bio-
107 ). Amino acids exist as zwitterions also in the solid
phase, and crystallize with salt-like properties unlike typ-
chemistry
ical organic acids or amines.
Primary Protein Structure
is sequence of a chain of amino acids

Isoelectric point
Amino Acids

The variation in titration curves when the amino acids are

grouped by category can be seen here. With the excep-
tion of tyrosine, using titration to differentiate between Amino group
hydrophobic amino acids is problematic.
Acidic
carboxyl
R group group

A polypeptide is an unbranched chain of amino acids.

Proteinogenic amino acids

See also: Protein primary structure and Posttranslational

modification
Amino acids are the structural units (monomers) that
make up proteins. They join together to form short
polymer chains called peptides or longer chains called ei-
ther polypeptides or proteins. These polymers are linear
and unbranched, with each amino acid within the chain
attached to two neighboring amino acids. The process
Composite of Titration Curves Grouped by Side Chain
Category using applet http://cti.itc.virginia.edu/~{}cmg/Demo/
of making proteins is called translation and involves the
compareAA/compareAAApplet.html step-by-step addition of amino acids to a growing protein
chain by a ribozyme that is called a ribosome.[46] The or-
At pH values between the two pKa values, the zwitte- der in which the amino acids are added is read through the
rion predominates, but coexists in dynamic equilibrium genetic code from an mRNA template, which is a RNA
with small amounts of net negative and net positive ions. copy of one of the organism’s genes.
At the exact midpoint between the two pKa values, the Twenty-three amino acids are naturally incorporated
trace amount of net negative and trace of net positive ions into polypeptides and are called proteinogenic or natu-
exactly balance, so that average net charge of all forms ral amino acids.[34] Of these, 21 are encoded by the uni-
present is zero.[45] This pH is known as the isoelectric versal genetic code. The remaining 2, selenocysteine and
point pI, so pI = ½(pKa1 + pKa2 ). The individual amino pyrrolysine, are incorporated into proteins by unique syn-
acids all have slightly different pKa values, so have dif- thetic mechanisms. Selenocysteine is incorporated when
ferent isoelectric points. For amino acids with charged the mRNA being translated includes a SECIS element,
side-chains, the pKa of the side-chain is involved. Thus which causes the UGA codon to encode selenocysteine
4.2. AMINO ACID 91

Non-proteinogenic amino acids that are found in proteins

are formed by post-translational modification, which is
modification after translation during protein synthesis.
These modifications are often essential for the function or
regulation of a protein; for example, the carboxylation of
glutamate allows for better binding of calcium cations,[50]
and the hydroxylation of proline is critical for maintain-
ing connective tissues.[51] Another example is the forma-
tion of hypusine in the translation initiation factor EIF5A,
through modification of a lysine residue.[52] Such modifi-
cations can also determine the localization of the protein,
e.g., the addition of long hydrophobic groups can cause a
protein to bind to a phospholipid membrane.[53]

HSe
Some non-proteinogenic amino acids are not found
in proteins. Examples include lanthionine, 2-
aminoisobutyric acid, dehydroalanine, and the
neurotransmitter gamma-aminobutyric acid. Non-
proteinogenic amino acids often occur as intermediates
in the metabolic pathways for standard amino acids – for
OH example, ornithine and citrulline occur in the urea cycle,
H2N part of amino acid catabolism (see below).[54] A rare
exception to the dominance of α-amino acids in biology
is the β-amino acid beta alanine (3-aminopropanoic

O
acid), which is used in plants and microorganisms in the
synthesis of pantothenic acid (vitamin B5 ), a component
of coenzyme A.[55]
The amino acid selenocysteine
Non-standard amino acids
[47]
instead of a stop codon. Pyrrolysine is used by some
methanogenic archaea in enzymes that they use to pro- The 20 amino acids that are encoded directly by the
duce methane. It is coded for with the codon UAG, which codons of the universal genetic code are called standard
is normally a stop codon in other organisms.[48] This UAG or canonical amino acids. The others are called non-
codon is followed by a PYLIS downstream sequence.[49] standard or non-canonical. Most of the non-standard
amino acids are also non-proteinogenic (i.e. they cannot
be used to build proteins), but three of them are proteino-
Non-proteinogenic amino acids genic, as they can be used to build proteins by exploiting
information not encoded in the universal genetic code.

+ The three non-standard proteinogenic amino acids

β H3N β are selenocysteine (present in many noneukaryotes as
C H3 C H2
well as most eukaryotes, but not coded directly by
α α α α2 DNA), pyrrolysine (found only in some archea and one
CH CH bacterium), and N-formylmethionine (which is often the
α1
COO- COO-
+
H3N H initial amino acid of proteins in bacteria, mitochondria,
and chloroplasts). For example, 25 human proteins in-
L-α-alanine β-alanine clude selenocysteine (Sec) in their primary structure,[56]
and the structurally characterized enzymes (selenoen-
zymes) employ Sec as the catalytic moiety in their active
β-alanine and its α-alanine isomer
sites.[57] Pyrrolysine and selenocysteine are encoded via
variant codons. For example, selenocysteine is encoded
Main article: Non-proteinogenic amino acids
by stop codon and SECIS element.[13][14][15]

Aside from the 23 proteinogenic amino acids, there are

many other amino acids that are called non-proteinogenic. In human nutrition
Those either are not found in proteins (for example
carnitine, GABA) or are not produced directly and in Main article: Essential amino acids
isolation by standard cellular machinery (for example, Further information: Protein in nutrition and Amino
hydroxyproline and selenomethionine). acid synthesis
92 CHAPTER 4. PROTEINS AND AMINO ACIDS

• Arginine is a precursor of nitric oxide.[69]

When taken up into the human body from the diet, the • Ornithine and S-adenosylmethionine are precursors
22 standard amino acids either are used to synthesize of polyamines.[70]
proteins and other biomolecules or are oxidized to urea
and carbon dioxide as a source of energy.[58] The oxida- • Aspartate, glycine, and glutamine are precursors of
tion pathway starts with the removal of the amino group nucleotides.[71]
by a transaminase; the amino group is then fed into the • Phenylalanine is a precursor of various
urea cycle. The other product of transamidation is a phenylpropanoids, which are important in plant
keto acid that enters the citric acid cycle.[59] Glucogenic metabolism.
amino acids can also be converted into glucose, through
gluconeogenesis.[60] However, not all of the functions of other abundant non-
Pyrrolysine trait is restricted to several microbes, and standard amino acids are known.
only one organism has both Pyl and Sec. Of the 22 Some non-standard amino acids are used as defenses
standard amino acids, 9 are called essential amino acids against herbivores in plants.[72] For example, canavanine
because the human body cannot synthesize them from is an analogue of arginine that is found in many
other compounds at the level needed for normal growth, legumes,[73] and in particularly large amounts in
so they must be obtained from food.[61] In addition, Canavalia gladiata (sword bean).[74] This amino acid
cysteine, taurine, tyrosine, and arginine are considered protects the plants from predators such as insects and
semiessential amino-acids in children (though taurine is can cause illness in people if some types of legumes
not technically an amino acid), because the metabolic are eaten without processing.[75] The non-protein amino
pathways that synthesize these amino acids are not fully acid mimosine is found in other species of legume, in
developed.[62][63] The amounts required also depend on particular Leucaena leucocephala.[76] This compound
the age and health of the individual, so it is hard to is an analogue of tyrosine and can poison animals that
make general statements about the dietary requirement graze on these plants.
for some amino acids. Dietary exposure to the non-
standard amino acid BMAA has been linked to human
neurodegenerative diseases, including ALS.[64] 4.2.5 Uses in industry
(*) Essential only in certain cases.[65][66]
Amino acids are used for a variety of applications in in-
dustry, but their main use is as additives to animal feed.
This is necessary, since many of the bulk components of
4.2.4 Classification these feeds, such as soybeans, either have low levels or
lack some of the essential amino acids: Lysine, methion-
Although there are many ways to classify amino acids,
ine, threonine, and tryptophan are most important in the
these molecules can be assorted into six main groups, on
production of these feeds.[77] In this industry, amino acids
the basis of their structure and the general chemical char-
are also used to chelate metal cations in order to improve
acteristics of their R groups.
the absorption of minerals from supplements, which may
be required to improve the health or production of these
Non-protein functions animals.[78]
The food industry is also a major consumer of amino
Further information: Amino acid neurotransmitter acids, in particular, glutamic acid, which is used
as a flavor enhancer,[79] and Aspartame (aspartyl-
In humans, non-protein amino acids also have important phenylalanine-1-methyl ester) as a low-calorie artificial
roles as metabolic intermediates, such as in the biosyn- sweetener.[80] Similar technology to that used for an-
thesis of the neurotransmitter gamma-amino-butyric acid imal nutrition is employed in the human nutrition in-
(GABA). Many amino acids are used to synthesize other dustry to alleviate symptoms of mineral deficiencies,
molecules, for example: such as anemia, by improving mineral absorption and
reducing negative side effects from inorganic mineral
supplementation.[81]
• Tryptophan is a precursor of the neurotransmitter
serotonin.[67] The chelating ability of amino acids has been used in fer-
tilizers for agriculture to facilitate the delivery of min-
• Tyrosine (and its precursor phenylalanine) are erals to plants in order to correct mineral deficiencies,
precursors of the catecholamine neurotransmitters such as iron chlorosis. These fertilizers are also used to
dopamine, epinephrine and norepinephrine. prevent deficiencies from occurring and improving the
overall health of the plants.[82] The remaining produc-
• Glycine is a precursor of porphyrins such as tion of amino acids is used in the synthesis of drugs and
heme.[68] cosmetics.[77]
4.2. AMINO ACID 93

Expanded genetic code diapers and agriculture.[92] Due to its solubility and abil-
ity to chelate metal ions, polyaspartate is also being used
Main article: Expanded genetic code as a biodegradeable anti-scaling agent and a corrosion
inhibitor.[93][94] In addition, the aromatic amino acid
tyrosine is being developed as a possible replacement for
Since 2001, 40 non-natural amino acids have been
toxic phenols such as bisphenol A in the manufacture of
added into protein by creating a unique codon (recoding)
polycarbonates.[95]
and a corresponding transfer-RNA:aminoacyl – tRNA-
synthetase pair to encode it with diverse physicochemical
and biological properties in order to be used as a tool to 4.2.6 Reactions
exploring protein structure and function or to create novel
or enhanced proteins.[16][17] As amino acids have both a primary amine group and
a primary carboxyl group, these chemicals can undergo
most of the reactions associated with these functional
Nullomers
groups. These include nucleophilic addition, amide
bond formation, and imine formation for the amine
Main article: Nullomers
group, and esterification, amide bond formation, and
decarboxylation for the carboxylic acid group.[96] The
Nullomers are codons that in theory code for an amino combination of these functional groups allow amino acids
acid, however in nature there is a selective bias against to be effective polydentate ligands for metal-amino acid
using this codon in favor of another, for example bac- chelates.[97] The multiple side-chains of amino acids can
teria prefer to use CGA instead of AGA to code for also undergo chemical reactions.[98] The types of these re-
arginine.[86] This creates some sequences that do not ap- actions are determined by the groups on these side-chains
pear in the genome. This characteristic can be taken and are, therefore, different between the various types of
advantage of and used to create new selective cancer- amino acid.
fighting drugs[87] and to prevent cross-contamination of
DNA samples from crime-scene investigations.[88]

Chemical building blocks

Further information: Asymmetric synthesis The Strecker amino acid synthesis

Amino acids are important as low-cost feedstocks.

These compounds are used in chiral pool synthesis as Chemical synthesis
enantiomerically pure building-blocks.[89]
Main article: Peptide synthesis
Amino acids have been investigated as precursors chiral
catalysts, e.g., for asymmetric hydrogenation reactions,
although no commercial applications exist.[90] Several methods exist to synthesize amino acids. One of
the oldest methods begins with the bromination at the
α-carbon of a carboxylic acid. Nucleophilic substitu-
Biodegradable plastics tion with ammonia then converts the alkyl bromide to
the amino acid.[99] In alternative fashion, the Strecker
Further information: Biodegradable plastic and amino acid synthesis involves the treatment of an alde-
Biopolymer hyde with potassium cyanide and ammonia, this produces
an α-amino nitrile as an intermediate. Hydrolysis of the
[100]
Amino acids are under development as components of nitrile in acid then yields a α-amino acid. Using am-
a range of biodegradable polymers. These materials monia or ammonium salts in this reaction gives unsub-
have applications as environmentally friendly packag- stituted amino acids, whereas substituting primary and
[101]
ing and in medicine in drug delivery and the construc- secondary amines will yield substituted amino acids.
tion of prosthetic implants. These polymers include Likewise, using ketones, instead [102]
of aldehydes, gives
polypeptides, polyamides, polyesters, polysulfides, and α,α-disubstituted amino acids. The classical synthe-
polyurethanes with amino acids either forming part of sis gives racemic mixtures of α-amino acids as prod-
their main chains or bonded as side-chains. These ucts, but several alternative procedures using asymmetric
[103] [104][105]
modifications alter the physical properties and reactivi- auxiliaries or asymmetric catalysts have been
[106]
ties of the polymers. [91]
An interesting example of such developed.
materials is polyaspartate, a water-soluble biodegrad- At the current time, the most-adopted method is an
able polymer that may have applications in disposable automated synthesis on a solid support (e.g., polystyrene
94 CHAPTER 4. PROTEINS AND AMINO ACIDS

beads), using protecting groups (e.g., Fmoc and t-Boc) as activated units. These are added in sequence onto the
and activating groups (e.g., DCC and DIC). growing peptide chain, which is attached to a solid resin
support.[111] The ability to easily synthesize vast num-
bers of different peptides by varying the types and or-
Peptide bond formation der of amino acids (using combinatorial chemistry) has
made peptide synthesis particularly important in creat-
For more details on this topic, see Peptide bond.
ing libraries of peptides for use in drug discovery through
As both the amine and carboxylic acid groups of
high-throughput screening.[112]
Amino acid (1) Amino acid (2)

Biosynthesis

In plants, nitrogen is first assimilated into organic

compounds in the form of glutamate, formed from
N-terminus C-terminus
alpha-ketoglutarate and ammonia in the mitochondrion.
In order to form other amino acids, the plant uses
transaminases to move the amino group to another alpha-
Peptide bond
keto carboxylic acid. For example, aspartate amino-
transferase converts glutamate and oxaloacetate to alpha-
ketoglutarate and aspartate.[113] Other organisms use
transaminases for amino acid synthesis, too.
Water
Nonstandard amino acids are usually formed through
Dipeptide
modifications to standard amino acids. For exam-
ple, homocysteine is formed through the transsulfuration
The condensation of two amino acids to form a dipeptide pathway or by the demethylation of methionine via the in-
through a peptide bond
termediate metabolite S-adenosyl methionine,[114] while
hydroxyproline is made by a posttranslational modifica-
amino acids can react to form amide bonds, one amino
tion of proline.[115]
acid molecule can react with another and become joined
through an amide linkage. This polymerization of amino Microorganisms and plants can synthesize many uncom-
acids is what creates proteins. This condensation reac- mon amino acids. For example, some microbes make 2-
tion yields the newly formed peptide bond and a molecule aminoisobutyric acid and lanthionine, which is a sulfide-
of water. In cells, this reaction does not occur di- bridged derivative of alanine. Both of these amino acids
rectly; instead, the amino acid is first activated by at- are found in peptidic lantibiotics such as alamethicin.[116]
tachment to a transfer RNA molecule through an ester However, in plants, 1-aminocyclopropane-1-carboxylic
bond. This aminoacyl-tRNA is produced in an ATP- acid is a small disubstituted cyclic amino acid that is a
dependent reaction carried out by an aminoacyl tRNA key intermediate in the production of the plant hormone
synthetase.[107] This aminoacyl-tRNA is then a substrate ethylene.[117]
for the ribosome, which catalyzes the attack of the
amino group of the elongating protein chain on the es-
ter bond.[108] As a result of this mechanism, all proteins Catabolism
made by ribosomes are synthesized starting at their N-
terminus and moving toward their C-terminus. Amino acids must first pass out of organelles and cells
into blood circulation via amino acid transporters, since
However, not all peptide bonds are formed in this way. In the amine and carboxylic acid groups are typically ion-
a few cases, peptides are synthesized by specific enzymes. ized. Degradation of an amino acid, occurring in the liver
For example, the tripeptide glutathione is an essential and kidneys, often involves deamination by moving its
part of the defenses of cells against oxidative stress. amino group to alpha-ketoglutarate, forming glutamate.
This peptide is synthesized in two steps from free amino This process involves transaminases, often the same as
acids.[109] In the first step, gamma-glutamylcysteine syn- those used in amination during synthesis. In many verte-
thetase condenses cysteine and glutamic acid through a brates, the amino group is then removed through the urea
peptide bond formed between the side-chain carboxyl of cycle and is excreted in the form of urea. However, amino
the glutamate (the gamma carbon of this side-chain) and acid degradation can produce uric acid or ammonia in-
the amino group of the cysteine. This dipeptide is then stead. For example, serine dehydratase converts serine
condensed with glycine by glutathione synthetase to form to pyruvate and ammonia.[119] After removal of one or
glutathione.[110] more amino groups, the remainder of the molecule can
In chemistry, peptides are synthesized by a variety of re- sometimes be used to synthesize new amino acids, or it
actions. One of the most-used in solid-phase peptide syn- can be used for energy by entering glycolysis or the citric
thesis uses the aromatic oxime derivatives of amino acids acid cycle, as detailed in image at right.
4.2. AMINO ACID 95

ifications, when additional chemical groups are attached

to the amino acids in proteins. Some modifications
can produce hydrophobic lipoproteins,[121] or hydrophilic
glycoproteins.[122] These type of modification allow the
reversible targeting of a protein to a membrane. For
example, the addition and removal of the fatty acid
palmitic acid to cysteine residues in some signaling pro-
teins causes the proteins to attach and then detach from
cell membranes.[123]

Table of standard amino acid abbreviations and

properties
Catabolism of proteinogenic amino acids. Amino acids can be
classified according to the properties of their main products as Main article: Proteinogenic amino acid
either of the following:[118]
* Glucogenic, with the products having the ability to form glucose
Two additional amino acids are in some species coded for
by gluconeogenesis
* Ketogenic, with the products not having the ability to form glu-
by codons that are usually interpreted as stop codons:
cose. These products may still be used for ketogenesis or lipid In addition to the specific amino acid codes, placeholders
synthesis. are used in cases where chemical or crystallographic anal-
* Amino acids catabolized into both glucogenic and ketogenic ysis of a peptide or protein cannot conclusively determine
products. the identity of a residue.
Unk is sometimes used instead of Xaa, but is less stan-
4.2.7 Physicochemical properties of amino dard.
acids In addition, many non-standard amino acids have a spe-
cific code. For example, several peptide drugs, such
The 20 amino acids encoded directly by the ge- as Bortezomib and MG132, are artificially synthesized
netic code can be divided into several groups based and retain their protecting groups, which have specific
on their properties. Important factors are charge, codes. Bortezomib is Pyz-Phe-boroLeu, and MG132 is
hydrophilicity or hydrophobicity, size, and functional Z-Leu-Leu-Leu-al. To aid in the analysis of protein struc-
groups.[34] These properties are important for protein ture, photo-reactive amino acid analogs are available.
structure and protein–protein interactions. The water- These include photoleucine (pLeu) and photomethionine
soluble proteins tend to have their hydrophobic residues (pMet).[128]
(Leu, Ile, Val, Phe, and Trp) buried in the middle of the
protein, whereas hydrophilic side-chains are exposed to
the aqueous solvent. (Note that in biochemistry, a residue 4.2.8 See also
refers to a specific monomer within the polymeric chain
of a polysaccharide, protein or nucleic acid.) The integral • Amino acid dating
membrane proteins tend to have outer rings of exposed
hydrophobic amino acids that anchor them into the lipid • Beta-peptide
bilayer. In the case part-way between these two extremes,
some peripheral membrane proteins have a patch of hy- • Degron
drophobic amino acids on their surface that locks onto
the membrane. In similar fashion, proteins that have to • Erepsin
bind to positively charged molecules have surfaces rich
with negatively charged amino acids like glutamate and • Homochirality
aspartate, while proteins binding to negatively charged
molecules have surfaces rich with positively charged • Hyperaminoacidemia
chains like lysine and arginine. There are different
hydrophobicity scales of amino acid residues.[120] • Leucines
Some amino acids have special properties such as
• Miller–Urey experiment
cysteine, that can form covalent disulfide bonds to other
cysteine residues, proline that forms a cycle to the
• Proteinogenic amino acid
polypeptide backbone, and glycine that is more flexible
than other amino acids. • Table of codons, 3-nucleotide sequences that encode
Many proteins undergo a range of posttranslational mod- each amino acid
96 CHAPTER 4. PROTEINS AND AMINO ACIDS

4.2.9 References and notes [17] Wang Q, Parrish AR, Wang L (March 2009). “Expanding
the genetic code for biological studies”. Chem. Biol.
[1] “Amino”. Dictionary.com. 2015. Retrieved 2015-07-03. 16 (3): 323–36. doi:10.1016/j.chembiol.2009.03.001.
PMC 2696486. PMID 19318213.
[2] “amino acid”. Cambridge Dictionaries Online. Cambridge
University Press. 2015. Retrieved 2015-07-03. [18] Simon M (2005). Emergent computation: emphasiz-
ing bioinformatics. New York: AIP Press/Springer Sci-
[3] “amino”. FreeDictionary.com. Farlex. 2015. Retrieved ence+Business Media. pp. 105–106. ISBN 0-387-
2015-07-03. 22046-1.

[4] Wagner I, Musso H (November 1983). “New Nat- [19] Petroff OA (December 2002). “GABA and glutamate
urally Occurring Amino Acids”. Angewandte in the human brain”. Neuroscientist 8 (6): 562–573.
Chemie International Edition 22 (22): 816–28. doi:10.1177/1073858402238515. PMID 12467378.
doi:10.1002/anie.198308161.
[20] For example, ruminants such as cows obtain a number of
[5] Latham, Michael C. (1997). “Chapter 8. Body composi- amino acids via microbes in the first two stomach cham-
tion, the functions of food, metabolism and energy”. Hu- bers.
man nutrition in the developing world. Food and Nutrition
Series - No. 29. Rome: Food and Agriculture Organiza- [21] Vauquelin LN, Robiquet PJ (1806). “The discovery of
tion of the United Nations. a new plant principle in Asparagus sativus”. Annales de
Chimie 57: 88–93.
[6] Proline is an exception to this general formula. It lacks
the NH2 group because of the cyclization of the side-chain [22] Anfinsen CB, Edsall JT, Richards FM (1972). Advances
and is known as an imino acid; it falls under the category in Protein Chemistry. New York: Academic Press. pp.
of special structured amino acids. 99, 103. ISBN 978-0-12-034226-6.

[23] Wollaston WH (1810). “On cystic oxide, a new species of

[7] Clark, Jim (August 2007). “an introduction to amino
urinary calculus”. Philosophical Transactions of the Royal
acids”. chemguide. Retrieved 2015-07-04.
Society 100: 223–30. doi:10.1098/rstl.1810.0015.
[8] Jakubke, Hans-Dieter; Sewald, Norbert (2008). “Amino
[24] Baumann E (1884). "Über cystin und cystein”. Z Physiol
acids”. Peptides from A to Z: A Concise Encyclopedia.
Chemie 8 (4): 299–305. Archived from the original on 14
Germany: Wiley-VCH. p. 20. ISBN 9783527621170 –
March 2011. Retrieved 28 March 2011.
via Google Books.
[25] Braconnot HM (1820). “Sur la conversion des matières
[9] Pollegioni, Loredano; Servi, Stefano, eds. (2012).
animales en nouvelles substances par le moyen de l'acide
Unnatural Amino Acids: Methods and Protocols. Meth-
sulfurique”. Annales de Chimie et Physique. Série 2 13:
ods in Molecular Biology - Volume 794. Humana Press.
113–25.
p. v. ISBN 978-1-61779-331-8. OCLC 756512314.
[26] Robert D. Simoni, Robert L. Hill and Martha Vaughan
[10] Hertweck C (2011). “Biosynthesis and Charging of (September 13, 2002). “The Discovery of the Amino
Pyrrolysine, the 22nd Genetically Encoded Amino Acid”. Acid Threonine: the Work of William C. Rose”. Jour-
Angewandte Chemie International Edition 50 (41): 9540– nal of Biological Chemistry 277 (37): 56-58. PMID
1. doi:10.1002/anie.201103769. PMID 21796749. 12218068.
[11] “Chapter 1: Proteins are the Body’s Worker Molecules”. [27] McCoy, R. H., Meyer, C. E., and Rose, W. C. (1935).
The Structures of Life. National Institute of General Med- “Feeding Experiments with Mixtures of Highly Purified
ical Sciences. 27 October 2011. Retrieved 2008-05-20. Amino Acids. VIII. Isolation and Identification of a New
Essential Amino Acid”. Journal of Biological Chemistry
[12] Michal, Gerhard; Schomburg, Dietmar, eds. (2012). Bio-
112: 283–302.
chemical Pathways: An Atlas of Biochemistry and Molec-
ular Biology (2nd ed.). Wiley. p. 5. [28] “etymonline.com entry for amino". www.etymonline.
com. Retrieved 19 July 2010.
[13] Modeling Electrostatic Contributions to Protein Folding
and Binding – Tjong, p.1 footnote [29] Joseph S. Fruton (1990). “Chapter 5- Emil Fischer and
Franz Hofmeister”. Contrasts in Scientific Style: Research
[14] Frontiers in Drug Design and Discovery ed. Atta-Ur- Groups in the Chemical and Biochemical Sciences, 191.
Rahman & others, p.299 American Philosophical Society. pp. 163–165. ISBN
0-87169-191-4.
[15] Elzanowski A, Ostell J (7 April 2008). “The Genetic
Codes”. National Center for Biotechnology Information [30] “Alpha amino acid - Medical definition”. Merriam-
(NCBI). Retrieved 10 March 2010. Webster dictionary.
[16] Xie J, Schultz PG (December 2005). “Adding [31] Proline at the US National Library of Medicine Medical
amino acids to the genetic repertoire”. Cur- Subject Headings (MeSH)
rent Opinion in Chemical Biology 9 (6): 548–54.
doi:10.1016/j.cbpa.2005.10.011. PMID 16260173. [32] http://opbs.okstate.edu/5753/Amino%20Acids.html
4.2. AMINO ACID 97

[33] IUPAC, Compendium of Chemical Terminology, 2nd ed. [47] Driscoll DM, Copeland PR (2003). “Mech-
(the “Gold Book”) (1997). Online corrected version: anism and regulation of selenoprotein synthe-
(2006–) "Imino acids". sis”. Annual Review of Nutrition 23 (1): 17–40.
doi:10.1146/annurev.nutr.23.011702.073318. PMID
[34] Creighton, Thomas H. (1993). “Chapter 1”. Proteins: 12524431.
structures and molecular properties. San Francisco: W.
H. Freeman. ISBN 978-0-7167-7030-5. [48] Krzycki JA (December 2005). “The direct genetic en-
coding of pyrrolysine”. Current Opinion in Microbiology
[35] Pisarewicz K, Mora D, Pflueger FC, Fields GB, Marí F 8 (6): 706–12. doi:10.1016/j.mib.2005.10.009. PMID
(May 2005). “Polypeptide chains containing D-gamma- 16256420.
hydroxyvaline”. Journal of the American Chemical Soci-
ety 127 (17): 6207–15. doi:10.1021/ja050088m. PMID [49] Théobald-Dietrich A, Giegé R, Rudinger-Thirion J
15853325. (2005). “Evidence for the existence in mRNAs of a hair-
pin element responsible for ribosome dependent pyrroly-
[36] van Heijenoort J (March 2001). “Formation of the glycan sine insertion into proteins”. Biochimie 87 (9–10): 813–7.
chains in the synthesis of bacterial peptidoglycan”. Glyco- doi:10.1016/j.biochi.2005.03.006. PMID 16164991.
biology 11 (3): 25R–36R. doi:10.1093/glycob/11.3.25R.
PMID 11320055. [50] Vermeer C (March 1990). “Gamma-carboxyglutamate-
containing proteins and the vitamin K-dependent car-
[37] Wolosker H, Dumin E, Balan L, Foltyn VN (July 2008). boxylase”. The Biochemical Journal 266 (3): 625–36.
“D-amino acids in the brain: D-serine in neurotrans- PMC 1131186. PMID 2183788.
mission and neurodegeneration”. The FEBS Journal 275
(14): 3514–26. doi:10.1111/j.1742-4658.2008.06515.x. [51] Bhattacharjee A, Bansal M (March 2005). “Col-
PMID 18564180. lagen structure: the Madras triple helix and the
current scenario”. IUBMB Life 57 (3): 161–72.
[38] Matthews BW (2009). “Racemic crystallography—easy doi:10.1080/15216540500090710. PMID 16036578.
crystals and easy structures: What’s not to like?". Protein
Science 18 (6): 1135–1138. doi:10.1002/pro.125. PMC [52] Park MH (February 2006). “The post-translational
2774423. PMID 19472321. synthesis of a polyamine-derived amino acid, hypu-
sine, in the eukaryotic translation initiation factor 5A
[39] Hatem, Salama Mohamed Ali (2006). “Gas chromato- (eIF5A)". Journal of Biochemistry 139 (2): 161–
graphic determination of Amino Acid Enantiomers in to- 9. doi:10.1093/jb/mvj034. PMC 2494880. PMID
bacco and bottled wines”. University of Giessen. Re- 16452303.
trieved 17 November 2008.
[53] Blenis J, Resh MD (December 1993). “Subcellular lo-
[40] “Nomenclature and Symbolism for Amino Acids and Pep- calization specified by protein acylation and phosphory-
tides”. IUPAC-IUB Joint Commission on Biochemical lation”. Current Opinion in Cell Biology 5 (6): 984–9.
Nomenclature. 1983. Archived from the original on 9 doi:10.1016/0955-0674(93)90081-Z. PMID 8129952.
October 2008. Retrieved 17 November 2008.
[54] Curis E, Nicolis I, Moinard C, Osowska S, Zerrouk N,
[41] Jodidi, S. L. (1 March 1926). “The Formol Titration of Bénazeth S et al. (November 2005). “Almost all about
Certain Amino Acids”. Journal of the American Chemical citrulline in mammals”. Amino Acids 29 (3): 177–205.
Society 48 (3): 751–753. doi:10.1021/ja01414a033. doi:10.1007/s00726-005-0235-4. PMID 16082501.

[42] Liebecq, Claude, ed. (1992). Biochemical Nomenclature [55] Coxon KM, Chakauya E, Ottenhof HH, Whitney HM,
and Related Documents (2nd ed.). Portland Press. pp. Blundell TL, Abell C et al. (August 2005). “Pantothenate
39–69. ISBN 978-1-85578-005-7. biosynthesis in higher plants”. Biochemical Society Trans-
actions 33 (Pt 4): 743–6. doi:10.1042/BST0330743.
[43] Smith, Anthony D. (1997). Oxford dictionary of bio- PMID 16042590.
chemistry and molecular biology. Oxford: Oxford Uni-
versity Press. p. 535. ISBN 978-0-19-854768-6. OCLC [56] Kryukov GV, Castellano S, Novoselov SV, Lobanov
37616711. AV, Zehtab O, Guigó R et al. (2003). “Charac-
terization of mammalian selenoproteomes”. Science
[44] Simmons, William J.; Gerhard Meisenberg (2006). Prin- 300 (5624): 1439–1443. Bibcode:2003Sci...300.1439K.
ciples of medical biochemistry. Mosby Elsevier. p. 19. doi:10.1126/science.1083516. PMID 12775843.
ISBN 0-323-02942-6.
[57] Gromer, S., Urig, S., Becker, K. (2004) The Thioredoxin
[45] Fennema OR. Food Chemistry 3rd Ed. CRC Press. pp. System – From Science to Clinic. Medicinal Research
327–8. ISBN 0-8247-9691-8. Reviews. 24(1):40–89.

[46] Rodnina MV, Beringer M, Wintermeyer W (Jan- [58] Sakami W, Harrington H (1963). “Amino acid
uary 2007). “How ribosomes make peptide bonds”. metabolism”. Annual Review of Biochemistry 32 (1):
Trends in Biochemical Sciences 32 (1): 20–6. 355–98. doi:10.1146/annurev.bi.32.070163.002035.
doi:10.1016/j.tibs.2006.11.007. PMID 17157507. PMID 14144484.
98 CHAPTER 4. PROTEINS AND AMINO ACIDS

[59] Brosnan JT (April 2000). “Glutamate, at the interface [71] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L.
between amino acid and carbohydrate metabolism”. The (2002). Biochemistry. San Francisco: W.H. Freeman. pp.
Journal of Nutrition 130 (4S Suppl): 988S–90S. PMID 693–8. ISBN 0-7167-4684-0.
10736367.
[72] Hylin, John W. (1969). “Toxic peptides and amino acids
[60] Young VR, Ajami AM (September 2001). “Glutamine: in foods and feeds”. Journal of Agricultural and Food
the emperor or his clothes?". The Journal of Nutrition Chemistry 17 (3): 492–6. doi:10.1021/jf60163a003.
131 (9 Suppl): 2449S–59S; discussion 2486S–7S. PMID
[73] Turner BL, Harborne JB (1967). “Distribution of canava-
11533293.
nine in the plant kingdom”. Phytochemistry 6 (6): 863–66.
[61] Young VR (August 1994). “Adult amino acid require- doi:10.1016/S0031-9422(00)86033-1.
ments: the case for a major revision in current recommen-
[74] Ekanayake S, Skog K, Asp NG (May 2007). “Canava-
dations”. The Journal of Nutrition 124 (8 Suppl): 1517S–
nine content in sword beans (Canavalia gladiata): analysis
1523S. PMID 8064412.
and effect of processing”. Food and Chemical Toxicology
[62] Imura K, Okada A (January 1998). “Amino acid 45 (5): 797–803. doi:10.1016/j.fct.2006.10.030. PMID
metabolism in pediatric patients”. Nutrition 14 (1): 17187914.
143–8. doi:10.1016/S0899-9007(97)00230-X. PMID [75] Rosenthal GA (2001). “L-Canavanine: a higher plant in-
9437700. secticidal allelochemical”. Amino Acids 21 (3): 319–30.
[63] Lourenço R, Camilo ME (2002). “Taurine: a condition- doi:10.1007/s007260170017. PMID 11764412.
ally essential amino acid in humans? An overview in [76] Hammond AC (May 1995). “Leucaena toxicosis and its
health and disease”. Nutrición Hospitalaria 17 (6): 262– control in ruminants”. Journal of Animal Science 73 (5):
70. PMID 12514918. 1487–92. PMID 7665380.
[64] Holtcamp, W. (2012). “The emerging science of [77] Leuchtenberger W, Huthmacher K, Drauz K (Novem-
BMAA: do cyanobacteria contribute to neurodegener- ber 2005). “Biotechnological production of amino
ative disease?". Environmental health perspective 120 acids and derivatives: current status and prospects”.
(3). doi:10.1289/ehp.120-a110. PMC 3295368. PMID Applied Microbiology and Biotechnology 69 (1): 1–8.
22382274. doi:10.1007/s00253-005-0155-y. PMID 16195792.
[65] Fürst P, Stehle P (June 2004). “What are the essential [78] Ashmead, H. DeWayne (1993). The Role of Amino Acid
elements needed for the determination of amino acid re- Chelates in Animal Nutrition. Westwood: Noyes Publica-
quirements in humans?". The Journal of Nutrition 134 (6 tions.
Suppl): 1558S–1565S. PMID 15173430.
[79] Garattini S (April 2000). “Glutamic acid, twenty years
[66] Reeds PJ (July 2000). “Dispensable and indispensable later”. The Journal of Nutrition 130 (4S Suppl): 901S–
amino acids for humans”. The Journal of Nutrition 130 9S. PMID 10736350.
(7): 1835S–40S. PMID 10867060.
[80] Stegink LD (July 1987). “The aspartame story: a model
[67] Savelieva KV, Zhao S, Pogorelov VM, Rajan I, Yang for the clinical testing of a food additive”. The American
Q, Cullinan E et al. (2008). Bartolomucci A, Journal of Clinical Nutrition 46 (1 Suppl): 204–15. PMID
ed. “Genetic disruption of both tryptophan hydrox- 3300262.
ylase genes dramatically reduces serotonin and affects
behavior in models sensitive to antidepressants”. PloS [81] Albion Laboratories, Inc. “Albion Ferrochel Website”.
ONE 3 (10): e3301. Bibcode:2008PLoSO...3.3301S. Retrieved 12 July 2011.
doi:10.1371/journal.pone.0003301. PMC 2565062. [82] Ashmead, H. DeWayne (1986). Foliar Feeding of Plants
PMID 18923670. with Amino Acid Chelates. Park Ridge: Noyes Publica-
tions.
[68] Shemin D, Rittenberg D (1 December 1946). “The bio-
logical utilization of glycine for the synthesis of the pro- [83] Turner EH, Loftis JM, Blackwell AD (March
toporphyrin of hemoglobin”. Journal of Biological Chem- 2006). “Serotonin a la carte: supplementation
istry 166 (2): 621–5. PMID 20276176. with the serotonin precursor 5-hydroxytryptophan”.
Pharmacology & Therapeutics 109 (3): 325–38.
[69] Tejero J, Biswas A, Wang ZQ, Page RC, Haque MM,
doi:10.1016/j.pharmthera.2005.06.004. PMID
Hemann C et al. (November 2008). “Stabilization
16023217.
and characterization of a heme-oxy reaction interme-
diate in inducible nitric-oxide synthase”. The Jour- [84] Kostrzewa RM, Nowak P, Kostrzewa JP, Kostrzewa RA,
nal of Biological Chemistry 283 (48): 33498–507. Brus R (March 2005). “Peculiarities of L: -DOPA treat-
doi:10.1074/jbc.M806122200. PMC 2586280. PMID ment of Parkinson’s disease”. Amino Acids 28 (2): 157–
18815130. 64. doi:10.1007/s00726-005-0162-4. PMID 15750845.
[70] Rodríguez-Caso C, Montañez R, Cascante M, Sánchez- [85] Heby O, Persson L, Rentala M (August 2007). “Target-
Jiménez F, Medina MA (August 2006). “Mathematical ing the polyamine biosynthetic enzymes: a promising ap-
modeling of polyamine metabolism in mammals”. The proach to therapy of African sleeping sickness, Chagas’
Journal of Biological Chemistry 281 (31): 21799–812. disease, and leishmaniasis”. Amino Acids 33 (2): 359–66.
doi:10.1074/jbc.M602756200. PMID 16709566. doi:10.1007/s00726-007-0537-9. PMID 17610127.
4.2. AMINO ACID 99

[86] Cruz-Vera LR, Magos-Castro MA, Zamora-Romo E, [99] McMurry, John (1996). Organic chemistry. Pacific
Guarneros G (2004). “Ribosome stalling and peptidyl- Grove, CA, USA: Brooks/Cole. p. 1064. ISBN 0-534-
tRNA drop-off during translational delay at AGA 23832-7.
codons”. Nucleic Acid Research. 32 18 (15): 4462–
8. doi:10.1093/nar/gkh784. PMC 516057. PMID [100] Strecker, Adolph (1850). “Ueber die künstliche Bildung
15317870. der Milchsäure und einen neuen, dem Glycocoll homolo-
gen Körper”. Justus Liebigs Annalen der Chemie 75 (1):
[87] “Molecules 'too dangerous for nature' kill cancer cells”. 27–45. doi:10.1002/jlac.18500750103.
Retrieved 28 October 2012.
[101] Strecker, Adolph (1854). “Ueber einen neuen aus Alde-
[88] “Lethal DNA tags could keep innocent people out of jail”. hyd – Ammoniak und Blausäure entstehenden Körper”.
New Scientist. Retrieved 27 May 2013. Justus Liebigs Annalen der Chemie 91 (3): 349–51.
doi:10.1002/jlac.18540910309.
[89] Hanessian S (1993). “Reflections on the total synthesis
[102] Masumoto S, Usuda H, Suzuki M, Kanai M, Shibasaki
of natural products: Art, craft, logic, and the chiron ap-
M (May 2003). “Catalytic enantioselective Strecker re-
proach”. Pure and Applied Chemistry 65 (6): 1189–204.
action of ketoimines”. Journal of the American Chemical
doi:10.1351/pac199365061189.
Society 125 (19): 5634–5. doi:10.1021/ja034980. PMID
[90] Blaser, Hans Ulrich (1992). “The chiral pool as a source 12733893.
of enantioselective catalysts and auxiliaries”. Chemical [103] Davis FA, Reddy RE, Portonovo PS (1994). “Asymmet-
Reviews 92 (5): 935–52. doi:10.1021/cr00013a009. ric strecker synthesis using enantiopure sulfinimines: A
convenient synthesis of α-amino acids”. Tetrahedron Let-
[91] Sanda F, Endo T (1999). “Syntheses and
ters 35 (50): 9351. doi:10.1016/S0040-4039(00)78540-
functions of polymers based on amino acids”.
6.
Macromolecular Chemistry and Physics 200
(12): 2651–61. doi:10.1002/(SICI)1521- [104] Ishitani H, Komiyama S, Hasegawa Y, Kobayashi
3935(19991201)200:12<2651::AID- S (2000). “Catalytic Asymmetric Strecker Syn-
MACP2651>3.0.CO;2-P. thesis. Preparation of Enantiomerically Pure α-
Amino Acid Derivatives from Aldimines and Tributyltin
[92] Gross RA, Kalra B (2002). “Biodegradable Cyanide or Achiral Aldehydes, Amines, and Hydrogen
Polymers for the Environment”. Science 297 Cyanide Using a Chiral Zirconium Catalyst”. Jour-
(5582): 803–807. Bibcode:2002Sci...297..803G. nal of the American Chemical Society 122 (5): 762–6.
doi:10.1126/science.297.5582.803. PMID 12161646. doi:10.1021/ja9935207.
[93] Low, K. C.; Wheeler, A. P.; Koskan, L. P. (1996). Com- [105] Huang J, Corey EJ (2004). “A New Chiral Catalyst for the
mercial poly(aspartic acid) and Its Uses. Advances in Enantioselective Strecker Synthesis of α-Amino Acids”.
Chemistry Series 248. Washington, D.C.: American Orgic Letters 62 (6): 5027–9. doi:10.1021/ol047698w.
Chemical Society. PMID 15606127.

[94] Thombre SM, Sarwade BD (2005). “Synthesis and [106] Duthaler, Rudolf O. (1994). “Recent developments in the
Biodegradability of Polyaspartic Acid: A Critical Re- stereoselective synthesis of α-aminoacids”. Tetrahedron
view” (PDF). Journal of Macromolecular Science, Part A 50 (6): 1539–1650. doi:10.1016/S0040-4020(01)80840-
42 (9): 1299–1315. doi:10.1080/10601320500189604. 1.

[95] Bourke SL, Kohn J (2003). “Polymers derived from the [107] Ibba M, Söll D (May 2001). “The renaissance of
amino acid l-tyrosine: polycarbonates, polyarylates and aminoacyl-tRNA synthesis”. EMBO Reports 2 (5): 382–
copolymers with poly(ethylene glycol)". Advanced Drug 7. doi:10.1093/embo-reports/kve095. PMC 1083889.
Delivery Reviews 55 (4): 447–466. doi:10.1016/S0169- PMID 11375928.
409X(03)00038-3. PMID 12706045.
[108] Lengyel P, Söll D (June 1969). “Mechanism of protein
[96] Elmore, Donald Trevor; Barrett, G. C. (1998). Amino biosynthesis”. Bacteriological Reviews 33 (2): 264–301.
acids and peptides. Cambridge, UK: Cambridge Univer- PMC 378322. PMID 4896351.
sity Press. pp. 48–60. ISBN 0-521-46827-2. [109] Wu G, Fang YZ, Yang S, Lupton JR, Turner ND (March
2004). “Glutathione metabolism and its implications for
[97] Konara S, Gagnona K, Clearfield A, Thompson C, Har-
health”. The Journal of Nutrition 134 (3): 489–92. PMID
tle J, Ericson C et al. (2010). “Structural deter-
14988435.
mination and characterization of copper and zinc bis-
glycinates with X-ray crystallography and mass spectrom- [110] Meister A (November 1988). “Glutathione metabolism
etry”. Journal of Coordination Chemistry 63 (19): 3335– and its selective modification”. The Journal of Biological
47. doi:10.1080/00958972.2010.514336. Chemistry 263 (33): 17205–8. PMID 3053703.

[98] Gutteridge A, Thornton JM (November 2005). “Under- [111] Carpino, Louis A. (1992). “1-Hydroxy-7-
standing nature’s catalytic toolkit”. Trends in Biochemical azabenzotriazole. An efficient peptide coupling
Sciences 30 (11): 622–9. doi:10.1016/j.tibs.2005.09.006. additive”. Journal of the American Chemical Society 115
PMID 16214343. (10): 4397–8. doi:10.1021/ja00063a082.
 100 CHAPTER 4. PROTEINS AND AMINO ACIDS

[112] Marasco D, Perretta G, Sabatella M, Ruvo M (Octo- [125] Kyte J, Doolittle RF (May 1982). “A simple method
ber 2008). “Past and future perspectives of synthetic for displaying the hydropathic character of a pro-
peptide libraries”. Current Protein & Peptide Science 9 tein”. Journal of Molecular Biology 157 (1): 105–32.
(5): 447–67. doi:10.2174/138920308785915209. PMID doi:10.1016/0022-2836(82)90515-0. PMID 7108955.
18855697.
[126] Freifelder, D. (1983). Physical Biochemistry (2nd ed.).
[113] Jones, Russell Celyn; Buchanan, Bob B.; Gruissem, Wil- W. H. Freeman and Company. ISBN 0-7167-1315-2.
helm (2000). Biochemistry & molecular biology of plants.
Rockville, Md: American Society of Plant Physiologists. [127] http://bcs.whfreeman.com/lehninger6e/#824263_
pp. 371–2. ISBN 0-943088-39-9. _839438__

[114] Brosnan JT, Brosnan ME (June 2006). “The sulfur- [128] Suchanek M, Radzikowska A, Thiele C (April 2005).
containing amino acids: an overview”. The Journal of “Photo-leucine and photo-methionine allow identification
Nutrition 136 (6 Suppl): 1636S–1640S. PMID 16702333. of protein-protein interactions in living cells”. Nature
Methods 2 (4): 261–7. doi:10.1038/nmeth752. PMID
[115] Kivirikko KI, Pihlajaniemi T (1998). “Collagen hy- 15782218.
droxylases and the protein disulfide isomerase subunit
of prolyl 4-hydroxylases”. Advances in Enzymology and
Related Areas of Molecular Biology. Advances in En-
zymology - and Related Areas of Molecular Biology
4.2.10 Further reading
72: 325–98. doi:10.1002/9780470123188.ch9. ISBN
9780470123188. PMID 9559057.
• Tymoczko, John L. (2012). “Protein Composi-
tion and Structure”. Biochemistry. New York: W.
[116] Whitmore L, Wallace BA (May 2004). “Analysis of H. Freeman and company. pp. 28–31. ISBN
peptaibol sequence composition: implications for in vivo 9781429229364.
synthesis and channel formation”. European Biophysics
Journal 33 (3): 233–7. doi:10.1007/s00249-003-0348-1. • Doolittle, Russell F. (1989). “Redundancies in pro-
PMID 14534753. tein sequences”. In Fasman, G.D. Predictions of
[117] Alexander L, Grierson D (October 2002). “Ethylene
Protein Structure and the Principles of Protein Con-
biosynthesis and action in tomato: a model for climacteric formation. New York: Plenum Press. pp. 599–623.
fruit ripening”. Journal of Experimental Botany 53 (377): ISBN 978-0-306-43131-9. LCCN 89008555.
2039–55. doi:10.1093/jxb/erf072. PMID 12324528.
• Nelson, David L.; Cox, Michael M. (2000).
[118] Stipanuk, M. H. (2006). Biochemical, physiological, & Lehninger Principles of Biochemistry (3rd ed.).
molecular aspects of human nutrition (2 ed.): Saunders Worth Publishers. ISBN 978-1-57259-153-0.
Elsevier. LCCN 99049137.
[119] Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L.
• Meierhenrich, Uwe (2008). Amino acids and
(2002). Biochemistry. San Francisco: W.H. Freeman. pp.
639–49. ISBN 0-7167-4684-0.
the asymmetry of life (PDF, 11.2 MB). Berlin:
Springer Verlag. ISBN 978-3-540-76885-2. LCCN
[120] Urry DW (2004). “The change in Gibbs free energy 2008930865.
for hydrophobic association: Derivation and evaluation
by means of inverse temperature transitions”. Chemical • Morelli, Robert J. (1952). Studies of amino acid ab-
Physics Letters 399 (1–3): 177–83. doi:10.1016/S0009- sorption from the small intestine. San Francisco.
2614(04)01565-9.

[121] Magee T, Seabra MC (April 2005). “Fatty acy-

lation and prenylation of proteins: what’s hot in
4.2.11 External links
fat”. Current Opinion in Cell Biology 17 (2): 190–6.
doi:10.1016/j.ceb.2005.02.003. PMID 15780596. • The origin of the single-letter code for the amino
acids
[122] Pilobello KT, Mahal LK (June 2007). “Deciphering
the glycocode: the complexity and analytical challenge
of glycomics”. Current Opinion in Chemical Biology 11
(3): 300–5. doi:10.1016/j.cbpa.2007.05.002. PMID 4.3 Properties of the twenty amino
17500024. acids
[123] Smotrys JE, Linder ME (2004). “Palmitoylation of
intracellular signaling proteins: regulation and func- Proteinogenic amino acids are amino acids that are pre-
tion”. Annual Review of Biochemistry 73 (1): 559– cursors to proteins, and are incorporated into proteins co-
87. doi:10.1146/annurev.biochem.73.011303.073954. translationally — that is, during translation.[1] There are
PMID 15189153. 22 proteinogenic amino acids in prokaryotes, but only
[124] Hausman, Robert E.; Cooper, Geoffrey M. (2004). The 21 are encoded by the nuclear genes of eukaryotes. Of
cell: a molecular approach. Washington, D.C: ASM the 22, pyrrolysine (O/Pyl) is incorporated into proteins
Press. p. 51. ISBN 0-87893-214-3. by distinct post-translational biosynthetic mechanisms, all
4.3. PROPERTIES OF THE TWENTY AMINO ACIDS 101

Amine on α-carbon 4.3.1 Structures

All amino acids The following illustrates the structures and abbreviations
of the 21 amino acids that are directly encoded for protein
One (or two)
hydrogen(s) synthesis by the genetic code of eukaryotes. The struc-
on α-carbon
D-stereo- L-stereo-
tures given below are standard chemical structures, not
isomers isomers the typical zwitterion forms that exist in aqueous solu-
tions.
20 3
Encoded Special
Added in Post-
Non-ribosomal translationally
Proteinogenic AAs added AAs
peptides
(Added during
translational)

Proteinogenic amino acids are a small fraction of all amino acids

the other 21 are directly encoded by the genetic code, in-

cluding selenocysteine (U/Sec), that uses a special case of
insertion during the translational incorporation, but that is
not considered a posttranslational modification . Humans
can synthesize 11 of these 20 from each other or from
other molecules of intermediary metabolism. The other 9
must be consumed (usually as their protein derivatives) in
the diet and so are thus called essential amino acids. The
essential amino acids are histidine, isoleucine, leucine,
lysine, methionine, phenylalanine, threonine, tryptophan,
and valine (i.e. H I L K M F T W V).
The word proteinogenic means “protein building”. Pro-
teinogenic amino acids can be condensed into a
polypeptide (the subunit of a protein) through a process Grouped table of 21 amino acids’ structures, nomenclature, and
called translation (the second stage of protein biosynthe- their side groups’ pKa values.
sis, part of the overall process of gene expression).
In contrast, non-proteinogenic amino acids are ei-
ther not incorporated in proteins (like GABA, L- • L-Alanine
DOPA, or triiodothyronine), or are not produced di- (Ala / A)
rectly and in isolation by standard cellular machinery (like
hydroxyproline and selenomethionine). The latter often • L-Arginine
results from posttranslational modification of proteins. (Arg / R)
The proteinogenic amino acids have been found to be re- • L-Asparagine
lated to the set of amino acids that can be recognized (Asn / N)
by ribozyme auto-aminoacylation systems.[2] Thus, non-
proteinogenic amino acids would have been excluded by • L-Aspartic acid
the contingent evolutionary success of nucleotide-based (Asp / D)
life forms. Other reasons have been offered to ex-
plain why certain specific non-proteinogenic amino acids • L-Cysteine
are not generally incorporated into proteins: for exam- (Cys / C)
ple, ornithine and homoserine cyclize against the peptide
backbone and fragment the protein with relatively short • L-Glutamic acid
half-lives, while others are toxic because they can be mis- (Glu / E)
takenly incorporated into proteins, such as the arginine
• L-Glutamine
analog canavanine.
(Gln / Q)
Non-proteinogenic amino acids are incorporated in
nonribosomal peptides, which are not produced by the • Glycine
ribosome during translation. (Gly / G)
102 CHAPTER 4. PROTEINS AND AMINO ACIDS

• L-Histidine 4.3.3 Chemical properties

(His / H)
Following is a table listing the one-letter symbols, the
• L-Isoleucine three-letter symbols, and the chemical properties of the
(Ile / I) side-chains of the standard amino acids. The masses
listed are based on weighted averages of the elemental
• L-Leucine
isotopes at their natural abundances. Note that forming
(Leu / L)
a peptide bond results in elimination of a molecule of
• L-Lysine water, so the mass of an amino acid unit within a protein
(Lys / K) chain is reduced by 18.01524 Da.
General chemical properties
• L-Methionine
(Met / M)

• L-Phenylalanine Side chain properties

(Phe / F)
Note: The pKa values of amino acids are typically slightly
• L-Proline different when the amino acid is inside a protein. Protein
(Pro / P) pKa calculations are sometimes used to calculate the
change in the pKa value of an amino acid in this situa-
• L-Serine
tion.
(Ser / S)

• L-Threonine
(Thr / T) Gene expression and biochemistry

• L-Tryptophan * UAG is normally the amber stop codon, but encodes

(Trp / W) pyrrolysine if a PYLIS element is present.
** UGA is normally the opal (or umber) stop codon, but
• L-Tyrosine encodes selenocysteine if a SECIS element is present.
(Tyr / Y) † The stop codon is not an amino acid, but is included for
• L-Valine completeness.
(Val / V) †† UAG and UGA do not always act as stop codons (see
above).
‡ An essential amino acid cannot be synthesized in hu-
IUPAC/IUBMB now also recommends standard abbre- mans and must, therefore, be supplied in the diet. Con-
viations for the following two amino acids: ditionally essential amino acids are not normally required
in the diet, but must be supplied exogenously to specific
• L-Selenocysteine populations that do not synthesize it in adequate amounts.
(Sec / U)

• L-Pyrrolysine Mass spectrometry

(Pyl / O)
In mass spectrometry of peptides and proteins, it is use-
ful to know the masses of the residues. The mass of the
4.3.2 Non-specific abbreviations
peptide or protein is the sum of the residue masses plus
the mass of water.[3]
Sometimes the specific identity of an amino acid cannot
be determined unambiguously. Certain protein sequenc- § Monoisotopic mass
ing techniques do not distinguish among certain pairs.
Thus, the following codes are used:
Stoichiometry and metabolic cost in cell
• Asx (B) is "asparagine or aspartic acid"
Following table lists the abundance of amino acids in
• Glx (Z) is "glutamic acid or glutamine" E.coli cell and the metabolic cost (ATP) for synthesis the
amino acids. Negative numbers indicate the metabolic
• Xle (J) is "leucine or isoleucine" processes are energy favorable and do not cost net ATP
of the cell.[4] Note that the abundance of amino acids
In addition, the symbol X is used to indicate an amino include amino acids in free-form and in polymerization
acid that is completely unidentified. form (proteins).
4.4. MYOGLOBIN 103

Remarks [4] Physical Biology of the Cell (Garland Science) p. 178

[5] Chapter 20 (Amino Acid Degradation and Synthesis) in:

Catabolism
Denise R., PhD. Ferrier. Lippincott’s Illustrated Reviews:
Biochemistry (Lippincott’s Illustrated Reviews). Hagerst-
won, MD: Lippincott Williams & Wilkins. ISBN 0-7817-
2265-9.

• Nelson, David L.; Cox, Michael M. (2000).

Lehninger Principles of Biochemistry (3rd ed.).
Worth Publishers. ISBN 1-57259-153-6.
• Kyte, J.; Doolittle, R. F. (1982). “A simple
method for displaying the hydropathic character
of a protein”. J. Mol. Biol. 157 (1): 105–
132. doi:10.1016/0022-2836(82)90515-0. PMID
7108955.
• Meierhenrich, Uwe J. (2008). Amino acids and the
Amino acids can be classified according to the properties of asymmetry of life (1st ed.). Springer. ISBN 978-3-
their main products as either of the following:[5] 540-76885-2.
• Biochemistry, Harpers (2015). Harpers Illustrated
• Glucogenic, with the products having the ability to form
Biochemistry (30st ed.). Lange. ISBN 978-0-07-
glucose by gluconeogenesis
182534-4.
• Ketogenic, with the products not having the ability to form
glucose. These products may still be used for ketogenesis or
lipid synthesis. 4.3.6 See also
• Amino acids catabolized into both glucogenic and ketogenic
products. • Glucogenic amino acid
• Ketogenic amino acid

4.3.4 Life based on alternative proteino-

genic sets 4.4 Myoglobin
The proteinogenic set used by known life on Earth ap- Myoglobin is an iron- and oxygen-binding protein found
pears to be arbitrarily selected by evolution, according in the muscle tissue of vertebrates in general and in almost
to current knowledge, from many hundreds of possi- all mammals. It is related to hemoglobin, which is the
ble alpha-type amino acids. Xenobiology studies hypo- iron- and oxygen-binding protein in blood, specifically in
thetical life forms that could be constructed using alter- the red blood cells. In humans, myoglobin is only found
native sets using expanded genetic codes. Miller type in the bloodstream after muscle injury. It is an abnormal
experiments on artificial abiogenesis show that alpha- finding, and can be diagnostically relevant when found in
type amino acids predominate in water-based 'primordial blood. [2]
soups’ but beta-type amino acids dominate when there is
Myoglobin is the primary oxygen-carrying pigment of
less water. Both alpha- and beta-based sets could form
muscle tissues.[3] High concentrations of myoglobin in
the basis for alternative protein constructions and life
muscle cells allow organisms to hold their breath for a
forms.
longer period of time. Diving mammals such as whales
and seals have muscles with particularly high abundance
4.3.5 References of myoglobin.[2] Myoglobin is found in Type I muscle,
Type II A and Type II B, but most texts consider myo-
[1] Ambrogelly A, Palioura S, Söll D (Jan 2007). “Natural globin not to be found in smooth muscle.
expansion of the genetic code”. Nat Chem Biol 3 (1): 29–
35. doi:10.1038/nchembio847. PMID 17173027.
Myoglobin was the first protein to have its three-
dimensional structure revealed by X-ray crystallogra-
[2] Erives A (2011). “A Model of Proto-Anti-Codon RNA phy.[4] This achievement was reported in 1958 by John
Enzymes Requiring L-Amino Acid Homochirality”. J Kendrew and associates.[5] For this discovery, John
Molecular Evolution 73: 10–22. doi:10.1007/s00239- Kendrew shared the 1962 Nobel Prize in chemistry with
011-9453-4. PMC 3223571. PMID 21779963.
Max Perutz.[6] Despite being one of the most studied pro-
[3] “The amino acid masses”. ExPASy. Retrieved 2009-01- teins in biology, its physiological function is not yet con-
06. clusively established: mice genetically engineered to lack
104 CHAPTER 4. PROTEINS AND AMINO ACIDS

myoglobin are viable, but showed a 30% reduction in vol-

ume of blood being pumped by the heart during a con-
traction. They adapted to this deficiency through natu-
ral reactions to inadequate oxygen supply (hypoxia) and
a widening of blood vessels (vasodilation).[7] In humans
myoglobin is encoded by the MB gene.[8]

4.4.1 Meat color

Myoglobin contains hemes, pigments responsible for the
color of red meat. The color that meat takes is partly de-
termined by the degree of oxidation of the myoglobin.
In fresh meat the iron atom is the ferrous state bound to a
dioxygen molecule (O2 ). Meat cooked well done is brown
because the iron atom is now in the ferric (+3) oxidation
state, having lost an electron. If meat has been exposed to
nitrites, it will remain pink because the iron atom is bound
to NO, nitric oxide (true of, e.g., corned beef or cured Molecular orbital description of Fe-O2 interaction in
hams). Grilled meats can also take on a pink "smoke ring" myoglobin.[14]
that comes from the iron binding to a molecule of carbon
monoxide.[9] Raw meat packed in a carbon monoxide at-
mosphere also shows this same pink “smoke ring” due directly to iron, and a distal histidine group (His-65) hov-
to the same principles. Notably, the surface of this raw ers near the opposite face.[15] The distal imidazole is not
meat also displays the pink color, which is usually asso- bonded to the iron but is available to interact with the sub-
ciated in consumers’ minds with fresh meat. This artifi- strate O2 . This interaction encourages the binding of O2 ,
cially induced pink color can persist, reportedly up to one but not carbon monoxide (CO), which still binds about
year.[10] Hormel and Cargill are both reported to use this 240× more strongly than O2 .
meat-packing process, and meat treated this way has been The binding of O2 causes substantial structural change at
in the consumer market since 2003.[11] the Fe center, which shrinks in radius and moves into the
center of N4 pocket. O2 -binding induces “spin-pairing":
the five-coordinate ferrous deoxy form is high spin and
4.4.2 Role in disease the six coordinate oxy form is low spin and diamagnetic.
Myoglobin is released from damaged muscle tissue
(rhabdomyolysis), which has very high concentrations of 4.4.4 Synthetic analogues
myoglobin. The released myoglobin is filtered by the
kidneys but is toxic to the renal tubular epithelium and so Many models of myoglobin have been synthesized as part
may cause acute renal failure.[12] It is not the myoglobin of a broad interest in transition metal dioxygen com-
itself that is toxic (it is a protoxin) but the ferrihemate plexes. A well known example is the picket fence por-
portion that is dissociated from myoglobin in acidic envi- phyrin, which consists of a ferrous complex of a steri-
ronments (e.g., acidic urine, lysosomes). cally bulky derivative of tetraphenylporphyrin.[16] In the
Myoglobin is a sensitive marker for muscle injury, mak- presence of an imidazole ligand, this ferrous complex re-
ing it a potential marker for heart attack in patients versibly binds O2 . The O2 substrate adopts a bent ge-
with chest pain.[13] However, elevated myoglobin has low ometry, occupying the sixth position of the iron cen-
specificity for acute myocardial infarction (AMI) and thus ter. A key property of this model is the slow formation
CK-MB, cTnT, ECG, and clinical signs should be taken of the μ-oxo dimer, which is an inactive diferric state.
into account to make the diagnosis. In nature, such deactivation pathways are suppressed by
protein matrix that prevents close approach of the Fe-
porphyrin assemblies.[17]
4.4.3 Structure and bonding
Myoglobin belongs to the globin superfamily of proteins, 4.4.5 See also
and as with other globins, consists of eight alpha helices
connected by loops. Human globin contains 154 amino • Cytoglobin
acids.[15]
• Hemoglobin
Myoglobin contains a porphyrin ring with an iron at its
center. A proximal histidine group (His-94) is attached • Hemoprotein
4.4. MYOGLOBIN 105

[10] Fraqueza MJ, Barreto AS (September 2011). “Gas

mixtures approach to improve turkey meat shelf life
under modified atmosphere packaging: the effect of
carbon monoxide”. Poult. Sci. 90 (9): 2076–84.
doi:10.3382/ps.2011-01366. PMID 21844276.

[11] Associated Press (2007-10-30). “Meat companies defend

use of carbon monoxide”. Business. Minneapolis Star Tri-
bune.

[12] Naka T, Jones D, Baldwin I, Fealy N, Bates S, Goehl

H, Morgera S, Neumayer HH, Bellomo R (April 2005).
“Myoglobin clearance by super high-flux hemofiltration
A picket-fence porphyrin complex of Fe, with axial coordination
in a case of severe rhabdomyolysis: a case report”. Crit
sites occupied by methylimidazole (green) and dioxygen. The R
Care 9 (2): R90–5. doi:10.1186/cc3034. PMC 1175920.
groups flank the O2 -binding site. PMID 15774055.

[13] Weber M, Rau M, Madlener K, Elsaesser A, Bankovic

• Neuroglobin D, Mitrovic V, Hamm C (November 2005). “Diagnos-
tic utility of new immunoassays for the cardiac markers
cTnI, myoglobin and CK-MB mass”. Clin. Biochem. 38
4.4.6 References (11): 1027–30. doi:10.1016/j.clinbiochem.2005.07.011.
PMID 16125162.
[1] PDB: 1MBO ; Takano T (March 1977). “Structure of
myoglobin refined at 2.0 Å resolution. II. Structure of de- [14] Drago RS (1980). “Free radical reactions of transition
oxymyoglobin from sperm whale”. J. Mol. Biol. 110 (3): metal systems”. Coordination Chemistry Reviews 32 (2):
569–84. doi:10.1016/S0022-2836(77)80112-5. PMID 97–110. doi:10.1016/S0010-8545(00)80372-0.
845960. [15] UniProt: P02144
[2] Nelson DL, Cox MM (2000). Lehninger Principles of Bio- [16] Collman JP, Brauman JI, Halbert TR, Suslick KS (Octo-
chemistry (3rd ed.). New York: Worth Publishers. p. ber 1976). “Nature of O2 and CO binding to metallopor-
206. ISBN 0-7167-6203-X. (Google books link is the phyrins and heme proteins”. Proc. Natl. Acad. Sci. U.S.A.
2008 edition) 73 (10): 3333–7. Bibcode:1976PNAS...73.3333C.
doi:10.1073/pnas.73.10.3333. PMC 431107. PMID
[3] Ordway GA, Garry DJ (September 2004). “Myoglobin: 1068445.
an essential hemoprotein in striated muscle”. J. Exp. Biol.
207 (Pt 20): 3441–6. doi:10.1242/jeb.01172. PMID [17] Lippard SJ, Berg JM (1994). Principles of Bioinorganic
15339940. Chemistry. Mill Valley, CA: University Science Books.
ISBN 0-935702-73-3.
[4] (U.S.) National Science Foundation: Protein Data Bank
Chronology (Jan. 21, 2004). Retrieved 3.17.2010
4.4.7 Further reading
[5] Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyck-
off H, Phillips DC (1958). “A Three-Dimensional
• Collman JP, Boulatov R, Sunderland CJ, Fu
Model of the Myoglobin Molecule Obtained by
X-Ray Analysis”. Nature 181 (4610): 662–6. L (February 2004). “Functional analogues
Bibcode:1958Natur.181..662K. doi:10.1038/181662a0. of cytochrome c oxidase, myoglobin, and
PMID 13517261. hemoglobin”. Chem. Rev. 104 (2): 561–88.
doi:10.1021/cr0206059. PMID 14871135.
[6] The Nobel Prize in Chemistry 1962
• Reeder BJ, Svistunenko DA, Cooper CE, Wilson
[7] Mammen PP, Kanatous SB, Yuhanna IS, Shaul PW, MT (December 2004). “The radical and redox
Garry MG, Balaban RS, Garry DJ (2003). “Hypoxia- chemistry of myoglobin and hemoglobin: from in
induced left ventricular dysfunction in myoglobin- vitro studies to human pathology”. Antioxid. Redox
deficient mice”. American Journal of Physiology. Signal. 6 (6): 954–66. doi:10.1089/ars.2004.6.954.
Heart and Circulatory Physiology 285 (5): H2132–41. PMID 15548893.
doi:10.1152/ajpheart.00147.2003. PMID 12881221.
• Schlieper G, Kim JH, Molojavyi A, Jacoby C,
[8] Akaboshi E (1985). “Cloning of the human myo-
Laussmann T, Flögel U, Gödecke A, Schrader J
globin gene”. Gene 33 (3): 241–9. doi:10.1016/0378-
(April 2004). “Adaptation of the myoglobin knock-
1119(85)90231-8. PMID 2989088.
out mouse to hypoxic stress”. Am. J. Phys-
[9] McGee H (2004). On Food and Cooking: The Science and iol. Regul. Integr. Comp. Physiol. 286
Lore of the Kitchen. New York: Scribner. p. 148. ISBN (4): R786–92. doi:10.1152/ajpregu.00043.2003.
0-684-80001-2. PMID 14656764.
106 CHAPTER 4. PROTEINS AND AMINO ACIDS

• Takano T (1977). “Structure of myoglobin refined iron-containing oxygen-transport metalloprotein in the

at 2.0 Å resolution. II. Structure of deoxymyoglobinred blood cells of all vertebrates[1] (with the exception of
from sperm whale”. J. Mol. Biol. 110 (3): 569– the fish family Channichthyidae[2] ) as well as the tissues
584. doi:10.1016/S0022-2836(77)80112-5. PMID of some invertebrates. Hemoglobin in the blood carries
845960. oxygen from the respiratory organs (lungs or gills) to the
rest of the body (i.e. the tissues). There it releases the
• Roy A, Sen S, Chakraborti AS (February 2004). oxygen to permit aerobic respiration to provide energy
“In vitro nonenzymatic glycation enhances the to power the functions of the organism in the process
role of myoglobin as a source of oxidative called metabolism.
stress”. Free Radic. Res. 38 (2): 139–
46. doi:10.1080/10715160310001638038. PMID In mammals, the protein makes up about 96% of the
15104207. red blood cells’ dry content (by weight), and around 35%
of the total content (including water).[3] Hemoglobin has
• Stewart JM, Blakely JA, Karpowicz PA, Kalanxhi an oxygen-binding capacity of 1.34 mL O2 per gram,[4]
E, Thatcher BJ, Martin BM (March 2004). “Un- which increases the total blood oxygen capacity seventy-
usually weak oxygen binding, physical properties, fold compared to dissolved oxygen in blood. The mam-
partial sequence, autoxidation rate and a poten- malian hemoglobin molecule can bind (carry) up to four
tial phosphorylation site of beluga whale (Delphi- oxygen molecules.[5]
napterus leucas) myoglobin”. Comp. Biochem.
Hemoglobin is involved in the transport of other gases:
Physiol. B, Biochem. Mol. Biol. 137 (3):
It carries some of the body’s respiratory carbon diox-
401–12. doi:10.1016/j.cbpc.2004.01.007. PMID
ide (about 10% of the total) as carbaminohemoglobin, in
15050527.
which CO2 is bound to the globin protein. The molecule
• Wu G, Wainwright LM, Poole RK (2003). “Mi- also carries the important regulatory molecule nitric ox-
crobial globins”. Adv. Microb. Physiol. ide bound to a globin protein thiol group, releasing it at
[6]
Advances in Microbial Physiology 47: 255– the same time as oxygen.
310. doi:10.1016/S0065-2911(03)47005-7. ISBN Hemoglobin is also found outside red blood cells and their
9780120277476. PMID 14560666. progenitor lines. Other cells that contain hemoglobin
include the A9 dopaminergic neurons in the substantia
nigra, macrophages, alveolar cells, and mesangial cells
4.4.8 External links in the kidney. In these tissues, hemoglobin has a non-
oxygen-carrying function as an antioxidant and a regula-
• The Myoglobin Protein
tor of iron metabolism.[7]
• Protein Database featured molecule Hemoglobin and hemoglobin-like molecules are also
• Online 'Mendelian Inheritance in Man' (OMIM) found in many invertebrates, fungi, and plants. In these
160000 human genetics organisms, hemoglobins may carry oxygen, or they may
act to transport and regulate other things such as carbon
• Which Cut Is Older? (It’s a Trick Question) New dioxide, nitric oxide, hydrogen sulfide and sulfide. A vari-
York Times, February 21, 2006 article regarding ant of the molecule, called leghemoglobin, is used to scav-
meat industry use of carbon monoxide to keep meat enge oxygen away from anaerobic systems, such as the
looking red. nitrogen-fixing nodules of leguminous plants, before the
oxygen can poison the system.
• Stores React to Meat Reports New York Times,
March 1, 2006 article on the use of carbon monox-
ide to make meat appear fresh.
4.5.1 Research history
• Mirceta, S.; Signore, A. V.; Burns, J. M.; Cossins,
In 1825 J.F. Engelhard[9] discovered that the ratio of Fe to
A. R.; Campbell, K. L.; Berenbrink, M. (2013).
“Evolution of Mammalian Diving Capacity Traced
protein is identical in the hemoglobins of several species.
by Myoglobin Net Surface Charge”. Science 340
From the known atomic mass of iron he calculated the
(6138): 1234192. doi:10.1126/science.1234192.
molecular mass of hemoglobin to n × 16000 (n = num-
PMID 23766330.. Also see Proteopedia article
ber of irons per hemoglobin, now known to be 4), the
about this finding first determination of a protein’s molecular mass. This
“hasty conclusion” drew a lot of ridicule at the time from
scientists who could not believe that any molecule could
4.5 Hemoglobin be that big. Gilbert Smithson Adair confirmed Engel-
hard’s results in 1925 by measuring the osmotic pressure
[10]
Hemoglobin (/ˈhiːməˌɡloʊbɪn/); also spelled of hemoglobin solutions.
haemoglobin and abbreviated Hb or Hgb, is the The oxygen-carrying protein hemoglobin was discovered
4.5. HEMOGLOBIN 107

There is more than one hemoglobin gene. The amino

acid sequences of the globin proteins in hemoglobins
usually differ between species. These differences grow
with evolutionary distance between species. For exam-
ple, the most common hemoglobin sequences in humans
and chimpanzees are nearly identical, differing by only
one amino acid in both the alpha and the beta globin pro-
tein chains. These differences grow larger between less
closely related species.
Even within a species, different variants of hemoglobin
always exist, although one sequence is usually a “most
common” one in each species. Mutations in the
genes for the hemoglobin protein in a species result
in hemoglobin variants.[17][18] Many of these mutant
forms of hemoglobin cause no disease. Some of these
mutant forms of hemoglobin, however, cause a group
of hereditary diseases termed the hemoglobinopathies.
The best known hemoglobinopathy is sickle-cell disease,
which was the first human disease whose mechanism was
understood at the molecular level. A (mostly) separate
set of diseases called thalassemias involves underproduc-
Max Perutz, one of the founding fathers of molecular biology[8] tion of normal and sometimes abnormal hemoglobins,
through problems and mutations in globin gene regula-
tion. All these diseases produce anemia.[19]
by Hünefeld in 1840.[11] In 1851,[12] German physiologist
Otto Funke published a series of articles in which he de-
scribed growing hemoglobin crystals by successively di-
luting red blood cells with a solvent such as pure water,
alcohol or ether, followed by slow evaporation of the sol-
vent from the resulting protein solution.[13] Hemoglobin’s
reversible oxygenation was described a few years later by
Felix Hoppe-Seyler.[14]
In 1959, Max Perutz determined the molecular structure
of myoglobin (similar to hemoglobin) by X-ray crystal- Protein alignment of human hemoglobin proteins, alpha, beta,
lography.[15][16] This work resulted in his sharing with and delta subunits respectively. The alignments were created us-
ing Uniprot’s alignment tool available online.
John Kendrew the 1962 Nobel Prize in Chemistry.
The role of hemoglobin in the blood was elucidated
by French physiologist Claude Bernard. The name
hemoglobin is derived from the words heme and globin, Variations in hemoglobin amino acid sequences, as with
reflecting the fact that each subunit of hemoglobin is a other proteins, may be adaptive. For example, recent
globular protein with an embedded heme group. Each studies have suggested genetic variants in deer mice that
heme group contains one iron atom, that can bind one help explain how deer mice that live in the mountains are
oxygen molecule through ion-induced dipole forces. The able to survive in the thin air that accompanies high al-
most common type of hemoglobin in mammals contains titudes. A researcher from the University of Nebraska-
four such subunits. Lincoln found mutations in four different genes that can
account for differences between deer mice that live in
lowland prairies versus the mountains. After examining
4.5.2 Genetics wild mice captured from both highlands and lowlands,
it was found that: the genes of the two breeds are “vir-
Hemoglobin consists mostly of protein subunits (the tually identical–except for those that govern the oxygen-
“globin” molecules), and these proteins, in turn, are carrying capacity of their hemoglobin”. “The genetic dif-
folded chains of a large number of different amino acids ference enables highland mice to make more efficient use
called polypeptides. The amino acid sequence of any of their oxygen”, since less is available at higher altitudes,
polypeptide created by a cell is in turn determined by the such as those in the mountains.[20] Mammoth hemoglobin
stretches of DNA called genes. In all proteins, it is the featured mutations that allowed for oxygen delivery at
amino acid sequence that determines the protein’s chem- lower temperatures, thus enabling mammoths to migrate
ical properties and function. to higher latitudes during the Pleistocene.[21]
108 CHAPTER 4. PROTEINS AND AMINO ACIDS

4.5.3 Synthesis this arrangement is the same folding motif used in other
heme/globin proteins such as myoglobin.[26][27] This fold-
Hemoglobin (Hb) is synthesized in a complex series of ing pattern contains a pocket that strongly binds the heme
steps. The heme part is synthesized in a series of steps in group.
the mitochondria and the cytosol of immature red blood A heme group consists of an iron (Fe) ion (charged atom)
cells, while the globin protein parts are synthesized by held in a heterocyclic ring, known as a porphyrin. This
ribosomes in the cytosol.[22] Production of Hb contin- porphyrin ring consists of four pyrrole molecules cycli-
ues in the cell throughout its early development from the cally linked together (by methine bridges) with the iron
proerythroblast to the reticulocyte in the bone marrow. ion bound in the center.[28] The iron ion, which is the site
At this point, the nucleus is lost in mammalian red blood of oxygen binding, coordinates with the four nitrogens in
cells, but not in birds and many other species. Even after the center of the ring, which all lie in one plane. The
the loss of the nucleus in mammals, residual ribosomal iron is bound strongly (covalently) to the globular pro-
RNA allows further synthesis of Hb until the reticulocyte tein via the imidazole ring of F8 histidine residue (also
loses its RNA soon after entering the vasculature (this known as the proximal histidine) below the porphyrin
hemoglobin-synthetic RNA in fact gives the reticulocyte ring. A sixth position can reversibly bind oxygen by a
its reticulated appearance and name).[23] coordinate covalent bond,[29] completing the octahedral
group of six ligands. Oxygen binds in an “end-on bent”
geometry where one oxygen atom binds Fe and the other
4.5.4 Structure protrudes at an angle. When oxygen is not bound, a very
weakly bonded water molecule fills the site, forming a dis-
torted octahedron.
Even though carbon dioxide is carried by hemoglobin, it
does not compete with oxygen for the iron-binding posi-
tions but is bound to the protein chains of the structure.
The iron ion may be either in the Fe2+ or in the Fe3+ state,
but ferrihemoglobin (methemoglobin) (Fe3+ ) cannot bind
oxygen.[30] In binding, oxygen temporarily and reversibly
oxidizes (Fe2+ ) to (Fe3+ ) while oxygen temporarily turns
into superoxide, thus iron must exist in the +2 oxidation
state to bind oxygen. If superoxide ion associated to Fe3+
is protonated, the hemoglobin iron will remain oxidized
and incapable of binding oxygen. In such cases, the en-
zyme methemoglobin reductase will be able to eventually
reactivate methemoglobin by reducing the iron center.
In adult humans, the most common hemoglobin type
is a tetramer (which contains 4 subunit proteins) called
hemoglobin A, consisting of two α and two β subunits
non-covalently bound, each made of 141 and 146 amino
acid residues, respectively. This is denoted as α2 β2 . The
Heme b group subunits are structurally similar and about the same size.
Each subunit has a molecular weight of about 16,000
daltons,[31] for a total molecular weight of the tetramer
Hemoglobin has a quaternary structure characteristic of
of about 64,000 daltons (64,458 g/mol).[32] Thus, 1 g/dL
many multi-subunit globular proteins.[24] Most of the
= 0.1551 mmol/L. Hemoglobin A is the most intensively
amino acids in hemoglobin form alpha helices, connected
studied of the hemoglobin molecules.
by short non-helical segments. Hydrogen bonds stabi-
lize the helical sections inside this protein, causing attrac- In human infants, the hemoglobin molecule is made up of
tions within the molecule, folding each polypeptide chain 2 α chains and 2 γ chains. The gamma chains are gradu-
into a specific shape.[25] Hemoglobin’s quaternary struc- ally replaced by β chains as the infant grows.[33]
ture comes from its four subunits in roughly a tetrahedral The four polypeptide chains are bound to each other by
arrangement.[24] salt bridges, hydrogen bonds, and the hydrophobic effect.
In most vertebrates, the hemoglobin molecule is an as-
sembly of four globular protein subunits. Each subunit
is composed of a protein chain tightly associated with Oxygen saturation
a non-protein heme group. Each protein chain arranges
into a set of alpha-helix structural segments connected In general, hemoglobin can be saturated with oxygen
together in a globin fold arrangement, so called because molecules (oxyhemoglobin), or desaturated with oxygen
4.5. HEMOGLOBIN 109

molecules (deoxyhemoglobin).[34] • Triplet oxygen, the lowest-energy molecular oxygen

species, has two unpaired electrons in antibonding
π* molecular orbitals.
Oxyhemoglobin Oxyhemoglobin is formed during
physiological respiration when oxygen binds to the heme • Iron(II) tends to exist in a high-spin configuration
component of the protein hemoglobin in red blood where unpaired electrons exist in E antibonding or-
cells. This process occurs in the pulmonary capillaries bitals.
adjacent to the alveoli of the lungs. The oxygen then
• Iron(III) has an odd number of electrons, and thus
travels through the blood stream to be dropped off at
must have one or more unpaired electrons, in any
cells where it is utilized as a terminal electron acceptor
energy state.
in the production of ATP by the process of oxidative
phosphorylation. It does not, however, help to counteract
a decrease in blood pH. Ventilation, or breathing, may All of these structures are paramagnetic (have unpaired
reverse this condition by removal of carbon dioxide, thus electrons), not diamagnetic. Thus, a non-intuitive (e.g.,
causing a shift up in pH.[35] a higher-energy for at least one species) distribution of
electrons in the combination of iron and oxygen must ex-
Hemoglobin exists in two forms, a taut (tense) form (T) ist, in order to explain the observed diamagnetism and no
and a relaxed form (R). Various factors such as low pH, unpaired electrons.
high CO2 and high 2,3 BPG at the level of the tissues
favor the taut form, which has low oxygen affinity and re- The three logical possibilities to produce diamagnetic (no
leases oxygen in the tissues. Conversely, a high pH, low net spin) Hb-O2 are:
CO2 , or low 2,3 BPG favors the relaxed form, which can
better bind oxygen.[36] The partial pressure of the system 1. Low-spin Fe2+ binds to singlet oxygen. Both low-
also affects O2 affinity where, at high partial pressures spin iron and singlet oxygen are diamagnetic. How-
of oxygen (such as those present in the alveoli), the re- ever, the singlet form of oxygen is the higher-energy
laxed (high affinity, R) state is favoured. Inversely, at low form of the molecule.
partial pressures (such as those present in respiring tis-
sues), the (low affinity, T) tense state is favoured.[37] Ad- 2. Low-spin Fe3+ binds to .O2 − (the superoxide ion)
ditionally, the binding of oxygen to the Iron-II heme pulls and the two unpaired electrons couple antiferromag-
the iron into the plane of the porphyrin ring, causing a netically, giving diamagnetic properties.
slight conformational shift. The shift encourages oxygen
3. Low-spin Fe4+ binds to peroxide, O2 2− . Both are
to bind to the three remaining hemes within hemoglobin
diamagnetic.
(thus, oxygen binding is cooperative).

Direct experimental data:

Deoxygenated hemoglobin Deoxygenated
hemoglobin is the form of hemoglobin without the bound • X-ray photoelectron spectroscopy suggests iron has
oxygen. The absorption spectra of oxyhemoglobin an oxidation state of approximately 3.2
and deoxyhemoglobin differ. The oxyhemoglobin has
significantly lower absorption of the 660 nm wavelength • Infrared vibrational frequencies of the O-O bond
than deoxyhemoglobin, while at 940 nm its absorption suggests a bond length fitting with superoxide (a
is slightly higher. This difference is used for measure- bond order of about 1.6, with superoxide being 1.5).
ment of the amount of oxygen in patient’s blood by an
instrument called pulse oximeter. This difference also • X-ray Absorption Near Edge Structures at the iron
accounts for the presentation of cyanosis, the blue to K-edge. The energy shift of 5 eV between Deoxyhe-
purplish color that tissues develop during hypoxia.[38] moglobin and Oxyhemoglobin, as for all the Methe-
moglobin species, strongly suggests an actual local
charge closer to Fe3+ than Fe2+ .[39][40][41]
4.5.5 Iron’s oxidation state in oxyhe-
moglobin Thus, the nearest formal oxidation state of iron in Hb-
O2 is the +3 state, with oxygen in the −1 state (as su-
Assigning oxygenated hemoglobin’s oxidation state is dif- peroxide .O2 − ). The diamagnetism in this configuration
ficult because oxyhemoglobin (Hb-O2 ), by experimental arises from the single unpaired electron on superoxide
measurement, is diamagnetic (no net unpaired electrons), aligning antiferromagnetically from the single unpaired
yet the low-energy electron configurations in both oxy- electron on iron, to give no net spin to the entire config-
gen and iron are paramagnetic (suggesting at least one un- uration, in accordance with diamagnetic oxyhemoglobin
paired electron in the complex). The lowest-energy form from experiment.[42][43]
of oxygen, and the lowest energy forms of the relevant The second choice of the three logical possibilities above
oxidation states of iron, are these: for diamagnetic oxyhemoglobin being found correct by
110 CHAPTER 4. PROTEINS AND AMINO ACIDS

experiment, is not surprising: singlet oxygen (possibil-

ity #1) and large separations of charge (possibility #3)
are both unfavorably high-energy states. Iron’s shift to a
higher oxidation state in Hb-O2 decreases the atom’s size,
and allows it into the plane of the porphyrin ring, pulling
on the coordinated histidine residue and initiating the al-
losteric changes seen in the globulins.
Early postulates by bio-inorganic chemists claimed that
possibility #1 (above) was correct and that iron should
exist in oxidation state II. This conclusion seemed likely,
since the iron oxidation state III as methemoglobin, when
not accompanied by superoxide .O2 − to “hold” the oxi-
dation electron, was known to render hemoglobin inca-
pable of binding normal triplet O2 as it occurs in the air.
It was thus assumed that iron remained as Fe(II) when A schematic visual model of oxygen-binding process, showing all
four monomers and hemes, and protein chains only as diagra-
oxygen gas was bound in the lungs. The iron chemistry
matic coils, to facilitate visualization into the molecule. Oxygen
in this previous classical model was elegant, but the re-
is not shown in this model, but, for each of the iron atoms, it
quired presence of the required diamagnetic high-energy binds to the iron (red sphere) in the flat heme. For example, in
singlet oxygen was never explained. It was classically ar- the upper-left of the four hemes shown, oxygen binds at the left
gued that the binding of an oxygen molecule placed high- of the iron atom shown in the upper-left of diagram. This causes
spin iron(II) in an octahedral field of strong-field ligands; the iron atom to move backward into the heme that holds it (the
this change in field would increase the crystal field split- iron moves upward as it binds oxygen, in this illustration), tug-
ting energy, causing iron’s electrons to pair into the low- ging the histidine residue (modeled as a red pentagon on the right
spin configuration, which would be diamagnetic in Fe(II). of the iron) closer, as it does. This, in turn, pulls on the protein
This forced low-spin pairing is indeed thought to happen chain holding the histidine.
in iron when oxygen binds, but is not enough to explain
iron’s change in size. Extraction of an additional elec-
binding affinity of hemoglobin for oxygen is increased by
tron from iron by oxygen is required to explain both iron’s
the oxygen saturation of the molecule, with the first oxy-
smaller size and observed increased oxidation state, and
gens bound influencing the shape of the binding sites for
oxygen’s weaker bond.
the next oxygens, in a way favorable for binding. This
The assignment of a whole-number oxidation state is a positive cooperative binding is achieved through steric
formalism, as the covalent bonds are not required to have conformational changes of the hemoglobin protein com-
perfect bond orders involving whole electron transfer. plex as discussed above; i.e., when one subunit protein
Thus, all three models for paramagnetic Hb-O2 may con- in hemoglobin becomes oxygenated, a conformational or
tribute to some small degree (by resonance) to the actual structural change in the whole complex is initiated, caus-
electronic configuration of Hb-O2 . However, the model ing the other subunits to gain an increased affinity for
of iron in Hb-O2 being Fe(III) is more correct than the oxygen. As a consequence, the oxygen binding curve of
classical idea that it remains Fe(II). hemoglobin is sigmoidal, or S-shaped, as opposed to the
normal hyperbolic curve associated with noncooperative
binding.
4.5.6 Cooperativity The dynamic mechanism of the cooperativity in
hemoglobin and its relation with the low-frequency
When oxygen binds to the iron complex, it causes the iron resonance has been discussed.[44]
atom to move back toward the center of the plane of the
porphyrin ring (see moving diagram). At the same time,
the imidazole side-chain of the histidine residue interact- 4.5.7 Binding for ligands other than oxy-
ing at the other pole of the iron is pulled toward the por- gen
phyrin ring. This interaction forces the plane of the ring
sideways toward the outside of the tetramer, and also in- Besides the oxygen ligand, which binds to hemoglobin in
duces a strain in the protein helix containing the histidine a cooperative manner, hemoglobin ligands also include
as it moves nearer to the iron atom. This strain is trans- competitive inhibitors such as carbon monoxide (CO) and
mitted to the remaining three monomers in the tetramer, allosteric ligands such as carbon dioxide (CO ) and nitric
2
where it induces a similar conformational change in the oxide (NO). The carbon dioxide is bound to amino groups
other heme sites such that binding of oxygen to these sites of the globin proteins as carbaminohemoglobin, and is
becomes easier. thought to account for about 10% of carbon dioxide trans-
In the tetrameric form of normal adult hemoglobin, the port in mammals. Nitric oxide is bound to specific thiol
binding of oxygen is, thus, a cooperative process. The groups in the globin protein to form an S-nitrosothiol,
4.5. HEMOGLOBIN 111

which dissociates into free nitric oxide and thiol again, in deoxygenated blood, facilitating its removal from the
as the hemoglobin releases oxygen from its heme site. body after the oxygen has been released to tissues un-
This nitric oxide transport to peripheral tissues is hypoth- dergoing metabolism. This increased affinity for carbon
esized to assist oxygen transport in tissues, by releasing dioxide by the venous blood is known as the Haldane ef-
vasodilatory nitric oxide to tissues in which oxygen levels fect. Through the enzyme carbonic anhydrase, carbon
are low.[45] dioxide reacts with water to give carbonic acid, which de-
composes into bicarbonate and protons:
Competitive CO2 + H2 O → H2 CO3 → HCO3 − + H+

The binding of oxygen is affected by molecules such

as carbon monoxide (CO) (for example, from tobacco 100
95.8
smoking, car exhaust, and incomplete combustion in fur-

Percent saturation (sO2, %)

naces). CO competes with oxygen at the heme binding
site. Hemoglobin binding affinity for CO is 250 times
greater than its affinity for oxygen,[46] meaning that small
amounts of CO dramatically reduce hemoglobin’s ability
to transport oxygen. Since carbon monoxide is a color- 50
less, odorless and tasteless gas, and poses a potentially
fatal threat, detectors have become commercially avail-
able to warn of dangerous levels in residences. When
hemoglobin combines with CO, it forms a very bright red
compound called carboxyhemoglobin, which may cause
the skin of CO poisoning victims to appear pink in death, 0 26.8 40 80 120
instead of white or blue. When inspired air contains CO Oxygen partial pressure (pO , mmHg) 2

levels as low as 0.02%, headache and nausea occur; if the

CO concentration is increased to 0.1%, unconsciousness The sigmoidal shape of hemoglobin’s oxygen-dissociation curve
will follow. In heavy smokers, up to 20% of the oxygen- results from cooperative binding of oxygen to hemoglobin.
active sites can be blocked by CO.
In similar fashion, hemoglobin also has competitive bind- Hence, blood with high carbon dioxide levels is also lower
ing affinity for cyanide (CN− ), sulfur monoxide (SO), in pH (more acidic). Hemoglobin can bind protons and
nitric oxide (NO), and sulfide (S2− ), including hydrogen carbon dioxide, which causes a conformational change in
sulfide (H2 S). All of these bind to iron in heme without the protein and facilitates the release of oxygen. Protons
changing its oxidation state, but they nevertheless inhibit bind at various places on the protein,[47]
while carbon diox-
oxygen-binding, causing grave toxicity. ide binds at the α-amino group. Carbon dioxide binds
to hemoglobin and forms carbaminohemoglobin.[48] This
The iron atom in the heme group must initially be decrease in hemoglobin’s affinity for oxygen by the bind-
in the ferrous (Fe2+ ) oxidation state to support oxy- ing of carbon dioxide and acid is known as the Bohr effect
gen and other gases’ binding and transport (it temporar- (shifts the O2 -saturation curve to the right). Conversely,
ily switches to ferric during the time oxygen is bound, when the carbon dioxide levels in the blood decrease (i.e.,
as explained above). Initial oxidation to the ferric in the lung capillaries), carbon dioxide and protons are
(Fe3+ ) state without oxygen converts hemoglobin into released from hemoglobin, increasing the oxygen affinity
“hemiglobin” or methemoglobin (pronounced “MET- of the protein. A reduction in the total binding capacity
hemoglobin”), which cannot bind oxygen. Hemoglobin of hemoglobin to oxygen (i.e. shifting the curve down,
in normal red blood cells is protected by a reduction sys- not just to the right) due to reduced pH is called the root
tem to keep this from happening. Nitric oxide is capable effect. This is seen in bony fish.
of converting a small fraction of hemoglobin to methe-
moglobin in red blood cells. The latter reaction is a rem- It is necessary for hemoglobin to release the oxygen that it
nant activity of the more ancient nitric oxide dioxygenase binds; if not, there is no point in binding it. The sigmoidal
function of globins. curve of hemoglobin makes it efficient in binding (taking
up O2 in lungs), and efficient in unloading (unloading O2
in tissues).[49]
Allosteric In people acclimated to high altitudes, the concentration
of 2,3-Bisphosphoglycerate (2,3-BPG) in the blood is in-
Further information: Oxygen-hemoglobin dissociation creased, which allows these individuals to deliver a larger
curve amount of oxygen to tissues under conditions of lower
oxygen tension. This phenomenon, where molecule Y af-
Carbon dioxide occupies a different binding site on the fects the binding of molecule X to a transport molecule
hemoglobin. Carbon dioxide is more readily dissolved Z, is called a heterotropic allosteric effect.
112 CHAPTER 4. PROTEINS AND AMINO ACIDS

Animals other than humans use different molecules to • Hemoglobin A (α2 β2 ) (PDB: 1BZ0 ) – The most
bind to hemoglobin and change its O2 affinity under un- common with a normal amount over 95%
favorable conditions. Fish use both ATP and GTP. These
• Hemoglobin A2 (α2 δ2 ) – δ chain synthesis begins
bind to a phosphate “pocket” on the fish hemoglobin
late in the third trimester and, in adults, it has a nor-
molecule, which stabilizes the tense state and therefore
mal range of 1.5–3.5%
decreases oxygen affinity.[50] GTP reduces hemoglobin
oxygen affinity much more than ATP, which is thought to • Hemoglobin F (α2 γ2 ) – In adults Hemoglobin F is
be due to an extra hydrogen bond formed that further sta- restricted to a limited population of red cells called
bilizes the tense state.[51] Under hypoxic conditions, the F-cells. However, the level of Hb F can be ele-
concentration of both ATP and GTP is reduced in fish vated in persons with sickle-cell disease and beta-
red blood cells to increase oxygen affinity.[52] thalassemia.
A variant hemoglobin, called fetal hemoglobin (HbF,
α2 γ2 ), is found in the developing fetus, and binds oxygen Types Megaloblast Macrocyte Normocyte
of cells
with greater affinity than adult hemoglobin. This means Yolk
Organs sac Liver Spleen Bone marrow
that the oxygen binding curve for fetal hemoglobin is left-
shifted (i.e., a higher percentage of hemoglobin has oxy- 50

synthesis of globin, %
gen bound to it at lower oxygen tension), in comparison 40

Part in the total

to that of adult hemoglobin. As a result, fetal blood in the
30
placenta is able to take oxygen from maternal blood.
20
Hemoglobin also carries nitric oxide (NO) in the globin
part of the molecule. This improves oxygen delivery in 10

the periphery and contributes to the control of respira-

tion. NO binds reversibly to a specific cysteine residue 6 12 18 24 30 36
Prenatal age (weeks) Birth
6 12 18 24 30 36 42
Postnatal age (weeks)
in globin; the binding depends on the state (R or T) of -similar globin chains
the hemoglobin. The resulting S-nitrosylated hemoglobin -similar globin chains

influences various NO-related activities such as the con-

trol of vascular resistance, blood pressure and respira- Gene expression of hemoglobin before and after birth. Also iden-
tion. NO is not released in the cytoplasm of erythrocytes tifies the types of cells and organs in which the gene expression
but transported by an anion exchanger called AE1 out of (data on Wood W.G., (1976). Br. Med. Bull. 32, 282.)
them.[53]
Variant forms that cause disease:

4.5.8 Types in humans • Hemoglobin D-Punjab – (α2 βD 2 ) – A variant form

of hemoglobin.
Hemoglobin variants are a part of the normal embryonic
and fetal development, but may also be pathologic mu- • Hemoglobin H (β4 ) – A variant form of hemoglobin,
tant forms of hemoglobin in a population, caused by vari- formed by a tetramer of β chains, which may be
ations in genetics. Some well-known hemoglobin variants present in variants of α thalassemia.
such as sickle-cell anemia are responsible for diseases,
• Hemoglobin Barts (γ4 ) – A variant form of
and are considered hemoglobinopathies. Other variants
hemoglobin, formed by a tetramer of γ chains,
cause no detectable pathology, and are thus considered
which may be present in variants of α thalassemia.
non-pathological variants.[54][55]
In the embryo: • Hemoglobin S (α2 βS 2 ) – A variant form of
hemoglobin found in people with sickle cell disease.
There is a variation in the β-chain gene, causing a
• Gower 1 (ζ2 ε2 ) change in the properties of hemoglobin, which re-
• Gower 2 (α2 ε2 ) (PDB: 1A9W ) sults in sickling of red blood cells.
• Hemoglobin C (α2 βC 2 ) – Another variant due to a
• Hemoglobin Portland I (ζ2 γ2 )
variation in the β-chain gene. This variant causes a
• Hemoglobin Portland II (ζ2 β2 ). mild chronic hemolytic anemia.
• Hemoglobin E (α2 βE 2 ) – Another variant due to a
In the fetus: variation in the β-chain gene. This variant causes a
mild chronic hemolytic anemia.
• Hemoglobin F (α2 γ2 ) (PDB: 1FDH ). • Hemoglobin AS – A heterozygous form causing
sickle cell trait with one adult gene and one sickle
After birth: cell disease gene
4.5. HEMOGLOBIN 113

• Hemoglobin SC disease – A compound heterozy- Decrease of hemoglobin, with or without an absolute de-
gous form with one sickle gene and another encod- crease of red blood cells, leads to symptoms of anemia.
ing Hemoglobin C. Anemia has many different causes, although iron defi-
ciency and its resultant iron deficiency anemia are the
most common causes in the Western world. As ab-
4.5.9 Degradation in vertebrate animals sence of iron decreases heme synthesis, red blood cells in
iron deficiency anemia are hypochromic (lacking the red
When red cells reach the end of their life due to ag- hemoglobin pigment) and microcytic (smaller than nor-
ing or defects, they are broken down in the spleen. The mal). Other anemias are rarer. In hemolysis (acceler-
hemoglobin molecule is broken up, and the iron gets re- ated breakdown of red blood cells), associated jaundice
cycled. This process also produces one molecule of car- is caused by the hemoglobin metabolite bilirubin, and the
bon monoxide for every molecule of heme degraded.[56] circulating hemoglobin can cause renal failure.
Heme degradation is one of the few natural sources of
Some mutations in the globin chain are associated with
carbon monoxide in the human body, and is responsible
the hemoglobinopathies, such as sickle-cell disease and
for the normal blood levels of carbon monoxide even in
thalassemia. Other mutations, as discussed at the begin-
people breathing pure air. The other major final prod-
ning of the article, are benign and are referred to merely
uct of heme degradation is bilirubin. Increased levels of
as hemoglobin variants.
this chemical are detected in the blood if red cells are
being destroyed more rapidly than usual. Improperly de- There is a group of genetic disorders, known as the
graded hemoglobin protein or hemoglobin that has been porphyrias that are characterized by errors in metabolic
released from the blood cells too rapidly can clog small pathways of heme synthesis. King George III of the
blood vessels, especially the delicate blood filtering ves- United Kingdom was probably the most famous por-
sels of the kidneys, causing kidney damage. Iron is re- phyria sufferer.
moved from heme and salvaged for later use, it is stored To a small extent, hemoglobin A slowly combines with
as hemosiderin or ferritin in tissues and transported in glucose at the terminal valine (an alpha aminoacid) of
plasma by beta globulins as transferrins. When the por- each β chain. The resulting molecule is often referred to
phyrin ring is broken up, the fragments are normally se- as Hb A₁ . As the concentration of glucose in the blood
creted as a yellow pigment called bilirubin, which is se- increases, the percentage of Hb A that turns into Hb A₁
creted into the intestines as bile. Intestines metabolise increases. In diabetics whose glucose usually runs high,
bilirubin into urobilinogen. Urobilinogen leaves the body the percent Hb A₁ also runs high. Because of the slow
in faeces, in a pigment called stercobilin. Globulin is rate of Hb A combination with glucose, the Hb A₁ per-
metabolised into amino acids that are then released into centage is representative of glucose level in the blood av-
circulation. eraged over a longer time (the half-life of red blood cells,
which is typically 50–55 days).
4.5.10 Role in disease Glycosylated hemoglobin is the form of hemoglobin to
which glucose is bound. The binding of glucose to amino
Hemoglobin deficiency can be caused either by a de- acids in the hemoglobin takes place spontaneously (with-
creased amount of hemoglobin molecules, as in anemia, out the help of an enzyme) in many proteins, and is not
or by decreased ability of each molecule to bind oxygen at known to serve a useful purpose. However, the bind-
the same partial pressure of oxygen. Hemoglobinopathies ing to hemoglobin does serve as a record for average
(genetic defects resulting in abnormal structure of the blood glucose levels over the lifetime of red cells, which
hemoglobin molecule)[57] may cause both. In any case, is approximately 120 days. The levels of glycosylated
hemoglobin deficiency decreases blood oxygen-carrying hemoglobin are therefore measured in order to monitor
capacity. Hemoglobin deficiency is, in general, strictly the long-term control of the chronic disease of type 2 dia-
distinguished from hypoxemia, defined as decreased betes mellitus (T2DM). Poor control of T2DM results in
partial pressure of oxygen in blood,[58][59][60][61] although high levels of glycosylated hemoglobin in the red blood
both are causes of hypoxia (insufficient oxygen supply to cells. The normal reference range is approximately 4–
tissues). 5.9 %. Though difficult to obtain, values less than 7%
are recommended for people with T2DM. Levels greater
Other common causes of low hemoglobin include loss
than 9% are associated with poor control of the glyco-
of blood, nutritional deficiency, bone marrow problems,
sylated hemoglobin, and levels greater than 12% are as-
chemotherapy, kidney failure, or abnormal hemoglobin
sociated with very poor control. Diabetics who keep
(such as that of sickle-cell disease).
their glycosylated hemoglobin levels close to 7% have a
The ability of each hemoglobin molecule to carry oxygen much better chance of avoiding the complications that
is normally modified by altered blood pH or CO2 , causing may accompany diabetes (than those whose levels are
an altered oxygen–hemoglobin dissociation curve. How- 8% or higher).[62] In addition, increased glycosylation
ever, it can also be pathologically altered in, e.g., carbon of hemoglobin increases its affinity for oxygen, therefore
monoxide poisoning.
114 CHAPTER 4. PROTEINS AND AMINO ACIDS

preventing its release at the tissue and inducing a level of version factor 0.155, which uses the tetramer weight of
hypoxia in extreme cases.[63] 64,500 Da, is more common.[67] Normal levels are:
Elevated levels of hemoglobin are associated with in-
creased numbers or sizes of red blood cells, called • Men: 13.8 to 18.0 g/dL (138 to 180 g/L, or 8.56 to
polycythemia. This elevation may be caused by 11.17 mmol/L)
congenital heart disease, cor pulmonale, pulmonary fi-
brosis, too much erythropoietin, or polycythemia vera.[64] • Women: 12.1 to 15.1 g/dL (121 to 151 g/L, or 7.51
High hemoglobin levels may also be caused by expo- to 9.37 mmol/L)
sure to high altitudes, smoking, dehydration (artificially
• Children: 11 to 16 g/dL (111 to 160 g/L, or 6.83 to
by concentrating Hb), advanced lung disease and certain
9.93 mmol/L)
tumors.[33]
A recent study done in Pondicherry, India, shows its im- • Pregnant women: 11 to 14 g/dL (110 to 140 g/L, or
portance in coronary artery disease.[65] 6.83 to 8.69 mmol/L)[68][69]

Normal values of hemoglobin in the 1st and 3rd trimesters

4.5.11 Diagnostic uses of pregnant women must be at least 11 g/dL and at least
10.5 g/dL during the 2nd trimester.[70]
Main article: Hemoglobinometer
Hemoglobin concentration measurement is among the Dehydration or hyperhydration can greatly influence mea-
sured hemoglobin levels. Albumin can indicate hydration
status.
If the concentration is below normal, this is called anemia.
Anemias are classified by the size of red blood cells, the
cells that contain hemoglobin in vertebrates. The anemia
is called “microcytic” if red cells are small, “macrocytic”
if they are large, and “normocytic” otherwise.
Hematocrit, the proportion of blood volume occupied
by red blood cells, is typically about three times the
hemoglobin concentration measured in g/dL. For exam-
ple, if the hemoglobin is measured at 17 g/dL, that com-
pares with a hematocrit of 51%.[71]
Laboratory hemoglobin test methods require a blood
sample (arterial, venous, or capillary) and analysis on
hematology analyzer and CO-oximeter. Additionally, a
new noninvasive hemoglobin (SpHb) test method called
Pulse CO-Oximetry is also available with comparable ac-
curacy to invasive methods.[72]
Concentrations of oxy- and deoxyhemoglobin can be
measured continuously, regionally and noninvasively us-
ing NIRS.[73][74][75][76][77] NIRS can be used both on the
head as on muscles. This technique is often used for
research in e.g. elite sports training, ergonomics, re-
habilition, patient monitoring, neonatal research, func-
A hemoglobin concentration measurement being administered tional brain monitoring, brain computer interface, urol-
before a blood donation at the American Red Cross Boston Blood ogy (bladder contraction), neurology (Neurovascular cou-
Donation Center.
pling) and more.
most commonly performed blood tests, usually as part Long-term control of blood sugar concentration can be
of a complete blood count. For example it is typically measured by the concentration of Hb A₁ . Measuring it
tested before or after blood donation. Results are re- directly would require many samples because blood sugar
ported in g/L, g/dL or mol/L. 1 g/dL equals about 0.6206 levels vary widely through the day. Hb A₁ is the product
mmol/L, although the latter units are not used as of- of the irreversible reaction of hemoglobin A with glucose.
ten due to uncertainty regarding the polymeric state of A higher glucose concentration results in more Hb A₁ .
the molecule.[66] This conversion factor, using the single Because the reaction is slow, the Hb A₁ proportion rep-
globin unit molecular weight of 16,000 Da, is more com- resents glucose level in blood averaged over the half-life
mon for hemoglobin concentration in blood. For MCHC of red blood cells, is typically 50–55 days. An Hb A₁
(mean corpuscular hemoglobin concentration) the con- proportion of 6.0% or less show good long-term glucose
4.5. HEMOGLOBIN 115

control, while values above 7.0% are elevated. This test much larger than those in vertebrates. In particular,
is especially useful for diabetics.[78] chimeric hemoglobins found in fungi and giant annelids
[81]
The functional magnetic resonance imaging (fMRI) ma- may contain both globin and other types of proteins.
chine uses the signal from deoxyhemoglobin, which is One of the most striking occurrences and uses of
sensitive to magnetic fields since it is paramagnetic. Com- hemoglobin in organisms is in the giant tube worm (Riftia
bined measurement with NIRS shows good correlation pachyptila, also called Vestimentifera), which can reach
with both the oxy- and deoxyhemoglobin signal com- 2.4 meters length and populates ocean volcanic vents. In-
pared to the BOLD signal.[79] stead of a digestive tract, these worms contain a popula-
tion of bacteria constituting half the organism’s weight.
The bacteria react with H2 S from the vent and O2 from
4.5.12 Analogues in non-vertebrate organ- the water to produce energy to make food from H2 O and
isms CO2 . The worms end with a deep-red fan-like structure
(“plume”), which extends into the water and absorbs H2 S
A variety of oxygen-transport and -binding proteins ex- and O2 for the bacteria, and CO2 for use as synthetic raw
ist in organisms throughout the animal and plant king- material similar to photosynthetic plants. The structures
doms. Organisms including bacteria, protozoans, and are bright-red due to their containing several extraordi-
fungi all have hemoglobin-like proteins whose known and narily complex hemoglobins that have up to 144 globin
predicted roles include the reversible binding of gaseous chains, each including associated heme structures. These
ligands. Since many of these proteins contain globins and hemoglobins are remarkable for being able to carry oxy-
the heme moiety (iron in a flat porphyrin support), they gen in the presence of sulfide, and even to carry sulfide,
are often called hemoglobins, even if their overall ter- without being completely “poisoned” or inhibited by it as
tiary structure is very different from that of vertebrate hemoglobins in most other species are.[82][83]
hemoglobin. In particular, the distinction of “myoglobin”
and hemoglobin in lower animals is often impossible, be-
cause some of these organisms do not contain muscles. 4.5.13 Other oxygen-binding proteins
Or, they may have a recognizable separate circulatory
system but not one that deals with oxygen transport (for Myoglobin Found in the muscle tissue of many verte-
example, many insects and other arthropods). In all brates, including humans, it gives muscle tissue a
these groups, heme/globin-containing molecules (even distinct red or dark gray color. It is very simi-
monomeric globin ones) that deal with gas-binding are re- lar to hemoglobin in structure and sequence, but is
ferred to as oxyhemoglobins. In addition to dealing with not a tetramer; instead, it is a monomer that lacks
transport and sensing of oxygen, they may also deal with cooperative binding. It is used to store oxygen rather
NO, CO2 , sulfide compounds, and even O2 scavenging in than transport it.
environments that must be anaerobic.[80] They may even
deal with detoxification of chlorinated materials in a way Hemocyanin The second most common oxygen-
analogous to heme-containing P450 enzymes and perox- transporting protein found in nature, it is found
idases. in the blood of many arthropods and molluscs.
Uses copper prosthetic groups instead of iron heme
groups and is blue in color when oxygenated.

Hemerythrin Some marine invertebrates and a few

species of annelid use this iron-containing non-heme
protein to carry oxygen in their blood. Appears
pink/violet when oxygenated, clear when not.

Chlorocruorin Found in many annelids, it is very simi-

lar to erythrocruorin, but the heme group is signif-
icantly different in structure. Appears green when
The giant tube worm Riftia pachyptila showing red hemoglobin- deoxygenated and red when oxygenated.
containing plumes
Vanabins Also known as vanadium chromagens, they
The structure of hemoglobins varies across species. are found in the blood of sea squirts. There were
Hemoglobin occurs in all kingdoms of organisms, but once hypothesized to use the rare metal vanadium
not in all organisms. Primitive species such as bacte- as an oxygen binding prosthetic group. However,
ria, protozoa, algae, and plants often have single-globin although they do contain vanadium by preference,
hemoglobins. Many nematode worms, molluscs, and they apparently bind little oxygen, and thus have
crustaceans contain very large multisubunit molecules, some other function, which has not been elucidated
116 CHAPTER 4. PROTEINS AND AMINO ACIDS

(sea squirts also contain some hemoglobin). They

may act as toxins.

Erythrocruorin Found in many annelids, including

earthworms, it is a giant free-floating blood pro-
tein containing many dozens—possibly hundreds—
of iron- and heme-bearing protein subunits bound
together into a single protein complex with a molec-
ular mass greater than 3.5 million daltons.
Heart of Steel (Hemoglobin) (2005) by Julian Voss-Andreae.
Pinnaglobin Only seen in the mollusc Pinna squamosa. The images show the 5-foot (1.60 m) tall sculpture right after
Brown manganese-based porphyrin protein. installation, after 10 days, and after several months of exposure
to the elements.
Leghemoglobin In leguminous plants, such as alfalfa or
soybeans, the nitrogen fixing bacteria in the roots are
the Roman god of war, since the planet is an orange-
protected from oxygen by this iron heme containing
oxygen-binding protein. The specific enzyme pro- red, which reminded the ancients of blood. Although the
color of the planet is due to iron compounds in combi-
tected is nitrogenase, which is unable to reduce ni-
trogen gas in the presence of free oxygen. nation with oxygen in the Martian soil, it is a common
misconception that the iron in hemoglobin and its ox-
Coboglobin A synthetic cobalt-based porphyrin. Cobo- ides gives blood its red color. The color is actually due
protein would appear colorless when oxygenated, to the porphyrin moiety of hemoglobin to which the iron
but yellow when in veins. is bound, not the iron itself,[87] although the ligation and
redox state of the iron can influence the pi to pi* or n to
pi* electronic transitions of the porphyrin and hence its
4.5.14 Presence in nonerythroid cells optical characteristics.
Artist Julian Voss-Andreae created a sculpture called
Some nonerythroid cells (i.e., cells other than the red
“Heart of Steel (Hemoglobin)" in 2005, based on the
blood cell line) contain hemoglobin. In the brain, these
protein’s backbone. The sculpture was made from glass
include the A9 dopaminergic neurons in the substantia ni-
and weathering steel. The intentional rusting of the ini-
gra, astrocytes in the cerebral cortex and hippocampus,
tially shiny work of art mirrors hemoglobin’s fundamental
and in all mature oligodendrocytes.[7] It has been sug-
chemical reaction of oxygen binding to iron.[88][89]
gested that brain hemoglobin in these cells may enable
the “storage of oxygen to provide a homeostatic mech-
anism in anoxic conditions, which is especially impor-
4.5.16 See also
tant for A9 DA neurons that have an elevated metabolism
with a high requirement for energy production”.[7] It has
been noted further that “A9 dopaminergic neurons may 4.5.17 References
be at particular risk since in addition to their high mito-
[1] Maton, Anthea; Jean Hopkins; Charles William
chondrial activity they are under intense oxidative stress McLaughlin; Susan Johnson; Maryanna Quon Warner;
caused by the production of hydrogen peroxide via au- David LaHart; Jill D. Wright (1993). Human Biology and
toxidation and/or monoamine oxidase (MAO)-mediated Health. Englewood Cliffs, New Jersey, USA: Prentice
deamination of dopamine and the subsequent reaction of Hall. ISBN 0-13-981176-1.
accessible ferrous iron to generate highly toxic hydroxyl
radicals”.[7] This may explain the risk of these cells for [2] Sidell, Bruce; Kristin O'Brien (2006). “When bad things
degeneration in Parkinson’s disease.[7] The hemoglobin- happen to good fish: the loss of hemoglobin and myo-
derived iron in these cells is not the cause of the post- globin expression in Antarctic icefishes”. The Jour-
nal of Experimental Biology 209 (Pt 10): 1791–1802.
mortem darkness of these cells (origin of the Latin name,
doi:10.1242/jeb.02091. PMID 16651546.
substantia nigra), but rather is due to neuromelanin.
Outside the brain, hemoglobin has non-oxygen-carrying [3] Weed, Robert I.; Reed, Claude F. and Berg, George
functions as an antioxidant and a regulator of iron (1963). “Is hemoglobin an essential structural component
of human erythrocyte membranes?". J Clin Invest. 42 (4):
metabolism in macrophages,[84] alveolar cells,[85] and
581–8. doi:10.1172/JCI104747. PMC 289318. PMID
mesangial cells in the kidney.[86] 13999462.

[4] Dominguez de Villota ED, Ruiz Carmona MT, Rubio JJ,

4.5.15 In history, art and music de Andrés S (1981). “Equality of the in vivo and in vitro
oxygen-binding capacity of haemoglobin in patients with
Historically, an association between the color of blood severe respiratory disease”. Br J Anaesth 53 (12): 1325–
and rust occurs in the association of the planet Mars, with 8. doi:10.1093/bja/53.12.1325. PMID 7317251.
4.5. HEMOGLOBIN 117

[5] Costanzo, Linda S. (2007). Physiology. Hagerstwon, MD: [23] Burka, Edward (1969). “Characteristics of RNA degrada-
Lippincott Williams & Wilkins. ISBN 0-7817-7311-3. tion in the erythroid cell.”. The Journal of Clinical Investi-
gation 48 (7): 1266–1272. doi:10.1172/jci106092. PMC
[6] Epstein, F. H.; Hsia, C. C. W. (1998). “Res- 322349. PMID 5794250. Retrieved 8 October 2014.
piratory Function of Hemoglobin”. New Eng-
land Journal of Medicine 338 (4): 239–247. [24] van Kessel et al. (2003) “2.4 Proteins – Natural
doi:10.1056/NEJM199801223380407. PMID 9435331. Polyamides.” Chemistry 12. Toronto: Nelson, p. 122.

[7] Biagioli M, Pinto M, Cesselli D et al. (2009). [25] “Hemoglobin Tutorial.” University of Massachusetts
“Unexpected expression of alpha- and beta-globin in Amherst. Web. 23 Oct. 2009.
mesencephalic dopaminergic neurons and glial cells”.
[26] Steinberg, MH (2001). Disorders of Hemoglobin: Ge-
Proc. Natl. Acad. Sci. U.S.A. 106 (36): 15454–9.
netics, Pathophysiology, and Clinical Management. Cam-
doi:10.1073/pnas.0813216106. PMC 2732704. PMID
bridge University Press. p. 95. ISBN 0-521-63266-8.
19717439.
[27] Hardison, RC (1996). “A brief history of hemoglobins:
[8] "Max Perutz, Father of Molecular Biology, Dies at 87".
plant, animal, protist, and bacteria”. Proc Natl Acad
The New York Times. February 8, 2002
Sci USA 93 (12): 5675–9. doi:10.1073/pnas.93.12.5675.
[9] Engelhard, Johann Friedrich (1825). Commentatio de PMC 39118. PMID 8650150.
vera materia sanguini purpureum colorem impertientis
[28] “Hemoglobin.” School of Chemistry – Bristol University
natura (in Latin). Göttingen: Dietrich.
– UK. Web. 12 Oct. 2009.
[10] Adair, Gilbert Smithson (1925). “A critical study of the [29] WikiPremed > Coordination Chemistry. Retrieved July
direct method of measuring the osmotic pressure of hǣ- 2, 2009
moglobin”. Proc. R. Soc. Lond. A 108 (750): 292–300.
doi:10.1098/rspa.1925.0126. [30] Linberg R, Conover CD, Shum KL, Shorr RG
(1998). “Hemoglobin based oxygen carriers: how
[11] Hünefeld F.L. (1840). “Die Chemismus in der thierischen much methemoglobin is too much?". Artif Cells
Organization”. Leipzig. Blood Substit Immobil Biotechnol 26 (2): 133–48.
doi:10.3109/10731199809119772. PMID 9564432.
[12] Funke O (1851). "Über das milzvenenblut”. Z Rat Med
1: 172–218. [31] Hemoglobin. Worthington-biochem.com. Retrieved
2013-09-05.
[13] “A NASA Recipe For Protein Crystallography” (PDF).
Educational Brief. National Aeronautics and Space Ad- [32] Van Beekvelt MC, Colier WN, Wevers RA, Van Engelen
ministration. Archived from the original (PDF) on 2008- BG (2001). “Performance of near-infrared spectroscopy
04-10. Retrieved 2008-10-12. in measuring local O2 consumption and blood flow in
skeletal muscle”. J Appl Physiol 90 (2): 511–519. PMID
[14] Hoppe-Seyler F (1866). "Über die oxydation in lebendem
11160049.
blute”. Med-chem Untersuch Lab 1: 133–140.
[33] “Hemoglobin.” MedicineNet. Web. 12 Oct. 2009.
[15] Perutz, M.F.; Rossmann, M.G.; Cullis, A.F.; Muirhead,
H.; Will, G.; North, A.C.T. (1960). “Structure of H”. [34] “Hemoglobin Home.” Biology @ Davidson. Web. 12 Oct.
Nature 185 (4711): 416–422. doi:10.1038/185416a0. 2009.
PMID 18990801.
[35] “Hemoglobin saturation graph”. altitude.org.
[16] Perutz MF (1960). “Structure of haemoglobin”.
Brookhaven symposia in biology 13: 165–83. PMID [36] King, Michael W. “The Medical Biochemistry Page –
13734651. Hemoglobin”.

[17] A Syllabus of Human Hemoglobin Variants (1996). [37] Voet, D. (2008) Fundamentals of Biochemistry, 3rd. ed.,
Globin.cse.psu.edu. Retrieved 2013-09-05. Fig. 07_06, John Wiley & Sons

[18] Hemoglobin Variants. Labtestsonline.org. Retrieved [38] Ahrens, Thomas; Kimberley, Basham (1993). Essentials
2013-09-05. of Oxygenation: Implication for Clinical Practice. Jones &
Bartlett Learning. p. 194. ISBN 0867203323.
[19] Uthman, MD, Ed. “Hemoglobinopathies and Tha-
[39] Pin S, Alpert B, Michalowicz A. (1982). “Oxygen
lassemias”. Retrieved 2007-12-26.
bonding in human hemoglobin and its isolated subunits:
[20] Reed, Leslie. “Adaptation found in mouse genes.” Om- A XANES study”. FEBS Lett. 147 (1): 106–10.
aha World-Herald 11 Aug. 2009: EBSCO. Web. 30 Oct. doi:10.1016/0014-5793(82)81021-1. PMID 7140986.
2009.
[40] Pin, S.; Valat, P.; Cortes, R.; Michalowicz, A.; Alpert,
[21] “Mammoths had ′anti-freeze′ blood”. BBC. 2010-05-02. B. (1985). “Ligand binding processes in hemoglobin.
Retrieved 2010-05-02. Chemical reactivity of iron studied by XANES spec-
troscopy”. Biophysical Journal 48 (6): 997–1001.
[22] “Hemoglobin Synthesis”. April 14, 2002. Retrieved doi:10.1016/S0006-3495(85)83862-5. PMC 1329432.
2007-12-26. PMID 4092074.
118 CHAPTER 4. PROTEINS AND AMINO ACIDS

[41] Bianconi A, Congiu-Castellano A, Dell'Ariccia M, Gio- [54] “Hemoglobin Variants”. Lab Tests Online. American As-
vannelli A, Burattini E, Durham PJ (1985). “Increase sociation for Clinical Chemistry. 2007-11-10. Retrieved
of the Fe effective charge in hemoproteins during oxy- 2008-10-12.
genation process”. Biochemical and Biophysical Research
Communications 30 (1): 98–102. doi:10.1016/0006- [55] Huisman THJ (1996). “A Syllabus of Human
291X(85)91775-9. PMID 4038310. Hemoglobin Variants”. Globin Gene Server. Penn-
sylvania State University. Retrieved 2008-10-12.
[42] Childs PE (2001). “Haemoglobin – a molecular lung: 2”.
Chemistry in Action (65). ISSN 0332-2637. [56] Kikuchi, G.; Yoshida, T.; Noguchi, M. (2005). “Heme
oxygenase and heme degradation”. Biochemical and Bio-
[43] Chen H, Ikeda-Saito M, Shaik S (2008). “Nature of physical Research Communications 338 (1): 558–567.
the Fe-O2 bonding in oxy-myoglobin: effect of the pro- doi:10.1016/j.bbrc.2005.08.020. PMID 16115609.
tein”. Journal of the American Chemical Society 130
(44): 14778–14790. doi:10.1021/ja805434m. PMID [57] "hemoglobinopathy" at Dorland’s Medical Dictionary
18847206.
[58] hypoxemia. Encyclopædia Britannica, stating hypoxemia
[44] Chou KC (1989). “Low-frequency resonance and co- (reduced oxygen tension in the blood).
operativity of hemoglobin”. Trends Biochem. Sci. 14
(6): 212–3. doi:10.1016/0968-0004(89)90026-1. PMID [59] Biology-Online.org --> Dictionary » H » Hypoxemia last
2763333. modified 29 December 2008

[45] Jensen, Frank B (2009). “The dual roles of red blood [60] William, C. Wilson; Grande, Christopher M. and Hoyt,
cells in tissue oxygen delivery: oxygen carriers and regula- David B. (2007). “Pathophysiology of acute respiratory
tors of local blood flow”. Journal of Experimental Biology failure”. Trauma, Volume II: Critical Care. Taylor &
(The Company of Biologists) 212 (Pt 21): 3387–3393. Francis. p. 430. ISBN 978-1-4200-1684-0.
doi:10.1242/jeb.023697. PMID 19837879.
[61] McGaffigan, P. A. (1996). “Hazards of hypoxemia: How
[46] Hall, John E. (2010). Guyton and Hall textbook of med- to protect your patient from low oxygen levels”. Nursing
ical physiology (12th ed.). Philadelphia, Pa.: Saun- 26 (5): 41–46; quiz 46. PMID 8710285.
ders/Elsevier. p. 502. ISBN 978-1416045748.
[62] “Definition of Glycosylated Hemoglobin.” Medicine Net.
[47] Nelson, D. L.; Cox, M. M. (2000). Lehninger Principles of Web. 12 Oct. 2009.
Biochemistry, 3rd ed. New York, NY: Worth Publishers.
p. 217, ISBN 1572599316. [63] Madsen, H; Ditzel, J (1984). “Blood-oxygen trans-
port in first trimester of diabetic pregnancy”. Acta Ob-
[48] Guyton, Arthur C.; John E. Hall (2006). Textbook of Med- stetricia et Gynecologica Scandinavica 63 (4): 317–20.
ical Physiology (11 ed.). Philadelphia: Elsevier Saunders. doi:10.3109/00016348409155523. PMID 6741458.
p. 511. ISBN 0-7216-0240-1.
[64] Hemoglobin at Medline Plus
[49] Lecture – 12 Myoglobin and Hemoglobin on YouTube
[65] Padmanaban, P.; Toora, B. (2011). “Hemoglobin:
[50] Rutjes, H. A.; Nieveen, M. C.; Weber, R. E.; Witte, F.; Emerging marker in stable coronary artery dis-
Van den Thillart, G. E. E. J. M. (20 June 2007). “Mul- ease”. Chronicles of Young Scientists 2 (2): 109.
tiple strategies of Lake Victoria cichlids to cope with doi:10.4103/2229-5186.82971.
lifelong hypoxia include hemoglobin switching”. AJP:
Regulatory, Integrative and Comparative Physiology 293 [66] Society for Biomedical Diabetes Research. SI Unit Con-
(3): R1376–R1383. doi:10.1152/ajpregu.00536.2006. version Calculator.
PMID 17626121.
[67] Handin, Robert I.; Lux, Samuel E. and StosselBlood,
[51] Gronenborn, Angela M.; Clore, G.Marius; Brunori, Mau- Thomas P. (2003). Blood: Principles & Practice of
rizio; Giardina, Bruno; Falcioni, Giancarlo; Perutz, Max Hematology. Lippincott Williams & Wilkins, ISBN
F. (1984). “Stereochemistry of ATP and GTP bound to 0781719933
fish haemoglobins”. Journal of Molecular Biology 178 (3):
731–742. doi:10.1016/0022-2836(84)90249-3. PMID [68] Hemoglobin Level Test. Ibdcrohns.about.com (2013-08-
6492161. 16). Retrieved 2013-09-05.

[52] Weber, Roy E.; Frank B. Jensen (1988). “Func- [69] Although other sources can have slightly differing values,
tional adaptations in hemoglobins from ectothermic in- such as haemoglobin (reference range). gpnotebook.co.uk
vertebrates”. Annual Review of Physiology 50: 161–
179. doi:10.1146/annurev.ph.50.030188.001113. PMID [70] Murray S.S. & McKinney E.S. (2006). Foundations of
3288089. Maternal-Newborn Nursing. 4th ed., p. 919. Philadel-
phia: Saunders Elsevier
[53] Rang, H.P.; Dale M.M.; Ritter J.M.; Moore P.K. (2003).
Pharmacology, Fifth Edition. Elsevier. ISBN 0-443- [71] “Hematocrit (HCT) or Packed Cell Volume (PCV)".
07202-7. DoctorsLounge.com. Retrieved 2007-12-26.
4.5. HEMOGLOBIN 119

[72] Frasca, D.; Dahyot-Fizelier, C.; Catherine, K.; Levrat, Q.; [82] Zal F, Lallier FH, Green BN, Vinogradov SN, Toulmond
Debaene, B.; Mimoz, O. (2011). “Accuracy of a con- A (1996). “The multi-hemoglobin system of the hy-
tinuous noninvasive hemoglobin monitor in intensive care drothermal vent tube worm Riftia pachyptila. II. Com-
unit patients*". Critical Care Medicine 39 (10): 2277– plete polypeptide chain composition investigated by max-
2282. doi:10.1097/CCM.0b013e3182227e2d. PMID imum entropy analysis of mass spectra”. J. Biol. Chem.
21666449. 271 (15): 8875–81. doi:10.1074/jbc.271.15.8875.
PMID 8621529.
[73] Ferrari, M.; Binzoni, T.; Quaresima, V. (1997).
“Oxidative metabolism in muscle”. Philosophical Trans- [83] Minic Z, Hervé G (2004). “Biochemical and enzy-
actions of the Royal Society B: Biological Sciences 352 mological aspects of the symbiosis between the deep-
(1354): 677–683. doi:10.1098/rstb.1997.0049. PMC sea tubeworm Riftia pachyptila and its bacterial en-
1691965. PMID 9232855. dosymbiont”. Eur. J. Biochem. 271 (15): 3093–
102. doi:10.1111/j.1432-1033.2004.04248.x. PMID
[74] Madsen, P. L.; Secher, N. H. (1999). “Near-infrared 15265029.
oximetry of the brain”. Progress in neurobiology 58 (6):
541–560. doi:10.1016/S0301-0082(98)00093-8. PMID [84] Liu L, Zeng M, Stamler JS (1999). “Hemoglobin in-
10408656. duction in mouse macrophages”. Proceedings of the Na-
tional Academy of Sciences of the United States of America
96 (12): 6643–7. doi:10.1073/pnas.96.12.6643. PMC
[75] McCully, K. K.; Hamaoka, T. (2000). “Near-infrared
21968. PMID 10359765.
spectroscopy: What can it tell us about oxygen saturation
in skeletal muscle?". Exercise and sport sciences reviews
[85] Newton DA, Rao KM, Dluhy RA, Baatz JE (2006).
28 (3): 123–127. PMID 10916704.
“Hemoglobin Is Expressed by Alveolar Epithelial Cells”.
Journal of Biological Chemistry 281 (9): 5668–76.
[76] Perrey, S. P. (2008). “Non-invasive NIR spectroscopy
doi:10.1074/jbc.M509314200. PMID 16407281.
of human brain function during exercise”. Methods 45
(4): 289–299. doi:10.1016/j.ymeth.2008.04.005. PMID [86] Nishi, H.; Inagi, R.; Kato, H.; Tanemoto, M.; Kojima, I.;
18539160. Son, D.; Fujita, T.; Nangaku, M. (2008). “Hemoglobin
is Expressed by Mesangial Cells and Reduces Oxidant
[77] Rolfe, P. (2000). “Invivonear-Infraredspectroscopy”. An- Stress”. Journal of the American Society of Nephrology 19
nual Review of Biomedical Engineering 2: 715–754. (8): 1500–1508. doi:10.1681/ASN.2007101085. PMC
doi:10.1146/annurev.bioeng.2.1.715. PMID 11701529. 2488266. PMID 18448584.

[78] This Hb A₁ level is only useful in individuals who [87] Boh, Larry (2001). Pharmacy Practice Manual: A Guide
have red blood cells (RBCs) with normal survivals (i.e., to the Clinical Experience. Lippincott Williams & Wilkins.
normal half-life). In individuals with abnormal RBCs, ISBN 0-7817-2541-0.
whether due to abnormal hemoglobin molecules (such as
Hemoglobin S in Sickle Cell Anemia) or RBC membrane [88] Holden, Constance (2005). “Blood and Steel”. Science
defects – or other problems, the RBC half-life is fre- 309 (5744): 2160. doi:10.1126/science.309.5744.2160d.
quently shortened. In these individuals, an alternative test
called “fructosamine level” can be used. It measures the [89] Moran L, Horton RA, Scrimgeour G, Perry M (2011).
degree of glycation (glucose binding) to albumin, the most Principles of Biochemistry. Boston, MA: Pearson. p. 127.
common blood protein, and reflects average blood glucose ISBN 0-321-70733-8.
levels over the previous 18–21 days, which is the half-life
of albumin molecules in the circulation.
4.5.18 Further reading
[79] Mehagnoul-Schipper DJ, van der Kallen BF, Colier WN,
van der Sluijs MC, van Erning LJ, Thijssen HO, Oese- • Campbell, MK (1999). “Biochemistry” (third ed.).
burg B, Hoefnagels WH, Jansen RW (2002). “Simul-
Harcourt. ISBN 0-03-024426-9.
taneous measurements of cerebral oxygenation changes
during brain activation by near-infrared spectroscopy and
• Eshaghian, S; Horwich, TB; Fonarow, GC
functional magnetic resonance imaging in healthy young
(2006). “An unexpected inverse relationship
and elderly subjects”. Hum Brain Mapp 16 (1): 14–23.
doi:10.1002/hbm.10026. PMID 11870923. between HbA1c levels and mortality in pa-
tients with diabetes and advanced systolic heart
[80] L. Int Panis, B. Goddeeris, R Verheyen (1995). “The failure”. Am Heart J 151 (1): 91.e1–91.e6.
hemoglobin concentration of Chironomus cf.Plumosus L. doi:10.1016/j.ahj.2005.10.008. PMID 16368297.
(Diptera: Chironomidae) larvae from two lentic habi-
tats”. Netherlands Journal of Aquatic Ecology 29 (1): 1–4. • Ganong, WF (2003). “Review of Medical Physiol-
doi:10.1007/BF02061785. ogy” (21st ed.). Lange. ISBN 0-07-140236-5.

[81] Weber RE, Vinogradov SN (2001). “Nonvertebrate • Hager, T (1995). “Force of Nature: The Life of
hemoglobins: functions and molecular adaptations”. Linus Pauling”. Simon and Schuster. ISBN 0-684-
Physiol. Rev. 81 (2): 569–628. PMID 11274340. 80909-5.
120 CHAPTER 4. PROTEINS AND AMINO ACIDS

• Kneipp J, Balakrishnan G, Chen R, Shen TJ,

Sahu SC, Ho NT, Giovannelli JL, Simplaceanu
V, Ho C, Spiro T (2005). “Dynamics of al-
lostery in hemoglobin: roles of the penultimate ty-
rosine H bonds”. J Mol Biol 356 (2): 335–53.
doi:10.1016/j.jmb.2005.11.006. PMID 16368110.

4.5.19 External links

• Proteopedia Hemoglobin

• National Anemia Action Council – anemia.org

• New hemoglobin type causes mock diagnosis with
pulse oxymeters
• Animation of hemoglobin: from deoxy to oxy form
Chapter 5

Enzyme mechanisms

5.1 Enzyme catalysis

Visualization of ubiquitylation

Enzyme catalysis is the increase in the rate of a chemical

reaction by the active site of a protein. The protein
catalyst (enzyme) may be part of a multi-subunit com-
plex, and/or may transiently or permanently associate
with a Cofactor (e.g. adenosine triphosphate). Cataly-
Enzyme changes shape by induced fit upon substrate binding to
sis of biochemical reactions in the cell is vital due to the form enzyme-substrate complex. Hexokinase has a large induced
very low reaction rates of the uncatalysed reactions. A fit motion that closes over the substrates adenosine triphosphate
key driver of protein evolution is the optimization of such and xylose. Binding sites in blue, substrates in black and Mg2+
catalytic activities via protein dynamics.[1] cofactor in yellow. (PDB: 2E2N , 2E2Q)
The mechanism of enzyme catalysis is similar in prin-
ciple to other types of chemical catalysis. By providing
an alternative reaction route the enzyme reduces the en- binding.
ergy required to reach the highest energy transition state
The advantages of the induced fit mechanism arise due
of the reaction. The reduction of activation energy (Ea)
to the stabilizing effect of strong enzyme binding. There
increases the amount of reactant molecules that achieve
are two different mechanisms of substrate binding: uni-
a sufficient level of energy, such that they reach the acti-
form binding, which has strong substrate binding, and dif-
vation energy and form the product. As with other cata-
ferential binding, which has strong transition state bind-
lysts, the enzyme is not consumed during the reaction (as
ing. The stabilizing effect of uniform binding increases
a substrate is) but is recycled such that a single enzyme
both substrate and transition state binding affinity, while
performs many rounds of catalysis.
differential binding increases only transition state bind-
ing affinity. Both are used by enzymes and have been
5.1.1 Induced fit evolutionarily chosen to minimize the Ea of the reaction.
Enzymes that are saturated, that is, have a high affinity
The favored model for the enzyme-substrate interaction is substrate binding, require differential binding to reduce
the induced fit model.[2] This model proposes that the ini- the Ea, whereas small substrate unbound enzymes may
tial interaction between enzyme and substrate is relatively use either differential or uniform binding.
weak, but that these weak interactions rapidly induce These effects have led to most proteins using the differ-
conformational changes in the enzyme that strengthen ential binding mechanism to reduce the Ea, so most pro-

121
122 CHAPTER 5. ENZYME MECHANISMS

viding an alternative chemical pathway for the reaction.

There are six possible mechanisms of “over the barrier”
catalysis as well as a “through the barrier” mechanism:

Proximity and orientation

This increases the rate of the reaction as enzyme-

substrate interactions align reactive chemical groups and
hold them close together. This reduces the entropy of the
reactants and thus makes reactions such as ligations or
addition reactions more favorable, there is a reduction in
the overall loss of entropy when two reactants become a
single product.
This effect is analogous to an effective increase in con-
centration of the reagents. The binding of the reagents to
the enzyme gives the reaction intramolecular character,
which gives a massive rate increase.
However, the situation might be more complex, since
modern computational studies have established that tra-
ditional examples of proximity effects cannot be re-
lated directly to enzyme entropic effects.[4][5][6] Also, the
original entropic proposal[7] has been found to largely
overestimate the contribution of orientation entropy to
catalysis.[8]
The different mechanisms of substrate binding

teins have high affinity of the enzyme to the transition Proton donors or acceptors
state. Differential binding is carried out by the induced
fit mechanism - the substrate first binds weakly, then the
See also: Protein pKa calculations
enzyme changes conformation increasing the affinity to
the transition state and stabilizing it, so reducing the ac-
tivation energy to reach it. Proton donors and acceptors, i.e. acids and base may do-
nate and accept protons in order to stabilize developing
It is important to clarify, however, that the induced fit
charges in the transition state.This typically has the ef-
concept cannot be used to rationalize catalysis. That is,
fect of activating nucleophile and electrophile groups, or
the chemical catalysis is defined as the reduction of Ea‡
stabilizing leaving groups. Histidine is often the residue
(when the system is already in the ES‡ ) relative to Ea‡ in
involved in these acid/base reactions, since it has a pKa
the uncatalyzed reaction in water (without the enzyme).
close to neutral pH and can therefore both accept and do-
The induced fit only suggests that the barrier is lower in
nate protons.
the closed form of the enzyme but does not tell us what
the reason for the barrier reduction is. Many reaction mechanisms involving acid/base catalysis
assume a substantially altered pKa. This alteration of pKa
Induced fit may be beneficial to the fidelity of molecular
is possible through the local environment of the residue.
recognition in the presence of competition and noise via
[3] pKa can also be influenced significantly by the surround-
the conformational proofreading mechanism .
ing environment, to the extent that residues which are ba-
sic in solution may act as proton donors, and vice versa.
5.1.2 Mechanisms of an alternative reac- It is important to clarify that the modification of the pKa’s
tion route is a pure part of the electrostatic mechanism.[9] Further-
more, the catalytic effect of the above example is mainly
These conformational changes also bring catalytic associated with the reduction of the pKa of the oxyan-
residues in the active site close to the chemical bonds in ion and the increase in the pKa of the histidine, while the
the substrate that will be altered in the reaction. After proton transfer from the serine to the histidine is not cat-
binding takes place, one or more mechanisms of catalysis alyzed significantly, since it is not the rate determining
lowers the energy of the reaction’s transition state, by pro- barrier.[10]
5.1. ENZYME CATALYSIS 123

Electrostatic catalysis lar to how covalent intermediates formed with active site
amino acid residues allow stabilization, but the capabili-
Stabilization of charged transition states can also be by ties of cofactors allow enzymes to carryout reactions that
residues in the active site forming ionic bonds (or partial amino acid side residues alone could not. Enzymes uti-
ionic charge interactions) with the intermediate. These lizing such cofactors include the PLP-dependent enzyme
bonds can either come from acidic or basic side chains aspartate transaminase and the TPP-dependent enzyme
found on amino acids such as lysine, arginine, aspartic pyruvate dehydrogenase.[17][18]
acid or glutamic acid or come from metal cofactors such Rather than lowering the activation energy for a reac-
as zinc. Metal ions are particularly effective and can re- tion pathway, covalent catalysis provides an alternative
duce the pKa of water enough to make it an effective nu- pathway for the reaction (via to the covalent intermediate)
cleophile. and so is distinct from true catalysis.[9] For example, the
Systematic computer simulation studies established that energetics of the covalent bond to the serine molecule in
electrostatic effects give, by far, the largest contribution chymotrypsin should be compared to the well-understood
to catalysis.[9] In particular, it has been found that enzyme covalent bond to the nucleophile in the uncatalyzed so-
provides an environment which is more polar than wa- lution reaction. A true proposal of a covalent catalysis
ter, and that the ionic transition states are stabilized by (where the barrier is lower than the corresponding barrier
fixed dipoles. This is very different from transition state in solution) would require, for example, a partial covalent
stabilization in water, where the water molecules must bond to the transition state by an enzyme group (e.g., a
pay with “reorganization energy”.[11] In order to stabilize very strong hydrogen bond), and such effects do not con-
ionic and charged states. Thus, the catalysis is associated tribute significantly to catalysis.
with the fact that the enzyme polar groups are preorga-
nized [12]
Bond strain
The magnitude of the electrostatic field exerted by an en-
zyme’s active site has been shown to be highly correlated
This is the principal effect of induced fit binding, where
with the enzyme’s catalytic rate enhancement[13][14]
the affinity of the enzyme to the transition state is greater
Binding of substrate usually excludes water from the ac- than to the substrate itself. This induces structural re-
tive site, thereby lowering the local dielectric constant to arrangements which strain substrate bonds into a posi-
that of an organic solvent. This strengthens the electro- tion closer to the conformation of the transition state, so
static interactions between the charged/polar substrates lowering the energy difference between the substrate and
and the active sites. In addition, studies have shown that transition state and helping catalyze the reaction.
the charge distributions about the active sites are arranged
However, the strain effect is, in fact, a ground state desta-
so as to stabilize the transition states of the catalyzed reac-
bilization effect, rather than transition state stabilization
tions. In several enzymes, these charge distributions ap-
effect.[9][19] Furthermore, enzymes are very flexible and
parently serve to guide polar substrates toward their bind-
they cannot apply large strain effect.[20]
ing sites so that the rates of these enzymatic reactions are
greater than their apparent diffusion-controlled limits. In addition to bond strain in the substrate, bond strain
may also be induced within the enzyme itself to activate
residues in the active site.
Covalent catalysis

Covalent catalysis involves the substrate forming a tran- Quantum tunneling

sient covalent bond with residues in the enzyme active
site or with a cofactor. This adds an additional covalent These traditional “over the barrier” mechanisms have
intermediate to the reaction, and helps to reduce the en- been challenged in some cases by models and observa-
ergy of later transition states of the reaction. The cova- tions of “through the barrier” mechanisms (quantum tun-
lent bond must, at a later stage in the reaction, be broken neling). Some enzymes operate with kinetics which are
to regenerate the enzyme. This mechanism is utilised faster than what would be predicted by the classical ΔG‡ .
by the catalytic triad of enzymes such as proteases like In “through the barrier” models, a proton or an electron
chymotrypsin and trypsin, where an acyl-enzyme inter- can tunnel through activation barriers.[22][23] Quantum
mediate is formed. An alternative mechanism is schiff tunneling for protons has been observed in tryptamine ox-
base formation using the free amine from a lysine residue, idation by aromatic amine dehydrogenase.[24]
as seen in the enzyme aldolase during glycolysis. Interestingly, quantum tunneling does not appear to pro-
Some enzymes utilize non-amino acid cofactors such vide a major catalytic advantage, since the tunneling con-
as pyridoxal phosphate (PLP) or thiamine pyrophos- tributions are similar in the catalyzed and the uncatalyzed
phate (TPP) to form covalent intermediates with reac- reactions in solution.[23][25][26][27] However, the tunneling
tant molecules.[15][16] Such covalent intermediates func- contribution (typically enhancing rate constants by a fac-
tion to reduce the energy of later transition states, simi- tor of ~1000[24] compared to the rate of reaction for the
124 CHAPTER 5. ENZYME MECHANISMS

classical 'over the barrier' route) is likely crucial to the vi- posed concept, the H transport from the enzyme pro-
ability of biological organisms. This emphasizes the gen- motes the first reactant conversion, breakdown of the first
eral importance of tunneling reactions in biology. initial chemical bond (between groups P1 and P2 ). The
In 1971-1972 the first quantum-mechanical model of en- step of hydrolysis leads to a breakdown of the second
zyme catalysis was formulated.[28][29] chemical bond and regeneration of the enzyme.
The proposed chemical mechanism does not depend on
the concentration of the substrates or products in the
Active enzyme medium. However, a shift in their concentration mainly
causes free energy changes in the first and final steps of
The binding energy of the enzyme-substrate complex the reactions (1) and (2) due to the changes in the free
cannot be considered as an external energy which is nec- energy content of every molecule, whether S or P, in wa-
essary for the substrate activation. The enzyme of high ter solution. This approach is in accordance with the
energy content may firstly transfer some specific ener- following mechanism of muscle contraction. The final
getic group X1 from catalytic site of the enzyme to the step of ATP hydrolysis in skeletal muscle is the product
final place of the first bound reactant, then another group release caused by the association of myosin heads with
X2 from the second bound reactant (or from the second actin.[33] The closing of the actin-binding cleft during the
group of the single reactant) must be transferred to active association reaction is structurally coupled with the open-
site to finish substrate conversion to product and enzyme ing of the nucleotide-binding pocket on the myosin active
regeneration.[30] site.[34]
We can present the whole enzymatic reaction as a two Notably, the final steps of ATP hydrolysis include the fast
coupling reactions: release of phosphate and the slow release of ADP.[35][36]
S1 + EX1 => S1 EX1 => P1 + EP2 (1) S2 + EP2 => S2 EP2 The release of a phosphate anion from bound ADP anion
=> P2 + EX2 (2) into water solution may be considered as an exergonic
reaction because the phosphate anion has low molecular
It may be seen from reaction (1) that the group X1 of the mass.
active enzyme appears in the product due to possibility of
the exchange reaction inside enzyme to avoid both elec- Thus, we arrive at the conclusion that the primary re-
−
trostatic inhibition and repulsion of atoms. So we rep- lease of the inorganic phosphate H2 PO4 leads to trans-
resent the active enzyme as a powerful reactant of the formation of a significant part of the free energy of ATP
enzymatic reaction. The reaction (2) shows incomplete hydrolysis into the kinetic energy of the solvated phos-
conversion of the substrate because its group X2 remains phate, producing active streaming. This assumption of
inside enzyme. This approach as idea had formerly pro- a local mechano-chemical transduction is in accord with
posed relying on the hypothetical extremely high enzy- Tirosh’s mechanism of muscle contraction, where the
matic conversions (catalytically perfect enzyme). [31] muscle force derives from an integrated action of active
streaming created by ATP hydrolysis.[37][38]
The crucial point for the verification of the present ap-
proach is that the catalyst must be a complex of the en-
zyme with the transfer group of the reaction. This chem-
ical aspect is supported by the well-studied mechanisms 5.1.3 Examples of catalytic mechanisms
of the several enzymatic reactions. Let us consider the
reaction of peptide bond hydrolysis catalyzed by a pure In reality, most enzyme mechanisms involve a combina-
protein α-chymotrypsin (an enzyme acting without a co- tion of several different types of catalysis.
factor), which is a well-studied member of the serine pro-
teases family, see.[32]
We present the experimental results for this reaction as Triose phosphate isomerase
two chemical steps:
Triose phosphate isomerase (EC 5.3.1.1) catalyses
S1 + EH => P1 + EP2 (3) EP2 + H–O–H => EH + P2 (4)
the reversible interconvertion of the two triose phos-
where S1 is a polypeptide, P1 and P2 are products. The phates isomers dihydroxyacetone phosphate and D-
first chemical step (3) includes the formation of a cova- glyceraldehyde 3-phosphate.
lent acyl-enzyme intermediate. The second step (4) is the
deacylation step. It is important to note that the group H+,
initially found on the enzyme, but not in water, appears in Trypsin
the product before the step of hydrolysis, therefore it may
be considered as an additional group of the enzymatic re- Trypsin (EC 3.4.21.4) is a serine protease that cleaves
action. protein substrates at lysine and arginine amino acid
Thus, the reaction (3) shows that the enzyme acts as a residues using a catalytic triad of active site residues to
powerful reactant of the reaction. According to the pro- perform nucleophilic, covalent catalysis.
5.1. ENZYME CATALYSIS 125

Aldolase ONE 2 (5): e468. Bibcode:2007PLoSO...2..468S.

doi:10.1371/journal.pone.0000468. PMC 1868595.
Aldolase (EC 4.1.2.13) catalyses the breakdown of PMID 17520027.
fructose 1,6-bisphosphate (F-1,6-BP) into glyceraldehyde
[4] Stanton, R.V.; Perakyla, M.; Bakowies, D.; Kollman,
3-phosphate and dihydroxyacetone phosphate (DHAP). P.A. (1998). “Combined ab initio and Free Energy
Calculations To Study Reactions in Enzymes and So-
lution: Amide Hydrolysis in Trypsin and Aqueous So-
5.1.4 Enzyme diffusivity lution”. J. Am. Chem. Soc 120 (14): 3448–3457.
doi:10.1021/ja972723x.
The advent of single-molecule studies led in the 2010s
to the observation that the movement of untethered en- [5] Kuhn, B.; Kollman, P.A. (2000). “QM-FE and Molecular
zymes increases with increasing substrate concentration Dynamics Calculations on Catechol O-Methyltransferase:
and increasing reaction enthalpy.[39] Subsequent observa- Free Energy of Activation in the Enzyme and in Aqueous
Solution and Regioselectivity of the Enzyme-Catalyzed
tions suggest that this increase in diffusivity is driven by
Reaction”. J. Am. Chem. Soc 122 (11): 2586–2596.
transient displacement of the enzyme’s center of mass,
doi:10.1021/ja992218v.
resulting in a “recoil effect that propels the enzyme”.[40]
[6] Bruice, T.C.; Lightstone, F.C. (1999). “Ground State and
Transition State Contributions to the Rates of Intramolec-
5.1.5 Reaction Similarity ular and Enzymatic Reactions”. Acc. Chem. Res. 32 (2):
127–136. doi:10.1021/ar960131y.
Similarity between enzymatic reactions (EC) can be cal-
culated by using bond changes, reaction centres or sub- [7] Page, M.I.; Jencks, W.P. (1971). “Entropic Con-
tributions to Rate Accelerations in Enzymic and
structure metrics (EC-BLAST).[41]
Intramolecular Reactions and the Chelate Ef-
fect”. Proc. Natl. Acad. Sci. USA 1971 (68):
1678–1683. Bibcode:1971PNAS...68.1678P.
5.1.6 See also doi:10.1073/pnas.68.8.1678. PMC 389269. PMID
5288752.
• Catalytic triad
[8] Warshel, A.; Parson, W.W. (2001). “Dynamics of Bio-
• Enzyme assay chemical and Biophysical Reactions: Insight from Com-
puter Simulations”. Quart. Rev. Biophys 34: 563–679.
• Enzyme kinetics
doi:10.1017/s0033583501003730.
• Protein dynamics
[9] Warshel, A.; Sharma, P.K.; Kato, M.; Xiang, Y.; Liu,
• Quantum tunnelling H.; Olsson, M.H.M. (2006). “Electrostatic Basis of
Enzyme Catalysis”. Chem. Rev. 106: 3210–3235.
• The Proteolysis Map doi:10.1021/cr0503106.

• Time resolved crystallography [10] Warshel, A.; Naray-Szabo, G.; Sussman, F.; Hwang,
J.-K. (1989). “How do Serine Proteases Re-
• Enzyme promiscuity ally Work?". Biochemistry 1989 (28): 3629–37.
doi:10.1021/bi00435a001. PMID 2665806.

5.1.7 References [11] Marcus, R. A. (1965). “On the Theory of Electron-

Transfer Reactions. VI. Unified Treatment for Homoge-
[1] Kamerlin, S. C.; Warshel, A (2010). “At the dawn neous and Electrode Reactions”. J. Chem. Phys. 43: 679–
of the 21st century: Is dynamics the missing link 701. doi:10.1063/1.1696792.
for understanding enzyme catalysis?". Proteins: Struc-
[12] Warshel, A (1978). “Energetics of Enzyme Cataly-
ture, Function, and Bioinformatics 78 (6): 1339–
sis”. Proc. Natl. Acad. Sci. USA 75: 5250.
75. doi:10.1002/prot.22654. PMC 2841229. PMID
doi:10.1073/pnas.75.11.5250.
20099310.
[13] “How Enzymes Work”
[2] Koshland DE (February 1958). “Application of
a Theory of Enzyme Specificity to Protein Syn- [14] “EXTREME ELECTRIC FIELDS POWER CATALY-
thesis”. Proc. Natl. Acad. Sci. U.S.A. 44 SIS IN THE ACTIVE SITE OF KETOSTEROID ISO-
(2): 98–104. Bibcode:1958PNAS...44...98K. MERASE”,
doi:10.1073/pnas.44.2.98. PMC 335371. PMID
16590179. [15] Toney, M. D. “Reaction specificity in pyridoxal enzymes.”
Archives of biochemistry and biophysics (2005) 433:
[3] Savir Y; Tlusty T (2007). Scalas, Enrico, 279-287
ed. “Conformational Proofreading: The Im-
pact of Conformational Changes on the Speci- [16] Micronutrient Information Center, Oregon State Univer-
ficity of Molecular Recognition” (PDF). PLOS sity
126 CHAPTER 5. ENZYME MECHANISMS

[17] Voet, Donald; Judith Voet (2004). Biochemistry. John [30] Foigel, A.G. (2011). “Is the enzyme a powerful reac-
Wiley & Sons Inc. pp. 986–989. ISBN 0-471-25090-2. tant of the biochemical reaction?". Mol. Cell. Biochem
352: 87-89 Foigel, Alexander G. (2011). “Is the en-
[18] Voet, Donald; Judith Voet (2004). Biochemistry. John zyme a powerful reactant of the biochemical reaction?".
Wiley & Sons Inc. pp. 604–606. ISBN 0-471-25090-2. Molecular and Cellular Biochemistry 352 (1–2): 87–9.
doi:10.1007/s11010-011-0742-4. PMID 21318350.
[19] Jencks, William P. (1987) [1969]. Catalysis in Chemistry
and Enzymology. McGraw-Hill series in advanced chem- [31] Fogel, A.G. (1982). “Cooperativity of enzymatic reac-
istry (reprint ed.). New York: Dover Publications. ISBN tions and molecular aspects of energy transduction”. Mol.
9780486654607. Cell. Biochem 47: 59–64. doi:10.1007/bf00241567.

[20] Warshel, A.; Levitt, M. (1976). “Theoretical Stud- [32] Hengge, AC; Stein, RL (2004). “Role of protein confor-
ies of Enzymatic Reactions: Dielectric Electrostatic and mational mobility in enzyme catalysis: acylation of alpha-
Steric Stabilization of the Carbonium Ion in the Reac- chymotrypsin by specific peptide substrates”. Biochem-
tion of Lysozyme”. Journal of Molecular Biology 103 (2): istry 43: 742–747. doi:10.1021/bi030222k.
227–49. doi:10.1016/0022-2836(76)90311-9. PMID
985660. [33] Lymn, RW; Taylor, EW. (1971). “Mechanism of adeno-
sine triphosphate hydrolysis by actomyosin”. Biochem-
[21] <fundamentals of biochemistry Voet, voet and Pratt 4th istry 10: 4617–4624. doi:10.1021/bi00801a004.
edition>, which is similar in shape to the transition state.
[34] Holmes, KC; Angert, I; Kull, FG; Jahn, W; Schroder,
[22] Garcia-Viloca, M; Gao, J; Karplus, M; Truhlar, DG RR. (2003). “Electron cryo-microscopy shows how strong
(2004). “How enzymes work: analysis by mod- binding of myosin to actin releases nucleotide”. Nature
ern rate theory and computer simulations”. Science 425: 423–427. doi:10.1038/nature02005.
303 (5655): 186–95. Bibcode:2004Sci...303..186G.
doi:10.1126/science.1088172. PMID 14716003. [35] Siemankowski, RF; Wiseman, MO; White, HD. (1985).
“ADP dissociation from actomyosin subfragment 1 is
[23] Olsson, MH; Siegbahn, PE; Warshel, A (2004). “Simula- sufficiently slow to limit the unloaded shortening veloc-
tions of the large kinetic isotope effect and the tempera- ity in vertebrate muscle”. Proc. Natl. Acad. Sci. USA 82:
ture dependence of the hydrogen atom transfer in lipoxy- 658–662. doi:10.1073/pnas.82.3.658.
genase”. Journal of the American Chemical Society 126
(9): 2820–8. doi:10.1021/ja037233l. PMID 14995199. [36] White, HD; Belknap, B; Webb, MR. (1997). “Kinetics
of nucleoside triphosphate cleavage and phosphate release
[24] Masgrau, L; Roujeinikova, A; Johannissen, LO; Hothi, steps by associated rabbit skeletal actomyosin, measured
P; Basran, J; Ranaghan, KE; Mulholland, AJ; Sutcliffe, using a novel fluorescent probe for phosphate”. Biochem-
MJ et al. (2006). “Atomic description of an en- istry 36: 11828–11836. doi:10.1021/bi970540h.
zyme reaction dominated by proton tunneling”. Science
312 (5771): 237–41. Bibcode:2006Sci...312..237M. [37] Tirosh, R; Low, WZ; Oplatka, A. (1990). “Transla-
doi:10.1126/science.1126002. PMID 16614214. tional motion of actin filaments in the presence of heavy
meromyosin and MgATP as measured by Doppler broad-
[25] Hwang, J.-K.; Warshel, A. (1996). “How important ening of laser light scattering”. Biochim. Biophys. Acta
are quantum mechanical nuclear motions in enzyme 1037: 274–280. doi:10.1016/0167-4838(90)90025-b.
catalysis”. J. Am. Chem. Soc 118: 11745–11751.
doi:10.1021/ja962007f. [38] Tirosh, R. (2006). “Ballistic protons and microwave-
induced water solutions (solitons) in bioenergetic trans-
[26] Ball, P. (2004). “Enzymes: By chance, or formations”. Int. J. Mol. Sci. 7: 320–345.
by design?". Nature 431 (7007): 396–397. doi:10.3390/i7090320.
Bibcode:2004Natur.431..396B. doi:10.1038/431396a.
[39] Muddana, Hari S.; Sengupta, Samudra; Mallouk, Thomas
[27] Olsson, M.H.M.; Parson, W.W.; Warshel, A. (2006). E. et al. (28 January 2010). “Substrate Catal-
“Dynamical Contributions to Enzyme Catalysis: Critical ysis Enhances Single-Enzyme Diffusion”. Journal
Tests of A Popular Hypothesis”. Chem. Rev. 106 (5): of the American Chemical Society 132 (7): 2110–1.
1737–1756. doi:10.1021/cr040427e. PMID 16683752. doi:10.1021/ja908773a.

[28] Volkenshtein M.V., Dogonadze R.R., Madumarov A.K., [40] Riedel, Clement; Gabizon, Ronen; Wilson, Christian A.
Urushadze Z.D., Kharkats Yu.I. Theory of Enzyme Catal- M. et al. (8 January 2015). “The heat released dur-
ysis.- Molekuliarnaya Biologia, Moscow, 6, 1972, 431- ing catalytic turnover enhances the diffusion of an en-
439 zyme”. Nature 517: 227–30. doi:10.1038/nature14043.
Lay summary – Nature: News & Views (8 January 2015).
[29] Volkenshtein M.V., Dogonadze R.R., Madumarov A.K.,
Urushadze Z.D., Kharkats Yu.I. Electronic and Con- [41] Rahman, SA; Cuesta, SM; Furnham, N; Holliday, GL;
formational Interactions in Enzyme Catalysis. In: Thornton, JM (2014). “EC-BLAST: a tool to automat-
E.L. Andronikashvili (Ed.), Konformatsionnie Izmenenia ically search and compare enzyme reactions”. Nature
Biopolimerov v Rastvorakh, Publishing House “Nauka”, Methods 11: 171–174. doi:10.1038/nmeth.2803. PMID
Moscow, 1973, 153-157 24412978.
5.1. ENZYME CATALYSIS 127

5.1.8 Further reading

• Alan Fersht, Structure and Mechanism in Protein Sci-
ence : A Guide to Enzyme Catalysis and Protein Fold-
ing. W. H. Freeman, 1998. ISBN 0-7167-3268-8
• Dedicated issue of Philosophical Transactions B on
Quantum catalysis in enzymes freely available.
Chapter 6

Enzyme kinetics

6.1 Enzyme kinetics the enzymatic mechanism

E + S <——> ES <——> ES*< ——> EP <——> E +
P
. These mechanisms can be divided into single-
substrate and multiple-substrate mechanisms. Kinetic
studies on enzymes that only bind one substrate, such as
triosephosphate isomerase, aim to measure the affinity
with which the enzyme binds this substrate and the
turnover rate. Some other examples of enzymes are phos-
phofructokinase and hexokinase, both of which are im-
portant for cellular respiration (glycolysis).
When enzymes bind multiple substrates, such as
dihydrofolate reductase (shown right), enzyme kinetics
can also show the sequence in which these substrates bind
and the sequence in which products are released. An ex-
ample of enzymes that bind a single substrate and release
multiple products are proteases, which cleave one pro-
tein substrate into two polypeptide products. Others join
two substrates together, such as DNA polymerase link-
ing a nucleotide to DNA. Although these mechanisms
are often a complex series of steps, there is typically one
rate-determining step that determines the overall kinetics.
This rate-determining step may be a chemical reaction
or a conformational change of the enzyme or substrates,
such as those involved in the release of product(s) from
the enzyme.
Dihydrofolate reductase from E. coli with its two substrates Knowledge of the enzyme’s structure is helpful in in-
dihydrofolate (right) and NADPH (left), bound in the active site.
terpreting kinetic data. For example, the structure can
The protein is shown as a ribbon diagram, with alpha helices
suggest how substrates and products bind during catal-
in red, beta sheets in yellow and loops in blue. Generated from
7DFR. ysis; what changes occur during the reaction; and even
the role of particular amino acid residues in the mecha-
Enzyme kinetics is the study of the chemical reactions nism. Some enzymes change shape significantly during
that are catalysed by enzymes. In enzyme kinetics, the the mechanism; in such cases, it is helpful to determine
reaction rate is measured and the effects of varying the the enzyme structure with and without bound substrate
conditions of the reaction are investigated. Studying an analogues that do not undergo the enzymatic reaction.
enzyme’s kinetics in this way can reveal the catalytic Not all biological catalysts are protein enzymes; RNA-
mechanism of this enzyme, its role in metabolism, how based catalysts such as ribozymes and ribosomes are es-
its activity is controlled, and how a drug or an agonist sential to many cellular functions, such as RNA splic-
might inhibit the enzyme. ing and translation. The main difference between ri-
Enzymes are usually protein molecules that manipulate bozymes and enzymes is that RNA catalysts are com-
other molecules — the enzymes’ substrates. These target posed of nucleotides, whereas enzymes are composed of
molecules bind to an enzyme’s active site and are trans- amino acids. Ribozymes also perform a more limited set
formed into products through a series of steps known as of reactions, although their reaction mechanisms and ki-

128
6.1. ENZYME KINETICS 129

netics can be analysed and classified by the same meth-

ods.

6.1.1 General principles

Product formed
Initial rate period

Time

Progress curve for an enzyme reaction. The slope in the initial

rate period is the initial rate of reaction v. The Michaelis–
Menten equation describes how this slope varies with the con-
As larger amounts of substrate are added to a reaction, the avail-
centration of substrate.
able enzyme binding sites become filled to the limit of Vmax . Be-
yond this limit the enzyme is saturated with substrate and the re-
action rate ceases to increase.
products and reactants; radiometric assays involve the
The reaction catalysed by an enzyme uses exactly the incorporation or release of radioactivity to measure the
same reactants and produces exactly the same products amount of product made over time. Spectrophotometric
as the uncatalysed reaction. Like other catalysts, en- assays are most convenient since they allow the rate of the
zymes do not alter the position of equilibrium between reaction to be measured continuously. Although radio-
substrates and products.[1] However, unlike uncatalysed metric assays require the removal and counting of sam-
chemical reactions, enzyme-catalysed reactions display ples (i.e., they are discontinuous assays) they are usually
saturation kinetics. For a given enzyme concentration and extremely sensitive and can measure very low levels of
for relatively low substrate concentrations, the reaction enzyme activity.[2] An analogous approach is to use mass
rate increases linearly with substrate concentration; the spectrometry to monitor the incorporation or release of
enzyme molecules are largely free to catalyse the reac- stable isotopes as substrate is converted into product.
tion, and increasing substrate concentration means an in-
creasing rate at which the enzyme and substrate molecules The most sensitive enzyme assays use lasers focused
encounter one another. However, at relatively high sub- through a microscope to observe changes in single en-
strate concentrations, the reaction rate asymptotically ap-zyme molecules as they catalyse their reactions. These
proaches the theoretical maximum; the enzyme active measurements either use changes in the fluorescence of
cofactors during an enzyme’s reaction mechanism, or of
sites are almost all occupied and the reaction rate is deter-
mined by the intrinsic turnover rate of the enzyme. The fluorescent dyes added onto specific sites of the protein
substrate concentration midway between these two limit- to report movements that occur during catalysis.[3] These
ing cases is denoted by KM. studies are providing a new view of the kinetics and dy-
namics of single enzymes, as opposed to traditional en-
The two most important kinetic properties of an enzyme zyme kinetics, which observes the average behaviour of
are how quickly the enzyme becomes saturated with a populations of millions of enzyme molecules.[4][5]
particular substrate, and the maximum rate it can achieve.
Knowing these properties suggests what an enzyme might An example progress curve for an enzyme assay is shown
do in the cell and can show how the enzyme will respond above. The enzyme produces product at an initial rate
to changes in these conditions. that is approximately linear for a short period after the
start of the reaction. As the reaction proceeds and sub-
strate is consumed, the rate continuously slows (so long
6.1.2 Enzyme assays as substrate is not still at saturating levels). To measure
the initial (and maximal) rate, enzyme assays are typi-
Main article: Enzyme assay cally carried out while the reaction has progressed only a
Enzyme assays are laboratory procedures that measure few percent towards total completion. The length of the
the rate of enzyme reactions. Because enzymes are not initial rate period depends on the assay conditions and
consumed by the reactions they catalyse, enzyme assays can range from milliseconds to hours. However, equip-
usually follow changes in the concentration of either sub- ment for rapidly mixing liquids allows fast kinetic mea-
strates or products to measure the rate of reaction. There surements on initial rates of less than one second.[6] These
are many methods of measurement. Spectrophotometric very rapid assays are essential for measuring pre-steady-
assays observe change in the absorbance of light between state kinetics, which are discussed below.
130 CHAPTER 6. ENZYME KINETICS

Most enzyme kinetics studies concentrate on this initial, the reaction rate (v) increases as [S] increases, as shown
approximately linear part of enzyme reactions. However, on the right. However, as [S] gets higher, the enzyme be-
it is also possible to measure the complete reaction curve comes saturated with substrate and the rate reaches V ₐₓ,
and fit this data to a non-linear rate equation. This way the enzyme’s maximum rate.
of measuring enzyme reactions is called progress-curve The Michaelis–Menten kinetic model of a single-
analysis.[7] This approach is useful as an alternative to substrate reaction is shown on the right. There is an ini-
rapid kinetics when the initial rate is too fast to measure tial bimolecular reaction between the enzyme E and sub-
accurately. strate S to form the enzyme–substrate complex ES but
the rate of enzymatic reaction increase with the increase
of the substrate concentration up to a certain level but
6.1.3 Single-substrate reactions then more increase in substrate concentration does not
cause any increase in reaction rate as there no more E
Enzymes with single-substrate mechanisms include
remain available for reacting with S and the rate of reac-
isomerases such as triosephosphateisomerase or
tion become dependent on ES and the reaction become
bisphosphoglycerate mutase, intramolecular lyases such
unimolecular reaction. Although the enzymatic mecha-
as adenylate cyclase and the hammerhead ribozyme, kcat
an RNA lyase.[8] However, some enzymes that only nism for the unimolecular reaction ES −→E + P can be
have a single substrate do not fall into this category quite complex, there is typically one rate-determining en-
of mechanisms. Catalase is an example of this, as the zymatic step that allows this reaction to be modelled as a
enzyme reacts with a first molecule of hydrogen peroxide single catalytic step with an apparent unimolecular rate
substrate, becomes oxidised and is then reduced by constant k ₐ . If the reaction path proceeds over one or
a second molecule of substrate. Although a single several intermediates, k ₐ will be a function of several el-
substrate is involved, the existence of a modified enzyme ementary rate constants, whereas in the simplest case of a
intermediate means that the mechanism of catalase is single elementary reaction (e.g. no intermediates) it will
actually a ping–pong mechanism, a type of mechanism be identical to the elementary unimolecular rate constant
that is discussed in the Multi-substrate reactions section k2 . The apparent unimolecular rate constant k ₐ is also
below. called turnover number and denotes the maximum num-
ber of enzymatic reactions catalysed per second.
The Michaelis–Menten equation[9] describes how the
Michaelis–Menten kinetics (initial) reaction rate v0 depends on the position of the
substrate-binding equilibrium and the rate constant k2 .

Vmax [S]
v0 = KM +[S]
(Michaelis–Menten equation)

with the constants

def k2 + k−1
A chemical reaction mechanism with or without enzyme KM = ≈ KD
catalysis. The enzyme (E) binds substrate (S) to produce k1
def
product (P). Vmax = kcat [E]tot
This Michaelis–Menten equation is the basis for most
single-substrate enzyme kinetics. Two crucial assump-
tions underlie this equation (apart from the general as-
sumption about the mechanism only involving no inter-
mediate or product inhibition, and there is no allostericity
or cooperativity). The first assumption is the so-called
quasi-steady-state assumption (or pseudo-steady-state hy-
pothesis), namely that the concentration of the substrate-
bound enzyme (and hence also the unbound enzyme)
Saturation curve for an enzyme reaction showing the
changes much more slowly than those of the product and
relation between the substrate concentration and reaction
substrate and thus the change over time of the complex
rate. !
Main article: Michaelis–Menten kinetics can be set to zero d[ES]/dt = 0 . The second as-
sumption is that the total enzyme concentration does not
!
As enzyme-catalysed reactions are saturable, their rate of change over time, thus [E]tot = [E] + [ES] = const . A
catalysis does not show a linear response to increasing complete derivation can be found here.
substrate. If the initial rate of the reaction is measured The Michaelis constant KM is experimentally defined as
over a range of substrate concentrations (denoted as [S]), the concentration at which the rate of the enzyme reaction
6.1. ENZYME KINETICS 131

is half V ₐₓ, which can be verified by substituting [S] =

K into the Michaelis–Menten equation and can also be [S]
seen graphically. If the rate-determining enzymatic step = W [F (t)]
KM
is slow compared to substrate dissociation ( k2 ≪ k−1
), the Michaelis constant KM is roughly the dissociation where W[] is the Lambert-W function.[14][15] and where
constant KD of the ES complex. F(t) is
If [S] is small compared to KM then the term [S]/(KM +
[S]) ≈ [S]/KM and also very little ES complex is ( )
formed, thus [E]0 ≈ [E] . Therefore, the rate of product F (t) = [S]0 exp [S]0 − Vmax t
formation is KM KM KM
This equation is encompassed by the equation below, ob-
tained by Berberan-Santos (MATCH Commun. Math.
kcat Comput. Chem. 63 (2010) 283), which is also valid
v0 ≈ [E][S] if[S] ≪ KM
KM when the initial substrate concentration is close to that
Thus the product formation rate depends on the enzyme of enzyme,
concentration as well as on the substrate concentration,
the equation resembles a bimolecular reaction with a cor-
[S] Vmax W [F (t)]
responding pseudo-second order rate constant k2 /KM . = W [F (t)] −
KM kcat KM 1 + W [F (t)]
This constant is a measure of catalytic efficiency. The
most efficient enzymes reach a k2 /KM in the range of where W[] is again the Lambert-W function.
108 – 1010 M−1 s−1 . These enzymes are so efficient they
effectively catalyse a reaction each time they encounter a
substrate molecule and have thus reached an upper theo- Linear plots of the Michaelis–Menten equation
retical limit for efficiency (diffusion limit); and are some-
times referred to as kinetically perfect enzymes.[10] See also: Lineweaver–Burk plot and Eadie-Hofstee dia-
gram
The plot of v versus [S] above is not linear; although ini-
Direct use of the Michaelis–Menten equation for time
course kinetic analysis

Further information: Rate equation

Further information: Reaction Progress Kinetic Analysis

The observed velocities predicted by the Michaelis–

Menten equation can be used to directly model the time
course disappearance of substrate and the production of
product through incorporation of the Michaelis–Menten
equation into the equation for first order chemical kinet-
ics. This can only be achieved however if one recognises
the problem associated with the use of Euler’s number
in the description of first order chemical kinetics. i.e. Lineweaver–Burk or double-reciprocal plot of kinetic data,
e−k is a split constant that introduces a systematic error showing the significance of the axis intercepts and gradient.
into calculations and can be rewritten as a single constant
tially linear at low [S], it bends over to saturate at high
which represents the remaining substrate after each time
period.[11] [S]. Before the modern era of nonlinear curve-fitting on
computers, this nonlinearity could make it difficult to
estimate KM and V ₐₓ accurately. Therefore, several
[S] = [S]0 (1 − k) t researchers developed linearisations of the Michaelis–
Menten equation, such as the Lineweaver–Burk plot, the
[S] = [S]0 (1 − v/[S]0 )t Eadie–Hofstee diagram and the Hanes–Woolf plot. All
of these linear representations can be useful for visual-
[S] = [S]0 (1 − (Vmax [S]0 /(KM + [S]0 )/[S]0 ))t ising data, but none should be used to determine kinetic
In 1983 Stuart Beal (and also independently Santiago parameters, as computer software is readily available that
Schnell and Claudio Mendoza in 1997) derived a closed allows for more accurate
[16]
determination by nonlinear re-
form solution for the time course kinetics analysis of gression methods.
the Michaelis-Menten mechanism.[12][13] The solution, The Lineweaver–Burk plot or double reciprocal plot is a
known as the Schnell-Mendoza equation, has the form: common way of illustrating kinetic data. This is produced
132 CHAPTER 6. ENZYME KINETICS

by taking the reciprocal of both sides of the Michaelis– Michaelis–Menten kinetics with intermediate
Menten equation. As shown on the right, this is a lin-
ear form of the Michaelis–Menten equation and produces One could also consider the less simple case
a straight line with the equation y = mx + c with a y-
intercept equivalent to 1/V ₐₓ and an x-intercept of the
k1
graph representing −1/KM.
E + S −→
k2 k3
←− ES −→EI −→E + P
k−1

where a complex with the enzyme and an intermedi-

1 KM 1 ate exists and the intermediate is converted into prod-
= +
v Vmax[ S] Vmax uct in a second step. In this case we have a very similar
equation[21]
Naturally, no experimental values can be taken at negative
1/[S]; the lower limiting value 1/[S] = 0 (the y-intercept)
[S][E]0
corresponds to an infinite substrate concentration, where v0 = kcat
KM′ + [S]
1/v=1/Vmax as shown at the right; thus, the x-intercept
is an extrapolation of the experimental data taken at pos- but the constants are different
itive concentrations. More generally, the Lineweaver–
Burk plot skews the importance of measurements taken
at low substrate concentrations and, thus, can yield inac- ′ def k3 k3 k2 + k−1
curate estimates of V ₐₓ and KM.[17] A more accurate KM = KM = ·
k2 + k3 k2 + k3 k1
linear plotting method is the Eadie-Hofstee plot. In this def k k
3 2
case, v is plotted against v/[S]. In the third common lin- kcat =
k2 + k3
ear representation, the Hanes-Woolf plot, [S]/v is plotted
against [S]. In general, data normalisation can help dimin- We see that for the limiting case k3 ≫ k2 , thus when the
ish the amount of experimental work and can increase the last step from EI to E + P is much faster than the previous
reliability of the output, and is suitable for both graphical step, we get again the original equation. Mathematically
′
and numerical analysis.[18] we have then KM ≈ KM and kcat ≈ k2 .

6.1.4 Multi-substrate reactions

Practical significance of kinetic constants
Multi-substrate reactions follow complex rate equations
that describe how the substrates bind and in what se-
The study of enzyme kinetics is important for two basic quence. The analysis of these reactions is much simpler
reasons. Firstly, it helps explain how enzymes work, and if the concentration of substrate A is kept constant and
secondly, it helps predict how enzymes behave in living substrate B varied. Under these conditions, the enzyme
organisms. The kinetic constants defined above, KM and behaves just like a single-substrate enzyme and a plot of
V ₐₓ, are critical to attempts to understand how enzymes v by [S] gives apparent KM and V ₐₓ constants for sub-
work together to control metabolism. strate B. If a set of these measurements is performed at
Making these predictions is not trivial, even for sim- different fixed concentrations of A, these data can be used
ple systems. For example, oxaloacetate is formed to work out what the mechanism of the reaction is. For
by malate dehydrogenase within the mitochondrion. an enzyme that takes two substrates A and B and turns
Oxaloacetate can then be consumed by citrate syn- them into two products P and Q, there are two types of
thase, phosphoenolpyruvate carboxykinase or aspartate mechanism: ternary complex and ping–pong.
aminotransferase, feeding into the citric acid cycle,
gluconeogenesis or aspartic acid biosynthesis, respec-
tively. Being able to predict how much oxaloacetate goes Ternary-complex mechanisms
into which pathway requires knowledge of the concen-
tration of oxaloacetate as well as the concentration and In these enzymes, both substrates bind to the enzyme
kinetics of each of these enzymes. This aim of predict- at the same time to produce an EAB ternary complex.
ing the behaviour of metabolic pathways reaches its most The order of binding can either be random (in a random
complex expression in the synthesis of huge amounts of mechanism) or substrates have to bind in a particular se-
kinetic and gene expression data into mathematical mod- quence (in an ordered mechanism). When a set of v by
els of entire organisms. Alternatively, one useful simplifi- [S] curves (fixed A, varying B) from an enzyme with a
cation of the metabolic modelling problem is to ignore the ternary-complex mechanism are plotted in a Lineweaver–
underlying enzyme kinetics and only rely on information Burk plot, the set of lines produced will intersect.
about the reaction network’s stoichiometry, a technique Enzymes with ternary-complex mechanisms include
called flux balance analysis.[19][20] glutathione S-transferase,[22] dihydrofolate reductase[23]
6.1. ENZYME KINETICS 133

6.1.5 Non-Michaelis–Menten kinetics

A B P Q
Main article: Allosteric regulation
E EA EQ E Some enzymes produce a sigmoid v by [S] plot, which of-
EAB EPQ
EB EP
B A Q P
25

Random-order ternary-complex mechanism for an enzyme reac- 20

tion. The reaction path is shown as a line and enzyme interme-

Rate of reaction
diates containing substrates A and B or products P and Q are 15

written below the line.

10

and DNA polymerase.[24] The following links show 5

short animations of the ternary-complex mechanisms

0
of the enzymes dihydrofolate reductase[β] and DNA 0 50 100 150 200
polymerase[γ] . Concentration of substrate

Saturation curve for an enzyme reaction showing sigmoid kinet-

Ping–pong mechanisms ics.

ten indicates cooperative binding of substrate to the ac-

A P B Q tive site. This means that the binding of one substrate
E EA E*P E* E*B EQ E
molecule affects the binding of subsequent substrate
molecules. This behavior is most common in multimeric
enzymes with several interacting active sites.[28] Here,
Ping–pong mechanism for an enzyme reaction. Intermediates
contain substrates A and B or products P and Q. the mechanism of cooperation is similar to that of
hemoglobin, with binding of substrate to one active site
altering the affinity of the other active sites for substrate
As shown on the right, enzymes with a ping-pong mech- molecules. Positive cooperativity occurs when binding
anism can exist in two states, E and a chemically mod- of the first substrate molecule increases the affinity of the
ified form of the enzyme E*; this modified enzyme is other active sites for substrate. Negative cooperativity
known as an intermediate. In such mechanisms, substrate occurs when binding of the first substrate decreases the
A binds, changes the enzyme to E* by, for example, trans- affinity of the enzyme for other substrate molecules.
ferring a chemical group to the active site, and is then re-
leased. Only after the first substrate is released can sub- Allosteric enzymes include mammalian tyrosyl tRNA-
synthetase, which shows negative cooperativity,[29]
strate B bind and react with the modified enzyme, regen-
erating the unmodified E form. When a set of v by [S] and bacterial aspartate transcarbamoylase[30] and
phosphofructokinase,[31] which show positive coopera-
curves (fixed A, varying B) from an enzyme with a ping–
pong mechanism are plotted in a Lineweaver–Burk plot, tivity.
a set of parallel lines will be produced. This is called a Cooperativity is surprisingly common and can help regu-
secondary plot. late the responses of enzymes to changes in the concen-
Enzymes with ping–pong mechanisms include trations of their substrates. Positive cooperativity makes
some oxidoreductases such as thioredoxin per- enzymes much more sensitive to [S] and their activities
oxidase,[25] transferases such as acylneuraminate can show large changes over a narrow range of substrate
cytidylyltransferase[26] and serine proteases such as concentration. Conversely, negative cooperativity makes
trypsin and chymotrypsin.[27] Serine proteases are a enzymes insensitive to small changes in [S].
very common and diverse family of enzymes, including The Hill equation (biochemistry)[32] is often used to de-
digestive enzymes (trypsin, chymotrypsin, and elastase), scribe the degree of cooperativity quantitatively in non-
several enzymes of the blood clotting cascade and many Michaelis–Menten kinetics. The derived Hill coefficient
others. In these serine proteases, the E* intermediate n measures how much the binding of substrate to one
is an acyl-enzyme species formed by the attack of an active site affects the binding of substrate to the other
active site serine residue on a peptide bond in a protein active sites. A Hill coefficient of <1 indicates negative
substrate. A short animation showing the mechanism of cooperativity and a coefficient of >1 indicates positive
chymotrypsin is linked here.[δ] cooperativity.
134 CHAPTER 6. ENZYME KINETICS

6.1.6 Pre-steady-state kinetics ditions or on slightly modified enzymes or substrates of-

ten shed light on this chemical mechanism, as they re-
veal the rate-determining step or intermediates in the re-
action. For example, the breaking of a covalent bond
to a hydrogen atom is a common rate-determining step.
Amount of product

Amount of enzyme Which of the possible hydrogen transfers is rate deter-

mining can be shown by measuring the kinetic effects
of substituting each hydrogen by deuterium, its stable
isotope. The rate will change when the critical hydro-
gen is replaced, due to a primary kinetic isotope effect,
which occurs because bonds to deuterium are harder to
Burst phase
break than bonds to hydrogen.[36] It is also possible to
measure similar effects with other isotope substitutions,
such as 13 C/12 C and 18 O/16 O, but these effects are more
Time (seconds)
subtle.[37]
Pre-steady state progress curve, showing the burst phase of an Isotopes can also be used to reveal the fate of various parts
enzyme reaction. of the substrate molecules in the final products. For ex-
ample, it is sometimes difficult to discern the origin of an
In the first moment after an enzyme is mixed with sub- oxygen atom in the final product; since it may have come
strate, no product has been formed and no intermediates from water or from part of the substrate. This may be
exist. The study of the next few milliseconds of the determined by systematically substituting oxygen’s sta-
reaction is called Pre-steady-state kinetics also referred ble isotope 18 O into the various molecules that partici-
to as Burst kinetics. Pre-steady-state kinetics is there- pate in the reaction and checking for the isotope in the
fore concerned with the formation and consumption of product.[38] The chemical mechanism can also be eluci-
enzyme–substrate intermediates (such as ES or E*) until dated by examining the kinetics and isotope effects un-
their steady-state concentrations are reached. der different pH conditions,[39] by altering the metal ions
or other bound cofactors,[40] by site-directed mutagene-
This approach was first applied to the hydrolysis reaction
sis of conserved amino acid residues, or by studying the
catalysed by chymotrypsin.[33] Often, the detection of an
behaviour of the enzyme in the presence of analogues of
intermediate is a vital piece of evidence in investigations
the substrate(s).[41]
of what mechanism an enzyme follows. For example, in
the ping–pong mechanisms that are shown above, rapid
kinetic measurements can follow the release of product
P and measure the formation of the modified enzyme in-
termediate E*.[34] In the case of chymotrypsin, this in-
termediate is formed by an attack on the substrate by the 6.1.8 Enzyme inhibition and activation
nucleophilic serine in the active site and the formation of
the acyl-enzyme intermediate. Main article: Enzyme inhibitor
In the figure to the right, the enzyme produces E* rapidly Enzyme inhibitors are molecules that reduce or abolish
in the first few seconds of the reaction. The rate then
slows as steady state is reached. This rapid burst phase
of the reaction measures a single turnover of the en- E+S ES E+P
zyme. Consequently, the amount of product released in + +
this burst, shown as the intercept on the y-axis of the I I
graph, also gives the amount of functional enzyme which
is present in the assay.[35]
Ki K'i

6.1.7 Chemical mechanism EI ESI

An important goal of measuring enzyme kinetics is to Kinetic scheme for reversible enzyme inhibitors.
determine the chemical mechanism of an enzyme reac-
tion, i.e., the sequence of chemical steps that transform
substrate into product. The kinetic approaches discussed
enzyme activity, while enzyme activators are molecules
above will show at what rates intermediates are formed that increase the catalytic rate of enzymes. These inter-
and inter-converted, but they cannot identify exactly what
actions can be either reversible (i.e., removal of the in-
these intermediates are. hibitor restores enzyme activity) or irreversible (i.e., the
Kinetic measurements taken under various solution con- inhibitor permanently inactivates the enzyme).
6.1. ENZYME KINETICS 135

Reversible inhibitors fraction of the enzyme population bound by inhibitor

Traditionally reversible enzyme inhibitors have been clas-

sified as competitive, uncompetitive, or non-competitive, [I]
according to their effects on K and V ₐₓ. These dif- [I] + Ki
ferent effects result from the inhibitor binding to the en-
zyme E, to the enzyme–substrate complex ES, or to both, the effect of the inhibitor is a result of the percent of the
respectively. The division of these classes arises from enzyme population interacting with inhibitor. The only
a problem in their derivation and results in the need to problem with this equation in its present form is that it
use two different binding constants for one binding event. assumes absolute inhibition of the enzyme with inhibitor
The binding of an inhibitor and its effect on the enzy- binding, when in fact there can be a wide range of effects
matic activity are two distinctly different things, another anywhere from 100% inhibition of substrate turn over to
problem the traditional equations fail to acknowledge. In just >0%. To account for this the equation can be easily
noncompetitive inhibition the binding of the inhibitor re- modified to allow for different degrees of inhibition by
sults in 100% inhibition of the enzyme only, and fails including a delta V ₐₓ term.
to consider the possibility of anything in between.[42]
The common form of the inhibitory term also obscures
the relationship between the inhibitor binding to the en- [I]
Vmax − ∆Vmax
zyme and its relationship to any other binding term be [I] + Ki
it the Michaelis–Menten equation or a dose response or
curve associated with ligand receptor binding. To demon-
strate the relationship the following rearrangement can be
made: [I]
Vmax 1 − (Vmax 1 − Vmax 2)
[I] + Ki
Vmax This term can then define the residual enzymatic activity
[I] present when the inhibitor is interacting with individual
1+
Ki enzymes in the population. However the inclusion of this
term has the added value of allowing for the possibility
Vmax
of activation if the secondary V ₐₓ term turns out to be
[I] + Ki higher than the initial term. To account for the possibly
Ki of activation as well the notation can then be rewritten
Adding zero to the bottom ([I]-[I]) replacing the inhibitor “I” with a modifier term denoted
here as “X”.

Vmax
[I] + Ki [X]
Vmax 1 − (Vmax 1 − Vmax 2)
[I] + Ki − [I] [X] + Kx
Dividing by [I]+Kᵢ While this terminology results in a simplified way of deal-
ing with kinetic effects relating to the maximum velocity
of the Michaelis–Menten equation, it highlights potential
Vmax problems with the term used to describe effects relating
1 to the K . The K relating to the affinity of the enzyme
[I] for the substrate should in most cases relate to potential
1− changes in the binding site of the enzyme which would di-
[I] + Ki
rectly result from enzyme inhibitor interactions. As such
[I] a term similar to the one proposed above to modulate
Vmax − Vmax V ₐₓ should be appropriate in most situations:[43][44]
[I] + Ki
This notation demonstrates that similar to the Michaelis–
Menten equation, where the rate of reaction depends on
[X]
the percent of the enzyme population interacting with Km 1 − (Km 1 − Km 2)
substrate [X] + Kx

fraction of the enzyme population bound by substrate

Irreversible inhibitors

[S] Enzyme inhibitors can also irreversibly inactivate en-

[S] + Km zymes, usually by covalently modifying active site
136 CHAPTER 6. ENZYME KINETICS

residues. These reactions, which may be called suicide 6.1.10 History

substrates, follow exponential decay functions and are
usually saturable. Below saturation, they follow first order In 1902 Victor Henri proposed a quantitative theory of
kinetics with respect to inhibitor. enzyme kinetics,[48] but at the time the experimental
significance of the hydrogen ion concentration was not
yet recognized. After Peter Lauritz Sørensen had de-
fined the logarithmic pH-scale and introduced the con-
6.1.9 Mechanisms of catalysis cept of buffering in 1909[49] the German chemist Leonor
Michaelis and his Canadian postdoc Maud Leonora
Menten repeated Henri’s experiments and confirmed his
Main article: Enzyme catalysis equation, which is now generally referred to as Michaelis-
The favoured model for the enzyme–substrate interac- Menten kinetics (sometimes also Henri-Michaelis-Menten
kinetics).[50] Their work was further developed by G. E.
Briggs and J. B. S. Haldane, who derived kinetic equa-
tions that are still widely considered today a starting point
without enzyme
in modeling enzymatic activity.[51]
The major contribution of the Henri-Michaelis-Menten
activation
energy without approach was to think of enzyme reactions in two stages.
enzyme
with enzyme activation In the first, the substrate binds reversibly to the enzyme,
energy with
forming the enzyme-substrate complex. This is some-
Energy

enzyme

reactants overall energy

times called the Michaelis complex. The enzyme then
e.g. C6 H12 O6 + O2 released during
reaction
catalyzes the chemical step in the reaction and releases
products
the product. The kinetics of many enzymes is adequately
CO2+H 2O described by the simple Michaelis-Menten model, but all
enzymes have internal motions that are not accounted
Reaction coordinate for in the model and can have significant contributions
to the overall reaction kinetics. This can be modeled
by introducing several Michaelis-Menten pathways that
The energy variation as a function of reaction coordinate shows are connected with fluctuating rates,[52][53][54] which is a
the stabilisation of the transition state by an enzyme. mathematical extension of the basic Michaelis Menten
mechanism.[55]
tion is the induced fit model.[45] This model proposes
that the initial interaction between enzyme and sub-
strate is relatively weak, but that these weak interactions
rapidly induce conformational changes in the enzyme that
6.1.11 Software
strengthen binding. These conformational changes also
bring catalytic residues in the active site close to the ENZO
chemical bonds in the substrate that will be altered in the
reaction.[46] Conformational changes can be measured us- ENZO (Enzyme Kinetics) is a graphical interface tool
ing circular dichroism or dual polarisation interferome- for building kinetic models of enzyme catalyzed reac-
try. After binding takes place, one or more mechanisms tions. ENZO automatically generates the corresponding
of catalysis lower the energy of the reaction’s transition differential equations from a stipulated enzyme reaction
state by providing an alternative chemical pathway for scheme. These differential equations are processed by
the reaction. Mechanisms of catalysis include catalysis by a numerical solver and a regression algorithm which fits
bond strain; by proximity and orientation; by active-site the coefficients of differential equations to experimen-
proton donors or acceptors; covalent catalysis and quan- tally observed time course curves. ENZO allows rapid
tum tunnelling.[34][47] evaluation of rival reaction schemes and can be used for
routine tests in enzyme kinetics.[56]
Enzyme kinetics cannot prove which modes of catalysis
are used by an enzyme. However, some kinetic data can
suggest possibilities to be examined by other techniques.
For example, a ping–pong mechanism with burst-phase
pre-steady-state kinetics would suggest covalent catalysis
6.1.12 See also
might be important in this enzyme’s mechanism. Alter-
natively, the observation of a strong pH effect on V ₐₓ • Protein dynamics
but not K might indicate that a residue in the active site
needs to be in a particular ionisation state for catalysis to
occur. • Diffusion limited enzyme
6.1. ENZYME KINETICS 137

6.1.13 Footnotes [12] Beal, S. L. (1983). “Computation of the explicit so-

lution to the Michaelis-Menten equation”. Journal of
α. ^ Link: Interactive Michaelis–Menten kinetics tutorial Pharmacokinetics and Biopharmaceutics 11 (6): 641–657.
(Java required) doi:10.1007/BF01059062. PMID 6689584.
^
β. Link: dihydrofolate reductase mechanism (Gif) [13] Schnell, S.; Mendoza, C. (1997). “Closed Form
^ Solution for Time-dependent Enzyme Kinetics”.
γ. Link: DNA polymerase mechanism (Gif) Journal of Theoretical Biology 187 (2): 207–212.
^ doi:10.1006/jtbi.1997.0425.
δ. Link: Chymotrypsin mechanism (Flash required)
[14] Goudar, CT; Sonnad, JR; Duggleby, RG (1999).
“Parameter estimation using a direct solution of the in-
6.1.14 References
tegrated Michaelis-Menten equation” (PDF). Biochimica
[1] Wrighton, Mark S.; Ebbing, Darrell D. (1993). General et Biophysica Acta 1429 (2): 377–83. doi:10.1016/s0167-
chemistry (4th ed.). Boston: Houghton Mifflin. ISBN 0- 4838(98)00247-7. PMID 9989222.
395-63696-5. [15] Goudar, C. T.; Harris, S. K.; McInerney, M. J.; Su-
[2] Danson, Michael; Eisenthal, Robert (2002). Enzyme as- flita, J. M. (2004). “Progress curve analysis for en-
says: a practical approach. Oxford [Oxfordshire]: Oxford zyme and microbial kinetic reactions using explicit so-
University Press. ISBN 0-19-963820-9. lutions based on the Lambert W function”. Jour-
nal of Microbiological Methods 59 (3): 317–326.
[3] Xie XS, Lu HP (June 1999). “Single-molecule en- doi:10.1016/j.mimet.2004.06.013. PMID 15488275.
zymology”. J. Biol. Chem. 274 (23): 15967–70.
doi:10.1074/jbc.274.23.15967. PMID 10347141. [16] Jones ME (1992). “Analysis of algebraic weighted least-
squares estimators for enzyme parameters”. Biochem. J.
[4] Lu H (2004). “Single-molecule spectroscopy studies 288 (Pt 2): 533–8. PMC 1132043. PMID 1463456.
of conformational change dynamics in enzymatic reac-
tions”. Current pharmaceutical biotechnology 5 (3): 261– [17] Tseng SJ, Hsu JP (August 1990). “A comparison of
9. doi:10.2174/1389201043376887. PMID 15180547. the parameter estimating procedures for the Michaelis-
Menten model”. J. Theor. Biol. 145 (4): 457–64.
[5] Schnell J, Dyson H, Wright P (2004). “Struc-
doi:10.1016/S0022-5193(05)80481-3. PMID 2246896.
ture, dynamics, and catalytic function of di-
hydrofolate reductase”. Annual review of bio- [18] Bravo IG, Busto F, De Arriaga D et al. (September 2001).
physics and biomolecular structure 33: 119–40. “A normalized plot as a novel and time-saving tool in com-
doi:10.1146/annurev.biophys.33.110502.133613. PMID plex enzyme kinetic analysis”. Biochem. J. 358 (Pt 3):
15139807. 573–83. PMC 1222113. PMID 11577687.
[6] Gibson QH (1969). “Rapid mixing: Stopped flow”. Meth- [19] Almaas E, Kovács B, Vicsek T, Oltvai ZN, Barabási
ods Enzymol. Methods in Enzymology 16: 187–228. AL (February 2004). “Global organization of metabolic
doi:10.1016/S0076-6879(69)16009-7. ISBN 978-0-12- fluxes in the bacterium Escherichia coli”. Nature 427
181873-9. (6977): 839–43. doi:10.1038/nature02289. PMID
[7] Duggleby RG (1995). “Analysis of enzyme progress 14985762.
curves by non-linear regression”. Methods Enzymol.
[20] Reed JL, Vo TD, Schilling CH, Palsson BO (2003). “An
Methods in Enzymology 249: 61–90. doi:10.1016/0076-
expanded genome-scale model of Escherichia coli K-
6879(95)49031-0. ISBN 978-0-12-182150-0. PMID
12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54.
7791628.
doi:10.1186/gb-2003-4-9-r54. PMC 193654. PMID
[8] Murray JB, Dunham CM, Scott WG (January 2002). 12952533.
“A pH-dependent conformational change, rather than the
chemical step, appears to be rate-limiting in the ham- [21] for a complete derivation, see here
merhead ribozyme cleavage reaction”. J. Mol. Biol. [22] Dirr H, Reinemer P, Huber R (1994). “X-ray crystal
315 (2): 121–30. doi:10.1006/jmbi.2001.5145. PMID structures of cytosolic glutathione S-transferases. Impli-
11779233. cations for protein architecture, substrate recognition and
[9] Michaelis L. and Menten M.L. Kinetik der Invertin- catalytic function”. Eur. J. Biochem. 220 (3): 645–
wirkung Biochem. Z. 1913; 49:333–369 English trans- 61. doi:10.1111/j.1432-1033.1994.tb18666.x. PMID
lation Accessed 6 April 2007 8143720.

[10] Stroppolo ME, Falconi M, Caccuri AM, Desideri A [23] Stone SR, Morrison JF (July 1988). “Dihydrofolate re-
(2001). “Superefficient enzymes”. Cell. Mol. Life Sci. ductase from Escherichia coli: the kinetic mechanism
58 (10): 1451–60. doi:10.1007/PL00000788. PMID with NADPH and reduced acetylpyridine adenine dinu-
11693526. cleotide phosphate as substrates”. Biochemistry 27 (15):
5493–9. doi:10.1021/bi00415a016. PMID 3052577.
[11] Walsh R, Martin E, Darvesh S. A method to describe
enzyme-catalyzed reactions by combining steady state and [24] Fisher PA (1994). “Enzymologic mechanism of replica-
time course enzyme kinetic parameters. Biochim Biophys tive DNA polymerases in higher eukaryotes”. Prog.
Acta. 2010 Jan;1800:1–5 Nucleic Acid Res. Mol. Biol. Progress in Nucleic
138 CHAPTER 6. ENZYME KINETICS

Acid Research and Molecular Biology 47: 371–97. [36] Cleland WW (January 2005). “The use of isotope ef-
doi:10.1016/S0079-6603(08)60257-3. ISBN 978-0-12- fects to determine enzyme mechanisms”. Arch. Biochem.
540047-3. PMID 8016325. Biophys. 433 (1): 2–12. doi:10.1016/j.abb.2004.08.027.
PMID 15581561.
[25] Akerman SE, Müller S (2003). “2-Cys peroxiredoxin
PfTrx-Px1 is involved in the antioxidant defence of Plas- [37] Northrop D (1981). “The expression of isotope effects
modium falciparum". Mol. Biochem. Parasitol. 130 (2): on enzyme-catalyzed reactions”. Annu. Rev. Biochem.
75–81. doi:10.1016/S0166-6851(03)00161-0. PMID 50: 103–31. doi:10.1146/annurev.bi.50.070181.000535.
12946843. PMID 7023356.

[26] Bravo IG, Barrallo S, Ferrero MA, Rodríguez-Aparicio [38] Baillie T, Rettenmeier A (1986). “Drug biotrans-
LB, Martínez-Blanco H, Reglero A (September 2001). formation: mechanistic studies with stable isotopes”.
“Kinetic properties of the acylneuraminate cytidylyltrans- Journal of clinical pharmacology 26 (6): 448–51.
ferase from Pasteurella haemolytica A2”. Biochem. J. 358 doi:10.1002/j.1552-4604.1986.tb03556.x. PMID
(Pt 3): 585–98. PMC 1222114. PMID 11577688. 3734135.

[39] Cleland WW (1982). “Use of isotope effects to eluci-

[27] Kraut J (1977). “Serine proteases: structure and mech-
date enzyme mechanisms”. CRC Crit. Rev. Biochem. 13
anism of catalysis”. Annu. Rev. Biochem. 46: 331–
(4): 385–428. doi:10.3109/10409238209108715. PMID
58. doi:10.1146/annurev.bi.46.070177.001555. PMID
6759038.
332063.
[40] Christianson DW, Cox JD (1999). “Catalysis by
[28] Ricard J, Cornish-Bowden A (July 1987). “Co-operative metal-activated hydroxide in zinc and manganese met-
and allosteric enzymes: 20 years on”. Eur. J. alloenzymes”. Annu. Rev. Biochem. 68: 33–
Biochem. 166 (2): 255–72. doi:10.1111/j.1432- 57. doi:10.1146/annurev.biochem.68.1.33. PMID
1033.1987.tb13510.x. PMID 3301336. 10872443.

[29] Ward WH, Fersht AR (July 1988). “Tyrosyl-tRNA syn- [41] Kraut D, Carroll K, Herschlag D (2003). “Chal-
thetase acts as an asymmetric dimer in charging tRNA. lenges in enzyme mechanism and energet-
A rationale for half-of-the-sites activity”. Biochemistry ics”. Annu. Rev. Biochem. 72: 517–71.
27 (15): 5525–30. doi:10.1021/bi00415a021. PMID doi:10.1146/annurev.biochem.72.121801.161617.
3179266. PMID 12704087.

[30] Helmstaedt K, Krappmann S, Braus GH (Septem- [42] Walsh, R.; Martin, E.; Darvesh, S. (2011). “Limitations
ber 2001). “Allosteric Regulation of Catalytic Ac- of conventional inhibitor classifications”. Integrative Bi-
tivity: Escherichia coli Aspartate Transcarbamoylase ology (Royal Society of Chemistry) 3 (12): 1197–1201.
versus Yeast Chorismate Mutase”. Microbiol. Mol. doi:10.1039/c1ib00053e. PMID 22038120.
Biol. Rev. 65 (3): 404–21, table of contents.
doi:10.1128/MMBR.65.3.404-421.2001. PMC 99034. [43] Walsh, R.; Martin, E.; Darvesh, S. (2007). “A ver-
PMID 11528003. satile equation to describe reversible enzyme inhibi-
tion and activation kinetics: Modeling β-galactosidase
[31] Schirmer T, Evans PR (January 1990). “Structural basis and butyrylcholinesterase”. Biochimica et Biophysica
of the allosteric behaviour of phosphofructokinase”. Na- Acta (BBA) - General Subjects 1770 (5): 733–746.
ture 343 (6254): 140–5. doi:10.1038/343140a0. PMID doi:10.1016/j.bbagen.2007.01.001. PMID 17307293.
2136935.
[44] Walsh, Ryan (2012). “Ch. 17. Alternative Perspectives of
Enzyme Kinetic Modeling”. In Ekinci, Deniz. Medicinal
[32] Hill, A. V. The possible effects of the aggregation of the
Chemistry and Drug Design (PDF). InTech. pp. 357–371.
molecules of haemoglobin on its dissociation curves. J.
ISBN 978-953-51-0513-8.
Physiol. (Lond.), 1910 40, iv–vii.
[45] Koshland DE (February 1958). “Application of a
[33] Hartley BS, Kilby BA (February 1954). “The reaction Theory of Enzyme Specificity to Protein Synthesis”.
of p-nitrophenyl esters with chymotrypsin and insulin”. Proc. Natl. Acad. Sci. U.S.A. 44 (2): 98–
Biochem. J. 56 (2): 288–97. PMC 1269615. PMID 104. doi:10.1073/pnas.44.2.98. PMC 335371. PMID
13140189. 16590179.
[34] Fersht, Alan (1999). Structure and mechanism in protein [46] Hammes G (2002). “Multiple conformational changes
science: a guide to enzyme catalysis and protein folding. in enzyme catalysis”. Biochemistry 41 (26): 8221–8.
San Francisco: W.H. Freeman. ISBN 0-7167-3268-8. doi:10.1021/bi0260839. PMID 12081470.

[35] Bender ML, Begué-Cantón ML, Blakeley RL et al. [47] Sutcliffe M, Scrutton N (2002). “A new conceptual
(December 1966). “The determination of the con- framework for enzyme catalysis. Hydrogen tunnelling
centration of hydrolytic enzyme solutions: alpha- coupled to enzyme dynamics in flavoprotein and quino-
chymotrypsin, trypsin, papain, elastase, subtilisin, and protein enzymes”. Eur. J. Biochem. 269 (13): 3096–
acetylcholinesterase”. J. Am. Chem. Soc. 88 (24): 5890– 102. doi:10.1046/j.1432-1033.2002.03020.x. PMID
913. doi:10.1021/ja00976a034. PMID 5980876. 12084049.
6.1. ENZYME KINETICS 139

[48] Henri V (1902). “Theorie generale de l'action de quelques • Stevens, Lewis; Price, Nicholas C. (1999). Funda-
diastases”. Compt. Rend. Hebd. Acad. Sci. Paris 135: mentals of enzymology: the cell and molecular biol-
916–9. ogy of catalytic proteins. Oxford [Oxfordshire]: Ox-
ford University Press. ISBN 0-19-850229-X.
[49] Sørensen PL (1909). “Enzymstudien {II}. Über die Mes-
sung und Bedeutung der Wasserstoffionenkonzentration • Bugg, Tim (2004). Introduction to Enzyme and
bei enzymatischen Prozessen” [Enzyme studies III: About Coenzyme Chemistry. Cambridge, MA: Blackwell
the measurement and significance of the hydrogen ion
Publishers. ISBN 1-4051-1452-5.
concentration in enzymatic processes]. Biochem. Z. (in
German) 21: 131–304.
Advanced
[50] Michaelis L, Menten M (1913). “Die Kinetik der In-
vertinwirkung” [The Kinetics of Invertase Action] (PDF).
Biochem. Z. (in German) 49: 333–369.; Michaelis L,
• Segel, Irwin H. (1993). Enzyme kinetics: behavior
Menten ML, Johnson KA, Goody RS (2011). “The and analysis of rapid equilibrium and steady state
original Michaelis constant: translation of the 1913 enzyme systems (New ed.). New York: Wiley. ISBN
Michaelis-Menten paper”. Biochemistry 50 (39): 8264– 0-471-30309-7.
9. doi:10.1021/bi201284u. PMC 3381512. PMID
21888353. • Fersht, Alan (1999). Structure and mechanism in
protein science: a guide to enzyme catalysis and pro-
[51] Briggs GE, Haldane JB (1925). “A Note on the Kinet- tein folding. San Francisco: W.H. Freeman. ISBN
ics of Enzyme Action”. The Biochemical Journal 19 (2): 0-7167-3268-8.
339–339. PMC 1259181. PMID 16743508.
• Santiago Schnell, Philip K. Maini (2004). “A
[52] Flomenbom O, Velonia K, Loos D, Masuo S, Cotlet M, century of enzyme kinetics: Reliability of
Engelborghs Y et al. (Feb 2005). “Stretched exponential the KM and v ₐₓ estimates” (PDF). Com-
decay and correlations in the catalytic activity of fluctuat- ments on Theoretical Biology 8 (2–3): 169–87.
ing single lipase molecules”. Proceedings of the National
doi:10.1080/08948550302453.
Academy of Sciences of the United States of America 102
(7): 2368–2372. doi:10.1073/pnas.0409039102. PMC • Walsh, Christopher (1979). Enzymatic reaction
548972. PMID 15695587.
mechanisms. San Francisco: W. H. Freeman. ISBN
[53] English BP, Min W, van Oijen AM, Lee KT, Luo 0-7167-0070-0.
G, Sun H et al. (Feb 2006). “Ever-fluctuating sin-
• Cleland, William Wallace; Cook, Paul (2007). En-
gle enzyme molecules: Michaelis-Menten equation re-
visited”. Nature Chemical Biology 2 (2): 87–94. zyme kinetics and mechanism. New York: Garland
doi:10.1038/nchembio759. PMID 16415859. Science. ISBN 0-8153-4140-7.

[54] Lu HP, Xun L, Xie XS (Dec 1998). “Single-molecule en-

zymatic dynamics”. Science (New York, N.Y.) 282 (5395): 6.1.16 External links
1877–1882. doi:10.1126/science.282.5395.1877. PMID
9836635. • Animation of an enzyme assay — Shows effects of
manipulating assay conditions
[55] Xue X, Liu F, Ou-Yang ZC (Sep 2006). “Single
molecule Michaelis-Menten equation beyond quasistatic • MACiE — A database of enzyme reaction mecha-
disorder”. Physical Review. E, Statistical, Nonlin- nisms
ear, and Soft Matter Physics 74 (3 Pt 1): 030902.
doi:10.1103/PhysRevE.74.030902. PMID 17025584. • ENZYME — Expasy enzyme nomenclature
database
[56] Bevc S., Konc J., Stojan J., Hodošček M., Penca M.,
Matej Praprotnik M., Janežič D. (2011). “ENZO: A • ENZO — Web application for easy construction and
Web Tool for Derivation and Evaluation of Kinetic Mod- quick testing of kinetic models of enzyme catalyzed
els of Enzyme Catalyzed Reactions”. PLoS ONE 6 reactions.
(7): e22265. doi:10.1371/journal.pone.0022265. PMC
3139599. PMID 21818304. ENZO server • ExCatDB — A database of enzyme catalytic mech-
anisms

6.1.15 Further reading • BRENDA — Comprehensive enzyme database,

giving substrates, inhibitors and reaction diagrams
Introductory
• SABIO-RK — A database of reaction kinetics

• Cornish-Bowden, Athel (2004). Fundamentals of • Joseph Kraut’s Research Group, University of Cali-
enzyme kinetics (3rd ed.). London: Portland Press. fornia San Diego — Animations of several enzyme
ISBN 1-85578-158-1. reaction mechanisms
140 CHAPTER 6. ENZYME KINETICS

• Symbolism and Terminology in Enzyme Kinetics —

A comprehensive explanation of concepts and ter-
minology in enzyme kinetics

• An introduction to enzyme kinetics — An accessible

set of on-line tutorials on enzyme kinetics

• Enzyme kinetics animated tutorial — An animated

tutorial with audio
Chapter 7

Lipids and membranes

7.1 Lipid polyketides (derived from condensation of ketoacyl sub-

units); and sterol lipids and prenol lipids (derived from
condensation of isoprene subunits).[4]
Although the term lipid is sometimes used as a synonym
for fats, fats are a subgroup of lipids called triglycerides.
Lipids also encompass molecules such as fatty acids
and their derivatives (including tri-, di-, monoglycerides,
and phospholipids), as well as other sterol-containing
metabolites such as cholesterol.[7] Although humans and
other mammals use various biosynthetic pathways to both
break down and synthesize lipids, some essential lipids
cannot be made this way and must be obtained from the
diet.

7.1.1 Categories of lipids

Fatty acids

Fatty acids or fatty acid residues when they form part of

a lipid, are a diverse group of molecules synthesized by
Structures of some common lipids. At the top are cholesterol[1] chain-elongation of an acetyl-CoA primer with malonyl-
and oleic acid.[2] The middle structure is a triglyceride com- CoA or methylmalonyl-CoA groups in a process called
posed of oleoyl, stearoyl, and palmitoyl chains attached to a fatty acid synthesis.[8][9] They are made of a hydrocarbon
glycerol backbone. At the bottom is the common phospholipid, chain that terminates with a carboxylic acid group; this ar-
phosphatidylcholine.[3] rangement confers the molecule with a polar, hydrophilic
end, and a nonpolar, hydrophobic end that is insoluble in
Lipids are a group of naturally occurring molecules water. The fatty acid structure is one of the most funda-
that include fats, waxes, sterols, fat-soluble vitamins mental categories of biological lipids, and is commonly
(such as vitamins A, D, E, and K), monoglycerides, used as a building-block of more structurally complex
diglycerides, triglycerides, phospholipids, and others. lipids. The carbon chain, typically between four and 24
The main biological functions of lipids include storing carbons long,[10] may be saturated or unsaturated, and
energy, signaling, and acting as structural components of may be attached to functional groups containing oxygen,
cell membranes.[4][5] Lipids have applications in the cos- halogens, nitrogen, and sulfur. If a fatty acid contains
metic and food industries as well as in nanotechnology.[6] a double bond, there is the possibility of either a cis or
Lipids may be broadly defined as hydrophobic or trans geometric isomerism, which significantly affects
amphiphilic small molecules; the amphiphilic nature the molecule’s configuration. Cis-double bonds cause the
of some lipids allows them to form structures such as fatty acid chain to bend, an effect that is compounded
vesicles, multilamellar/unilamellar liposomes, or mem- with more double bonds in the chain. Three double
branes in an aqueous environment. Biological lipids bonds in 18-carbon linolenic acid, the most abundant
originate entirely or in part from two distinct types of fatty-acyl chains of plant thylakoid membranes, render
biochemical subunits or “building-blocks": ketoacyl and these membranes highly fluid despite environmental low-
isoprene groups.[4] Using this approach, lipids may be temperatures,[11] and also makes linolenic acid give dom-
divided into eight categories: fatty acids, glycerolipids, inating sharp peaks in high resolution 13-C NMR spectra
glycerophospholipids, sphingolipids, saccharolipids, and of chloroplasts. This in turn plays an important role in the

141
142 CHAPTER 7. LIPIDS AND MEMBRANES

structure and function of cell membranes.[12] Most nat- R O

urally occurring fatty acids are of the cis configuration, C CH2

although the trans form does exist in some natural and

partially hydrogenated fats and oils.[13] R O O C H
O
C
Examples of biologically important fatty acids include –
H2 +
H2C P C NH3
the eicosanoids, derived primarily from arachidonic acid
O O O C
and eicosapentaenoic acid, that include prostaglandins, O
H2
leukotrienes, and thromboxanes. Docosahexaenoic acid
is also important in biological systems, particularly with Phosphatidylethanolamine[3]
respect to sight.[14][15] Other major lipid classes in the
fatty acid category are the fatty esters and fatty amides.
Fatty esters include important biochemical intermedi-
ates such as wax esters, fatty acid thioester coenzyme GPEtn) and phosphatidylserine (PS or GPSer). In ad-
A derivatives, fatty acid thioester ACP derivatives and dition to serving as a primary component of cellu-
fatty acid carnitines. The fatty amides include N-acyl lar membranes and binding sites for intra- and inter-
ethanolamines, such as the cannabinoid neurotransmitter cellular proteins, some glycerophospholipids in eukary-
anandamide.[16] otic cells, such as phosphatidylinositols and phosphatidic
acids are either precursors of or, themselves, membrane-
derived second messengers.[25] Typically, one or both
Glycerolipids of these hydroxyl groups are acylated with long-chain
fatty acids, but there are also alkyl-linked and 1Z-alkenyl-
Glycerolipids are composed of mono-, di-, and tri- linked (plasmalogen) glycerophospholipids, as well as di-
substituted glycerols,[17] the best-known being the fatty alkylether variants in archaebacteria.[26]
acid triesters of glycerol, called triglycerides. The word
“triacylglycerol” is sometimes used synonymously with
“triglyceride”. In these compounds, the three hydroxyl Sphingolipids
groups of glycerol are each esterified, typically by differ- [27]
ent fatty acids. Because they function as an energy store, Sphingolipids are a complicated family of compounds
these lipids comprise the bulk of storage fat in animal tis- that share a common structural feature, a sphingoid base
sues. The hydrolysis of the ester bonds of triglycerides backbone that is synthesized de novo from the amino
and the release of glycerol and fatty acids from adipose acid serine and a long-chain fatty acyl CoA, then con-
tissue are the initial steps in metabolizing fat.[18] verted into ceramides, phosphosphingolipids, glycosph-
ingolipids and other compounds. The major sphingoid
Additional subclasses of glycerolipids are represented by base of mammals is commonly referred to as sphingosine.
glycosylglycerols, which are characterized by the pres- Ceramides (N-acyl-sphingoid bases) are a major subclass
ence of one or more sugar residues attached to glycerol of sphingoid base derivatives with an amide-linked fatty
via a glycosidic linkage. Examples of structures in this acid. The fatty acids are typically saturated or mono-
category are the digalactosyldiacylglycerols found in plant unsaturated with chain lengths from 16 to 26 carbon
membranes[19] and seminolipid from mammalian sperm atoms.[28]
cells.[20]

Glycerophospholipids

Glycerophospholipids, usually referred to as

phospholipids, are ubiquitous in nature and are key
components of the lipid bilayer of cells,[21] as well as Sphingomyelin[3]
being involved in metabolism and cell signaling.[22]
Neural tissue (including the brain) contains relatively
high amounts of glycerophospholipids, and alterationsThe major phosphosphingolipids of mammals are
in their composition has been implicated in various sphingomyelins (ceramide phosphocholines),[29]
neurological disorders.[23] Glycerophospholipids may be
whereas insects contain mainly ceramide
subdivided into distinct classes, based on the nature of
phosphoethanolamines[30] and fungi have phytoce-
the polar headgroup at the sn−3 position of the glycerol
ramide phosphoinositols and mannose-containing
backbone in eukaryotes and eubacteria, or the sn−1 headgroups.[31] The glycosphingolipids are a diverse
position in the case of archaebacteria.[24] family of molecules composed of one or more sugar
Examples of glycerophospholipids found in biological residues linked via a glycosidic bond to the sphingoid
membranes are phosphatidylcholine (also known as PC, base. Examples of these are the simple and complex
GPCho or lecithin), phosphatidylethanolamine (PE or glycosphingolipids such as cerebrosides and gangliosides.
7.1. LIPID 143

Sterol lipids

Sterol lipids, such as cholesterol and its derivatives,

are an important component of membrane lipids,[32]
along with the glycerophospholipids and sphingomyelins.
The steroids, all derived from the same fused four-
ring core structure, have different biological roles as
hormones and signaling molecules. The eighteen-carbon
(C18) steroids include the estrogen family whereas
the C19 steroids comprise the androgens such as
testosterone and androsterone. The C21 subclass in-
cludes the progestogens as well as the glucocorticoids
and mineralocorticoids.[33] The secosteroids, comprising
various forms of vitamin D, are characterized by cleav-
age of the B ring of the core structure.[34] Other exam-
ples of sterols are the bile acids and their conjugates,[35]
which in mammals are oxidized derivatives of cholesterol Structure of the saccharolipid Kdo2 -lipid A.[42] Glucosamine
and are synthesized in the liver. The plant equivalents residues in blue, Kdo residues in red, acyl chains in black and
are the phytosterols, such as β-sitosterol, stigmasterol, phosphate groups in green.
and brassicasterol; the latter compound is also used as a
biomarker for algal growth.[36] The predominant sterol in
fungal cell membranes is ergosterol.[37] fatty-acyl chains. The minimal lipopolysaccharide re-
quired for growth in E. coli is Kdo2 -Lipid A, a hexa-
acylated disaccharide of glucosamine that is glycosy-
Prenol lipids lated with two 3-deoxy-D-manno-octulosonic acid (Kdo)
residues.[42]
Prenol lipids are synthesized from the five-carbon-unit
precursors isopentenyl diphosphate and dimethylallyl
diphosphate that are produced mainly via the mevalonic Polyketides
acid (MVA) pathway.[38] The simple isoprenoids (linear
alcohols, diphosphates, etc.) are formed by the succes- Polyketides are synthesized by polymerization of acetyl
sive addition of C5 units, and are classified according and propionyl subunits by classic enzymes as well as it-
to number of these terpene units. Structures contain- erative and multimodular enzymes that share mechanis-
ing greater than 40 carbons are known as polyterpenes. tic features with the fatty acid synthases. They com-
Carotenoids are important simple isoprenoids that func- prise a large number of secondary metabolites and natural
tion as antioxidants and as precursors of vitamin A.[39] products from animal, plant, bacterial, fungal and ma-
Another biologically important class of molecules is ex- rine sources, and have great structural diversity.[43][44]
emplified by the quinones and hydroquinones, which con- Many polyketides are cyclic molecules whose backbones
tain an isoprenoid tail attached to a quinonoid core of non- are often further modified by glycosylation, methylation,
isoprenoid origin.[40] Vitamin E and vitamin K, as well as hydroxylation, oxidation, and/or other processes. Many
the ubiquinones, are examples of this class. Prokaryotes commonly used anti-microbial, anti-parasitic, and anti-
synthesize polyprenols (called bactoprenols) in which the cancer agents are polyketides or polyketide derivatives,
terminal isoprenoid unit attached to oxygen remains un- such as erythromycins, tetracyclines, avermectins, and
saturated, whereas in animal polyprenols (dolichols) the antitumor epothilones.[45]
terminal isoprenoid is reduced.[41]

7.1.2 Biological functions

Saccharolipids
Membranes
Saccharolipids describe compounds in which fatty acids
are linked directly to a sugar backbone, forming struc- Eukaryotic cells are compartmentalized into membrane-
tures that are compatible with membrane bilayers. In the bound organelles that carry out different biological func-
saccharolipids, a monosaccharide substitutes for the glyc- tions. The glycerophospholipids are the main struc-
erol backbone present in glycerolipids and glycerophos- tural component of biological membranes, such as
pholipids. The most familiar saccharolipids are the acy- the cellular plasma membrane and the intracellular
lated glucosamine precursors of the Lipid A compo- membranes of organelles; in animal cells the plasma
nent of the lipopolysaccharides in Gram-negative bacte- membrane physically separates the intracellular compo-
ria. Typical lipid A molecules are disaccharides of glu- nents from the extracellular environment. The glyc-
cosamine, which are derivatized with as many as seven erophospholipids are amphipathic molecules (contain-
144 CHAPTER 7. LIPIDS AND MEMBRANES

ing both hydrophobic and hydrophilic regions) that con- aggregations are also observed and form part of the poly-
tain a glycerol core linked to two fatty acid-derived morphism of amphiphile (lipid) behavior. Phase behav-
“tails” by ester linkages and to one “head” group by a ior is an area of study within biophysics and is the sub-
phosphate ester linkage. While glycerophospholipids are ject of current academic research.[50][51] Micelles and bi-
the major component of biological membranes, other layers form in the polar medium by a process known as
non-glyceride lipid components such as sphingomyelin the hydrophobic effect.[52] When dissolving a lipophilic
and sterols (mainly cholesterol in animal cell mem- or amphiphilic substance in a polar environment, the
branes) are also found in biological membranes.[46] In polar molecules (i.e., water in an aqueous solution) be-
plants and algae, the galactosyldiacylglycerols,[47] and come more ordered around the dissolved lipophilic sub-
sulfoquinovosyldiacylglycerol,[19] which lack a phosphate stance, since the polar molecules cannot form hydrogen
group, are important components of membranes of bonds to the lipophilic areas of the amphiphile. So in
chloroplasts and related organelles and are the most abun- an aqueous environment, the water molecules form an
dant lipids in photosynthetic tissues, including those of ordered "clathrate" cage around the dissolved lipophilic
higher plants, algae and certain bacteria. molecule.[53]
Plant thylakoid membranes have the largest lipid compo- The formation of lipids into protocell membranes is a key
nent of a non-bilayer forming monogalactosyl diglyceride step in models of abiogenesis, the origin of life.[54]
(MGDG), and little phospholipids; despite this unique
lipid composition, chloroplast thylakoid membranes have
been shown to contain a dynamic lipid-bilayer matrix as Energy storage
revealed by magnetic resonance and electron microscope
Triglycerides, stored in adipose tissue, are a major
studies.[48]
form of energy storage both in animals and plants.
The adipocyte, or fat cell, is designed for continuous
synthesis and breakdown of triglycerides in animals,
with breakdown controlled mainly by the activation of
hormone-sensitive enzyme lipase.[55] The complete ox-
idation of fatty acids provides high caloric content, about
9 kcal/g, compared with 4 kcal/g for the breakdown of
carbohydrates and proteins. Migratory birds that must fly
long distances without eating use stored energy of triglyc-
erides to fuel their flights.[56]

Signaling

In recent years, evidence has emerged showing that

lipid signaling is a vital part of the cell signaling.[57][58]
Lipid signaling may occur via activation of G protein-
coupled or nuclear receptors, and members of several
different lipid categories have been identified as sig-
naling molecules and cellular messengers.[59] These in-
clude sphingosine-1-phosphate, a sphingolipid derived
from ceramide that is a potent messenger molecule
involved in regulating calcium mobilization,[60] cell
growth, and apoptosis;[61] diacylglycerol (DAG) and
Self-organization of phospholipids: a spherical liposome, a the phosphatidylinositol phosphates (PIPs), involved in
micelle, and a lipid bilayer. calcium-mediated activation of protein kinase C;[62] the
prostaglandins, which are one type of fatty-acid derived
A biological membrane is a form of lamellar phase lipid eicosanoid involved in inflammation and immunity;[63]
bilayer. The formation of lipid bilayers is an energet- the steroid hormones such as estrogen, testosterone and
ically preferred process when the glycerophospholipids cortisol, which modulate a host of functions such as
described above are in an aqueous environment.[49] This reproduction, metabolism and blood pressure; and the
is known as the hydrophobic effect. In an aqueous sys- oxysterols such as 25-hydroxy-cholesterol that are liver X
tem, the polar heads of lipids align towards the polar, receptor agonists.[64] Phosphatidylserine lipids are known
aqueous environment, while the hydrophobic tails mini- to be involved in signaling for the phagocytosis of apop-
mize their contact with water and tend to cluster together, totic cells and/or pieces of cells. They accomplish this by
forming a vesicle; depending on the concentration of the being exposed to the extracellular face of the cell mem-
lipid, this biophysical interaction may result in the for- brane after the inactivation of flippases which place them
mation of micelles, liposomes, or lipid bilayers. Other exclusively on the cytosolic side and the activation of
7.1. LIPID 145

scramblases, which scramble the orientation of the phos- the liver.

pholipids. After this occurs, other cells recognize the The synthesis of unsaturated fatty acids involves a
phosphatidylserines and phagocytosize the cells or cell desaturation reaction, whereby a double bond is intro-
fragments exposing them.[65] duced into the fatty acyl chain. For example, in hu-
mans, the desaturation of stearic acid by stearoyl-CoA
Other functions desaturase-1 produces oleic acid. The doubly unsaturated
fatty acid linoleic acid as well as the triply unsaturated
The “fat-soluble” vitamins (A, D, E and K) – which α-linolenic acid cannot be synthesized in mammalian tis-
are isoprene-based lipids – are essential nutrients stored sues, and are therefore[77]essential fatty acids and must be
in the liver and fatty tissues, with a diverse range of obtained from the diet.
functions. Acyl-carnitines are involved in the trans- Triglyceride synthesis takes place in the endoplasmic
port and metabolism of fatty acids in and out of reticulum by metabolic pathways in which acyl groups in
mitochondria, where they undergo beta oxidation.[66] fatty acyl-CoAs are transferred to the hydroxyl groups of
Polyprenols and their phosphorylated derivatives also glycerol-3-phosphate and diacylglycerol.[78]
play important transport roles, in this case the trans-
Terpenes and isoprenoids, including the carotenoids, are
port of oligosaccharides across membranes. Polyprenol
made by the assembly and modification of isoprene units
phosphate sugars and polyprenol diphosphate sugars
donated from the reactive precursors isopentenyl py-
function in extra-cytoplasmic glycosylation reactions, in
rophosphate and dimethylallyl pyrophosphate.[38] These
extracellular polysaccharide biosynthesis (for instance,
precursors can be made in different ways. In animals
peptidoglycan polymerization in bacteria), and in eu-
[67][68] and archaea, the mevalonate pathway produces these
karyotic protein N-glycosylation. Cardiolipins are
compounds from acetyl-CoA,[79] while in plants and
a subclass of glycerophospholipids containing four acyl
bacteria the non-mevalonate pathway uses pyruvate and
chains and three glycerol groups that are particularly
glyceraldehyde 3-phosphate as substrates.[38][80] One im-
abundant in the inner mitochondrial membrane.[69][70]
portant reaction that uses these activated isoprene donors
They are believed to activate enzymes involved with
is steroid biosynthesis. Here, the isoprene units are joined
oxidative phosphorylation.[71] Lipids also form the basis
together to make squalene and then folded up and formed
of steroid hormones.[72]
into a set of rings to make lanosterol.[81] Lanosterol can
then be converted into other steroids such as cholesterol
and ergosterol.[81][82]
7.1.3 Metabolism

The major dietary lipids for humans and other animals Degradation
are animal and plant triglycerides, sterols, and membrane
phospholipids. The process of lipid metabolism synthe- Beta oxidation is the metabolic process by which fatty
sizes and degrades the lipid stores and produces the struc- acids are broken down in the mitochondria and/or in
tural and functional lipids characteristic of individual tis- peroxisomes to generate acetyl-CoA. For the most part,
sues. fatty acids are oxidized by a mechanism that is similar
to, but not identical with, a reversal of the process of
fatty acid synthesis. That is, two-carbon fragments are
Biosynthesis removed sequentially from the carboxyl end of the acid
after steps of dehydrogenation, hydration, and oxidation
In animals, when there is an oversupply of dietary carbo- to form a beta-keto acid, which is split by thiolysis. The
hydrate, the excess carbohydrate is converted to triglyc- acetyl-CoA is then ultimately converted into ATP, CO2 ,
erides. This involves the synthesis of fatty acids from and H2 O using the citric acid cycle and the electron trans-
acetyl-CoA and the esterification of fatty acids in the pro- port chain. Hence the citric acid cycle can start at acetyl-
duction of triglycerides, a process called lipogenesis.[73] CoA when fat is being broken down for energy if there is
Fatty acids are made by fatty acid synthases that polymer- little or no glucose available. The energy yield of the com-
ize and then reduce acetyl-CoA units. The acyl chains in plete oxidation of the fatty acid palmitate is 106 ATP.[83]
the fatty acids are extended by a cycle of reactions that Unsaturated and odd-chain fatty acids require additional
add the acetyl group, reduce it to an alcohol, dehydrate it enzymatic steps for degradation.
to an alkene group and then reduce it again to an alkane
group. The enzymes of fatty acid biosynthesis are divided
into two groups, in animals and fungi all these fatty acid 7.1.4 Nutrition and health
synthase reactions are carried out by a single multifunc-
tional protein,[74] while in plant plastids and bacteria sep- Most of the fat found in food is in the form of triglyc-
arate enzymes perform each step in the pathway.[75][76] erides, cholesterol, and phospholipids. Some dietary fat
The fatty acids may be subsequently converted to triglyc- is necessary to facilitate absorption of fat-soluble vita-
erides that are packaged in lipoproteins and secreted from mins (A, D, E, and K) and carotenoids.[84] Humans and
146 CHAPTER 7. LIPIDS AND MEMBRANES

other mammals have a dietary requirement for certain [2] Stryer et al., p. 328.
essential fatty acids, such as linoleic acid (an omega-
6 fatty acid) and alpha-linolenic acid (an omega-3 fatty [3] Stryer et al., p. 330.
acid) because they cannot be synthesized from simple
[4] Fahy E, Subramaniam S, Murphy RC, Nishijima
precursors in the diet.[77] Both of these fatty acids are 18- M, Raetz CR, Shimizu T, Spener F, van Meer G,
carbon polyunsaturated fatty acids differing in the num- Wakelam MJ, Dennis EA. (2009). “Update of the
ber and position of the double bonds. Most vegetable oils LIPID MAPS comprehensive classification system for
are rich in linoleic acid (safflower, sunflower, and corn lipids”. Journal of Lipid Research 50 (S1): S9–
oils). Alpha-linolenic acid is found in the green leaves 14. doi:10.1194/jlr.R800095-JLR200. PMC 2674711.
of plants, and in selected seeds, nuts, and legumes (in PMID 19098281.
particular flax, rapeseed, walnut, and soy).[85] Fish oils
are particularly rich in the longer-chain omega-3 fatty [5] Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes
acids eicosapentaenoic acid (EPA) and docosahexaenoic RW, Cotter D, Dinasarapu AR, Maurya MR.
(2011). “Bioinformatics and systems biology of the
acid (DHA).[86] A large number of studies have shown
lipidome”. Chemical Reviews 111 (10): 6452–6490.
positive health benefits associated with consumption of doi:10.1021/cr200295k. PMC 3383319. PMID
omega-3 fatty acids on infant development, cancer, car- 21939287.
diovascular diseases, and various mental illnesses, such as
depression, attention-deficit hyperactivity disorder, and [6] Mashaghi S, Jadidi T, Koenderink G, Mashaghi
dementia.[87][88] In contrast, it is now well-established A. (2013). “Lipid nanotechnology”. International
that consumption of trans fats, such as those present in Journal of Molecular Sciences 14 (2): 4242–4282.
partially hydrogenated vegetable oils, are a risk factor for doi:10.3390/ijms14024242. PMID 23429269.
cardiovascular disease.[89][90][91]
[7] Michelle A, Hopkins J, McLaughlin CW, Johnson S,
A few studies have suggested that total dietary fat in- Warner MQ, LaHart D, Wright JD. (1993). Human Bi-
take is linked to an increased risk of obesity[92][93] and ology and Health. Englewood Cliffs, New Jersey, USA:
diabetes.[94] However, a number of very large studies, Prentice Hall. ISBN 978-0-13-981176-0.
including the Women’s Health Initiative Dietary Mod-
ification Trial, an eight-year study of 49,000 women, [8] Vance JE, Vance DE. (2002). Biochemistry of Lipids,
the Nurses’ Health Study and the Health Professionals Lipoproteins and Membranes. Amsterdam: Elsevier.
[95][96] ISBN 978-0-444-51139-3.
Follow-up Study, revealed no such links. None of
these studies suggested any connection between percent- [9] Brown HA, ed. (2007). Lipodomics and Bioactive Lipids:
age of calories from fat and risk of cancer, heart dis- Mass Spectrometry Based Lipid Analysis. Methods in En-
ease, or weight gain. The Nutrition Source, a web- zymology 423. Boston: Academic Press. ISBN 978-0-
site maintained by the Department of Nutrition at the 12-373895-0.
Harvard School of Public Health, summarizes the cur-
rent evidence on the impact of dietary fat: “Detailed [10] Hunt SM, Groff JL, Gropper SAS. (1995). Advanced
research—much of it done at Harvard—shows that the to- Nutrition and Human Metabolism. Belmont, California:
tal amount of fat in the diet isn't really linked with weight West Pub. Co. p. 98. ISBN 978-0-314-04467-9.
[97]
or disease.” [11] Yashroy RC. (1987). "13 C NMR studies of lipid fatty acyl
chains of chloroplast membranes”. Indian Journal of Bio-
chemistry and Biophysics 24 (6): 177–178.
7.1.5 See also
[12] Devlin, pp. 193–195.
• Emulsion test
[13] Hunter JE. (2006). “Dietary trans fatty acids: review
• Lipid microdomain of recent human studies and food industry responses”.
• Lipid signaling Lipids 41 (11): 967–992. doi:10.1007/s11745-006-5049-
y. PMID 17263298.
• Lipidomics
[14] Furse, Samuel (2011-12-02). “A Long Lipid, a Long
• Protein-lipid interaction Name: Docosahexaenoic Acid”. The Lipid Chronicles.

• Phenolic lipids, a class of natural products com- [15] “DHA for Optimal Brain and Visual Functioning”.
posed of long aliphatic chains and phenolic rings DHA/EPA Omega-3 Institute.
that occur in plants, fungi and bacteria
[16] Fezza F, De Simone C, Amadio D, Maccarrone M.
(2008). “Fatty acid amide hydrolase: a gate-keeper of the
7.1.6 References endocannabinoid system”. Subcellular Biochemistry. Sub-
cellular Biochemistry 49: 101–132. doi:10.1007/978-
[1] Maitland, Jr Jones (1998). Organic Chemistry. W W Nor- 1-4020-8831-5_4. ISBN 978-1-4020-8830-8. PMID
ton & Co Inc (Np). p. 139. ISBN 978-0-393-97378-5. 18751909.
7.1. LIPID 147

[17] Coleman RA, Lee DP. (2004). “Enzymes of triglyceride [33] Stryer et al., p. 749.
synthesis and their regulation”. Progress in Lipid Research
43 (2): 134–176. doi:10.1016/S0163-7827(03)00051-1. [34] Bouillon R, Verstuyf A, Mathieu C, Van Cromphaut S,
PMID 14654091. Masuyama R, Dehaes P, Carmeliet G. (2006). “Vi-
tamin D resistance”. Best Practice & Research Clin-
[18] van Holde and Mathews, pp. 630–31. ical Endocrinology & Metabolism 20 (4): 627–645.
doi:10.1016/j.beem.2006.09.008. PMID 17161336.
[19] Hölzl G, Dörmann P. (2007). “Structure and
function of glycoglycerolipids in plants and bacte- [35] Russell DW. (2003). “The enzymes, regula-
ria”. Progress in Lipid Research 46 (5): 225–243. tion, and genetics of bile acid synthesis”. An-
doi:10.1016/j.plipres.2007.05.001. PMID 17599463. nual Review of Biochemistry 72: 137–174.
doi:10.1146/annurev.biochem.72.121801.161712.
[20] Honke K, Zhang Y, Cheng X, Kotani N,
PMID 12543708.
Taniguchi N. (2004). “Biological roles of sul-
foglycolipids and pathophysiology of their defi- [36] Villinski JC, Hayes JM, Brassell SC, Riggert VL, Dunbar
ciency”. Glycoconjugate Journal 21 (1–2): 59–62. R. (2008). “Sedimentary sterols as biogeochemical indi-
doi:10.1023/B:GLYC.0000043749.06556.3d. cators in the Southern Ocean”. Organic Geochemistry 39
(5): 567–588. doi:10.1016/j.orggeochem.2008.01.009.
[21] “The Structure of a Membrane”. The Lipid Chronicles.
Retrieved 2011-12-31. [37] Deacon J. (2005). Fungal Biology. Cambridge, Mas-
[22] Berridge MJ, Irvine RF. (1989). “Inositol phos- sachusetts: Blackwell Publishers. p. 342. ISBN 978-1-
phates and cell signalling”. Nature 341: 197–205. 4051-3066-0.
doi:10.1038/341197a0. [38] Kuzuyama T, Seto H. (2003). “Diversity of the biosyn-
[23] Farooqui, A. A.; Horrocks, L. A.; Farooqui, T (2000). thesis of the isoprene units”. Natural Product Reports 20
“Glycerophospholipids in brain: Their metabolism, incor- (2): 171–183. doi:10.1039/b109860h. PMID 12735695.
poration into membranes, functions, and involvement in [39] Rao AV, Rao LG. (2007). “Carotenoids and human
neurological disorders”. Chemistry and physics of lipids health”. Pharmacological Research: the Official Journal
106 (1): 1–29. doi:10.1016/S0009-3084(00)00128-6. of the Italian Pharmacological Society 55 (3): 207–216.
PMID 10878232. doi:10.1016/j.phrs.2007.01.012. PMID 17349800.
[24] Ivanova PT, Milne SB, Byrne MO, Xiang Y, Brown HA.
[40] Brunmark A, Cadenas E. (1989). “Redox and addi-
(2007). “Glycerophospholipid identification and quantita-
tion chemistry of quinoid compounds and its biological
tion by electrospray ionization mass spectrometry”. Meth-
implications”. Free Radical Biology & Medicine 7 (4):
ods in Enzymology. Methods in Enzymology 432: 21–57.
435–477. doi:10.1016/0891-5849(89)90126-3. PMID
doi:10.1016/S0076-6879(07)32002-8. ISBN 978-0-12-
2691341.
373895-0. PMID 17954212.
[41] Swiezewska E, Danikiewicz W. (2005). “Poly-
[25] van Holde and Mathews, p. 844.
isoprenoids: structure, biosynthesis and func-
[26] Paltauf F. (1994). “Ether lipids in biomembranes”. tion”. Progress in Lipid Research 44 (4): 235–258.
Chemistry and Physics of Lipids 74 (2): 101–139. doi:10.1016/j.plipres.2005.05.002. PMID 16019076.
doi:10.1016/0009-3084(94)90054-X. PMID 7859340.
[42] Raetz CR1, Garrett TA, Reynolds CM, Shaw WA, Moore
[27] Merrill AH, Sandhoff K. (2002). “Sphingolipids: JD, Smith DC Jr et al. (2006). “Kdo2-Lipid A
metabolism and cell signaling”, Ch. 14 in New Com- of Escherichia coli, a defined endotoxin that activates
prehensive Biochemistry: Biochemistry of Lipids, Lipopro- macrophages via TLR-4”. The Journal of Lipid Research
teins, and Membranes, Vance, D.E. and Vance, J.E., eds. 47 (5): 1097–1111. doi:10.1194/jlr.M600027-JLR200.
Elsevier Science, NY, ISBN 978-0-12-182212-5.

[28] Devlin, pp. 421–422. [43] Walsh CT. (2004). “Polyketide and nonribosomal pep-
tide antibiotics: modularity and versatility”. Science
[29] Hori T, Sugita M. (1993). “Sphingolipids in lower an-
303 (5665): 1805–1810. doi:10.1126/science.1094318.
imals”. Progress in Lipid Research 32 (1): 25–45.
PMID 15031493.
doi:10.1016/0163-7827(93)90003-F. PMID 8415797.
[44] Caffrey P, Aparicio JF, Malpartida F, Zotchev SB.
[30] Wiegandt H. (1992). “Insect glycolipids”. Biochimica et
(2008). “Biosynthetic engineering of polyene macrolides
Biophysica Acta 1123 (2): 117–126. doi:10.1016/0005-
towards generation of improved antifungal and antipara-
2760(92)90101-Z. PMID 1739742.
sitic agents”. Current Topics in Medicinal Chemistry 8 (8):
[31] Guan X, Wenk MR. (2008). “Biochemistry of inosi- 639–640. doi:10.2174/156802608784221479. PMID
tol lipids”. Frontiers in Bioscience 13 (13): 3239–3251. 18473889.
doi:10.2741/2923. PMID 18508430.
[45] Minto RE, Blacklock BJ. (2008). “Biosynthesis and
[32] Bach D, Wachtel E. (2003). “Phospholipid/cholesterol function of polyacetylenes and allied natural prod-
model membranes: formation of cholesterol crystal- ucts”. Progress in Lipid Research 47 (4): 233–
lites”. Biochim Biophys Acta 1610 (2): 187–197. 306. doi:10.1016/j.plipres.2008.02.002. PMC 2515280.
doi:10.1016/S0005-2736(03)00017-8. PMID 12648773. PMID 18387369.
148 CHAPTER 7. LIPIDS AND MEMBRANES

[46] Stryer et al., pp. 329–331. [60] Hinkovska-Galcheva V, VanWay SM, Shanley TP,
Kunkel RG. (2008). “The role of sphingosine-1-
[47] Heinz E. (1996). “Plant glycolipids: structure, isolation phosphate and ceramide-1-phosphate in calcium home-
and analysis”, pp. 211–332 in Advances in Lipid Method- ostasis”. Current Opinion in Investigational Drugs 9 (11):
ology, Vol. 3. W.W. Christie (ed.). Oily Press, Dundee. 1191–1205. PMID 18951299.
ISBN 978-0-9514171-6-4
[61] Saddoughi SA, Song P, Ogretmen B. (2008). “Roles
[48] Yashroy RC. (1990). “Magnetic resonance studies of bioactive sphingolipids in cancer biology and ther-
of dynamic organisation of lipids in chloroplast mem- apeutics”. Subcellular Biochemistry. Subcellular Bio-
branes”. Journal of Biosciences 15 (4): 281–288. chemistry 49: 413–440. doi:10.1007/978-1-4020-8831-
doi:10.1007/BF02702669. 5_16. ISBN 978-1-4020-8830-8. PMC 2636716. PMID
18751921.
[49] Stryer et al., pp. 333–334.
[62] Klein C, Malviya AN. (2008). “Mechanism of nuclear
calcium signaling by inositol 1,4,5-trisphosphate pro-
[50] van Meer G, Voelker DR, Feigenson GW. (2008).
duced in the nucleus, nuclear located protein kinase C and
“Membrane lipids: where they are and how they be-
cyclic AMP-dependent protein kinase”. Frontiers in Bio-
have”. Nature Reviews Molecular Cell Biology 9 (2): 112–
science 13 (13): 1206–1226. doi:10.2741/2756. PMID
124. doi:10.1038/nrm2330. PMC 2642958. PMID
17981624.
18216768.
[63] Boyce JA. (2008). “Eicosanoids in asthma, al-
[51] Feigenson GW. (2006). “Phase behavior of lipid mix- lergic inflammation, and host defense”. Cur-
tures”. Nature Chemical Biology 2 (11): 560–563. rent Molecular Medicine 8 (5): 335–349.
doi:10.1038/nchembio1106-560. PMC 2685072. PMID doi:10.2174/156652408785160989. PMID 18691060.
17051225.
[64] Bełtowski J. (2008). “Liver X receptors (LXR) as
[52] Wiggins PM. (1990). “Role of water in some biologi- therapeutic targets in dyslipidemia”. Cardiovascu-
cal processes”. Microbiological Reviews 54 (4): 432–449. lar Therapy 26 (4): 297–316. doi:10.1111/j.1755-
PMC 372788. PMID 2087221. 5922.2008.00062.x. PMID 19035881.

[53] Raschke TM, Levitt M. (2005). “Nonpolar solutes en- [65] Biermann M, Maueröder C, Brauner JM,Chaurio R,
hance water structure within hydration shells while reduc- Janko C, Herrmann M, Muñoz LE. (2013). “Surface
ing interactions between them”. Proceedings of the Na- code—biophysical signals for apoptotic cell clearance”.
tional Academy of Sciences of the United States of America Physical Biology 10 (6): 065007. doi:10.1088/1478-
102 (19): 6777–6782. doi:10.1073/pnas.0500225102. 3975/10/6/065007. PMID 24305041.
PMC 1100774. PMID 15867152.
[66] Indiveri, C; Tonazzi, A; Palmieri, F (1991). “Charac-
terization of the unidirectional transport of carnitine cat-
[54] Segré D, Ben-Eli D, Deamer D, Lancet D. (2001).
alyzed by the reconstituted carnitine carrier from rat liver
“The Lipid World” (PDF). Origins of Life and
mitochondria”. Biochimica et biophysica acta 1069 (1):
Evolution of Biospheres 31 (1–2): 119–145.
110–6. PMID 1932043.
doi:10.1023/A:1006746807104. PMID 11296516.
[67] Parodi AJ, Leloir LF. (1979). “The role of lipid inter-
[55] Brasaemle DL. (2007). “Thematic review series: mediates in the glycosylation of proteins in the eucary-
adipocyte biology. The perilipin family of structural lipid otic cell”. Biochimica et Biophysica Acta 559 (1): 1–37.
droplet proteins: stabilization of lipid droplets and con- doi:10.1016/0304-4157(79)90006-6. PMID 375981.
trol of lipolysis”. Journal of Lipid Research 48 (12):
2547–2559. doi:10.1194/jlr.R700014-JLR200. PMID [68] Helenius A, Aebi M. (2001). “Intracellular functions
17878492. of N-linked glycans”. Science 291 (5512): 2364–2369.
doi:10.1126/science.291.5512.2364. PMID 11269317.
[56] Stryer et al., p. 619.
[69] Nowicki M, Frentzen M. (2005). “Cardiolipin syn-
[57] Wang X. (2004). “Lipid signaling”. Cur- thase of Arabidopsis thaliana". FEBS Letters 579 (10):
rent Opinion in Plant Biology 7 (3): 329–236. 2161–2165. doi:10.1016/j.febslet.2005.03.007. PMID
doi:10.1016/j.pbi.2004.03.012. PMID 15134755. 15811335.

[70] Gohil VM, Greenberg ML. (2009). “Mitochondrial mem-

[58] Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subra-
brane biogenesis: phospholipids and proteins go hand
maniam S. (2011). “Signaling gateway molecule pages—
in hand”. Journal of Cell Biology 184 (4): 469–472.
a data model perspective”. Bioinformatics 27 (12):
doi:10.1083/jcb.200901127. PMC 2654137. PMID
1736–1738. doi:10.1093/bioinformatics/btr190. PMC
19237595.
3106186. PMID 21505029.
[71] Hoch FL. (1992). “Cardiolipins and biomembrane func-
[59] Eyster KM. (2007). “The membrane and lipids tion”. Biochimica et Biophysica Acta 1113 (1): 71–133.
as integral participants in signal transduction”. doi:10.1016/0304-4157(92)90035-9. PMID 10206472.
Advances in Physiology Education 31 (1): 5–16.
doi:10.1152/advan.00088.2006. PMID 17327576. [72] Steroids. Elmhurst.edu. Retrieved on 2013-10-10.
7.1. LIPID 149

[73] Stryer et al., p. 634. [89] Micha R, Mozaffarian D. (2008). “Trans fatty
acids: effects on cardiometabolic health and impli-
[74] Chirala S, Wakil S. (2004). “Structure and function of cations for policy”. Prostaglandins, Leukotrienes,
animal fatty acid synthase”. Lipids 39 (11): 1045–1053. and Essential Fatty Acids 79 (3–5): 147–152.
doi:10.1007/s11745-004-1329-9. PMID 15726818. doi:10.1016/j.plefa.2008.09.008. PMC 3588097.
PMID 18996687.
[75] White SW, Zheng J, Zhang YM, Rock CO. (2005).
“The structural biology of type II fatty acid biosyn- [90] Dalainas I, Ioannou HP. (2008). “The role of trans fatty
thesis”. Annual Review of Biochemistry 74: 791– acids in atherosclerosis, cardiovascular disease and infant
831. doi:10.1146/annurev.biochem.74.082803.133524. development”. International Angiology: a Journal of the
PMID 15952903. International Union of Angiology 27 (2): 146–156. PMID
18427401.
[76] Ohlrogge J, Jaworski J. (1997). “Regulation of
fatty acid synthesis”. Annual Review of Plant Phys- [91] Mozaffarian D, Willett WC. (2007). “Trans fatty acids
iology and Plant Molecular Biology 48: 109–136. and cardiovascular risk: a unique cardiometabolic im-
doi:10.1146/annurev.arplant.48.1.109. PMID 15012259. print?". Current Atherosclerosis Reports 9 (6): 486–93.
doi:10.1007/s11883-007-0065-9. PMID 18377789.
[77] Stryer et al., p. 643.
[92] Astrup A, Dyerberg J, Selleck M, Stender S. (2008),
[78] Stryer et al., pp. 733–739. Nutrition transition and its relationship to the develop-
ment of obesity and related chronic diseases 9 (S1), pp.
[79] Grochowski L, Xu H, White R. (2006). 48–52, doi:10.1111/j.1467-789X.2007.00438.x, PMID
"Methanocaldococcus jannaschii uses a modified 18307699
mevalonate pathway for biosynthesis of isopentenyl
diphosphate”. Journal of Bacteriology 188 (9): 3192– [93] Astrup A. (2005). “The role of dietary fat in obesity”.
3198. doi:10.1128/JB.188.9.3192-3198.2006. PMC Seminars in Vascular Medicine 5 (1): 40–47. PMID
1447442. PMID 16621811. 15968579.

[80] Lichtenthaler H. (1999). “The 1-dideoxy-D-xylulose-5- [94] Astrup A. (2008). “Dietary management of obesity”.
phosphate pathway of isoprenoid biosynthesis in plants”. JPEN Journal of Parenteral and Enteral Nutrition 32
Annual Review of Plant Physiology and Plant Molecular (5): 575–577. doi:10.1177/0148607108321707. PMID
Biology 50: 47–65. doi:10.1146/annurev.arplant.50.1.47. 18753397.
PMID 15012203.
[95] Beresford SA, Johnson KC, Ritenbaugh C, Lasser NL,
[81] Schroepfer G. (1981). “Sterol biosynthesis”. Snetselaar LG, Black HR et al. (2006). “Low-fat di-
Annual Review of Biochemistry 50: 585–621. etary pattern and risk of colorectal cancer: the Women’s
doi:10.1146/annurev.bi.50.070181.003101. PMID Health Initiative Randomized Controlled Dietary Modi-
7023367. fication Trial”. Journal of the American Medical Asso-
ciation 295 (6): 643–654. doi:10.1001/jama.295.6.643.
[82] Lees N, Skaggs B, Kirsch D, Bard M. (1995). “Cloning PMID 16467233.
of the late genes in the ergosterol biosynthetic pathway of
Saccharomyces cerevisiae—a review”. Lipids 30 (3): 221– [96] Howard BV, Manson JE, Stefanick ML, Beresford SA,
226. doi:10.1007/BF02537824. PMID 7791529. Frank G, Jones B et al. (2006). “Low-fat dietary
pattern and weight change over 7 years: the Women’s
[83] Stryer et al., pp. 625–626. Health Initiative Dietary Modification Trial”. Journal
of the American Medical Association 295 (1): 39–49.
[84] Bhagavan, p. 903.
doi:10.1001/jama.295.1.39. PMID 16391215.
[85] Russo GL. (2009). “Dietary n-6 and n-3 polyunsaturated [97] “Fats and Cholesterol: Out with the Bad, In with the Good
fatty acids: from biochemistry to clinical implications in — What Should You Eat? – The Nutrition Source”. Har-
cardiovascular prevention”. Biochemical Pharmacology vard School of Public Health.
77 (6): 937–946. doi:10.1016/j.bcp.2008.10.020. PMID
19022225.
Bibliography
[86] Bhagavan, p. 388.

[87] Riediger ND, Othman RA, Suh M, Moghadasian MH. • Bhagavan NV (2002). Medical Biochemistry. San
(2009). “A systemic review of the roles of n- Diego: Harcourt/Academic Press. ISBN 978-0-12-
3 fatty acids in health and disease”. Journal of 095440-7.
the American Dietic Association 109 (4): 668–679.
doi:10.1016/j.jada.2008.12.022. PMID 19328262. • Devlin TM (1997). Textbook of Biochemistry: With
Clinical Correlations (4th ed.). Chichester: John
[88] Galli C, Risé P. (2009). “Fish consumption, omega Wiley & Sons. ISBN 978-0-471-17053-2.
3 fatty acids and cardiovascular disease. The
science and the clinical trials”. Nutrition and • Stryer L, Berg JM, Tymoczko JL (2007). Biochem-
Health (Berkhamsted, Hertfordshire) 20 (1): 11–20. istry (6th ed.). San Francisco: W.H. Freeman.
doi:10.1177/026010600902000102. PMID 19326716. ISBN 978-0-7167-8724-2.
150 CHAPTER 7. LIPIDS AND MEMBRANES

• van Holde KE, Mathews CK (1996). Biochem-

istry (2nd ed.). Menlo Park, California: Ben-
jamin/Cummings Pub. Co. ISBN 978-0-8053-
3931-4.

7.1.7 External links

Introductory

• List of lipid-related web sites

• Nature Lipidomics Gateway – Round-up and sum-

maries of recent lipid research

• Lipid Library – General reference on lipid chemistry

and biochemistry

• Cyberlipid.org – Resources and history for lipids.

• Molecular Computer Simulations – Modeling of

Lipid Membranes Cross-section view of the structures that can be formed by phos-
pholipids in aqueous
• Lipids, Membranes and Vesicle Trafficking – The
Virtual Library of Biochemistry and Cell Biology
7.2 Biological membrane
Nomenclature This article is about various membranes in living things.
For the membranes surrounding cells, see cell membrane.
A biological membrane or biomembrane is an en-
• IUPAC nomenclature of lipids
closing or separating membrane that acts as a selectively
permeable barrier within living things. Biological mem-
• IUPAC glossary entry for the lipid class of branes, in the form of cell membranes, often consist
molecules of a phospholipid bilayer with embedded, integral and
peripheral proteins used in communication and trans-
Databases portation of chemicals and ions. Bulk lipid in membrane
provides a fluid matrix for proteins to rotate and later-
ally diffuse for physiological functioning. Proteins are
• LIPID MAPS – Comprehensive lipid and lipid- adapted to high membrane fluidity environment of lipid
associated gene/protein databases. bilayer with the presence of an annular lipid shell, consist-
ing of lipid molecules bound tightly to surface of integral
• LipidBank – Japanese database of lipids and related membrane proteins. The cellular membranes should not
properties, spectral data and references. be confused with isolating tissues formed by layers of
cells, such as mucous membranes and basement mem-
branes.
General

• ApolloLipids – Provides dyslipidemia and cardio- 7.2.1 Function

vascular disease prevention and treatment informa-
tion as well as continuing medical education pro- The phospholipid bilayer contains charged hydrophilic
grams headgroups, which interact with polar water. The lipids
also contain hydrophobic tails, which meet with the
• National Lipid Association – Professional medical hydrophobic tails of the complementary layer. The
education organization for health care profession- interactions of lipids, especially the hydrophobic tails, de-
als who seek to prevent morbidity and mortality termine the lipid bilayer physical properties such as fluid-
stemming from dyslipidemias and other cholesterol- ity.
related disorders. Membranes in cells typically define enclosed spaces or
7.3. MEMBRANE PROTEIN 151

compartments in which cells may maintain a chemical or 7.2.2 See also

biochemical environment that differs from the outside.
For example, the membrane around peroxisomes shields • Membrane lipids
the rest of the cell from peroxides, chemicals that can be
• Membrane protein
toxic to the cell, and the cell membrane separates a cell
from its surrounding medium. Peroxisomes are one form • Annular lipid shell
of vacuole found in the cell that contain by-products of
chemical reactions within the cell. Most organelles are • Lipid bilayer
defined by such membranes, and are called “membrane-
• Membrane fluidity
bound” organelles.
• Osmosis
• Membrane biology
Selective Permeability
7.2.3 References
Probably the most important feature of a biomembrane
is that it is a selectively permeable structure. This means [1] Brown
that the size, charge, and other chemical properties of the
atoms and molecules attempting to cross it will determine
General
whether they succeed in doing so. Selective permeability
is essential for effective separation of a cell or organelle
from its surroundings. Biological membranes also have • von Heijne G, Rees D (August 2008). “Membranes:
certain mechanical or elastic properties that allow them reading between the lines”. Curr. Opin. Struct. Biol.
to change shape and move as required. 18 (4): 403–5. doi:10.1016/j.sbi.2008.06.003.
PMID 18634876.
Generally, small hydrophobic molecules can readily cross
phospholipid bilayers by simple diffusion.[1] • Brown, Bernard (1996). Biological Membranes
(PDF). London, U.K.: The Biochemical Society. p.
Particles that are required for cellular function but are un-
21. ISBN 0904498328.
able to diffuse freely across a membrane enter through a
membrane transport protein or are taken in by means of
endocytosis, where the membrane allows for a vacuole 7.2.4 External links
to join onto it and push its contents into the cell. Many
types of specialized plasma membranes can separate cell • Membranes at the US National Library of Medicine
from external environment: apical, basolateral, presynap- Medical Subject Headings (MeSH)
tic and postsynaptic ones, membranes of flagella, cilia,
microvillus, filopodia and lamellipodia, the sarcolemma
of muscle cells, as well as specialized myelin and den-
dritic spine membranes of neurons. Plasma membranes
7.3 Membrane protein
can also form different types of “supramembrane” struc-
tures such as caveola, postsynaptic density, podosome, in- Membrane proteins are proteins that interact with
vadopodium, desmosome, hemidesmosome, focal adhe- biological membranes. They are one of the common
sion, and cell junctions. These types of membranes differ types of protein along with soluble globular proteins,
in lipid and protein composition. fibrous proteins, and disordered proteins.[1] They are tar-
gets of over 50% of all modern medicinal drugs.[2] It is
Distinct types of membranes also create intracellular estimated that 20–30% of all genes in most genomes en-
organelles: endosome; smooth and rough endoplasmic code membrane proteins.[3]
reticulum; sarcoplasmic reticulum; Golgi apparatus; lyso-
some; mitochondrion (inner and outer membranes); nu-
cleus (inner and outer membranes); peroxisome; vac- 7.3.1 Function
uole; cytoplasmic granules; cell vesicles (phagosome, au-
tophagosome, clathrin-coated vesicles, COPI-coated and Membrane proteins perform a variety of functions vital
COPII-coated vesicles) and secretory vesicles (including to the survival of organisms:[4]
synaptosome, acrosomes, melanosomes, and chromaffin
granules). Different types of biological membranes have • Membrane receptor proteins relay signals between
diverse lipid and protein compositions. The content of the cell’s internal and external environments.
membranes defines their physical and biological proper-
ties. Some components of membranes play a key role in • Transport proteins move molecules and ions across
medicine, such as the efflux pumps that pump drugs out the membrane. They can be categorized according
of a cell. to the Transporter Classification database.
152 CHAPTER 7. LIPIDS AND MEMBRANES

Schematic representation of transmembrane proteins: 1. a single

transmembrane α-helix (bitopic membrane protein) 2. a poly-
topic transmembrane α-helical protein 3. a polytopic transmem-
brane β-sheet protein
The membrane is represented in light-brown.

Integral membrane proteins are permanently attached to

the membrane. Such proteins can be separated from
the biological membranes only using detergents, nonpolar
solvents, or sometimes denaturing agents. They can be
classified according to their relationship with the bilayer:
Crystal structure of Potassium channel Kv1.2/2.1 Chimera. Cal-
culated hydrocarbon boundaries of the lipid bilayer are indicated • Integral polytopic proteins, also known as “trans-
by red and blue dots. membrane proteins,” are integral membrane pro-
teins that span across the membrane at least once.
They have one of two tertiary structures:
• Membrane enzymes may have many activities, such
as oxidoreductase, transferase or hydrolase. • helix bundle proteins, which are present in all
types of biological membranes;
• Cell adhesion molecules allow cells to identify each
• beta barrel proteins, which are found only
other and interact. For example proteins involved in
in outer membranes of Gram-negative bac-
immune response.
teria, lipid-rich cell walls of a few Gram-
positive bacteria, and outer membranes of
mitochondria and chloroplasts.
7.3.2 Topology

The topology of an integral membrane protein describes • Integral monotopic proteins are integral membrane
the number of transmembrane segments, as well as the proteins that are attached to only one side of the
orientation in the membrane.[5] Membrane proteins have membrane and do not span the whole way across.
several different topologies:[6]
A slightly different classification is to divide all mem- Peripheral membrane proteins
brane proteins to integral and amphitropic.[7] The am-
phitropic are proteins that can exist in two alterna- Main article: Peripheral membrane protein
tive states: a water-soluble and a lipid bilayer-bound.
The amphitropic protein category includes water-soluble
channel-forming polypeptide toxins, which associate ir- Peripheral membrane proteins are temporarily attached
reversibly with membranes, but excludes peripheral pro- either to the lipid bilayer or to integral proteins by a
teins that interact with other membrane proteins rather combination of hydrophobic, electrostatic, and other non-
than with lipid bilayer. covalent interactions. Peripheral proteins dissociate fol-
lowing treatment with a polar reagent, such as a solution
with an elevated pH or high salt concentrations.
Integral membrane proteins Integral and peripheral proteins may be post-
translationally modified, with added fatty acid or
Main article: Integral membrane protein prenyl chains, or GPI (glycosylphosphatidylinositol),
which may be anchored in the lipid bilayer.
7.3. MEMBRANE PROTEIN 153

Membrane proteins have hydrophobic surfaces, are rel-

atively flexible and are expressed at relatively low lev-
els. This creates difficulties in obtaining enough protein
and then growing crystals. Hence, despite the signifi-
cant functional importance of membrane proteins, de-
termining atomic resolution structures for these proteins
1 2 3 4 is more difficult than globular proteins.[9] As of January
2013 less than 0.1% of protein structures determined
Schematic representation of the different types of interaction be- were membrane proteins despite being 20-30% of the to-
tween monotopic membrane proteins and the cell membrane: 1. tal proteome.[10]
interaction by an amphipathic α-helix parallel to the membrane
plane (in-plane membrane helix) 2. interaction by a hydropho- Many of the successful membrane protein structures are
bic loop 3. interaction by a covalently bound membrane lipid characterized by X-ray crystallography and are very large
(lipidation) 4. electrostatic or ionic interactions with membrane structures in which the interactions with the membrane
lipids (e.g. through a calcium ion) mimetic environments can be anticipated to be small in
comparison to those within the protein structures. The
small domains are particularly sensitive to the influence of
Polypeptide toxins membrane mimetic environments, with potential to lead
to non-native structures. However, there are many sam-
Main article: Pore-forming toxin ple preparation conditions that can be chosen for crys-
tallization and for solution NMR. All membrane pro-
Polypeptide toxins and many antibacterial peptides, such tein structural biology should be subjected to careful
as colicins or hemolysins, and certain proteins involved in scrutiny; through a combination of structural method-
apoptosis, are sometimes considered a separate category. ologies it should be possible to achieve an understand-
These proteins are water-soluble but can aggregate and ing of the native functional state for membrane protein
associate irreversibly with the lipid bilayer and become structures.[11] Coevolution information has been success-
reversibly or irreversibly membrane-associated. fully exploited for prediction of multiple large (mem-
brane) protein structures.[12][13][14]
Due to this difficulty and the importance of this class of
7.3.3 3D Structure proteins methods of protein structure prediction based on
hydropathy plots and the positive inside rule have been
developed.[15][16]

7.3.4 Membrane proteins in genomes

A large fraction of all proteins are thought to be

membrane proteins. For instance, about 1000 of the
~4200 proteins of E. coli are thought to be membrane
proteins.[17] The membrane localization has been con-
firmed for more than 600 of them experimentally.[17] The
localization of proteins in membranes can be predicted
very reliably using hydrophobicity analyses of protein se-
quences, i.e. the localization of hydrophobic amino acid
sequences.

Increase in the number of 3D structures of membrane proteins 7.3.5 See also

known
• Integral membrane proteins
The most common tertiary structures are helix bundle and
beta barrel. The portion of the membrane proteins that • Transmembrane proteins
are attached to the lipid bilayer (see annular lipid shell)
are consisting of hydrophobic amino acids only. This • Peripheral membrane proteins
is done so that the peptide bonds’ carbonyl and amine
• Annular lipid shell
will react with each other instead of the hydrophobic sur-
rounding. The portion of the protein that is not touching • Ion pump (biology)
the lipid bilayer and is protruding out of the cell mem-
brane are usually hydrophilic amino acids.[8] • Carrier protein
154 CHAPTER 7. LIPIDS AND MEMBRANES

• Ion channel [3] Krogh, A.; Larsson, B. R.; Von Heijne, G.; Sonnham-
mer, E. L. L. (2001). “Predicting transmembrane pro-
• Receptor (biochemistry) * List of MeSH codes tein topology with a hidden markov model: Application
(D12.776) to complete genomes”. Journal of Molecular Biology
305 (3): 567–580. doi:10.1006/jmbi.2000.4315. PMID
• Inner nuclear membrane proteins 11152613.

[4] Almén, M.; Nordström, K. J.; Fredriksson, R.; Schiöth,

7.3.6 External links H. B. (2009). “Mapping the human membrane proteome:
A majority of the human membrane proteins can be
Organizations classified according to function and evolutionary origin”.
BMC Biology 7: 50. doi:10.1186/1741-7007-7-50. PMC
• Membrane Protein Structural Dynamics Consor- 2739160. PMID 19678920.
tium [5] Von Heijne, G. (2006). “Membrane-protein topology”.
Nature Reviews Molecular Cell Biology 7 (12): 909–918.
doi:10.1038/nrm2063. PMID 17139331.
Membrane protein databases
[6] Gerald Karp (2009). Cell and Molecular Biology: Con-
• TCDB - Transporter Classification database, a com- cepts and Experiments. John Wiley and Sons. pp. 128–
prehensive classification of transmembrane trans- . ISBN 978-0-470-48337-4. Retrieved 13 November
porter proteins 2010.

• Orientations of Proteins in Membranes (OPM) [7] Johnson JE, Cornell RB (1999). “Amphitropic pro-
database 3D structures of integral and peripheral teins: regulation by reversible membrane interactions
membrane proteins arranged in the lipid bilayer (review)". Mol. Membr. Biol. 16 (3): 217–235.
doi:10.1080/096876899294544. PMID 10503244.
• Protein Data Bank of Transmembrane Proteins 3D
[8] White, Stephen. “General Principle of Membrane Protein
models of all transmembrane proteins currently in
Folding and Stability.” Stephen White Laboratory Home-
PDB. Approximate positions of membrane bound-
page. 10 Nov. 2009. web.
ary planes were calculated for each PDB entry.
[9] Carpenter, E. P.; Beis, K.; Cameron, A. D.; Iwata, S.
• TransportDB Genomics-oriented database of trans- (2008). “Overcoming the challenges of membrane pro-
porters from TIGR tein crystallography”. Current Opinion in Structural Bi-
ology 18 (5): 581–586. doi:10.1016/j.sbi.2008.07.001.
• Membrane PDB Database of 3D structures of inte- PMC 2580798. PMID 18674618.
gral membrane proteins and hydrophobic peptides
with an emphasis on crystallization conditions [10] Membrane Proteins of known 3D Structure

• List of transmembrane proteins of known 3D struc- [11] Cross, Timothy, Mukesh Sharma, Myunggi Yi, Huan-
ture, incomplete list of transmembrane proteins cur- Xiang Zhou (2010). “Influence of Solubilizing Environ-
rently used in to the Protein Data Bank ments on Membrane Protein Structures”

• Membrane targeting domains (MeTaDoR), a [12] Hopf TA, Colwell LJ, Sheridan R, Rost B, Sander C,
database of membrane targeting domains Marks DS (June 2012). “Three-dimensional structures of
membrane proteins from genomic sequencing” 149 (7).
pp. 1607–21. doi:10.1016/j.cell.2012.04.012. PMC
Further reading 3641781. PMID 22579045.

[13] Marks DS, Colwell LJ, Sheridan R et al. (2011).

• The Human Membrane Proteome - A compre- “Protein 3D structure computed from evolution-
hensive article covering the transmembrane protein ary sequence variation” 6 (12). pp. e28766.
component of the human proteome doi:10.1371/journal.pone.0028766. PMC 3233603.
PMID 22163331.

7.3.7 References [14] Flock T, Venkatakrishnan A, Vinothkumar K, Babu MM

(June 2012). “Deciphering membrane protein structures
[1] Andreeva, A (2014). “SCOP2 prototype: a new ap- from protein sequences” 13 (6). p. 160. doi:10.1186/gb-
proach to protein structure mining”. Nucleic Acids Res. 2012-13-6-160. PMID 22738306.
doi:10.1093/nar/gkt1242. PMID 24293656.
[15] Elofsson, A.; Heijne, G. V. (2007). “Membrane
[2] Overington JP, Al-Lazikani B, Hopkins AL (December Protein Structure: Prediction versus Reality”.
2006). “How many drug targets are there?". Nat Rev Annual Review of Biochemistry 76: 125–140.
Drug Discov 5 (12): 993–6. doi:10.1038/nrd2199. PMID doi:10.1146/annurev.biochem.76.052705.163539.
17139284. PMID 17579561.
7.4. CELL MEMBRANE 155

[16] State of the art in membrane protein prediction adhesion, ion conductivity and cell signalling and serve
as the attachment surface for several extracellular struc-
[17] Daley, D. O.; Rapp, M; Granseth, E; Melén, K; Drew, D; tures, including the cell wall, glycocalyx, and intracellular
von Heijne, G (2005). “Global topology analysis of the
cytoskeleton. Cell membranes can be artificially reassem-
Escherichia coli inner membrane proteome”. Science 308
bled.[4][5][6]
(5726): 1321–3. doi:10.1126/science.1109730. PMID
15919996.
7.4.1 Function
7.4 Cell membrane
Not to be confused with cell walls.

Cell

Extracellular fluid
Nucleus
Cytoplasm

A detailed diagram of the cell membrane

Cell membrane
Carbohydrate

Glycoprotein

Globular protein
Protein Channel
(Transport protein)

Cholesterol

Glycolipid

Surface protein Alpha-helix protein

Globular protein Filaments of (Integral protein)
(Integral) cytoskeleton Peripheral protein

Phospholipid bilayer Phospholipid

(Phosphatidylcholine)

Hydrophilic head

Hydrophobic tail

Illustration of a Eukaryotic cell membrane

Illustration depicting cellular diffusion

The cell membrane (or plasma membrane or plas-

malemma) surrounds the cytoplasm of living cells, phys-
ically separating the intracellular components from the
extracellular environment. Fungi, bacteria and plants also
have a cell wall in addition, which provides a mechani-
cal support to the cell and precludes the passage of larger
molecules. The cell membrane also plays a role in an-
Comparison of Eukaryotes vs. Prokaryotes choring the cytoskeleton to provide shape to the cell, and
in attaching to the extracellular matrix and other cells to
The cell membrane (also known as the plasma mem- help group cells together to form tissues.
brane or cytoplasmic membrane) is a biological mem- The cell membrane is selectively permeable and able to
brane that separates the interior of all cells from regulate what enters and exits the cell, thus facilitating
the outside environment.[1][2] The cell membrane is the transport of materials needed for survival. The move-
selectively permeable to ions and organic molecules and ment of substances across the membrane can be either
controls the movement of substances in and out of cells.[3] "passive", occurring without the input of cellular energy,
The basic function of the cell membrane is to protect the or "active", requiring the cell to expend energy in trans-
cell from its surroundings. It consists of the phospholipid porting it. The membrane also maintains the cell poten-
bilayer with embedded proteins. Cell membranes are tial. The cell membrane thus works as a selective filter
involved in a variety of cellular processes such as cell that allows only certain things to come inside or go outside
156 CHAPTER 7. LIPIDS AND MEMBRANES

the cell. The cell employs a number of transport mecha- peptidoglycan (amino acids and sugars). Some eukary-
nisms that involve biological membranes: otic cells also have cell walls, but none that are made of
1. Passive osmosis and diffusion: Some substances (small peptidoglycan. The outer membrane of gram negative
molecules, ions) such as carbon dioxide (CO2 ) and oxy- microbes is rich in lipopolysaccharide and thus is dif-
gen (O2 ), can move across the plasma membrane by dif- ferent from cell membrane of the microbes. The outer
fusion, which is a passive transport process. Because the membrane can bleb out into periplasmic protrusions un-
membrane acts as a barrier for certain molecules and ions, der stess conditions or upon virulence requirements while
they can occur in different concentrations on the two sides encountering a host target cell, and thus such blebs may
work as virulence organelles.[7]
of the membrane. Such a concentration gradient across
a semipermeable membrane sets up an osmotic flow for
the water.
7.4.3 Structures
2. Transmembrane protein channels and transporters:
Nutrients, such as sugars or amino acids, must enter the Fluid mosaic model
cell, and certain products of metabolism must leave the
cell. Such molecules diffuse passively through protein According to the fluid mosaic model of S. J. Singer and
channels such as aquaporins (in the case of water (H2 O)) G. L. Nicolson (1972), which replaced the earlier model
in facilitated diffusion or are pumped across the mem- of Davson and Danielli, biological membranes can be
brane by transmembrane transporters. Protein channel considered as a two-dimensional liquid in which lipid
proteins, also called permeases, are usually quite specific, and protein molecules diffuse more or less easily.[8] Al-
recognizing and transporting only a limited food group of though the lipid bilayers that form the basis of the mem-
chemical substances, often even only a single substance. branes do indeed form two-dimensional liquids by them-
3. Endocytosis: Endocytosis is the process in which cells selves, the plasma membrane also contains a large quan-
absorb molecules by engulfing them. The plasma mem- tity of proteins, which provide more structure. Examples
brane creates a small deformation inward, called an in- of such structures are protein-protein complexes, pickets
vagination, in which the substance to be transported is and fences formed by the actin-based cytoskeleton, and
captured. The deformation then pinches off from the potentially lipid rafts.
membrane on the inside of the cell, creating a vesi-
cle containing the captured substance. Endocytosis is
Lipid bilayer
a pathway for internalizing solid particles (“cell eating”
or phagocytosis), small molecules and ions (“cell drink-
ing” or pinocytosis), and macromolecules. Endocytosis
requires energy and is thus a form of active transport.
4. Exocytosis: Just as material can be brought into the cell
by invagination and formation of a vesicle, the membrane
of a vesicle can be fused with the plasma membrane, ex-
truding its contents to the surrounding medium. This is
the process of exocytosis. Exocytosis occurs in various
cells to remove undigested residues of substances brought
in by endocytosis, to secrete substances such as hormones
and enzymes, and to transport a substance completely
across a cellular barrier. In the process of exocytosis, the Diagram of the arrangement of amphipathic lipid molecules to
undigested waste-containing food vacuole or the secre- form a lipid bilayer. The yellow polar head groups separate the
tory vesicle budded from Golgi apparatus, is first moved grey hydrophobic tails from the aqueous cytosolic and extracel-
by cytoskeleton from the interior of the cell to the sur- lular environments.
face. The vesicle membrane comes in contact with the
plasma membrane. The lipid molecules of the two bi- Lipid bilayers form through the process of self-assembly.
layers rearrange themselves and the two membranes are, The cell membrane consists primarily of a thin layer of
thus, fused. A passage is formed in the fused membrane amphipathic phospholipids which spontaneously arrange
and the vesicles discharges its contents outside the cell. so that the hydrophobic “tail” regions are isolated from
the surrounding polar fluid, causing the more hydrophilic
“head” regions to associate with the intracellular (cytoso-
7.4.2 Prokaryotes lic) and extracellular faces of the resulting bilayer. This
forms a continuous, spherical lipid bilayer. Forces such as
Gram-negative bacteria have both a plasma membrane van der Waals, electrostatic, hydrogen bonds, and nonco-
and an outer membrane separated by periplasm. Other valent interactions all contribute to the formation of the
prokaryotes have only a plasma membrane. Prokary- lipid bilayer. Overall, hydrophobic interactions are the
otic cells are also surrounded by a cell wall composed of major driving force in the formation of lipid bilayers.
7.4. CELL MEMBRANE 157

Lipid bilayers are generally impermeable to ions and po- model. Tight junctions join epithelial cells near their api-
lar molecules. The arrangement of hydrophilic heads and cal surface to prevent the migration of proteins from the
hydrophobic tails of the lipid bilayer prevent polar so- basolateral membrane to the apical membrane. The basal
lutes (ex. amino acids, nucleic acids, carbohydrates, pro- and lateral surfaces thus remain roughly equivalent to one
teins, and ions) from diffusing across the membrane, but another, yet distinct from the apical surface.
generally allows for the passive diffusion of hydrophobic
molecules. This affords the cell the ability to control the
movement of these substances via transmembrane protein Membrane structures
complexes such as pores, channels and gates.
Cell membrane can form different types of “supramem-
Flippases and scramblases concentrate phosphatidyl ser-
brane” structures such as caveola, postsynaptic den-
ine, which carries a negative charge, on the inner mem-
sity, podosome, invadopodium, focal adhesion, and dif-
brane. Along with NANA, this creates an extra barrier to
ferent types of cell junctions. These structures are
charged moieties moving through the membrane.
usually responsible for cell adhesion, communication,
Membranes serve diverse functions in eukaryotic and endocytosis and exocytosis. They can be visualized by
prokaryotic cells. One important role is to regulate the electron microscopy or fluorescence microscopy. They
movement of materials into and out of cells. The phos- are composed of specific proteins, such as integrins and
pholipid bilayer structure (fluid mosaic model) with spe- cadherins.
cific membrane proteins accounts for the selective perme-
ability of the membrane and passive and active transport
mechanisms. In addition, membranes in prokaryotes and Cytoskeleton
in the mitochondria and chloroplasts of eukaryotes facil-
itate the synthesis of ATP through chemiosmosis. The cytoskeleton is found underlying the cell membrane
in the cytoplasm and provides a scaffolding for membrane
proteins to anchor to, as well as forming organelles that
Membrane polarity
extend from the cell. Indeed, cytoskeletal elements inter-
act extensively and intimately with the cell membrane.[9]
See also: Epithelial polarity
Anchoring proteins restricts them to a particular cell
The apical membrane of a polarized cell is the surface
surface — for example, the apical surface of epithelial
+
H +
H cells that line the vertebrate gut — and limits how far
Apical Surface they may diffuse within the bilayer. The cytoskeleton
is able to form appendage-like organelles, such as cilia,
K +
which are microtubule-based extensions covered by the
cell membrane, and filopodia, which are actin-based ex-
tensions. These extensions are ensheathed in membrane
and project from the surface of the cell in order to sense
Carbonic
Anhydrase 2 the external environment and/or make contact with the
substrate or other cells. The apical surfaces of epithelial
cells are dense with actin-based finger-like projections
-
Cl +
K
-
Cl known as microvilli, which increase cell surface area and
thereby increase the absorption rate of nutrients. Local-
kAE1
Basolateral Surface ized decoupling of the cytoskeleton and cell membrane
results in formation of a bleb.
Alpha intercalated cell

of the plasma membrane that faces inward to the lumen.

7.4.4 Composition
This is particularly evident in epithelial and endothelial
Cell membranes contain a variety of biological
cells, but also describes other polarized cells, such as
molecules, notably lipids and proteins. Material is
neurons. The basolateral membrane of a polarized cell
incorporated into the membrane, or deleted from it, by a
is the surface of the plasma membrane that forms its
variety of mechanisms:
basal and lateral surfaces. It faces outwards, towards the
interstitium, and away from the lumen. Basolateral mem-
brane is a compound phrase referring to the terms “basal • Fusion of intracellular vesicles with the membrane
(base) membrane” and “lateral (side) membrane”, which, (exocytosis) not only excretes the contents of the
especially in epithelial cells, are identical in composition vesicle but also incorporates the vesicle membrane’s
and activity. Proteins (such as ion channels and pumps) components into the cell membrane. The membrane
are free to move from the basal to the lateral surface of may form blebs around extracellular material that
the cell or vice versa in accordance with the fluid mosaic pinch off to become vesicles (endocytosis).
158 CHAPTER 7. LIPIDS AND MEMBRANES

• If a membrane is continuous with a tubular structure is quite fluid and not fixed rigidly in place. Under
made of membrane material, then material from the physiological conditions phospholipid molecules in the
tube can be drawn into the membrane continuously. cell membrane are in the liquid crystalline state. It means
the lipid molecules are free to diffuse and exhibit rapid
• Although the concentration of membrane compo- lateral diffusion along the layer in which they are present.
nents in the aqueous phase is low (stable membrane However, the exchange of phospholipid molecules be-
components have low solubility in water), there is an tween intracellular and extracellular leaflets of the bilayer
exchange of molecules between the lipid and aque- is a very slow process. Lipid rafts and caveolae are ex-
ous phases. amples of cholesterol-enriched microdomains in the cell
membrane. Also, a fraction of the lipid in direct contact
Lipids with integral membrane proteins, which is tightly bound
to the protein surface is called annular lipid shell; it be-
haves as a part of protein complex.
In animal cells cholesterol is normally found dispersed in
varying degrees throughout cell membranes, in the irreg-
ular spaces between the hydrophobic tails of the mem-
brane lipids, where it confers a stiffening and strengthen-
ing effect on the membrane.[3]

Phospholipids forming lipid vesicles

Lipid vesicles or liposomes are circular pockets that are

enclosed by a lipid bilayer. These structures are used
in laboratories to study the effects of chemicals in cells
by delivering these chemicals directly to the cell, as well
as getting more insight into cell membrane permeability.
Lipid vesicles and liposomes are formed by first suspend-
ing a lipid in an aqueous solution then agitating the mix-
ture through sonication, resulting in a vesicle. By measur-
ing the rate of efflux from that of the inside of the vesicle
to the ambient solution, allows researcher to better under-
Examples of the major membrane phospholipids and glycol-
stand membrane permeability. Vesicles can be formed
ipids: phosphatidylcholine (PtdCho), phosphatidylethanolamine
(PtdEtn), phosphatidylinositol (PtdIns), phosphatidylserine
with molecules and ions inside the vesicle by forming the
(PtdSer). vesicle with the desired molecule or ion present in the so-
lution. Proteins can also be embedded into the membrane
The cell membrane consists of three classes of through solubilizing the desired proteins in the presence
amphipathic lipids: phospholipids, glycolipids, and of detergents and attaching them to the phospholipids in
sterols. The amount of each depends upon the type of which the liposome is formed. These provide researchers
cell, but in the majority of cases phospholipids are the with a tool to examine various membrane protein func-
most abundant.[10] In RBC studies, 30% of the plasma tions.
membrane is lipid.
The fatty chains in phospholipids and glycolipids usually Carbohydrates
contain an even number of carbon atoms, typically be-
tween 16 and 20. The 16- and 18-carbon fatty acids are Plasma membranes also contain carbohydrates, pre-
the most common. Fatty acids may be saturated or unsat- dominantly glycoproteins, but with some glycolipids
urated, with the configuration of the double bonds nearly(cerebrosides and gangliosides). For the most part, no
always “cis”. The length and the degree of unsaturation glycosylation occurs on membranes within the cell; rather
of fatty acid chains have a profound effect on membrane generally glycosylation occurs on the extracellular sur-
fluidity[11] as unsaturated lipids create a kink, preventing
face of the plasma membrane. The glycocalyx is an im-
the fatty acids from packing together as tightly, thus de-
portant feature in all cells, especially epithelia with mi-
creasing the melting temperature (increasing the fluidity)
crovilli. Recent data suggest the glycocalyx participates
of the membrane. The ability of some organisms to reg- in cell adhesion, lymphocyte homing, and many others.
ulate the fluidity of their cell membranes by altering lipid
The penultimate sugar is galactose and the terminal sugar
composition is called homeoviscous adaptation. is sialic acid, as the sugar backbone is modified in the
The entire membrane is held together via non-covalent golgi apparatus. Sialic acid carries a negative charge, pro-
interaction of hydrophobic tails, however the structure viding an external barrier to charged particles.
7.4. CELL MEMBRANE 159

Proteins • Annular lipid shell

The cell membrane has large content of proteins, typically • AP2 adaptors
around 50% of membrane volume[11] These proteins are
• Artificial cell
important for cell because they are responsible for various
biological activities. Approximately a third of the genes • Bacterial cell structure
in yeast code specifically for them, and this number is
even higher in multicellular organisms.[10] • Bangstad syndrome
The cell membrane, being exposed to the outside envi- • Cell damage, including damage to cell membrane
ronment, is an important site of cell–cell communication.
As such, a large variety of protein receptors and identifi- • Cell theory
cation proteins, such as antigens, are present on the sur-
face of the membrane. Functions of membrane proteins • Elasticity of cell membranes
can also include cell–cell contact, surface recognition, cy-
toskeleton contact, signaling, enzymatic activity, or trans- • Gram-positive bacteria
porting substances across the membrane. • History of cell membrane theory
Most membrane proteins must be inserted in some way
into the membrane. For this to occur, an N-terminus • Lipid raft
“signal sequence” of amino acids directs proteins to the
• Trogocytosis
endoplasmic reticulum, which inserts the proteins into a
lipid bilayer. Once inserted, the proteins are then trans-
ported to their final destination in vesicles, where the vesi- 7.4.8 Notes and references
cle fuses with the target membrane.
[1] Kimball’s Biology pages, Cell Membranes

7.4.5 Variation [2] Singleton P, (1999). Bacteria in Biology, Biotechnology

and Medicine (5th ed.). New York: Wiley. ISBN 0-471-
The cell membrane has different lipid and protein com- 98880-4.
positions in distinct types of cells and may have therefore
[3] Alberts B, Johnson A, Lewis J et al. (2002). Molecular
specific names for certain cell types:
Biology of the Cell (4th ed.). New York: Garland Science.
ISBN 0-8153-3218-1.
• Sarcolemma in myocytes
[4] Budin, Itay; Devaraj, Neal K. (December 29, 2011).
• Oolemma in oocytes “Membrane Assembly Driven by a Biomimetic Coupling
Reaction”. Journal of the American Chemical Society 134
• Axolemma in neuronal processes - axons (2): 751–753. doi:10.1021/ja2076873. Retrieved Febru-
ary 18, 2012.
• Historically, the plasma membrane was also referred
to as the plasmalemma [5] Staff (January 25, 2012). “Chemists Synthesize Artificial
Cell Membrane”. ScienceDaily. Retrieved February 18,
2012.
7.4.6 Permeability
[6] Staff (January 26, 2012). “Chemists create artificial
The permeability of a membrane is the rate of passive cell membrane”. kurzweilai.net. Retrieved February 18,
2012.
diffusion of molecules through the membrane. These
molecules are known as permeant molecules. Permeabil- [7] YashRoy, R.C. (1999). “A structural model for virulence
ity depends mainly on the electric charge and polarity of organellae of gram negative organisms with reference to
the molecule and to a lesser extent the molar mass of the Salmonella pathogenicity in chicken ileum”. Indian Jour-
molecule. Due to the cell membrane’s hydrophobic na- nal of Poultry Science 34 (2): 213–219.
ture, small electrically neutral molecules pass through the
membrane more easily than charged, large ones. The in- [8] Singer SJ, Nicolson GL (Feb 1972). “The fluid mo-
saic model of the structure of cell membranes”. Science
ability of charged molecules to pass through the cell mem-
175 (4023): 720–31. doi:10.1126/science.175.4023.720.
brane results in pH partition of substances throughout the PMID 4333397.
fluid compartments of the body.
[9] Doherty GJ and McMahon HT (2008). “Mediation, Mod-
ulation and Consequences of Membrane-Cytoskeleton In-
7.4.7 See also teractions”. Annual Review of Biophysics 37: 65–95.
doi:10.1146/annurev.biophys.37.032807.125912. PMID
• Ammonium transporter 18573073.
160 CHAPTER 7. LIPIDS AND MEMBRANES

[10] Lodish H, Berk A, Zipursky LS et al. (2004). Molecular

Cell Biology (4th ed.). New York: Scientific American
Books. ISBN 0-7167-3136-3.

[11] Jesse Gray, Shana Groeschler, Tony Le, Zara Gonzalez

(2002). “Membrane Structure” (SWF). Davidson Col-
lege. Retrieved 2007-01-11.

7.4.9 External links

• Lipids, Membranes and Vesicle Trafficking - The
Virtual Library of Biochemistry and Cell Biology
• Cell membrane protein extraction protocol

• Membrane homeostasis, tension regulation,

mechanosensitive membrane exchange and mem-
brane traffic
• 3D structures of proteins associated with plasma
membrane of eukaryotic cells
• Lipid composition and proteins of some eukariotic
membranes
•
Chapter 8

Carbohydrate structure

8.1 Carbohydrate 5-carbon monosaccharide ribose is an important compo-

nent of coenzymes (e.g., ATP, FAD and NAD) and the
backbone of the genetic molecule known as RNA. The
related deoxyribose is a component of DNA. Saccha-
HO OH rides and their derivatives include many other important
OH biomolecules that play key roles in the immune system,
O fertilization, preventing pathogenesis, blood clotting, and
O O development.[7]
HO HO OH
OH In food science and in many informal contexts, the term
OH carbohydrate often means any food that is particularly
rich in the complex carbohydrate starch (such as cereals,
Lactose is a disaccharide found in milk. It consists of a molecule bread and pasta) or simple carbohydrates, such as sugar
of D-galactose and a molecule of D-glucose bonded by beta-1-4 (found in candy, jams, and desserts).
glycosidic linkage. It has a formula of C12 H22 O11 .

A carbohydrate is a biological molecule consisting of 8.1.1 Structure

carbon (C), hydrogen (H) and oxygen (O) atoms, usually
with a hydrogen:oxygen atom ratio of 2:1 (as in water); Formerly the name “carbohydrate” was used in chemistry
in other words, with the empirical formula Cm(H2 O)n for any compound with the formula Cm (H2 O) n.
(where m could be different from n).[1] Some exceptions Following this definition, some chemists considered
exist; for example, deoxyribose, a sugar component of formaldehyde (CH2 O) to be the simplest carbohydrate,[8]
DNA,[2] has the empirical formula C5 H10 O4 .[3] Carbo- while others claimed that title for glycolaldehyde.[9] To-
hydrates are technically hydrates of carbon;[4] structurally day the term is generally understood in the biochemistry
it is more accurate to view them as polyhydroxy aldehydes sense, which excludes compounds with only one or two
and ketones.[5] carbons.
The term is most common in biochemistry, where it is Natural saccharides are generally built of simple carbo-
a synonym of saccharide, a group that includes sugars, hydrates called monosaccharides with general formula
starch, and cellulose. The saccharides are divided into (CH2 O)n where n is three or more. A typical monosac-
four chemical groups: monosaccharides, disaccharides, charide has the structure H-(CHOH)x(C=O)-(CHOH)y-
oligosaccharides, and polysaccharides. In general, the H, that is, an aldehyde or ketone with many hydroxyl
monosaccharides and disaccharides, which are smaller groups added, usually one on each carbon atom that is
(lower molecular weight) carbohydrates, are commonly not part of the aldehyde or ketone functional group. Ex-
referred to as sugars.[6] The word saccharide comes amples of monosaccharides are glucose, fructose, and
from the Greek word σάκχαρον (sákkharon), meaning glyceraldehydes. However, some biological substances
“sugar.” While the scientific nomenclature of carbohy- commonly called “monosaccharides” do not conform
drates is complex, the names of the monosaccharides and to this formula (e.g., uronic acids and deoxy-sugars
disaccharides very often end in the suffix -ose. For ex- such as fucose) and there are many chemicals that do
ample, grape sugar is the monosaccharide glucose, cane conform to this formula but are not considered to be
sugar is the disaccharide sucrose and milk sugar is the monosaccharides (e.g., formaldehyde CH2 O and inositol
disaccharide lactose (see illustration). (CH2 O)6 ).[10]
Carbohydrates perform numerous roles in living organ- The open-chain form of a monosaccharide often coex-
isms. Polysaccharides serve for the storage of energy ists with a closed ring form where the aldehyde/ketone
(e.g., starch and glycogen) and as structural components carbonyl group carbon (C=O) and hydroxyl group (-OH)
(e.g., cellulose in plants and chitin in arthropods). The react forming a hemiacetal with a new C-O-C bridge.

161
162 CHAPTER 8. CARBOHYDRATE STRUCTURE

Monosaccharides can be linked together into what are Classification of monosaccharides

called polysaccharides (or oligosaccharides) in a large va-
riety of ways. Many carbohydrates contain one or more
modified monosaccharide units that have had one or more
groups replaced or removed. For example, deoxyribose,
a component of DNA, is a modified version of ribose;
chitin is composed of repeating units of N-acetyl glu-
cosamine, a nitrogen-containing form of glucose.

8.1.2 Monosaccharides
Main article: Monosaccharide
Monosaccharides are the simplest carbohydrates in that

The α and β anomers of glucose. Note the position of the

hydroxyl group (red or green) on the anomeric carbon rel-
ative to the CH2 OH group bound to carbon 5: they either
have identical absolute configurations (R,R or S,S) (α), or
opposite absolute configurations (R,S or S,R) (β).[11]
Monosaccharides are classified according to three differ-
ent characteristics: the placement of its carbonyl group,
the number of carbon atoms it contains, and its chiral
handedness. If the carbonyl group is an aldehyde, the
monosaccharide is an aldose; if the carbonyl group is a
ketone, the monosaccharide is a ketose. Monosaccha-
rides with three carbon atoms are called trioses, those
with four are called tetroses, five are called pentoses, six
are hexoses, and so on.[12] These two systems of clas-
sification are often combined. For example, glucose
is an aldohexose (a six-carbon aldehyde), ribose is an
aldopentose (a five-carbon aldehyde), and fructose is a
ketohexose (a six-carbon ketone).
Each carbon atom bearing a hydroxyl group (-OH),
with the exception of the first and last carbons, are
asymmetric, making them stereo centers with two possi-
ble configurations each (R or S). Because of this asym-
metry, a number of isomers may exist for any given
monosaccharide formula. Using Le Bel-van't Hoff rule,
the aldohexose D-glucose, for example, has the for-
mula (C·H2 O) 6 , of which four of its six carbons atoms
are stereogenic, making D-glucose one of 24 =16 pos-
D-glucose is an aldohexose with the formula (C·H2 O)6 . The red sible stereoisomers. In the case of glyceraldehydes,
atoms highlight the aldehyde group and the blue atoms highlight an aldotriose, there is one pair of possible stereoiso-
the asymmetric center furthest from the aldehyde; because this mers, which are enantiomers and epimers. 1, 3-
-OH is on the right of the Fischer projection, this is a D sugar. dihydroxyacetone, the ketose corresponding to the aldose
glyceraldehydes, is a symmetric molecule with no stereo
they cannot be hydrolyzed to smaller carbohydrates. centers. The assignment of D or L is made according
They are aldehydes or ketones with two or more hydroxyl to the orientation of the asymmetric carbon furthest from
groups. The general chemical formula of an unmodi- the carbonyl group: in a standard Fischer projection if the
fied monosaccharide is (C•H2 O) , literally a “carbon hy- hydroxyl group is on the right the molecule is a D sugar,
drate.” Monosaccharides are important fuel molecules as otherwise it is an L sugar. The “D-" and “L-" prefixes
well as building blocks for nucleic acids. The smallest should not be confused with “d-" or “l-", which indicate
monosaccharides, for which n=3, are dihydroxyacetone the direction that the sugar rotates plane polarized light.
and D- and L-glyceraldehydes. This usage of “d-" and “l-" is no longer followed in car-
8.1. CARBOHYDRATE 163

bohydrate chemistry.[13] a component of lyxoflavin found in the human heart.[15]

Ribulose and xylulose occur in the pentose phosphate
pathway. Galactose, a component of milk sugar lactose,
Ring-straight chain isomerism is found in galactolipids in plant cell membranes and in
glycoproteins in many tissues. Mannose occurs in human
metabolism, especially in the glycosylation of certain pro-
teins. Fructose, or fruit sugar, is found in many plants and
in humans, it is metabolized in the liver, absorbed directly
into the intestines during digestion, and found in semen.
Trehalose, a major sugar of insects, is rapidly hydrolyzed
into two glucose molecules to support continuous flight.

8.1.3 Disaccharides

Glucose can exist in both a straight-chain and ring form.

The aldehyde or ketone group of a straight-chain

monosaccharide will react reversibly with a hydroxyl
group on a different carbon atom to form a hemiacetal Sucrose, also known as table sugar, is a common disaccharide.
or hemiketal, forming a heterocyclic ring with an oxy- It is composed of two monosaccharides: D-glucose (left) and D-
fructose (right).
gen bridge between two carbon atoms. Rings with five
and six atoms are called furanose and pyranose forms, re-
spectively, and exist in equilibrium with the straight-chain Main article: Disaccharide
form.[14]
During the conversion from straight-chain form to the Two joined monosaccharides are called a disaccharide
cyclic form, the carbon atom containing the carbonyl oxy- and these are the simplest polysaccharides. Examples in-
gen, called the anomeric carbon, becomes a stereogenic clude sucrose and lactose. They are composed of two
center with two possible configurations: The oxygen atom monosaccharide units bound together by a covalent bond
may take a position either above or below the plane of known as a glycosidic linkage formed via a dehydration
the ring. The resulting possible pair of stereoisomers is reaction, resulting in the loss of a hydrogen atom from
called anomers. In the α anomer, the -OH substituent on one monosaccharide and a hydroxyl group from the other.
the anomeric carbon rests on the opposite side (trans) of The formula of unmodified disaccharides is C12 H22 O11 .
the ring from the CH2 OH side branch. The alternative Although there are numerous kinds of disaccharides, a
form, in which the CH2 OH substituent and the anomeric handful of disaccharides are particularly notable.
hydroxyl are on the same side (cis) of the plane of the Sucrose, pictured to the right, is the most abundant
ring, is called the β anomer. disaccharide, and the main form in which carbohy-
drates are transported in plants. It is composed of
one D-glucose molecule and one D-fructose molecule.
Use in living organisms The systematic name for sucrose, O-α-D-glucopyranosyl-
(1→2)-D-fructofuranoside, indicates four things:
Monosaccharides are the major source of fuel for
metabolism, being used both as an energy source (glucose • Its monosaccharides: glucose and fructose
being the most important in nature) and in biosynthesis.
When monosaccharides are not immediately needed by • Their ring types: glucose is a pyranose and fructose
many cells they are often converted to more space- is a furanose
efficient forms, often polysaccharides. In many animals, • How they are linked together: the oxygen on carbon
including humans, this storage form is glycogen, espe- number 1 (C1) of α-D-glucose is linked to the C2
cially in liver and muscle cells. In plants, starch is used of D-fructose.
for the same purpose. The most abundant carbohydrate,
cellulose, is a structural component of the cell wall of • The -oside suffix indicates that the anomeric carbon
plants and many forms of algae. Ribose is a component of both monosaccharides participates in the glyco-
of RNA. Deoxyribose is a component of DNA. Lyxose is sidic bond.
164 CHAPTER 8. CARBOHYDRATE STRUCTURE

Lactose, a disaccharide composed of one D-galactose tential for some negative health effects of extreme carbo-
molecule and one D-glucose molecule, occurs naturally hydrate restriction remains, as the issue has not been stud-
in mammalian milk. The systematic name for lac- ied extensively so far.[19] However, in the case of dietary
tose is O-β-D-galactopyranosyl-(1→4)-D-glucopyranose. fiber – indigestible carbohydrates which are not a source
Other notable disaccharides include maltose (two D- of energy – inadequate intake can lead to significant in-
glucoses linked α−1,4) and cellulobiose (two D-glucoses creases in mortality.[20]
linked β−1,4). Disaccharides can be classified into two Following a diet consisting of very low amounts of daily
types.They are reducing and non-reducing disaccharides. carbohydrate for several days will usually result in higher
If the functional group is present in bonding with another
levels of blood ketone bodies than an isocaloric diet with
sugar unit, it is called a reducing disaccharide or biose. similar protein content.[21] This relatively high level of ke-
tone bodies is commonly known as ketosis and is very
often confused with the potentially fatal condition often
8.1.4 Nutrition seen in type 1 diabetics known as diabetic ketoacidosis.
Somebody suffering ketoacidosis will have much higher
levels of blood ketone bodies along with high blood sugar,
dehydration and electrolyte imbalance.
Long-chain fatty acids cannot cross the blood–brain bar-
rier, but the liver can break these down to produce ke-
tones. However the medium-chain fatty acids octanoic
and heptanoic acids can cross the barrier and be used
by the brain, which normally relies upon glucose for its
energy.[22][23][24] Gluconeogenesis allows humans to syn-
thesize some glucose from specific amino acids: from the
glycerol backbone in triglycerides and in some cases from
fatty acids.
Organisms typically cannot metabolize all types of car-
bohydrate to yield energy. Glucose is a nearly universal
and accessible source of energy. Many organisms also
have the ability to metabolize other monosaccharides and
disaccharides but glucose is often metabolized first. In
Escherichia coli, for example, the lac operon will express
enzymes for the digestion of lactose when it is present,
but if both lactose and glucose are present the lac operon
is repressed, resulting in the glucose being used first (see:
Diauxie). Polysaccharides are also common sources of
energy. Many organisms can easily break down starches
into glucose, however, most organisms cannot metab-
olize cellulose or other polysaccharides like chitin and
arabinoxylans. These carbohydrate types can be metab-
Grain products: rich sources of carbohydrates olized by some bacteria and protists. Ruminants and
termites, for example, use microorganisms to process cel-
Carbohydrate consumed in food yields 3.87 calories of lulose. Even though these complex carbohydrates are not
energy per gram for simple sugars,[16] and 3.57 to 4.12 very digestible, they represent an important dietary el-
calories per gram for complex carbohydrate in most other ement for humans, called dietary fiber. Fiber enhances
foods.[17] High levels of carbohydrate are often associ- digestion, among other benefits.[25]
ated with highly processed foods or refined foods made
Based on the effects on risk of heart disease and
from plants, including sweets, cookies and candy, ta-
obesity,[26] the Institute of Medicine recommends that
ble sugar, honey, soft drinks, breads and crackers, jams
American and Canadian adults get between 45–65% of
and fruit products, pastas and breakfast cereals. Lower
dietary energy from carbohydrates.[27] The Food and
amounts of carbohydrate are usually associated with un-
Agriculture Organization and World Health Organiza-
refined foods, including beans, tubers, rice, and unrefined
tion jointly recommend that national dietary guidelines
fruit.[18] Foods from animal carcass have the lowest car-
set a goal of 55–75% of total energy from carbohydrates,
bohydrate, but milk does contain lactose.
but only 10% directly from sugars (their term for simple
Carbohydrates are a common source of energy in living carbohydrates).[28]
organisms; however, no carbohydrate is an essential nutri-
ent in humans.[19] Humans are able to obtain most of their
energy requirement from protein and fats, though the po-
8.1. CARBOHYDRATE 165

Classification Catabolism

Catabolism is the metabolic reaction which cells undergo

Nutritionists often refer to carbohydrates as either sim-
to extract energy. There are two major metabolic path-
ple or complex. However, the exact distinction between
ways of monosaccharide catabolism: glycolysis and the
these groups can be ambiguous. The term complex car-
citric acid cycle.
bohydrate was first used in the U.S. Senate Select Com-
mittee on Nutrition and Human Needs publication Di- In glycolysis, oligo/polysaccharides are cleaved first to
etary Goals for the United States (1977) where it was smaller monosaccharides by enzymes called glycoside hy-
intended to distinguish sugars from other carbohydrates drolases. The monosaccharide units can then enter into
(which were perceived to be nutritionally superior).[29] monosaccharide catabolism. In some cases, as with hu-
However, the report put “fruit, vegetables and whole- mans, not all carbohydrate types are usable as the diges-
grains” in the complex carbohydrate column, despite the tive and metabolic enzymes necessary are not present.
fact that these may contain sugars as well as polysaccha-
rides. This confusion persists as today some nutritionists
use the term complex carbohydrate to refer to any sort 8.1.6 Carbohydrate chemistry
of digestible saccharide present in a whole food, where
fiber, vitamins and minerals are also found (as opposed to Carbohydrate chemistry is a large and economically im-
processed carbohydrates, which provide energy but few portant branch of organic chemistry. Some of the main
other nutrients). The standard usage, however, is to clas- organic reactions that involve carbohydrates are:
sify carbohydrates chemically: simple if they are sugars
(monosaccharides and disaccharides) and complex if they • Carbohydrate acetalisation
are polysaccharides (or oligosaccharides).[30]
• Cyanohydrin reaction
In any case, the simple vs. complex chemical distinc-
tion has little value for determining the nutritional qual- • Lobry-de Bruyn-van Ekenstein transformation
ity of carbohydrates.[30] Some simple carbohydrates (e.g. • Amadori rearrangement
fructose) raise blood glucose slowly, while some complex
carbohydrates (starches), especially if processed, raise • Nef reaction
blood sugar rapidly. The speed of digestion is deter-
• Wohl degradation
mined by a variety of factors including which other nutri-
ents are consumed with the carbohydrate, how the food • Koenigs–Knorr reaction
is prepared, individual differences in metabolism, and the
chemistry of the carbohydrate.[31] • Carbohydrate digestion
The USDA’s Dietary Guidelines for Americans 2010 call
for moderate- to high-carbohydrate consumption from 8.1.7 See also
a balanced diet that includes six one-ounce servings of
grain foods each day, at least half from whole grain • Bioplastic
sources and the rest from enriched.[32]
• Fermentation
The glycemic index (GI) and glycemic load concepts have
been developed to characterize food behavior during hu- • Gluconeogenesis
man digestion. They rank carbohydrate-rich foods based
• Glycoinformatics
on the rapidity and magnitude of their effect on blood glu-
cose levels. Glycemic index is a measure of how quickly • Glycolipid
food glucose is absorbed, while glycemic load is a mea-
sure of the total absorbable glucose in foods. The insulin • Glycoprotein
index is a similar, more recent classification method that • Low-carbohydrate diet
ranks foods based on their effects on blood insulin levels,
which are caused by glucose (or starch) and some amino • Macromolecule
acids in food.
• No-carbohydrate diet
• Nutrition
• Pentose phosphate pathway
8.1.5 Metabolism • Photosynthesis
• Saccharic acid
Main article: Carbohydrate metabolism
• Carbohydrate NMR
166 CHAPTER 8. CARBOHYDRATE STRUCTURE

8.1.8 References [19] Westman, EC (2002). “Is dietary carbohydrate essential

for human nutrition?". The American journal of clini-
[1] Western Kentucky University (May 29, 2013). “WKU BIO cal nutrition 75 (5): 951–3; author reply 953–4. PMID
113 Carbohydrates”. wku.edu. 11976176.

[2] Eldra Pearl Solomon, Linda R. Berg, Diana W. Martin; [20] Park, Y; Subar, AF; Hollenbeck, A; Schatzkin, A (2011).
Cengage Learning (2004). Biology. google.books.com. p. “Dietary fiber intake and mortality in the NIH-AARP
52. ISBN 978-0534278281. diet and health study”. Archives of Internal Medicine
171 (12): 1061–8. doi:10.1001/archinternmed.2011.18.
[3] National Institute of Standards and Technology (2011). PMC 3513325. PMID 21321288.
“Material Measurement Library D-erythro-Pentose, 2-
deoxy-". nist.gov. [21] http://ajcn.nutrition.org/content/83/5/1055.full.pdf+
html
[4] Long Island University (May 29, 2013). “The Chemistry
of Carbohydrates” (PDF). brooklyn.liu.edu.
[22] http://www.jneurosci.org/content/23/13/5928.full
[5] Purdue University (May 29, 2013). “Carbohydrates: The
Monosaccharides”. purdue.edu. [23] http://www.nature.com/jcbfm/journal/v33/n2/abs/
jcbfm2012151a.html
[6] Flitsch, Sabine L.; Ulijn, Rein V (2003). “Sug-
ars tied to the spot”. Nature 421 (6920): 219–20. [24] MedBio.info > Integration of Metabolism Professor em.
doi:10.1038/421219a. PMID 12529622. Robert S. Horn, Oslo, Norway. Retrieved on May 1,
2010.
[7] Maton, Anthea; Jean Hopkins; Charles William
McLaughlin; Susan Johnson; Maryanna Quon Warner; [25] Pichon, L; Huneau, JF; Fromentin, G; Tomé, D (2006).
David LaHart; Jill D. Wright (1993). Human Biology and “A high-protein, high-fat, carbohydrate-free diet reduces
Health. Englewood Cliffs, New Jersey, USA: Prentice energy intake, hepatic lipogenesis, and adiposity in rats”.
Hall. pp. 52–59. ISBN 0-13-981176-1. The Journal of nutrition 136 (5): 1256–60. PMID
16614413.
[8] John Merle Coulter, Charler Reid Barnes, Henry Chan-
dler Cowles (1930), A Textbook of Botany for Colleges [26] Tighe, P; Duthie, G; Vaughan, N; Brittenden, J; Simpson,
and Universities" WG; Duthie, S; Mutch, W; Wahle, K; Horgan, G; Thies,
F. (2010). “Effect of increased consumption of whole-
[9] Carl A. Burtis, Edward R. Ashwood, Norbert W. Tietz
grain foods on blood pressure and other cardiovascular
(2000), Tietz fundamentals of clinical chemistry
risk markers in healthy middle-aged persons: a random-
ized, controlled trial”. The American journal of clinical
[10] Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999)
nutrition 92 (4): 733–40. doi:10.3945/ajcn.2010.29417.
Biochemistry. 3rd edition. Benjamin Cummings. ISBN
PMID 20685951.
0-8053-3066-6

[11] http://www.ncbi.nlm.nih.gov/books/NBK1955/#_ch2_ [27] Food and Nutrition Board (2002/2005). Dietary Refer-
s4_ ence Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty
Acids, Cholesterol, Protein and Amino Acids. Washington,
[12] Campbell, Neil A.; Brad Williamson; Robin J. Heyden D.C.: The National Academies Press. Page 769. ISBN
(2006). Biology: Exploring Life. Boston, Massachusetts: 0-309-08537-3.
Pearson Prentice Hall. ISBN 0-13-250882-6.
[28] Joint WHO/FAO expert consultation (2003). (PDF).
[13] Pigman, Ward; Horton, D. (1972). “Chapter 1: Stereo- Geneva: World Health Organization. pp. 55–56. ISBN
chemistry of the Monosaccharides”. In Pigman and Hor- 92-4-120916-X.
ton. The Carbohydrates: Chemistry and Biochemistry Vol
1A (2nd ed.). San Diego: Academic Press. pp. 1–67. [29] Joint WHO/FAO expert consultation (1998), Carbohy-
drates in human nutrition, chapter 1. ISBN 92-5-104114-
[14] Pigman, Ward; Anet, E.F.L.J. (1972). “Chapter 4: Mu- 8.
tarotations and Actions of Acids and Bases”. In Pigman
and Horton. The Carbohydrates: Chemistry and Biochem- [30] “Carbohydrates”. The Nutrition Source. Harvard School
istry Vol 1A (2nd ed.). San Diego: Academic Press. pp. of Public Health. Retrieved 3 April 2013.
165–194.
[31] Jenkins, David; Alexandra L. Jenkins, Thomas M.S.
[15] “lyxoflavin”. Merriam-Webster.
Woleve, Lilian H. Thompson and A. Venkat Rao (Febru-
[16] http://ndb.nal.usda.gov/ndb/foods/show/6202 ary 1986). “Simple and Complex Carbohydrates”. Nu-
trition Reviews 44 (2): 44–49. doi:10.1111/j.1753-
[17] http://www.fao.org/docrep/006/y5022e/y5022e04.htm 4887.1986.tb07585.x.

[18] http://www.diabetes.org.uk/upload/How%20we% [32] DHHS and USDA, Dietary Guidelines for Americans
20help/catalogue/carb-reference-list-0511.pdf 2010.
8.2. POLYSACCHARIDE 167

8.1.9 External links They may be amorphous or even insoluble in water.[1][2]

When all the monosaccharides in a polysaccharide are the
• Carbohydrates, including interactive models and an- same type, the polysaccharide is called a homopolysac-
imations (Requires MDL Chime) charide or homoglycan, but when more than one type of
monosaccharide is present they are called heteropolysac-
• IUPAC-IUBMB Joint Commission on Biochemi-
charides or heteroglycans.[3][4]
cal Nomenclature (JCBN): Carbohydrate Nomen-
clature Natural saccharides are generally of simple carbohydrates
called monosaccharides with general formula (CH2 O)n
• Carbohydrates detailed where n is three or more. Examples of monosaccharides
[5]
• Carbohydrates and Glycosylation – The Virtual Li- are glucose, fructose, and glyceraldehyde. Polysaccha-
brary of Biochemistry and Cell Biology rides, meanwhile, have a general formula of Cx(H2 O)y
where x is usually a large number between 200 and 2500.
• Functional Glycomics Gateway, a collaboration be- Considering that the repeating units in the polymer back-
tween the Consortium for Functional Glycomics and bone are often six-carbon monosaccharides, the general
Nature Publishing Group formula can also be represented as (C6 H10 O5 )n where
40≤n≤3000.
• Carbohydrate: Biochemistry Course
Polysaccharides contain more than ten monosaccha-
ride units. Definitions of how large a carbohydrate
must be to fall into the categories polysaccharides or
8.2 Polysaccharide oligosaccharides vary according to personal opinion.
Polysaccharides are an important class of biological poly-
mers. Their function in living organisms is usually either
structure- or storage-related. Starch (a polymer of glu-
cose) is used as a storage polysaccharide in plants, be-
ing found in the form of both amylose and the branched
amylopectin. In animals, the structurally similar glucose
polymer is the more densely branched glycogen, some-
times called 'animal starch'. Glycogen’s properties allow
it to be metabolized more quickly, which suits the active
3D structure of cellulose, a beta-glucan polysaccharide. lives of moving animals.
Cellulose and chitin are examples of structural polysac-
charides. Cellulose is used in the cell walls of plants
and other organisms, and is said to be the most abun-
dant organic molecule on earth.[6] It has many uses
such as a significant role in the paper and textile indus-
tries, and is used as a feedstock for the production of
rayon (via the viscose process), cellulose acetate, cel-
luloid, and nitrocellulose. Chitin has a similar struc-
ture, but has nitrogen-containing side branches, increas-
ing its strength. It is found in arthropod exoskeletons
Amylose is a linear polymer of glucose mainly linked with and in the cell walls of some fungi. It also has mul-
α(1→4) bonds. It can be made of several thousands of glucose tiple uses, including surgical threads. Polysaccharides
units. It is one of the two components of starch, the other being also include callose or laminarin, chrysolaminarin, xylan,
amylopectin. arabinoxylan, mannan, fucoidan and galactomannan.

Polysaccharides are polymeric carbohydrate molecules

composed of long chains of monosaccharide units bound 8.2.1 Function
together by glycosidic linkages and on hydrolysis give the
constituent monosaccharides or oligosaccharides. They Structure
range in structure from linear to highly branched. Exam-
ples include storage polysaccharides such as starch and Nutrition polysaccharides are common sources of en-
glycogen, and structural polysaccharides such as cellulose ergy. Many organisms can easily break down starches
and chitin. into glucose; however, most organisms cannot metab-
Polysaccharides are often quite heterogeneous, contain- olize cellulose or other polysaccharides like chitin and
ing slight modifications of the repeating unit. Depending arabinoxylans. These carbohydrate types can be metab-
on the structure, these macromolecules can have distinct olized by some bacteria and protists. Ruminants and
properties from their monosaccharide building blocks. termites, for example, use microorganisms to process
168 CHAPTER 8. CARBOHYDRATE STRUCTURE

cellulose. and plays an important role in the glucose cycle. Glyco-

Even though these complex to carbohydrates are not very gen forms an energy reserve that can be quickly mobi-
digestible, they provide important dietary elements for lized to meet a sudden need for glucose, but one that is
humans. Called dietary fiber, these carbohydrates en- less compact and more immediately available as an en-
hance digestion among other benefits. The main action ergy reserve than triglycerides (lipids).
of dietary fiber is to change the nature of the contents ofIn the liver hepatocytes, glycogen can compose up to eight
the gastrointestinal tract, and to change how other nutri-percent (100–120 g in an adult) of the fresh weight soon
ents and chemicals are absorbed.[7][8] Soluble fiber binds after a meal.[15] Only the glycogen stored in the liver can
to bile acids in the small intestine, making them less likely
be made accessible to other organs. In the muscles, glyco-
to enter the body; this in turn lowers cholesterol levels gen is found in a low concentration of one to two percent
in the blood.[9] Soluble fiber also attenuates the absorp- of the muscle mass. The amount of glycogen stored in
tion of sugar, reduces sugar response after eating, normal-
the body—especially within the muscles, liver, and red
izes blood lipid levels and, once fermented in the colon, blood cells[16][17][18] —varies with physical activity, basal
produces short-chain fatty acids as byproducts with wide- metabolic rate, and eating habits such as intermittent fast-
ranging physiological activities (discussion below). Al- ing. Small amounts of glycogen are found in the kidneys,
though insoluble fiber is associated with reduced diabetes and even smaller amounts in certain glial cells in the brain
risk, the mechanism by which this occurs is unknown.[10] and white blood cells. The uterus also stores glycogen
[15]
Not yet formally proposed as an essential macronutri- during pregnancy, to nourish the embryo.
ent (as of 2005), dietary fiber is nevertheless regarded Glycogen is composed of a branched chain of glucose
as important for the diet, with regulatory authorities in residues. It is stored in liver and muscles.
many developed countries recommending increases in
fiber intake.[7][8][11][12] • It is an energy reserve for animals.
• It is the chief form of carbohydrate stored in animal
body.
8.2.2 Storage polysaccharides
• It is insoluble in water. It turns red when mixed with
Starches iodine.
• It also yields glucose on hydrolysis.
Starch is glucose polymer in which glucopyranose units
are bonded by alpha-linkages. It is made up of a mixture
• Schematic 2-D cross-sectional view of glycogen. A
of amylose (15–20%) and amylopectin (80–85%). Amy-
core protein of glycogenin is surrounded by branches
lose consists of a linear chain of several hundred glucose
of glucose units. The entire globular granule may
molecules and Amylopectin is a branched molecule made
contain approximately 30,000 glucose units.[1]
of several thousand glucose units (every chain of 24–30
glucose units is one unit of Amylopectin). Starches are • A view of the atomic structure of a single branched
insoluble in water. They can be digested which can break strand of glucose units in a glycogen molecule.
the alpha-linkages (glycosidic bonds). Both humans
and animals have amylases, so they can digest starches. 1. ^ Page 12 in: Exercise physiology: energy, nu-
Potato, rice, wheat, and maize are major sources of starch trition, and human performance, By William D.
in the human diet. The formations of starches are the McArdle, Frank I. Katch, Victor L. Katch, Edition:
ways that plants store glucose. 6, illustrated, Published by Lippincott Williams &
Wilkins, 2006, ISBN 0-7817-4990-5, ISBN 978-0-
7817-4990-9, 1068 pages
Glycogen

Glycogen serves as the secondary long-term energy stor- 8.2.3 Structural polysaccharides
age in animal and fungal cells, with the primary energy
stores being held in adipose tissue. Glycogen is made pri- Arabinoxylans
marily by the liver and the muscles, but can also be made
by glycogenesis within the brain and stomach.[13] Arabinoxylans are found in both the primary and sec-
ondary cell walls of plants and are the copolymers of two
Glycogen is the analogue of starch, a glucose polymer in
pentose sugars: arabinose and xylose.
plants, and is sometimes referred to as animal starch,[14]
having a similar structure to amylopectin but more ex-
tensively branched and compact than starch. Glycogen Cellulose
is a polymer of α(1→4) glycosidic bonds linked, with
α(1→6)-linked branches. Glycogen is found in the form The structural component of plants are formed primarily
of granules in the cytosol/cytoplasm in many cell types, from cellulose. Wood is largely cellulose and lignin, while
8.2. POLYSACCHARIDE 169

paper and cotton are nearly pure cellulose. Cellulose is produced by E. coli alone. Mixtures of capsular polysac-
a polymer made with repeated glucose units bonded to- charides, either conjugated or native are used as vaccines.
gether by beta-linkages. Humans and many animals lack Bacteria and many other microbes, including fungi and
an enzyme to break the beta-linkages, so they do not di- algae, often secrete polysaccharides to help them adhere
gest cellulose. Certain animals such as termites can di- to surfaces and to prevent them from drying out. Humans
gest cellulose, because bacteria possessing the enzyme have developed some of these polysaccharides into use-
are present in their gut. Cellulose is insoluble in water. ful products, including xanthan gum, dextran, welan gum,
It does not change color when mixed with iodine. On gellan gum, diutan gum and pullulan.
hydrolysis, it yields glucose. It is the most abundant car-
bohydrate in nature. Most of these polysaccharides exhibit useful visco-elastic
properties when dissolved in water at very low levels.[19]
This makes various liquids used in everyday life, such as
Chitin some foods, lotions, cleaners, and paints, viscous when
stationary, but much more free-flowing when even slight
Chitin is one of many naturally occurring polymers. It shear is applied by stirring or shaking, pouring, wip-
forms a structural component of many animals, such as ing, or brushing. This property is named pseudoplastic-
exoskeletons. Over time it is bio-degradable in the nat- ity or shear thinning; the study of such matters is called
ural environment. Its breakdown may be catalyzed by rheology.
enzymes called chitinases, secreted by microorganisms
Aqueous solutions of the polysaccharide alone have a cu-
such as bacteria and fungi, and produced by some plants.
rious behavior when stirred: after stirring ceases, the so-
Some of these microorganisms have receptors to simple
lution initially continues to swirl due to momentum, then
sugars from the decomposition of chitin. If chitin is de-
slows to a standstill due to viscosity and reverses direction
tected, they then produce enzymes to digest it by cleaving
briefly before stopping. This recoil is due to the elastic ef-
the glycosidic bonds in order to convert it to simple sugars
fect of the polysaccharide chains, previously stretched in
and ammonia.
solution, returning to their relaxed state.
Chemically, chitin is closely related to chitosan (a more
Cell-surface polysaccharides play diverse roles in bacte-
water-soluble derivative of chitin). It is also closely re-
rial ecology and physiology. They serve as a barrier be-
lated to cellulose in that it is a long unbranched chain of
tween the cell wall and the environment, mediate host-
glucose derivatives. Both materials contribute structure
pathogen interactions, and form structural components
and strength, protecting the organism.
of biofilms. These polysaccharides are synthesized from
nucleotide-activated precursors (called nucleotide sugars)
Pectins and, in most cases, all the enzymes necessary for biosyn-
thesis, assembly and transport of the completed poly-
Pectins are a family of complex polysaccharides that con- mer are encoded by genes organized in dedicated clusters
tain 1,4-linked α-D-galactosyluronic acid residues. They within the genome of the organism. Lipopolysaccharide
are present in most primary cell walls and in the non- is one of the most important cell-surface polysaccharides,
woody parts of terrestrial plants. as it plays a key structural role in outer membrane in-
tegrity, as well as being an important mediator of host-
pathogen interactions.
8.2.4 Acidic polysaccharides The enzymes that make the A-band (homopolymeric) and
B-band (heteropolymeric) O-antigens have been iden-
Acidic polysaccharides are polysaccharides that contain tified and the metabolic pathways defined.[20] The ex-
carboxyl groups, phosphate groups and/or sulfuric ester opolysaccharide alginate is a linear copolymer of β−1,4-
groups. linked D-mannuronic acid and L-guluronic acid residues,
and is responsible for the mucoid phenotype of late-
stage cystic fibrosis disease. The pel and psl loci are
8.2.5 Bacterial capsular polysaccharides
two recently discovered gene clusters that also encode
exopolysaccharides found to be important for biofilm for-
Pathogenic bacteria commonly produce a thick, mucous-
mation. Rhamnolipid is a biosurfactant whose production
like, layer of polysaccharide. This “capsule” cloaks
is tightly regulated at the transcriptional level, but the pre-
antigenic proteins on the bacterial surface that would oth-
cise role that it plays in disease is not well understood at
erwise provoke an immune response and thereby lead to
present. Protein glycosylation, particularly of pilin and
the destruction of the bacteria. Capsular polysaccharides
flagellin, became a focus of research by several groups
are water-soluble, commonly acidic, and have molecular
from about 2007, and has been shown to be important
weights on the order of 100-2000 kDa. They are lin-
for adhesion and invasion during bacterial infection.[21]
ear and consist of regularly repeating subunits of one to
six monosaccharides. There is enormous structural di-
versity; nearly two hundred different polysaccharides are
170 CHAPTER 8. CARBOHYDRATE STRUCTURE

8.2.6 Chemical identification tests for [9] Anderson JW; Baird P; Davis RH et al. (2009). “Health
polysaccharides benefits of dietary fiber”. Nutr Rev 67 (4): 188–
205. doi:10.1111/j.1753-4887.2009.00189.x. PMID
19335713.
Periodic acid-Schiff stain (PAS)
[10] Weickert MO, Pfeiffer AF (2008). “Metabolic effects
Polysaccharides with unprotected vicinal diols or amino of dietary fiberand any other substance that consume and
sugars (i.e. some OH groups replaced with amine) give prevention of diabetes”. J Nutr 138 (3): 439–42. PMID
a positive Periodic acid-Schiff stain (PAS). The list of 18287346.
polysaccharides that stain with PAS is long. Although
[11] “Dietary reference values for carbohydrates and dietary
mucins of epithelial origins stain with PAS, mucins of fiber” (PDF). European Food Safety Authority.
connective tissue origin have so many acidic substitu-
tions that they do not have enough glycol or amino-alcohol [12] Jones PJ, Varady KA (2008). “Are functional foods
groups left to react with PAS. redefining nutritional requirements?" (PDF). Appl Phys-
iol Nutr Metab 33 (1): 118–23. doi:10.1139/H07-134.
PMID 18347661.
8.2.7 See also [13] Anatomy and Physiology. Saladin, Kenneth S. McGraw-
Hill, 2007.
• Glycan
[14] “Animal starch”. Merriam Webster. Retrieved May 11,
• Oligosaccharide nomenclature 2014.

• Polysaccharide encapsulated bacteria [15] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
(2006). Biology: Exploring Life. Boston, Massachusetts:
Pearson Prentice Hall. ISBN 0-13-250882-6.
8.2.8 References [16] Moses SW, Bashan N, Gutman A (December 1972).
“Glycogen metabolism in the normal red blood cell”.
[1] Varki A, Cummings R, Esko J, Freeze H, Stanley P, Blood 40 (6): 836–43. PMID 5083874.
Bertozzi C, Hart G, Etzler M (2008). Essentials of glyco-
biology. Essentials of Glycobiology (Cold Spring Harbor [17] http://jeb.biologists.org/cgi/reprint/129/1/141.pdf
Laboratory Press; 2nd edition). ISBN 0-87969-770-9.
[18] Miwa I, Suzuki S (November 2002). “An im-
[2] Varki A, Cummings R, Esko J, Jessica Freeze, Hart G, proved quantitative assay of glycogen in erythrocytes”.
Marth J (1999). Essentials of glycobiology. Essentials Annals of Clinical Biochemistry 39 (Pt 6): 612–3.
of glycobiology (Cold Spring Harbor Laboratory Press). doi:10.1258/000456302760413432. PMID 12564847.
ISBN 0-87969-560-9.
[19] Viscosity of Welan Gum vs. Concentration in Wa-
[3] IUPAC, Compendium of Chemical Terminology, 2nd ed. ter. http://www.xydatasource.com/xy-showdatasetpage.
(the “Gold Book”) (1997). Online corrected version: php?datasetcode=345115&dsid=80
(2006–) "homopolysaccharide (homoglycan)".
[20] Guo H, Yi W, Song JK, Wang PG (2008). “Cur-
[4] IUPAC, Compendium of Chemical Terminology, 2nd ed. rent understanding on biosynthesis of microbial polysac-
(the “Gold Book”) (1997). Online corrected version: charides”. Curr Top Med Chem 8 (2): 141–51.
(2006–) "heteropolysaccharide (heteroglycan)". doi:10.2174/156802608783378873. PMID 18289083.

[21] Cornelis P (editor). (2008). Pseudomonas: Genomics

[5] Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999)
and Molecular Biology (1st ed.). Caister Academic Press.
Biochemistry. 3rd edition. Benjamin Cummings. ISBN
ISBN 978-1-904455-19-6. .
0-8053-3066-6

[6] N.A.Campbell (1996) Biology (4th edition). Benjamin

Cummings NY. p.23 ISBN 0-8053-1957-3 8.2.9 External links
[7] “Dietary Reference Intakes for Energy, Carbohydrate, • Polysaccharide Structure
fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino
Acids (Macronutrients) (2005), Chapter 7: Dietary, • Applications and commercial sources of polysac-
Functional and Total fiber.” (PDF). US Department of charides
Agriculture, National Agricultural Library and National
Academy of Sciences, Institute of Medicine, Food and • European Polysaccharide Network of Excellence
Nutrition Board.

[8] Eastwood M, Kritchevsky D (2005). “Dietary fiber: how

did we get where we are?". Annu Rev Nutr 25: 1–
8. doi:10.1146/annurev.nutr.25.121304.131658. PMID
16011456.
Chapter 9

Intermediary metabolism

171
Chapter 10

Metabolism

10.1 Overview of metabolism able reactions that require energy that will not occur by
themselves, by coupling them to spontaneous reactions
“Cell metabolism” redirects here. For the journal, see that release energy. Enzymes act as catalysts that allow
Cell Metabolism. the reactions to proceed more rapidly. Enzymes also al-
For the architectural movement, see Metabolism (archi- low the regulation of metabolic pathways in response to
tecture). changes in the cell’s environment or to signals from other
Metabolism (from Greek: μεταβολή metabolē, cells.
The metabolic system of a particular organism deter-
mines which substances it will find nutritious and which
poisonous. For example, some prokaryotes use hydrogen
sulfide as a nutrient, yet this gas is poisonous to animals.[1]
The speed of metabolism, the metabolic rate, influences
how much food an organism will require, and also affects
how it is able to obtain that food.
A striking feature of metabolism is the similarity of
the basic metabolic pathways and components between
even vastly different species.[2] For example, the set of
carboxylic acids that are best known as the intermediates
in the citric acid cycle are present in all known organ-
isms, being found in species as diverse as the unicellular
bacterium Escherichia coli and huge multicellular or-
Structure of adenosine triphosphate (ATP), a central intermediate ganisms like elephants.[3] These striking similarities in
in energy metabolism metabolic pathways are likely due to their early appear-
ance in evolutionary history, and their retention because
“change”) is the set of life-sustaining chemical trans- of their efficacy.[4][5]
formations within the cells of living organisms. These
enzyme-catalyzed reactions allow organisms to grow and
reproduce, maintain their structures, and respond to their
environments. The word metabolism can also refer to all
chemical reactions that occur in living organisms, includ-
ing digestion and the transport of substances into and be- 10.1.1 Key biochemicals
tween different cells, in which case the set of reactions
within the cells is called intermediary metabolism or
intermediate metabolism. Further information: Biomolecule, cell (biology) and
biochemistry
Metabolism is usually divided into two categories. Most of the structures that make up animals, plants and
Catabolism, that breaks down organic matter and har- microbes are made from three basic classes of molecule:
vests energy by way of cellular respiration, and anabolism amino acids, carbohydrates and lipids (often called fats).
that uses energy to construct components of cells such as As these molecules are vital for life, metabolic reac-
proteins and nucleic acids. tions either focus on making these molecules during the
The chemical reactions of metabolism are organized into construction of cells and tissues, or by breaking them
metabolic pathways, in which one chemical is trans- down and using them as a source of energy, by their
formed through a series of steps into another chemi- digestion. These biochemicals can be joined together
cal, by a sequence of enzymes. Enzymes are crucial to to make polymers such as DNA and proteins, essential
metabolism because they allow organisms to drive desir- macromolecules of life.

172
10.1. OVERVIEW OF METABOLISM 173

Glucose can exist in both a straight-chain and ring form.

Structure of a triacylglycerol lipid

cal molecules, and fill numerous roles, such as the storage

Amino acids and proteins
and transport of energy (starch, glycogen) and structural
components (cellulose in plants, chitin in animals).[7]
Proteins are made of amino acids arranged in a lin-
The basic carbohydrate units are called monosaccharides
ear chain joined together by peptide bonds. Many pro-
and include galactose, fructose, and most importantly
teins are enzymes that catalyze the chemical reactions in
glucose. Monosaccharides can be linked together to form
metabolism. Other proteins have structural or mechan-
polysaccharides in almost limitless ways.[13]
ical functions, such as those that form the cytoskeleton,
a system of scaffolding that maintains the cell shape.[6]
Proteins are also important in cell signaling, immune Nucleotides
responses, cell adhesion, active transport across mem-
branes, and the cell cycle.[7] Amino acids also contribute The two nucleic acids, DNA and RNA, are polymers of
to cellular energy metabolism by providing a carbon nucleotides. Each nucleotide is composed of a phosphate
source for entry into the citric acid cycle (tricarboxylic attached to a ribose or deoxyribose sugar group which is
acid cycle),[8] especially when a primary source of en- attached to a nitrogenous base. Nucleic acids are criti-
ergy, such as glucose, is scarce, or when cells undergo cal for the storage and use of genetic information, and its
metabolic stress.[9] interpretation through the processes of transcription and
protein biosynthesis.[7] This information is protected by
DNA repair mechanisms and propagated through DNA
Lipids
replication. Many viruses have an RNA genome, such
as HIV, which uses reverse transcription to create a
Lipids are the most diverse group of biochemicals. Their
DNA template from its viral RNA genome.[14] RNA in
main structural uses are as part of biological mem-
ribozymes such as spliceosomes and ribosomes is similar
branes both internal and external, such as the cell mem-
to enzymes as it can catalyze chemical reactions. Indi-
brane, or as a source of energy.[7] Lipids are usually de-
vidual nucleosides are made by attaching a nucleobase
fined as hydrophobic or amphipathic biological molecules
to a ribose sugar. These bases are heterocyclic rings
but will dissolve in organic solvents such as benzene
containing nitrogen, classified as purines or pyrimidines.
or chloroform.[10] The fats are a large group of com-
Nucleotides also act as coenzymes in metabolic-group-
pounds that contain fatty acids and glycerol; a glycerol
transfer reactions.[15]
molecule attached to three fatty acid esters is called
a triacylglyceride.[11] Several variations on this basic
structure exist, including alternate backbones such as Coenzymes
sphingosine in the sphingolipids, and hydrophilic groups
such as phosphate as in phospholipids. Steroids such as Main article: Coenzyme
cholesterol are another major class of lipids.[12]

Metabolism involves a vast array of chemical reactions,

Carbohydrates but most fall under a few basic types of reactions that
involve the transfer of functional groups of atoms and
Carbohydrates are aldehydes or ketones, with many their bonds within molecules.[16] This common chem-
hydroxyl groups attached, that can exist as straight chains istry allows cells to use a small set of metabolic in-
or rings. Carbohydrates are the most abundant biologi- termediates to carry chemical groups between differ-
174 CHAPTER 10. METABOLISM

NH2
HO O N
O O N
P
S O O O
N N P N N
H H O
O OH O OH

HO
O OH
P
HO
O

Structure of the coenzyme acetyl-CoA.The transferable acetyl

group is bonded to the sulfur atom at the extreme left.

ent reactions.[15] These group-transfer intermediates are

called coenzymes. Each class of group-transfer reactions
is carried out by a particular coenzyme, which is the
substrate for a set of enzymes that produce it, and a set of
enzymes that consume it. These coenzymes are therefore
continuously made, consumed and then recycled.[17]
One central coenzyme is adenosine triphosphate (ATP),
the universal energy currency of cells. This nucleotide is Structure of hemoglobin. The protein subunits are in red and
used to transfer chemical energy between different chem- blue, and the iron-containing heme groups in green. From PDB:
ical reactions. There is only a small amount of ATP in 1GZX .
cells, but as it is continuously regenerated, the human
body can use about its own weight in ATP per day.[17] hydrogen, phosphorus, oxygen and sulfur.[20] Organic
ATP acts as a bridge between catabolism and anabolism. compounds (proteins, lipids and carbohydrates) contain
Catabolism breaks down molecules and anabolism puts the majority of the carbon and nitrogen; most of the oxy-
them together. Catabolic reactions generate ATP and an- gen and hydrogen is present as water.[20]
abolic reactions consume it. It also serves as a carrier of
phosphate groups in phosphorylation reactions. The abundant inorganic elements act as ionic electrolytes.
The most important ions are sodium, potassium, calcium,
A vitamin is an organic compound needed in small quan- magnesium, chloride, phosphate and the organic ion
tities that cannot be made in cells. In human nutrition, bicarbonate. The maintenance of precise ion gradients
most vitamins function as coenzymes after modification; across cell membranes maintains osmotic pressure and
for example, all water-soluble vitamins are phosphory- pH.[21] Ions are also critical for nerve and muscle func-
lated or are coupled to nucleotides when they are used in tion, as action potentials in these tissues are produced
cells.[18] Nicotinamide adenine dinucleotide (NAD+ ), a by the exchange of electrolytes between the extracellular
derivative of vitamin B3 (niacin), is an important coen- fluid and the cell’s fluid, the cytosol.[22] Electrolytes en-
zyme that acts as a hydrogen acceptor. Hundreds of ter and leave cells through proteins in the cell membrane
separate types of dehydrogenases remove electrons from called ion channels. For example, muscle contraction de-
their substrates and reduce NAD+ into NADH. This re- pends upon the movement of calcium, sodium and potas-
duced form of the coenzyme is then a substrate for any sium through ion channels in the cell membrane and T-
of the reductases in the cell that need to reduce their tubules.[23]
substrates.[19] Nicotinamide adenine dinucleotide exists
in two related forms in the cell, NADH and NADPH. Transition metals are usually present as trace elements
The NAD+ /NADH form is more important in catabolic in organisms, with zinc and iron being most abundant
reactions, while NADP+ /NADPH is used in anabolic re- of those.[24][25] These metals are used in some proteins
actions. as cofactors and are essential for the activity of en-
zymes such as catalase and oxygen-carrier proteins such
as hemoglobin.[26] Metal cofactors are bound tightly to
Minerals and cofactors specific sites in proteins; although enzyme cofactors can
be modified during catalysis, they always return to their
original state by the end of the reaction catalyzed. Metal
Further information: Metal Ions in Life Sciences, Metal
micronutrients are taken up into organisms by specific
metabolism, and bioinorganic chemistry
transporters and bind to storage proteins such as ferritin
or metallothionein when not in use.[27][28]
Inorganic elements play critical roles in metabolism;
some are abundant (e.g. sodium and potassium) while
others function at minute concentrations. About 99% 10.1.2 Catabolism
of a mammal’s mass is made up of the elements
carbon, nitrogen, calcium, sodium, chlorine, potassium, Catabolism is the set of metabolic processes that break
10.1. OVERVIEW OF METABOLISM 175

down large molecules. These include breaking down and Proteins, polysaccharides and fats
oxidizing food molecules. The purpose of the catabolic
reactions is to provide the energy and components needed
by anabolic reactions. The exact nature of these catabolic
reactions differ from organism to organism and organ- Amino acids, monosaccharides, fatty acids
isms can be classified based on their sources of energy
and carbon (their primary nutritional groups), as shown
in the table below. Organic molecules are used as a
source of energy by organotrophs, while lithotrophs use
inorganic substrates and phototrophs capture sunlight as AcetylCoA
chemical energy. However, all these different forms
of metabolism depend on redox reactions that involve ADP
NAD+
the transfer of electrons from reduced donor molecules Citric Oxidative
such as organic molecules, water, ammonia, hydrogen acid phosphorylation
sulfide or ferrous ions to acceptor molecules such as cycle
oxygen, nitrate or sulfate.[29] In animals these reactions NADH ATP
involve complex organic molecules that are broken down
to simpler molecules, such as carbon dioxide and wa- A simplified outline of the catabolism of proteins, carbohydrates
ter. In photosynthetic organisms such as plants and and fats
cyanobacteria, these electron-transfer reactions do not re-
lease energy, but are used as a way of storing energy ab-
sorbed from sunlight.[7] Energy from organic compounds

The most common set of catabolic reactions in animals Further information: Cellular respiration, fermentation,
can be separated into three main stages. In the first, large carbohydrate catabolism, fat catabolism and protein
organic molecules such as proteins, polysaccharides or catabolism
lipids are digested into their smaller components outside
cells. Next, these smaller molecules are taken up by cells
and converted to yet smaller molecules, usually acetyl Carbohydrate catabolism is the breakdown of carbo-
coenzyme A (acetyl-CoA), which releases some energy. hydrates into smaller units. Carbohydrates are usu-
Finally, the acetyl group on the CoA is oxidised to water ally taken into cells once they have been digested into
and carbon dioxide in the citric acid cycle and electron monosaccharides.[35] Once inside, the major route of
breakdown is glycolysis, where sugars such as glucose
transport chain, releasing the energy that is stored by re-
ducing the coenzyme nicotinamide adenine dinucleotide and fructose are converted into pyruvate and some ATP
(NAD+ ) into NADH. is generated.[36] Pyruvate is an intermediate in several
metabolic pathways, but the majority is converted to
acetyl-CoA and fed into the citric acid cycle. Although
some more ATP is generated in the citric acid cycle,
the most important product is NADH, which is made
from NAD+ as the acetyl-CoA is oxidized. This oxi-
Digestion dation releases carbon dioxide as a waste product. In
anaerobic conditions, glycolysis produces lactate, through
the enzyme lactate dehydrogenase re-oxidizing NADH
Further information: Digestion and gastrointestinal tract to NAD+ for re-use in glycolysis. An alternative route
for glucose breakdown is the pentose phosphate path-
Macromolecules such as starch, cellulose or proteins can- way, which reduces the coenzyme NADPH and produces
not be rapidly taken up by cells and must be broken pentose sugars such as ribose, the sugar component of
into their smaller units before they can be used in cell nucleic acids.
metabolism. Several common classes of enzymes di- Fats are catabolised by hydrolysis to free fatty acids and
gest these polymers. These digestive enzymes include glycerol. The glycerol enters glycolysis and the fatty acids
proteases that digest proteins into amino acids, as well are broken down by beta oxidation to release acetyl-CoA,
as glycoside hydrolases that digest polysaccharides into which then is fed into the citric acid cycle. Fatty acids re-
simple sugars known as monosaccharides. lease more energy upon oxidation than carbohydrates be-
Microbes simply secrete digestive enzymes into their cause carbohydrates contain more oxygen in their struc-
surroundings,[30][31] while animals only secrete these tures. Steroids are also broken down by some bacteria
enzymes from specialized cells in their guts.[32] The in a process similar to beta oxidation, and this break-
amino acids or sugars released by these extracellular en- down process involves the release of significant amounts
zymes are then pumped into cells by active transport of acetyl-CoA, propionyl-CoA, and pyruvate, which can
proteins.[33][34] all be used by the cell for energy. M. tuberculosis can also
176 CHAPTER 10. METABOLISM

grow on the lipid cholesterol as a sole source of carbon, an enzyme called ATP synthase. The flow of protons
and genes involved in the cholesterol use pathway(s) have makes the stalk subunit rotate, causing the active site of
been validated as important during various stages of the the synthase domain to change shape and phosphorylate
infection lifecycle of M. tuberculosis.[37] adenosine diphosphate – turning it into ATP.[17]
Amino acids are either used to synthesize proteins and
other biomolecules, or oxidized to urea and carbon
Energy from inorganic compounds
dioxide as a source of energy.[38] The oxidation path-
way starts with the removal of the amino group by a
Further information: Microbial metabolism and nitrogen
transaminase. The amino group is fed into the urea cy-
cycle
cle, leaving a deaminated carbon skeleton in the form of
a keto acid. Several of these keto acids are intermedi-
Chemolithotrophy is a type of metabolism found in
ates in the citric acid cycle, for example the deamination
of glutamate forms α-ketoglutarate.[39] The glucogenic
prokaryotes where energy is obtained from the ox-
idation of inorganic compounds. These organisms
amino acids can also be converted into glucose, through
gluconeogenesis (discussed below).[40] can use hydrogen,[44] reduced sulfur compounds (such
as sulfide, hydrogen sulfide and thiosulfate),[1] ferrous
iron (FeII)[45] or ammonia[46] as sources of reducing
10.1.3 Energy transformations power and they gain energy from the oxidation of
these compounds with electron acceptors such as oxygen
Oxidative phosphorylation or nitrite.[47] These microbial processes are important
in global biogeochemical cycles such as acetogenesis,
Further information: Oxidative phosphorylation, nitrification and denitrification and are critical for soil fer-
chemiosmosis and mitochondrion tility.[48][49]

In oxidative phosphorylation, the electrons removed from

Energy from light
organic molecules in areas such as the protagon acid cy-
cle are transferred to oxygen and the energy released is
used to make ATP. This is done in eukaryotes by a series Further information: Phototroph, photophosphorylation,
of proteins in the membranes of mitochondria called the chloroplast
electron transport chain. In prokaryotes, these proteins
are found in the cell’s inner membrane.[41] These pro- The energy in sunlight is captured by plants,
teins use the energy released from passing electrons from cyanobacteria, purple bacteria, green sulfur bacteria
reduced molecules like NADH onto oxygen to pump and some protists. This process is often coupled to the
protons across a membrane.[42] conversion of carbon dioxide into organic compounds,
as part of photosynthesis, which is discussed below. The
energy capture and carbon fixation systems can however
operate separately in prokaryotes, as purple bacteria
and green sulfur bacteria can use sunlight as a source of
energy, while switching between carbon fixation and the
fermentation of organic compounds.[50][51]
In many organisms the capture of solar energy is sim-
ilar in principle to oxidative phosphorylation, as it in-
volves the storage of energy as a proton concentration
gradient. This proton motive force then drives ATP
synthesis.[17] The electrons needed to drive this electron
transport chain come from light-gathering proteins called
photosynthetic reaction centres or rhodopsins. Reaction
centers are classed into two types depending on the type
of photosynthetic pigment present, with most photosyn-
thetic bacteria only having one type, while plants and
cyanobacteria have two.[52]
Mechanism of ATP synthase. ATP is shown in red, ADP and
phosphate in pink and the rotating stalk subunit in black. In plants, algae, and cyanobacteria, photosystem II uses
light energy to remove electrons from water, releasing
Pumping protons out of the mitochondria creates a proton oxygen as a waste product. The electrons then flow
concentration difference across the membrane and gen- to the cytochrome b6f complex, which uses their en-
erates an electrochemical gradient.[43] This force drives ergy to pump protons across the thylakoid membrane in
protons back into the mitochondrion through the base of the chloroplast.[7] These protons move back through the
10.1. OVERVIEW OF METABOLISM 177

membrane as they drive the ATP synthase, as before. The sunlight and carbon dioxide (CO2 ). In plants, cyanobac-
electrons then flow through photosystem I and can then teria and algae, oxygenic photosynthesis splits water, with
either be used to reduce the coenzyme NADP+ , for use oxygen produced as a waste product. This process uses
in the Calvin cycle, which is discussed below, or recycled the ATP and NADPH produced by the photosynthetic re-
for further ATP generation.[53] action centres, as described above, to convert CO2 into
glycerate 3-phosphate, which can then be converted into
glucose. This carbon-fixation reaction is carried out by
10.1.4 Anabolism the enzyme RuBisCO as part of the Calvin – Benson cy-
cle.[54] Three types of photosynthesis occur in plants, C3
Further information: Anabolism carbon fixation, C4 carbon fixation and CAM photosyn-
thesis. These differ by the route that carbon dioxide takes
Anabolism is the set of constructive metabolic pro- to the Calvin cycle, with C3 plants fixing CO2 directly,
cesses where the energy released by catabolism is used while C4 and CAM photosynthesis incorporate the CO2
to synthesize complex molecules. In general, the com- into other compounds first, as adaptations to deal with in-
plex molecules that make up cellular structures are con- tense sunlight and dry conditions.[55]
structed step-by-step from small and simple precursors. In photosynthetic prokaryotes the mechanisms of car-
Anabolism involves three basic stages. First, the produc- bon fixation are more diverse. Here, carbon dioxide can
tion of precursors such as amino acids, monosaccharides, be fixed by the Calvin – Benson cycle, a reversed citric
isoprenoids and nucleotides, secondly, their activation acid cycle,[56] or the carboxylation of acetyl-CoA.[57][58]
into reactive forms using energy from ATP, and thirdly, Prokaryotic chemoautotrophs also fix CO2 through the
the assembly of these precursors into complex molecules Calvin – Benson cycle, but use energy from inorganic
such as proteins, polysaccharides, lipids and nucleic acids. compounds to drive the reaction.[59]
Organisms differ in how many of the molecules in their
cells they can construct for themselves. Autotrophs such
as plants can construct the complex organic molecules in Carbohydrates and glycans
cells such as polysaccharides and proteins from simple
molecules like carbon dioxide and water. Heterotrophs, Further information: Gluconeogenesis, glyoxylate cycle,
on the other hand, require a source of more complex glycogenesis and glycosylation
substances, such as monosaccharides and amino acids, to
produce these complex molecules. Organisms can be fur-
In carbohydrate anabolism, simple organic acids can be
ther classified by ultimate source of their energy: pho-
converted into monosaccharides such as glucose and then
toautotrophs and photoheterotrophs obtain energy from
used to assemble polysaccharides such as starch. The
light, whereas chemoautotrophs and chemoheterotrophs
generation of glucose from compounds like pyruvate,
obtain energy from inorganic oxidation reactions.
lactate, glycerol, glycerate 3-phosphate and amino acids is
called gluconeogenesis. Gluconeogenesis converts pyru-
Carbon fixation vate to glucose-6-phosphate through a series of interme-
diates, many of which are shared with glycolysis.[36] How-
Further information: Photosynthesis, carbon fixation and ever, this pathway is not simply glycolysis run in reverse,
chemosynthesis as several steps are catalyzed by non-glycolytic enzymes.
Photosynthesis is the synthesis of carbohydrates from This is important as it allows the formation and break-
down of glucose to be regulated separately, and prevents
both pathways from running simultaneously in a futile cy-
cle.[60][61]
Although fat is a common way of storing energy, in
vertebrates such as humans the fatty acids in these stores
cannot be converted to glucose through gluconeogenesis
as these organisms cannot convert acetyl-CoA into
pyruvate; plants do, but animals do not, have the nec-
essary enzymatic machinery.[62] As a result, after long-
term starvation, vertebrates need to produce ketone bod-
ies from fatty acids to replace glucose in tissues such as
the brain that cannot metabolize fatty acids.[63] In other
organisms such as plants and bacteria, this metabolic
problem is solved using the glyoxylate cycle, which by-
passes the decarboxylation step in the citric acid cycle and
Plant cells (bounded by purple walls) filled with chloroplasts allows the transformation of acetyl-CoA to oxaloacetate,
(green), which are the site of photosynthesis where it can be used for the production of glucose.[62][64]
178 CHAPTER 10. METABOLISM

Polysaccharides and glycans are made by the sequential from the reactive precursors isopentenyl pyrophosphate
addition of monosaccharides by glycosyltransferase from and dimethylallyl pyrophosphate.[72] These precursors
a reactive sugar-phosphate donor such as uridine diphos- can be made in different ways. In animals and archaea,
phate glucose (UDP-glucose) to an acceptor hydroxyl the mevalonate pathway produces these compounds from
group on the growing polysaccharide. As any of the acetyl-CoA,[73] while in plants and bacteria the non-
hydroxyl groups on the ring of the substrate can be ac- mevalonate pathway uses pyruvate and glyceraldehyde
ceptors, the polysaccharides produced can have straight 3-phosphate as substrates.[72][74] One important reaction
or branched structures.[65] The polysaccharides produced that uses these activated isoprene donors is steroid biosyn-
can have structural or metabolic functions themselves, or thesis. Here, the isoprene units are joined together to
be transferred to lipids and proteins by enzymes called make squalene and then folded up and formed into a
oligosaccharyltransferases.[66][67] set of rings to make lanosterol.[75] Lanosterol can then
be converted into other steroids such as cholesterol and
ergosterol.[75][76]
Fatty acids, isoprenoids and steroids

Further information: Fatty acid synthesis, steroid Proteins

metabolism
Fatty acids are made by fatty acid synthases that polymer- Further information: Protein biosynthesis, amino acid
synthesis
O O O O
– –
O P O P O O P O P O Organisms vary in their ability to synthesize the 20 com-
– – – –
O O O O
mon amino acids. Most bacteria and plants can synthe-
DMAPP IPP
size all twenty, but mammals can only synthesize eleven
nonessential amino acids, so nine essential amino acids
O O
–
GPP
must be obtained from food.[7] Some simple parasites,
O P O P O
O
– –
O
such as the bacteria Mycoplasma pneumoniae, lack all
amino acid synthesis and take their amino acids directly
from their hosts.[77] All amino acids are synthesized from
intermediates in glycolysis, the citric acid cycle, or the
pentose phosphate pathway. Nitrogen is provided by
Squalene
glutamate and glutamine. Amino acid synthesis depends
on the formation of the appropriate alpha-keto acid,
which is then transaminated to form an amino acid.[78]
Amino acids are made into proteins by being joined to-
gether in a chain of peptide bonds. Each different pro-
tein has a unique sequence of amino acid residues: this
Lanosterol
HO is its primary structure. Just as the letters of the al-
phabet can be combined to form an almost endless va-
riety of words, amino acids can be linked in varying se-
Simplified version of the steroid synthesis pathway with the quences to form a huge variety of proteins. Proteins are
intermediates isopentenyl pyrophosphate (IPP), dimethylallyl made from amino acids that have been activated by at-
pyrophosphate (DMAPP), geranyl pyrophosphate (GPP) and tachment to a transfer RNA molecule through an ester
squalene shown. Some intermediates are omitted for clarity. bond. This aminoacyl-tRNA precursor is produced in
an ATP-dependent reaction carried out by an aminoacyl
ize and then reduce acetyl-CoA units. The acyl chains in tRNA synthetase.[79] This aminoacyl-tRNA is then a sub-
the fatty acids are extended by a cycle of reactions that strate for the ribosome, which joins the amino acid onto
add the acyl group, reduce it to an alcohol, dehydrate it the elongating protein chain, using the sequence informa-
to an alkene group and then reduce it again to an alkane tion in a messenger RNA.[80]
group. The enzymes of fatty acid biosynthesis are divided
into two groups: in animals and fungi all these fatty acid
synthase reactions are carried out by a single multifunc- Nucleotide synthesis and salvage
tional type I protein,[68] while in plant plastids and bac-
teria separate type II enzymes perform each step in the Further information: Nucleotide salvage, pyrimidine
pathway.[69][70] biosynthesis, and purine metabolism
Terpenes and isoprenoids are a large class of lipids that
include the carotenoids and form the largest class of Nucleotides are made from amino acids, carbon dioxide
plant natural products.[71] These compounds are made by and formic acid in pathways that require large amounts of
the assembly and modification of isoprene units donated metabolic energy.[81] Consequently, most organisms have
10.1. OVERVIEW OF METABOLISM 179

efficient systems to salvage preformed nucleotides.[81][82] the amount of entropy (disorder) cannot decrease. Al-
Purines are synthesized as nucleosides (bases attached to though living organisms’ amazing complexity appears to
ribose).[83] Both adenine and guanine are made from the contradict this law, life is possible as all organisms are
precursor nucleoside inosine monophosphate, which is open systems that exchange matter and energy with their
synthesized using atoms from the amino acids glycine, surroundings. Thus living systems are not in equilibrium,
glutamine, and aspartic acid, as well as formate trans- but instead are dissipative systems that maintain their
ferred from the coenzyme tetrahydrofolate. Pyrimidines, state of high complexity by causing a larger increase in
on the other hand, are synthesized from the base orotate, the entropy of their environments.[95] The metabolism of
which is formed from glutamine and aspartate.[84] a cell achieves this by coupling the spontaneous processes
of catabolism to the non-spontaneous processes of an-
abolism. In thermodynamic terms, metabolism maintains
10.1.5 Xenobiotics and redox metabolism order by creating disorder.[96]

Further information: Xenobiotic metabolism, drug

metabolism, Alcohol metabolism and antioxidants 10.1.7 Regulation and control
Further information: Metabolic pathway, metabolic
All organisms are constantly exposed to compounds control analysis, hormone, regulatory enzymes, and cell
that they cannot use as foods and would be harm- signaling
ful if they accumulated in cells, as they have no
metabolic function. These potentially damaging com-
pounds are called xenobiotics.[85] Xenobiotics such as As the environments of most organisms are constantly
synthetic drugs, natural poisons and antibiotics are detox- changing, the reactions of metabolism must be finely
ified by a set of xenobiotic-metabolizing enzymes. In regulated to maintain a constant set of conditions within
humans, these include cytochrome P450 oxidases,[86] cells, a condition called homeostasis.[97][98] Metabolic
UDP-glucuronosyltransferases,[87] and glutathione S- regulation also allows organisms to respond to signals
transferases.[88] This system of enzymes acts in three and interact actively with their environments.[99] Two
stages to firstly oxidize the xenobiotic (phase I) and closely linked concepts are important for understanding
then conjugate water-soluble groups onto the molecule how metabolic pathways are controlled. Firstly, the reg-
(phase II). The modified water-soluble xenobiotic can ulation of an enzyme in a pathway is how its activity
then be pumped out of cells and in multicellular organ- is increased and decreased in response to signals. Sec-
isms may be further metabolized before being excreted ondly, the control exerted by this enzyme is the effect that
(phase III). In ecology, these reactions are particularly these changes in its activity have on the overall rate of the
important in microbial biodegradation of pollutants and pathway (the flux through the pathway).[100] For example,
the bioremediation of contaminated land and oil spills.[89] an enzyme may show large changes in activity (i.e. it is
Many of these microbial reactions are shared with multi- highly regulated) but if these changes have little effect on
cellular organisms, but due to the incredible diversity of the flux of a metabolic pathway, then this enzyme is not
types of microbes these organisms are able to deal with involved in the control of the pathway.[101]
a far wider range of xenobiotics than multicellular organ-
insulin
isms, and can degrade even persistent organic pollutants glucose
such as organochloride compounds.[90] 3
1
glucose
A related problem for aerobic organisms is oxidative transporter-4 insulin
receptor
stress.[91] Here, processes including oxidative phosphory-
lation and the formation of disulfide bonds during protein 2
folding produce reactive oxygen species such as hydrogen glycogen
4
6
peroxide.[92] These damaging oxidants are removed by
antioxidant metabolites such as glutathione and enzymes fatty acids
such as catalases and peroxidases.[93][94] pyruvate

Effect of insulin on glucose uptake and metabolism. Insulin

10.1.6 Thermodynamics of living organ- binds to its receptor (1), which in turn starts many protein ac-
isms tivation cascades (2). These include: translocation of Glut-4
transporter to the plasma membrane and influx of glucose (3),
glycogen synthesis (4), glycolysis (5) and fatty acid synthesis (6).
Further information: Biological thermodynamics
There are multiple levels of metabolic regulation. In in-
Living organisms must obey the laws of thermodynamics, trinsic regulation, the metabolic pathway self-regulates to
which describe the transfer of heat and work. The second respond to changes in the levels of substrates or products;
law of thermodynamics states that in any closed system, for example, a decrease in the amount of product can in-
180 CHAPTER 10. METABOLISM

crease the flux through the pathway to compensate.[100] lipid metabolism.[109][110] The retention of these ancient
This type of regulation often involves allosteric regulation
pathways during later evolution may be the result of
of the activities of multiple enzymes in the pathway.[102] these reactions having been an optimal solution to their
Extrinsic control involves a cell in a multicellular organ-particular metabolic problems, with pathways such as
ism changing its metabolism in response to signals from glycolysis and the citric acid cycle producing their end
other cells. These signals are usually in the form of products highly efficiently and in a minimal number of
soluble messengers such as hormones and growth fac- steps.[4][5] Mutation changes that affect non-coding DNA
tors and are detected by specific receptors on the cell segments may merely affect the metabolic efficiency
surface.[103] These signals are then transmitted inside theof the individual for whom the mutation occurs.[111]
cell by second messenger systems that often involved the The first pathways of enzyme-based metabolism may
phosphorylation of proteins.[104] have been parts of purine nucleotide metabolism, while
A very well understood example of extrinsic control is previous metabolic pathways were a part of the ancient
RNA world.[112]
the regulation of glucose metabolism by the hormone
insulin.[105] Insulin is produced in response to rises in Many models have been proposed to describe the mech-
blood glucose levels. Binding of the hormone to insulin anisms by which novel metabolic pathways evolve. These
receptors on cells then activates a cascade of protein ki- include the sequential addition of novel enzymes to a
nases that cause the cells to take up glucose and con- short ancestral pathway, the duplication and then diver-
vert it into storage molecules such as fatty acids and gence of entire pathways as well as the recruitment of pre-
glycogen.[106] The metabolism of glycogen is controlled existing enzymes and their assembly into a novel reac-
by activity of phosphorylase, the enzyme that breaks tion pathway.[113] The relative importance of these mech-
down glycogen, and glycogen synthase, the enzyme that anisms is unclear, but genomic studies have shown that
makes it. These enzymes are regulated in a recip- enzymes in a pathway are likely to have a shared ances-
rocal fashion, with phosphorylation inhibiting glycogen try, suggesting that many pathways have evolved in a step-
synthase, but activating phosphorylase. Insulin causes by-step fashion with novel functions created from pre-
glycogen synthesis by activating protein phosphatases and existing steps in the pathway.[114] An alternative model
producing a decrease in the phosphorylation of these comes from studies that trace the evolution of proteins’
enzymes.[107] structures in metabolic networks, this has suggested that
enzymes are pervasively recruited, borrowing enzymes
to perform similar functions in different metabolic path-
10.1.8 Evolution ways (evident in the MANET database)[115] These re-
cruitment processes result in an evolutionary enzymatic
Further information: Molecular evolution and mosaic.[116] A third possibility is that some parts of
phylogenetics metabolism might exist as “modules” that can be reused
The central pathways of metabolism described above, in different pathways and perform similar functions on
different molecules.[117]
Firmicutes As well as the evolution of new metabolic pathways, evo-
Animalia
Chlamydiae lution can also cause the loss of metabolic functions. For
Planctomycetes
example, in some parasites metabolic processes that are
Plantae
not essential for survival are lost and preformed amino
Protozoa Actinobacteria acids, nucleotides and carbohydrates may instead be scav-
Euryarchaeota enged from the host.[118] Similar reduced metabolic ca-
Fusobacteria pabilities are seen in endosymbiotic organisms.[119]
Crenarchaeota Cyanobacteria

10.1.9 Investigation and manipulation

Proteobacteria
Further information: Protein methods, proteomics,
metabolomics and metabolic network modelling
Evolutionary tree showing the common ancestry of organisms Classically, metabolism is studied by a reductionist ap-
from all three domains of life. Bacteria are colored blue, proach that focuses on a single metabolic pathway. Par-
eukaryotes red, and archaea green. Relative positions of some ticularly valuable is the use of radioactive tracers at the
of the phyla included are shown around the tree. whole-organism, tissue and cellular levels, which define
the paths from precursors to final products by identify-
such as glycolysis and the citric acid cycle, are present ing radioactively labelled intermediates and products.[120]
in all three domains of living things and were present in The enzymes that catalyze these chemical reactions can
the last universal ancestor.[3][108] This universal ancestral then be purified and their kinetics and responses to
cell was prokaryotic and probably a methanogen that inhibitors investigated. A parallel approach is to identify
had extensive amino acid, nucleotide, carbohydrate and the small molecules in a cell or tissue; the complete set of
10.1. OVERVIEW OF METABOLISM 181

as 1,3-propanediol and shikimic acid.[131] These genetic

modifications usually aim to reduce the amount of energy
used to produce the product, increase yields and reduce
the production of wastes.[132]

10.1.10 History

Further information: History of biochemistry and history

of molecular biology
The term metabolism is derived from the Greek

Metabolic network of the Arabidopsis thaliana citric acid cycle.

Enzymes and metabolites are shown as red squares and the in-
teractions between them as black lines.

these molecules is called the metabolome. Overall, these

studies give a good view of the structure and function of
simple metabolic pathways, but are inadequate when ap-
plied to more complex systems such as the metabolism of
a complete cell.[121]
An idea of the complexity of the metabolic networks in
cells that contain thousands of different enzymes is given
by the figure showing the interactions between just 43
proteins and 40 metabolites to the right: the sequences of
genomes provide lists containing anything up to 45,000
genes.[122] However, it is now possible to use this ge-
nomic data to reconstruct complete networks of biochem-
ical reactions and produce more holistic mathematical
models that may explain and predict their behavior.[123]
These models are especially powerful when used to inte-
grate the pathway and metabolite data obtained through Santorio Santorio in his steelyard balance, from Ars de statica
classical methods with data on gene expression from medicina, first published 1614
proteomic and DNA microarray studies.[124] Using these
techniques, a model of human metabolism has now been Μεταβολισμός – “Metabolismos” for “change”, or
produced, which will guide future drug discovery and “overthrow”.[133] The first documented references of
biochemical research.[125] These models are now used in metabolism were made by Ibn al-Nafis in his 1260
network analysis, to classify human diseases into groups AD work titled Al-Risalah al-Kamiliyyah fil Siera al-
that share common proteins or metabolites.[126][127] Nabawiyyah (The Treatise of Kamil on the Prophet’s Bi-
ography) which included the following phrase “Both the
Bacterial metabolic networks are a striking example of body and its parts are in a continuous state of dissolu-
bow-tie[128][129][130] organization, an architecture able to tion and nourishment, so they are inevitably undergo-
input a wide range of nutrients and produce a large va- ing permanent change.”.[134] The history of the scien-
riety of products and complex macromolecules using a tific study of metabolism spans several centuries and has
relatively few intermediate common currencies. moved from examining whole animals in early studies,
A major technological application of this information is to examining individual metabolic reactions in modern
metabolic engineering. Here, organisms such as yeast, biochemistry. The first controlled experiments in human
plants or bacteria are genetically modified to make them metabolism were published by Santorio Santorio in 1614
more useful in biotechnology and aid the production of in his book Ars de statica medicina.[135] He described how
drugs such as antibiotics or industrial chemicals such he weighed himself before and after eating, sleep, work-
182 CHAPTER 10. METABOLISM

ing, sex, fasting, drinking, and excreting. He found that • Sulfur metabolism
most of the food he took in was lost through what he
called “insensible perspiration”. • Thermic effect of food

In these early studies, the mechanisms of these metabolic • Water metabolism

processes had not been identified and a vital force was
thought to animate living tissue.[136] In the 19th century,
when studying the fermentation of sugar to alcohol by 10.1.12 References
yeast, Louis Pasteur concluded that fermentation was cat-
[1] Friedrich C (1998). “Physiology and genetics of sulfur-
alyzed by substances within the yeast cells he called “fer- oxidizing bacteria”. Adv Microb Physiol. Advances in
ments”. He wrote that “alcoholic fermentation is an act Microbial Physiology 39: 235–89. doi:10.1016/S0065-
correlated with the life and organization of the yeast cells, 2911(08)60018-1. ISBN 9780120277391. PMID
not with the death or putrefaction of the cells.”[137] This 9328649.
discovery, along with the publication by Friedrich Wöhler
in 1828 of a paper on the chemical synthesis of urea,[138] [2] Pace NR (January 2001). “The universal nature
of biochemistry”. Proc. Natl. Acad. Sci.
and is notable for being the first organic compound pre-
U.S.A. 98 (3): 805–8. Bibcode:2001PNAS...98..805P.
pared from wholly inorganic precursors. This proved that doi:10.1073/pnas.98.3.805. PMC 33372. PMID
the organic compounds and chemical reactions found in 11158550.
cells were no different in principle than any other part of
chemistry. [3] Smith E, Morowitz H (2004). “Universality in in-
termediary metabolism”. Proc Natl Acad Sci USA
It was the discovery of enzymes at the beginning of the 101 (36): 13168–73. Bibcode:2004PNAS..10113168S.
20th century by Eduard Buchner that separated the study doi:10.1073/pnas.0404922101. PMC 516543. PMID
of the chemical reactions of metabolism from the bi- 15340153.
ological study of cells, and marked the beginnings of
biochemistry.[139] The mass of biochemical knowledge [4] Ebenhöh O, Heinrich R (2001). “Evolutionary opti-
mization of metabolic pathways. Theoretical recon-
grew rapidly throughout the early 20th century. One
struction of the stoichiometry of ATP and NADH pro-
of the most prolific of these modern biochemists was ducing systems”. Bull Math Biol 63 (1): 21–55.
Hans Krebs who made huge contributions to the study doi:10.1006/bulm.2000.0197. PMID 11146883.
of metabolism.[140] He discovered the urea cycle and
later, working with Hans Kornberg, the citric acid cy- [5] Meléndez-Hevia E, Waddell T, Cascante M (1996). “The
cle and the glyoxylate cycle.[141][64] Modern biochemical puzzle of the Krebs citric acid cycle: assembling the pieces
research has been greatly aided by the development of of chemically feasible reactions, and opportunism in the
new techniques such as chromatography, X-ray diffrac- design of metabolic pathways during evolution”. J Mol
Evol 43 (3): 293–303. doi:10.1007/BF02338838. PMID
tion, NMR spectroscopy, radioisotopic labelling, electron
8703096.
microscopy and molecular dynamics simulations. These
techniques have allowed the discovery and detailed anal- [6] Michie K, Löwe J (2006). “Dynamic filaments of the
ysis of the many molecules and metabolic pathways in bacterial cytoskeleton”. Annu Rev Biochem 75: 467–
cells. 92. doi:10.1146/annurev.biochem.75.103004.142452.
PMID 16756499.

[7] Nelson, David L.; Michael M. Cox (2005). Lehninger

10.1.11 See also Principles of Biochemistry. New York: W. H. Freeman
and company. p. 841. ISBN 0-7167-4339-6.
• Anthropogenic metabolism
[8] Kelleher, J,Bryan 3rd, B, Mallet,R, Holleran, A, Mur-
• Antimetabolite phy, A, and Fiskum, G (1987). “Analysis of tricarboxylic
acid-cycle metabolism of hepatoma cells by comparison
• Basal metabolic rate of 14 CO2 ratios”. Biochem J 246 (3): 633–639. PMC
• Calorimetry 346906. PMID 6752947.

[9] Hothersall, J and Ahmed, A (2013). “Metabolic fate

• Isothermal microcalorimetry
of the increased yeast amino acid uptake subsequent to
• Inborn error of metabolism catabolite derepression”. J Amino Acids 2013: e461901.
doi:10.1155/2013/461901. PMC 3575661. PMID
• Iron-sulfur world theory, a “metabolism first” theory 23431419.
of the origin of life.
[10] Fahy E, Subramaniam S, Brown H, Glass C, Merrill A,
• Primary nutritional groups Murphy R, Raetz C, Russell D, Seyama Y, Shaw W,
Shimizu T, Spener F, van Meer G, VanNieuwenhze M,
• Respirometry White S, Witztum J, Dennis E (2005). “A comprehensive
classification system for lipids”. J Lipid Res 46 (5): 839–
• Stream metabolism 61. doi:10.1194/jlr.E400004-JLR200. PMID 15722563.
10.1. OVERVIEW OF METABOLISM 183

[11] “Nomenclature of Lipids”. IUPAC-IUB Commission on [23] Dulhunty A (2006). “Excitation-contraction coupling
Biochemical Nomenclature (CBN). Retrieved 2007-03- from the 1950s into the new millennium”. Clin Exp
08. Pharmacol Physiol 33 (9): 763–72. doi:10.1111/j.1440-
1681.2006.04441.x. PMID 16922804.
[12] Hegardt F (1999). “Mitochondrial 3-hydroxy-3-
methylglutaryl-CoA synthase: a control enzyme [24] Mahan D, Shields R (1998). “Macro- and micromineral
in ketogenesis”. Biochem J 338 (Pt 3): 569–82. composition of pigs from birth to 145 kilograms of body
doi:10.1042/0264-6021:3380569. PMC 1220089. weight”. J Anim Sci 76 (2): 506–12. PMID 9498359.
PMID 10051425.
[25] Husted S, Mikkelsen B, Jensen J, Nielsen N (2004).
[13] Raman R, Raguram S, Venkataraman G, Paulson “Elemental fingerprint analysis of barley (Hordeum vul-
J, Sasisekharan R (2005). “Glycomics: an inte- gare) using inductively coupled plasma mass spectrom-
grated systems approach to structure-function relation- etry, isotope-ratio mass spectrometry, and multivari-
ships of glycans”. Nat Methods 2 (11): 817–24. ate statistics”. Anal Bioanal Chem 378 (1): 171–82.
doi:10.1038/nmeth807. PMID 16278650. doi:10.1007/s00216-003-2219-0. PMID 14551660.

[14] Sierra S, Kupfer B, Kaiser R (2005). “Basics of the vi- [26] Finney L, O'Halloran T (2003). “Transition
rology of HIV-1 and its replication”. J Clin Virol 34 metal speciation in the cell: insights from the
(4): 233–44. doi:10.1016/j.jcv.2005.09.004. PMID chemistry of metal ion receptors”. Science 300
16198625. (5621): 931–6. Bibcode:2003Sci...300..931F.
doi:10.1126/science.1085049. PMID 12738850.
[15] Wimmer M, Rose I (1978). “Mechanisms
of enzyme-catalyzed group transfer reac- [27] Cousins R, Liuzzi J, Lichten L (2006). “Mammalian
tions”. Annu Rev Biochem 47: 1031–78. zinc transport, trafficking, and signals”. J Biol Chem 281
doi:10.1146/annurev.bi.47.070178.005123. PMID (34): 24085–9. doi:10.1074/jbc.R600011200. PMID
354490. 16793761.
[16] Mitchell P (1979). “The Ninth Sir Hans Krebs Lec-
[28] Dunn L, Rahmanto Y, Richardson D (2007). “Iron uptake
ture. Compartmentation and communication in living
and metabolism in the new millennium”. Trends Cell Biol
systems. Ligand conduction: a general catalytic princi-
17 (2): 93–100. doi:10.1016/j.tcb.2006.12.003. PMID
ple in chemical, osmotic and chemiosmotic reaction sys-
17194590.
tems”. Eur J Biochem 95 (1): 1–20. doi:10.1111/j.1432-
1033.1979.tb12934.x. PMID 378655.
[29] Nealson K, Conrad P (1999). “Life: past, present and
future”. Philos Trans R Soc Lond B Biol Sci 354 (1392):
[17] Dimroth P, von Ballmoos C, Meier T (March 2006).
1923–39. doi:10.1098/rstb.1999.0532. PMC 1692713.
“Catalytic and mechanical cycles in F-ATP synthases:
PMID 10670014.
Fourth in the Cycles Review Series”. EMBO Rep 7 (3):
276–82. doi:10.1038/sj.embor.7400646. PMC 1456893.
[30] Häse C, Finkelstein R (December 1993). “Bacterial extra-
PMID 16607397.
cellular zinc-containing metalloproteases”. Microbiol Rev
[18] Coulston, Ann; Kerner, John; Hattner, JoAnn; Srivastava, 57 (4): 823–37. PMC 372940. PMID 8302217.
Ashini (2006). “Nutrition Principles and Clinical Nu-
trition”. Stanford School of Medicine Nutrition Courses. [31] Gupta R, Gupta N, Rathi P (2004). “Bacterial lipases:
SUMMIT. an overview of production, purification and biochemical
properties”. Appl Microbiol Biotechnol 64 (6): 763–81.
[19] Pollak N, Dölle C, Ziegler M (2007). “The power to doi:10.1007/s00253-004-1568-8. PMID 14966663.
reduce: pyridine nucleotides – small molecules with a
multitude of functions”. Biochem J 402 (2): 205– [32] Hoyle T (1997). “The digestive system: linking the-
18. doi:10.1042/BJ20061638. PMC 1798440. PMID ory and practice”. Br J Nurs 6 (22): 1285–91. PMID
17295611. 9470654.

[20] Heymsfield S, Waki M, Kehayias J, Lichtman S, Dilma- [33] Souba W, Pacitti A (1992). “How amino acids get
nian F, Kamen Y, Wang J, Pierson R (1991). “Chemical into cells: mechanisms, models, menus, and media-
and elemental analysis of humans in vivo using improved tors”. JPEN J Parenter Enteral Nutr 16 (6): 569–78.
body composition models”. Am J Physiol 261 (2 Pt 1): doi:10.1177/0148607192016006569. PMID 1494216.
E190–8. PMID 1872381.
[34] Barrett M, Walmsley A, Gould G (1999). “Structure
[21] Sychrová H (2004). “Yeast as a model organism to study and function of facilitative sugar transporters”. Curr
transport and homeostasis of alkali metal cations” (PDF). Opin Cell Biol 11 (4): 496–502. doi:10.1016/S0955-
Physiol Res. 53 Suppl 1: S91–8. PMID 15119939. 0674(99)80072-6. PMID 10449337.

[22] Levitan I (1988). “Modulation of ion channels in neu- [35] Bell G, Burant C, Takeda J, Gould G (1993). “Struc-
rons and other cells”. Annu Rev Neurosci 11: 119– ture and function of mammalian facilitative sugar trans-
36. doi:10.1146/annurev.ne.11.030188.001003. PMID porters”. J Biol Chem 268 (26): 19161–4. PMID
2452594. 8366068.
184 CHAPTER 10. METABOLISM

[36] Bouché C, Serdy S, Kahn C, Goldfine A (2004). “The cel- [49] Barea J, Pozo M, Azcón R, Azcón-Aguilar C (2005).
lular fate of glucose and its relevance in type 2 diabetes”. “Microbial co-operation in the rhizosphere”. J Exp Bot
Endocr Rev 25 (5): 807–30. doi:10.1210/er.2003-0026. 56 (417): 1761–78. doi:10.1093/jxb/eri197. PMID
PMID 15466941. 15911555.

[37] Wipperman, Matthew, F.; Thomas, Suzanne, T.; Samp- [50] van der Meer M, Schouten S, Bateson M, Nübel U,
son, Nicole, S. (2014). “Pathogen roid rage: Choles- Wieland A, Kühl M, de Leeuw J, Sinninghe Damsté
terol utilization by Mycobacterium tuberculosis". Crit. J, Ward D (July 2005). “Diel Variations in Carbon
Rev. Biochem. Mol. Biol. 49 (4): 269–93. Metabolism by Green Nonsulfur-Like Bacteria in Al-
doi:10.3109/10409238.2014.895700. PMID 24611808. kaline Siliceous Hot Spring Microbial Mats from Yel-
lowstone National Park”. Appl Environ Microbiol 71
[38] Sakami W, Harrington H (1963). “Amino acid
(7): 3978–86. doi:10.1128/AEM.71.7.3978-3986.2005.
metabolism”. Annu Rev Biochem 32: 355–98.
PMC 1168979. PMID 16000812.
doi:10.1146/annurev.bi.32.070163.002035. PMID
14144484.
[51] Tichi M, Tabita F (2001). “Interactive Control of
[39] Brosnan J (2000). “Glutamate, at the interface between Rhodobacter capsulatus Redox-Balancing Systems during
amino acid and carbohydrate metabolism”. J Nutr 130 Phototrophic Metabolism”. J Bacteriol 183 (21): 6344–
(4S Suppl): 988S–90S. PMID 10736367. 54. doi:10.1128/JB.183.21.6344-6354.2001. PMC
100130. PMID 11591679.
[40] Young V, Ajami A (2001). “Glutamine: the emperor or
his clothes?". J Nutr 131 (9 Suppl): 2449S–59S; discus- [52] Allen J, Williams J (1998). “Photosynthetic reaction cen-
sion 2486S–7S. PMID 11533293. ters”. FEBS Lett 438 (1–2): 5–9. doi:10.1016/S0014-
5793(98)01245-9. PMID 9821949.
[41] Hosler J, Ferguson-Miller S, Mills D (2006). “Energy
Transduction: Proton Transfer Through the Respira- [53] Munekage Y, Hashimoto M, Miyake C, Tomizawa
tory Complexes”. Annu Rev Biochem 75: 165–87. K, Endo T, Tasaka M, Shikanai T (2004).
doi:10.1146/annurev.biochem.75.062003.101730. PMC “Cyclic electron flow around photosystem I
2659341. PMID 16756489. is essential for photosynthesis”. Nature 429
(6991): 579–82. Bibcode:2004Natur.429..579M.
[42] Schultz B, Chan S (2001). “Structures and proton-
doi:10.1038/nature02598. PMID 15175756.
pumping strategies of mitochondrial respiratory en-
zymes”. Annu Rev Biophys Biomol Struct 30: 23–65.
[54] Miziorko H, Lorimer G (1983). “Ribulose-
doi:10.1146/annurev.biophys.30.1.23. PMID 11340051.
1,5-bisphosphate carboxylase-oxygenase”.
[43] Capaldi R, Aggeler R (2002). “Mechanism of the Annu Rev Biochem 52: 507–35.
F(1)F(0)-type ATP synthase, a biological rotary motor”. doi:10.1146/annurev.bi.52.070183.002451. PMID
Trends Biochem Sci 27 (3): 154–60. doi:10.1016/S0968- 6351728.
0004(01)02051-5. PMID 11893513.
[55] Dodd A, Borland A, Haslam R, Griffiths H, Maxwell
[44] Friedrich B, Schwartz E (1993). “Molecu- K (2002). “Crassulacean acid metabolism: plas-
lar biology of hydrogen utilization in aerobic tic, fantastic”. J Exp Bot 53 (369): 569–80.
chemolithotrophs”. Annu Rev Microbiol 47: 351– doi:10.1093/jexbot/53.369.569. PMID 11886877.
83. doi:10.1146/annurev.mi.47.100193.002031. PMID
8257102. [56] Hügler M, Wirsen C, Fuchs G, Taylor C, Sievert S (May
2005). “Evidence for Autotrophic CO2 Fixation via the
[45] Weber K, Achenbach L, Coates J (2006). “Microor- Reductive Tricarboxylic Acid Cycle by Members of the
ganisms pumping iron: anaerobic microbial iron oxida- ɛ Subdivision of Proteobacteria”. J Bacteriol 187 (9):
tion and reduction”. Nat Rev Microbiol 4 (10): 752–64. 3020–7. doi:10.1128/JB.187.9.3020-3027.2005. PMC
doi:10.1038/nrmicro1490. PMID 16980937. 1082812. PMID 15838028.
[46] Jetten M, Strous M, van de Pas-Schoonen K, Schalk J,
[57] Strauss G, Fuchs G (1993). “Enzymes of a novel
van Dongen U, van de Graaf A, Logemann S, Muyzer
autotrophic CO2 fixation pathway in the pho-
G, van Loosdrecht M, Kuenen J (1998). “The anaero-
totrophic bacterium Chloroflexus aurantiacus, the
bic oxidation of ammonium”. FEMS Microbiol Rev 22
3-hydroxypropionate cycle”. Eur J Biochem 215 (3):
(5): 421–37. doi:10.1111/j.1574-6976.1998.tb00379.x.
633–43. doi:10.1111/j.1432-1033.1993.tb18074.x.
PMID 9990725.
PMID 8354269.
[47] Simon J (2002). “Enzymology and bioenergetics
of respiratory nitrite ammonification”. FEMS Mi- [58] Wood H (1991). “Life with CO or CO2 and H2 as a source
crobiol Rev 26 (3): 285–309. doi:10.1111/j.1574- of carbon and energy”. FASEB J 5 (2): 156–63. PMID
6976.2002.tb00616.x. PMID 12165429. 1900793.

[48] Conrad R (1996). “Soil microorganisms as controllers [59] Shively J, van Keulen G, Meijer W (1998). “Some-
of atmospheric trace gases (H2, CO, CH4, OCS, N2O, thing from almost nothing: carbon dioxide fixation in
and NO)". Microbiol Rev 60 (4): 609–40. PMC 239458. chemoautotrophs”. Annu Rev Microbiol 52: 191–230.
PMID 8987358. doi:10.1146/annurev.micro.52.1.191. PMID 9891798.
10.1. OVERVIEW OF METABOLISM 185

[60] Boiteux A, Hess B (1981). “Design of glycoly- doi:10.1128/JB.188.9.3192-3198.2006. PMC 1447442.

sis”. Philos Trans R Soc Lond B Biol Sci 293 PMID 16621811.
(1063): 5–22. Bibcode:1981RSPTB.293....5B.
doi:10.1098/rstb.1981.0056. PMID 6115423. [74] Lichtenthaler H (1999). “The 1-Ddeoxy-D-xylulose-5-
phosphate pathway of isoprenoid biosynthesis in plants”.
[61] Pilkis S, el-Maghrabi M, Claus T (1990). “Fructose-2,6- Annu Rev Plant Physiol Plant Mol Biol 50: 47–65.
bisphosphate in control of hepatic gluconeogenesis. From doi:10.1146/annurev.arplant.50.1.47. PMID 15012203.
metabolites to molecular genetics”. Diabetes Care 13 (6):
582–99. doi:10.2337/diacare.13.6.582. PMID 2162755. [75] Schroepfer G (1981). “Sterol biosynthe-
sis”. Annu Rev Biochem 50: 585–621.
[62] Ensign S (2006). “Revisiting the glyoxylate cycle: doi:10.1146/annurev.bi.50.070181.003101. PMID
alternate pathways for microbial acetate assimilation”. 7023367.
Mol Microbiol 61 (2): 274–6. doi:10.1111/j.1365-
2958.2006.05247.x. PMID 16856935. [76] Lees N, Skaggs B, Kirsch D, Bard M (1995). “Cloning
of the late genes in the ergosterol biosynthetic pathway
[63] Finn P, Dice J (2006). “Proteolytic and lipolytic re-
of Saccharomyces cerevisiae—a review”. Lipids 30 (3):
sponses to starvation”. Nutrition 22 (7–8): 830–44.
221–6. doi:10.1007/BF02537824. PMID 7791529.
doi:10.1016/j.nut.2006.04.008. PMID 16815497.
[77] Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC,
[64] Kornberg H, Krebs H (1957). “Synthesis of cell
Herrmann R (November 1996). “Complete sequence
constituents from C2-units by a modified tricar-
analysis of the genome of the bacterium Mycoplasma
boxylic acid cycle”. Nature 179 (4568): 988–91.
pneumoniae”. Nucleic Acids Res. 24 (22): 4420–
Bibcode:1957Natur.179..988K. doi:10.1038/179988a0.
49. doi:10.1093/nar/24.22.4420. PMC 146264. PMID
PMID 13430766.
8948633.
[65] Rademacher T, Parekh R, Dwek R (1988). “Gly-
cobiology”. Annu Rev Biochem 57: 785–838. [78] Guyton, Arthur C.; John E. Hall (2006). Textbook of Med-
doi:10.1146/annurev.bi.57.070188.004033. PMID ical Physiology. Philadelphia: Elsevier. pp. 855–6. ISBN
3052290. 0-7216-0240-1.

[66] Opdenakker G, Rudd P, Ponting C, Dwek R (1993). [79] Ibba M, Söll D (2001). “The renaissance of
“Concepts and principles of glycobiology”. FASEB J 7 aminoacyl-tRNA synthesis”. EMBO Rep 2 (5): 382–7.
(14): 1330–7. PMID 8224606. doi:10.1093/embo-reports/kve095. PMC 1083889.
PMID 11375928.
[67] McConville M, Menon A (2000). “Recent develop-
ments in the cell biology and biochemistry of glyco- [80] Lengyel P, Söll D (1969). “Mechanism of protein biosyn-
sylphosphatidylinositol lipids (review)". Mol Membr Biol thesis”. Bacteriol Rev 33 (2): 264–301. PMC 378322.
17 (1): 1–16. doi:10.1080/096876800294443. PMID PMID 4896351.
10824734.
[81] Rudolph F (1994). “The biochemistry and physiology of
[68] Chirala S, Wakil S (2004). “Structure and function of nucleotides”. J Nutr 124 (1 Suppl): 124S–127S. PMID
animal fatty acid synthase”. Lipids 39 (11): 1045–53. 8283301. Zrenner R, Stitt M, Sonnewald U, Boldt R
doi:10.1007/s11745-004-1329-9. PMID 15726818. (2006). “Pyrimidine and purine biosynthesis and degra-
dation in plants”. Annu Rev Plant Biol 57: 805–36.
[69] White S, Zheng J, Zhang Y (2005). “The
doi:10.1146/annurev.arplant.57.032905.105421. PMID
structural biology of type II fatty acid biosyn-
16669783.
thesis”. Annu Rev Biochem 74: 791–831.
doi:10.1146/annurev.biochem.74.082803.133524. [82] Stasolla C, Katahira R, Thorpe T, Ashihara H (2003).
PMID 15952903. “Purine and pyrimidine nucleotide metabolism in
higher plants”. J Plant Physiol 160 (11): 1271–95.
[70] Ohlrogge J, Jaworski J (1997). “Regulation of fatty acid
doi:10.1078/0176-1617-01169. PMID 14658380.
synthesis”. Annu Rev Plant Physiol Plant Mol Biol 48:
109–136. doi:10.1146/annurev.arplant.48.1.109. PMID [83] Davies O, Mendes P, Smallbone K, Malys N (2012).
15012259. “Characterisation of multiple substrate-specific
[71] Dubey V, Bhalla R, Luthra R (2003). “An overview (d)ITP/(d)XTPase and modelling of deaminated
of the non-mevalonate pathway for terpenoid biosyn- purine nucleotide metabolism”. BMB Reports 45 (4):
thesis in plants” (PDF). J Biosci 28 (5): 637–46. 259–64. doi:10.5483/BMBRep.2012.45.4.259. PMID
doi:10.1007/BF02703339. PMID 14517367. 22531138.

[72] Kuzuyama T, Seto H (2003). “Diversity of the biosynthe- [84] Smith J (1995). “Enzymes of nucleotide synthesis”.
sis of the isoprene units”. Nat Prod Rep 20 (2): 171–83. Curr Opin Struct Biol 5 (6): 752–7. doi:10.1016/0959-
doi:10.1039/b109860h. PMID 12735695. 440X(95)80007-7. PMID 8749362.

[73] Grochowski L, Xu H, White R (May 2006). [85] Testa B, Krämer S (2006). “The biochemistry of
“Methanocaldococcus jannaschii Uses a Modified drug metabolism—an introduction: part 1. Principles
Mevalonate Pathway for Biosynthesis of Isopen- and overview”. Chem Biodivers 3 (10): 1053–101.
tenyl Diphosphate”. J Bacteriol 188 (9): 3192–8. doi:10.1002/cbdv.200690111. PMID 17193224.
186 CHAPTER 10. METABOLISM

[86] Danielson P (2002). “The cytochrome P450 super- [100] Salter M, Knowles R, Pogson C (1994). “Metabolic con-
family: biochemistry, evolution and drug metabolism trol”. Essays Biochem 28: 1–12. PMID 7925313.
in humans”. Curr Drug Metab 3 (6): 561–97.
doi:10.2174/1389200023337054. PMID 12369887. [101] Westerhoff H, Groen A, Wanders R (1984). “Modern the-
ories of metabolic control and their applications (review)".
[87] King C, Rios G, Green M, Tephly T (2000). “UDP- Biosci Rep 4 (1): 1–22. doi:10.1007/BF01120819. PMID
glucuronosyltransferases”. Curr Drug Metab 1 (2): 143– 6365197.
61. doi:10.2174/1389200003339171. PMID 11465080.
[102] Fell D, Thomas S (1995). “Physiological control of
[88] Sheehan D, Meade G, Foley V, Dowd C (Novem-
metabolic flux: the requirement for multisite modulation”.
ber 2001). “Structure, function and evolution of glu-
Biochem J 311 (Pt 1): 35–9. PMC 1136115. PMID
tathione transferases: implications for classification of
7575476.
non-mammalian members of an ancient enzyme super-
family”. Biochem J 360 (Pt 1): 1–16. doi:10.1042/0264-
[103] Hendrickson W (2005). “Transduction of biochemi-
6021:3600001. PMC 1222196. PMID 11695986.
cal signals across cell membranes”. Q Rev Biophys 38
[89] Galvão T, Mohn W, de Lorenzo V (2005). “Explor- (4): 321–30. doi:10.1017/S0033583506004136. PMID
ing the microbial biodegradation and biotransformation 16600054.
gene pool”. Trends Biotechnol 23 (10): 497–506.
doi:10.1016/j.tibtech.2005.08.002. PMID 16125262. [104] Cohen P (2000). “The regulation of protein function by
multisite phosphorylation—a 25 year update”. Trends
[90] Janssen D, Dinkla I, Poelarends G, Terpstra P (2005). Biochem Sci 25 (12): 596–601. doi:10.1016/S0968-
“Bacterial degradation of xenobiotic compounds: evolu- 0004(00)01712-6. PMID 11116185.
tion and distribution of novel enzyme activities”. En-
viron Microbiol 7 (12): 1868–82. doi:10.1111/j.1462- [105] Lienhard G, Slot J, James D, Mueckler M (1992).
2920.2005.00966.x. PMID 16309386. “How cells absorb glucose”. Sci Am 266 (1): 86–
91. doi:10.1038/scientificamerican0192-86. PMID
[91] Davies K (1995). “Oxidative stress: the paradox of aero- 1734513.
bic life”. Biochem Soc Symp 61: 1–31. PMID 8660387.
[106] Roach P (2002). “Glycogen and its
[92] Tu B, Weissman J (2004). “Oxidative protein folding metabolism”. Curr Mol Med 2 (2): 101–20.
in eukaryotes: mechanisms and consequences”. J Cell doi:10.2174/1566524024605761. PMID 11949930.
Biol 164 (3): 341–6. doi:10.1083/jcb.200311055. PMC
2172237. PMID 14757749. [107] Newgard C, Brady M, O'Doherty R, Saltiel A
[93] Sies H (1997). “Oxidative stress: oxidants and (2000). “Organizing glucose disposal: emerging
antioxidants” (PDF). Exp Physiol 82 (2): 291– roles of the glycogen targeting subunits of protein
5. doi:10.1113/expphysiol.1997.sp004024. PMID phosphatase-1” (PDF). Diabetes 49 (12): 1967–77.
9129943. doi:10.2337/diabetes.49.12.1967. PMID 11117996.

[94] Vertuani S, Angusti A, Manfredini S (2004). “The [108] Romano A, Conway T (1996). “Evolution of carbohy-
antioxidants and pro-antioxidants network: an drate metabolic pathways”. Res Microbiol 147 (6–7):
overview”. Curr Pharm Des 10 (14): 1677–94. 448–55. doi:10.1016/0923-2508(96)83998-2. PMID
doi:10.2174/1381612043384655. PMID 15134565. 9084754.

[95] von Stockar U, Liu J (1999). “Does microbial life al- [109] Koch A (1998). “How did bacteria come to be?". Adv Mi-
ways feed on negative entropy? Thermodynamic analy- crob Physiol. Advances in Microbial Physiology 40: 353–
sis of microbial growth”. Biochim Biophys Acta 1412 (3): 99. doi:10.1016/S0065-2911(08)60135-6. ISBN 978-0-
191–211. doi:10.1016/S0005-2728(99)00065-1. PMID 12-027740-7. PMID 9889982.
10482783.
[110] Ouzounis C, Kyrpides N (1996). “The emergence of ma-
[96] Demirel Y, Sandler S (2002). “Thermodynamics and jor cellular processes in evolution”. FEBS Lett 390 (2):
bioenergetics”. Biophys Chem 97 (2–3): 87–111. 119–23. doi:10.1016/0014-5793(96)00631-X. PMID
doi:10.1016/S0301-4622(02)00069-8. PMID 12050002. 8706840.
[97] Albert R (2005). “Scale-free networks in cell biology”.
[111] C.Michael Hogan. 2010. Mutation. ed. E.Monosson and
J Cell Sci 118 (Pt 21): 4947–57. doi:10.1242/jcs.02714.
C.J.Cleveland. Encyclopedia of Earth. National Council
PMID 16254242.
for Science and the Environment. Washington DC
[98] Brand M (1997). “Regulation analysis of energy
metabolism”. J Exp Biol 200 (Pt 2): 193–202. PMID [112] Caetano-Anolles G, Kim HS, Mittenthal JE (2007).
9050227. “The origin of modern metabolic networks in-
ferred from phylogenomic analysis of protein
[99] Soyer O, Salathé M, Bonhoeffer S (2006). “Sig- architecture”. Proc Natl Acad Sci USA 104
nal transduction networks: topology, response and bio- (22): 9358–63. Bibcode:2007PNAS..104.9358C.
chemical processes”. J Theor Biol 238 (2): 416–25. doi:10.1073/pnas.0701214104. PMC 1890499. PMID
doi:10.1016/j.jtbi.2005.05.030. PMID 16045939. 17517598.
 10.1. OVERVIEW OF METABOLISM 187

[113] Schmidt S, Sunyaev S, Bork P, Dandekar T (2003). [124] Gianchandani E, Brautigan D, Papin J (2006). “Sys-
“Metabolites: a helping hand for pathway evolution?". tems analyses characterize integrated functions of bio-
Trends Biochem Sci 28 (6): 336–41. doi:10.1016/S0968- chemical networks”. Trends Biochem Sci 31 (5): 284–91.
0004(03)00114-2. PMID 12826406. doi:10.1016/j.tibs.2006.03.007. PMID 16616498.

[114] Light S, Kraulis P (2004). “Network analysis of metabolic [125] Duarte NC, Becker SA, Jamshidi N et al. (Febru-
enzyme evolution in Escherichia coli”. BMC Bioinfor- ary 2007). “Global reconstruction of the human
matics 5: 15. doi:10.1186/1471-2105-5-15. PMC metabolic network based on genomic and bib-
394313. PMID 15113413. Alves R, Chaleil R, Stern- liomic data”. Proc. Natl. Acad. Sci. U.S.A. 104
berg M (2002). “Evolution of enzymes in metabolism: (6): 1777–82. Bibcode:2007PNAS..104.1777D.
a network perspective”. J Mol Biol 320 (4): 751–70. doi:10.1073/pnas.0610772104. PMC 1794290. PMID
doi:10.1016/S0022-2836(02)00546-6. PMID 12095253. 17267599.

[115] Kim HS, Mittenthal JE, Caetano-Anolles G (2006). [126] Goh KI, Cusick ME, Valle D, Childs B, Vidal M,
“MANET: tracing evolution of protein architecture in Barabási AL (May 2007). “The human disease net-
metabolic networks”. BMC Bioinformatics 7: 351. work”. Proc. Natl. Acad. Sci. U.S.A.
doi:10.1186/1471-2105-7-351. PMC 1559654. PMID 104 (21): 8685–90. Bibcode:2007PNAS..104.8685G.
16854231. doi:10.1073/pnas.0701361104. PMC 1885563. PMID
17502601.
[116] Teichmann SA, Rison SC, Thornton JM, Riley M, Gough
J, Chothia C (2001). “Small-molecule metabolsim: an [127] Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN,
enzyme mosaic”. Trends Biotechnol 19 (12): 482–6. Barabási AL (July 2008). “The implications of hu-
doi:10.1016/S0167-7799(01)01813-3. PMID 11711174. man metabolic network topology for disease comor-
bidity”. Proc. Natl. Acad. Sci. U.S.A. 105
[117] Spirin V, Gelfand M, Mironov A, Mirny L (June 2006). (29): 9880–9885. Bibcode:2008PNAS..105.9880L.
“A metabolic network in the evolutionary context: Multi- doi:10.1073/pnas.0802208105. PMC 2481357. PMID
scale structure and modularity”. Proc Natl Acad Sci USA 18599447.
103 (23): 8774–9. Bibcode:2006PNAS..103.8774S.
[128] Csete M, Doyle J (2004). “Bow ties, metabolism
doi:10.1073/pnas.0510258103. PMC 1482654. PMID
and disease”. Trends Biotechnol. 22 (9): 446–50.
16731630.
doi:10.1016/j.tibtech.2004.07.007. PMID 15331224.
[118] Lawrence J (2005). “Common themes in the genome
[129] Ma HW, Zeng AP (2003). “The connectivity
strategies of pathogens”. Curr Opin Genet Dev 15
structure, giant strong component and centrality of
(6): 584–8. doi:10.1016/j.gde.2005.09.007. PMID
metabolic networks”. Bioinformatics 19 (11): 1423–30.
16188434. Wernegreen J (2005). “For better or worse:
doi:10.1093/bioinformatics/btg177. PMID 12874056.
genomic consequences of intracellular mutualism and
parasitism”. Curr Opin Genet Dev 15 (6): 572–83. [130] Zhao J, Yu H, Luo JH, Cao ZW, Li YX (2006).
doi:10.1016/j.gde.2005.09.013. PMID 16230003. “Hierarchical modularity of nested bow-ties in
metabolic networks”. BMC Bioinformatics 7: 386.
[119] Pál C, Papp B, Lercher M, Csermely P, Oliver S, doi:10.1186/1471-2105-7-386. PMC 1560398. PMID
Hurst L (2006). “Chance and necessity in the 16916470.
evolution of minimal metabolic networks”. Nature
440 (7084): 667–70. Bibcode:2006Natur.440..667P. [131] Thykaer J, Nielsen J (2003). “Metabolic engi-
doi:10.1038/nature04568. PMID 16572170. neering of beta-lactam production”. Metab Eng 5
(1): 56–69. doi:10.1016/S1096-7176(03)00003-X.
[120] Rennie M (1999). “An introduction to the use of tracers in PMID 12749845. González-Pajuelo M, Meynial-
nutrition and metabolism”. Proc Nutr Soc 58 (4): 935–44. Salles I, Mendes F, Andrade J, Vasconcelos I, Sou-
doi:10.1017/S002966519900124X. PMID 10817161. caille P (2005). “Metabolic engineering of Clostrid-
ium acetobutylicum for the industrial production of
[121] Phair R (1997). “Development of kinetic models in the 1,3-propanediol from glycerol”. Metab Eng 7 (5–6):
nonlinear world of molecular cell biology”. Metabolism 329–36. doi:10.1016/j.ymben.2005.06.001. PMID
46 (12): 1489–95. doi:10.1016/S0026-0495(97)90154- 16095939. Krämer M, Bongaerts J, Bovenberg R,
2. PMID 9439549. Kremer S, Müller U, Orf S, Wubbolts M, Raeven L
(2003). “Metabolic engineering for microbial produc-
[122] Sterck L, Rombauts S, Vandepoele K, Rouzé P, Van de tion of shikimic acid”. Metab Eng 5 (4): 277–83.
Peer Y (2007). “How many genes are there in plants doi:10.1016/j.ymben.2003.09.001. PMID 14642355.
(... and why are they there)?". Curr Opin Plant Biol 10
(2): 199–203. doi:10.1016/j.pbi.2007.01.004. PMID [132] Koffas M, Roberge C, Lee K, Stephanopoulos G (1999).
17289424. “Metabolic engineering”. Annu Rev Biomed Eng 1:
535–57. doi:10.1146/annurev.bioeng.1.1.535. PMID
[123] Borodina I, Nielsen J (2005). “From genomes to in silico 11701499.
cells via metabolic networks”. Curr Opin Biotechnol 16
(3): 350–5. doi:10.1016/j.copbio.2005.04.008. PMID [133] “Metabolism”. The Online Etymology Dictionary. Re-
15961036. trieved 2007-02-20.
 188 CHAPTER 10. METABOLISM

[134] Dr. Abu Shadi Al-Roubi (1982), “Ibn Al-Nafis as a • Berg, J. Tymoczko, J. and Stryer, L., Biochemistry.
philosopher”, Symposium on Ibn al-Nafis, Second Inter- (W. H. Freeman and Company, 2002), ISBN 0-
national Conference on Islamic Medicine: Islamic Medi- 7167-4955-6
cal Organization, Kuwait (cf. Ibn al-Nafis As a Philoso-
pher, Encyclopedia of Islamic World [1]) • Cox, M. and Nelson, D. L., Lehninger Principles of
Biochemistry. (Palgrave Macmillan, 2004), ISBN 0-
[135] Eknoyan G (1999). “Santorio Sanctorius (1561–1636)
7167-4339-6
– founding father of metabolic balance studies”. Am J
Nephrol 19 (2): 226–33. doi:10.1159/000013455. PMID • Brock, T. D. Madigan, M. T. Martinko, J. and
10213823.
Parker J., Brock’s Biology of Microorganisms. (Ben-
[136] Williams, H. S. (1904) A History of Science: in Five Vol- jamin Cummings, 2002), ISBN 0-13-066271-2
umes. Volume IV: Modern Development of the Chemical
and Biological Sciences Harper and Brothers (New York) • Da Silva, J.J.R.F. and Williams, R. J. P., The Bi-
Retrieved on 2007-03-26 ological Chemistry of the Elements: The Inorganic
Chemistry of Life. (Clarendon Press, 1991), ISBN
[137] Dubos J. (1951). “Louis Pasteur: Free Lance of 0-19-855598-9
Science, Gollancz. Quoted in Manchester K. L.
(1995) Louis Pasteur (1822–1895)—chance and the pre- • Nicholls, D. G. and Ferguson, S. J., Bioenergetics.
pared mind”. Trends Biotechnol 13 (12): 511–515. (Academic Press Inc., 2002), ISBN 0-12-518121-3
doi:10.1016/S0167-7799(00)89014-9. PMID 8595136.

[138] Kinne-Saffran E, Kinne R (1999). “Vitalism and synthesis

of urea. From Friedrich Wöhler to Hans A. Krebs”. Am J
10.1.14 External links
Nephrol 19 (2): 290–4. doi:10.1159/000013463. PMID
10213830. External links

[139] Eduard Buchner’s 1907 Nobel lecture at http://nobelprize.

org Accessed 2007-03-20 General information

[140] Kornberg H (2000). “Krebs and his trinity of cycles”. Nat • Metabolism, Cellular Respiration and Photosynthe-
Rev Mol Cell Biol 1 (3): 225–8. doi:10.1038/35043073.
sis The Virtual Library of Biochemistry and Cell Bi-
PMID 11252898.
ology at biochemweb.org
[141] Krebs HA, Henseleit K (1932). “Untersuchungen über die
Harnstoffbildung im tierkorper”. Z. Physiol. Chem. 210: • The Biochemistry of Metabolism
33–66. doi:10.1515/bchm2.1932.210.1-2.33.
Krebs H, Johnson W (April 1937). “Metabolism of ke-
• Advanced Animal Metabolism Calculators/ Interac-
tonic acids in animal tissues”. Biochem J 31 (4): 645–60. tive Learning Tools
PMC 1266984. PMID 16746382.
• Microbial metabolism Simple overview. School
level.
10.1.13 Further reading • Metabolic Pathways of Biochemistry Graphical rep-
resentations of major metabolic pathways.
Introductory
• Chemistry for biologists Introduction to the chem-
• Rose, S. and Mileusnic, R., The Chemistry of Life. istry of metabolism. School level.
(Penguin Press Science, 1999), ISBN 0-14-027273-
• Sparknotes SAT biochemistry Overview of bio-
9
chemistry. School level.
• Schneider, E. D. and Sagan, D., Into the Cool: En-
• MIT Biology Hypertextbook Undergraduate-level
ergy Flow, Thermodynamics, and Life. (University
guide to molecular biology.
Of Chicago Press, 2005), ISBN 0-226-73936-8
• Lane, N., Oxygen: The Molecule that Made the Human metabolism
World. (Oxford University Press, USA, 2004),
ISBN 0-19-860783-0
• Topics in Medical Biochemistry Guide to human
metabolic pathways. School level.
Advanced
• http://themedicalbiochemistrypage.org/ THE Med-
• Price, N. and Stevens, L., Fundamentals of Enzy- ical Biochemistry Page] Comprehensive resource on
mology: Cell and Molecular Biology of Catalytic Pro- human metabolism.
teins. (Oxford University Press, 1999), ISBN 0-19-
850229-X Databases
10.1. OVERVIEW OF METABOLISM 189

• Flow Chart of Metabolic Pathways at ExPASy

• IUBMB-Nicholson Metabolic Pathways Chart

• SuperCYP: Database for Drug-Cytochrome-
Metabolism

Metabolic pathways

• Interactive Flow Chart of the Major Metabolic Path-

ways

• Metabolism reference Pathway

• Guide to Glycolysis School level.

• The Nitrogen cycle and Nitrogen fixation at the

Wayback Machine

• Downloadable guide to photosynthesis School level.

• What is Photosynthesis? Collection of photosynthe-
sis articles and resources.
Chapter 11

Carbohydrate metabolism

11.1 Glycolysis Parnas pathway.[8]

The entire glycolysis pathway can be separated into two
phases:[2]
Glycolysis (from glycose, an older term[1] for glucose
+ -lysis degradation) is the metabolic pathway that con-
verts glucose C6 H12 O6 , into pyruvate, CH3 COCOO− + 1. The Preparatory Phase – in which ATP is consumed
H+ . The free energy released in this process is used and is hence also known as the investment phase
to form the high-energy compounds ATP (adenosine 2. The Pay Off Phase – in which ATP is produced.
triphosphate) and NADH (reduced nicotinamide adenine
dinucleotide).[2][3]
Glycolysis is a determined sequence of ten enzyme- 11.1.1 Overview
catalyzed reactions. The intermediates provide entry
The overall reaction of glycolysis is:
points to glycolysis. For example, most monosaccha-
rides, such as fructose and galactose, can be converted The use of symbols in this equation makes it appear not
to one of these intermediates. The intermediates may balanced with respect to oxygen atoms, hydrogen atoms,
also be directly useful. For example, the intermediate and charges. Atom balance is maintained by the two
dihydroxyacetone phosphate (DHAP) is a source of the phosphate (Pᵢ) groups:[9]
glycerol that combines with fatty acids to form fat.
Glycolysis is an oxygen independent metabolic pathway, • Each exists in the form of a hydrogen phosphate an-
meaning that it does not use molecular oxygen (i.e. at- ion (HPO4 2− ), dissociating to contribute 2 H+ over-
mospheric oxygen) for any of its reactions. However all
the products of glycolysis (pyruvate and NADH + H+ ) • Each liberates an oxygen atom when it binds to an
are sometimes disposed of using atmospheric oxygen.[4] ADP (adenosine diphosphate) molecule, contribut-
When molecular oxygen is used in the disposal of the ing 2 O overall
products of glycolysis the processed is usually referred
to as aerobic, whereas if the disposal uses no oxygen the
process is said to be anaerobic.[5] Thus, glycolysis occurs, Charges are balanced by the difference between ADP
and ATP. In the cellular environment, all three hy-
with variations, in nearly all organisms, both aerobic and
anaerobic. The wide occurrence of glycolysis indicates droxyl groups of ADP dissociate into −O− and H+ , giving
ADP3− , and this ion tends to exist in an ionic bond with
that it is one of the most ancient metabolic pathways.[6]
Indeed, the reactions that constitute glycolysis and its Mg2+ , giving ADPMg− . ATP behaves identically except
parallel pathway, the pentose phosphate pathway, occur that it has four hydroxyl groups, giving ATPMg2− . When
metal-catalyzed under the oxygen-free conditions of the these differences along with the true charges on the two
Archean oceans, also in the absence of enzymes.[7] Gly- phosphate groups are considered together, the net charges
colysis could thus have originated from chemical con- of −4 on each side are balanced.
straints of the prebiotic world. For simple fermentations, the metabolism of one
Glycolysis occurs in most organisms in the cytosol of the molecule of glucose to two molecules of pyruvate has a
cell. The most common type of glycolysis is the Embden– net yield of two molecules of ATP. Most cells will then
Meyerhof–Parnas (EMP pathway), which was discovered carry out further reactions to 'repay' the used NAD+ and
by Gustav Embden, Otto Meyerhof, and Jakub Karol Par- produce a final product of ethanol or lactic acid. Many
nas. Glycolysis also refers to other pathways, such as the bacteria use inorganic compounds as hydrogen acceptors
Entner–Doudoroff pathway and various heterofermenta- to regenerate the NAD+ .
tive and homofermentative pathways. However, the dis- Cells performing aerobic respiration synthesize much
cussion here will be limited to the Embden–Meyerhof– more ATP, but not as part of glycolysis. These further

190
11.1. GLYCOLYSIS 191

aerobic reactions use pyruvate and NADH + H+ from gly- plished by inhibiting or activating the enzymes that are
colysis. Eukaryotic aerobic respiration produces approx- involved. The steps that are regulated may be determined
imately 34 additional molecules of ATP for each glucose by calculating the change in free energy, ΔG, for each
molecule, however most of these are produced by a vastly step. If a step’s products and reactants are in equilibrium,
different mechanism to the substrate-level phosphoryla- then the step is assumed not to be regulated. Since the
tion in glycolysis. change in free energy is zero for a system at equilibrium,
The lower-energy production, per glucose, of anaero- any step with a free energy change near zero is not being
bic respiration relative to aerobic respiration, results in regulated. If a step is being regulated, then that step’s en-
zyme is not converting reactants into products as fast as
greater flux through the pathway under hypoxic (low-
oxygen) conditions, unless alternative sources of anaer- it could, resulting in a build-up of reactants, which would
be converted to products if the enzyme were operating
obically oxidizable substrates, such as fatty acids, are
found. faster. Since the reaction is thermodynamically favorable,
the change in free energy for the step will be negative. A
step with a large negative change in free energy is assumed
11.1.2 Elucidation of the pathway to be regulated.

In 1860, Louis Pasteur discovered that microorganisms

Free energy changes
are responsible for fermentation. In 1897, Eduard Buch-
ner found that extracts of certain cells can cause fermen- The change in free energy, ΔG, for each step in the glycol-
tation. In 1905, Arthur Harden and William Young along ysis pathway can be calculated using ΔG = ΔG°' + RTln
with Nick Sheppard determined that a heat-sensitive Q, where Q is the reaction quotient. This requires know-
high-molecular-weight subcellular fraction (the enzymes) ing the concentrations of the metabolites. All of these
and a heat-insensitive low-molecular-weight cytoplasm values are available for erythrocytes, with the exception
fraction (ADP, ATP and NAD+ and other cofactors) are of the concentrations of NAD+ and NADH. The ratio
required together for fermentation to proceed. The de- of NAD+ to NADH in the cytoplasm is approximately
tails of the pathway were eventually determined by 1940, 1000, which makes the oxidation of glyceraldehyde-3-
with a major input from Otto Meyerhof and some years phosphate (step 6) more favourable.
later by Luis Leloir. The biggest difficulties in determin-
ing the intricacies of the pathway were due to the very Using the measured concentrations of each step, and
short lifetime and low steady-state concentrations of the the standard free energy changes, the actual free energy
intermediates of the fast glycolytic reactions. change can be calculated. (Neglecting this is very com-
mon - the delta G of ATP hydrolysis in cells is not the
standard free energy change of ATP hydrolysis quoted in
11.1.3 Sequence of reactions textbooks).
From measuring the physiological concentrations of
Preparatory phase metabolites in an erythrocyte it seems that about seven
of the steps in glycolysis are in equilibrium for that cell
The first five steps are regarded as the preparatory (or
type. Three of the steps — the ones with large negative
investment) phase, since they consume energy to con-
free energy changes — are not in equilibrium and are re-
vert the glucose into two three-carbon sugar phosphates[2]
ferred to as irreversible; such steps are often subject to
(G3P).
regulation.
Step 5 in the figure is shown behind the other steps,
Pay-off phase because that step is a side-reaction that can de-
crease or increase the concentration of the intermedi-
The second half of glycolysis is known as the pay-off ate glyceraldehyde-3-phosphate. That compound is con-
phase, characterised by a net gain of the energy-rich verted to dihydroxyacetone phosphate by the enzyme
molecules ATP and NADH.[2] Since glucose leads to two triose phosphate isomerase, which is a catalytically per-
triose sugars in the preparatory phase, each reaction in the fect enzyme; its rate is so fast that the reaction can be as-
pay-off phase occurs twice per glucose molecule. This sumed to be in equilibrium. The fact that ΔG is not zero
yields 2 NADH molecules and 4 ATP molecules, leading indicates that the actual concentrations in the erythrocyte
to a net gain of 2 NADH molecules and 2 ATP molecules are not accurately known.
from the glycolytic pathway per glucose.

Biochemical logic
11.1.4 Regulation
The existence of more than one point of regulation indi-
Glycolysis is regulated by slowing down or speeding up cates that intermediates between those points enter and
certain steps in the glycolysis pathway. This is accom- leave the glycolysis pathway by other processes. For ex-
192 CHAPTER 11. CARBOHYDRATE METABOLISM

ample, in the first regulated step, hexokinase converts tal part of homeostasis. In liver cells, extra G6P (glucose-
glucose into glucose-6-phosphate. Instead of contin- 6-phosphate) may be converted to G1P for conversion to
uing through the glycolysis pathway, this intermediate glycogen, or it is alternatively converted by glycolysis to
can be converted into glucose storage molecules, such acetyl-CoA and then citrate. Excess citrate is exported
as glycogen or starch. The reverse reaction, break- to the cytosol, where ATP citrate lyase will regenerate
ing down, e.g., glycogen, produces mainly glucose-6- acetyl-CoA and OAA. The acetyl-CoA is then used for
phosphate; very little free glucose is formed in the re- fatty acid synthesis and cholesterol synthesis, two impor-
action. The glucose-6-phosphate so produced can enter tant ways of utilizing excess glucose when its concentra-
glycolysis after the first control point. tion is high in blood. Liver contains both hexokinase and
In the second regulated step (the third step of glycolysis), glucokinase; both catalyse the phosphorylation of glu-
cose to G6P but the latter is not inhibited by G6P. Thus,
phosphofructokinase converts fructose-6-phosphate into
fructose-1,6-bisphosphate, which then is converted into glucokinase allows glucose to be converted into glyco-
gen, fatty acids, and cholesterol even as G6P accumulates
glyceraldehyde-3-phosphate and dihydroxyacetone phos-
phate. The dihydroxyacetone phosphate can be removed in hepatocytes.[15] This is important when blood glucose
from glycolysis by conversion into glycerol-3-phosphate, levels are high. During hypoglycemia, the glycogen can
which can be used to form triglycerides.[14] On the con- be converted back to G6P and then converted to glucose
verse, triglycerides can be broken down into fatty acids by the liver-specific enzyme glucose 6-phosphatase and
and glycerol; the latter, in turn, can be converted into di- released into the blood without taking up the low con-
hydroxyacetone phosphate, which can enter glycolysis af- centration of glucose it releases. This reverse reaction is
ter the second control point. an important role of liver cells to maintain blood sugars
levels during fasting. This is critical for brain function,
since the brain utilizes glucose as an energy source under
Regulation most conditions.

The three regulated enzymes are hexokinase,

phosphofructokinase, and pyruvate kinase.
The flux through the glycolytic pathway is adjusted in re-
sponse to conditions both inside and outside the cell. The
rate in liver is regulated to meet major cellular needs:
(1) the production of ATP, (2) the provision of building
blocks for biosynthetic reactions, and (3) to lower blood
glucose, one of the major functions of the liver. When
blood sugar falls, glycolysis is halted in the liver to allow
the reverse process, gluconeogenesis. In glycolysis, the
reactions catalyzed by hexokinase, phosphofructokinase,
and pyruvate kinase are effectively irreversible in most
organisms. In metabolic pathways, such enzymes are po-
tential sites of control, and all three enzymes serve this
purpose in glycolysis.

Bacillus stearothermophilus phosphofructokinase. PDB: 6PFK .

Phosphofructokinase Phosphofructokinase is an im-

portant control point in the glycolytic pathway, since it is
one of the irreversible steps and has key allosteric effec-
tors, AMP and fructose 2,6-bisphosphate (F2,6BP).
Fructose 2,6-bisphosphate (F2,6BP) is a very potent acti-
vator of phosphofructokinase (PFK-1), which is synthe-
sized when F6P is phosphorylated by a second phospho-
fructokinase (PFK2). In liver, when blood sugar is low
and glucagon elevates cAMP, PFK2 is phosphorylated by
protein kinase A. The phosphorylation inactivates PFK2,
and another domain on this protein becomes active as
Yeast hexokinase B. PDB: 1IG8 . fructose bisphosphatase-2, which converts F2,6BP back
to F6P. Both glucagon and epinephrine cause high lev-
Hexokinase In animals, regulation of blood glucose els of cAMP in the liver. The result of lower levels
levels by the pancreas in conjunction with the liver is a vi- of liver fructose-2,6-bisphosphate is a decrease in activ-
11.1. GLYCOLYSIS 193

ity of phosphofructokinase and an increase in activity of Anoxic regeneration of NAD+

fructose 1,6-bisphosphatase, so that gluconeogenesis (in
essence, “glycolysis in reverse”) is favored. This is con- One method of doing this is to simply have the pyruvate
sistent with the role of the liver in such situations, since do the oxidation; in this process, pyruvate is converted
the response of the liver to these hormones is to release to lactate (the conjugate base of lactic acid) in a process
glucose to the blood. called lactic acid fermentation:
ATP competes with AMP for the allosteric effector
site on the PFK enzyme. ATP concentrations in cells Pyruvate + NADH + H+ → Lactate + NAD+
are much higher than those of AMP, typically 100-fold
higher,[16] but the concentration of ATP does not change
more than about 10% under physiological conditions, This process occurs in the bacteria involved in making
whereas a 10% drop in ATP results in a 6-fold increase yogurt (the lactic acid causes the milk to curdle). This
in AMP.[17] Thus, the relevance of ATP as an allosteric process also occurs in animals under hypoxic (or partially
effector is questionable. An increase in AMP is a conse- anaerobic) conditions, found, for example, in overworked
quence of a decrease in energy charge in the cell. muscles that are starved of oxygen, or in infarcted heart
Citrate inhibits phosphofructokinase when tested in vitro muscle cells. In many tissues, this is a cellular last resort
by enhancing the inhibitory effect of ATP. However, it is for energy; most animal tissue cannot tolerate anaerobic
doubtful that this is a meaningful effect in vivo, because conditions for an extended period of time.
citrate in the cytosol is utilized mainly for conversion to Some organisms, such as yeast, convert NADH back to
acetyl-CoA for fatty acid and cholesterol synthesis. NAD+ in a process called ethanol fermentation. In this
process, the pyruvate is converted first to acetaldehyde
and carbon dioxide, then to ethanol.
Lactic acid fermentation and ethanol fermentation can
occur in the absence of oxygen. This anaerobic fermen-
tation allows many single-cell organisms to use glycolysis
as their only energy source.
Anoxic regeneration of NADH is only an effective means
of energy production during short, intense exercise, pro-
viding energy for a period ranging from 10 seconds to 2
minutes and is dominant from about 10–30 seconds dur-
ing a maximal effort. It replenishes very quickly over
this period and produces 2 ATP molecules per glucose
molecule, or about 5% of glucose’s energy potential (38
ATP molecules in bacteria). The speed at which ATP is
produced is about 100 times that of oxidative phospho-
rylation. The pH in the cytoplasm quickly drops when
hydrogen ions accumulate in the muscle, eventually in-
hibiting enzymes involved in glycolysis.
Yeast pyruvate kinase. PDB: 1A3W .
The burning sensation in muscles during hard exercise
Pyruvate kinase This enzyme catalyzes the last step can be attributed to the production of hydrogen ions dur-
of glycolysis, in which pyruvate and ATP are formed. ing a shift to lactic acid fermentation as oxygen is con-
Regulation of this enzyme is discussed in the main topic, verted to carbon dioxide by aerobic respiration faster than
pyruvate kinase. the body can replenish it. These hydrogen ions form a part
of lactic acid along with lactate. The body falls back on
this less efficient but faster method of producing ATP un-
11.1.5 Post-glycolysis processes der low oxygen conditions. This is thought to have been
the primary means of energy production in earlier organ-
The overall process of glycolysis is: isms before oxygen was at high concentration in the atmo-
sphere and thus would represent a more ancient form of
Glucose + 2 NAD+ + 2 ADP + 2 Pᵢ → 2 Pyru-
energy production in cells. The liver later gets rid of this
vate + 2 NADH + 2 H+ + 2 ATP + 2 H2 O
excess lactate by transforming it back into an important
If glycolysis were to continue indefinitely, all of the glycolytic intermediate called pyruvate; see Cori cycle.
NAD+ would be used up, and glycolysis would stop. To Fermenation of pyruvate to lactate is sometimes also
allow glycolysis to continue, organisms must be able to called “anaerobic glycolysis”, however, glycolysis ends
oxidize NADH back to NAD+ . How this is performed with the production of pyruvate regardless in the pres-
depends on which external electron acceptor is available. ence or absence of oxygen.
194 CHAPTER 11. CARBOHYDRATE METABOLISM

Anaerobic respiration Pyruvate can enter the mitochondrion to boost the

amount of oxaloacetate available to combine with
In the above two examples of fermentation, NADH is ox- acetyl CoA in the citric acid cycle
idized by transferring two electrons to pyruvate. How-
ever, anaerobic bacteria use a wide variety of compounds Pyruvate molecules produced by glycolysis are actively
as the terminal electron acceptors in cellular respiration: transported across the inner mitochondrial membrane,
nitrogenous compounds, such as nitrates and nitrites; sul- and into the matrix where they can either be oxidized
fur compounds, such as sulfates, sulfites, sulfur dioxide, and combined with coenzyme A to form CO2 , acetyl-
and elemental sulfur; carbon dioxide; iron compounds; CoA, and NADH,[15] or they can be carboxylated (by
manganese compounds; cobalt compounds; and uranium pyruvate carboxylase) to form oxaloacetate. This latter
compounds. reaction ”fills up” the amount of oxaloacetate in the citric
acid cycle, and is therefore an anaplerotic reaction (from
the Greek meaning to “fill up”), increasing the cycle’s ca-
Aerobic respiration
pacity to metabolize acetyl-CoA when the tissue’s energy
needs (e.g. in heart and skeletal muscle) are suddenly in-
In aerobic organisms, a complex mechanism has been de-
creased by activity.[19] In the citric acid cycle all the in-
veloped to use the oxygen in air as the final electron ac-
termediates (e.g. citrate, iso-citrate, alpha-ketoglutarate,
ceptor.
succinate, fumarate, malate and oxaloacetate) are regen-
erated during each turn of the cycle. Adding more of
• First, pyruvate is converted to acetyl-CoA and CO2
any of these intermediates to the mitochondrion there-
within the mitochondria in a process called pyruvate
fore means that that additional amount is retained within
decarboxylation.
the cycle, increasing all the other intermediates as one is
• Second, the acetyl-CoA enters the citric acid cycle, converted into the other. Hence the addition of oxaloac-
also known as Krebs Cycle, where it is fully oxidized etate greatly increases the amounts of all the citric acid
to carbon dioxide and water, producing yet more intermediates, thereby increasing the cycle’s capacity to
NADH. metabolize acetyl CoA, converting its acetate component
into CO2 and water, with the release of enough energy
• Third, the NADH is oxidized to NAD by the +
to form 11 ATP and 1 GTP molecule for each additional
electron transport chain, using oxygen as the final
molecule of acetyl CoA that combines with oxaloacetate
electron acceptor. This process creates a hydrogen
in the cycle.[19]
ion gradient across the inner membrane of the mi-
tochondria.
• Fourth, the proton gradient is used to produce about 11.1.6 Intermediates for other pathways =
2.5 ATP for every NADH oxidized in a process
called oxidative phosphorylation. This article concentrates on the catabolic role of glycoly-
sis with regard to converting potential chemical energy to
usable chemical energy during the oxidation of glucose to
Glycolytic end products are used in the conversion of pyruvate. Many of the metabolites in the glycolytic path-
carbohydrates into fatty acids and cholesterol way are also used by anabolic pathways, and, as a conse-
quence, flux through the pathway is critical to maintain a
The pyruvate produced by glycolysis is an important in- supply of carbon skeletons for biosynthesis.
termediary in the conversion of carbohydrates into fatty
acids and cholesterol.[18] This occurs via the conversion In addition, not all carbon entering the pathway leaves as
of pyruvate into acetyl-CoA in the mitochondrion. How- pyruvate and may be extracted at earlier stages to provide
ever, this acetyl CoA needs to be transported into cy- carbon compounds for other pathways.
tosol where the synthesis of fatty acids and cholesterol These metabolic pathways are all strongly reliant on gly-
occurs. This cannot occur directly. To obtain cytoso- colysis as a source of metabolites: and many more.
lic acetyl-CoA, citrate (produced by the condensation
of acetyl CoA with oxaloacetate) is removed from the
• Gluconeogenesis
citric acid cycle and carried across the inner mitochon-
drial membrane into the cytosol.[18] There it is cleaved • Lipid metabolism (glycerol synthesis, and the post-
by ATP citrate lyase into acetyl-CoA and oxaloacetate. glycolytic production of fatty acids and cholesterol)
The oxaloacetate can be used for gluconeogenesis (in the
liver), or it can be returned into mitochondrion as malate. • Pentose phosphate pathway
The cytosolic acetyl-CoA is carboxylated by acetyl CoA
carboxylase into malonyl CoA, the first committed step in • Citric acid cycle, a post-glycolytic process which in
the synthesis of fatty acids and the production of choles- turn leads to:
terol. Cholesterol can, in turn, be used to synthesize the
steroid hormones, bile salts, and vitamin D.[15][18] • Amino acid synthesis
11.1. GLYCOLYSIS 195

• Nucleotide synthesis top:828px; background:transparent; border-top:3px

• Tetrapyrrole synthesis blue solid"></div>]]
[[<div style="display:block; width:63.
6666666666666px; height:0px; overflow:hidden;
From an anabolic metabolism perspective, the NADH has position:relative; left:695.6666666666667px;
a role to drive synthetic reactions, doing so by directly top:1197px; background:transparent; border-top:3px
or indirectly reducing the pool of NADP+ in the cell to blue solid"></div>]]
NADPH, which is another important reducing agent for [[<div style="display:block; width:100px; height:0px;
biosynthetic pathways in a cell. overflow:hidden; position:relative; left:801.0px;
top:1029.66666666667px; background:transparent;
border-top:3px blue solid"></div>]]
11.1.7 Glycolysis in disease [[<div style="display:block; width:60px;
height:0px; overflow:hidden; position:relative;
Genetic diseases left:555.3333333333333px; top:991.166666666667px;
background:transparent; border-top:3px blue
Glycolytic mutations are generally rare due to importance solid"></div>]]
of the metabolic pathway, this means that the majority of [[<div style="display:block; width:100px; height:0px;
occurring mutations result in an inability for the cell to overflow:hidden; position:relative; left:386.0px;
respire, and therefore cause the death of the cell at an top:594px; background:transparent; border-top:3px
early stage. However, some mutations are seen with one blue solid"></div>]]
notable example being Pyruvate kinase deficiency, lead- [[<div style="display:block; width:100px; height:0px;
ing to chronic hemolytic anemia. overflow:hidden; position:relative; left:723.0px;
top:1086px; background:transparent; border-top:3px
Cancer blue solid"></div>]]
[[<div style="display:block; width:60px; height:0px;
Malignant rapidly growing tumor cells typically have gly- overflow:hidden; position:relative; left:386.0px;
colytic rates that are up to 200 times higher than those top:140.655462184874px; background:transparent;
of their normal tissues of origin. This phenomenon was border-top:3px blue solid"></div>]]
first described in 1930 by Otto Warburg and is referred [[<div style="display:block; width:60px;
to as the Warburg effect. The Warburg hypothesis claims height:0px; overflow:hidden; position:relative;
that cancer is primarily caused by dysfunctionality in mi- left:386.9999999999999px; top:882.666666666667px;
tochondrial metabolism, rather than because of uncon- background:transparent; border-top:3px blue
trolled growth of cells. A number of theories have been solid"></div>]]
advanced to explain the Warburg effect. One such theory [[<div style="display:block; width:100px;
suggests that the increased glycolysis is a normal protec- height:0px; overflow:hidden; position:relative;
tive process of the body and that malignant change could left:477.6500000000001px; top:942.5px; background:
be primarily caused by energy metabolism.[20] transparent; border-top:3px blue solid"></div>]]
[[<div style="display:block; width:60px; height:
This high glycolysis rate has important medical ap- 0px; overflow:hidden; position:relative; left:
plications, as high aerobic glycolysis by malignant tu- 386.99999999999994px; top:432.616246498599px;
mors is utilized clinically to diagnose and monitor treat- background:transparent; border-top:3px blue
ment responses of cancers by imaging uptake of 2- solid"></div>]]
18
F-2-deoxyglucose (FDG) (a radioactive modified hex- [[<div style="display:block; width:60px;
okinase substrate) with positron emission tomography height:0px; overflow:hidden; position:relative;
(PET).[21][22] left:384.8991596638656px; top:277.627450980392px;
There is ongoing research to affect mitochondrial background:transparent; border-top:3px blue
metabolism and treat cancer by reducing glycolysis and solid"></div>]]
thus starving cancerous cells in various new ways, includ- [[<div style="display:block; width:60px; height:0px;
ing a ketogenic diet.[23] overflow:hidden; position:relative; left:386.0px;
top:200.655462184874px; background:transparent;
border-top:3px blue solid"></div>]]
11.1.8 Interactive pathway map [[<div style="display:block; width:100px; height:0px;
overflow:hidden; position:relative; left:222.5px;
Click on genes, proteins and metabolites below to link to top:390.333333333333px; background:transparent;
respective articles. [§ 1] border-top:3px blue solid"></div>]]
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196 CHAPTER 11. CARBOHYDRATE METABOLISM

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[[<div style="display:block; width:60px; transparent; border-top:3px blue solid"></div>]]
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solid"></div>]] background:transparent; border-top:3px blue
[[<div style="display:block; width:60px; solid"></div>]]
height:0px; overflow:hidden; position:relative; [[<div style="display:block; width:63.
left:386.9999999999999px; top:843.666666666667px; 6666666666666px; height:0px; overflow:hidden;
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solid"></div>]] top:1217px; background:transparent; border-top:3px
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0px; overflow:hidden; position:relative; left: [[<div style="display:block; width:100px;
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11.1. GLYCOLYSIS 197

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border-top:3px blue solid"></div>]] [[<div style="display:block; width:63.
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solid"></div>]] background:transparent; border-top:3px blue
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overflow:hidden; position:relative; left:386.0px; [[<div style="display:block; width:60px; height:
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0px; overflow:hidden; position:relative; left: solid"></div>]]
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height:0px; overflow:hidden; position:relative; solid"></div>]]
left:119.22128851540629px; top:306.67787114846px; [[<div style="display:block; width:60px; height:
198 CHAPTER 11. CARBOHYDRATE METABOLISM

0px; overflow:hidden; position:relative; left: 11.1.9 Alternative nomenclature

104.29411764705867px; top:932.333333333333px;
background:transparent; border-top:3px blue Some of the metabolites in glycolysis have alternative
solid"></div>]] names and nomenclature. In part, this is because some of
[[<div style="display:block; width:60px; height:0px; them are common to other pathways, such as the Calvin
overflow:hidden; position:relative; left:89.0px; cycle.
top:1044.66666666667px; background:transparent;
border-top:3px blue solid"></div>]]
[[<div style="display:block; width:60px; height:0px; 11.1.10 See also
overflow:hidden; position:relative; left:89.0px;
top:1064.66666666667px; background:transparent; • Carbohydrate catabolism
border-top:3px blue solid"></div>]]
[[<div style="display:block; width:60px; height:0px; • Citric acid cycle
overflow:hidden; position:relative; left:89.0px;
• Cori cycle
top:1104.66666666667px; background:transparent;
border-top:3px blue solid"></div>]] • Fermentation (biochemistry)
[[<div style="display:block; width:60px; height:0px;
overflow:hidden; position:relative; left:89.0px; • Gluconeogenesis
top:1084.66666666667px; background:transparent;
border-top:3px blue solid"></div>]] • Glycolytic oscillation
[[<div style="display:block; width:100px;
height:0px; overflow:hidden; position:relative; • Pentose phosphate pathway
left:197.3666666666667px; top:1129.36666666667px;
• Pyruvate decarboxylation
background:transparent; border-top:3px blue
solid"></div>]] • Triose kinase
[[<div style="display:block; width:193px;
height:0px; overflow:hidden; position:relative;
left:539.9495798319327px; top:314.941176470588px; 11.1.11 References
background:transparent; border-top:3px blue
solid"></div>]] [1] Webster’s New International Dictionary of the English
[[<div style="display:block; width:163px; Language, 2nd ed. (1937) Merriam Company, Spring-
height:0px; overflow:hidden; position:relative; field, Mass.
left:541.9495798319327px; top:358.941176470588px;
background:transparent; border-top:3px green [2] Glycolysis – Animation and Notes
solid"></div>]]
[3] Bailey, Regina. “10 Steps of Glycolysis”.
[[<div style="display:block; width:95px; height:0px;
overflow:hidden; position:relative; left:870.0px; [4] Stryer, Lubert (1995). “Glycolysis.”. In: Biochemistry.
top:1149px; background:transparent; border-top:3px (Fourth ed.). New York: W.H. Freeman and Company.
blue solid"></div>]] pp. 483–508. ISBN 0 7167 2009 4.
[[<div style="display:block; width:80px; height:0px;
overflow:hidden; position:relative; left:593.0px; [5] Anderson, Douglas M., ed. (2003). Dorland’s Illustrated
Medical Dictionary (30th ed.). Philadelphia, PA: Saun-
top:1076px; background:transparent; border-top:3px
ders. pp. 35, 71. ISBN 0 8089 2288 2.
green solid"></div>]]
[[<div style="display:block; width:80px; height:0px; [6] Romano, AH; Conway, T (1996). “Evolution of car-
overflow:hidden; position:relative; left:593.0px; bohydrate metabolic pathways”. Res Microbiol 147 (6–
top:1096px; background:transparent; border-top:3px 7): 448–55. doi:10.1016/0923-2508(96)83998-2. PMID
blue solid"></div>]] 9084754.

[7] Keller; Ralser; Turchyn (Apr 2014). “Non-enzymatic gly-

|{{{bSize}}}px|alt=Glycolysis and Gluconeogenesis colysis and pentose phosphate pathway-like reactions in
edit]] a plausible Archean ocean”. Mol Syst Biol. 10: 725.
doi:10.1002/msb.20145228. PMID 24771084.
File:WP534.png
[8] Kim BH, Gadd GM. (2011) Bacterial Physiology and
Glycolysis and Gluconeogenesis edit Metabolism, 3rd edition.

[9] Lane, A. N.; Fan, T. W. -M.; Higashi, R. M.

(2009). “Metabolic acidosis and the importance of
[1] The interactive pathway map can be edited at WikiPath- balanced equations”. Metabolomics 5 (2): 163–165.
ways: “GlycolysisGluconeogenesis_WP534”. doi:10.1007/s11306-008-0142-2.
11.2. GLUCONEOGENESIS 199

[10] Reeves, R. E.; South D. J.; Blytt H. J.; Warren L. • Metabolism, Cellular Respiration and Photosynthe-
G. (1974). “Pyrophosphate: D-fructose 6-phosphate 1- sis - The Virtual Library of Biochemistry and Cell
phosphotransferase. A new enzyme with the glycolytic Biology at biochemweb.org
function 6-phosphate 1-phosphotransferase”. J Biol Chem
249 (24): 7737–7741. PMID 4372217. • notes on glycolysis at rahulgladwin.com
[11] Selig, M.; Xavier K. B.; Santos H.; Schönheit P. (1997). • The chemical logic behind glycolysis at ufp.pt
“Comparative analysis of Embden-Meyerhof and Entner-
Doudoroff glycolytic pathways in hyperthermophilic ar- • Expasy biochemical pathways poster at ExPASy
chaea and the bacterium Thermotoga". Arch Microbiol
167 (4): 217–232. PMID 9075622. • MedicalMnemonics.com: 317 5468
[12] Garrett, R.; Grisham, C. M. (2005). Biochemistry (3rd • metpath: Interactive representation of glycolysis
ed.). Belmont, CA: Thomson Brooks/Cole. p. 584. ISBN
0-534-49033-6.

[13] Garrett, R.; Grisham, C. M. (2005). Biochemistry (3rd 11.2 Gluconeogenesis

ed.). Belmont, CA: Thomson Brooks/Cole. pp. 582–583.
ISBN 0-534-49033-6.
Not to be confused with Glycogenesis or
[14] Berg, J. M.; Tymoczko, J. L.; Stryer, L. (2007). Bio- Glyceroneogenesis.
chemistry (6th ed.). New York: Freeman. p. 622. ISBN
0716787245.
Gluconeogenesis (GNG) is a metabolic pathway that re-
[15] Voet, Donald; Judith G. Voet; Charlotte W. Pratt (2006). sults in the generation of glucose from non-carbohydrate
Fundamentals of Biochemistry, 2nd Edition. John Wiley carbon substrates such as pyruvate, lactate, glycerol, and
and Sons, Inc. pp. 547, 556. ISBN 0-471-21495-7. glucogenic amino acids. While primarily odd-chain fatty
acids can be converted into glucose, it is possible for at
[16] Beis, I.; Newsholme, E. A. (1975). “The contents of ade-
least some even-chain fatty acids.
nine nucleotides, phosphagens and some glycolytic inter-
mediates in resting muscles from vertebrates and inverte- It is one of the two main mechanisms used by humans
brates”. Biochem J 152: 23–32. and many other animals to maintain blood glucose lev-
els, avoiding low blood glucose level (hypoglycemia).
[17] Voet D., and Voet J. G. (2004). Biochemistry 3rd Edition
(New York, John Wiley & Sons, Inc.). The other means of maintaining blood glucose levels is
through the degradation of glycogen (glycogenolysis).[1]
[18] Stryer, Lubert (1995). “Fatty acid metabolism.”. In: Bio-
Gluconeogenesis is a ubiquitous process, present
chemistry. (Fourth ed.). New York: W.H. Freeman and
Company. pp. 603–628. ISBN 0 7167 2009 4.
in plants, animals, fungi, bacteria, and other
microorganisms.[2] In vertebrates, gluconeogenesis
[19] Stryer, Lubert (1995). “Citric acid cycle.”. In: Biochem- takes place mainly in the liver and, to a lesser extent,
istry. (Fourth ed.). New York: W.H. Freeman and Com- in the cortex of the kidneys. In ruminants, this tends
pany. pp. 509–527, 569–579, 614–616, 638–641, 732– to be a continuous process.[3] In many other animals,
735, 739–748, 770–773. ISBN 0 7167 2009 4. the process occurs during periods of fasting, starvation,
[20] “What is Cancer?". Retrieved September 8, 2012. low-carbohydrate diets, or intense exercise. The process
is highly endergonic until it is coupled to the hydrolysis of
[21] “PET Scan: PET Scan Info Reveals ...”. Retrieved De- ATP or GTP, effectively making the process exergonic.
cember 5, 2005. For example, the pathway leading from pyruvate to
glucose-6-phosphate requires 4 molecules of ATP and 2
[22] “4320139 549..559” (PDF). Retrieved December 5,
2005.
molecules of GTP to proceed spontaneously. Gluconeo-
genesis is often associated with ketosis. Gluconeogenesis
[23] Maroon, J; Bost J; Amos A; Zuccoli G (May 2013). is also a target of therapy for type 2 diabetes, such as
“Restricted Calorie Ketogenic Diet for the Treatment of the antidiabetic drug, metformin, which inhibits glucose
Glioblastoma Multiforme”. Journal of Child Neurology. formation and stimulates glucose uptake by cells.[4] In
doi:10.1177/0883073813488670. ruminants, because metabolizable dietary carbohydrates
tend to be metabolized by rumen organs, gluconeogene-
sis occurs regardless of fasting, low-carbohydrate diets,
11.1.12 External links exercise, etc.[5]
• A Detailed Glycolysis Animation provided by
IUBMB (Adobe Flash Required) 11.2.1 Precursors
• The Glycolytic enzymes in Glycolysis at RCSB PDB
In humans the main gluconeogenic precursors are lactate,
• Glycolytic cycle with animations at wdv.com glycerol (which is a part of the triacylglycerol molecule),
200 CHAPTER 11. CARBOHYDRATE METABOLISM

(platypus) and marsupials (opossum) but not placental

mammals. Genes for isocitrate lyase are found only in
nematodes, in which, it is apparent, they originated in
horizontal gene transfer from bacteria.
The existence of glyoxylate cycles in humans has not been
established, and it is widely held that fatty acids cannot
be converted to glucose in humans directly. However,
carbon-14 has been shown to end up in glucose when it
is supplied in fatty acids.[13] Despite these findings, it is
considered unlikely that the 2-carbon acetyl-CoA derived
from the oxidation of fatty acids would produce a net yield
of glucose via the citric acid cycle - however, acetyl-CoA
can be converted into pyruvate and lactate through the
Catabolism of proteinogenic amino acids. Amino acids are ketogenic pathway.[10][14] Put simply, acetic acid (in the
classified according the abilities of their products to enter form of acetyl-CoA) is used to partially produce glucose;
gluconeogenesis:[6] acetyl groups can only form part of the glucose molecules
(not the 5th carbon atom) and require extra substrates
• Glucogenic amino acids have this ability (such as pyruvate) in order to form the rest of the glu-
• Ketogenic amino acids do not. These products may still be cose molecule. But a roundabout pathway does lead
used for ketogenesis or lipid synthesis. from acetyl-coA to pyruvate, via acetoacetate, acetone,
• Some amino acids are catabolized into both glucogenic and hydroxyacetone (acetol) and then either propylene glycol
ketogenic products. or methylglyoxal.[14][15][16]

11.2.2 Location
alanine and glutamine. Altogether, they account for over
90% of the overall gluconeogenesis.[7] Other glucogenic In mammals, gluconeogenesis is restricted to the liver,[17]
amino acids as well as all citric acid cycle interme- the kidney[17] and possibly the intestine.[18] However
diates, the latter through conversion to oxaloacetate, these organs use somewhat different gluconeogenic pre-
can also function as substrates for gluconeogenesis.[8] cursors. The liver uses primarily lactate, alanine and
In ruminants, propionate is the principal gluconeogenic glycerol while the kidney uses lactate, glutamine and
substrate.[5][9] glycerol.[19] Propionate is the principal substrate for glu-
coneogenesis in the ruminant liver, and the ruminant liver
Lactate is transported back to the liver where it is con- may make increased use of gluconeogenic amino acids,
verted into pyruvate by the Cori cycle using the enzyme e.g. alanine, when glucose demand is increased.[20] The
lactate dehydrogenase. Pyruvate, the first designated sub- capacity of liver cells to use lactate for gluconeogene-
strate of the gluconeogenic pathway, can then be used sis declines from the preruminant stage to the ruminant
to generate glucose.[8] Transamination or deamination of
stage in calves and lambs.[21] In sheep kidney tissue, very
amino acids facilitates entering of their carbon skeleton high rates of gluconeogenesis from propionate have been
into the cycle directly (as pyruvate or oxaloacetate), or
observed.[22] The intestine uses mostly glutamine and
indirectly via the citric acid cycle. glycerol.[18]
Whether even-chain fatty acids can be converted into In all species, the formation of oxaloacetate from
glucose in animals has been a longstanding question in pyruvate and TCA cycle intermediates is restricted
biochemistry.[10] It is known that odd-chain fatty acids to the mitochondrion, and the enzymes that convert
can be oxidized to yield propionyl-CoA, a precursor Phosphoenolpyruvic acid (PEP) to glucose are found
for succinyl-CoA, which can be converted to pyruvate in the cytosol.[23] The location of the enzyme that
and enter into gluconeogenesis. In plants, specifically links these two parts of gluconeogenesis by converting
seedlings, the glyoxylate cycle can be used to convert fatty oxaloacetate to PEP—PEP carboxykinase (PEPCK)—is
acids (acetate) into the primary carbon source of the or- variable by species: it can be found entirely within the
ganism. The glyoxylate cycle produces four-carbon di- mitochondria, entirely within the cytosol, or dispersed
carboxylic acids that can enter gluconeogenesis.[8] evenly between the two, as it is in humans.[23] Transport
In 1995, researchers identified the glyoxylate cycle of PEP across the mitochondrial membrane is accom-
in nematodes.[11] In addition, the glyoxylate enzymes plished by dedicated transport proteins; however no such
malate synthase and isocitrate lyase have been found in proteins exist for oxaloacetate.[23] Therefore, in species
animal tissues.[12] Genes coding for malate synthase have that lack intra-mitochondrial PEPCK, oxaloacetate must
been identified in other metazoans including arthropods, be converted into malate or aspartate, exported from the
echinoderms, and even some vertebrates. Mam- mitochondrion, and converted back into oxaloacetate in
mals found to possess these genes include monotremes order to allow gluconeogenesis to continue.[23]
11.2. GLUCONEOGENESIS 201

• Oxaloacetate is reduced to malate using NADH, a

step required for its transportation out of the mito-
chondria.

• Malate is oxidized to oxaloacetate using NAD+ in

the cytosol, where the remaining steps of gluconeo-
genesis take place.

• Oxaloacetate is decarboxylated and then phospho-

rylated to form phosphoenolpyruvate using the en-
zyme PEPCK. A molecule of GTP is hydrolyzed to
GDP during this reaction.

• The next steps in the reaction are the same

as reversed glycolysis. However, fructose 1,6-
bisphosphatase converts fructose 1,6-bisphosphate
to fructose 6-phosphate, using one water molecule
and releasing one phosphate (in glycolysis
phosphofructokinase 1 converts F6P to F1,6BP).
This is also the rate-limiting step of gluconeogene-
sis.

• Glucose-6-phosphate is formed from fructose 6-

phosphate by phosphoglucoisomerase (the reverse
of step 2 in glycolysis). Glucose-6-phosphate can
be used in other metabolic pathways or dephospho-
rylated to free glucose. Whereas free glucose can
easily diffuse in and out of the cell, the phospho-
rylated form (glucose-6-phosphate) is locked in the
cell, a mechanism by which intracellular glucose lev-
els are controlled by cells.

• The final reaction of gluconeogenesis, the formation

of glucose, occurs in the lumen of the endoplasmic
reticulum, where glucose-6-phosphate is hydrolyzed
by glucose-6-phosphatase to produce glucose and
release an inorganic phosphate. Like two steps
prior, this step is not a simple reversal of glycol-
ysis, in which hexokinase catalyzes the conversion
of glucose and ATP into G6P and ADP. Glucose is
Gluconeogenesis pathway with key molecules and enzymes. shuttled into the cytoplasm by glucose transporters
Many steps are the opposite of those found in the glycolysis. located in the endoplasmic reticulum’s membrane.

11.2.3 Pathway 11.2.4 Regulation

Gluconeogenesis is a pathway consisting of a series While most steps in gluconeogenesis are the reverse of
of eleven enzyme-catalyzed reactions. The pathway those found in glycolysis, three regulated and strongly
may begin in the mitochondria or cytoplasm (of the endergonic reactions are replaced with more kinet-
liver/kidney), this being dependent on the substrate be- ically favorable reactions. Hexokinase/glucokinase,
ing used. Many of the reactions are the reversible steps phosphofructokinase, and pyruvate kinase enzymes
found in glycolysis. of glycolysis are replaced with glucose-6-phosphatase,
fructose-1,6-bisphosphatase, and PEP carboxykinase.
• Gluconeogenesis begins in the mitochondria with This system of reciprocal control allow glycolysis and glu-
the formation of oxaloacetate by the carboxyla- coneogenesis to inhibit each other and prevent the forma-
tion of pyruvate. This reaction also requires one tion of a futile cycle.
molecule of ATP, and is catalyzed by pyruvate car- The majority of the enzymes responsible for gluco-
boxylase. This enzyme is stimulated by high levels neogenesis are found in the cytoplasm; the exceptions
of acetyl-CoA (produced in β-oxidation in the liver) are mitochondrial pyruvate carboxylase and, in animals,
and inhibited by high levels of ADP and glucose. phosphoenolpyruvate carboxykinase. The latter exists
202 CHAPTER 11. CARBOHYDRATE METABOLISM

as an isozyme located in both the mitochondrion and [8] Garrett, Reginald H.; Charles M. Grisham (2002). Prin-
the cytosol.[24] The rate of gluconeogenesis is ultimately ciples of Biochemistry with a Human Focus. USA:
controlled by the action of a key enzyme, fructose-1,6- Brooks/Cole, Thomson Learning. pp. 578, 585. ISBN
bisphosphatase, which is also regulated through signal 0-03-097369-4.
transduction by cAMP and its phosphorylation. [9] Van Soest, P. J. 1994. Nutritional ecology of the rumi-
Most factors that regulate the activity of the gluconeogen- nant. 2nd Ed. Cornell Univ. Press. 476 pp.
esis pathway do so by inhibiting the activity or expression
[10] de Figueiredo LF, Schuster S, Kaleta C, Fell DA (2009).
of key enzymes. However, both acetyl CoA and citrate “Can sugars be produced from fatty acids? A test case for
activate gluconeogenesis enzymes (pyruvate carboxylase pathway analysis tools”. Bioinformatics 25 (1): 152–158.
and fructose-1,6-bisphosphatase, respectively). Due to doi:10.1093/bioinformatics/btn621. PMID 19117076.
the reciprocal control of the cycle, acetyl-CoA and cit-
rate also have inhibitory roles in the activity of pyruvate [11] Liu F, Thatcher JD, Barral JM, Epstein HF (1995). “Bi-
kinase. functional glyoxylate cycle protein of Caenorhabditis el-
egans: a developmentally regulated protein of intestine
Global control of gluconeogenesis is mediated by and muscle”. Developmental Biology 169 (2): 399–414.
glucagon (released when blood glucose is low); it triggers doi:10.1006/dbio.1995.1156. PMID 7781887.
phosphorylation of enzymes and regulatory proteins by
Protein Kinase A (a cyclic AMP regulated kinase) result- [12] Kondrashov FA, Koonin EV, Morgunov IG, Finogenova
TV, Kondrashova MN (2006). “Evolution of glyoxylate
ing in inhibition of glycolysis and stimulation of gluco-
cycle enzymes in Metazoa: evidence of multiple hori-
neogenesis. Recent studies have shown that the absence zontal transfer events and pseudogene formation”. Biol-
of hepatic glucose production has no major effect on the ogy Direct 1: 31. doi:10.1186/1745-6150-1-31. PMC
control of fasting plasma glucose concentration. Com- 1630690. PMID 17059607.
pensatory induction of gluconeogenesis occurs in the kid-
neys and intestine, driven by glucagon, glucocorticoids, [13] Weinman EO, Strisower EH, Chaikoff IL (1957). “Con-
and acidosis.[25] version of fatty acids to carbohydrate: application of iso-
topes to this problem and role of the Krebs cycle as a syn-
thetic pathway”. Physiol. Rev. 37 (2): 252–72. PMID
13441426.
11.2.5 References
[14] Glew RH (2010). “You can get there from here: acetone,
[1] Silva, Pedro. “The Chemical Logic Behind Gluconeoge- anionic ketones and even-carbon fatty acids can provide
nesis”. Retrieved September 8, 2009. substrates for gluconeogenesis”. Niger J Physiol Sci 25 (1):
2–4. PMID 22314896.
[2] David L Nelson and Michael M Cox (2000). Lehninger
Principles of Biochemistry. USA: Worth Publishers. p. [15] Miller ON, Bazzano G; Bazzano (1965). “Propane-
724. ISBN 1-57259-153-6. diol metabolism and its relation to lactic acid
metabolism”. Ann NY Acad Sci 119 (3): 957–973.
[3] Young JW (1977). “Gluconeogenesis in cattle: signif-
Bibcode:1965NYASA.119..957M. doi:10.1111/j.1749-
icance and methodology”. J. Dairy Sci. 60 (1): 1–
6632.1965.tb47455.x. PMID 4285478.
15. doi:10.3168/jds.S0022-0302(77)83821-6. PMID
320235. [16] Ruddick JA (1972). “Toxicology, metabolism, and bio-
chemistry of 1,2-propanediol”. Toxicol App Pharmacol
[4] Hundal RS, Krssak M, Dufour S, Laurent D, Lebon 21: 102–111. doi:10.1016/0041-008X(72)90032-4.
V, Chandramouli V, Inzucchi SE, Schumann WC, Pe-
tersen KF, Landau BR, Shulman GI (2000). “Mechanism [17] Widmaier, Eric (2006). Vander’s Human Physiology.
by Which Metformin Reduces Glucose Production McGraw Hill. p. 96. ISBN 0-07-282741-6.
in Type 2 Diabetes”. Diabetes 49 (12): 2063–
9. doi:10.2337/diabetes.49.12.2063. PMC 2995498. [18] Mithieux G, Rajas F, Gautier-Stein A (2004). “A
PMID 11118008. Free full text PDF (82 KiB) novel role for glucose 6-phosphatase in the small intes-
tine in the control of glucose homeostasis.”. The Jour-
[5] Beitz, D. C. 2004. Carbohydrate metabolism. In: Reese, nal of Biological Chemistry 279 (43): 44231–44238.
W. O. Dukes’ physiology of domestic animals. 12th ed. doi:10.1074/jbc.R400011200. PMID 15302872.
Cornell Univ. Press. pp. 501-515.
[19] Gerich JE (2010). “Role of the kidney in normal glucose
[6] Ferrier, Denise R; Champe, Pamela C; Harvey, Richard homeostasis and in the hyperglycaemia of diabetes mel-
A (1 August 2004). “20. Amino Acid Degradation and litus: Therapeutic implications”. Diabetic Medicine 27
Synthesis”. Biochemistry (Lippincott’s Illustrated Reviews). (2): 136–142. doi:10.1111/j.1464-5491.2009.02894.x.
Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN PMID 20546255.
0-7817-2265-9.
[20] Overton, T. R., J. K. Drackley, C. J. Ottemann-
[7] Gerich JE, Meyer C, Woerle HJ, Stumvoll M (2001). Abbamonte, A. D. Beaulieu, L. S. Emmert and J. H.
“Renal gluconeogenesis: Its importance in human glu- Clark. 1999. Substrate utilization for hepatic gluconeoge-
cose homeostasis”. Diabetes Care 24 (2): 382–391. nesis is altered by increased glucose demand in ruminants.
doi:10.2337/diacare.24.2.382. PMID 11213896. J. Anim. Sci. 77: 1940-1951.
11.3. GLYCOGEN 203

[21] Donkin, S. S. and L. E. Armentano. 1995. Insulin and

glucagon regulation of gluconeogenesis in preruminating
and ruminating bovine. J. Anim. Sci. 73: 546-551.

[22] Donkin SS, Armentano LE (1995). “Insulin and glucagon

regulation of gluconeogenesis in preruminating and rumi-
nating bovine”. J. Anim. Sci. 73 (2): 546–51. PMID
7601789.

[23] Voet, Donald; Judith Voet; Charlotte Pratt (2008). Fun-

damentals of Biochemistry. John Wiley & Sons Inc. p.
556. ISBN 978-0-470-12930-2.

[24] Chakravarty K, Cassuto H, Reshef L, Hanson RW

(2005). “Factors that control the tissue-specific transcrip-
tion of the gene for phosphoenolpyruvate carboxykinase-
C”. Crit. Rev. Biochem. Mol. Biol. 40 (3): 129–54.
doi:10.1080/10409230590935479. PMID 15917397.

[25] Mutel E, Gautier-Stein A, Abdul-Wahed A, Amigó-

Correig M, Zitoun C, Stefanutti A, Houberdon I, Tourette
JA, Mithieux G, Rajas F (2011). “Control of blood glu- Schematic two-dimensional cross-sectional view of glycogen: A
cose in the absence of hepatic glucose production dur- core protein of glycogenin is surrounded by branches of glucose
ing prolonged fasting in mice: induction of renal and in- units. The entire globular granule may contain around 30,000
testinal gluconeogenesis by glucagon”. Diabetes 60 (12): glucose units.[1]
3121–3131. doi:10.2337/db11-0571. PMC 3219939.
PMID 22013018.

11.2.6 External links

• Overview at indstate.edu
• Interactive diagram at uakron.edu
• The chemical logic behind gluconeogenesis
• metpath: Interactive representation of gluconeogen-
esis

11.3 Glycogen
Glycogen is a multibranched polysaccharide of glucose
that serves as a form of energy storage in animals[2] and
fungi. The polysaccharide structure represents the main
storage form of glucose in the body. A view of the atomic structure of a single branched strand of
glucose units in a glycogen molecule.
In humans, glycogen is made and stored primarily in the
cells of the liver and the muscles hydrated with three
or four parts of water.[3] Glycogen functions as the sec-
ondary long-term energy storage, with the primary energy
stores being fats held in adipose tissue. Muscle glycogen
is converted into glucose by muscle cells, and liver glyco-
gen converts to glucose for use throughout the body in-
cluding the central nervous system.
Glycogen is the analogue of starch, a glucose polymer
that functions as energy storage in plants. It has a sim-
ilar structure to amylopectin (a component of starch),
Glycogen (black granules) in spermatozoa of a flatworm; trans-
but is more extensively branched and compact than
mission electron microscopy, scale: 0.3 µm
starch. Glycogen is found in the form of granules in the
cytosol/cytoplasm in many cell types, and plays an impor-
tant role in the glucose cycle. Glycogen forms an energy
204 CHAPTER 11. CARBOHYDRATE METABOLISM

reserve that can be quickly mobilized to meet a sudden

need for glucose, but one that is less compact than the
energy reserves of triglycerides (lipids).
In the liver cells (hepatocytes), glycogen can compose
up to 8% of its fresh weight (100–120 g in an adult)
soon after a meal.[4] Only the glycogen stored in the liver
can be made accessible to other organs. In the mus-
cles, glycogen is found in a low concentration (1-2% of
the muscle mass). The amount of glycogen stored in
the body—especially within the muscles, liver, and red
blood cells[5][6][7] —mostly depends on physical training,
basal metabolic rate, and eating habits. Small amounts
of glycogen are found in the kidneys, and even smaller
amounts in certain glial cells in the brain and white blood
cells. The uterus also stores glycogen during pregnancy
to nourish the embryo.[8]

11.3.1 Structure

1,4-α-glycosidic and 1,6-glycosidic linkages in the glycogen

oligomer

drated form, composed of three or four parts of water

per part of glycogen associated with 0.45 millimoles of
potassium per gram of glycogen.[3]

11.3.2 Function
Liver

As a meal containing carbohydrates or protein is eaten

and digested, blood glucose levels rise, and the pancreas
secretes insulin. Blood glucose from the portal vein en-
ters liver cells (hepatocytes). Insulin acts on the hepato-
cytes to stimulate the action of several enzymes, includ-
ing glycogen synthase. Glucose molecules are added to
the chains of glycogen as long as both insulin and glucose
remain plentiful. In this postprandial or “fed” state, the
liver takes in more glucose from the blood than it releases.
1,4-α-glycosidic linkages in the glycogen oligomer
After a meal has been digested and glucose levels begin to
fall, insulin secretion is reduced, and glycogen synthesis
Glycogen is a branched biopolymer consisting of linear stops. When it is needed for energy, glycogen is broken
chains of glucose residues with further chains branching down and converted again to glucose. Glycogen phospho-
off every 8 to 12 glucoses or so. Glucoses are linked to- rylase is the primary enzyme of glycogen breakdown. For
gether linearly by α(1→4) glycosidic bonds from one glu- the next 8–12 hours, glucose derived from liver glycogen
cose to the next. Branches are linked to the chains from is the primary source of blood glucose used by the rest of
which they are branching off by α(1→6) glycosidic bonds the body for fuel.
between the first glucose of the new branch and a glucose
on the stem chain.[9] Glucagon, another hormone produced by the pancreas, in
many respects serves as a countersignal to insulin. In re-
Due to the way glycogen is synthesised, every glycogen sponse to insulin levels being above normal (when blood
granule has at its core a glycogenin protein.[10] levels of glucose begin to fall below the normal range),
Glycogen in muscle, liver, and fat cells is stored in a hy- glucagon is secreted in increasing amounts and stimu-
11.3. GLYCOGEN 205

lates both glycogenolysis (the breakdown of glycogen) into the interior of the glycogen molecule. The branch-
and gluconeogenesis. ing enzyme can act upon only a branch having at least 11
residues, and the enzyme may transfer to the same glu-
cose chain or adjacent glucose chains.
Muscle

Muscle cell glycogen appears to function as an immedi- Breakdown

ate reserve source of available glucose for muscle cells.
Other cells that contain small amounts use it locally, as Main article: Glycogenolysis
well. As muscle cells lack glucose-6-phosphatase, which Glycogen is cleaved from the nonreducing ends of the
is required to pass glucose into the blood, the glyco-
gen they store is available solely for internal use and is
not shared with other cells. This is in contrast to liver
cells, which, on demand, readily do break down their
stored glycogen into glucose and send it through the blood
stream as fuel for other organs. Glycogen is also a suitable
storage substance due to its insolubility in water, which Action of glycogen phosphorylase on glycogen
means it does not affect the osmotic pressure of a cell.
chain by the enzyme glycogen phosphorylase to produce
monomers of glucose-1-phosphate, which is then con-
11.3.3 History verted to glucose 6-phosphate by phosphoglucomutase.
A special debranching enzyme is needed to remove the
Glycogen was discovered by Claude Bernard. His exper- α(1-6) branches in branched glycogen and reshape the
iments showed that the liver contained a substance that chain into linear polymer. The G6P monomers produced
could give rise to reducing sugar by the action of a “fer- have three possible fates:
ment” in the liver. By 1857, he described the isolation of
a substance he called "la matière glycogène", or “sugar- • G6P can continue on the glycolysis pathway and be
forming substance”. Soon after the discovery of glyco- used as fuel.
gen in the liver, A. Sanson found that muscular tissue also
contains glycogen. The empirical formula for glycogen of • G6P can enter the pentose phosphate pathway via
(C the enzyme glucose-6-phosphate dehydrogenase to
6H produce NADPH and 5-carbon sugars.
10O
5) was established by Kekule in 1858.[11] • In the liver and kidney, G6P can be dephospho-
rylated back to glucose by the enzyme glucose
6-phosphatase. This is the final step in the
11.3.4 Metabolism gluconeogenesis pathway.

Synthesis
11.3.5 Clinical relevance
Main article: Glycogenesis
Disorders of glycogen metabolism

Glycogen synthesis is, unlike its breakdown, endergonic The most common disease in which glycogen metabolism
- it requires the input of energy. Energy for glyco- becomes abnormal is diabetes, in which, because of ab-
gen synthesis comes from uridine triphosphate (UTP), normal amounts of insulin, liver glycogen can be ab-
which reacts with glucose-1-phosphate, forming UDP- normally accumulated or depleted. Restoration of nor-
glucose, in a reaction catalysed by UTP—glucose-1- mal glucose metabolism usually normalizes glycogen
phosphate uridylyltransferase. Glycogen is synthesized metabolism, as well.
from monomers of UDP-glucose initially by the protein
glycogenin, which has two tyrosine anchors for the re- In hypoglycemia caused by excessive insulin, liver glyco-
ducing end of glycogen, since glycogenin is a homodimer. gen levels are high, but the high insulin levels prevent the
After about eight glucose molecules have been added to a glycogenolysis necessary to maintain normal blood sugar
tyrosine residue, the enzyme glycogen synthase progres- levels. Glucagon is a common treatment for this type of
sively lengthens the glycogen chain using UDP-glucose, hypoglycemia.
adding α(1→4)-bonded glucose. The glycogen branch- Various inborn errors of metabolism are caused by defi-
ing enzyme catalyzes the transfer of a terminal fragment ciencies of enzymes necessary for glycogen synthesis or
of six or seven glucose residues from a nonreducing end breakdown. These are collectively referred to as glycogen
to the C-6 hydroxyl group of a glucose residue deeper storage diseases.
206 CHAPTER 11. CARBOHYDRATE METABOLISM

Glycogen depletion and endurance exercise [3] Kreitzman SN, Coxon AY, Szaz KF (1992). “Glycogen
storage: illusions of easy weight loss, excessive weight re-
Long-distance athletes, such as marathon runners, cross- gain, and distortions in estimates of body composition”
country skiers, and cyclists, often experience glycogen (PDF). The American Journal of Clinical Nutrition 56 (1
Suppl): 292s–293s. PMID 1615908.
depletion, where almost all of the athlete’s glycogen
stores are depleted after long periods of exertion with- [4] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
out enough energy consumption. This phenomenon is re- (2006). Biology: Exploring Life. Boston, Massachusetts:
ferred to as "hitting the wall". Pearson Prentice Hall. ISBN 0-13-250882-6.
Glycogen depletion can be forestalled in three possible [5] Moses SW, Bashan N, Gutman A (December 1972).
ways. First, during exercise, carbohydrates with the high- “Glycogen metabolism in the normal red blood cell”.
est possible rate of conversion to blood glucose (high Blood 40 (6): 836–43. PMID 5083874.
glycemic index) are ingested continuously. The best pos-
[6] Ingermann RL, Virgin GL (1987). “Glycogen content and
sible outcome of this strategy replaces about 35% of glu- release of glucose from red blood cells of the sipunculan
cose consumed at heart rates above about 80% of max- worm themiste dyscrita” (PDF). J Exp Biol 129: 141–9.
imum. Second, through endurance training adaptations
and specialized regimens (e.g. fasted low-intensity en- [7] Miwa I, Suzuki S (November 2002). “An im-
durance training), the body can condition type I muscle proved quantitative assay of glycogen in erythrocytes”.
fibers to improve both fuel use efficiency and workload Annals of Clinical Biochemistry 39 (Pt 6): 612–3.
doi:10.1258/000456302760413432. PMID 12564847.
capacity to increase the percentage of fatty acids used
[12][13]
as fuel, sparing carbohydrate use from all sources. [8] Campbell, Neil A.; Brad Williamson; Robin J. Heyden
Third, by consuming large quantities of carbohydrates af- (2006). Biology: Exploring Life. Boston: Pearson Pren-
ter depleting glycogen stores as a result of exercise or tice Hall. ISBN 0-13-250882-6.
diet, the body can increase storage capacity of intramus-
[9] Berg, Tymoczko & Stryer (2012). Biochemistry (7th,
cular glycogen stores.[14][15][16] This process is known as International ed.). W. H. Freeman. p. 338. ISBN
carbohydrate loading. In general, glycemic index of car- 1429203145.
bohydrate source does not matter since muscular insulin
sensitivity is increased as a result of temporary glycogen [10] Berg et al. (2012). Biochemistry (7th, International ed.).
depletion.[17][18] W. H. Freeman. p. 650.

When experiencing glycogen debt, athletes often expe- [11] F. G. Young (1957). “Claude Bernard and the Discovery
rience extreme fatigue to the point that it is difficult to of Glycogen”. British Medical Journal 1 (5033 (Jun. 22,
move. As a reference, the very best professional cyclists 1957)): 1431–7. doi:10.1136/bmj.1.5033.1431. JSTOR
in the world will usually finish a 4- to 5-hr stage race 25382898.
right at the limit of glycogen depletion using the first three [12] http://www.bodyrecomposition.com/training/
strategies. methods-of-endurance-training-part-1.html
When athletes ingest both carbohydrate and caffeine fol- [13] http://www.bodyrecomposition.com/fat-loss/
lowing exhaustive exercise, their glycogen is replenished qa-steady-state-vs-tempo-training-and-fat-loss.html
more rapidly.[19][20][21]
[14] http://www.simplyshredded.com/
research-review-an-in-depth-look-into-carbing-up-on-the-cyclical-ketogeni
html
11.3.6 See also
[15] McDonald, Lyle. The Ketogenic Diet: A Complete Guide
for the Dieter and the Practitioner. Lyle McDonald, 1998
• Chitin
[16] “Costill DL et. al. Muscle glycogen utilization during pro-
• Peptidoglycan longed exercise on successive days. J Appl Physiol (1971)
31: 834-838.”
• Triglyceride
[17] Glycogen depletion and increased insulin sensitivity and
responsiveness in muscle after exerciseAm J Physiol En-
docrinol MetabDecember 1, 1986 251:(6) E664-E669
11.3.7 References
[18] McDonald, Lyle. The Ultimate Diet 2.0. Lyle McDonald,
2003
[1] William D. McArdle, Frank I. Katch, Victor L. Katch
(2006). Exercise physiology: energy, nutrition, and human [19] Pedersen DJ, Lessard SJ, Coffey VG et al. (July 2008).
performance (6 ed.). Lippincott Williams & Wilkins. p. “High rates of muscle glycogen resynthesis after exhaus-
12. ISBN 978-0-7817-4990-9. tive exercise when carbohydrate is coingested with caf-
feine”. Journal of Applied Physiology (Original article)
[2] Sadava et al. (2011). Life (9th, International ed.). W. H. 105 (1): 7–13. doi:10.1152/japplphysiol.01121.2007.
Freeman. ISBN 9781429254311. PMID 18467543.
11.4. PENTOSE PHOSPHATE PATHWAY 207

[20] “Post-exercise Caffeine Helps Muscles Refuel” (Press re- monophosphate shunt) is a metabolic pathway paral-
lease). American Physiological Society. Newswise. Re- lel to glycolysis that generates NADPH and pentoses
trieved July 6, 2008. (5-carbon sugars). While it does involve oxidation of
[21] Gaudet, Laura; Jackson, Allen; Streitz, Carmyn; McIn- glucose, its primary role is anabolic rather than catabolic.
tire, Kyle; McDaniel, Larry. “The Effects Of Caffeine On There are two distinct phases in the pathway. The first is
Athletic Performance”. http://journals.cluteonline.com/ the oxidative phase, in which NADPH is generated, and
index.php/CTMS/article/view/5518''. Clute Institute. Re- the second is the non-oxidative synthesis of 5-carbon sug-
trieved 17 June 2014.
ars. For most organisms, the pentose phosphate pathway
takes place in the cytosol; in plants, most steps take place
11.3.8 External links in plastids.[1]
Similar to glycolysis, the pentose phosphate pathway
• Glycogen detection using Periodic Acid Schiff appears to have a very ancient evolutionary origin.
Staining The reactions of this pathway are mostly enzyme-
• Glycogen storage disease - McArdle’s Disease Web- catalyzed in modern cells. They also occur however non-
site enzymatically under conditions that replicate those of the
Archean ocean, and are catalyzed by metal ions, ferrous
• Glycogen at the US National Library of Medicine ions (Fe(II)) in particular.[2] The origins of the pathway
Medical Subject Headings (MeSH) could thus date back to the prebiotic world.

11.4 Pentose phosphate pathway 11.4.1 Outcome

The primary results of the pathway are:

• The generation of reducing equivalents, in the form

of NADPH, used in reductive biosynthesis reactions
within cells (e.g. fatty acid synthesis).
• Production of ribose 5-phosphate (R5P), used in the
synthesis of nucleotides and nucleic acids.
• Production of erythrose 4-phosphate (E4P) used in
the synthesis of aromatic amino acids.

Aromatic amino acids, in turn, are precursors for many

biosynthetic pathways, including the lignin in wood.
Dietary pentose sugars derived from the digestion of nu-
cleic acids may be metabolized through the pentose phos-
phate pathway, and the carbon skeletons of dietary carbo-
hydrates may be converted into glycolytic/gluconeogenic
intermediates.
In mammals, the PPP occurs exclusively in the cyto-
plasm, and is found to be most active in the liver, mam-
mary gland and adrenal cortex in the human. The PPP
is one of the three main ways the body creates molecules
with reducing power, accounting for approximately 60%
of NADPH production in humans.
One of the uses of NADPH in the cell is to prevent
oxidative stress. It reduces glutathione via glutathione
reductase, which converts reactive H2 O2 into H2 O by
glutathione peroxidase. If absent, the H2 O2 would be
converted to hydroxyl free radicals by Fenton chemistry,
which can attack the cell. Erythrocytes, for example,
generate a large amount of NADPH through the pentose
The Pentose Phosphate Pathway
phosphate pathway to use in the reduction of glutathione.
In biochemistry, the pentose phosphate pathway (also Hydrogen peroxide is also generated for phagocytes in a
called the phosphogluconate pathway and the hexose process often referred to as a respiratory burst.[3]
208 CHAPTER 11. CARBOHYDRATE METABOLISM

11.4.2 Phases 11.4.3 Erythrocytes and the pentose phos-

phate pathway
Oxidative phase
Several deficiencies in the level of activity (not func-
In this phase, two molecules of NADP are reduced to tion) of glucose-6-phosphate dehydrogenase have been
+

NADPH, utilizing the energy from the conversion of observed to be associated with resistance to the malar-
glucose-6-phosphate into ribulose 5-phosphate. ial parasite Plasmodium falciparum among individuals of
Mediterranean and African descent. The basis for this
resistance may be a weakening of the red cell membrane
(the erythrocyte is the host cell for the parasite) such that
it cannot sustain the parasitic life cycle long enough for
productive growth.[4]

Oxidative phase of pentose phosphate pathway.

Glucose-6-phosphate (1), 6-phosphoglucono-δ-lactone (2), 6-
11.4.4 See also
phosphogluconate (3), ribulose 5-phosphate (4)
• G6PDH deficiency - A hereditary disease that dis-
rupts the pentose phosphate pathway
The entire set of reactions can be summarized as follows:
• RNA
The overall reaction for this process is:
• Thiamine deficiency

Glucose 6-phosphate + 2 NADP+ + H2 O → • Frank Dickens FRS

ribulose 5-phosphate + 2 NADPH + 2 H+ +
CO2
11.4.5 References
[1] Kruger, Nicholas J; von Schaewen, Antje (June 2003).
Non-oxidative phase “The oxidative pentose phosphate pathway: structure and
organisation”. Current Opinion in Plant Biology 6 (3):
236–246. doi:10.1016/S1369-5266(03)00039-6. Re-
trieved 23 February 2015.

[2] Keller, Markus A.; Turchyn, Alexandra V.; Ralser,

Markus (25 April 2014). “Non-enzymatic glycolysis and
pentose phosphate pathway-like reactions in a plausible
Archean ocean”. Molecular Systems Biology 10 (4): 725–
725. doi:10.1002/msb.20145228. Retrieved 23 February
2015.

[3] Immunology at MCG 1/cytotox

[4] Cappadoro M, Giribaldi G, O'Brien E et al. (October

The pentose phosphate pathway’s nonoxidative phase 1998). “Early phagocytosis of glucose-6-phosphate dehy-
drogenase (G6PD)-deficient erythrocytes parasitized by
Plasmodium falciparum may explain malaria protection
Net reaction: 3 ribulose-5-phosphate → 1 ribose-5- in G6PD deficiency”. Blood 92 (7): 2527–34. PMID
phosphate + 2 xylulose-5-phosphate → 2 fructose-6- 9746794.
phosphate + glyceraldehyde-3-phosphate

11.4.6 External links

Regulation • The chemical logic behind the pentose phosphate
pathway
Glucose-6-phosphate dehydrogenase is the rate-
controlling enzyme of this pathway. It is allosterically • Pentose Phosphate Pathway at the US National
stimulated by NADP+ . The ratio of NADPH:NADP+ is Library of Medicine Medical Subject Headings
normally about 100:1 in liver cytosol. This makes the (MeSH)
cytosol a highly-reducing environment. An NADPH-
• Pentose phosphate pathway Map - Homo sapiens
utilizing pathway forms NADP+ , which stimulates
Glucose-6-phosphate dehydrogenase to produce more
NADPH. This step is also inhibited by acetyl CoA.
Chapter 12

Citric acid cycle

12.1 Citric acid cycle trix of the mitochondrion. In prokaryotic cells, such as
bacteria which lack mitochondria, the TCA reaction se-
O
quence is performed in the cytosol with the proton gra-
O

Acetyl
Pyruvate C
C
C

O
Legend dient for ATP production being across the cell’s surface
Hydrogen Adenosine
NAD+
O

C
S
CoA
CoA -SH +
Pyruvate dehydrogenase
CO2+NADH, H
+
O
C
O
C

O
Carbon
Oxygen
ATP triphosphate
Guanosine
(plasma membrane) rather than the inner membrane of
O O GTP triphosphate

the mitochondrion.
C O
C S Sulfur
Acetyl-CoA CoA -SH C
C C
C

O
O
Q Coenzyme Q CoA Coenzyme A
HCO- + ATP Water NADH Nicotinamide adenine dinucleotide
3 Citrate
Pyruvate dehydrogenase Enzyme
Pyruvate carboxylase
ADP + Pi Citrate synthase Aconitase O O

Oxaloacetate Water O
C
O
O cis-Aconitate
C

C
O C C

12.1.1 Discovery
C C C
Water
C

C O
O + O
NADH, H Aconitase
C C
O

O Malate dehydrogenase O O

NAD+ D-Isocitrate O
C
O

NAD+ C
C
C
O C C
O
Malate O
O

Several of the components and reactions of the citric acid

C O
C
C C Citric acid cycle NADH, H +
O Isocitrate dehydrogenase
O O CO2 O O
Fumarase
Water α-ketoglutarate O
C
C
C

C
C

O
cycle were established in the 1930s by the research of
O

O
Fumarate
NAD+ + CoA

α--ketoglutarate dehydrogenase
-SH
the Nobel laureate Albert Szent-Györgyi, for which he
C O +
NADH, H + CO2
O
C
C C

O QH2
Succinyl-CoA
O
received the Nobel Prize in 1937 for his discoveries per-
Succinyl-CoA synthetase
taining to fumaric acid, a key component of the cycle.[5]
C
Q C S
CoA
GDP + Pi C C

Succinic dehydrogenase Succinate

O

O
O

O
C
C
C

C
O
CoA -SH + GTP
The citric acid cycle itself was finally identified in 1937
O

by Hans Adolf Krebs while at the University of Sheffield,

for which he received the Nobel Prize for Physiology or
Overview of the citric acid cycle (click to enlarge)
Medicine in 1953.[6]
The citric acid cycle – also known as the tricarboxylic
acid (TCA) cycle or the Krebs cycle[1][2] – is a series
of chemical reactions used by all aerobic organisms to 12.1.2 Evolution
generate energy through the oxidation of acetate derived
from carbohydrates, fats and proteins into carbon dioxide Components of the TCA cycle were derived from
and chemical energy in the form of adenosine triphos- anaerobic bacteria, and the TCA cycle itself may have
phate (ATP). In addition, the cycle provides precursors of evolved more than once.[7] Theoretically there are several
certain amino acids as well as the reducing agent NADH alternatives to the TCA cycle; however, the TCA cycle
that is used in numerous other biochemical reactions. Its appears to be the most efficient. If several TCA alterna-
central importance to many biochemical pathways sug- tives had evolved independently, they all appear to have
gests that it was one of the earliest established compo- converged to the TCA cycle.[8][9]
nents of cellular metabolism and may have originated
abiogenically.[3][4]
12.1.3 Overview
The name of this metabolic pathway is derived from citric
acid (a type of tricarboxylic acid) that is consumed and The citric acid cycle is a key metabolic pathway that uni-
then regenerated by this sequence of reactions to com- fies carbohydrate, fat, and protein metabolism. The re-
plete the cycle. In addition, the cycle consumes acetate actions of the cycle are carried out by 8 enzymes that
(in the form of acetyl-CoA) and water, reduces NAD+ to completely oxidize acetate, in the form of acetyl-CoA,
NADH, and produces carbon dioxide as a waste byprod- into two molecules each of carbon dioxide and water.
uct. The NADH generated by the TCA cycle is fed into Through catabolism of sugars, fats, and proteins, a two-
the oxidative phosphorylation (electron transport) path- carbon organic product acetate in the form of acetyl-
way. The net result of these two closely linked pathways CoA is produced which enters the citric acid cycle. The
is the oxidation of nutrients to produce usable chemical reactions of the cycle also convert three equivalents of
energy in the form of ATP. nicotinamide adenine dinucleotide (NAD+ ) into three
In eukaryotic cells, the citric acid cycle occurs in the ma- equivalents of reduced NAD+ (NADH), one equivalent

209
210 CHAPTER 12. CITRIC ACID CYCLE

of flavin adenine dinucleotide (FAD) into one equiva- drive ATP synthesis; FADH2 is covalently attached to
lent of FADH2 , and one equivalent each of guanosine succinate dehydrogenase, an enzyme functioning both in
diphosphate (GDP) and inorganic phosphate (Pᵢ) into one the TCA cycle and the mitochondrial electron transport
equivalent of guanosine triphosphate (GTP). The NADH chain in oxidative phosphorylation. FADH2 , therefore,
and FADH2 generated by the citric acid cycle are in turn facilitates transfer of electrons to coenzyme Q, which is
used by the oxidative phosphorylation pathway to gener- the final electron acceptor of the reaction catalyzed by the
ate energy-rich adenosine triphosphate (ATP). Succinate:ubiquinone oxidoreductase complex, also act-
[11]
One of the primary sources of acetyl-CoA is from the ing as an intermediate in the electron transport chain.
breakdown of sugars by glycolysis which yield pyruvate The citric acid cycle is continuously supplied with new
that in turn is decarboxylated by the enzyme pyruvate de- carbon in the form of acetyl-CoA, entering at step 0
hydrogenase generating acetyl-CoA according to the fol- below.[12]
lowing reaction scheme: Mitochondria in animals, including humans, possess two
succinyl-CoA synthetases: one that produces GTP from
• CH3 C(=O)C(=O)O− (pyruvate) + HSCoA + NAD+ GDP, and another that produces ATP from ADP.[13]
→ CH3 C(=O)SCoA (acetyl-CoA) + NADH + CO2 Plants have the type that produces ATP (ADP-forming
succinyl-CoA synthetase).[12] Several of the enzymes in
The product of this reaction, acetyl-CoA, is the starting the cycle may be loosely associated in a multienzyme
point for the citric acid cycle. Acetyl-CoA may also be protein complex within the mitochondrial matrix.[14]
obtained from the oxidation of fatty acids. Below is a The GTP that is formed by GDP-forming succinyl-CoA
schematic outline of the cycle: synthetase may be utilized by nucleoside-diphosphate ki-
nase to form ATP (the catalyzed reaction is GTP + ADP
• The citric acid cycle begins with the transfer of a → GDP + ATP).[11]
two-carbon acetyl group from acetyl-CoA to the
four-carbon acceptor compound (oxaloacetate) to
form a six-carbon compound (citrate). 12.1.5 Products
• The citrate then goes through a series of chemical
Products of the first turn of the cycle are: one GTP (or
transformations, losing two carboxyl groups as CO2 .
ATP), three NADH, one QH2 , two CO2 .
The carbons lost as CO2 originate from what was ox-
aloacetate, not directly from acetyl-CoA. The car- Because two acetyl-CoA molecules are produced from
bons donated by acetyl-CoA become part of the ox- each glucose molecule, two cycles are required per glu-
aloacetate carbon backbone after the first turn of the cose molecule. Therefore, at the end of two cycles, the
citric acid cycle. Loss of the acetyl-CoA-donated products are: two GTP, six NADH, two QH2 , and four
carbons as CO2 requires several turns of the citric CO2
acid cycle. However, because of the role of the citric The above reactions are balanced if Pᵢ represents the
acid cycle in anabolism, they might not be lost, since H2 PO4 − ion, ADP and GDP the ADP2− and GDP2− ions,
many TCA cycle intermediates are also used as pre- respectively, and ATP and GTP the ATP3− and GTP3−
cursors for the biosynthesis of other molecules.[10] ions, respectively.
• Most of the energy made available by the oxida- The total number of ATP obtained after complete oxi-
tive steps of the cycle is transferred as energy- dation of one glucose in glycolysis, citric acid cycle, and
rich electrons to NAD+ , forming NADH. For each oxidative phosphorylation is estimated to be between 30
acetyl group that enters the citric acid cycle, three and 38.[15]
molecules of NADH are produced.
• Electrons are also transferred to the electron accep-
12.1.6 Efficiency
tor Q, forming QH2 .
• At the end of each cycle, the four-carbon oxaloac- The theoretical maximum yield of ATP through oxida-
etate has been regenerated, and the cycle continues. tion of one molecule of glucose in glycolysis, citric acid
cycle, and oxidative phosphorylation is 38 (assuming 3
molar equivalents of ATP per equivalent NADH and 2
12.1.4 Steps ATP per FADH2 ). In eukaryotes, two equivalents of
NADH are generated in glycolysis, which takes place in
Two carbon atoms are oxidized to CO2 , the energy from the cytoplasm. Transport of these two equivalents into
these reactions being transferred to other metabolic pro- the mitochondria consumes two equivalents of ATP, thus
cesses by GTP (or ATP), and as electrons in NADH reducing the net production of ATP to 36. Furthermore,
and QH2 . The NADH generated in the TCA cycle may inefficiencies in oxidative phosphorylation due to leak-
later donate its electrons in oxidative phosphorylation to age of protons across the mitochondrial membrane and
12.1. CITRIC ACID CYCLE 211

slippage of the ATP synthase/proton pump commonly re- 12.1.8 Regulation

duces the ATP yield from NADH and FADH2 to less than
the theoretical maximum yield.[15] The observed yields
are, therefore, closer to ~2.5 ATP per NADH and ~1.5
ATP per FADH2 , further reducing the total net produc-
tion of ATP to approximately 30.[16] An assessment of
the total ATP yield with newly revised proton-to-ATP
ratios provides an estimate of 29.85 ATP per glucose The regulation of the TCA cycle is largely determined by
molecule.[17] product inhibition and substrate availability. If the cy-
cle were permitted to run unchecked, large amounts of
metabolic energy could be wasted in overproduction of
reduced coenzyme such as NADH and ATP. The major
eventual substrate of the cycle is ADP which gets con-
verted to ATP. A reduced amount of ADP causes ac-
12.1.7 Variation cumulation of precursor NADH which in turn can in-
hibit a number of enzymes. NADH, a product of all
dehydrogenases in the TCA cycle with the exception
While the TCA cycle is in general highly conserved, there of succinate dehydrogenase, inhibits pyruvate dehydro-
is significant variability in the enzymes found in different genase, isocitrate dehydrogenase, α-ketoglutarate dehy-
taxa[18] (note that the diagrams on this page are specific drogenase, and also citrate synthase. Acetyl-coA in-
to the mammalian pathway variant). hibits pyruvate dehydrogenase, while succinyl-CoA in-
hibits alpha-ketoglutarate dehydrogenase and citrate syn-
Some differences exist between eukaryotes and prokary-
otes. The conversion of D-threo-isocitrate to 2- thase. When tested in vitro with TCA enzymes, ATP
oxoglutarate is catalyzed in eukaryotes by the NAD+ - inhibits citrate synthase and α-ketoglutarate dehydroge-
dependent EC 1.1.1.41, while prokaryotes employ the nase; however, ATP levels do not change more than 10%
NADP+ -dependent EC 1.1.1.42.[19] Similarly, the con- in vivo between rest and vigorous exercise. There is no
version of (S)-malate to oxaloacetate is catalyzed in eu- known allosteric mechanism that can account for large
karyotes by the NAD+ -dependent EC 1.1.1.37, while changes in reaction rate from an allosteric [26]
effector whose
most prokaryotes utilize a quinone-dependent enzyme, concentration changes less than 10%.
EC 1.1.5.4.[20] Calcium is used as a regulator. Mitochondrial matrix
A step with significant variability is the conversion of calcium levels can reach the tens of micromolar lev-
succinyl-CoA to succinate. Most organisms utilize EC els during cellular activation.[27] It activates pyruvate
6.2.1.5, succinate–CoA ligase (ADP-forming) (despite dehydrogenase phosphatase which in turn activates the
its name, the enzyme operates in the pathway in the pyruvate dehydrogenase complex. Calcium also activates
direction of ATP formation). In mammals a GTP- isocitrate dehydrogenase and α-ketoglutarate dehydroge-
forming enzyme, succinate–CoA ligase (GDP-forming) nase.[28] This increases the reaction rate of many of the
steps in the cycle, and therefore increases flux throughout
(EC 6.2.1.4) also operates. The level of utilization of
each isoform is tissue dependent.[21] In some acetate- the pathway.
producing bacteria, such as Acetobacter aceti, an entirely Citrate is used for feedback inhibition, as it inhibits
different enzyme catalyzes this conversion – EC 2.8.3.18, phosphofructokinase, an enzyme involved in glycolysis
succinyl-CoA:acetate CoA-transferase. This specialized that catalyses formation of fructose 1,6-bisphosphate,a
enzyme links the TCA cycle with acetate metabolism in precursor of pyruvate. This prevents a constant high rate
these organisms.[22] Some bacteria, such as Helicobac- of flux when there is an accumulation of citrate and a de-
ter pylori, employ yet another enzyme for this conver- crease in substrate for the enzyme.
sion – succinyl-CoA:acetoacetate CoA-transferase (EC Recent work has demonstrated an important link between
2.8.3.5).[23] intermediates of the citric acid cycle and the regulation of
Some variability also exists at the previous step – the hypoxia-inducible factors (HIF). HIF plays a role in the
conversion of 2-oxoglutarate to succinyl-CoA. While regulation of oxygen homeostasis, and is a transcription
most organisms utilize the ubiquitous NAD+ -dependent factor that targets angiogenesis, vascular remodeling, glu-
2-oxoglutarate dehydrogenase, some bacteria utilize cose utilization, iron transport and apoptosis. HIF is syn-
a ferredoxin-dependent 2-oxoglutarate synthase (EC thesized consititutively, and hydroxylation of at least one
1.2.7.3).[24] Other organisms, including obligately au- of two critical proline residues mediates their interaction
totrophic and methanotrophic bacteria and archaea, by- with the von Hippel Lindau E3 ubiquitin ligase complex,
pass succinyl-CoA entirely, and convert 2-oxoglutarate which targets them for rapid degradation. This reaction
to succinate via succinate semialdehyde, using EC is catalysed by prolyl 4-hydroxylases. Fumarate and suc-
4.1.1.71, 2-oxoglutarate decarboxylase, and EC 1.2.1.79, cinate have been identified as potent inhibitors of prolyl
succinate-semialdehyde dehydrogenase.[25] hydroxylases, thus leading to the stabilisation of HIF.[29]
212 CHAPTER 12. CITRIC ACID CYCLE

12.1.9 Major metabolic pathways converg- into cytosolic oxaloacetate, which is ultimately converted
ing on the TCA cycle into glucose, in a process that is almost the reverse of
glycolysis.[31]
Several catabolic pathways converge on the TCA cycle. In protein catabolism, proteins are broken down by
Most of these reactions add intermediates to the TCA proteases into their constituent amino acids. Their carbon
cycle, and are therefore known as anaplerotic reactions, skeletons (i.e. the de-aminated amino acids) may either
from the Greek meaning to “fill up”. Processes that enter the citric acid cycle as intermediates (e.g. alpha-
remove intermediates from the cycle are termed “cata- ketoglutarate derived from glutamate or glutamine), hav-
plerotic” reactions. ing an anaplerotic effect on the cycle, or, in the case
of leucine, isoleucine, lysine, phenylalanine, tryptophan,
In this section and in the next, the citric acid cycle inter-
and tyrosine, they are converted into acetyl-CoA which
mediates are indicated in italics to distinguish them from
can be burned to CO2 and water, or used to form ketone
other substrates and end-products.
bodies, which too can only be burned in tissues other
Pyruvate molecules produced by glycolysis are actively than the liver where they are formed, or excreted via the
transported across the inner mitochondrial membrane, urine or breath.[31] These latter amino acids are therefore
and into the matrix where they can either be oxidized and termed “ketogenic” amino acids, whereas those that en-
combined with coenzyme A to form CO2 , acetyl-CoA, ter the citric acid cycle as intermediates can only be cata-
and NADH,[30] or they can be carboxylated (by pyruvate plerotically removed by entering the gluconeogenic path-
carboxylase) to form oxaloacetate. This latter reaction way via malate which is transported out of the mitochon-
”fills up” the amount of oxaloacetate in the citric acid cy- drion to be converted into cytosolic oxaloacetate and ulti-
cle, and is therefore an anaplerotic reaction, increasing mately into glucose. These are the so-called “glucogenic”
the cycle’s capacity to metabolize acetyl-CoA when the amino acids. De-aminated alanine, cysteine, glycine, ser-
tissue’s energy needs (e.g. in muscle) are suddenly in- ine, and threonine are converted to pyruvate and can con-
creased by activity.[31] sequently either enter the citric acid cycle as oxaloacetate
In the citric acid cycle all the intermediates (e.g. cit- (an anaplerotic reaction) or as acetyl-CoA to be disposed
rate, iso-citrate, alpha-ketoglutarate, succinate, fumarate, of as CO2 and water.[31]
malate and oxaloacetate) are regenerated during each turn In fat catabolism, triglycerides are hydrolyzed to break
of the cycle. Adding more of any of these intermedi- them into fatty acids and glycerol. In the liver the glycerol
ates to the mitochondrion therefore means that that ad- can be converted into glucose via dihydroxyacetone phos-
ditional amount is retained within the cycle, increasing phate and glyceraldehyde-3-phosphate by way of gluco-
all the other intermediates as one is converted into the neogenesis. In many tissues, especially heart and skele-
other. Hence the addition of any one of them to the cy- tal muscle tissue, fatty acids are broken down through
cle has an anaplerotic effect, and its removal has a cat- a process known as beta oxidation, which results in the
aplerotic effect. These anaplerotic and cataplerotic re- production of mitochondrial acetyl-CoA, which can be
actions will, during the course of the cycle, increase or used in the citric acid cycle. Beta oxidation of fatty
decrease the amount of oxaloacetate available to combine acids with an odd number of methylene bridges produces
with acetyl-CoA to form citric acid. This in turn increases propionyl-CoA, which is then converted into succinyl-
or decreases the rate of ATP production by the mitochon- CoA and fed into the citric acid cycle as an anaplerotic
drion, and thus the availability of ATP to the cell.[31] intermediate.[32]
Acetyl-CoA, on the other hand, derived from pyruvate ox- The total energy gained from the complete breakdown of
idation, or from the beta-oxidation of fatty acids, is the one (six-carbon) molecule of glucose by glycolysis, the
only fuel to enter the citric acid cycle. With each turn formation of 2 acetyl-CoA molecules, their catabolism in
of the cycle one molecule of acetyl-CoA is consumed for the citric acid cycle, and oxidative phosphorylation equals
every molecule of oxaloacetate present in the mitochon- about 30 ATP molecules, in eukaryotes. The number of
drial matrix, and is never regenerated. It is the oxidation ATP molecules derived from the beta oxidation of a 6
of the acetate portion of acetyl-CoA that produces CO2 carbon segment of a fatty acid chain, and the subsequent
and water, with the energy thus released captured in the oxidation of the resulting 3 molecules of acetyl-CoA is 40.
form of ATP.[31]
In the liver, the carboxylation of cytosolic pyruvate into
intra-mitochondrial oxaloacetate is an early step in the 12.1.10 Citric acid cycle intermediates
gluconeogenic pathway which converts lactate and de- serve as substrates for biosyn-
aminated alanine into glucose,[30][31] under the influence
thetic processes
of high levels of glucagon and/or epinephrine in the
blood.[31] Here the addition of oxaloacetate to the mito-
chondrion does not have a net anaplerotic effect, as an- In this subheading, as in the previous one, the TCA inter-
other citric acid cycle intermediate (malate) is immedi- mediated are identified by italics.
ately removed from the mitochondrion to be converted Several of the citric acid cycle intermediates are used for
12.1. CITRIC ACID CYCLE 213

the synthesis of important compounds, which will have 12.1.11 Interactive pathway map
significant cataplerotic effects on the cycle.[31] Acetyl-
CoA cannot be transported out of the mitochondrion. Click on genes, proteins and metabolites below to link to
To obtain cytosolic acetyl-CoA, citrate is removed from respective articles. [§ 1]
the citric acid cycle and carried across the inner mito-
[[File:
chondrial membrane into the cytosol. There it is cleaved
[[<div style="display:block; width:30.
by ATP citrate lyase into acetyl-CoA and oxaloacetate.
1834671470831px; height:0px; overflow:hidden;
The oxaloacetate can be used for gluconeogenesis (in the
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liver), or it can be returned into mitochondrion as malate.
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The cytosolic acetyl-CoA is used for fatty acid synthe-
border-top:3px blue solid"></div>]]
sis and the production of cholesterol. Cholesterol can,
[[<div style="display:block; width:30.
in turn, be used to synthesize the steroid hormones, bile
9999999999983px; height:0px; overflow:hidden;
salts, and vitamin D.[30][31]
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them into amino acids the alpha keto-acids formed from [[<div style="display:block; width:29.
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ketoglutarate, which is a citric acid cycle intermediate. [[<div style="display:block; width:41.841620626151px;
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Of these amino acids, aspartate and glutamine are used, [[<div style="display:block; width:33.
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[[<div style="display:block; width:32.582089552239px;
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border-top:3px blue solid"></div>]]
tochondrion, to be oxidized back to oxaloacetate in the
[[<div style="display:block; width:80px; height:0px;
cytosol. Cytosolic oxaloacetate is then decarboxylated to
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of nearly all the gluconeogenic precursors (such as the
[[<div style="display:block; width:84.
glucogenic amino acids and lactate) into glucose by the
9238578680197px; height:0px; overflow:hidden;
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214 CHAPTER 12. CITRIC ACID CYCLE

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12.1. CITRIC ACID CYCLE 215

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[[<div style="display:block; width:70.
9637798844278px; height:0px; overflow:hidden; |{{{bSize}}}px|alt=TCA Cycle edit]]
position:relative; left:302.78215871956456px;
top:542.264367816092px; background:transparent; File:TCACycle WP78.png
216 CHAPTER 12. CITRIC ACID CYCLE

[12] Jones RC, Buchanan BB, Gruissem W (2000). Biochem-

istry & molecular biology of plants (1st ed.). Rockville,
TCA Cycle edit Md: American Society of Plant Physiologists. ISBN 0-
943088-39-9.
[1] The interactive pathway map can be edited at WikiPath-
ways: “TCACycle_WP78”. [13] Johnson JD, Mehus JG, Tews K, Milavetz BI, Lam-
beth DO (October 1998). “Genetic evidence for the ex-
pression of ATP- and GTP-specific succinyl-CoA syn-
12.1.12 See also thetases in multicellular eucaryotes”. J. Biol. Chem. 273
(42): 27580–6. doi:10.1074/jbc.273.42.27580. PMID
9765291.
• Calvin cycle
[14] Barnes SJ, Weitzman PD (June 1986). “Organization
• Glyoxylate cycle of citric acid cycle enzymes into a multienzyme clus-
ter”. FEBS Lett. 201 (2): 267–70. doi:10.1016/0014-
• Reverse (Reductive) Krebs cycle
5793(86)80621-4. PMID 3086126.

[15] Porter RK, Brand MD (September 1995). “Mitochondrial

12.1.13 References proton conductance and H+/O ratio are independent of
electron transport rate in isolated hepatocytes”. Biochem.
[1] Lowenstein JM (1969). Methods in Enzymology, Volume J. 310 (2): 379–82. PMC 1135905. PMID 7654171.
13: Citric Acid Cycle. Boston: Academic Press. ISBN
0-12-181870-5. [16] Stryer L, Berg JM, Tymoczko JL (2002). “Section 18.6:
The Regulation of Cellular Respiration Is Governed Pri-
[2] Krebs HA, Weitzman PDJ (1987). Krebs’ citric acid cy- marily by the Need for ATP”. Biochemistry. San Fran-
cle: half a century and still turning. London: Biochemical cisco: W.H. Freeman. ISBN 0-7167-4684-0.
Society. p. 25. ISBN 0-904498-22-0.
[17] Rich PR (December 2003). “The molecular machinery
[3] Wagner, Andreas (2014). Arrival of the Fittest (first of Keilin’s respiratory chain”. Biochem. Soc. Trans.
ed.). New York: Penguin Group. p. 100. ISBN 31 (Pt 6): 1095–105. doi:10.1042/BST0311095. PMID
9781591846468. 14641005.

[4] Lane, Nick (2009). Life Ascending: The Ten Great Inven- [18] “Citric acid cycle variants at MetaCyc”.
tions of Evolution. New York: W.W. Norton & Co. ISBN
0-393-06596-0. [19] Sahara T, Takada Y, Takeuchi Y, Yamaoka N, Fuku-
naga N (March 2002). “Cloning, sequencing, and expres-
[5] “The Nobel Prize in Physiology or Medicine 1937”. The sion of a gene encoding the monomeric isocitrate dehy-
Nobel Foundation. Retrieved 2011-10-26. drogenase of the nitrogen-fixing bacterium, Azotobacter
vinelandii”. Biosci. Biotechnol. Biochem. 66 (3): 489–
[6] “The Nobel Prize in Physiology or Medicine 1953”. The 500. doi:10.1271/bbb.66.489. PMID 12005040.
Nobel Foundation. Retrieved 2011-10-26.
[20] van der Rest ME, Frank C, Molenaar D (December
[7] Gest H (1987). “Evolutionary roots of the citric acid cycle 2000). “Functions of the membrane-associated and cy-
in prokaryotes”. Biochem. Soc. Symp. 54: 3–16. PMID toplasmic malate dehydrogenases in the citric acid cy-
3332996. cle of Escherichia coli”. J. Bacteriol. 182 (24): 6892–
9. doi:10.1128/jb.182.24.6892-6899.2000. PMC 94812.
[8] Meléndez-Hevia E, Waddell TG, Cascante M (Septem- PMID 11092847.
ber 1996). “The puzzle of the Krebs citric acid cy-
cle: assembling the pieces of chemically feasible reac- [21] Lambeth DO, Tews KN, Adkins S, Frohlich D, Milavetz
tions, and opportunism in the design of metabolic path- BI (August 2004). “Expression of two succinyl-CoA syn-
ways during evolution”. J. Mol. Evol. 43 (3): 293–303. thetases with different nucleotide specificities in mam-
doi:10.1007/BF02338838. PMID 8703096. malian tissues”. J. Biol. Chem. 279 (35): 36621–4.
doi:10.1074/jbc.M406884200. PMID 15234968.
[9] Ebenhöh O, Heinrich R (January 2001). “Evolutionary
optimization of metabolic pathways. Theoretical recon- [22] Mullins EA, Francois JA, Kappock TJ (July 2008). “A
struction of the stoichiometry of ATP and NADH pro- specialized citric acid cycle requiring succinyl-coenzyme
ducing systems”. Bull. Math. Biol. 63 (1): 21–55. A (CoA):acetate CoA-transferase (AarC) confers acetic
doi:10.1006/bulm.2000.0197. PMID 11146883. acid resistance on the acidophile Acetobacter aceti”. J.
Bacteriol. 190 (14): 4933–40. doi:10.1128/JB.00405-08.
[10] Wolfe RR, Jahoor F (February 1990). “Recovery of la- PMC 2447011. PMID 18502856.
beled CO2 during the infusion of C-1- vs C-2-labeled
acetate: implications for tracer studies of substrate ox- [23] Corthésy-Theulaz IE, Bergonzelli GE, Henry H et al. (Oc-
idation”. Am. J. Clin. Nutr. 51 (2): 248–52. PMID tober 1997). “Cloning and characterization of Helicobac-
2106256. ter pylori succinyl CoA:acetoacetate CoA-transferase,
a novel prokaryotic member of the CoA-transferase
[11] Stryer L, Berg J, Tymoczko JL (2002). Biochemistry. San family”. J. Biol. Chem. 272 (41): 25659–67.
Francisco: W.H. Freeman. ISBN 0-7167-4684-0. doi:10.1074/jbc.272.41.25659. PMID 9325289.
12.1. CITRIC ACID CYCLE 217

[24] Baughn AD, Garforth SJ, Vilchèze C, Jacobs WR

(November 2009). “An anaerobic-type alpha-
ketoglutarate ferredoxin oxidoreductase completes
the oxidative tricarboxylic acid cycle of Mycobac-
terium tuberculosis”. PLoS Pathog. 5 (11): e1000662.
doi:10.1371/journal.ppat.1000662. PMC 2773412.
PMID 19936047.

[25] Zhang S, Bryant DA (December 2011). “The tri-

carboxylic acid cycle in cyanobacteria”. Science 334
(6062): 1551–3. doi:10.1126/science.1210858. PMID
22174252.

[26] Voet D, Voet JG (2004). Biochemistry (3rd ed.). New

York: John Wiley & Sons, Inc. p. 615.

[27] Ivannikov, M. et al. (2013). “Mitochondrial Free

Ca2+ Levels and Their Effects on Energy Metabolism in
Drosophila Motor Nerve Terminals”. Biophys. J. 104
(11): 2353–2361. doi:10.1016/j.bpj.2013.03.064. PMC
3672877. PMID 23746507.

[28] Denton RM, Randle PJ, Bridges BJ, Cooper RH, Ker-
bey AL, Pask HT, Severson DL, Stansbie D, Whitehouse
S (October 1975). “Regulation of mammalian pyruvate
dehydrogenase”. Mol. Cell. Biochem. 9 (1): 27–53.
doi:10.1007/BF01731731. PMID 171557.

[29] Koivunen P, Hirsilä M, Remes AM, Hassinen IE,

Kivirikko KI, Myllyharju J (February 2007). “Inhibition
of hypoxia-inducible factor (HIF) hydroxylases by cit-
ric acid cycle intermediates: possible links between cell
metabolism and stabilization of HIF”. J. Biol. Chem. 282
(7): 4524–32. doi:10.1074/jbc.M610415200. PMID
17182618.

[30] Voet, Donald; Judith G. Voet; Charlotte W. Pratt (2006).

Fundamentals of Biochemistry, 2nd Edition. John Wiley
and Sons, Inc. pp. 547, 556. ISBN 0-471-21495-7.

[31] Stryer, Lubert (1995). “Citric acid cycle.”. In: Biochem-

istry. (Fourth ed.). New York: W.H. Freeman and Com-
pany. pp. 509–527, 569–579, 614–616, 638–641, 732–
735, 739–748, 770–773. ISBN 0 7167 2009 4.

[32] Halarnkar PP, Blomquist GJ (1989). “Comparative as-

pects of propionate metabolism”. Comp. Biochem.
Physiol., B 92 (2): 227–31. doi:10.1016/0305-
0491(89)90270-8. PMID 2647392.

12.1.14 External links

• An animation of the citric acid cycle at Smith Col-
lege
• Citric acid cycle variants at MetaCyc

• Pathways connected to the citric acid cycle at Kyoto

Encyclopedia of Genes and Genomes

• Introduction at Khan Academy

• metpath: Interactive representation of the TCA cy-

cle
Chapter 13

Oxidative phosphorylation

13.1 Oxidative phosphorylation main protein complexes are involved, whereas in prokary-
otes many different enzymes are present, using a variety
of electron donors and acceptors.
The energy released by electrons flowing through this
Outer membrane
electron transport chain is used to transport protons
across the inner mitochondrial membrane, in a process
called electron transport. This generates potential energy
ATP
Synthase
in the form of a pH gradient and an electrical potential
NADH
across this membrane. This store of energy is tapped by
ATP Citric allowing protons to flow back across the membrane and
acid down this gradient, through a large enzyme called ATP
Matrix cycle
synthase; this process is known as chemiosmosis. This
Fumarate
Succinate enzyme uses this energy to generate ATP from adenosine
Inner membrane
diphosphate (ADP), in a phosphorylation reaction. This
reaction is driven by the proton flow, which forces the
rotation of a part of the enzyme; the ATP synthase is a
Intermembrane space rotary mechanical motor.
Although oxidative phosphorylation is a vital part of
metabolism, it produces reactive oxygen species such as
The electron transport chain in the cell is the site of oxidative superoxide and hydrogen peroxide, which lead to propa-
phosphorylation in prokaryotes. The NADH and succinate gen- gation of free radicals, damaging cells and contributing to
erated in the citric acid cycle are oxidized, releasing energy to disease and, possibly, aging (senescence). The enzymes
power the ATP synthase. carrying out this metabolic pathway are also the target of
many drugs and poisons that inhibit their activities.
Oxidative phosphorylation (or OXPHOS in short) is
the metabolic pathway in which the mitochondria in cells
use their structure, enzymes, and energy released by the 13.1.1 Overview of energy transfer by
oxidation of nutrients to reform ATP. Although the many chemiosmosis
forms of life on earth use a range of different nutrients,
ATP is the molecule that supplies energy to metabolism. Further information: Chemiosmosis and Bioenergetics
Almost all aerobic organisms carry out oxidative phos-
phorylation. This pathway is probably so pervasive be- Oxidative phosphorylation works by using energy-
cause it is a highly efficient way of releasing energy, com- releasing chemical reactions to drive energy-requiring re-
pared to alternative fermentation processes such as anaer- actions: The two sets of reactions are said to be cou-
obic glycolysis. pled. This means one cannot occur without the other.
During oxidative phosphorylation, electrons are trans- The flow of electrons through the electron transport chain,
ferred from electron donors to electron acceptors such as from electron donors such as NADH to electron acceptors
oxygen, in redox reactions. These redox reactions release such as oxygen, is an exergonic process – it releases en-
energy, which is used to form ATP. In eukaryotes, these ergy, whereas the synthesis of ATP is an endergonic pro-
redox reactions are carried out by a series of protein com- cess, which requires an input of energy. Both the elec-
plexes within the cell’s intermembrane wall mitochondria, tron transport chain and the ATP synthase are embed-
whereas, in prokaryotes, these proteins are located in the ded in a membrane, and energy is transferred from elec-
cells’ intermembrane space. These linked sets of proteins tron transport chain to the ATP synthase by movements
are called electron transport chains. In eukaryotes, five of protons across this membrane, in a process called

218
13.1. OXIDATIVE PHOSPHORYLATION 219

chemiosmosis.[1] In practice, this is like a simple electric

O
circuit, with a current of protons being driven from the
O
negative N-side of the membrane to the positive P-side
by the proton-pumping enzymes of the electron transport
chain. These enzymes are like a battery, as they perform O
work to drive current through the circuit. The movement O 2e +2H
of protons creates an electrochemical gradient across the
membrane, which is often called the proton-motive force. OH
It has two components: a difference in proton concen- O
tration (a H+ gradient, ΔpH) and a difference in electric
potential, with the N-side having a negative charge.[2] O
ATP synthase releases this stored energy by completing OH
the circuit and allowing protons to flow down the electro-
chemical gradient, back to the N-side of the membrane.[3] Reduction of coenzyme Q from its ubiquinone form (Q) to the
This kinetic energy drives the rotation of part of the en- reduced ubiquinol form (QH2 ).
zymes structure and couples this motion to the synthesis
of ATP.
The two components of the proton-motive force are soluble electron carrier coenzyme Q10 (Q) [8]
carries both
thermodynamically equivalent: In mitochondria, the electrons and protons by a redox cycle. This small
largest part of energy is provided by the potential; in benzoquinone molecule is very hydrophobic, so it dif-
alkaliphile bacteria the electrical energy even has to com- fuses freely within the membrane. When Q accepts
pensate for a counteracting inverse pH difference. In- two electrons and two protons, it becomes reduced to
versely, chloroplasts operate mainly on ΔpH. However, the ubiquinol form (QH 2 ); when QH 2 releases two elec-
they also require a small membrane potential for the ki- trons and two protons, it becomes oxidized back to the
netics of ATP synthesis. At least in the case of the ubiquinone (Q) form. As a result, if two enzymes are
fusobacterium P. modestum it drives the counter-rotation arranged so that Q is reduced on one side of the mem-
of subunits a and c of the FO motor of ATP synthase.[2] brane and QH2 oxidized on the other, ubiquinone will
couple these reactions and shuttle protons across the
The amount of energy released by oxidative phospho- membrane.[9] Some bacterial electron transport chains
rylation is high, compared with the amount produced use different quinones, such as menaquinone, in addition
by anaerobic fermentation. Glycolysis produces only 2 to ubiquinone.[10]
ATP molecules, but somewhere between 30 and 36 ATPs
are produced by the oxidative phosphorylation of the 10 Within proteins, [3][11]
electrons are transferred between flavin
NADH and 2 succinate molecules made by converting cofactors, iron–sulfur clusters, and cytochromes.
[4] There are several types of iron–sulfur cluster. The sim-
one molecule of glucose to carbon dioxide and water,
while each cycle of beta oxidation of a fatty acid yields plest kind found in the electron transfer chain consists of
about 14 ATPs. These ATP yields are theoretical max- two iron atoms joined by two atoms of inorganic sulfur;
imum values; in practice, some protons leak across the these are called [2Fe–2S] clusters. The second kind,
membrane, lowering the yield of ATP.[5] called [4Fe–4S], contains a cube of four iron atoms and
four sulfur atoms. Each iron atom in these clusters is
coordinated by an additional amino acid, usually by the
13.1.2 Electron and proton transfer sulfur atom of cysteine. Metal ion cofactors undergo re-
molecules dox reactions without binding or releasing protons, so in
the electron transport chain they serve solely to transport
Further information: Coenzyme and Cofactor electrons through proteins. Electrons move quite long dis-
The electron transport chain carries both protons and tances through proteins by hopping along chains of these
[12]
electrons, passing electrons from donors to acceptors, cofactors. This occurs by quantum tunnelling, which
and transporting protons across a membrane. These is rapid over distances of less than 1.4×10−9 m.[13]
processes use both soluble and protein-bound transfer
molecules. In mitochondria, electrons are transferred
within the intermembrane space by the water-soluble 13.1.3 Eukaryotic electron transport
[6]
electron transfer protein cytochrome c. This carries chains
only electrons, and these are transferred by the reduc-
tion and oxidation of an iron atom that the protein holds Further information: Electron transport chain and
within a heme group in its structure. Cytochrome c is Chemiosmosis
also found in some bacteria, where it is located within
the periplasmic space.[7] Many catabolic biochemical processes, such as glycolysis,
Within the inner mitochondrial membrane, the lipid- the citric acid cycle, and beta oxidation, produce the re-
220 CHAPTER 13. OXIDATIVE PHOSPHORYLATION

duced coenzyme NADH. This coenzyme contains elec- bles a boot with a large “ball” poking out from the mem-
trons that have a high transfer potential; in other words, brane into the mitochondrion.[20][21] The genes that en-
they will release a large amount of energy upon oxida- code the individual proteins are contained in both the cell
tion. However, the cell does not release this energy all nucleus and the mitochondrial genome, as is the case for
at once, as this would be an uncontrollable reaction. In- many enzymes present in the mitochondrion.
stead, the electrons are removed from NADH and passed The reaction that is catalyzed by this enzyme is the
to oxygen through a series of enzymes that each release two electron oxidation of NADH by coenzyme Q10 or
a small amount of the energy. This set of enzymes, con- ubiquinone (represented as Q in the equation below), a
sisting of complexes I through IV, is called the electron
lipid-soluble quinone that is found in the mitochondrion
transport chain and is found in the inner membrane of the membrane:
mitochondrion. Succinate is also oxidized by the electron
matrix → NAD + QH2 + 4 Hintermembrane
NADH + Q + 5 H+ + +
transport chain, but feeds into the pathway at a different
point. The start of the reaction, and indeed of the entire electron
In eukaryotes, the enzymes in this electron transport sys- chain, is the binding of a NADH molecule to complex
tem use the energy released from the oxidation of NADH I and the donation of two electrons. The electrons en-
to pump protons across the inner membrane of the mi- ter complex I via a prosthetic group attached to the com-
tochondrion. This causes protons to build up in the plex, flavin mononucleotide (FMN). The addition of elec-
intermembrane space, and generates an electrochemical trons to FMN converts it to its reduced form, FMNH2 .
gradient across the membrane. The energy stored in this The electrons are then transferred through a series of
potential is then used by ATP synthase to produce ATP. iron–sulfur clusters: the second kind of prosthetic group
Oxidative phosphorylation in the eukaryotic mitochon- present in the complex.[18] There are both [2Fe–2S] and
drion is the best-understood example of this process. The [4Fe–4S] iron–sulfur clusters in complex I.
mitochondrion is present in almost all eukaryotes, with As the electrons pass through this complex, four pro-
the exception of anaerobic protozoa such as Trichomonas tons are pumped from the matrix into the intermem-
vaginalis that instead reduce protons to hydrogen in a brane space. Exactly how this occurs is unclear, but
remnant mitochondrion called a hydrogenosome.[14] it seems to involve conformational changes in complex
I that cause the protein to bind protons on the N-side
of the membrane and release them on the P-side of the
NADH-coenzyme Q oxidoreductase (complex I)
membrane.[22] Finally, the electrons are transferred from
the chain of iron–sulfur clusters to a ubiquinone molecule
in the membrane.[16] Reduction of ubiquinone also con-
tributes to the generation of a proton gradient, as two
Fe-S protons are taken up from the matrix as it is reduced to
centers Q ubiquinol (QH2 ).
QH2

Succinate-Q oxidoreductase (complex II)

2e

Fe-S Fe
Q
FMN
centers QH2
Heme
NADH

Complex I or NADH-Q oxidoreductase. The abbreviations are 2H

discussed in the text. In all diagrams of respiratory complexes in
this article, the matrix is at the bottom, with the intermembrane
space above. FAD FADH
NADH-coenzyme Q oxidoreductase, also known as
NADH dehydrogenase or complex I, is the first protein
in the electron transport chain.[16] Complex I is a giant
enzyme with the mammalian complex I having 46 sub-
units and a molecular mass of about 1,000 kilodaltons Succinate Fumarate +2H
[17]
(kDa). The structure is known in detail only from a
bacterium;[18][19] in most organisms the complex resem- Complex II: Succinate-Q oxidoreductase.
13.1. OXIDATIVE PHOSPHORYLATION 221

Succinate-Q oxidoreductase, also known as complex II Step 1 Step 2

Cyt c Cyt c
or succinate dehydrogenase, is a second entry point to 2H (ox) 2H (ox)
the electron transport chain.[23] It is unusual because it is
Cyt c Cyt c
the only enzyme that is part of both the citric acid cycle 1e (red) 1e (red)
and the electron transport chain. Complex II consists of Q Q
QH2 QH2
four protein subunits and contains a bound flavin adenine QH2
Q
dinucleotide (FAD) cofactor, iron–sulfur clusters, and a Q 1e Q 1e
heme group that does not participate in electron transfer
to coenzyme Q, but is believed to be important in de- 2H
creasing production of reactive oxygen species.[24][25] It
oxidizes succinate to fumarate and reduces ubiquinone. The two electron transfer steps in complex III: Q-cytochrome c ox-
As this reaction releases less energy than the oxidation of idoreductase. After each step, Q (in the upper part of the figure)
NADH, complex II does not transport protons across the leaves the enzyme.
membrane and does not contribute to the proton gradient.
tochrome c reductase, cytochrome bc1 complex, or sim-
ply complex III.[33][34] In mammals, this enzyme is
Succinate + Q → Fumarate + QH2
a dimer, with each subunit complex containing 11
In some eukaryotes, such as the parasitic worm Ascaris protein subunits, an [2Fe-2S] iron–sulfur cluster and
suum, an enzyme similar to complex II, fumarate re- three cytochromes: one cytochrome c1 and two b
ductase (menaquinol:fumarate oxidoreductase, or QFR), cytochromes.[35] A cytochrome is a kind of electron-
operates in reverse to oxidize ubiquinol and reduce fu- transferring protein that contains at least one heme group.
marate. This allows the worm to survive in the anaer- The iron atoms inside complex III’s heme groups alternate
obic environment of the large intestine, carrying out between a reduced ferrous (+2) and oxidized ferric (+3)
anaerobic oxidative phosphorylation with fumarate as the state as the electrons are transferred through the protein.
electron acceptor.[26] Another unconventional function of The reaction catalyzed by complex III is the oxidation
complex II is seen in the malaria parasite Plasmodium of one molecule of ubiquinol and the reduction of two
falciparum. Here, the reversed action of complex II molecules of cytochrome c, a heme protein loosely as-
as an oxidase is important in regenerating ubiquinol, sociated with the mitochondrion. Unlike coenzyme Q,
which the parasite uses in an unusual form of pyrimidine which carries two electrons, cytochrome c carries only
biosynthesis.[27] one electron.

Electron transfer flavoprotein-Q oxidoreductase

matrix → Q + 2 Cyt cred + 4 Hintermembrane
QH2 + 2 Cyt cox + 2 H+ +

Electron transfer flavoprotein-ubiquinone oxidoreduc-

tase (ETF-Q oxidoreductase), also known as electron As only one of the electrons can be transferred from the
transferring-flavoprotein dehydrogenase, is a third entry QH2 donor to a cytochrome c acceptor at a time, the re-
point to the electron transport chain. It is an enzyme that action mechanism of complex III is more elaborate than
accepts electrons from electron-transferring flavoprotein those of the other respiratory complexes, and occurs in
in the mitochondrial matrix, and uses these electrons to two steps called the Q cycle.[36] In the first step, the en-
reduce ubiquinone.[28] This enzyme contains a flavin and zyme binds three substrates, first, QH2 , which is then
a [4Fe–4S] cluster, but, unlike the other respiratory com- oxidized, with one electron being passed to the second
plexes, it attaches to the surface of the membrane and substrate, cytochrome c. The two protons released from
does not cross the lipid bilayer.[29] QH2 pass into the intermembrane space. The third sub-
strate is Q, which accepts the second electron from the
QH2 and is reduced to Q.− , which is the ubisemiquinone
ETFred + Q → ETFox + QH2 free radical. The first two substrates are released, but this
ubisemiquinone intermediate remains bound. In the sec-
In mammals, this metabolic pathway is important in beta ond step, a second molecule of QH2 is bound and again
oxidation of fatty acids and catabolism of amino acids and passes its first electron to a cytochrome c acceptor. The
choline, as it accepts electrons from multiple acetyl-CoA second electron is passed to the bound ubisemiquinone,
dehydrogenases.[30][31] In plants, ETF-Q oxidoreductase reducing it to QH2 as it gains two protons from the mi-
is also important in the metabolic responses that allow tochondrial matrix. This QH2 is then released from the
survival in extended periods of darkness.[32] enzyme.[37]
As coenzyme Q is reduced to ubiquinol on the inner side
Q-cytochrome c oxidoreductase (complex III) of the membrane and oxidized to ubiquinone on the other,
a net transfer of protons across the membrane occurs,
Q-cytochrome c oxidoreductase is also known as cy- adding to the proton gradient.[3] The rather complex two-
222 CHAPTER 13. OXIDATIVE PHOSPHORYLATION

step mechanism by which this occurs is important, as it rather than in the mitochondrial matrix, and pass these
increases the efficiency of proton transfer. If, instead electrons to the ubiquinone pool.[41] These enzymes do
of the Q cycle, one molecule of QH2 were used to di- not transport protons, and, therefore, reduce ubiquinone
rectly reduce two molecules of cytochrome c, the effi- without altering the electrochemical gradient across the
ciency would be halved, with only one proton transferred inner membrane.[42]
per cytochrome c reduced.[3] Another example of a divergent electron transport chain
is the alternative oxidase, which is found in plants, as well
Cytochrome c oxidase (complex IV) as some fungi, protists, and possibly some animals.[43][44]
This enzyme transfers electrons directly from ubiquinol
[45]
For more details on this topic, see cytochrome c oxidase. to oxygen.
Cytochrome c oxidase, also known as complex IV, is the The electron transport pathways produced by these alter-
native NADH and ubiquinone oxidases have lower ATP
yields than the full pathway. The advantages produced

4 Cyt c 4H by a shortened pathway are not entirely clear. How-

ever, the alternative oxidase is produced in response to
(red)
stresses such as cold, reactive oxygen species, and infec-
tion by pathogens, as well as other factors that inhibit the
Cyt c 4e full electron transport chain.[46][47] Alternative pathways
4 (ox) might, therefore, enhance an organisms’ resistance to in-
Cu
jury, by reducing oxidative stress.[48]

Fe
Organization of complexes

Fe The original model for how the respiratory chain com-

plexes are organized was that they diffuse freely and in-
4H +O Cu dependently in the mitochondrial membrane.[17] How-
ever, recent data suggest that the complexes might
form higher-order structures called supercomplexes or
4H "respirasomes.”[49] In this model, the various complexes
2H O exist as organized sets of interacting enzymes.[50] These
associations might allow channeling of substrates be-
tween the various enzyme complexes, increasing the
Complex IV: cytochrome c oxidase.
rate and efficiency of electron transfer.[51] Within such
final protein complex in the electron transport chain.[38] mammalian supercomplexes, some components would be
The mammalian enzyme has an extremely complicated present in higher amounts than others, with some data
structure and contains 13 subunits, two heme groups, as suggesting a ratio between complexes I/II/III/IV and the
well as multiple metal ion cofactors – in all, three atoms ATP synthase of approximately 1:1:3:7:4.[52] However,
of copper, one of magnesium and one of zinc.[39] the debate over this supercomplex hypothesis is not com-
pletely resolved, as some data do not appear to fit with
This enzyme mediates the final reaction in the elec- this model.[17][53]
tron transport chain and transfers electrons to oxygen,
while pumping protons across the membrane.[40] The fi-
nal electron acceptor oxygen, which is also called the ter- 13.1.4 Prokaryotic electron transport
minal electron acceptor, is reduced to water in this step.
Both the direct pumping of protons and the consumption
chains
of matrix protons in the reduction of oxygen contribute
Further information: Microbial metabolism
to the proton gradient. The reaction catalyzed is the oxi-
dation of cytochrome c and the reduction of oxygen:
+ In contrast to the general similarity in structure and
4 Cyt cred + O2 + 8 H+ matrix → 4 Cyt cox + 2 H2 O + 4 Hintermembrane
function of the electron transport chains in eukaryotes,
bacteria and archaea possess a large variety of electron-
Alternative reductases and oxidases transfer enzymes. These use an equally wide set of
chemicals as substrates.[54] In common with eukaryotes,
Many eukaryotic organisms have electron transport prokaryotic electron transport uses the energy released
chains that differ from the much-studied mammalian en- from the oxidation of a substrate to pump ions across a
zymes described above. For example, plants have alterna- membrane and generate an electrochemical gradient. In
tive NADH oxidases, which oxidize NADH in the cytosol the bacteria, oxidative phosphorylation in Escherichia coli
13.1. OXIDATIVE PHOSPHORYLATION 223

is understood in most detail, while archaeal systems are 13.1.5 ATP synthase (complex V)
at present poorly understood.[55]
The main difference between eukaryotic and prokaryotic Further information: ATP synthase
oxidative phosphorylation is that bacteria and archaea use
many different substances to donate or accept electrons. ATP synthase, also called complex V, is the final enzyme
This allows prokaryotes to grow under a wide variety of in the oxidative phosphorylation pathway. This enzyme
environmental conditions.[56] In E. coli, for example, ox- is found in all forms of life and functions in the same way
idative phosphorylation can be driven by a large number in both prokaryotes and eukaryotes.[64] The enzyme uses
of pairs of reducing agents and oxidizing agents, which the energy stored in a proton gradient across a membrane
are listed below. The midpoint potential of a chemical to drive the synthesis of ATP from ADP and phosphate
measures how much energy is released when it is oxi- (Pᵢ). Estimates of the number of protons required to syn-
dized or reduced, with reducing agents having negative thesize one ATP have ranged from three to four,[65][66]
potentials and oxidizing agents positive potentials. with some suggesting cells can vary this ratio, to suit dif-
[67]
As shown above, E. coli can grow with reducing agents ferent conditions.
such as formate, hydrogen, or lactate as electron donors,
and nitrate, DMSO, or oxygen as acceptors.[56] The larger
the difference in midpoint potential between an oxidizing ADP + Pi + 4 H+ intermembrane ⇌ ATP + H2 O + 4 Hmatrix
+

and reducing agent, the more energy is released when they

react. Out of these compounds, the succinate/fumarate This phosphorylation reaction is an equilibrium, which
pair is unusual, as its midpoint potential is close to zero. can be shifted by altering the proton-motive force. In the
Succinate can therefore be oxidized to fumarate if a absence of a proton-motive force, the ATP synthase re-
strong oxidizing agent such as oxygen is available, or fu- action will run from right to left, hydrolyzing ATP and
marate can be reduced to succinate using a strong reduc- pumping protons out of the matrix across the membrane.
ing agent such as formate. These alternative reactions are However, when the proton-motive force is high, the reac-
catalyzed by succinate dehydrogenase and fumarate re- tion is forced to run in the opposite direction; it proceeds
ductase, respectively.[58] from left to right, allowing protons to flow down their con-
centration gradient and turning ADP into ATP.[64] In-
Some prokaryotes use redox pairs that have only a small
deed, in the closely related vacuolar type H+-ATPases,
difference in midpoint potential. For example, nitrifying
the hydrolysis reaction is used to acidify cellular com-
bacteria such as Nitrobacter oxidize nitrite to nitrate, do-
partments, by pumping protons and hydrolysing ATP.[68]
nating the electrons to oxygen. The small amount of en-
ergy released in this reaction is enough to pump protons ATP synthase is a massive protein complex with a
and generate ATP, but not enough to produce NADH mushroom-like shape. The mammalian enzyme complex
or NADPH directly for use in anabolism.[59] This prob- contains 16 subunits and has a mass of approximately 600
[69]
lem is solved by using a nitrite oxidoreductase to produce kilodaltons. The portion embedded within the mem-
enough proton-motive force to run part of the electron brane is called FO and contains a ring of c subunits and
transport chain in reverse, causing complex I to generate the proton channel. The stalk and the ball-shaped head-
NADH.[60][61] piece is called F1 and is the site of ATP synthesis. The
ball-shaped complex at the end of the F1 portion con-
Prokaryotes control their use of these electron donors and
tains six proteins of two different kinds (three α subunits
acceptors by varying which enzymes are produced, in re-
and three β subunits), whereas the “stalk” consists of one
sponse to environmental conditions.[62] This flexibility is
protein: the γ subunit, with the tip of the stalk extend-
possible because different oxidases and reductases use
ing into the ball of α and β subunits.[70] Both the α and
the same ubiquinone pool. This allows many combina-
β subunits bind nucleotides, but only the β subunits cat-
tions of enzymes to function together, linked by the com-
alyze the ATP synthesis reaction. Reaching along the side
mon ubiquinol intermediate.[57] These respiratory chains
of the F1 portion and back into the membrane is a long
therefore have a modular design, with easily interchange-
rod-like subunit that anchors the α and β subunits into the
able sets of enzyme systems.
base of the enzyme.
In addition to this metabolic diversity, prokaryotes also
As protons cross the membrane through the channel in
possess a range of isozymes – different enzymes that cat-
the base of ATP synthase, the FO proton-driven motor
alyze the same reaction. For example, in E. coli, there
rotates.[71] Rotation might be caused by changes in the
are two different types of ubiquinol oxidase using oxygen
ionization of amino acids in the ring of c subunits caus-
as an electron acceptor. Under highly aerobic conditions,
ing electrostatic interactions that propel the ring of c sub-
the cell uses an oxidase with a low affinity for oxygen that
units past the proton channel.[72] This rotating ring in turn
can transport two protons per electron. However, if lev-
drives the rotation of the central axle (the γ subunit stalk)
els of oxygen fall, they switch to an oxidase that transfers
within the α and β subunits. The α and β subunits are pre-
only one proton per electron, but has a high affinity for
vented from rotating themselves by the side-arm, which
oxygen.[63]
acts as a stator. This movement of the tip of the γ subunit
224 CHAPTER 13. OXIDATIVE PHOSPHORYLATION

within the ball of α and β subunits provides the energy or peroxide anions, which are dangerously reactive.
for the active sites in the β subunits to undergo a cycle of
movements that produces and then releases ATP.[2]
e− e−
•
O2 −→ O2 −→ O2−
2
Superoxide Peroxide

These reactive oxygen species and their reaction prod-

ucts, such as the hydroxyl radical, are very harmful to
cells, as they oxidize proteins and cause mutations in
DNA. This cellular damage might contribute to disease
and is proposed as one cause of aging.[78][79]
The cytochrome c oxidase complex is highly efficient at
reducing oxygen to water, and it releases very few partly
reduced intermediates; however small amounts of super-
oxide anion and peroxide are produced by the electron
transport chain.[80] Particularly important is the reduc-
tion of coenzyme Q in complex III, as a highly reactive
ubisemiquinone free radical is formed as an intermediate
Mechanism of ATP synthase. ATP is shown in red, ADP and in the Q cycle. This unstable species can lead to elec-
phosphate in pink and the rotating γ subunit in black. tron “leakage” when electrons transfer directly to oxy-
gen, forming superoxide.[81] As the production of reac-
This ATP synthesis reaction is called the binding change tive oxygen species by these proton-pumping complexes
mechanism and involves the active site of a β subunit cy- is greatest at high membrane potentials, it has been pro-
cling between three states.[73] In the “open” state, ADP posed that mitochondria regulate their activity to main-
and phosphate enter the active site (shown in brown in tain the membrane potential within a narrow range that
the diagram). The protein then closes up around the balances ATP production against oxidant generation.[82]
molecules and binds them loosely – the “loose” state For instance, oxidants can activate uncoupling proteins
(shown in red). The enzyme then changes shape again and that reduce membrane potential.[83]
forces these molecules together, with the active site in the
To counteract these reactive oxygen species, cells con-
resulting “tight” state (shown in pink) binding the newly
tain numerous antioxidant systems, including antioxidant
produced ATP molecule with very high affinity. Finally,
vitamins such as vitamin C and vitamin E, and antioxi-
the active site cycles back to the open state, releasing ATP
dant enzymes such as superoxide dismutase, catalase, and
and binding more ADP and phosphate, ready for the next
peroxidases,[77] which detoxify the reactive species, lim-
cycle.
iting damage to the cell.
In some bacteria and archaea, ATP synthesis is driven by
the movement of sodium ions through the cell membrane,
rather than the movement of protons.[74][75] Archaea such 13.1.7 Inhibitors
as Methanococcus also contain the A1 Aₒ synthase, a form
of the enzyme that contains additional proteins with lit- There are several well-known drugs and toxins that inhibit
tle similarity in sequence to other bacterial and eukary- oxidative phosphorylation. Although any one of these
otic ATP synthase subunits. It is possible that, in some toxins inhibits only one enzyme in the electron trans-
species, the A1 Aₒ form of the enzyme is a specialized port chain, inhibition of any step in this process will halt
sodium-driven ATP synthase,[76] but this might not be the rest of the process. For example, if oligomycin in-
true in all cases.[75] hibits ATP synthase, protons cannot pass back into the
mitochondrion.[84] As a result, the proton pumps are un-
able to operate, as the gradient becomes too strong for
13.1.6 Reactive oxygen species them to overcome. NADH is then no longer oxidized and
the citric acid cycle ceases to operate because the concen-
Further information: Oxidative stress and Antioxidant tration of NAD+ falls below the concentration that these
enzymes can use.
Molecular oxygen is an ideal terminal electron accep- Not all inhibitors of oxidative phosphorylation are toxins.
tor because it is a strong oxidizing agent. The re- In brown adipose tissue, regulated proton channels called
duction of oxygen does involve potentially harmful uncoupling proteins can uncouple respiration from ATP
intermediates.[77] Although the transfer of four electrons synthesis.[89] This rapid respiration produces heat, and is
and four protons reduces oxygen to water, which is harm- particularly important as a way of maintaining body tem-
less, transfer of one or two electrons produces superoxide perature for hibernating animals, although these proteins
13.1. OXIDATIVE PHOSPHORYLATION 225

may also have a more general function in cells’ responses 13.1.11 References
to stress.[90]
[1] Mitchell P, Moyle J (1967). “Chemiosmotic hypothesis of
oxidative phosphorylation”. Nature 213 (5072): 137–9.
13.1.8 History Bibcode:1967Natur.213..137M. doi:10.1038/213137a0.
PMID 4291593.
Further information: History of biochemistry and [2] Dimroth P, Kaim G, Matthey U (1 January 2000).
History of molecular biology “Crucial role of the membrane potential for ATP synthe-
sis by F(1)F(o) ATP synthases”. J. Exp. Biol. 203 (Pt 1):
The field of oxidative phosphorylation began with the re- 51–9. PMID 10600673.
port in 1906 by Arthur Harden of a vital role for phos- [3] Schultz BE, Chan SI (2001). “Structures and proton-
phate in cellular fermentation, but initially only sugar pumping strategies of mitochondrial respiratory en-
phosphates were known to be involved.[91] However, in zymes”. Annu Rev Biophys Biomol Struct 30: 23–65.
the early 1940s, the link between the oxidation of sug- doi:10.1146/annurev.biophys.30.1.23. PMID 11340051.
ars and the generation of ATP was firmly established by
[4] Rich PR (2003). “The molecular machinery of Keilin’s
Herman Kalckar,[92] confirming the central role of ATP
respiratory chain” (PDF). Biochem. Soc. Trans. 31 (Pt 6):
in energy transfer that had been proposed by Fritz Albert 1095–105. doi:10.1042/bst0311095. PMID 14641005.
Lipmann in 1941.[93] Later, in 1949, Morris Friedkin and
Albert L. Lehninger proved that the coenzyme NADH [5] Porter RK, Brand MD (1995). “Mitochondrial proton
linked metabolic pathways such as the citric acid cycle conductance and H+/O ratio are independent of electron
and the synthesis of ATP.[94] The term oxidative phospho- transport rate in isolated hepatocytes”. Biochem. J. 310 (
rylation was coined by Volodymyr Belitser in 1939.[95][96] Pt 2) ((Pt 2)): 379–82. PMC 1135905. PMID 7654171.

For another twenty years, the mechanism by which ATP [6] Mathews FS (1985). “The structure, function and evo-
is generated remained mysterious, with scientists search- lution of cytochromes”. Prog. Biophys. Mol. Biol. 45
ing for an elusive “high-energy intermediate” that would (1): 1–56. doi:10.1016/0079-6107(85)90004-5. PMID
link oxidation and phosphorylation reactions. [97]
This 3881803.
puzzle was solved by Peter D. Mitchell with the publi- [7] Wood PM (1983). “Why do c-type cytochromes ex-
cation of the chemiosmotic theory in 1961.[98] At first, ist?". FEBS Lett. 164 (2): 223–6. doi:10.1016/0014-
this proposal was highly controversial, but it was slowly 5793(83)80289-0. PMID 6317447.
accepted and Mitchell was awarded a Nobel prize in
1978.[99][100] Subsequent research concentrated on pu- [8] Crane FL (1 December 2001). “Biochemical func-
tions of coenzyme Q10”. J Am Coll Nutr 20 (6):
rifying and characterizing the enzymes involved, with
591–8. doi:10.1080/07315724.2001.10719063. PMID
major contributions being made by David E. Green on
11771674.
the complexes of the electron-transport chain, as well as
Efraim Racker on the ATP synthase.[101] A critical step [9] Mitchell P (1979). “Keilin’s respiratory chain con-
towards solving the mechanism of the ATP synthase was cept and its chemiosmotic consequences”. Science
provided by Paul D. Boyer, by his development in 1973 of 206 (4423): 1148–59. Bibcode:1979Sci...206.1148M.
the “binding change” mechanism, followed by his radical doi:10.1126/science.388618. PMID 388618.
[73][102]
proposal of rotational catalysis in 1982. More re- [10] Søballe B, Poole RK (1999). “Microbial ubiquinones:
cent work has included structural studies on the enzymes multiple roles in respiration, gene regulation and oxida-
involved in oxidative phosphorylation by John E. Walker, tive stress management” (PDF). Microbiology (Reading,
with Walker and Boyer being awarded a Nobel Prize in Engl.) 145 (8): 1817–30. doi:10.1099/13500872-145-8-
1997.[103] 1817. PMID 10463148.

[11] Johnson DC, Dean DR, Smith AD, Johnson MK (2005).

13.1.9 See also “Structure, function, and formation of biological iron-
sulfur clusters”. Annu. Rev. Biochem. 74: 247–
81. doi:10.1146/annurev.biochem.74.082803.133518.
• Respirometry
PMID 15952888.
• TIM/TOM Complex [12] Page CC, Moser CC, Chen X, Dutton PL (1999). “Nat-
ural engineering principles of electron tunnelling in bi-
ological oxidation-reduction”. Nature 402 (6757): 47–
13.1.10 Notes 52. Bibcode:1999Natur.402...47P. doi:10.1038/46972.
PMID 10573417.
[1] DNP was extensively used as an anti-obesity medica-
tion in the 1930s but was ultimately discontinued due [13] Leys D, Scrutton NS (2004). “Electrical circuitry
to its dangerous side effects. However, illicit use of in biology: emerging principles from protein struc-
the drug for this purpose continues today. See 2,4- ture”. Curr. Opin. Struct. Biol. 14 (6): 642–7.
Dinitrophenol#Dieting_aid for more information. doi:10.1016/j.sbi.2004.10.002. PMID 15582386.
226 CHAPTER 13. OXIDATIVE PHOSPHORYLATION

[14] Boxma B, de Graaf RM, van der Staay GW, van Alen 123–39. doi:10.1016/S0005-2728(01)00237-7. PMID
TA, Ricard G, Gabaldón T et al. (2005). “An 11803022.
anaerobic mitochondrion that produces hydrogen”. Na-
ture 434 (7029): 74–9. Bibcode:2005Natur.434...74B. [27] Painter HJ, Morrisey JM, Mather MW, Vaidya AB
doi:10.1038/nature03343. PMID 15744302. (2007). “Specific role of mitochondrial electron trans-
port in blood-stage Plasmodium falciparum”. Nature
[15] Medical CHEMISTRY Compendium. By Anders Over- 446 (7131): 88–91. Bibcode:2007Natur.446...88P.
gaard Pedersen and Henning Nielsen. Aarhus University. doi:10.1038/nature05572. PMID 17330044.
2008
[28] Ramsay RR, Steenkamp DJ, Husain M (1987).
[16] Hirst J (2005). “Energy transduction by respira- “Reactions of electron-transfer flavoprotein and electron-
tory complex I--an evaluation of current knowledge” transfer flavoprotein: ubiquinone oxidoreductase”.
(PDF). Biochem. Soc. Trans. 33 (Pt 3): 525–9. Biochem. J. 241 (3): 883–92. PMC 1147643. PMID
doi:10.1042/BST0330525. PMID 15916556. 3593226.

[17] Lenaz G, Fato R, Genova ML, Bergamini C, Bianchi C, [29] Zhang J, Frerman FE, Kim JJ (2006). “Structure
Biondi A (2006). “Mitochondrial Complex I: structural of electron transfer flavoprotein-ubiquinone oxidore-
and functional aspects”. Biochim. Biophys. Acta 1757 ductase and electron transfer to the mitochondrial
(9-10): 1406–20. doi:10.1016/j.bbabio.2006.05.007. ubiquinone pool”. Proc. Natl. Acad. Sci. U.S.A.
PMID 16828051. 103 (44): 16212–7. Bibcode:2006PNAS..10316212Z.
doi:10.1073/pnas.0604567103. PMC 1637562. PMID
[18] Sazanov LA, Hinchliffe P (2006). “Structure 17050691.
of the hydrophilic domain of respiratory com-
[30] Ikeda Y, Dabrowski C, Tanaka K (25 January 1983).
plex I from Thermus thermophilus”. Science 311
“Separation and properties of five distinct acyl-CoA de-
(5766): 1430–6. Bibcode:2006Sci...311.1430S.
hydrogenases from rat liver mitochondria. Identification
doi:10.1126/science.1123809. PMID 16469879.
of a new 2-methyl branched chain acyl-CoA dehydroge-
[19] Efremov R.G., Baradaran R., & Sazanov L.A., (2010) nase”. J. Biol. Chem. 258 (2): 1066–76. PMID 6401712.
The arcdhitecture of respiratory complex I, Nature 465,
[31] Ruzicka FJ, Beinert H (1977). “A new iron-sulfur flavo-
441-445
protein of the respiratory chain. A component of the fatty
[20] Baranova EA, Holt PJ, Sazanov LA (2007). “Projection acid beta oxidation pathway” (PDF). J. Biol. Chem. 252
structure of the membrane domain of Escherichia coli res- (23): 8440–5. PMID 925004.
piratory complex I at 8 A resolution”. J. Mol. Biol. 366 [32] Ishizaki K, Larson TR, Schauer N, Fernie AR, Gra-
(1): 140–54. doi:10.1016/j.jmb.2006.11.026. PMID ham IA, Leaver CJ (2005). “The critical role of Ara-
17157874. bidopsis electron-transfer flavoprotein:ubiquinone oxi-
doreductase during dark-induced starvation”. Plant Cell
[21] Friedrich T, Böttcher B (2004). “The gross struc-
17 (9): 2587–600. doi:10.1105/tpc.105.035162. PMC
ture of the respiratory complex I: a Lego Sys-
1197437. PMID 16055629.
tem”. Biochim. Biophys. Acta 1608 (1): 1–9.
doi:10.1016/j.bbabio.2003.10.002. PMID 14741580. [33] Berry EA, Guergova-Kuras M, Huang LS, Crofts AR
(2000). “Structure and function of cytochrome bc
[22] Hirst J (January 2010). “Towards the molecular mech-
complexes”. Annu. Rev. Biochem. 69: 1005–
anism of respiratory complex I”. Biochem. J. 425 (2):
75. doi:10.1146/annurev.biochem.69.1.1005. PMID
327–39. doi:10.1042/BJ20091382. PMID 20025615.
10966481.
[23] Cecchini G (2003). “Function and structure of complex II [34] Crofts AR (2004). “The cytochrome bc1
of the respiratory chain”. Annu. Rev. Biochem. 72: 77– complex: function in the context of struc-
109. doi:10.1146/annurev.biochem.72.121801.161700. ture”. Annu. Rev. Physiol. 66: 689–733.
PMID 14527321. doi:10.1146/annurev.physiol.66.032102.150251.
[24] Yankovskaya V, Horsefield R, Törnroth S, Luna-Chavez PMID 14977419.
C, Miyoshi H, Léger C, Byrne B, Cecchini G, Iwata [35] Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen
S et al. (2003). “Architecture of succinate dehydro- B et al. (1998). “Complete structure of the 11-subunit
genase and reactive oxygen species generation”. Sci- bovine mitochondrial cytochrome bc1 complex”. Sci-
ence 299 (5607): 700–4. Bibcode:2003Sci...299..700Y. ence 281 (5373): 64–71. Bibcode:1998Sci...281...64I.
doi:10.1126/science.1079605. PMID 12560550. doi:10.1126/science.281.5373.64. PMID 9651245.
[25] Horsefield R, Iwata S, Byrne B (2004). “Complex II from [36] Trumpower BL (1990). “The protonmotive Q cycle. En-
a structural perspective”. Curr. Protein Pept. Sci. 5 ergy transduction by coupling of proton translocation to
(2): 107–18. doi:10.2174/1389203043486847. PMID electron transfer by the cytochrome bc1 complex” (PDF).
15078221. J. Biol. Chem. 265 (20): 11409–12. PMID 2164001.
[26] Kita K, Hirawake H, Miyadera H, Amino H, Takeo S [37] Hunte C, Palsdottir H, Trumpower BL (2003). “Pro-
(2002). “Role of complex II in anaerobic respiration of tonmotive pathways and mechanisms in the cytochrome
the parasite mitochondria from Ascaris suum and Plas- bc1 complex”. FEBS Lett. 545 (1): 39–46.
modium falciparum”. Biochim. Biophys. Acta 1553 (1-2): doi:10.1016/S0014-5793(03)00391-0. PMID 12788490.
13.1. OXIDATIVE PHOSPHORYLATION 227

[38] Calhoun MW, Thomas JW, Gennis RB (1994). “The [49] Heinemeyer J, Braun HP, Boekema EJ, Kouril R
cytochrome oxidase superfamily of redox-driven pro- (2007). “A structural model of the cytochrome C
ton pumps”. Trends Biochem. Sci. 19 (8): 325–30. reductase/oxidase supercomplex from yeast mitochon-
doi:10.1016/0968-0004(94)90071-X. PMID 7940677. dria”. J. Biol. Chem. 282 (16): 12240–8.
doi:10.1074/jbc.M610545200. PMID 17322303.
[39] Tsukihara T, Aoyama H, Yamashita E, Tomizaki
T, Yamaguchi H, Shinzawa-Itoh K et al. (1996). [50] Schägger H, Pfeiffer K (2000). “Supercomplexes
“The whole structure of the 13-subunit oxidized in the respiratory chains of yeast and mam-
cytochrome c oxidase at 2.8 A”. Science 272 malian mitochondria”. EMBO J. 19 (8): 1777–83.
(5265): 1136–44. Bibcode:1996Sci...272.1136T. doi:10.1093/emboj/19.8.1777. PMC 302020. PMID
doi:10.1126/science.272.5265.1136. PMID 8638158. 10775262.

[40] Yoshikawa S, Muramoto K, Shinzawa-Itoh K, Aoyama [51] Schägger H (2002). “Respiratory chain supercomplexes
H, Tsukihara T, Shimokata K et al. (2006). “Proton of mitochondria and bacteria”. Biochim. Biophys. Acta
pumping mechanism of bovine heart cytochrome c ox- 1555 (1-3): 154–9. doi:10.1016/S0005-2728(02)00271-
idase”. Biochim. Biophys. Acta 1757 (9-10): 1110–6. 2. PMID 12206908.
doi:10.1016/j.bbabio.2006.06.004. PMID 16904626. [52] Schägger H, Pfeiffer K (2001). “The ratio of oxida-
tive phosphorylation complexes I-V in bovine heart mi-
[41] Rasmusson AG, Soole KL, Elthon TE (2004).
tochondria and the composition of respiratory chain su-
“Alternative NAD(P)H dehydrogenases of plant
percomplexes”. J. Biol. Chem. 276 (41): 37861–7.
mitochondria”. Annu Rev Plant Biol 55: 23–39.
doi:10.1074/jbc.M106474200. PMID 11483615.
doi:10.1146/annurev.arplant.55.031903.141720. PMID
15725055. [53] Gupte S, Wu ES, Hoechli L, Hoechli M, Jacobson K,
Sowers AE et al. (1984). “Relationship between lat-
[42] Menz RI, Day DA (1996). “Purification and characteri- eral diffusion, collision frequency, and electron trans-
zation of a 43-kDa rotenone-insensitive NADH dehydro- fer of mitochondrial inner membrane oxidation-reduction
genase from plant mitochondria”. J. Biol. Chem. 271 components”. Proc. Natl. Acad. Sci. U.S.A.
(38): 23117–20. doi:10.1074/jbc.271.38.23117. PMID 81 (9): 2606–10. Bibcode:1984PNAS...81.2606G.
8798503. doi:10.1073/pnas.81.9.2606. PMC 345118. PMID
6326133.
[43] McDonald A, Vanlerberghe G (2004). “Branched mi-
tochondrial electron transport in the Animalia: presence [54] Nealson KH (1999). “Post-Viking microbiology: new ap-
of alternative oxidase in several animal phyla”. IUBMB proaches, new data, new insights”. Orig Life Evol Biosph
Life 56 (6): 333–41. doi:10.1080/1521-6540400000876. 29 (1): 73–93. doi:10.1023/A:1006515817767. PMID
PMID 15370881. 11536899.

[44] Sluse FE, Jarmuszkiewicz W (1998). “Alternative ox- [55] Schäfer G, Engelhard M, Müller V (1999). “Bioenergetics
idase in the branched mitochondrial respiratory net- of the Archaea”. Microbiol. Mol. Biol. Rev. 63 (3): 570–
work: an overview on structure, function, regulation, 620. PMC 103747. PMID 10477309.
and role”. Braz. J. Med. Biol. Res. 31 (6): 733–
47. doi:10.1590/S0100-879X1998000600003. PMID [56] Ingledew WJ, Poole RK (1984). “The respiratory chains
9698817. of Escherichia coli”. Microbiol. Rev. 48 (3): 222–71.
PMC 373010. PMID 6387427.
[45] Moore AL, Siedow JN (1991). “The regulation and nature
[57] Unden G, Bongaerts J (1997). “Alternative respira-
of the cyanide-resistant alternative oxidase of plant mito-
tory pathways of Escherichia coli: energetics and tran-
chondria”. Biochim. Biophys. Acta 1059 (2): 121–40.
scriptional regulation in response to electron accep-
doi:10.1016/S0005-2728(05)80197-5. PMID 1883834.
tors”. Biochim. Biophys. Acta 1320 (3): 217–34.
[46] Vanlerberghe GC, McIntosh L (1997). “ALTERNA- doi:10.1016/S0005-2728(97)00034-0. PMID 9230919.
TIVE OXIDASE: From Gene to Function”. Annu. [58] Cecchini G, Schröder I, Gunsalus RP, Maklashina E
Rev. Plant Physiol. Plant Mol. Biol. 48: 703–734. (2002). “Succinate dehydrogenase and fumarate reduc-
doi:10.1146/annurev.arplant.48.1.703. PMID 15012279. tase from Escherichia coli”. Biochim. Biophys. Acta 1553
(1-2): 140–57. doi:10.1016/S0005-2728(01)00238-9.
[47] Ito Y, Saisho D, Nakazono M, Tsutsumi N, Hirai A
PMID 11803023.
(1997). “Transcript levels of tandem-arranged alterna-
tive oxidase genes in rice are increased by low tem- [59] Freitag A, Bock E; Bock (1990). “Energy conservation in
perature”. Gene 203 (2): 121–9. doi:10.1016/S0378- Nitrobacter”. FEMS Microbiology Letters 66 (1–3): 157–
1119(97)00502-7. PMID 9426242. 62. doi:10.1111/j.1574-6968.1990.tb03989.x.

[48] Maxwell DP, Wang Y, McIntosh L (1999). “The alter- [60] Starkenburg SR, Chain PS, Sayavedra-Soto LA, Hauser L,
native oxidase lowers mitochondrial reactive oxygen pro- Land ML, Larimer FW et al. (2006). “Genome sequence
duction in plant cells”. Proc. Natl. Acad. Sci. U.S.A. of the chemolithoautotrophic nitrite-oxidizing bacterium
96 (14): 8271–6. Bibcode:1999PNAS...96.8271M. Nitrobacter winogradskyi Nb-255”. Appl. Environ. Mi-
doi:10.1073/pnas.96.14.8271. PMC 22224. PMID crobiol. 72 (3): 2050–63. doi:10.1128/AEM.72.3.2050-
10393984. 2063.2006. PMC 1393235. PMID 16517654.
228 CHAPTER 13. OXIDATIVE PHOSPHORYLATION

[61] Yamanaka T, Fukumori Y (1988). “The nitrite oxidiz- F1 adenosine triphosphatase. Correlations of initial ve-
ing system of Nitrobacter winogradskyi”. FEMS Mi- locity, bound intermediate, and oxygen exchange mea-
crobiol. Rev. 4 (4): 259–70. doi:10.1111/j.1574- surements with an alternating three-site model”. J. Biol.
6968.1988.tb02746.x. PMID 2856189. Chem. 257 (20): 12030–8. PMID 6214554.

[62] Iuchi S, Lin EC (1993). “Adaptation of Escherichia coli to [74] Dimroth P (1994). “Bacterial sodium ion-coupled en-
redox environments by gene expression”. Mol. Microbiol. ergetics”. Antonie Van Leeuwenhoek 65 (4): 381–95.
9 (1): 9–15. doi:10.1111/j.1365-2958.1993.tb01664.x. doi:10.1007/BF00872221. PMID 7832594.
PMID 8412675.
[75] Becher B, Müller V (1994). “Delta mu Na+ drives the
[63] Calhoun MW, Oden KL, Gennis RB, de Mattos MJ, Nei- synthesis of ATP via an delta mu Na(+)-translocating
jssel OM (1993). “Energetic efficiency of Escherichia F1F0-ATP synthase in membrane vesicles of the archaeon
coli: effects of mutations in components of the aerobic Methanosarcina mazei Gö1”. J. Bacteriol. 176 (9): 2543–
respiratory chain” (PDF). J. Bacteriol. 175 (10): 3020–5. 50. PMC 205391. PMID 8169202.
PMC 204621. PMID 8491720.
[76] Müller V (2004). “An exceptional variability in
[64] Boyer PD (1997). “The ATP synthase--a splendid
the motor of archael A1A0 ATPases: from multi-
molecular machine”. Annu. Rev. Biochem. 66:
meric to monomeric rotors comprising 6-13 ion bind-
717–49. doi:10.1146/annurev.biochem.66.1.717. PMID
ing sites”. J. Bioenerg. Biomembr. 36 (1): 115–
9242922.
25. doi:10.1023/B:JOBB.0000019603.68282.04. PMID
[65] Van Walraven HS, Strotmann H, Schwarz O, Rumberg B 15168615.
(1996). “The H+/ATP coupling ratio of the ATP synthase
from thiol-modulated chloroplasts and two cyanobacte- [77] Davies KJ (1995). “Oxidative stress: the paradox of aer-
rial strains is four”. FEBS Lett. 379 (3): 309–13. obic life”. Biochem. Soc. Symp. 61: 1–31. PMID
doi:10.1016/0014-5793(95)01536-1. PMID 8603713. 8660387.

[66] Yoshida M, Muneyuki E, Hisabori T (2001). “ATP [78] Rattan SI (2006). “Theories of biological aging: genes,
synthase--a marvellous rotary engine of the cell”. proteins, and free radicals”. Free Radic. Res. 40
Nat. Rev. Mol. Cell Biol. 2 (9): 669–77. (12): 1230–8. doi:10.1080/10715760600911303. PMID
doi:10.1038/35089509. PMID 11533724. 17090411.

[67] Schemidt RA, Qu J, Williams JR, Brusilow WS (1998). [79] Valko M, Leibfritz D, Moncol J, Cronin MT, Mazur
“Effects of carbon source on expression of F0 genes and M, Telser J (2007). “Free radicals and antioxidants
on the stoichiometry of the c subunit in the F1F0 AT- in normal physiological functions and human disease”.
Pase of Escherichia coli”. J. Bacteriol. 180 (12): 3205–8. Int. J. Biochem. Cell Biol. 39 (1): 44–84.
PMC 107823. PMID 9620972. doi:10.1016/j.biocel.2006.07.001. PMID 16978905.

[68] Nelson N, Perzov N, Cohen A, Hagai K, Padler V, Nel- [80] Raha S, Robinson BH (2000). “Mitochondria, oxygen
son H (1 January 2000). “The cellular biology of proton- free radicals, disease and ageing”. Trends Biochem. Sci.
motive force generation by V-ATPases”. J. Exp. Biol. 203 25 (10): 502–8. doi:10.1016/S0968-0004(00)01674-1.
(Pt 1): 89–95. PMID 10600677. PMID 11050436.

[69] Rubinstein JL, Walker JE, Henderson R (2003). [81] Finkel T, Holbrook NJ (2000). “Oxidants, oxidative stress
“Structure of the mitochondrial ATP synthase by elec- and the biology of ageing”. Nature 408 (6809): 239–47.
tron cryomicroscopy”. EMBO J. 22 (23): 6182–92. doi:10.1038/35041687. PMID 11089981.
doi:10.1093/emboj/cdg608. PMC 291849. PMID
14633978. [82] Kadenbach B, Ramzan R, Wen L, Vogt S (March
2010). “New extension of the Mitchell Theory for ox-
[70] Leslie AG, Walker JE (2000). “Structural model of F1-
idative phosphorylation in mitochondria of living organ-
ATPase and the implications for rotary catalysis”. Philos.
isms”. Biochim. Biophys. Acta 1800 (3): 205–12.
Trans. R. Soc. Lond., B, Biol. Sci. 355 (1396): 465–
doi:10.1016/j.bbagen.2009.04.019. PMID 19409964.
71. doi:10.1098/rstb.2000.0588. PMC 1692760. PMID
10836500.
[83] Echtay KS, Roussel D, St-Pierre J, Jekabsons MB, Ca-
[71] Noji H, Yoshida M (2001). “The rotary machine in the denas S, Stuart JA et al. (January 2002). “Superox-
cell, ATP synthase”. J. Biol. Chem. 276 (3): 1665–8. ide activates mitochondrial uncoupling proteins”. Na-
doi:10.1074/jbc.R000021200. PMID 11080505. ture 415 (6867): 96–9. Bibcode:2002Natur.415...96E.
doi:10.1038/415096a. PMID 11780125.
[72] Capaldi RA, Aggeler R (2002). “Mechanism of the
F(1)F(0)-type ATP synthase, a biological rotary mo- [84] Joshi S, Huang YG (1991). “ATP synthase complex
tor”. Trends Biochem. Sci. 27 (3): 154–60. from bovine heart mitochondria: the oligomycin sen-
doi:10.1016/S0968-0004(01)02051-5. PMID 11893513. sitivity conferring protein is essential for dicyclohexyl
carbodiimide-sensitive ATPase”. Biochim. Biophys. Acta
[73] Gresser MJ, Myers JA, Boyer PD (25 October 1982). 1067 (2): 255–8. doi:10.1016/0005-2736(91)90051-9.
“Catalytic site cooperativity of beef heart mitochondrial PMID 1831660.
13.1. OXIDATIVE PHOSPHORYLATION 229

[85] Tsubaki M (1993). “Fourier-transform infrared study of [98] Mitchell P (1961). “Coupling of phosphorylation to
cyanide binding to the Fea3-CuB binuclear site of bovine electron and hydrogen transfer by a chemi-osmotic
heart cytochrome c oxidase: implication of the redox- type of mechanism”. Nature 191 (4784): 144–8.
linked conformational change at the binuclear site”. Bio- Bibcode:1961Natur.191..144M. doi:10.1038/191144a0.
chemistry 32 (1): 164–73. doi:10.1021/bi00052a022. PMID 13771349.
PMID 8380331.
[99] Milton H. Saier Jr. “Peter Mitchell and the Vital Force”.
[86] Heytler PG (1979). “Uncouplers of oxidative phospho- Retrieved 2014-05-25.
rylation”. Meth. Enzymol. Methods in Enzymology
55: 462–42. doi:10.1016/0076-6879(79)55060-5. ISBN [100] Mitchell, Peter (1978). “David Keilin’s Respiratory Chain
978-0-12-181955-2. PMID 156853. Concept and Its Chemiosmotic Consequences” (PDF).
Nobel lecture. Nobel Foundation. Retrieved 2007-07-21.
[87] Lambert AJ, Brand MD (2004). “Inhibitors of the
quinone-binding site allow rapid superoxide production [101] Pullman ME, Penefsky HS, Datta A, Racker E (1 Novem-
from mitochondrial NADH:ubiquinone oxidoreductase ber 1960). “Partial resolution of the enzymes catalyz-
(complex I)". J. Biol. Chem. 279 (38): 39414–20. ing oxidative phosphorylation. I. Purification and proper-
doi:10.1074/jbc.M406576200. PMID 15262965. ties of soluble dinitrophenol-stimulated adenosine triphos-
phatase”. J. Biol. Chem. 235 (11): 3322–9. PMID
[88] Dervartanian DV, Veeger C (November 1964). “STUD- 13738472.
IES ON SUCCINATE DEHYDROGENASE. I. SPEC-
TRAL PROPERTIES OF THE PURIFIED ENZYME [102] Boyer PD, Cross RL, Momsen W (1973). “A new
AND FORMATION OF ENZYME-COMPETITIVE concept for energy coupling in oxidative phosphoryla-
INHIBITOR COMPLEXES”. Biochim. Biophys. Acta tion based on a molecular explanation of the oxygen ex-
92 (2): 233–47. doi:10.1016/0926-6569(64)90182-8. change reactions”. Proc. Natl. Acad. Sci. U.S.A.
PMID 14249115. 70 (10): 2837–9. Bibcode:1973PNAS...70.2837B.
doi:10.1073/pnas.70.10.2837. PMC 427120. PMID
[89] Ricquier D, Bouillaud F (2000). “The uncoupling protein 4517936.
homologues: UCP1, UCP2, UCP3, StUCP and AtUCP”.
Biochem. J. 345 (2): 161–79. doi:10.1042/0264- [103] “The Nobel Prize in Chemistry 1997”. Nobel Foundation.
6021:3450161. PMC 1220743. PMID 10620491. Retrieved 2007-07-21.

[90] Borecký J, Vercesi AE (2005). “Plant uncoupling

mitochondrial protein and alternative oxidase: energy 13.1.12 Further reading
metabolism and stress”. Biosci. Rep. 25 (3-4): 271–86.
doi:10.1007/s10540-005-2889-2. PMID 16283557.
Introductory
[91] Harden A, Young WJ.; Young (1906). “The alcoholic fer-
ment of yeast-juice”. Proceedings of the Royal Society B • Nelson DL; Cox MM (2004). Lehninger Principles
(77): 405–20. doi:10.1098/rspb.1906.0029. of Biochemistry (4th ed.). W. H. Freeman. ISBN
0-7167-4339-6.
[92] Kalckar HM (1974). “Origins of the concept oxidative
phosphorylation”. Mol. Cell. Biochem. 5 (1-2): 55–63. • Schneider ED; Sagan D (2006). Into the Cool: En-
doi:10.1007/BF01874172. PMID 4279328. ergy Flow, Thermodynamics and Life (1st ed.). Uni-
[93] Lipmann F, (1941). “Metabolic generation and utiliza- versity of Chicago Press. ISBN 0-226-73937-6.
tion of phosphate bond energy”. Adv Enzymol 1: 99–162.
doi:10.4159/harvard.9780674366701.c141.
• Lane N (2006). Power, Sex, Suicide: Mitochondria
and the Meaning of Life (1st ed.). Oxford University
[94] Friedkin M, Lehninger AL (1 April 1949). “Esterification Press, USA. ISBN 0-19-920564-7.
of inorganic phosphate coupled to electron transport be-
tween dihydrodiphosphopyridine nucleotide and oxygen”.
J. Biol. Chem. 178 (2): 611–44. PMID 18116985. Advanced
[95] H. M. Kalckar (1991). “50 years of biological research-- • Nicholls DG; Ferguson SJ (2002). Bioenergetics 3
from oxidative phosphorylation to energy requiring trans- (1st ed.). Academic Press. ISBN 0-12-518121-3.
port regulation”. Annual review of biochemistry 60: 1–
37. doi:10.1146/annurev.bi.60.070191.000245. PMID • Haynie D (2001). Biological Thermodynamics (1st
1883194. ed.). Cambridge University Press. ISBN 0-521-
[96] Belitser, V. A., Tsibakova, E. T. (1939). “About phospho- 79549-4.
rilation mechanism coupled with respiration”. Biokhimya
4: 516–534.
• Rajan SS (2003). Introduction to Bioenergetics (1st
ed.). Anmol. ISBN 81-261-1364-2.
[97] Slater EC (1953). “Mechanism of phosphorylation
in the respiratory chain”. Nature 172 (4387): 975–8. • Wikstrom M (Ed) (2005). Biophysical and Struc-
Bibcode:1953Natur.172..975S. doi:10.1038/172975a0. tural Aspects of Bioenergetics (1st ed.). Royal Soci-
PMID 13111237. ety of Chemistry. ISBN 0-85404-346-2.
230 CHAPTER 13. OXIDATIVE PHOSPHORYLATION

13.1.13 External links

General resources

• Animated diagrams illustrating oxidative phospho-

rylation Wiley and Co Concepts in Biochemistry

• On-line biophysics lectures Antony Crofts,

University of Illinois at Urbana-Champaign

• ATP Synthase Graham Johnson

Structural resources

• PDB molecule of the month:

• ATP synthase
• Cytochrome c
• Cytochrome c oxidase
• Interactive molecular models at Universidade Fer-
nando Pessoa:
• NADH dehydrogenase
• succinate dehydrogenase
• Coenzyme Q - cytochrome c reductase
• cytochrome c oxidase
Chapter 14

Photosynthesis

14.1 Photosynthesis

Composite image showing the global distribution of photosyn-

thesis, including both oceanic phytoplankton and terrestrial
vegetation. Dark red and blue-green indicate regions of high
photosynthetic activity in ocean and land respectively.

σύνθεσις, synthesis, “putting together”.[1][2][3] In most

cases, oxygen is also released as a waste product. Most
plants, most algae, and cyanobacteria perform photosyn-
thesis; such organisms are called photoautotrophs. Pho-
tosynthesis maintains atmospheric oxygen levels and sup-
plies all of the organic compounds and most of the energy
necessary for life on Earth.[4]
Although photosynthesis is performed differently by dif-
ferent species, the process always begins when energy
from light is absorbed by proteins called reaction centres
Schematic of photosynthesis in plants. The carbohydrates pro-
duced are stored in or used by the plant.
that contain green chlorophyll pigments. In plants, these
proteins are held inside organelles called chloroplasts,
which are most abundant in leaf cells, while in bacteria
6CO2 6H2O Light C 6H12O6 6O2
they are embedded in the plasma membrane. In these
Carbon dioxide Water Sugar Oxygen
light-dependent reactions, some energy is used to strip
electrons from suitable substances, such as water, produc-
ing oxygen gas. Furthermore, two further compounds are
Overall equation for the type of photosynthesis that occurs in
generated: reduced nicotinamide adenine dinucleotide
plants
phosphate (NADPH) and adenosine triphosphate (ATP),
Photosynthesis is a process used by plants and other or- the “energy currency” of cells.
ganisms to convert light energy, normally from the Sun, In plants, algae and cyanobacteria, sugars are produced
into chemical energy that can be later released to fuel the by a subsequent sequence of light-independent reactions
organisms’ activities. This chemical energy is stored in called the Calvin cycle, but some bacteria use different
carbohydrate molecules, such as sugars, which are syn- mechanisms, such as the reverse Krebs cycle. In the
thesized from carbon dioxide and water – hence the name Calvin cycle, atmospheric carbon dioxide is incorporated
photosynthesis, from the Greek φῶς, phōs, “light”, and into already existing organic carbon compounds, such

231
232 CHAPTER 14. PHOTOSYNTHESIS

as ribulose bisphosphate (RuBP).[5] Using the ATP and these organisms. However, there are some types of bacte-
NADPH produced by the light-dependent reactions, the ria that carry out anoxygenic photosynthesis. These con-
resulting compounds are then reduced and removed to sume carbon dioxide but do not release oxygen.
form further carbohydrates, such as glucose. Carbon dioxide is converted into sugars in a process
The first photosynthetic organisms probably evolved early called carbon fixation. Carbon fixation is an endothermic
in the evolutionary history of life and most likely used redox reaction, so photosynthesis needs to supply both a
reducing agents, such as hydrogen or hydrogen sulfide, source of energy to drive this process, and the electrons
as sources of electrons, rather than water.[6] Cyanobacte- needed to convert carbon dioxide into a carbohydrate.
ria appeared later; the excess oxygen they produced con- This addition of the electrons is a reduction reaction. In
tributed to the oxygen catastrophe,[7] which rendered the general outline and in effect, photosynthesis is the op-
evolution of complex life possible. Today, the average posite of cellular respiration, in which glucose and other
rate of energy capture by photosynthesis globally is ap- compounds are oxidized to produce carbon dioxide and
proximately 130 terawatts,[8][9][10] which is about three water, and to release exothermic chemical energy to drive
times the current power consumption of human civiliza- the organism’s metabolism. However, the two processes
tion.[11] Photosynthetic organisms also convert around take place through a different sequence of chemical re-
100–115 thousand million metric tonnes of carbon into actions and in different cellular compartments.
biomass per year.[12][13] The general equation for photosynthesis as first proposed
by Cornelius van Niel is therefore:[14]
14.1.1 Overview
CO2 + 2H2 A + photons → [CH2 O] + 2A +
H2 O
carbon dioxide + electron donor + light energy
Light → carbohydrate + oxidized electron donor +
water
H 2O O2
Since water is used as the electron donor in oxygenic pho-
tosynthesis, the equation for this process is:

Light reactions n CO2 + 2n H2 O + photons → (CH2 O)n + n

+
O2 + n H2 O
NAD

Pi
P
AT

carbon dioxide + water + light energy → car-

D

CO2
NA
P

P
PH

AD

bohydrate + oxygen + water

This equation emphasizes that water is both a reactant (in

Calvin the light-dependent reaction) and a product (in the light-
independent reaction), but canceling n water molecules
Cycle from each side gives the net equation:

n CO2 + n H2 O + photons → (CH2 O)n + n O2

sugar carbon dioxide + water + light energy → car-
bohydrate + oxygen

Photosynthesis changes sunlight into chemical energy, splits water

Other processes substitute other compounds (such as
to liberate O2 , and fixes CO2 into sugar.
arsenite) for water in the electron-supply role; for ex-
ample some microbes use sunlight to oxidize arsenite to
Photosynthetic organisms are photoautotrophs, which arsenate:[15] The equation for this reaction is:
means that they are able to synthesize food directly from
carbon dioxide and water using energy from light. How-
CO2 + (AsO3 3− ) + photons → (AsO4 3− ) +
ever, not all organisms that use light as a source of en-
CO[16]
ergy carry out photosynthesis, since photoheterotrophs
use organic compounds, rather than carbon dioxide, as carbon dioxide + arsenite + light energy → ar-
[4]
a source of carbon. In plants, algae and cyanobacte- senate + carbon monoxide (used to build other
ria, photosynthesis releases oxygen. This is called oxy- compounds in subsequent reactions)
genic photosynthesis. Although there are some differ-
ences between oxygenic photosynthesis in plants, algae, Photosynthesis occurs in two stages. In the first stage,
and cyanobacteria, the overall process is quite similar in light-dependent reactions or light reactions capture the
14.1. PHOTOSYNTHESIS 233

energy of light and use it to make the energy-storage In plants and algae, photosynthesis takes place in
molecules ATP and NADPH. During the second stage, organelles called chloroplasts. A typical plant cell con-
the light-independent reactions use these products to cap- tains about 10 to 100 chloroplasts. The chloroplast is
ture and reduce carbon dioxide. enclosed by a membrane. This membrane is composed
Most organisms that utilize photosynthesis to produce of a phospholipid inner membrane, a phospholipid outer
oxygen use visible light to do so, although at least three membrane, and an intermembrane space between them.
use shortwave infrared or, more specifically, far-red Within the membrane is an aqueous fluid called the
radiation.[17] stroma. The stroma contains stacks (grana) of thylakoids,
which are the site of photosynthesis. The thylakoids are
Archaeobacteria use a simpler method using a pig- flattened disks, bounded by a membrane with a lumen
ment similar to the pigments used for vision. The or thylakoid space within it. The site of photosynthesis
archaearhodopsin changes its configuration in response to is the thylakoid membrane, which contains integral and
sunlight, acting as a proton pump. This produces a proton peripheral membrane protein complexes, including the
gradient more directly which is then converted to chem- pigments that absorb light energy, which form the pho-
ical energy. The process does not involve carbon dioxide tosystems.
fixation and does not release oxygen. It seems to have
evolved separately.[18][19] Plants absorb light primarily using the pigment
chlorophyll, which is the reason that most plants
have a green color. Besides chlorophyll, plants also
use pigments such as carotenes and xanthophylls.[23]
14.1.2 Photosynthetic membranes and or- Algae also use chlorophyll, but various other pig-
ganelles ments are present, such as phycocyanin, carotenes,
and xanthophylls in green algae, phycoerythrin in red
algae (rhodophytes) and fucoxanthin in brown algae and
7
1
diatoms resulting in a wide variety of colors.
8
2
3 These pigments are embedded in plants and algae in com-
plexes called antenna proteins. In such proteins, all the
pigments are ordered to work well together. Such a pro-
9
tein is also called a light-harvesting complex.

4
10
Although all cells in the green parts of a plant have chloro-
11
5 plasts, most of the energy in higher plants is captured
12
6
in the leaves - certain species adapted to conditions of
strong sunlight and aridity, such as many Euphorbia and
Chloroplast ultrastructure: cactus species, have their main photosynthetic organs in
1. outer membrane their stems. The cells in the interior tissues of a leaf,
2. intermembrane space
called the mesophyll, can contain between 450,000 and
3. inner membrane (1+2+3: envelope)
4. stroma (aqueous fluid)
800,000 chloroplasts for every square millimeter of leaf.
5. thylakoid lumen (inside of thylakoid) The surface of the leaf is uniformly coated with a water-
6. thylakoid membrane resistant waxy cuticle that protects the leaf from exces-
7. granum (stack of thylakoids) sive evaporation of water and decreases the absorption
8. thylakoid (lamella) of ultraviolet or blue light to reduce heating. The trans-
9. starch parent epidermis layer allows light to pass through to the
10. ribosome palisade mesophyll cells where most of the photosynthe-
11. plastidial DNA sis takes place.
12. plastoglobule (drop of lipids)

Main articles: Chloroplast and Thylakoid 14.1.3 Light-dependent reactions

In photosynthetic bacteria, the proteins that gather light Main article: Light-dependent reactions
for photosynthesis are embedded in cell membranes. In
its simplest form, this involves the membrane surround- In the light-dependent reactions, one molecule of the
ing the cell itself.[20] However, the membrane may be pigment chlorophyll absorbs one photon and loses one
tightly folded into cylindrical sheets called thylakoids,[21] electron. This electron is passed to a modified form of
or bunched up into round vesicles called intracytoplasmic chlorophyll called pheophytin, which passes the electron
membranes.[22] These structures can fill most of the inte- to a quinone molecule, allowing the start of a flow of
rior of a cell, giving the membrane a very large surface electrons down an electron transport chain that leads to
area and therefore increasing the amount of light that the the ultimate reduction of NADP to NADPH. In addi-
bacteria can absorb.[21] tion, this creates a proton gradient across the chloroplast
234 CHAPTER 14. PHOTOSYNTHESIS

by chlorophyll and other accessory pigments (see dia-

gram at right). When a chlorophyll molecule at the
core of the photosystem II reaction center obtains suf-
ficient excitation energy from the adjacent antenna pig-
ments, an electron is transferred to the primary electron-
acceptor molecule, pheophytin, through a process called
photoinduced charge separation. These electrons are
shuttled through an electron transport chain, the so-called
Z-scheme shown in the diagram, that initially functions to
generate a chemiosmotic potential across the membrane.
An ATP synthase enzyme uses the chemiosmotic poten-
Light-dependent reactions of photosynthesis at the thylakoid tial to make ATP during photophosphorylation, whereas
membrane NADPH is a product of the terminal redox reaction in
the Z-scheme. The electron enters a chlorophyll molecule
membrane; its dissipation is used by ATP synthase for the in Photosystem I. The electron is excited due to the light
concomitant synthesis of ATP. The chlorophyll molecule absorbed by the photosystem. A second electron carrier
regains the lost electron from a water molecule through a accepts the electron, which again is passed down lower-
process called photolysis, which releases a dioxygen (O2 ) ing energies of electron acceptors. The energy created
molecule. The overall equation for the light-dependent by the electron acceptors is used to move hydrogen ions
reactions under the conditions of non-cyclic electron flow across the thylakoid membrane into the lumen. The elec-
in green plants is:[24] tron is used to reduce the co-enzyme NADP, which has
functions in the light-independent reaction. The cyclic re-
action is similar to that of the non-cyclic, but differs in the
2 H2 O + 2 NADP+ + 3 ADP + 3 Pᵢ + light → form that it generates only ATP, and no reduced NADP
2 NADPH + 2 H+ + 3 ATP + O2 (NADPH) is created. The cyclic reaction takes place only
at photosystem I. Once the electron is displaced from the
Not all wavelengths of light can support photosynthesis. photosystem, the electron is passed down the electron
The photosynthetic action spectrum depends on the type acceptor molecules and returns to photosystem I, from
of accessory pigments present. For example, in green where it was emitted, hence the name cyclic reaction.
plants, the action spectrum resembles the absorption
spectrum for chlorophylls and carotenoids with peaks for
violet-blue and red light. In red algae, the action spectrum Water photolysis
overlaps with the absorption spectrum of phycobilins for
red blue-green light, which allows these algae to grow in Main articles: Photodissociation and Oxygen evolution
deeper waters that filter out the longer wavelengths used
by green plants. The non-absorbed part of the light spec-
The NADPH is the main reducing agent in chloroplasts,
trum is what gives photosynthetic organisms their color
providing a source of energetic electrons to other reac-
(e.g., green plants, red algae, purple bacteria) and is the
tions. Its production leaves chlorophyll with a deficit of
least effective for photosynthesis in the respective organ-
electrons (oxidized), which must be obtained from some
isms.
other reducing agent. The excited electrons lost from
chlorophyll in photosystem I are replaced from the elec-
Z scheme tron transport chain by plastocyanin. However, since
photosystem II includes the first steps of the Z-scheme,
an external source of electrons is required to reduce its
oxidized chlorophyll a molecules. The source of elec-
trons in green-plant and cyanobacterial photosynthesis is
water. Two water molecules are oxidized by four suc-
cessive charge-separation reactions by photosystem II to
yield a molecule of diatomic oxygen and four hydrogen
ions; the electron yielded in each step is transferred to a
The “Z scheme” redox-active tyrosine residue that then reduces the pho-
toxidized paired-chlorophyll a species called P680 that
In plants, light-dependent reactions occur in the thylakoid serves as the primary (light-driven) electron donor in the
membranes of the chloroplasts and use light energy to photosystem II reaction center. The oxidation of water
synthesize ATP and NADPH. The light-dependent re- is catalyzed in photosystem II by a redox-active structure
action has two forms: cyclic and non-cyclic. In the that contains four manganese ions and a calcium ion; this
non-cyclic reaction, the photons are captured in the oxygen-evolving complex binds two water molecules and
light-harvesting antenna complexes of photosystem II stores the four oxidizing equivalents that are required to
14.1. PHOTOSYNTHESIS 235

drive the water-oxidizing reaction. Photosystem II is the The fixation or reduction of carbon dioxide is a pro-
only known biological enzyme that carries out this ox- cess in which carbon dioxide combines with a five-carbon
idation of water. The hydrogen ions contribute to the sugar, ribulose 1,5-bisphosphate, to yield two molecules
transmembrane chemiosmotic potential that leads to ATP of a three-carbon compound, glycerate 3-phosphate, also
synthesis. Oxygen is a waste product of light-dependent known as 3-phosphoglycerate. Glycerate 3-phosphate,
reactions, but the majority of organisms on Earth use in the presence of ATP and NADPH produced during
oxygen for cellular respiration, including photosynthetic the light-dependent stages, is reduced to glyceraldehyde
organisms.[25][26] 3-phosphate. This product is also referred to as 3-
phosphoglyceraldehyde (PGAL) or, more generically, as
triose phosphate. Most (5 out of 6 molecules) of the
14.1.4 Light-independent reactions glyceraldehyde 3-phosphate produced is used to regen-
erate ribulose 1,5-bisphosphate so the process can con-
Calvin cycle tinue. The triose phosphates not thus “recycled” often
condense to form hexose phosphates, which ultimately
Main articles: Calvin cycle, Carbon fixation and Light- yield sucrose, starch and cellulose. The sugars produced
independent reactions during carbon metabolism yield carbon skeletons that can
be used for other metabolic reactions like the production
In the light-independent (or “dark”) reactions, the enzyme of amino acids and lipids.
RuBisCO captures CO2 from the atmosphere and, in
a process called the Calvin-Benson cycle that requires
Carbon concentrating mechanisms
the newly formed NADPH, releases three-carbon sug-
ars, which are later combined to form sucrose and starch.
The overall equation for the light-independent reactions
in green plants is[24]:128

3 CO2 + 9 ATP + 6 NADPH + 6 H+ →

C3 H6 O3 -phosphate + 9 ADP + 8 Pᵢ + 6
NADP+ + 3 H2 O

ADP

ATP

ATP

ADP

NADPH

NADP+

Overview of the Calvin cycle and carbon fixation Overview of C4 carbon fixation

Carbon fixation produces an intermediate product, which On land In hot and dry conditions, plants close their
is then converted to the final carbohydrate products. The stomata to prevent water loss. Under these conditions,
carbon skeletons produced by photosynthesis are then CO2 will decrease and oxygen gas, produced by the
variously used to form other organic compounds, such light reactions of photosynthesis, will increase, causing
as the building material cellulose, as precursors for lipid an increase of photorespiration by the oxygenase activity
and amino acid biosynthesis, or as a fuel in cellular res- of ribulose-1,5-bisphosphate carboxylase/oxygenase and
piration. The latter occurs not only in plants but also in decrease in carbon fixation. Some plants have evolved
animals when the energy from plants gets passed through mechanisms to increase the CO2 concentration in the
a food chain. leaves under these conditions.[27]
236 CHAPTER 14. PHOTOSYNTHESIS

Main article: C4 carbon fixation carbonic anhydrase. This causes the HCO3 − ions to ac-
cumulate within the cell from where they diffuse into the
[31]
C4 plants chemically fix carbon dioxide in the cells of carboxysomes. Pyrenoids in algae and [32]
hornworts also
the mesophyll by adding it to the three-carbon molecule act to concentrate CO 2 around rubisco.

phosphoenolpyruvate (PEP), a reaction catalyzed by an

enzyme called PEP carboxylase, creating the four-carbon
organic acid oxaloacetic acid. Oxaloacetic acid or malate
14.1.5 Order and kinetics
synthesized by this process is then translocated to special-
ized bundle sheath cells where the enzyme RuBisCO and The overall [13]
process of photosynthesis takes place in four
other Calvin cycle enzymes are located, and where CO2 stages:
released by decarboxylation of the four-carbon acids is
then fixed by RuBisCO activity to the three-carbon 3-
phosphoglyceric acids. The physical separation of Ru- 14.1.6 Efficiency
BisCO from the oxygen-generating light reactions re-
duces photorespiration and increases CO2 fixation and,
thus, photosynthetic capacity of the leaf.[28] C4 plants
can produce more sugar than C3 plants in conditions of
high light and temperature. Many important crop plants
are C4 plants, including maize, sorghum, sugarcane, and
millet. Plants that do not use PEP-carboxylase in car-
bon fixation are called C3 plants because the primary
carboxylation reaction, catalyzed by RuBisCO, produces
the three-carbon 3-phosphoglyceric acids directly in the
Calvin-Benson cycle. Over 90% of plants use C3 carbon
fixation, compared to 3% that use C4 carbon fixation;[29]
however, the evolution of C4 in over 60 plant lineages
makes it a striking example of convergent evolution.[27]
Probability distribution resulting from one-dimensional discrete
Main article: CAM photosynthesis time random walks. The quantum walk created using the
Hadamard coin is plotted (blue) vs a classical walk (red) after
50 time steps.
Xerophytes, such as cacti and most succulents, also use
PEP carboxylase to capture carbon dioxide in a process
called Crassulacean acid metabolism (CAM). In contrast Main article: Photosynthetic efficiency
to C4 metabolism, which physically separates the CO2
fixation to PEP from the Calvin cycle, CAM temporally Plants usually convert light into chemical energy with
separates these two processes. CAM plants have a dif- a photosynthetic efficiency of 3–6%.[33] Absorbed light
ferent leaf anatomy from C3 plants, and fix the CO2 at that is unconverted is dissipated primarily as heat, with a
night, when their stomata are open. CAM plants store small fraction (1-2%) [34] re-emitted as chlorophyll fluo-
the CO2 mostly in the form of malic acid via carboxy- rescence at longer (redder) wavelengths.
lation of phosphoenolpyruvate to oxaloacetate, which is
Actual plants’ photosynthetic efficiency varies with the
then reduced to malate. Decarboxylation of malate dur-
frequency of the light being converted, light intensity,
ing the day releases CO2 inside the leaves, thus allowing
temperature and proportion of carbon dioxide in the at-
carbon fixation to 3-phosphoglycerate by RuBisCO. Six-
mosphere, and can vary from 0.1% to 8%.[35] By com-
teen thousand species of plants use CAM.[30]
parison, solar panels convert light into electric energy at
an efficiency of approximately 6–20% for mass-produced
panels, and above 40% in laboratory devices.
In water Cyanobacteria possess carboxysomes, which
increase the concentration of CO2 around RuBisCO to Photosynthesis measurement systems are not designed to
increase the rate of photosynthesis. An enzyme, carbonic directly measure the amount of light absorbed by the
anhydrase, located within the carboxysome releases CO2 leaf. But analysis of chlorophyll-fluorescence, P700- and
from the dissolved hydrocarbonate ions (HCO3 − ). Be- P515-absorbance and gas exchange measurements reveal
fore the CO2 diffuses out it is quickly sponged up by Ru- detailed information about e.g. the photosystems, quan-
BisCO, which is concentrated within the carboxysomes. tum efficiency and the CO2 assimilation rates. With some
HCO3 − ions are made from CO2 outside the cell by an- instruments even wavelength-dependency of the photo-
other carbonic anhydrase and are actively pumped into synthetic efficiency can be analyzed.[36]
the cell by a membrane protein. They cannot cross the A phenomenon known as quantum walk increases the ef-
membrane as they are charged, and within the cytosol ficiency of the energy transport of light significantly. In
they turn back into CO2 very slowly without the help of the photosynthetic cell of an algae, bacterium, or plant,
14.1. PHOTOSYNTHESIS 237

there are light-sensitive molecules called chromophores thetic organisms have been dated at 3.4 billion years
arranged in an antenna-shaped structure named a photo- old.[40][41]
complex. When a photon is absorbed by a chromophore, The main source of oxygen in the atmosphere is oxygenic
it is converted into a quasiparticle referred to as an photosynthesis, and its first appearance is sometimes re-
exciton, which jumps from chromophore to chromophore ferred to as the oxygen catastrophe. Geological ev-
towards the reaction center of the photocomplex, a col- idence suggests that oxygenic photosynthesis, such as
lection of molecules that traps its energy in a chemical that in cyanobacteria, became important during the
form that makes it accessible for the cell’s metabolism. Paleoproterozoic era around 2 billion years ago. Mod-
The particle’s wave properties enable it to cover a wider
ern photosynthesis in plants and most photosynthetic
area and try out several possible paths simultaneously, al- prokaryotes is oxygenic. Oxygenic photosynthesis uses
lowing it to instantaneously “choose” the most efficient
water as an electron donor, which is oxidized to molecu-
route, where it will have the highest probability of ar- lar oxygen (O
riving at its destination in the minimum possible time.
2) in the photosynthetic reaction center.
Because it takes place at temperatures far higher than
quantum phenomena usually occur in, quantum walking
is only possible over very short distances, due to obstacles Symbiosis and the origin of chloroplasts
in the form of destructive interference that will come into
play. These cause the particle to lose its wave properties Several groups of animals have formed symbiotic rela-
for an instant before it regains them once again after it tionships with photosynthetic algae. These are most com-
is freed from its locked position through a classic “hop”. mon in corals, sponges and sea anemones. It is presumed
The distance towards the center is therefore covered in a that this is due to the particularly simple body plans and
series of conventional hops and quantum walks.[37][38][39] large surface areas of these animals compared to their
volumes.[42] In addition, a few marine mollusks Elysia
viridis and Elysia chlorotica also maintain a symbiotic re-
14.1.7 Evolution lationship with chloroplasts they capture from the algae
in their diet and then store in their bodies. This allows
the mollusks to survive solely by photosynthesis for sev-
eral months at a time.[43][44] Some of the genes from the
plant cell nucleus have even been transferred to the slugs,
so that the chloroplasts can be supplied with proteins that
they need to survive.[45]
An even closer form of symbiosis may explain the ori-
gin of chloroplasts. Chloroplasts have many similar-
ities with photosynthetic bacteria, including a circular
chromosome, prokaryotic-type ribosomes, and similar
proteins in the photosynthetic reaction center.[46][47] The
endosymbiotic theory suggests that photosynthetic bac-
teria were acquired (by endocytosis) by early eukaryotic
cells to form the first plant cells. Therefore, chloroplasts
may be photosynthetic bacteria that adapted to life inside
Plant cells with visible chloroplasts (from a moss, Plagiomnium plant cells. Like mitochondria, chloroplasts still possess
affine) their own DNA, separate from the nuclear DNA of their
plant host cells and the genes in this chloroplast DNA re-
Main article: Evolution of photosynthesis semble those in cyanobacteria.[48] DNA in chloroplasts
codes for redox proteins such as photosynthetic reaction
centers. The CoRR Hypothesis proposes that this Co-
Early photosynthetic systems, such as those from green
location is required for Redox Regulation.
and purple sulfur and green and purple nonsulfur bacte-
ria, are thought to have been anoxygenic, using various
molecules as electron donors. Green and purple sulfur Cyanobacteria and the evolution of photosynthesis
bacteria are thought to have used hydrogen and sulfur as
an electron donor. Green nonsulfur bacteria used various The biochemical capacity to use water as the source for
amino and other organic acids. Purple nonsulfur bacte- electrons in photosynthesis evolved once, in a common
ria used a variety of nonspecific organic molecules. The ancestor of extant cyanobacteria. The geological record
use of these molecules is consistent with the geological indicates that this transforming event took place early
evidence that the atmosphere was highly reduced at that in Earth’s history, at least 2450–2320 million years ago
time. (Ma), and, it is speculated, much earlier.[49][50] Be-
Fossils of what are thought to be filamentous photosyn- cause the Earth’s atmosphere contained almost no oxy-
238 CHAPTER 14. PHOTOSYNTHESIS

gen during the estimated development of photosynthe- uralist, demonstrated that green plants consume carbon
sis, many scientists believe that the first photosynthetic dioxide and release oxygen under the influence of light.
cyanobacteria did not generate oxygen.[51] Available ev- Soon afterward, Nicolas-Théodore de Saussure showed
idence from geobiological studies of Archean (>2500 that the increase in mass of the plant as it grows could
Ma) sedimentary rocks indicates that life existed 3500 not be due only to uptake of CO2 but also to the incorpo-
Ma, but the question of when oxygenic photosynthe- ration of water. Thus, the basic reaction by which pho-
sis evolved is still unanswered. A clear paleontologi- tosynthesis is used to produce food (such as glucose) was
cal window on cyanobacterial evolution opened about outlined.
2000 Ma, revealing an already-diverse biota of blue-
Cornelis Van Niel made key discoveries explaining the
greens. Cyanobacteria remained principal primary pro- chemistry of photosynthesis. By studying purple sul-
ducers throughout the Proterozoic Eon (2500–543 Ma),
fur bacteria and green bacteria he was the first scientist
in part because the redox structure of the oceans favored to demonstrate that photosynthesis is a light-dependent
photoautotrophs capable of nitrogen fixation. Green al-
redox reaction, in which hydrogen reduces carbon diox-
gae joined blue-greens as major primary producers on ide.
continental shelves near the end of the Proterozoic, but
only with the Mesozoic (251–65 Ma) radiations of di- Robert Emerson discovered two light reactions by testing
noflagellates, coccolithophorids, and diatoms did primary plant productivity using different wavelengths of light.
production in marine shelf waters take modern form. With the red alone, the light reactions were suppressed.
Cyanobacteria remain critical to marine ecosystems as When blue and red were combined, the output was much
primary producers in oceanic gyres, as agents of biologi- more substantial. Thus, there were two photosystems,
cal nitrogen fixation, and, in modified form, as the plastids one absorbing up to 600 nm wavelengths, the other up
of marine algae.[52] to 700 nm. The former is known as PSII, the latter is
PSI. PSI contains only chlorophyll a, PSII contains pri-
The Oriental hornet (Vespa orientalis) converts sunlight marily chlorophyll a with most of the available chloro-
into electric power using a pigment called xanthopterin. phyll b, among other pigment. These include phycobilins,
This is the first evidence of a member of the animal king- which are the red and blue pigments of red and blue al-
dom engaging in photosynthesis.[53] gae respectively, and fucoxanthol for brown algae and di-
atoms. The process is most productive when absorption
of quanta are equal in both the PSII and PSI, assuring
14.1.8 Discovery that input energy from the antenna complex is divided
between the PSI and PSII system, which in turn powers
Although some of the steps in photosynthesis are still not the photochemistry.[13]
completely understood, the overall photosynthetic equa-
tion has been known since the 19th century.
Jan van Helmont began the research of the process in the
mid-17th century when he carefully measured the mass
of the soil used by a plant and the mass of the plant as
it grew. After noticing that the soil mass changed very
little, he hypothesized that the mass of the growing plant
must come from the water, the only substance he added to
the potted plant. His hypothesis was partially accurate —
much of the gained mass also comes from carbon dioxide
as well as water. However, this was a signaling point to
the idea that the bulk of a plant’s biomass comes from the
inputs of photosynthesis, not the soil itself.
Joseph Priestley, a chemist and minister, discovered that,
when he isolated a volume of air under an inverted jar,
and burned a candle in it, the candle would burn out very
quickly, much before it ran out of wax. He further dis-
covered that a mouse could similarly “injure” air. He then
showed that the air that had been “injured” by the candle
and the mouse could be restored by a plant.
In 1778, Jan Ingenhousz, court physician to the Austrian
Empress, repeated Priestley’s experiments. He discov-
ered that it was the influence of sunlight on the plant that
could cause it to revive a mouse in a matter of hours.
In 1796, Jean Senebier, a Swiss pastor, botanist, and nat- Melvin Calvin works in his photosynthesis laboratory.
14.1. PHOTOSYNTHESIS 239

Robert Hill thought that a complex of reactions consist-

ing of an intermediate to cytochrome b6 (now a plasto-
quinone), another is from cytochrome f to a step in the
carbohydrate-generating mechanisms. These are linked
by plastoquinone, which does require energy to reduce
cytochrome f for it is a sufficient reductant. Further
experiments to prove that the oxygen developed dur-
ing the photosynthesis of green plants came from wa-
ter, were performed by Hill in 1937 and 1939. He
showed that isolated chloroplasts give off oxygen in the
presence of unnatural reducing agents like iron oxalate,
ferricyanide or benzoquinone after exposure to light. The
Hill reaction[54] is as follows:

The leaf is the primary site of photosynthesis in plants.

2 H2 O + 2 A + (light, chloroplasts) → 2 AH2
+ O2
14.1.9 Factors

There are three main factors affecting photosynthesis and

where A is the electron acceptor. Therefore, in light, the
several corollary factors. The three main are:
electron acceptor is reduced and oxygen is evolved.
Samuel Ruben and Martin Kamen used radioactive iso-
• Light irradiance and wavelength
topes to determine that the oxygen liberated in photosyn-
thesis came from the water. • Carbon dioxide concentration
Melvin Calvin and Andrew Benson, along with James
• Temperature.
Bassham, elucidated the path of carbon assimilation (the
photosynthetic carbon reduction cycle) in plants. The
carbon reduction cycle is known as the Calvin cycle, Light intensity (irradiance), wavelength and temper-
which ignores the contribution of Bassham and Benson. ature
Many scientists refer to the cycle as the Calvin-Benson
Cycle, Benson-Calvin, and some even call it the Calvin- See also: PI (photosynthesis-irradiance) curve
Benson-Bassham (or CBB) Cycle. The process of photosynthesis provides the main input
Nobel Prize-winning scientist Rudolph A. Marcus was
able to discover the function and significance of the elec-
tron transport chain.
Otto Heinrich Warburg and Dean Burk discovered the I- Chlorophyll b

quantum photosynthesis reaction that splits the CO2 , ac- Chlorophyll a

Absorbance

tivated by the respiration.[55]

Louis N.M. Duysens and Jan Amesz discovered that
chlorophyll a will absorb one light, oxidize cytochrome
f, chlorophyll a (and other pigments) will absorb another
light, but will reduce this same oxidized cytochrome, stat-
ing the two light reactions are in series.

400 500 600 700

Wavelength [nm]
Development of the concept
400 500 600 700

In 1893, Charles Reid Barnes proposed two terms, pho-

tosyntax and photosynthesis, for the biological process of
synthesis of complex carbon compounds out of carbonic Absorbance spectra of free chlorophyll a (green) and b (red) in a
acid, in the presence of chlorophyll, under the influence solvent. The action spectra of chlorophyll molecules are slightly
of light. Over time, the term photosynthesis came into modified in vivo depending on specific pigment-protein interac-
common usage as the term of choice. Later discovery of tions.
anoxygenic photosynthetic bacteria and photophosphory-
lation necessitated redefinition of the term.[56] of free energy into the biosphere, and is one of four main
240 CHAPTER 14. PHOTOSYNTHESIS

ways in which radiation is important for plant life (Jones Carbon dioxide levels and photorespiration
1992).[57]
Spectral responses of various physiological processes dif-
fer; therefore, instruments for measuring them must be
appropriately sensitive. Combinations of photocells and
filters can approximate the responses needed to mea-
sure either irradiance in the PAR or photon irradiance
in the PAR. Such instruments are often called photosyn-
thetic energy and quantum sensors, respectively (Jones
1992).[57] Radiometers measure radiant flux density, and
pyranometers or solarimeters measure total shortwave ra-
diation incident upon a surface. Photosynthesis does not
respond linearly to light, hence the average irradiance Photorespiration
cannot be expected to predict CO2 uptake well. Further-
more, the high irradiance within sunflecks may even cause As carbon dioxide concentrations rise, the rate at which
photoinhibitory damage to the chloroplasts. For many sugars are made by the light-independent reactions in-
purposes, especially in studies of photosynthesis, the av- creases until limited by other factors. RuBisCO,
erage irradiance on a horizontal surface at any depth in the enzyme that captures carbon dioxide in the light-
the canopy is not the value of interest (Jones 1992).[57] independent reactions, has a binding affinity for both car-
bon dioxide and oxygen. When the concentration of car-
The radiation climate within plant communities is ex-
bon dioxide is high, RuBisCO will fix carbon dioxide.
tremely variable, both spatially and temporally.
However, if the carbon dioxide concentration is low, Ru-
In the early 20th century, Frederick Blackman and BisCO will bind oxygen instead of carbon dioxide. This
Gabrielle Matthaei investigated the effects of light inten- process, called photorespiration, uses energy, but does
sity (irradiance) and temperature on the rate of carbon not produce sugars.
assimilation.
RuBisCO oxygenase activity is disadvantageous to plants
for several reasons:
• At constant temperature, the rate of carbon assim-
ilation varies with irradiance, initially increasing as 1. One product of oxygenase activity is phosphoglyco-
the irradiance increases. However, at higher irradi- late (2 carbon) instead of 3-phosphoglycerate (3 car-
ance, this relationship no longer holds and the rate bon). Phosphoglycolate cannot be metabolized by
of carbon assimilation reaches a plateau. the Calvin-Benson cycle and represents carbon lost
from the cycle. A high oxygenase activity, there-
• At constant irradiance, the rate of carbon assimila- fore, drains the sugars that are required to recycle
tion increases as the temperature is increased over ribulose 5-bisphosphate and for the continuation of
a limited range. This effect is seen only at high ir- the Calvin-Benson cycle.
radiance levels. At low irradiance, increasing the
temperature has little influence on the rate of car- 2. Phosphoglycolate is quickly metabolized to glyco-
bon assimilation. late that is toxic to a plant at a high concentration; it
inhibits photosynthesis.

These two experiments illustrate several important 3. Salvaging glycolate is an energetically expensive
points: First, from research it is known that, in general, process that uses the glycolate pathway, and only
photochemical reactions are not affected by temperature. 75% of the carbon is returned to the Calvin-Benson
However, these experiments clearly show that tem- cycle as 3-phosphoglycerate. The reactions also pro-
perature affects the rate of carbon assimilation, so duce ammonia (NH3 ), which is able to diffuse out of
there must be two sets of reactions in the full pro- the plant, leading to a loss of nitrogen.
cess of carbon assimilation. These are, of course,
the light-dependent 'photochemical' stage and the light- A highly simplified summary is:
independent, temperature-dependent stage. Second,
Blackman’s experiments illustrate the concept of limiting
factors. Another limiting factor is the wavelength of light. 2 glycolate + ATP → 3-
Cyanobacteria, which reside several meters underwater, phosphoglycerate + car-
cannot receive the correct wavelengths required to cause bon dioxide + ADP +
photoinduced charge separation in conventional photo- NH3
synthetic pigments. To combat this problem, a series
of proteins with different pigments surround the reaction The salvaging pathway for the products of RuBisCO
center. This unit is called a phycobilisome. oxygenase activity is more commonly known as
14.1. PHOTOSYNTHESIS 241

photorespiration, since it is characterized by light- [6] Olson JM (May 2006). “Photosynthesis in the
dependent oxygen consumption and the release of Archean era”. Photosyn. Res. 88 (2): 109–17.
carbon dioxide. doi:10.1007/s11120-006-9040-5. PMID 16453059.

[7] Buick R (August 2008). “When did oxygenic photosyn-

thesis evolve?". Philos. Trans. R. Soc. Lond., B, Biol.
14.1.10 See also
Sci. 363 (1504): 2731–43. doi:10.1098/rstb.2008.0041.
PMC 2606769. PMID 18468984.
• Jan Anderson (scientist)
[8] Nealson KH, Conrad PG (December 1999). “Life: past,
• Artificial photosynthesis present and future”. Philos. Trans. R. Soc. Lond., B, Biol.
Sci. 354 (1392): 1923–39. doi:10.1098/rstb.1999.0532.
• Calvin-Benson cycle
PMC 1692713. PMID 10670014.
• Carbon fixation
[9] Whitmarsh J, Govindjee (1999). “The photosynthetic
• Cellular respiration process”. In Singhal GS, Renger G, Sopory SK, Irrgang
KD, Govindjee. Concepts in photobiology: photosynthe-
• Chemosynthesis sis and photomorphogenesis. Boston: Kluwer Academic
Publishers. pp. 11–51. ISBN 0-7923-5519-9. 100 x 1015
• Integrated fluorometer grams of carbon/year fixed by photosynthetic organisms,
which is equivalent to 4 x 1018 kJ/yr = 4 x 1021 J/yr of
• Light-dependent reaction free energy stored as reduced carbon; (4 x 1018 kJ/yr) /
(31,556,900 sec/yr) = 1.27 x 1014 J/yr; (1.27 x 1014 J/yr)
• Organic reaction / (1012 J/sec / TW) = 127 TW.

• Photobiology [10] Steger U, Achterberg W, Blok K, Bode H, Frenz W,

Gather C, Hanekamp G, Imboden D, Jahnke M, Kost M,
• Photoinhibition Kurz R, Nutzinger HG, Ziesemer T (2005). Sustainable
development and innovation in the energy sector. Berlin:
• Photosynthetic reaction center Springer. p. 32. ISBN 3-540-23103-X. The average
global rate of photosynthesis is 130 TW (1 TW = 1 ter-
• Photosynthetically active radiation awatt = 1012 watt).
• Photosystem [11] “World Consumption of Primary Energy by Energy Type
and Selected Country Groups, 1980–2004” (XLS). En-
• Photosystem I
ergy Information Administration. July 31, 2006. Re-
• Photosystem II trieved 2007-01-20.

• Quantum biology [12] Field CB, Behrenfeld MJ, Randerson JT, Falkowski P
(July 1998). “Primary production of the biosphere:
• Red edge integrating terrestrial and oceanic components”. Sci-
ence 281 (5374): 237–40. Bibcode:1998Sci...281..237F.
• Vitamin D doi:10.1126/science.281.5374.237. PMID 9657713.

[13] “Photosynthesis”. McGraw-Hill Encyclopedia of Science

& Technology 13. New York: McGraw-Hill. 2007. ISBN
14.1.11 References
0-07-144143-3.
[1] “photosynthesis”. Online Etymology Dictionary.
[14] Whitmarsh J, Govindjee (1999). “Chapter 2: The Ba-
[2] φῶς. Liddell, Henry George; Scott, Robert; A Greek– sic Photosynthetic Process”. In Singhal GS, Renger G,
English Lexicon at the Perseus Project Sopory SK, Irrgang KD, Govindjee. Concepts in Photobi-
ology: Photosynthesis and Photomorphogenesis. Boston:
[3] σύνθεσις. Liddell, Henry George; Scott, Robert; A Kluwer Academic Publishers. p. 13. ISBN 978-
Greek–English Lexicon at the Perseus Project 0792355199.

[4] Bryant DA, Frigaard NU (November 2006). [15] Anaerobic Photosynthesis, Chemical & Engineering
“Prokaryotic photosynthesis and phototrophy illu- News, 86, 33, August 18, 2008, p. 36
minated”. Trends Microbiol. 14 (11): 488–96.
doi:10.1016/j.tim.2006.09.001. PMID 16997562. [16] Kulp TR, Hoeft SE, Asao M, Madigan MT, Hol-
libaugh JT, Fisher JC, Stolz JF, Culbertson CW,
[5] Reece J, Urry L, Cain M, Wasserman S, Minorsky P, Miller LG, Oremland RS (August 2008). “Ar-
Jackson R. Biology (International ed.). Upper Saddle senic(III) fuels anoxygenic photosynthesis in hot
River, NJ: Pearson Education. pp. 235, 244. ISBN 0- spring biofilms from Mono Lake, California”. Science
321-73975-2. This initial incorporation of carbon into 321 (5891): 967–70. Bibcode:2008Sci...321..967K.
organic compounds is known as carbon fixation. doi:10.1126/science.1160799. PMID 18703741.
242 CHAPTER 14. PHOTOSYNTHESIS

[17] “Scientists discover unique microbe in California’s largest [32] Badger MR, Andrews JT, Whitney SM, Ludwig M, Yel-
lake”. Retrieved 2009-07-20. lowlees DC, Leggat W, Price GD (1998). “The diver-
sity and coevolution of Rubisco, plastids, pyrenoids, and
[18] Plants: Diversity and Evolution, page 14, Martin In- chloroplast-based CO2 -concentrating mechanisms in al-
grouille, Bill Eddie gae”. Canadian Journal of Botany 76 (6): 1052–1071.
doi:10.1139/b98-074. ISSN 0008-4026.
[19] Evolution of Photosynthesis
[33] Miyamoto K. “Chapter 1 – Biological energy production”.
[20] Tavano CL, Donohue TJ (December 2006).
Renewable biological systems for alternative sustainable
“Development of the bacterial photosynthetic ap-
energy production (FAO Agricultural Services Bulletin –
paratus”. Curr. Opin. Microbiol. 9 (6): 625–31.
128). Food and Agriculture Organization of the United
doi:10.1016/j.mib.2006.10.005. PMC 2765710. PMID
Nations. Retrieved 2009-01-04.
17055774.
[34] Maxwell K, Johnson GN (April 2000). “Chlorophyll
[21] Mullineaux CW (1999). “The thylakoid membranes of
fluorescence--a practical guide”. J. Exp. Bot. 51
cyanobacteria: structure, dynamics and function”. Aus-
(345): 659–68. doi:10.1093/jexbot/51.345.659. PMID
tralian Journal of Plant Physiology 26 (7): 671–677.
10938857.
doi:10.1071/PP99027.
[35] Govindjee R. “What is Photosynthesis”. Biology at Illi-
[22] Sener MK, Olsen JD, Hunter CN, Schulten K (Oc- nois.
tober 2007). “Atomic-level structural and func-
tional model of a bacterial photosynthetic membrane [36] Schreiber U, Klughammer C, Kolbowski J (2012).
vesicle”. Proc. Natl. Acad. Sci. U.S.A. “Assessment of wavelength-dependent parameters of
104 (40): 15723–8. Bibcode:2007PNAS..10415723S. photosynthetic electron transport with a new type of
doi:10.1073/pnas.0706861104. PMC 2000399. PMID multi-color PAM chlorophyll fluorometer”. Photosynthe-
17895378. sis research 113 (1-3): 127–144.
[23] Campbell NA, Williamson B, Heyden RJ (2006). Biology [37] Palmer J (21 June 2013). “Plants 'seen doing quantum
Exploring Life. Upper Saddle River, NJ: Pearson Prentice physics’". BBC News.
Hall. ISBN 0-13-250882-6.
[38] Lloyd S (10 March 2014). “Quantum Biology: Better Liv-
[24] Raven PH, Evert RF, Eichhorn SE (2005). Biology of ing Through Quantum Mechanics - The Nature of Real-
Plants, (7th ed.). New York: W.H. Freeman and Com- ity”. Nova: PBS Online, WGBH Boston.
pany Publishers. pp. 124–127. ISBN 0-7167-1007-2.
[39] Hildner R, Brinks D, Nieder JB, Cogdell RJ, van Hulst NF
[25] “Yachandra Group Home page”. (2013). “Quantum coherent energy transfer over varying
pathways in single light-harvesting complexes”. Science
[26] Pushkar Y, Yano J, Sauer K, Boussac A, Yachan- 340 (6139): 1448–51. doi:10.1126/science.1235820.
dra VK (February 2008). “Structural changes in the PMID 23788794.
Mn4Ca cluster and the mechanism of photosynthetic
water splitting”. Proc. Natl. Acad. Sci. U.S.A. [40] Photosynthesis got a really early start, New Scientist, 2
105 (6): 1879–84. Bibcode:2008PNAS..105.1879P. October 2004
doi:10.1073/pnas.0707092105. PMC 2542863. PMID
18250316. [41] Revealing the dawn of photosynthesis, New Scientist, 19
August 2006
[27] Williams BP, Johnston IG, Covshoff S, Hibberd JM
(September 2013). “Phenotypic landscape inference re- [42] Venn AA, Loram JE, Douglas AE (2008). “Photosyn-
veals multiple evolutionary paths to C₄ photosynthesis”. thetic symbioses in animals”. J. Exp. Bot. 59 (5): 1069–
eLife 2: e00961. doi:10.7554/eLife.00961. 80. doi:10.1093/jxb/erm328. PMID 18267943.

[28] L. Taiz, E. Zeiger (2006). Plant Physiology (4 ed.). Sin- [43] Rumpho ME, Summer EJ, Manhart JR (May 2000).
auer Associates. ISBN 978-0-87893-856-8. “Solar-powered sea slugs. Mollusc/algal chloro-
plast symbiosis”. Plant Physiol. 123 (1): 29–38.
[29] Monson RK, Sage RF (1999). “16”. C₄ plant biology. doi:10.1104/pp.123.1.29. PMC 1539252. PMID
Boston: Academic Press. pp. 551–580. ISBN 0-12- 10806222.
614440-0.
[44] Muscatine L, Greene RW (1973). “Chloroplasts and algae
[30] Dodd AN, Borland AM, Haslam RP, Griffiths H, Maxwell as symbionts in molluscs”. Int. Rev. Cytol. International
K (April 2002). “Crassulacean acid metabolism: plas- Review of Cytology 36: 137–69. doi:10.1016/S0074-
tic, fantastic”. J. Exp. Bot. 53 (369): 569–80. 7696(08)60217-X. ISBN 9780123643360. PMID
doi:10.1093/jexbot/53.369.569. PMID 11886877. 4587388.

[31] Badger, M. R.; Price, GD (2003). “CO2 concentrat- [45] Rumpho ME, Worful JM, Lee J, Kannan K, Tyler
ing mechanisms in cyanobacteria: molecular components, MS, Bhattacharya D, Moustafa A, Manhart JR (Novem-
their diversity and evolution”. Journal of Experimen- ber 2008). “Horizontal gene transfer of the algal nu-
tal Botany 54 (383): 609–22. doi:10.1093/jxb/erg076. clear gene psbO to the photosynthetic sea slug Elysia
PMID 12554704. chlorotica”. Proc. Natl. Acad. Sci. U.S.A.
14.1. PHOTOSYNTHESIS 243

105 (46): 17867–71. Bibcode:2008PNAS..10517867R. • Blankenship RE (2014). Molecular Mechanisms of

doi:10.1073/pnas.0804968105. PMC 2584685. PMID Photosynthesis (2nd ed.). John Wiley & Sons. ISBN
19004808. 978-1-4051-8975-0.
[46] Douglas SE (December 1998). “Plastid evolution: ori- • Govindjee, Beatty JT, Gest H, Allen JF (2006). Dis-
gins, diversity, trends”. Curr. Opin. Genet. Dev. 8 (6): coveries in Photosynthesis. Advances in Photosyn-
655–61. doi:10.1016/S0959-437X(98)80033-6. PMID thesis and Respiration 20. Berlin: Springer. ISBN
9914199. 1-4020-3323-0.
[47] Reyes-Prieto A, Weber AP, Bhattacharya D (2007). • Reece JB et al. (2013). Campbell Biology.
“The origin and establishment of the plastid in algae Benjamin Cummings. ISBN 978-0321775658.
and plants”. Annu. Rev. Genet. 41: 147–68.
doi:10.1146/annurev.genet.41.110306.130134. PMID
17600460. Papers
[48] Raven JA, Allen JF (2003). “Genomics and chloro- • Gupta RS, Mukhtar T, Singh B (June 1999).
plast evolution: what did cyanobacteria do for plants?".
“Evolutionary relationships among photosynthetic
Genome Biol. 4 (3): 209. doi:10.1186/gb-2003-4-3-209.
PMC 153454. PMID 12620099.
prokaryotes (Heliobacterium chlorum, Chloroflexus
aurantiacus, cyanobacteria, Chlorobium tepidum
[49] Akiko Tomitani (April 2006). “The evolutionary diver- and proteobacteria): implications regarding the ori-
sification of cyanobacteria: Molecular–phylogenetic and gin of photosynthesis”. Mol. Microbiol. 32 (5):
paleontological perspectives”. PNAS 103 (14): 5442– 893–906. doi:10.1046/j.1365-2958.1999.01417.x.
5447. doi:10.1073/pnas.0600999103. PMC 1459374. PMID 10361294. implications regarding the origin
PMID 16569695. of photosynthesis
[50] “Cyanobacteria: Fossil Record”. Ucmp.berkeley.edu. • Rutherford AW, Faller P (January 2003).
Retrieved 2010-08-26. “Photosystem II: evolutionary perspectives”.
[51] Smith, Alison (2010). Plant biology. New York, NY: Philos. Trans. R. Soc. Lond., B, Biol. Sci. 358
Garland Science. p. 5. ISBN 0815340257. (1429): 245–53. doi:10.1098/rstb.2002.1186.
PMC 1693113. PMID 12594932.
[52] Herrero A, Flores E (2008). The Cyanobacteria: Molec-
ular Biology, Genomics and Evolution (1st ed.). Caister
Academic Press. ISBN 978-1-904455-15-8. 14.1.13 External links
[53] Plotkin M, Hod I, Zaban A, Boden SA, Bagnall DM, • A collection of photosynthesis pages for all levels
Galushko D, Bergman DJ (2010). “Solar energy har- from a renowned expert (Govindjee)
vesting in the epicuticle of the oriental hornet (Vespa
orientalis)". Naturwissenschaften 97 (12): 1067–76. • In depth, advanced treatment of photosynthesis, also
doi:10.1007/s00114-010-0728-1. PMID 21052618. from Govindjee
[54] Walker, D. A. (2002). "'And whose bright pres- • Science Aid: Photosynthesis Article appropriate for
ence' - an appreciation of Robert Hill and his reac- high school science
tion” (PDF). Photosynthesis Research 73 (1–3): 51–54.
doi:10.1023/A:1020479620680. PMID 16245102. • Metabolism, Cellular Respiration and Photosynthe-
sis – The Virtual Library of Biochemistry and Cell
[55] Otto Warburg – Biography. Nobelprize.org (1970-08- Biology
01). Retrieved on 2011-11-03.
• Overall examination of Photosynthesis at an inter-
[56] Gest, Howard (2002). “History of the word photosynthe- mediate level
sis and evolution of its definition.”. Photosynthesis Re-
search 73 (1-3): 7–10. doi:10.1023/A:1020419417954. • Overall Energetics of Photosynthesis

[57] Jones, H.G. 1992. Plants and Microclimate: A Quantita- • Photosynthesis Discovery Milestones – experiments
tive Approach to Environmental Plant Physiology. Cam- and background
bridge Univ. Press, Cambridge, U.K. 428 p.
• The source of oxygen produced by photosynthesis
Interactive animation, a textbook tutorial
14.1.12 Further reading • Jessica Marshall (2011-03-29). “First practical arti-
ficial leaf makes debut”. Discovery News.
Books
• Photosynthesis – Light Dependent & Light Indepen-
• Bidlack JE, Stern KR, Jansky S (2003). Introductory dent Stages
plant biology. New York: McGraw-Hill. ISBN 0- • Khan Academy, video introduction
07-290941-2.
Chapter 15

Lipid metabolism

15.1 Fatty acid synthesis present in prokaryotes, plants, fungi, and parasites, as
well as in mitochondria.[3]
Fatty acid synthesis is the creation of fatty acids from In animals, as well as some fungi such as yeast, these
acetyl-CoA and malonyl-CoA precursors through action same reactions occur on fatty acid synthase I (FASI), a
of enzymes called fatty acid synthases. It is an impor- large dimeric protein that has all of the enzymatic activ-
tant part of the lipogenesis process, which – together with ities required to create a fatty acid. FASI is less efficient
glycolysis – functions to create fats from blood sugar in than FASII; however, it allows for the formation of more
living organisms. molecules, including “medium-chain” fatty acids via early
chain termination.[3]

15.1.1 Straight-chain fatty acids Once a 16:0 carbon fatty acid has been formed, it can
undergo a number of modifications, resulting in de-
Straight-chain fatty acids occur in two types: saturated saturation and/or elongation. Elongation, starting with
and unsaturated. stearate (18:0), is performed mainly in the ER by sev-
eral membrane-bound enzymes. The enzymatic steps in-
volved in the elongation process are principally the same
Saturated straight-chain fatty acids as those carried out by FAS, but the four principal succes-
sive steps of the elongation are performed by individual
proteins, which may be physically associated.[4][5]
Abbreviations: ACP – Acyl carrier protein, CoA –
Coenzyme A, NADP – Nicotinamide adenine dinu-
cleotide phosphate.
Regulation
Acetyl-CoA is formed into malonyl-CoA by acetyl-CoA
carboxylase, at which point malonyl-CoA is destined
to feed into the fatty acid synthesis pathway. Acetyl-
CoA carboxylase is the point of regulation in saturated
straight-chain fatty acid synthesis, and is subject to both
phosphorylation and allosteric regulation. Regulation by
phosphorylation occurs mostly in mammals, while al-
losteric regulation occurs in most organisms. Allosteric
control occurs as feedback inhibition by palmitoyl-CoA
and activation by citrate. When there are high levels
Synthesis of saturated fatty acids via Fatty Acid Synthase II in E. of palmitoyl-CoA, the final product of saturated fatty
coli acid synthesis, it allosterically inactivates acetyl-CoA car-
boxylase to prevent a build-up of fatty acids in cells. Cit-
Much like β-oxidation, straight-chain fatty acid synthesis rate acts to activate acetyl-CoA carboxylase under high
occurs via the six recurring reactions shown below, until levels, because high levels indicate that there is enough
the 16-carbon palmitic acid is produced.[1][2] acetyl-CoA to feed into the Krebs cycle and produce
[6]
The diagrams presented show how fatty acids are syn- energy.
thesized in microorganisms and list the enzymes found De Novo Synthesis in Humans
in Escherichia coli.[1] These reactions are performed by
fatty acid synthase II (FASII), which in general contain In humans, fatty acids are formed predominantly in the
multiple enzymes that act as one complex. FASII is liver and lactating mammary glands, and, to a lesser ex-

244
15.1. FATTY ACID SYNTHESIS 245

tent, the adipose tissue. Most acetyl-CoA is formed

from pyruvate by pyruvate dehydrogenase in the mito-
chondria. Acetyl-CoA produced in the mitochondria is
condensed with oxaloacetate by citrate synthase to form
citrate, which is then transported into the cytosol and bro-
ken down to yield acetyl-CoA and oxaloacetate by ATP
citrate lyase. Oxaloacetate in the cytosol is reduced to
malate by cytoplasmic malate dehydrogenase, and malate
is transported back into the mitochondria to participate in
the Citric acid cycle.[7]

Desaturation

Desaturation of fatty acids involves a process that re-

quires molecular oxygen (O2 ), NADH, and cytochrome
b5 . The reaction, which occurs in the endoplasmic retic-
ulum, results in the oxidation of both the fatty acid and
NADH. The most common desaturation reactions involve Synthesis of unsaturated fatty acids via anaerobic desaturation
the placement of a double bond between carbons 9 and 10
(as in the conversion of palmitic acid to palmitoleic acid
and the conversion of stearic acid to oleic acid, facilitated fatty acid synthesis pathway. When FabB reacts
9
by the action of Δ -desaturase). Other positions that can with the cis-decenoyl intermediate, the final product
be desaturated in humans include carbon 4, 5, and 6, via after elongation will be an unsaturated fatty acid.[9]
Δ4 -, Δ5 -, and Δ6 -desaturases, respectively.
• The two main unsaturated fatty acids made are
Unsaturated fatty acids are essential components to Palmitoleoyl-ACP (16:1ω7) and cis-vaccenoyl-
prokaryotic and eukaryotic cell membranes. These ACP (18:1ω7).[10]
fatty acids function primarily in maintaining membrane
fluidity.[8] They have also been associated with serving as
Most bacteria that undergo anaerobic desaturation con-
signaling molecules in other processes such as cell differ-
tain homologues of FabA and FabB.[11] Clostridia are
entiation and DNA replication.[8] There are two pathways
the main exception; they have a novel enzyme, yet to be
organisms use for desaturation: Aerobic and Anaerobic.
identified, that catalyzes the formation of the cis double
bond.[10]
Anaerobic desaturation Many bacteria use the anaer- Regulation
obic pathway for synthesizing unsaturated fatty acids.
This pathway does not utilize oxygen and is dependent This pathway undergoes transcriptional regulation by
on enzymes to insert the double bond before elongation FadR and FabR. FadR is the more extensively studied
utilizing the normal fatty acid synthesis machinery. In protein and has been attributed bifunctional characteris-
Escherichia coli, this pathway is well understood. tics. It acts as an activator of fabA and fabB transcription
and as a repressor for the β-oxidation regulon. In contrast,
• FabA is a β-hydroxydecanoyl-ACP dehydrase – it is FabR acts as a repressor for the transcription of fabA and
[9]
specific for the 10-carbon saturated fatty acid syn- fabB.
thesis intermediate (β-hydroxydecanoyl-ACP).
• FabA catalyzes the dehydration of β- Aerobic desaturation Aerobic desaturation is the
hydroxydecanoyl-ACP, causing the release of most widespread pathway for the synthesis of unsatu-
water and insertion of the double bond between C7 rated fatty acids. It is utilized in all eukaryotes and some
and C8 counting from the methyl end. This creates prokaryotes. This pathway utilizes desaturases to syn-
the trans-2-decenoyl intermediate. thesize unsaturated fatty acids from full-length saturated
fatty acid substrates.[12] All desaturases require oxygen
• Either the trans-2-decenoyl intermediate can be and ultimately consume NADH even though desaturation
shunted to the normal saturated fatty acid synthe- is an oxidative process. Desaturases are specific for the
sis pathway by FabB, where the double bond will be double bond they induce in the substrate. In Bacillus sub-
hydrolyzed and the final product will be a saturated tilis, the desaturase, Δ5 -Des, is specific for inducing a cis-
fatty acid, or FabA will catalyze the isomerization double bond at the Δ5 position.[8][12] Saccharomyces cere-
into the cis-3-decenoyl intermediate. visiae contains one desaturase, Ole1p, which induces the
• FabB is a β-ketoacyl-ACP synthase that elongates cis-double bond at Δ9 .[8]
and channels intermediates into the mainstream Regulation
246 CHAPTER 15. LIPID METABOLISM

15.1.2 Branched-chain fatty acids

Branched-chain fatty acids are usually saturated and are

found in two distinct families: the iso-series and anteiso-
series. It has been found that Actinomycetales contain
unique branch-chain fatty acid synthesis mechanisms, in-
cluding that which forms tuberculosteric acid.

Synthesis of unsaturated fatty acids via aerobic desaturation

Branch-chain fatty acid synthesizing system

In B. subtilis, this pathway is regulated by a two-
component system: DesK and DesR. DesK is a
membrane-associated kinase and DesR is a transcrip-
tional regulator of the des gene.[8][12] The regulation re-
sponds to temperature; when there is a drop in temper-
ature, this gene is upregulated. Unsaturated fatty acids
increase the fluidity of the membrane and stabilize it un-
der lower temperatures. DesK is the sensor protein that,
when there is a decrease in temperature, will autophos-
phorylate. DesK-P will transfer its phosphoryl group to
DesR. Two DesR-P proteins will dimerize and bind to the
DNA promoters of the des gene and recruit RNA poly-
merase to begin transcription.[8][12]
Pseudomonas aeruginosa
In general, both anaerobic and aerobic unsaturated fatty
acid synthesis will not occur within the same system,
however Pseudomonas aeruginosa and Vibrio ABE-1 are
exceptions.[13][14][15] While P. aeruginosa undergoes pri-
marily anaerobic desaturation, it also undergoes two aer-
obic pathways. One pathway utilizes a Δ9 -desaturase
(DesA) that catalyzes a double bond formation in mem-
brane lipids. Another pathway uses two proteins, DesC
and DesB, together to act as a Δ9 -desaturase, which
inserts a double bond into a saturated fatty acid-CoA
molecule. This second pathway is regulated by repres-
sor protein DesT. DesT is also a repressor of fabAB ex-
pression for anaerobic desaturation when in presence of
exogenous unsaturated fatty acids. This functions to co-
ordinate the expression of the two pathways within the
organism.[14][16] Valine primer
15.1. FATTY ACID SYNTHESIS 247

Isoleucine primer
Synthetic pathways of the branched-chain fatty acid
synthesizing system given differing primers

The branched-chain fatty acid synthesizing system uses

α-keto acids as primers. This system is distinct
from the branched-chain fatty acid synthetase that uti-
lizes short-chain acyl-CoA esters as primers.[17] α-Keto
acid primers are derived from the transamination and
decarboxylation of valine, leucine, and isoleucine to form
2-methylpropanyl-CoA, 3-methylbutyryl-CoA, and 2-
Methylbutyryl-CoA, respectively.[18] 2-Methylpropanyl-
CoA primers derived from valine are elongated to
produce even-numbered iso-series fatty acids such as
14-methyl-pentadecanoic (isopalmitic) acid, and 3-
methylbutyryl-CoA primers from leucine may be used
to form odd-numbered iso-series fatty acids such as
13-methyl-tetradecanoic acid. 2-Methylbutyryl-CoA
primers from isoleucine are elongated to form anteiso-
series fatty acids containing an odd number of carbon
atoms such as 12-Methyl tetradecanoic acid.[19] Decar-
boxylation of the primer precursors occurs through the
branched-chain α-keto acid decarboxylase (BCKA) en-
zyme. Elongation of the fatty acid follows the same
biosynthetic pathway in Escherichia coli used to produce
straight-chain fatty acids where malonyl-CoA is used as
a chain extender.[20] The major end products are 12–17
carbon branched-chain fatty acids and their composition
tends to be uniform and characteristic for many bacterial
Leucine primer species.[19]
BCKA decarboxylase and relative activities of α-keto
acid substrates
The BCKA decarboxylase enzyme is composed of two
subunits in a tetrameric structure (A2 B2 ) and is essential
for the synthesis of branched-chain fatty acids. It is re-
sponsible for the decarboxylation of α-keto acids formed
by the transamination of valine, leucine, and isoleucine
and produces the primers used for branched-chain fatty
acid synthesis. The activity of this enzyme is much
higher with branched-chain α-keto acid substrates than
with straight-chain substrates, and in Bacillus species its
specificity is highest for the isoleucine-derived α-keto-
β-methylvaleric acid, followed by α-ketoisocaproate and
α-ketoisovalerate.[19][20] The enzyme’s high affinity to-
ward branched-chain α-keto acids allows it to function as
the primer donating system for branched-chain fatty acid
synthetase.[20]
Factors affecting chain length and pattern distribu-
tion
α-Keto acid primers are used to produce branched-chain
fatty acids that, in general, are between 12 and 17 carbons
in length. The proportions of these branched-chain fatty
acids tend to be uniform and consistent among a particu-
lar bacterial species but may be altered due to changes in
malonyl-CoA concentration, temperature, or heat-stable
factors (HSF) present.[19] All of these factors may af-
248 CHAPTER 15. LIPID METABOLISM

fect chain length, and HSFs have been demonstrated to of sugars to shikimic acid which is then converted to cy-
alter the specificity of BCKA decarboxylase for a par- clohexylcarboxylic acid-CoA esters that serve as primers
ticular α-keto acid substrate, thus shifting the ratio of for omega-alicyclic fatty acid synthesis [21]
branched-chain fatty acids produced.[19] An increase in
malonyl-CoA concentration has been shown to result in
a larger proportion of C17 fatty acids produced, up un- Tuberculostearic acid synthesis
til the optimal concentration (≈20μM) of malonyl-CoA
is reached. Decreased temperatures also tend to shift the
fatty-acid distribution slightly toward C17 fatty-acids in
Bacillus species.[17][19]

Branch-chain fatty acid synthase

This system functions similarly to the branch-chain fatty

acid synthesizing system, however it uses short-chain car-
boxylic acids as primers instead of alpha-keto acids. In
general, this method is used by bacteria that do not have
the ability to perform the branch-chain fatty acid system
using alpha-keto primers. Typical short-chain primers
include isovalerate, isobutyrate, and 2-methyl butyrate.
In general, the acids needed for these primers are taken
up from the environment; this is often seen in ruminal
bacteria.[21]
The overall reaction is:

Isobutyryl-CoA + 6 malonyl-CoA +12

NADPH + 12H+ → Isopalmitic acid + 6 CO2 Mechanism of the synthesis of Tuberculostearic acid
12 NADP + 5 H2 O + 7 CoA[17]
Tuberculostearic acid (D−10-Methylstearic acid) is a
saturated fatty acid that is known to be produced by
The difference between (straight-chain) fatty acid syn-
Mycobacterium spp. and two species of Streptomyces. It
thase and branch-chain fatty acid synthase is substrate
is formed from the precursor oleic acid (a monosaturated
specificity of the enzyme that catalyzes the reaction of
[17] fatty acid).[22] After oleic acid is esterified to a phospho-
acyl-CoA to acyl-ACP.
lipid, S-adenosyl-methionine donates a methyl group to
the double bond of oleic acid.[23] This methylation reac-
Omega-alicyclic fatty acids tion forms the intermediate 10-methylene-octadecanoyal.
Successive reduction of the residue, with NADPH as a
cofactor, results in 10-methylstearic acid [18]

15.1.3 See also

• Fatty acid

• Essential fatty acid

• Fatty acid metabolism

Omega-alicyclic fatty acids typically contain an omega-
terminal propyl or butyryl cyclic group and are some of • Fatty acid synthase
the major membrane fatty acids found in several species
of bacteria. The fatty acid synthetase used to produce
omega-alicyclic fatty acids is also used to produce mem- 15.1.4 References
brane branched-chain fatty acids. In bacteria with mem-
[1] Dijkstra, Albert J., R. J. Hamilton, and Wolf Hamm.
branes composed mainly of omega-alicyclic fatty acids,
“Fatty Acid Biosynthesis.” Trans Fatty Acids. Oxford:
the supply of cyclic carboxylic acid-CoA esters is much Blackwell Pub., 2008. 12. Print.
greater than that of branched-chain primers.[17] The syn-
thesis of cyclic primers is not well understood but it has [2] “MetaCyc pathway: superpathway of fatty acids biosyn-
been suggested that mechanism involves the conversion thesis (E. coli)".
15.2. LIPOGENESIS 249

[3] “Fatty Acids: Straight-chain Saturated, Structure, Occur- [17] Kaneda, Toshi. “Iso- and Anteiso-Fatty Acids in Bac-
rence and Biosynthesis.” Lipid Library – Lipid Chemistry, teria: Biosynthesis, Function, and Taxonomic Signifi-
Biology, Technology and Analysis. Web. 30 Apr. 2011. cance.” Microbiological Reviews 55.2 (1991): 288–302
<http://lipidlibrary.aocs.org/lipids/fa_sat/index.htm>.
[18] “Branched-chain Fatty Acids, Phytanic Acid, Tubercu-
[4] “MetaCyc pathway: stearate biosynthesis I (animals)". lostearic Acid Iso/anteiso- Fatty Acids.” Lipid Library
– Lipid Chemistry, Biology, Technology and Analysis.
[5] “MetaCyc pathway: very long chain fatty acid biosynthesis Web. 1 May 2011. http://lipidlibrary.aocs.org/lipids/fa_
II”. branc/index.htm.
[6] Diwan, Joyce J. “Fatty Acid Synthesis.” Rensselaer Poly- [19] Naik, Devaray N., and Toshi Kaneda. “Biosynthesis of
technic Institute (RPI) :: Architecture, Business, En- Branched Long-chain Fatty Acids by Species of Bacil-
gineering, IT, Humanities, Science. Web. 30 Apr. lus: Relative Activity of Three α-keto Acid Substrates and
2011. <http://rpi.edu/dept/bcbp/molbiochem/MBWeb/ Factors Affecting Chain Length.” Can. J. Microbiol. 20
mb2/part1/fasynthesis.htm>. (1974): 1701–708.
[7] Ferre, P.; F. Foufelle (2007). “SREBP-1c Tran- [20] Oku, Hirosuke, and Toshi Kaneda. “Biosynthesis of
scription Factor and Lipid Homeostasis: Clinical Branched-chain Fatty Acids in Bacillis Subtilis.” The
Perspective”. Hormone Research 68 (2): 72–82. Journal of Biological Chemistry 263.34 (1988): 18386-
doi:10.1159/000100426. PMID 17344645. Retrieved 8396.
2010-08-30. this process is outlined graphically in page
73 [21] Christie, William W. “Fatty Acids: Natural Alicyclic
Structures, Occurrence, and Biochemistry.” The AOCS
[8] Aguilar, Pablo S, and Diegode Mendoza. “Control of fatty Lipid Library. 5 Apr. 2011. Web. 24 Apr. 2011.
acid desaturation: a mechanism conserved from bacteria <http://lipidlibrary.aocs.org/lipids/fa_cycl/file.pdf>.
to humans.” Molecular microbiology 62.6 (2006):1507–
14. [22] Ratledge, Colin, and John Stanford. The Biology of the
Mycobacteria. London: Academic, 1982. Print.
[9] Feng, Youjun, and John ECronan. “Complex binding
of the FabR repressor of bacterial unsaturated fatty acid [23] Kubica, George P., and Lawrence G. Wayne. The My-
biosynthesis to its cognate promoters.” Molecular micro- cobacteria: a Sourcebook. New York: Dekker, 1984.
biology 80.1 (2011):195–218. Print.
[10] Zhu, Lei, et al. “Functions of the Clostridium acetobutyli-
cium FabF and FabZ proteins in unsaturated fatty acid
biosynthesis.” BMC microbiology 9(2009):119.
15.1.5 External links

[11] Wang, Haihong, and John ECronan. “Functional re- • Overview at Rensselaer Polytechnic Institute
placement of the FabA and FabB proteins of Escherichia
coli fatty acid synthesis by Enterococcus faecalis FabZ • Overview at Indiana State University
and FabF homologues.” Journal of biological chemistry
279.33 (2004):34489-95.

[12] Mansilla, Mara C, and Diegode Mendoza. “The Bacillus

15.2 Lipogenesis
subtilis desaturase: a model to understand phospholipid
modification and temperature sensing.” Archives of mi- Lipogenesis is the process by which acetyl-CoA is con-
crobiology 183.4 (2005):229-35. verted to fatty acids. The former is an intermediate stage
in metabolism of simple sugars, such as glucose, a source
[13] Wada, M, N. Fukunaga, and S. Sasaki. “Mechanism of
biosynthesis of unsaturated fatty acids in Pseudomonas sp. of energy of living organisms. Through lipogenesis and
strain E-3, a psychrotrophic bacterium.” Journal of bac- subsequent triglyceride synthesis, the energy can be effi-
teriology 171.8 (1989):4267-71. ciently stored in the form of fats.

[14] Subramanian, Chitra, Charles ORock, and Yong-

Lipogenesis encompasses both the process of fatty acid
MeiZhang. “DesT coordinates the expression of anaero- synthesis and triglyceride synthesis (where fatty acids are
bic and aerobic pathways for unsaturated fatty acid biosyn- esterified with glycerol to form fats).[1] The products are
thesis in Pseudomonas aeruginosa.” Journal of bacteriol- secreted from the liver in the form of very-low-density
ogy 192.1 (2010):280-5. lipoproteins (VLDL). VLDL are secreted directly into
blood, where they mature and function to deliver the en-
[15] Morita, N, et al. “Both the anaerobic pathway and aer- dogenously derived lipids to peripheral tissues.
obic desaturation are involved in the synthesis of unsatu-
rated fatty acids in Vibrio sp. strain ABE-1.” FEBS letters
297.1–2 (1992):9–12.
15.2.1 Fatty acid synthesis
[16] Zhu, Kun, et al. “Two aerobic pathways for the formation
of unsaturated fatty acids in Pseudomonas aeruginosa.” Main article: Fatty acid synthesis
Molecular microbiology 60.2 (2006):260-73.
250 CHAPTER 15. LIPID METABOLISM

Fatty acids synthesis starts with acetyl-CoA and builds up ACC is also activated by citrate. When there is abundant
by the addition of two-carbon units. The synthesis occurs acetyl-CoA in the cell cytoplasm for fat synthesis, it pro-
in the cytoplasm of the cell, in contrast to the degradation ceeds at an appropriate rate.
(oxidation), which occurs in the mitochondria. Many of Note: Research now shows that glucose metabolism (ex-
the enzymes for the fatty acid synthesis are organized into act metabolite to be determined), aside from insulin’s in-
a multienzyme complex called fatty acid synthetase.[2] fluence on lipogenic enzyme genes, can induce the gene
The major sites of fatty acid synthesis are adipose tissue products for liver’s pyruvate kinase, acetyl-CoA carboxy-
and the liver.[3] lase, and fatty acid synthase. These genes are induced
by the transcription factors ChREBP/Mlx via high blood
Control and regulation glucose levels[4] and presently unknown signaling events.
Insulin induction is due to SREBP-1c, which is also in-
Insulin is a peptide hormone that is critical for managing volved in cholesterol metabolism.
the body’s metabolism. Insulin is released by the pancreas
when blood sugar levels rise, and it has many effects that
broadly promote the absorption and storage of sugars, in- 15.2.2 Fatty acid esterification
cluding lipogenesis.
Experiments were conducted to study in vivo the over-
Insulin stimulates lipogenesis primarily by activating two
all fatty acid specificity of the mechanisms involved
enzymatic pathways. Pyruvate dehydrogenase (PDH),
in chylomicron cholesterol ester and triglyceride forma-
converts pyruvate into acetyl-CoA. Acetyl-CoA carboxy-
tion during fat absorption in the rat. Mixtures contain-
lase (ACC), converts acetyl-CoA produced by PDH into
ing similar amounts of two, three, or four C14-labeled
malonyl-CoA. Malonyl-CoA provides the two-carbon
fatty acids (palmitic, stearic, oleic, and linoleic acids),
building blocks that are used to create larger fatty acids.
but with varying ratios of unlabeled fatty acids, were
given by gastric intubation to rats with cannulated tho-
PDH dephosphorylation Insulin stimulates the activ- racic ducts. The chyle or chylomicron lipid so obtained
ity of pyruvate dehydrogenase phosphatase. This enzyme was chromatographed on silicic acid columns to separate
removes the phosphate from pyruvate dehydrogenase, al- cholesterol esters and glycerides (the latter being 98.2%
lowing for conversion of pyruvate to acetyl-CoA. This triglycerides). After assaying each lipid class for total
mechanism leads to the increased rate of catalysis of this radioactivity, gas-liquid chromatography was employed
enzyme, so increases the levels of acetyl-CoA. Increased to measure the total mass and the distribution of mass
levels of acetyl-CoA will increase the flux through not and of radioactivity in the individual fatty acid compo-
only the fat synthesis pathway but also the citric acid cy- nents of each lipid fraction. The specific radioactivity
cle. of each fatty acid in each fraction could then be calcu-
lated. The data provided quantitative information on the
relative specificity of incorporation of each fatty acid into
Acetyl-CoA carboxylase Main article: Acetyl-CoA each chylomicron lipid class and on the relative extent to
carboxylase which each fatty acid in each lipid fraction was diluted
with endogenous fatty acid. With the exception of a slight
Insulin affects ACC in a similar way to PDH. It leads discrimination against stearic acid, the processes of fatty
to its dephosphorylation which activates the enzyme. acid absorption and chylomicron triglyceride formation
Glucagon has an antagonistic effect and increases phos- displayed no specificity for one fatty acid relative to an-
phorylation, deactivation, thereby inhibiting ACC and other. In contrast, chylomicron cholesterol ester forma-
slowing fat synthesis. tion showed marked specificity for oleic acid, relative to
the other three fatty acids. This specificity was not signifi-
Affecting ACC affects the rate of acetyl-CoA conversion cantly altered by varying the composition of the test meal,
to malonyl-CoA. Increased malonyl-CoA level pushes the by including cholesterol in the test meal, or by feeding the
equilibrium over to increase production of fatty acids animal a high-cholesterol diet for several weeks preceding
through biosynthesis. Long chain fatty acids are negative the study. Considerable dilution of the dietary fatty acids
allosteric regulators of ACC and so when the cell has suf- with endogenous fatty acids was observed. In one exper-
ficient long chain fatty acids, they will eventually inhibit iment, 43% of the chylomicron triglyceride fatty acids
ACC activity and stop fatty acid synthesis. was of endogenous origin. Relatively more (54%) of the
AMP and ATP concentrations of the cell act as a measure cholesterol ester fatty acids was of endogenous origin.[5]
of the ATP needs of a cell. When ATP is depleted, there
is a rise in 5'AMP. This rise activates AMP-activated pro-
tein kinase, which phosphorylates ACC and thereby in- 15.2.3 In industry
hibits fat synthesis. This is a useful way to ensure that
glucose is not diverted down a storage pathway in times About 100,000 metric tons of the natural fatty acids are
when energy levels are low. consumed in the preparation of various fatty acid esters.
15.3. ACETYL-COA CARBOXYLASE 251

The simple esters with lower chain alcohols (methyl-, biotin carboxyl carrier domains on a single polypeptide.
ethyl-, n-propyl-, isopropyl- and butyl esters) are used as ACC functional regions, starting from the N-terminus to
emollients in cosmetics and other personal care products C-terminus are the biotin carboxylase (BC), biotin bind-
and as lubricants. Esters of fatty acids with more complex ing (BB), carboxyltransferase (CT), and ATP-binding
alcohols, such as sorbitol, ethylene glycol, diethylene gly- (AB). AB lies within BC. Biotin is covalently attached
col, and polyethylene glycol are consumed in foods, per- through an amide bond to the long side chain of a lysine
sonal care, paper, water treatment, metal working fluids, reside in BB. As BB is between BC and CT regions, bi-
rolling oils, and synthetic lubricants. otin can easily translocate to both of the active sites where
it is required.

15.2.4 References In mammals where two isoforms of ACC are expressed,

the main structural difference between these isoforms is
[1] Kersten S (April 2001). “Mechanisms of nutritional and the extended ACC2 N-terminus containing a mitochon-
[1]
hormonal regulation of lipogenesis”. EMBO Rep. 2 dria targeting sequence.
(4): 282–6. doi:10.1093/embo-reports/kve071. PMC
1083868. PMID 11306547.
15.3.2 Mechanism
[2] Elmhurst College. “Lipogenesis”. Retrieved 2007-12-22.

[3] J. Pearce (1983). “Fatty acid synthesis in liver and adipose The overall reaction of ACAC(A,B) proceeds by a two-
tissue”. Proceedings of the Nutrition Society 2: 263–271. step mechanism.[5] The first reaction is carried out by BC
doi:10.1079/PNS19830031. and involves the ATP-dependent carboxylation of biotin
with bicarbonate serving as the source of CO2 . The car-
[4] Work from Howard Towle, Catherine Postic, and K. boxyl group is transferred from biotin to acetyl CoA to
Uyeda. form malonyl CoA in the second reaction, which is cat-
[5] Karmen, Arthur; Whyte, Malcolm; Goodman, DeWitt alyzed by CT.
S. (July 1963). “Fatty acid esterification and chylomi-
cron formation during fat absorption: 1. Triglycerides and
cholesterol esters”. The Journal of Lipid Research 4: 312–
321. PMID 14168169. Retrieved 24 August 2013.

15.3 Acetyl-CoA carboxylase

Acetyl-CoA carboxylase (ACC) is a biotin-dependent The reaction mechanism of ACAC(A,B).
enzyme that catalyzes the irreversible carboxylation of The color scheme is as follows: enzyme, coenzymes, substrate
acetyl-CoA to produce malonyl-CoA through its two cat- names, metal ions, phosphate, and carbonate
alytic activities, biotin carboxylase (BC) and carboxyl-
transferase (CT). ACC is a multi-subunit enzyme in most In the active site, the reaction proceeds with extensive in-
prokaryotes and in the chloroplasts of most plants and al- teraction of the residues Glu296 and positively charged
gae, whereas it is a large, multi-domain enzyme in the Arg338 and Arg292 with the substrates.[6] Two Mg2+
endoplasmic reticulum of most eukaryotes. The most im- are coordinated by the phosphate groups on the ATP, and
portant function of ACC is to provide the malonyl-CoA are required for ATP binding to the enzyme. Bicarbon-
substrate for the biosynthesis of fatty acids.[1] The activity ate is deprotonated by Glu296, although in solution, this
of ACC can be controlled at the transcriptional level as proton transfer is unlikely as the pKa of bicarbonate is
well as by small molecule modulators and covalent mod- 10.3. The enzyme apparently manipulates pKas to fa-
ification. The human genome contains the genes for two cilitate the deprotonation of bicarbonate. The pKa of
different ACCs[2] — ACACA[3] and ACACB.[4] bicarbonate is decreased by its interaction with positively
charged side chains of Arg338 and Arg292. Further-
more, Glu296 interacts with the side chain of Glu211,
15.3.1 Structure an interaction that has been shown to cause an increase in
the apparent pKa. Following deprotonation of bicarbon-
Prokaryotes and plants have multi-subunit ACCs com- ate, the oxygen of the bicarbonate acts as a nucleophile
posed of several polypeptides encoded by distinct genes. and attacks the gamma phosphate on ATP. The car-
Biotin carboxylase (BC) activity, biotin carboxyl carrier boxyphosphate intermediate quickly decomposes to CO2
protein (BCCP), and carboxyl transferase (CT) activity and PO4 3− . The PO4 3− deprotonates biotin, creating
are each contained on a different subunit. The stoichiom- an enolate, stabilized by Arg338, that subsequently at-
etry of these subunits in the ACC holoenzyme differs tacks [[CO₂]] resulting in the production of
amongst organisms.[1] Humans and most eukaryotes have carboxybiotin.[6] The carboxybiotin translocates to the
evolved an ACC with CT and BC catalytic domains and carboxytransferase (CT) active site, where the carboxyl
252 CHAPTER 15. LIPID METABOLISM

group is transferred to acetyl-CoA. In contrast to the BC tional level, and ChREBP, which increases in expression
domain, little is known about the reaction mechanism of with high carbohydrates diets.[10][11]
CT. A proposed mechanism is the release of carbon diox- Through a feedforward loop, citrate allosterically acti-
ide from biotin, which subsequently abstracts a proton vates ACC.[12] Citrate may increase ACC polymerization
from the methyl group from acetyl CoA carboxylase. The to increases enzymatic activity; however, it is unclear
resulting enolate attacks CO2 to form malonyl CoA. In if polymerization is citrate’s main mechanism of in-
a competing mechanism, proton abstraction is concerted creasing ACC activity or if polymerization is an artifact
with the attack of acetyl CoA. of in vitro experiments. Other allosteric activators in-
clude glutamate and other dicarboxylic acids.[13] Long
and short chain fatty acyl CoAs are negative feedback in-
15.3.3 Function hibitors of ACC.[14]

The function of ACC is to regulate the metabolism of Phosphorylation can result when the hormones glucagon
fatty acids. When the enzyme is active, the product, or epinephrine bind to cell surface receptors, but the main
malonyl-CoA, is produced which is a building block for cause of phosphorylation is due to a rise in AMP levels
new fatty acids and can inhibit the transfer of the fatty acyl when the energy status of the cell is low, leading to the
group from acyl CoA to carnitine with carnitine acyltrans- activation of the AMP-activated protein kinase (AMPK).
ferase, which inhibits the beta-oxidation of fatty acids in AMPK is the main kinase regulator of ACC, able to phos-
the mitochondria. phorylate a number of serine residues on both isoforms
of ACC.[15] On ACC1, AMPK phosphorylates Ser79,
In mammals, two main isoforms of ACC are expressed, Ser1200, and Ser1215. Protein kinase A also has the abil-
ACC1 and ACC2, which differ in both tissue distribution ity to phosphorylate ACC, with a much greater ability to
and function. ACC1 is found in the cytoplasm of all cells phosphorylate ACC2 than ACC1. However, the physio-
but is enriched in lipogenic tissue, such as adipose tissue logical significance of protein kinase A in the regulation
and lactating mammary glands, where fatty acid synthesis of ACC is currently unknown. Researchers hypothesize
is important.[7] In oxidative tissues, such as the skeletal there are other ACC kinases important to its regulation
muscle and the heart, the ratio of ACC2 expressed is as there are many other possible phosphorylation sites on
higher. ACC1 and ACC2 are both highly expressed in ACC.[16]
the liver where both fatty acid oxidation and synthesis are
important.[8] The differences in tissue distribution indi- When insulin binds to its receptors on the cellular
cate that ACC1 maintains regulation of fatty acid synthe- membrane, it activates a phosphatase enzyme called pro-
sis whereas ACC2 mainly regulates fatty acid oxidation. tein phosphatase 2A (PP2A) to dephosphorylate the en-
zyme; thereby removing the inhibitory effect. Further-
more, insulin induces a phosphodiesterase that lowers the
15.3.4 Regulation level of cAMP in the cell, thus inhibiting PKA, and also
inhibits AMPK directly.
This protein may use the morpheein model of allosteric
regulation.[17]

15.3.5 Clinical implications

Control of Acetyl CoA Carboxylase. The AMP regulated kinase At the juncture of lipid synthesis and oxidation path-
triggers the phosphorylation of the enzyme (thus inactivating it)
ways, ACC presents many clinical possibilities for the
and the phosphatase enzyme removes the phosphate group.
production of novel antibiotics and the development of
new therapies for diabetes, obesity, and other manifesta-
The regulation of mammalian ACC is complex, in order tions of metabolic syndrome.[18] Researchers aim to take
to control two distinct pools of malonyl CoA that direct advantage of structural differences between bacterial and
either the inhibition of beta oxidation or the activation of human ACCs to create antibiotics specific to the bacte-
lipid biosynthesis.[9] rial ACC, in efforts to minimize side effects to patients.
Mammalian ACC1 and ACC2 are regulated transcrip- Promising results for the usefulness of an ACC inhibitor
tionally by multiple promoters which mediate ACC abun- include the finding that ACC2 -/- mice (mice with no ex-
dance in response to the cells nutritional status. Ac- pression of ACC2) have continuous fatty acid oxidation,
tivation of gene expression through different promot- reduced body fat mass, and reduced body weight despite
ers results in alternative splicing; however, the physio- an increase in food consumption. ACC2 -/- mice are also
logical significance of specific ACC isozymes remains protected from diabetes.[9] It should be noted that mutant
unclear.[8] The sensitivity to nutritional status results from mice lacking ACC1 are embryonically lethal. However,
the control of these promoters by transcription factors it is unknown whether drugs targeting ACCs in humans
such as SREBP1c, controlled by insulin at the transcrip- must be specific for ACC2.[19]
15.3. ACETYL-COA CARBOXYLASE 253

15.3.6 See also [11] Ishii S, Iizuka K, Miller BC, Uyeda K (October
2004). “Carbohydrate response element binding pro-
• Malonyl-CoA decarboxylase tein directly promotes lipogenic enzyme gene transcrip-
tion”. Proc Natl Acad Sci USA 101 (44): 15597–602.
doi:10.1073/pnas.0405238101. PMC 524841. PMID
15.3.7 References 15496471.

[12] Martin DB, Vagelos PR (June 1962). “The Mechanism of

[1] Tong L (August 2005). “Acetyl-coenzyme A carboxy-
Tricarboxylic Acid Cycle Regulation of Fatty Acid Syn-
lase: crucial metabolic enzyme and attractive target for
thesis”. J Biol Chem 237: 1787–92. PMID 14470343.
drug discovery”. Cell. Mol. Life Sci. 62 (16): 1784–803.
doi:10.1007/s00018-005-5121-4. PMID 15968460. [13] Boone AN, Chan A, Kulpa JE, Brownsey RW (April
2000). “Bimodal Activation of Acetyl-CoA Carboxy-
[2] Brownsey RW, Zhande R, Boone AN (November 1997).
lase by Glutamate”. J Biol Chem 275 (15): 10819–25.
“Isoforms of acetyl-CoA carboxylase: structures, regula-
doi:10.1074/jbc.275.15.10819. PMID 10753875.
tory properties and metabolic functions”. Biochem. Soc.
Trans. 25 (4): 1232–8. PMID 9449982. [14] Faergeman NJ, Knudsen J (April 1997). “Role of
long chain fatty acyl-CoA esters in the regulation of
[3] Abu-Elheiga L, Jayakumar A, Baldini A, Chirala SS,
metabolism and in cell signalling”. Biochem J. 323 (Pt
Wakil SJ (April 1995). “Human acetyl-CoA carboxy-
1): 1–12. PMC 1218279. PMID 9173866.
lase: characterization, molecular cloning, and evidence
for two isoforms”. Proc. Natl. Acad. Sci. U.S.A. 92 [15] Park SH, Gammon SR, Knippers JD, Paulsen SR, Ru-
(9): 4011–5. doi:10.1073/pnas.92.9.4011. PMC 42092. bink DS, Winder WW (June 2002). “Phosphorylation-
PMID 7732023. activity relationships of AMPK and acetyl-CoA carboxy-
lase in muscle”. J. Appl. Physiol. 92 (6): 2475–82.
[4] Widmer J, Fassihi KS, Schlichter SC, Wheeler KS, Crute doi:10.1152/japplphysiol.00071.2002. PMID 12015362.
BE, King N, Nutile-McMenemy N, Noll WW, Daniel S,
Ha J, Kim KH, Witters LA (June 1996). “Identification of [16] Brownsey RW, Boone AN, Elliott JE, Kulpa JE, Lee
a second human acetyl-CoA carboxylase gene”. Biochem. WM (April 2006). “Regulation of acetyl-CoA carboxy-
J. 316. ( Pt 3): 915–22. PMC 1217437. PMID 8670171. lase”. Biochem. Soc. Trans. 34 (Pt 2): 223–7.
doi:10.1042/BST20060223. PMID 16545081.
[5] Lee CK, Cheong HK, Ryu KS, Lee JI, Lee W, Jeon YH,
Cheong C (August 2008). “Biotinoyl domain of human [17] T. Selwood and E. K. Jaffe. (2011). “Dynamic disso-
acetyl-CoA carboxylase: Structural insights into the car- ciating homo-oligomers and the control of protein func-
boxyl transfer mechanism”. Proteins 72 (2): 613–24. tion.”. Arch. Biochem. Biophys. 519 (2): 131–43.
doi:10.1002/prot.21952. PMID 18247344. doi:10.1016/j.abb.2011.11.020. PMC 3298769. PMID
22182754.
[6] Chou CY, Yu LP, Tong L (April 2009). “Crystal structure
of biotin carboxylase in complex with substrates and im- [18] Corbett JW, Harwood JH (November 2007). “In-
plications for its catalytic mechanism”. J. Biol. Chem. 284 hibitors of mammalian acetyl-CoA carboxylase”. Re-
(17): 11690–7. doi:10.1074/jbc.M805783200. PMC cent Patents Cardiovasc Drug Discov 2 (3): 162–80.
2670172. PMID 19213731. doi:10.2174/157489007782418928. PMID 18221116.

[7] Kim TS, Leahy P, Freake HC (August 1996). “Pro- [19] Lutfi Abu-Elheiga, Martin M Matzuk, Parichher Ko-
moter usage determines tissue specific responsiveness rdari, WonKeun Oh, Tattym Shaikenov, Ziwei Gu,
of the rat acetyl-CoA carboxylase gene”. Biochem. Salih J Wakil (August 2005). “Mutant Mice Lack-
Biophys. Res. Commun. 225 (2): 647–53. ing Acetyl CoA Carboxylase are Embryonically Lethal”.
doi:10.1006/bbrc.1996.1224. PMID 8753813. Proc. Natl. Acad. Sci. USA 102 (34): 1211–6.
doi:10.1073/pnas.0505714102. PMC 1189351. PMID
[8] Barber MC, Price NT, Travers MT (March 2005). “Struc- 16103361.
ture and regulation of acetyl-CoA carboxylase genes of
metazoa”. Biochim. Biophys. Acta 1733 (1): 1–28.
doi:10.1016/j.bbalip.2004.12.001. PMID 15749055. 15.3.8 Further reading
[9] L Abu-Elheiga, M M Matzuk, K A Abo-Hashema, S J
Wakil (March 2001). “Continuous Fatty Acid Oxida-
• Voet, Donald; Voet, Judith G. (2004). Biochemistry
tion and Reduced Fat Storage in Mice Lacking Acetyl- (3rd ed.). Wiley. ISBN 0-471-19350-X.
CoA Carboxylase 2”. Science 291 (5513): 2613–6.
• edited by (2000). Buchanan, Bob B.; Gruissem,
doi:10.1126/science.1056843. PMID 11283375.
Wilhelm; Jones, Russell L., eds. Biochemistry and
[10] Field F. J., Born E., Murthy S. and Mathur S. N. (De- molecular biology of plants. American Society of
cember 2002). “Polyunsaturated fatty acids decrease the Plant Physiologists. ISBN 0-943088-37-2.
expression of sterol regulatory element binding protein-
1 in CaCo-2 cells: effect on fatty acid synthesis and tri- • Levert K, Waldrop G, Stephens J (2002). “A biotin
acylglycerol transport.”. Biochem. J. 368 (Pt 3): 855– analog inhibits acetyl-CoA carboxylase activity and
64. doi:10.1042/BJ20020731. PMC 1223029. PMID adipogenesis”. J. Biol. Chem. 277 (19): 16347–50.
12213084. doi:10.1074/jbc.C200113200. PMID 11907024.
254 CHAPTER 15. LIPID METABOLISM

15.4 Fatty acid degradation the reaction is coupled to a strongly exergonic hydrolysis
reaction: the enzyme inorganic pyrophosphatase cleaves
Fatty acid degradation is the process in which fatty the pyrophosphate liberated from ATP to two phosphate
acids are broken down into their metabolites, in the end ions, consuming one water molecule in the process. Thus
generating acetyl-CoA, the entry molecule for the citric the net reaction becomes:
acid cycle, the main energy supply of animals. It includes RCOO− + CoA + ATP + H2 O → RCO-CoA + AMP +
three major steps: 2Pᵢ + 2H+

• Lipolysis of and release from adipose tissue

Transport into the mitochondrial matrix
• Activation and transport into mitochondria
The inner mitochondrial membrane is impermeable to
• β-oxidation fatty acids and a specialized carnitine carrier system
operates to transport activated fatty acids from cytosol to
mitochondria.
15.4.1 Lipolysis and release Once activated, the acyl CoA is transported into the
mitochondrial matrix. This occurs via a series of simi-
Initially in the process of degradation, fatty acids are
lar steps:
stored in fat cells (adipocytes). The breakdown of this
fat is known as lipolysis. The products of lipolysis, free
1. Acyl CoA is conjugated to carnitine by carnitine
fatty acids, are released into the bloodstream and cir-
acyltransferase I (palmitoyltransferase) I located on
culate throughout the body. During the breakdown of
the outer mitochondrial membrane
triacylglycerols into fatty acids, more than 75% of the
fatty acids are reconverted to triacylglycerol (a body’s nat- 2. Acyl carnitine is shuttled inside by a translocase
ural mechanism to regulate energy resources), even in
cases of starvation and exercise. 3. Acyl carnitine (such as Palmitoylcarnitine) is con-
verted to acyl CoA by carnitine acyltransferase
(palmitoyltransferase) II located on the inner mi-
15.4.2 Activation and transport into mito- tochondrial membrane. The liberated carnitine re-
chondria turns to the cytosol.

Fatty acids must be activated before they can be carried It is important to note that carnitine acyltransferase I un-
into the mitochondria, where fatty acid oxidation occurs. dergoes allosteric inhibition as a result of malonyl-CoA,
This process occurs in two steps catalyzed by the enzyme an intermediate in fatty acid biosynthesis, in order to pre-
fatty acyl-CoA synthetase. vent futile cycling between beta-oxidation and fatty acid
synthesis.
the mitochondrial oxidation of fatty acids takes place
Formation of an activated thioester bond
in three major steps: 1.β-oxidation: conversion of fatty
acids into 2-carbon acetyl Co-A units. 2.entry of acetyl
The enzyme first catalyzes nucleophilic attack on the α-
Co-A into TCA cycle to yield energy. 3.finally, the
phosphate of ATP to form pyrophosphate and an acyl
electron transport chain in the mitochondria.though in
chain linked to AMP. The next step is formation of an
this step, no direct participation of fatty acids, the reac-
activated thioester bond between the fatty acyl chain and
tion continues.
Coenzyme A.

15.4.3 β-oxidation
Main article: Beta oxidation

Once inside the mitochondria, the β-oxidation of fatty

acids occurs via five recurring steps:

1. Activation by ATP
The balanced equation for the above is:
RCOO− + CoA + ATP → RCO-CoA + AMP + PPᵢ + 2. Oxidation by FAD,
2H+ 3. Hydration,
This two-step reaction is freely reversible and its
equilibrium lies near 1. To drive the reaction forward, 4. Oxidation by NAD+ ,
15.5. BETA OXIDATION 255

5. Thiolysis, 15.5.2 Activation and membrane transport

6. The final product is acetyl-CoA, the entry molecule Free fatty acids cannot penetrate any biological mem-
for the citric acid cycle. brane due to their negative charge. Free fatty acids
must cross the cell membrane through specific transport
15.4.4 See also proteins, such as the SLC27 family fatty acid transport
protein.[1][2] Once in the cytosol, the following processes
• Reverse cholesterol transport bring fatty acids into the mitochondrial matrix so that
beta-oxidation can take place.

15.4.5 References 1. Long-chain-fatty-acid—CoA ligase catalyzes the re-

action between a fatty acid with ATP to give a fatty
15.5 Beta oxidation acyl adenylate, plus inorganic pyrophosphate, which
then reacts with free coenzyme A to give a fatty acyl-
CoA ester and AMP.

2. If the fatty acyl-CoA has a long chain, then the car-

nitine shuttle must be utilized:

(a) Acyl-CoA is transferred to the hydroxyl group

of carnitine by carnitine palmitoyltransferase
I, located on the cytosolic faces of the outer
and inner mitochondrial membranes.
(b) Acyl-carnitine is shuttled inside by a carnitine-
acylcarnitine translocase, as a carnitine is shut-
tled outside.
(c) Acyl-carnitine is converted back to acyl-CoA
Schematic demonstrating mitochondrial fatty acid beta-oxidation by carnitine palmitoyltransferase II, located on
and effects of long-chain 3-hydroxyacyl-coenzyme A dehydroge- the interior face of the inner mitochondrial
nase deficiency, LCHAD deficiency membrane. The liberated carnitine is shuttled
back to the cytosol, as an acyl-carnitine is shut-
In biochemistry and metabolism, beta-oxidation is the tled into the matrix.
catabolic process by which fatty acid molecules are bro-
3. If the fatty acyl-CoA contains a short chain, these
ken down in the mitochondria to generate acetyl-CoA,
short-chain fatty acids can simply diffuse through the
which enters the citric acid cycle, and NADH and
inner mitochondrial membrane.[3]
FADH2, which are co-enzymes used in the electron trans-
port chain. It is named as such because the beta carbon
of the fatty acid undergoes oxidation to a carbonyl group.
Various mechanisms have evolved to handle the large va-
15.5.3 General mechanism
riety of fatty acids.
Once the fatty acid is inside the mitochondrial matrix,
beta-oxidation occurs by cleaving two carbons every cy-
15.5.1 Overview cle to form acetyl-CoA. The process consists of 4 steps.

Fatty acid catabolism consists of: 1. A long-chain fatty acid is dehydrogenated to create
a trans double bond between C2 and C3. This is
1. Activation and membrane transport of free fatty catalyzed by acyl CoA dehydrogenase to produce
acids by binding to coenzyme A. trans-delta 2-enoyl CoA. It uses FAD as an electron
acceptor and it is reduced to FADH2.
2. Oxidation of the beta carbon to a carbonyl group.
2. Trans-delta2-enoyl CoA is hydrated at the double
3. Cleavage of two-carbon segments resulting in
bond to produce L-B-hydroxyacyl CoA by enoyl-
acetyl-CoA.
CoA hydratase.
4. Oxidation of acetyl-CoA to carbon dioxide in the
citric acid cycle. 3. L-B-hydroxyacyl CoA is dehydrogenated again to
create B-ketoacyl CoA by B-hydroxyacyl CoA de-
5. Electron transfer from electron carriers to the hydrogenase. This enzyme uses NAD as an electron
electron transfer chain in oxidative phosphorylation. acceptor.
256 CHAPTER 15. LIPID METABOLISM

4. Thiolysis occurs between C2 and C3 (alpha and beta cle by condensing with an existing molecule of oxaloac-
carbons) of B-ketoacyl CoA. Thiolase enzyme cat- etate, succinyl-CoA enters the cycle as a principal in its
alyzes the reaction when a new molecule of coen- own right. Thus the succinate just adds to the population
zyme A breaks the bond by nucleophilic attack on of circulating molecules in the cycle and undergoes no
C3. This releases the first two carbon units, as acetyl net metabolization while in it. When this infusion of cit-
CoA, and a fatty acyl CoA minus two carbons. The ric acid cycle intermediates exceeds cataplerotic demand
process continues until all of the carbons in the fatty (such as for aspartate or glutamate synthesis), some of
acid are turned into acetyl CoA. them can be extracted to the gluconeogenesis pathway, in
the liver and kidneys, through phosphoenolpyruvate car-
[5]
Fatty acids are oxidized by most of the tissues in the body. boxykinase, and converted to free glucose.
However, some tissues such as the adrenal medulla do not
use fatty acids for their energy requirements, but instead
15.5.6 Unsaturated fatty acids
use carbohydrates.
Because many fatty acids are not fully saturated or do not β-Oxidation of unsaturated fatty acids poses a problem
have an even number of carbons, several different mech- since the location of a cis bond can prevent the forma-
anisms have evolved, described below. tion of a trans-Δ2 bond. These situations are handled by
an additional two enzymes, Enoyl CoA isomerase or 2,4
Dienoyl CoA reductase.
15.5.4 Even-numbered saturated fatty
acids
Once inside the mitochondria, each cycle of β-oxidation,
liberating a two carbon unit (acetyl-CoA), occurs in a se-
quence of four reactions:
This process continues until the entire chain is cleaved
into acetyl CoA units. The final cycle produces two sepa-
rate acetyl CoAs, instead of one acyl CoA and one acetyl
CoA. For every cycle, the Acyl CoA unit is shortened
by two carbon atoms. Concomitantly, one molecule of
FADH2 , NADH and acetyl CoA are formed.
This describes how unsaturated fatty acids are divided in Beta
oxidation.
15.5.5 Odd-numbered saturated fatty
acids Whatever the conformation of the hydrocarbon chain, β-
oxidation occurs normally until the acyl CoA (because
In general, fatty acids with an odd number of carbons are of the presence of a double bond) is not an appropriate
found in the lipids of plants and some marine organisms. substrate for acyl CoA dehydrogenase, or enoyl CoA hy-
Many ruminant animals form a large amount of 3-carbon dratase:
propionate during the fermentation of carbohydrates in
the rumen.[4]
• If the acyl CoA contains a cis-Δ3 bond, then cis-
Chains with an odd-number of carbons are oxidized in Δ3 -Enoyl CoA isomerase will convert the bond to
the same manner as even-numbered chains, but the final a trans-Δ2 bond, which is a regular substrate.
products are propionyl-CoA and acetyl-CoA.
Propionyl-CoA is first carboxylated using a bicarbonate • If the acyl CoA contains a cis-Δ4 double bond, then
ion into D-stereoisomer of methylmalonyl-CoA, in a re- its dehydrogenation yields a 2,4-dienoyl interme-
action that involves a biotin co-factor, ATP, and the en- diate, which is not a substrate for enoyl CoA hy-
zyme propionyl-CoA carboxylase. The bicarbonate ion’s dratase. However, the enzyme 2,4 Dienoyl CoA
carbon is added to the middle carbon of propionyl-CoA, reductase reduces the intermediate, using NADPH,
forming a D-methylmalonyl-CoA. However, the D con- into trans-Δ3 -enoyl CoA. As in the above case, this
formation is enzymatically converted into the L confor- compound is converted into a suitable intermediate
mation by methylmalonyl-CoA epimerase, then it under- by 3,2-Enoyl CoA isomerase.
goes intramolecular rearrangement, which is catalyzed
by methylmalonyl-CoA mutase (requiring B12 as a coen- To summarize:
zyme) to form succinyl-CoA. The succinyl-CoA formed
can then enter the citric acid cycle. • Odd-numbered double bonds are handled by the iso-
However, whereas acetyl-CoA enters the citric acid cy- merase.
15.5. BETA OXIDATION 257

• Even-numbered double bonds by the reductase For an even-numbered saturated fat (C₂ ), n - 1 oxidations
(which creates an odd-numbered double bond) are necessary, and the final process yields an additional
acetyl CoA. In addition, two equivalents of ATP are lost
during the activation of the fatty acid. Therefore, the total
15.5.7 Peroxisomal beta-oxidation ATP yield can be stated as:

Fatty acid oxidation also occurs in peroxisomes when the (n - 1) * 14 + 10 - 2 = total ATP
fatty acid chains are too long to be handled by the mito-
chondria. The same enzymes are used in peroxisomes as or
in the mitochondrial matrix, and acetyl-CoA is generated.
It is believed that very long chain (greater than C-22) fatty 14n-6 (alternatively)
acids, branched fatty acids,[6] some prostaglandins and
leukotrienes[7] undergo initial oxidation in peroxisomes For instance, the ATP yield of palmitate (C16 , n = 8) is:
until octanoyl-CoA is formed, at which point it undergoes
mitochondrial oxidation.[8] (8 - 1) * 14 + 10 - 2 = 106 ATP
One significant difference is that oxidation in peroxi-
Represented in table form:
somes is not coupled to ATP synthesis. Instead, the high-
potential electrons are transferred to O2 , which yields For sources that use the larger ATP production num-
H2 O2 . It does generate heat however. The enzyme bers described above, the total would be 129 ATP ={(8-
catalase, found exclusively in peroxisomes, converts the 1)*17+12-2} equivalents per palmitate.
hydrogen peroxide into water and oxygen. Beta-oxidation of unsaturated fatty acids changes the
Peroxisomal β-oxidation also requires enzymes specific ATP yield due to the requirement of two possible addi-
to the peroxisome and to very long fatty acids. There are tional enzymes.
three key differences between the enzymes used for mi-
tochondrial and peroxisomal β-oxidation:
15.5.9 History and discovery
1. The NADH formed in the third oxidative step can- In 1904, the German chemist Franz Knoop elucidated the
not be reoxidized in the peroxisome, so reducing steps in beta-oxidation by feeding dogs odd- and even-
equivalents are exported to the cytosol. chain ω-phenyl fatty acids, such as ω-phenylvaleric acid
2. β-oxidation in the peroxisome requires the use of and ω-phenylbutyric acid, respectively. The mechanism
a peroxisomal carnitine acyltransferase (instead of of beta-oxidation, i.e. successive removal of two carbons,
carnitine acyltransferase I and II used by the mito- was realized when it was discovered that the odd-chain
chondria) for transport of the activated acyl group ω-phenylvaleric acid was metabolized to hippuric acid,
into the mitochondria for further breakdown. and that the even-chain ω-phenylbutyric acid was metab-
olized to phenaceturic acid. At this time, any reaction
3. The first oxidation step in the peroxisome is cat- mechanism involving oxidation at the beta carbon was as
alyzed by the enzyme acyl-CoA oxidase. yet unknown in organic chemistry.[9][10]

4. The β-ketothiolase used in peroxisomal β-oxidation

has an altered substrate specificity, different from 15.5.10 Clinical significance
the mitochondrial β-ketothiolase.
There are at least 25 enzymes and specific transport pro-
teins in the β-oxidation pathway.[11] Of these, 18 have
Peroxisomal oxidation is induced by a high-fat diet and
been associated with human disease as inborn errors of
administration of hypolipidemic drugs like clofibrate.
metabolism.

15.5.8 Energy yield 15.5.11 See also

The ATP yield for every oxidation cycle is theoretically at • Fatty acid metabolism
maximum yield 17, as NADH produces 3 ATP, FADH2
produces 2 and a full rotation of the Citric Acid Cy- • Fatty-acid metabolism disorder
cle produces 12. In practice it’s closer to 14 ATP for • Lipolysis
a full oxidation cycle as in practice the theoretical yield
isn't attained, it’s generally closer to 2.5 ATP per NADH • Krebs cycle
molecule produced, 1.5 for each FADH2 Molecule pro-
• Omega oxidation
duced and this equates to 10 per cycle of the TCA (ac-
cording to the P/O ratio), broken down as follows: • Alpha oxidation
258 CHAPTER 15. LIPID METABOLISM

15.5.12 External links

• The chemical logic behind fatty acid metabolism at
ufp.pt
• JEREMY M. BERG,JOHN L. TYMOCZKO and
LUBERT STRYER Biochemistry, 2002
• Animations at brookscole.com

15.5.13 References
[1] Stahl, Andreas (1 February 2004). “A current re-
view of fatty acid transport proteins (SLC27)". Pflügers
Archiv European Journal of Physiology 447 (5): 722–727.
doi:10.1007/s00424-003-1106-z. PMID 12856180. Re-
trieved 2 March 2015.

[2] Anderson, Courtney M.; Stahl, Andreas (April

2013). “SLC27 fatty acid transport proteins”.
Molecular Aspects of Medicine 34 (2-3): 516–528.
doi:10.1016/j.mam.2012.07.010. Retrieved 2 March
2015.

[3] Charney, Alan N.; Micic, Ljubisa; Egnor, Richard W. (3

December 1997). “Nonionic diffusion of short-chain fatty
acids across rat colon.”. The American Journal of Physi-
ology 274 (3 Pt 1): G518–24. PMID 9530153. Retrieved
2 March 2015.

[4] Nelson, D. L. & Cox, M. M. (2005). Lehninger Principles

of Biochemistry, 4th Edition. New York: W. H. Freeman
and Company, pp. 648-649. ISBN 0-7167-4339-6.

[5] King, Michael. “Gluconeogenesis: Synthesis of New Glu-

cose”. Subsection: “Propionate”. themedicalbiochem-
istrypage.org, LLC. Retrieved 20 March 2013.

[6] Singh I (February 1997). “Biochemistry of peroxisomes

in health and disease”. Mol. Cell. Biochem. 167 (1-2):
1–29. doi:10.1023/A:1006883229684. PMID 9059978.

[7] G. Gordon Gibson; Brian G. Lake (2013-04-08).

Peroxisomes: Biology and Importance in Toxicology and
Medicine. CRC Press. pp. 69–. ISBN 978-0-203-48151-
6.

[8] Lazarow, Paul B. (10 March 1978). “Rat liver peroxi-

somes catalyze the beta oxidation of fatty acids.”. Journal
of Biological Chemistry (253): 1522–1528. Retrieved 2
March 2015.

[9] Knoop, Franz (1904). “Der Abbau aromatischer

Fettsäuren im Tierkörper”. Beitr Chem Physiol Pathol 6:
150–162.

[10] Houten, Sander Michel; Wanders, Ronald J. A. (2 March

2010). “A general introduction to the biochemistry of mi-
tochondrial fatty acid β-oxidation”. Journal of Inherited
Metabolic Disease 33 (5): 469–477. doi:10.1007/s10545-
010-9061-2. Retrieved 2 March 2015.

[11] Tein, Ingrid (2013). “Disorders of fatty acid oxida-

tion”. Handbook of Clinical Neurology 113: 1675–1688.
doi:10.1016/B978-0-444-59565-2.00035-6.
Chapter 16

Nitrogen metabolism

16.1 Nitrogen fixation

Nitrogen fixation is a process in which nitrogen (N2 ) in
the atmosphere is converted into ammonium (NH4 + ) or
nitrogen dioxide (NO
2), for example.[1] Atmospheric nitrogen or molecular
nitrogen (N2 ) is relatively inert: it does not easily react
with other chemicals to form new compounds. The fixa-
tion process frees up the nitrogen atoms from their triply
bonded diatomic form, N≡N, to be used in other ways.
Nitrogen fixation, natural and synthetic, is essential for all
forms of life because nitrogen is required to biosynthesize
basic building blocks of plants, animals and other life
forms, e.g., nucleotides for DNA and RNA and amino Schematic representation of the nitrogen cycle. Abiotic nitrogen
acids for proteins. Therefore, nitrogen fixation is essential fixation has been omitted.
for agriculture and the manufacture of fertilizer. It is also
an important process in the manufacture of explosives
(e.g. gunpowder, dynamite, TNT, etc.). Nitrogen fixa- occurs at a cluster called FeMoco, an abbreviation for the
tion occurs naturally in the air by means of lightning.[2][3]
iron-molybdenum cofactor. The mechanism proceeds via
Biological nitrogen fixation can include conversion to a series of protonation and reduction steps wherein [5]
the
nitrogen dioxide. All biological nitrogen fixation is FeMoco active site hydrogenates the N2 substrate.
done by way of nitrogenase metalo-enzymes which con- In free-living diazotrophs, the nitrogenase-generated
tain iron, molybdenum, or vanadium. Microorganisms ammonium is assimilated into glutamate through the
that can fix nitrogen are prokaryotes (both bacteria and glutamine synthetase/glutamate synthase pathway.
archaea, distributed throughout their respective king-
The microbial genes required for nitrogen fixation are
doms) called diazotrophs. Some higher plants, and some
widely distributed in diverse environments.[6][7]
animals (termites), have formed associations (symbiosis)
with diazotrophs. Enzymes responsible for nitrogenase action are very sus-
ceptible to destruction by oxygen. For this reason, many
bacteria cease production of the enzyme in the pres-
16.1.1 Biological nitrogen fixation ence of oxygen. Many nitrogen-fixing organisms exist
only in anaerobic conditions, respiring to draw down oxy-
Biological nitrogen fixation was discovered by the Ger- gen levels, or binding the oxygen with a protein such as
man agronomist Hermann Hellriegel and Dutch microbi- leghemoglobin.[1]
ologist Martinus Beijerinck. Biological nitrogen fixation
(BNF) occurs when atmospheric nitrogen is converted to
ammonia by an enzyme called nitrogenase.[1] The overall Microorganisms that fix nitrogen
reaction for BNF is:
Main article: Diazotroph
N2 + 8 H+ + 8 e− → 2 NH3 + H2
Diazotrophs are a diverse group of prokaryotes that
The process is coupled to the hydrolysis of 16 equivalents includes cyanobacteria (e.g. the highly significant
of ATP and is accompanied by the co-formation of one Trichodesmium and Cyanothece), green sulfur bac-
molecule of H2 .[4] The conversion of N2 into ammonia teria,and diazotrophs Azotobacteraceae, rhizobia and

259
260 CHAPTER 16. NITROGEN METABOLISM

Frankia. Non-leguminous Although by far the majority of

Cyanobacteria inhabit nearly all illuminated environ- plants able to form nitrogen-fixing root nodules are in the
ments on Earth and play key roles in the carbon legume family Fabaceae, there are a few exceptions:
and nitrogen cycle of the biosphere. In general,
cyanobacteria are able to utilize a variety of inorganic • Parasponia, a tropical genus in the Cannabaceae
and organic sources of combined nitrogen, like nitrate, also able to interact with rhizobia and form nitrogen-
nitrite, ammonium, urea, or some amino acids. Several fixing nodules[12]
cyanobacterial strains are also capable of diazotrophic
growth, an ability that may have been present in their last • Actinorhizal plants such as alder and bayberry can
common ancestor in the Archean eon.[8] Nitrogen fixation also form nitrogen-fixing nodules, thanks to a symbi-
by cyanobacteria in coral reefs can fix twice the amount of otic association with Frankia bacteria. These plants
nitrogen than on land—around 1.8 kg of nitrogen is fixed belong to 25 genera[13] distributed among 8 plant
per hectare per day. The colonial marine cyanobacterium families.
Trichodesmium is thought to fix nitrogen on such a scale
that it accounts for almost half of the nitrogen-fixation in
The ability to fix nitrogen is far from universally present
marine systems on a global scale.[9]
in these families. For instance, of 122 genera in the
Rosaceae, only 4 genera are capable of fixing nitro-
gen. All these families belong to the orders Cucurbitales,
Root nodule symbioses Fagales, and Rosales, which together with the Fabales
form a clade of eurosids. In this clade, Fabales were the
Legume family Plants that contribute to nitrogen fix- first lineage to branch off; thus, the ability to fix nitrogen
ation include the legume family – Fabaceae – with taxa may be plesiomorphic and subsequently lost in most de-
such as kudzu, clovers, soybeans, alfalfa, lupines, peanuts, scendants of the original nitrogen-fixing plant; however,
and rooibos. They contain symbiotic bacteria called it may be that the basic genetic and physiological require-
rhizobia within nodules in their root systems, producing ments were present in an incipient state in the last com-
nitrogen compounds that help the plant to grow and com- mon ancestors of all these plants, but only evolved to full
pete with other plants. When the plant dies, the fixed function in some of them:
nitrogen is released, making it available to other plants
There are also several nitrogen-fixing symbiotic associa-
and this helps to fertilize the soil.[1][10] The great majority
tions that involve cyanobacteria (such as Nostoc):
of legumes have this association, but a few genera (e.g.,
Styphnolobium) do not. In many traditional and organic
farming practices, fields are rotated through various types • Some lichens such as Lobaria and Peltigera
of crops, which usually includes one consisting mainly
• Mosquito fern (Azolla species)
or entirely of clover or buckwheat (non-legume family
Polygonaceae), which are often referred to as "green ma- • Cycads
nure".
• Gunnera
Inga alley farming relies on the leguminous genus Inga, a
small tropical, tough-leaved, nitrogen-fixing tree.[11]
Endosymbiosis in diatoms

Rhopalodia gibba, a diatom algae, is probably the only eu-

karyote with cyanobacterial N2-fixing endosymbiont or-
ganelles. The spheroid bodies reside in the cytoplasm of
the diatoms and are inseparable from their hosts.[14][15]

16.1.2 Industrial nitrogen fixation

The possibility that atmospheric nitrogen reacts with cer-
tain chemicals was first observed by Desfosses in 1828.
He observed that mixtures of alkali metal oxides and
carbon react at high temperatures with nitrogen. With
the use of barium carbonate as starting material the first
commercially used process became available in the 1860s
developed by Margueritte and Sourdeval. The result-
A sectioned alder tree root nodule. ing barium cyanide could be reacted with steam yield-
ing ammonia. In 1898 Adolph Frank and Nikodem Caro
16.1. NITROGEN FIXATION 261

decoupled the process and first produced calcium car- is ongoing, with particular emphasis on hydrogenation to
bide and in a subsequent step reacted it with nitrogen to give ammonia.[22]
calcium cyanamide. The Ostwald process for the pro- Metallic lithium has long been known for burning in an
duction of nitric acid was discovered in 1902. Frank- atmosphere of nitrogen and then converting to lithium
Caro process and Ostwald process dominated the indus- nitride. Hydrolysis of the resulting nitride gives ammo-
trial fixation of nitrogen until the discovery of the Haber nia. In a related process, trimethylsilyl chloride, lithium,
process in 1909.[16][17] Prior to 1900, Nikola Tesla also and nitrogen react in the presence of a catalyst to give
experimented with the industrial fixation of nitrogen “by tris(trimethylsilyl)amine. Tris(trimethylsilyl)amine can
using currents of extremely high frequency or rate of
then be used for reaction with α,δ,ω-triketones to give tri-
vibration”.[18][19] cyclic pyrroles.[23] Processes involving Li metal are how-
ever of no practical interest since they are noncatalytic
Haber process and re-reducing the Li+ ion residue is difficult.
Beginning in the 1960s several homogeneous systems
Main article: Haber process were identified that convert nitrogen to ammonia, some-
Artificial fertilizer production is now the largest times even catalytically but often operating via ill-defined
mechanisms. The original discovery is described in an
early review, “Vol'pin and co-workers, using a non-protic
Lewis acid, aluminium tribromide, were able to demon-
strate the truly catalytic effect of titanium by treating dini-
trogen with a mixture of titanium tetrachloride, metallic
aluminium, and aluminium tribromide at 50 °C, either in
the absence or in the presence of a solvent, e.g. benzene.
As much as 200 mol of ammonia per mol of TiCl4 was
obtained after hydrolysis....”[24]
The quest for well defined intermediates led to the charac-
terization of many transition metal dinitrogen complexes.
Few of these well defined complexes function catalyti-
cally, their behavior illuminated likely stages in nitrogen
fixation. Most fruitful of all of these early studies focused
on M(N2 )2 (dppe)2 (M = Mo, W). For example double
protonation of such low valent complexes gave interme-
Equipment for a study of nitrogen fixation by alpha rays, Fixed diates with the linkage M=N-NH2 . In 1995, a molybde-
Nitrogen Research Laboratory, 1926 num(III) amido complex was discovered that cleaved N2
to give the corresponding molybdenum(VI) nitride.[25]
source of human-produced fixed nitrogen in the Earth's This and related terminal nitrido complexes have been
[26]
ecosystem. Ammonia is a required precursor to used to make nitriles.
fertilizers, explosives, and other products. The most com-
mon method is the Haber process. The Haber process re-
quires high pressures (around 200 atm) and high temper-
atures (at least 400 °C), routine conditions for industrial
catalysis. This highly efficient process uses natural gas as
a hydrogen source and air as a nitrogen source.[20]
Much research has been conducted on the discovery of
catalysts for nitrogen fixation, often with the goal of re-
ducing the energy required for this conversion. However,
such research has thus far failed to even approach the ef-
ficiency and ease of the Haber process. Many compounds
react with atmospheric nitrogen to give dinitrogen com-
plexes. The first dinitrogen complex to be reported was
Ru(NH3 )5 (N2 )2+ .[21]
Synthetic nitrogen reduction Yandulov 2003

Ambient nitrogen reduction In 2003 a related molybdenum amido complex was

found to catalyze the reduction of N2 . In addition to a
Catalytic chemical nitrogen fixation at ambient condi- source of protons, the catalyst requires a strong reducing
tions is an ongoing scientific endeavor. Guided by the ex- agent.[27][28][29][30] However, this catalytic reduction fix-
ample of nitrogenase, this area of homogeneous catalysis ates only a few nitrogen molecules. In these systems, like
262 CHAPTER 16. NITROGEN METABOLISM

the biological one, hydrogen is provided to the substrate [7] Hoppe, B.; Kahl, T.; Karasch, P.; Wubet, T.; Bauhus,
heterolytically, by means of protons and reducing equiv- J.; Buscot, F.; Krüger, D. (2014). “Network anal-
alents rather than with H2 itself. ysis reveals ecological links between N-fixing
bacteria and wood-decaying fungi”. PLoS ONE
In 2011 Arashiba et al. reported yet another system with 9 (2): e88141. Bibcode:2014PLoSO...988141H.
a catalyst again based on molybdenum but with a diphos- doi:10.1371/journal.pone.0088141. PMC 3914916.
phorus pincer ligand.[31] Photolytic nitrogen splitting is PMID 24505405.
also considered.[32][33][34][35][36]
[8] Latysheva, N.; Junker, V. L.; Palmer, W. J.; Codd, G.
A.; Barker, D. (2012). “The evolution of nitrogen fixa-
16.1.3 See also tion in cyanobacteria”. Bioinformatics 28 (5): 603–606.
doi:10.1093/bioinformatics/bts008.
• Birkeland–Eyde process: an industrial fertiliser pro-
[9] Bergman, B.; Sandh, G.; Lin, S.; Larsson, H.; and Car-
duction process
penter, E. J. (2012). "Trichodesmium – a widespread
• Denitrification: an organic process of nitrogen re- marine cyanobacterium with unusual nitrogen fixation
lease properties”. FEMS Microbiology Reviews 37 (3): 1–17.
doi:10.1111/j.1574-6976.2012.00352.x.
• George Washington Carver: an American botanist
[10] Smil, V (2000). Cycles of Life. Scientific American Li-
• Nif gene: a gene found in nitrogen fixing bacteria brary.

• Nitrification: biological production of nitrogen [11] Elkan, Daniel. “Slash-and-burn farming has become a
major threat to the world’s rainforest”. The Guardian, 21
• Nitrogen cycle: the flow and transformation of ni- April 2004.
trogen through the environment
[12] Op den Camp, Rik; Streng, A. et al. (2010).
• Nitrogen deficiency “LysM-Type Mycorrhizal Receptor Recruited for Rhi-
zobium Symbiosis in Nonlegume Parasponia". Science
• Nitrogenase: enzymes used by organisms to fix ni-
331 (6019): 909–912. Bibcode:2011Sci...331..909O.
trogen doi:10.1126/science.1198181.
• Ostwald process: a chemical process for making ni-
[13] Dawson, J. O. (2008). “Ecology of actinorhizal plants”.
tric acid HNO3 Nitrogen-fixing Actinorhizal Symbioses 6. Springer. pp.
• Push–pull technology: the use of both repellent and 199–234. doi:10.1007/978-1-4020-3547-0_8.
attractive organisms in agriculture [14] Prechtl, J. et al. (2004). Intracellular spheroid bodies
of Rhopalodia gibba have nitrogen-fixing apparatus of
cyanobacterial origin. Molecular biology and evolution,
16.1.4 References 21(8), 1477–1481, .
[1] Postgate, J. (1998). Nitrogen Fixation, 3rd Edition. Cam- [15] Nakayama, T., & Inagaki, Y. (2014). Unique genome
bridge University Press, Cambridge UK. evolution in an intracellular N2-fixing symbiont of a
rhopalodiacean diatom. Acta Societatis Botanicorum Polo-
[2] Slosson, Edwin (1919). Creative Chemistry. New York:
niae, 83 (4), 409-413, .
The Century Co. pp. 19–37.

[3] http://journals.ametsoc.org/doi/abs/10.1175/ [16] Heinrich, H.; Nevbner, Rolf (1934). “Die Umwand-
1520-0469%281980%29037%3C0179%3AANFBL% lungsgleichung Ba(Cn)2 → BaCN2 + C Im Temperaturge-
3E2.0.CO%3B2 biet von 500 Bis 1000 °C”. Zeitschrift für Elektrochemie
und angewandte physikalische Chemie 40 (10): 693–698.
[4] Chi Chung, Lee; Markus W., Ribbe; Yilin, Hu (2014). doi:10.1002/bbpc.19340401005 (inactive 2015-02-01).
“Chapter 7. Cleaving the N,N Triple Bond: The Transfor-
mation of Dinitrogen to Ammonia by Nitrogenases". In Pe- [17] Curtis, Harry Alfred (1932). Fixed nitrogen.
ter M.H. Kroneck and Martha E. Sosa Torres. The Metal-
Driven Biogeochemistry of Gaseous Compounds in the En- [18] http://www.tfcbooks.com/tesla/1900-06-00.htm
vironment. Metal Ions in Life Sciences 14. Springer. pp.
[19] Tesla, Nikola (1900). “The Problem of Increasing Human
147–174. doi:10.1007/978-94-017-9269-1_6.
Energy”. The Century Magazine. 60 (n.s. v. 38) (1900
[5] Hoffman, B. M.; Lukoyanov, D.; Dean, D. R.; Seefeldt, May–Oct): 175.
L. C. (2013). “Nitrogenase: A Draft Mechanism”. Acc.
Chem. Res. 46: 587. doi:10.1021/ar300267m. [20] http://cfpub.epa.gov/watertrain/pdf/issue1.pdf US Envi-
ronmental Protection Agency: Human Alteration of the
[6] Gaby, J.C.; Buckley, D.H. (2011). “A global census of ni- Global Nitrogen Cycle: Causes and Consequences by Pe-
trogenase diversity”. Environmental Microbiology 13 (7): ter M. Vitousek, Chair, John Aber, Robert W. Howarth,
1790–1799. doi:10.1111/j.1462-2920.2011.02488.x. Gene E. Likens, Pamela A. Matson, David W. Schindler,
PMID 21535343. William H. Schlesinger, and G. David Tilman
16.2. AMINO ACID SYNTHESIS 263

[21] A. D. Allen, C. V. Senoff; Senoff (1965). “Ni- [33] Solari, E., Da Silva, C., Iacono, B., Hesschen-
trogenopentammineruthenium(II) complexes”. Journal brouck, J., Rizzoli, C., Scopelliti, R. and Flo-
of the Chemical Society, Chemical Communications (24): riani, C. (2001) “Photochemical Activation of
621. doi:10.1039/C19650000621. the N≡N Bond in a Dimolybdenum–Dinitrogen
Complex: Formation of a Molybdenum Ni-
[22] “Reduction of dinitrogen” Richard R. Schrock PNAS tride” Angew. Chem. Int. Ed 40: 3907–3909
14 November 2006 vol. 103 no. 46 17087 doi:10.1002/1521-3773(20011015)40:20<3907::AID-
doi:10.1073/pnas.0603633103 ANIE3907>3.0.CO;2-#

[23] Brook, Michael A. (2000). Silicon in Organic, [34] Huss, Adam S.; Curley, John J.; Cummins, Christopher
Organometallic, and Polymer Chemistry. New York: John C.; Blank, David A. (2013). “Relaxation and Dissoci-
Wiley & Sons, Inc. pp. 193–194. ation Following Photoexcitation of the (?-N2)[Mo(N[t-
Bu]Ar)3]2 Dinitrogen Cleavage Intermediate”. The
[24] Chatt, J.; Leigh, G. J., “Nitrogen Fixation”, Chem. Soc. Journal of Physical Chemistry B 117 (5): 1429–1436.
Rev. 1972, vol. 1, 121. doi:10.1021/jp310122x.

[25] “Dinitrogen Cleavage by a Three-Coordinate Molybde- [35] Kunkely, H.; Vogler, A. (2010). “Photolysis of
num(III) Complex” Catalina E. Laplaza and Christo- Aqueous [(NH3)5Os(μ-N2)Os(NH3)5]5+: Cleavage of
pher C. Cummins Science 12 May 1995: 861– Dinitrogen by an Intramolecular Photoredox Reac-
863.10.1126/science.268.5212.861 tion”. Angew. Chem. Int. Ed. 49: 1591–1593.
doi:10.1002/anie.200905026.
[26] “A Cycle for Organic Nitrile Synthesis via Dinitrogen
Cleavage” John J. Curley, Emma L. Sceats, and Christo- [36] Miyazaki, T.; Tanaka, H.; Tanabe, Y.; Yuki, M.;
pher C. Cummins J. Am. Chem. Soc., 2006, 128 (43), pp. Nakajima, K.; Yoshizawa, K.; Nishibayashi, Y. (2014).
14036–14037 doi:10.1021/ja066090a “Cleavage and Formation of Molecular Dinitrogen in a
Single System Assisted by Molybdenum Complexes Bear-
[27] Synthesis and Reactions of Molybdenum Triamidoamine ing Ferrocenyldiphosphine”. Angew. Chem. Int. Ed 53:
Complexes Containing Hexaisopropylterphenyl Substituents 11488–11492. doi:10.1002/anie.201405673.
Dmitry V. Yandulov, Richard R. Schrock, Arnold L.
Rheingold, Christopher Ceccarelli, and William M. Davis
Inorg. Chem.; 2003; 42(3) pp 796–813; (Article) 16.1.5 External links
doi:10.1021/ic020505l
• “A Brief History of the Discovery of Nitrogen-fixing
[28] “Catalytic Reduction of Dinitrogen to Ammonia at a Organisms”, Ann M. Hirsch (2009)
Single Molybdenum Center” Dmitry V. Yandulov and
Richard R. Schrock Science 4 July 2003: Vol. 301. no. • Marine Nitrogen Fixation laboratory at the Univer-
5629, pp. 76–78 doi:10.1126/science.1085326 sity of Southern California
[29] The catalyst is derived from molybdenum(V) chloride and
tris(2-aminoethyl)amine N-substituted with three very
bulky hexa-isopropylterphenyl (HIPT) groups. Nitrogen 16.2 Amino acid synthesis
adds end-on to the molybdenum atom, and the bulky
HIPT substituents prevent the formation of the stable and For the non-biological synthesis of amino acids, see
nonreactive Mo-N=N-Mo dimer. In this isolated pocket
Strecker amino acid synthesis.
the Mo-N2 . The proton donor is a pyridinium salt of
weakly coordinating counter anion. The reducing agent
is decamethylchromocene. All ammonia formed is col- Amino acid synthesis is the set of biochemical processes
lected as the HCl salt by trapping the distillate with a HCl (metabolic pathways) by which the various amino acids
solution are produced from other compounds. The substrates for
these processes are various compounds in the organism's
[30] Note also that, although the dinitrogen complex is shown
diet or growth media. Not all organisms are able to syn-
in brackets, this species can be isolated and characterized.
Here the brackets do not indicate that the intermediate is thesise all amino acids. For example, humans are able to
not observed. synthesise only 12 of the 20 standard amino acids (some
textbooks argue 10 are made in the body, while others
[31] Arashiba, Kazuya; Yoshihiro; Yoshiaki Nishibayashi, argue that 11 are) .
Miyake (2011). “A molybdenum complex bearing PNP-
A fundamental problem for biological systems is to ob-
type pincer ligands leads to the catalytic reduction of dini-
tain nitrogen in an easily usable form. This problem is
trogen into ammonia”. Nature Chemistry 3: 120–125.
doi:10.1038/nchem.906. solved by certain microorganisms capable of reducing the
inert N≡N molecule (nitrogen gas) to two molecules of
[32] Rebreyend, C. and de Bruin, B. (2014), Photolytic N2 ammonia in one of the most remarkable reactions in bio-
Splitting: A Road to Sustainable NH3 Production?. Angew. chemistry. Ammonia is the source of nitrogen for all
Chem. Int. Ed.doi:10.1002/anie.201409727 the amino acids. The carbon backbones come from the
264 CHAPTER 16. NITROGEN METABOLISM

glycolytic pathway, the pentose phosphate pathway, or 16.2.3 From intermediates of the citric
the citric acid cycle. acid cycle and other pathways
In amino acid production, one encounters an important
problem in biosynthesis, namely stereochemical control. Of the basic set of twenty amino acids (not counting
Because all amino acids except glycine are chiral, biosyn- selenocysteine), there are eight that human beings can-
thetic pathways must generate the correct isomer with not synthesize. In addition, the amino acids arginine,
high fidelity. In each of the 19 pathways for the gener- cysteine, glycine, glutamine, histidine, proline, serine,
ation of chiral amino acids, the stereochemistry at the and tyrosine are considered conditionally essential,
α-carbon atom is established by a transamination reac- meaning they are not normally required in the diet, but
tion that involves pyridoxal phosphate. Almost all the must be supplied exogenously to specific populations that
transaminases that catalyze these reactions descend from do not synthesize it in adequate amounts.[1][2] For exam-
a common ancestor, illustrating once again that effective ple, enough arginine is synthesized by the urea cycle to
solutions to biochemical problems are retained through- meet the needs of an adult but perhaps not those of a
out evolution. growing child. Amino acids that must be obtained from
the diet are called essential amino acids. Nonessential
Biosynthetic pathways are often highly regulated such amino acids are produced in the body. The pathways
that building-blocks are synthesized only when supplies for the synthesis of nonessential amino acids are quite
are low. Very often, a high concentration of the final simple. Glutamate dehydrogenase catalyzes the reductive
product of a pathway inhibits the activity of enzymes that amination of α-ketoglutarate to glutamate. A transami-
function early in the pathway. Often present are allosteric nation reaction takes place in the synthesis of most amino
enzymes capable of sensing and responding to concentra- acids. At this step, the chirality of the amino acid is
tions of regulatory species. These enzymes are similar in established. Alanine and aspartate are synthesized by
functional properties to aspartate transcarbamoylase and the transamination of pyruvate and oxaloacetate, respec-
its regulators. Feedback and allosteric mechanisms en- tively. Glutamine is synthesized from NH4+ and gluta-
sure that all twenty amino acids are maintained in suffi- mate, and asparagine is synthesized similarly. Proline
cient amounts for protein synthesis and other processes. and arginine are derived from glutamate. Serine, formed
from 3-phosphoglycerate, is the precursor of glycine
and cysteine. Tyrosine is synthesized by the hydroxy-
16.2.1 Nitrogen fixation lation of phenylalanine, an essential amino acid. The
pathways for the biosynthesis of essential amino acids
Microorganisms use ATP and reduced ferredoxin, a pow- are much more complex than those for the nonessen-
erful reductant, to reduce atmospheric nitrogen (N2 ) to tial ones. Activated Tetrahydrofolate, a carrier of one-
ammonia (NH3 ). An iron-molybdenum cluster in ni- carbon units, plays an important role in the metabolism
trogenase deftly catalyzes the fixation of N2 , a very in- of amino acids and nucleotides. This coenzyme carries
ert molecule. Higher organisms consume the fixed ni- one-carbon units at three oxidation states, which are in-
trogen to synthesize amino acids, nucleotides, and other terconvertible: most reduced—methyl; intermediate—
nitrogen-containing biomolecules. The major points of methylene; and most oxidized—formyl, formimino, and
entry of ammonia into metabolism are glutamine or methenyl. The major donor of activated methyl groups is
glutamate. S-adenosylmethionine, which is synthesized by the trans-
fer of an adenosyl group from ATP to the sulfur atom
of methionine. S-Adenosylhomocysteine is formed when
the activated methyl group is transferred to an acceptor.
16.2.2 Transamination
It is hydrolyzed to adenosine and homocysteine, the latter
of which is then methylated to methionine to complete
Most amino acids are synthesized from α-ketoacids, and
the activated methyl cycle.
later transaminated from another amino acid, usually
glutamate. The enzyme involved in this reaction is an Cortisol inhibits protein synthesis.[3]
aminotransferase.

16.2.4 Regulation by feedback inhibition

α-ketoacid + glutamate ⇄ amino acid + α-
ketoglutarate Most of the pathways of amino acid biosynthesis are
regulated by feedback inhibition, in which the commit-
Glutamate itself is formed by amination of α- ted step is allosterically inhibited by the final product.
ketoglutarate: Branched pathways require extensive interaction among
the branches that includes both negative and positive reg-
ulation. The regulation of glutamine synthetase from E.
α-ketoglutarate + NH+ coli is a striking demonstration of cumulative feedback
4 ⇄ glutamate inhibition and of control by a cascade of reversible cova-
16.2. AMINO ACID SYNTHESIS 265

lent modifications. Glutamate 5-kinase which catalyzes the reaction from

L-glutamate to an unstable intermediate L-γ-Glutamyl
phosphate.[6]
α-Ketoglutarates Arginine synthesis also utilizes negative feedback as well
as repression through a repressor encoded by the gene
The α-ketoglutarate family of amino acid synthesis (syn- argR. The gene product of argR, ArgR an aporepressor,
thesis of glutamate, glutamine, proline and arginine) be- and arginine as a corepressor affect the operon of arginine
gins with α-ketoglutarate, an intermediate in the Citric biosynthesis. The degree of repression is determined by
Acid Cycle. The concentration of α-ketoglutarate is de- the concentrations of the repressor protein and corepres-
pendent on the activity and metabolism within the cell sor level.[7]
along with the regulation of enzymatic activity. In E. coli
citrate synthase, the enzyme involved in the condensation
reaction initiating the Citric Acid Cycle is strongly inhib- Erythrose 4-phosphate and phosphoenolpyruvate
ited by α-ketoglutarate feedback inhibition and can be in-
hibited by DPNH as well high concentrations of ATP.[4] Phenylalanine, tyrosine, and tryptophan are known as
This is one of the initial regulations of the α-ketoglutarate
the aromatic amino acids. The synthesis of all three
family of amino acid synthesis. share a common beginning to their pathways; the for-
The regulation of the synthesis of glutamate from α- mation of chorismate from phosphoenolpyruvate (PEP)
ketoglutarate is subject to regulatory control of the Citric and erythrose 4- phosphate (E4P). The first step, con-
Acid Cycle as well as mass action dependent on the con- densation of 3-deoxy-D-arabino-heptulosonic acid 7-
centrations of reactants involved due to the reversible na- phosphate (DAHP) from PEP/E4P, uses three isoen-
ture of the transamination and glutamate dehydrogenase zymes AroF, AroG, and AroH. Each one of these has
reactions.[4] its synthesis regulated from tyrosine, phenylalanine, and
The conversion of glutamate to glutamine is regulated tryptophan, respectively. These isoenzymes all have the
by glutamine synthetase (GS) and is a highly significant ability to help regulate synthesis of DAHP by the method
step in nitrogen metabolism.[4] This enzyme is regulated of feedback inhibition. This acts in the cell by monitoring
by at least four different mechanisms: 1. Repression the concentrations of each of the three aromatic amino
and depression due to nitrogen levels; 2. Activation and acids. When there is too much of any one of them, that
inactivation due to enzymatic forms (taut and relaxed); one will allosterically control the DAHP synthetase by
3. Cumulative feedback inhibition through end prod- “turning it off”. With the first step of the common path-
uct metabolites; and 4. Alterations of the enzyme due way shut off, synthesis of the three amino acids can not
to adenylation and deadenylation.[4] In rich nitrogenous proceed. The rest of the enzymes in the common pathway
media or growth conditions containing high quantities of (conversion of DAHP to chorismate) appear to be syn-
ammonia there is a low level of GS, whereas in limit- thesized constitutively, except for shikimate kinase which
ing quantities of ammonia the specific activity of the en- can be inhibited by shikimate through linear mixed-type
zyme is 20-fold higher.[4] The confirmation of the enzyme inhibition. If too much shikimate has been produced then
it can bind to shikimate kinase to stop further production.
plays a role in regulation depending on if GS is in the
taut or relaxed form. The taut form of GS is fully ac- Besides the regulations described above, each amino
tive but, the removal of manganese converts the enzyme acids terminal pathway can be regulated. These terminal
to the relaxed state. The specific conformational state pathways progress from chorismate to the final end prod-
occurs based on the binding of specific divalent cations uct, either tyrosine, phenylalanine, or tryptophan. Each
and is also related to adenylation.[4] The feedback inhibi- one of these pathways is regulated in a similar fashion
tion of GS is due to a cumulative feedback due to several to the common pathway; with feedback inhibition on the
metabolites including L-tryptophan, L-histidine, AMP, first committed step of the pathway.
CTP, glucosamine-6-phosphate and carbamyl phosphate, Tyrosine and phenylalanine share the same initial step
alanine, and glycine.[4] An excess of any one product does in their terminal pathways, chorismate converted to
not individually inhibit the enzyme but a combination prephenate which is converted to an amino acid-
or accumulation of all the end products have a strong specific intermediate. This process is mediated by a
inhibitory effect on the synthesis of glutamine.[4] Glu- phenylalanine (PheA) or tyrosine (TyrA) specific cho-
tamine synthase activity is also inhibited via adenylation. rismate mutase-prephenate dehydrogenase. The reason
The adenylation activity is catalyzed by the bifunctional for the amino acid-specific enzymes is because PheA
adenylyltransferase/adenylyl removal (AT/AR) enzyme. uses a simple dehydrogenase to convert prephenate to
Glutamine and a regulatory protein called PII act together phenylpyruvate, while TyrA uses a NAD-dependent de-
to stimulate adenylation.[5] hydrogenase to make 4-hydroxylphenylpyruvate. Both
The regulation of proline biosynthesis can be depen- PheA and TyrA are feedback inhibited by their respec-
dent on the initial controlling step through negative feed- tive amino acids. Tyrosine can also be inhibited at the
back inhibition.[6] In E. coli, proline allosterically inhibits transcriptional level by the TyrR repressor. TyrR binds
266 CHAPTER 16. NITROGEN METABOLISM

to the TyrR boxes on the operon near the promoter of the functional aspartokinase, LysC. Transcription of aspar-
gene that it wants to repress. tokinase genes is regulated by concentrations of the sub-
In the terminal-tryptophan synthesis pathway, the ini- sequently produced amino acids, lysine, threonine and
tial step converts chorismate to anthranilate using methionine. The higher these amino acids concentra-
anthranilate synthase. This enzyme requires either tions, the less the gene is transcribed. ThrA and LysC
ammonia or glutamine as the amino group donor. are also feed-back inhibited by threonine and lysine. Fi-
Anthranilate synthase is regulated by the gene products nally, DAP decarboxylase LysA mediates the last step of
of trpE and trpD. trpE encodes the first subunit, which the lysine synthesis and is common for all studied bac-
terial species. The formation of aspartate kinase (AK),
binds to chorismate and moves the amino group from the
donor to chorismate. trpD encodes the second subunit, which catalyzes the phosphorylation of aspartate and ini-
tiates its conversion into other amino acids, is also inhib-
which is simply used to bind glutamine and use it as the
amino group donor so that the amine group can transfer to ited by both lysine and threonine, which prevents the for-
mation of the amino acids derived from aspartate. Ad-
the chorismate. Anthranilate synthase is also regulated by
feedback inhibition. The finished product of tryptophan, ditionally, high lysine concentrations inhibit the activity
of dihydrodipicolinate synthase (DHPS). So, in addition
once produced in great enough quantities, is able to act
as the co-repressor to the TrpR repressor which represses to inhibiting the first enzyme of the aspartate families
expression of the trp operon. biosynthetic pathway, lysine also inhibits the activity of
the first enzyme after the branch point, i.e. the enzyme
that is specific for lysine’s own synthesis.
Oxaloacetate/aspartate

The oxaloacetate/aspartate family of amino acids is com- Asparagine There are two different asparagine syn-
posed of lysine, asparagine, methionine, threonine, and thetases found in bacterial species. These two syn-
isoleucine. Aspartate can be converted into lysine, as- thetases, which are both referred to as the AsnC protein,
paragine, methionine and threonine. Threonine also gives are coded for by two genes: AsnA and AsnB. AsnC is
rise to isoleucine. All of these amino acids contain dif- autogenously regulated, which is where the product of a
ferent mechanisms for their regulation, some being more structural gene regulates the expression of the operon in
complex than others. All the enzymes in this biosynthetic which the genes reside. The stimulating effect of AsnC
pathway are subject to regulation via feedback inhibition on AsnA transcription is downregulated by asparagine.
and/or repression at the genetic level. As is typical in However, the autoregulation of AsnC is not affected by
highly branched metabolic pathways, there is additional asparagine.
regulation at each branch point of the pathway. This type
of regulatory scheme allows control over the total flux
Methionine Methionine synthesis is under tight regu-
of the aspartate pathway in addition to the total flux of
lation. The repressor protein MetJ, in cooperation with
individual amino acids. The aspartate pathway uses L-
the corepressor protein S-adenosyl-methionine, mediates
aspartic acid as the precursor for the biosynthesis of one
the repression of methionine’s biosynthetic pathway. Re-
fourth of the building block amino acids. Without this
cently, a new regulator focus, MetR has been identified.
pathway, protein synthesis would not be possible.
The MetR protein is required for MetE and MetH gene
expression and functions as a transactivator of transcrip-
Aspartate The enzyme aspartokinase, which catalyzes tion for these genes. MetR transcriptional activity is reg-
the phosphorylation of aspartate and initiates its conver- ulated by homocystein, which is the metabolic precursor
sion into other amino acids, can be broken up into 3 of methionine. It is also known that vitamin B12 can re-
isozymes, AK-I, II and III. AK-I is feed-back inhibited press MetE gene expression, which is mediated by the
by threonine, while AK-II and III are inhibited by lysine. MetH holoenzyme.
As a sidenote, AK-III catalyzes the phosphorylation of
aspartic acid that is the commitment step in this biosyn-
thetic pathway. The higher the concentration of threonine Threonine The biosynthesis of threonine is regulated
or lysine, the more aspartate kinase becomes downregu- via allosteric regulation of its precursor, homoserine, by
lated. structurally altering the enzyme homoserine dehydroge-
nase. This reaction occurs at a key branch point in the
pathway, with the substrate homoserine serving as the
Lysine Lysine is synthesized from aspartate via the di- precursor for the biosynthesis of lysine, methionine, thre-
aminopimelate (DAP) pathway. The initial two stages of onin and isoleucine. High levels of threonine result in
the DAP pathway are catalyzed by aspartokinase and as- low levels of homoserine synthesis. The synthesis of
partate semialdehyde dehydrogenase and play a key role aspartate kinase (AK), which catalyzes the phosphory-
in the biosynthesis of lysine, threonine and methionine. lation of aspartate and initiates its conversion into other
There are two bifunctional aspartokinase/homoserine de- amino acids, is feed-back inhibited by lysine, isoleucine,
hydrogenases, ThrA and MetL, in addition to a mono- and threonine, which prevents the synthesis of the amino
16.2. AMINO ACID SYNTHESIS 267

acids derived from aspartate. So, in addition to inhibit- contact with the loop, it will be “knocked off” the tran-
ing the first enzyme of the aspartate families biosynthetic script. When the ribosome is removed the his genes will
pathway, threonine also inhibits the activity of the first not be translated and histidine will not be produced by
enzyme after the branch point, i.e. the enzyme that is the cell.[9]
specific for threonine’s own synthesis.

3-Phosphoglycerates
Isoleucine The enzymes threonine deaminase, dihy-
droxy acid dehydrase and transaminase are controlled by Serine Serine is the first amino acid in this family to
end-product regulation. I.e. the presence of isoleucine be produced; it is then modified to produce both glycine
will downregulate the formation of all three enzymes, re- and cysteine (and many other biologically important
sulting in the downregulation of threonine biosynthesis. molecules). Serine is formed from 3-phosphoglycerate
High concentrations of isoleucine also result in the down- in the following pathway:
regulation of aspartate’s conversion into the aspartyl-
3-phosphoglycerate-> phosphohydroxyl-pyruvate->
phosphate intermediate, hence halting further biosynthe-
phosphoserine-> serine
sis of lysine, methionine, threonine, and isoleucine.
The conversion from 3-phosphoglycerate to
phosphohydroxyl-pyruvate is achieved by the en-
Ribose 5-phosphates zyme phosphoglycerate dehydrogenase. This enzyme is
the key regulatory step in this pathway. Phosphoglycer-
The synthesis of histidine in “E. coli” is a complex path- ate dehydrogenase is regulated by the concentration of
way involving 10 reactions and 10 enzymes. Synthesis be- serine in the cell. At high concentrations this enzyme
gins with 5-phosphoribosyl-pyrophosphate (PRPP) and will be inactive and serine will not be produced. At low
finishes with histidine and occurs through the reactions concentrations of serine the enzyme will be fully active
of the following enzymes:[8] and serine will be produced by the bacterium.[10] Since
serine is the first amino acid produced in this family both
HisG-> HisE/HisI-> HisA-> HisH-> HisF-> HisB->
glycine and cysteine will be regulated by the available
HisC-> HisB-> HisD (HisE/I and HisB are both bifunc-
concentration of serine in the cell.[11]
tional enzymes)
All of the enzymes are coded for on the his operon. This
operon has a distinct block of the leader sequence, called Glycine Glycine is synthesized from serine using the
block 1: enzyme serine hydromethyltransferase (SHMT), which is
coded by the gene glyA. The enzyme effectively removes
Met-Thr-Arg-Val-Gln-Phe-Lys-His-His-His-His-His-
a hydroxyl group from serine and replaces it with a methyl
His-His-Pro-Asp
group to yield glycine. This reaction is the only way E.
This leader sequence is very important for the regulation coli can produce glycine. The regulation of glyA is very
of histidine in “E. coli”. The his operon operates under a complex and is known to incorporate serine, glycine, me-
system of coordinated regulation where all the gene prod- thionine, purines, thymine, and folates however, the full
ucts will be repressed or depressed equally. The main mechanism has yet to be elucidated.[12] The methionine
factor in the repression or derepression of histidine syn- gene product MetR and the methionine intermediate ho-
thesis is the concentration of histidine charged tRNAs. mocysteine are known to positively regulate glyA. Ho-
The regulation of histidine is actually quite simple con- mocysteine is a coactivator of glyA and must act in con-
sidering the complexity of its biosynthesis pathway and, cert with MetR.[12][13] On the other hand, PurR, a pro-
it closely resembles regulation of tryptophan. In this sys- tein which plays a role in purine synthesis and S-adeno-
tem the full leader sequence has 4 blocks of comple- sylmethionine are known to down regulate glyA. PurR
mentary strands that can form hairpin loops structures.[8] binds directly to the control region of glyA and effectively
Block one, shown above, is the key to regulation. When turns the gene off so that glycine will not be produced by
histidine charged tRNA levels are low in the cell the ri- the bacterium.
bosome will stall at the string of His residues in block 1.
This stalling of the ribosome will allow complementary
strands 2 and 3 to form a hairpin loop. The loop formed Cysteine Cysteine is a very important molecule for a
by strands 2 and 3 forms an anti-terminator and transla- bacterium’s survival. This amino acid harbors a sulfur
tion of the his genes will continue and histidine will be atom and can actively participate in disulfide bond for-
produced. However when histidine charged tRNA levels mation. The genes required for the synthesis of cysteine
are high the ribosome will not stall at block 1, this will not are coded for on the cys regulon. The integration of sulfur
allow strands 2 and 3 to form a hairpin. Instead strands into the molecule is positively regulated by CysB. CysB is
3 and 4 will form a hairpin loop further downstream of the main focus of cysteine regulation. Effective inducers
the ribosome. The hairpin loop formed by strands 3 and of this regulon are N-acetyl-serine (NAS) and very small
4 is a terminating loop, when the ribosome comes into amounts of reduced sulfur. CysB functions by binding
268 CHAPTER 16. NITROGEN METABOLISM

to DNA half sites on the cys regulon. These half sites This is catalyzed by Acetohydroxy isomeroreductase.
differ in quantity and arrangement depending on the pro- The third reaction is the dehydration reaction of α, β-
moter of interest. There is however one half site that is dihydroxyisovalerate catalyzed by Dihydroxy acid dehy-
conserved. It lies just upstream of the −35 site of the pro- drase resulting in α-ketoisovalerate. Finally, a transami-
moter. There are also multiple accessory sites depending nation catalyzed either by an alanine-valine transaminase
on the promoter. In the absence of the inducer, NAS, or a glutamate-valine transaminase results in valine.
CysB will bind the DNA and cover many of the accessory Valine performs feedback inhibition to inhibit the Aceto-
half sites. Without the accessory half sites the regulon hydroxy acid synthase used to combine the first two pyru-
cannot be transcribed and cysteine will not be produced.
vate molecules.[16]
It is believed that the presence of NAS causes CysB to
undergo a conformational change. This conformational
change allows CysB to bind properly to all the half sites Leucine The leucine synthesis pathway diverges from
and causes the recruitment of the RNA polymerase. The the valine pathway beginning with α-ketoisovalerate. α-
RNA polymerase will then transcribe the cys regulon and Isopropylmalate synthase reacts with this substrate and
cysteine will be produced. Acetyl CoA to produce α-isopropylmalate. An isomerase
Further regulation is required for this pathway, however. then isomerizes α-isopropylmalate to β-isopropylmalate.
CysB can actually down regulate its own transcription The third step is the NAD+-dependent oxidation of β-
by binding to its own DNA sequence and blocking the isopropylmalate via the action of a dehydrogenase to yield
RNA polymerase. In this case NAS will act to disallow α-ketoisocaproate. Finally is the transamination via the
the binding of CysB to its own DNA sequence. OAS action of a glutamate-leucine transaminase to result in
is a precursor of NAS, cysteine itself can inhibit CysE leucine.
which functions to create OAS. Without the necessary Leucine, like valine, regulates the first step of its path-
OAS, NAS will not be produced and cysteine will not way by inhibiting the action of the α-Isopropylmalate
be produced. There are two other negative regulators of synthase.[16] Because leucine is synthesized by a diversion
cysteine. These are the molecules sulfide and thiosulfate, from the valine synthetic pathway, the feedback inhibi-
they act to bind to CysB and they compete with NAS for tion of valine on its pathway also can inhibit the synthesis
the binding of CysB.[14] of leucine.

Pyruvates ilvEDA operon The genes that encode both the Di-
hydroxy acid dehydrase used in the creation of α-
Pyruvate is the end result of glycolysis and can feed into ketoisovalerate and Transaminase E, as well as other en-
both the TCA cycle and fermentation processes.[15] Reac- zymes are encoded on the ilvEDA operon. This operon is
tions beginning with either one or two molecules of pyru- bound and inactivated by valine, leucine, and isoleucine.
vate cause the synthesis of alanine, valine, and leucine. (Isoleucine is not a direct derivative of pyruvate, but is
Feedback inhibition of final products is the main method produced by the use of many of the same enzymes used
of inhibition, and, in E. coli, the ilvEDA operon also plays to produce valine and, indirectly, leucine.) When one of
a part in this regulation. these amino acids is limited, the gene furthest from the
amino-acid binding site of this operon can be transcribed.
When a second of these amino acids is limited, the next-
Alanine Alanine is produced by the transamination closest gene to the binding site can be transcribed, and so
of one molecule of pyruvate using two alternate steps: forth.[16]
1) conversion of glutamate to α-ketoglutarate using a
glutamate-alanine transaminase, and 2) conversion of va-
line to α-ketoisovalerate via Transaminase C. 16.2.5 Amino acids as precursors to other
Not much is known about the regulation of alanine syn- biomolecules
thesis. The only definite method is the bacterium’s abil-
ity to repress Transaminase C activity by either valine or Amino acids are precursors of a variety of biomolecules.
leucine (see ilvEDA operon). Other than that, alanine Glutathione (γ-Glu-Cys-Gly) serves as a sulfhydryl buffer
biosynthesis does not seem to be regulated.[16] and detoxifying agent. Glutathione peroxidase, a sele-
noenzyme, catalyzes the reduction of hydrogen perox-
ide and organic peroxides by glutathione. Nitric ox-
Valine Valine is produced by a four-enzyme pathway. ide, a short-lived messenger, is formed from arginine.
It begins with the reaction of two pyruvate molecules Porphyrins are synthesized from glycine and succinyl
catalyzed by Acetohydroxy acid synthase yielding α- CoA, which condense to give δ-aminolevulinate. Two
acetolactate. Step two is the NADPH+ + H+ - depen- molecules of this intermediate become linked to form
dent reduction of α-acetolactate and migration of the porphobilinogen. Four molecules of porphobilinogen
methane groups to produce α, β-dihydroxyisovalerate. combine to form a linear tetrapyrrole, which cyclizes to
16.3. NUCLEOTIDE 269

uroporphyrinogen III. Oxidation and side-chain modifi- [14] Figge RM (2007). “Methione biosynthesis”. In Wendisch
cations lead to the synthesis of protoporphyrin IX, which VF. Amino acid biosynthesis: pathways, regulation, and
acquires an iron atom to form heme.[17] metabolic engineering. Berlin: Springer. pp. 206–208.
ISBN 3540485953.

16.2.6 References [15] Lehninger AL, Cox MM, Nelson DL (2008). Lehninger
principles of biochemistry (5th ed.). New York: W.H.
[1] Fürst P, Stehle P (1 June 2004). “What are the essential Freeman. p. 528. ISBN 978-0-7167-7108-1.
elements needed for the determination of amino acid re-
[16] Umbarger HE (1978). “Amino Acid Biosynthesis and its
quirements in humans?". J. Nutr. 134 (6 Suppl): 1558S–
Regulation”. Annual Review of Biochemistry 47: 533–
1565S. PMID 15173430.
606. doi:10.1146/annurev.bi.47.070178.002533. PMID
[2] Reeds PJ (1 July 2000). “Dispensable and indispensable 354503.
amino acids for humans”. J. Nutr. 130 (7): 1835S–40S.
PMID 10867060. [17] Berg JM, Tymoczko JL, Stryer L (2002). Biochemistry
(5th ed.). New York, NY: W. H. Freeman. ISBN 0-7167-
[3] Manchester KL (1964). “Sites of Hormonal Regulation 3051-0.
of Protein Metabolism”. In Munro HN, Allison JB. Mam-
malian protein metabolism 4. New York: Academic Press.
p. 229. ISBN 978-0-12-510604-7. 16.2.7 External links
[4] Shapiro BM, Stadtman ER (1970). “The Regula-
tion of Glutamine Synthesis in Microorganisms”. • NCBI Bookshelf Free Textbook Access
Annual Review of Microbiology 24: 501–524.
doi:10.1146/annurev.mi.24.100170.002441. PMID
4927139. 16.3 Nucleotide
[5] White D (2007). The physiology and biochemistry of
prokaryotes (3rd ed.). New York: Oxford Univ. Press.
ISBN 0195301684.

[6] Marco-Marín C, Gil-Ortiz F, Pérez-Arellano I, Cervera

J, Fita I, Rubio V (2007). “A Novel Two-domain Ar-
chitecture Within the Amino Acid Kinase Enzyme Fam-
ily Revealed by the Crystal Structure of Escherichia coli
Glutamate 5-kinase”. Journal of Molecular Biology 367
(5): 1431–1446. doi:10.1016/j.jmb.2007.01.073. PMID
17321544.

[7] Maas WK (1991). “The regulation of arginine biosynthe-

sis: its contribution to understanding the control of gene
expression”. Genetics 128 (3): 489–94. PMC 1204522.
PMID 1874410.

[8] Cohen GN (2007). The Biosynthesis of Histidine and Its

Regulation. Springer. pp. 399–407.

[9] “Regulation of Histidine and Hut Operons”. Retrieved 29 This nucleotide contains the five-carbon sugar deoxyribose, a
April 2012. nitrogenous base called adenine, and one phosphate group.
Together, the deoxyribose and adenine make up a nucleoside
[10] Bridgers WF (1970). “The relationship of the metabolic (specifically, a deoxyribonucleoside) called deoxyadenosine.
regulation of serine to phospholipids and one-carbon With the one phosphate group included, whole structure is con-
metabolism”. International Journal of Biochemistry 1 (4): sidered a deoxyribonucleotide (a nucleotide constituent of DNA)
495–505. doi:10.1016/0020-711X(70)90065-0. with the name deoxyadenosine monophosphate.
[11] Pilzer LI (December 1963). “The Pathway and Control of
Serine Biosynthesis in Escherichia coli”. J. Biol. Chem. Nucleotides are organic molecules that serve as the
238: 3934–44. PMID 14086727. monomers, or subunits, of nucleic acids like DNA and
[12] Steiert JG, Rolfes RJ, Zalkin H, Stauffer GV (1990).
RNA. The building blocks of nucleic acids, nucleotides
“Regulation of the Escherichia coli glyA gene by the purR are composed of a nitrogenous base, a five-carbon sugar
gene product”. J. Bacteriol. 172 (7): 3799–803. PMC (ribose or deoxyribose), and at least one phosphate group.
213358. PMID 2113912. Thus a nucleoside plus a phosphate group yields a nu-
cleotide.
[13] Plamann MD, Stauffer GV (1989). “Regulation of the
Escherichia coli glyA gene by the metR gene product and Nucleotides serve to carry packets of energy within
homocysteine”. J. Bacteriol. 171 (9): 4958–62. PMC the cell in the form of the nucleoside triphosphates
210303. PMID 2670901. (ATP, GTP, CTP and UTP), playing a central role
270 CHAPTER 16. NITROGEN METABOLISM

in metabolism.[1] In addition, nucleotides participate in and cytosine. RNA uses uracil in place of thymine. Ade-
cell signaling (cGMP and cAMP), and are incorporated nine always pairs with thymine by 2 hydrogen bonds,
into important cofactors of enzymatic reactions (e.g. while guanine pairs with cytosine through 3 hydrogen
coenzyme A, FAD, FMN, NAD, and NADP+ ). bonds, each due to their unique structures.
In experimental biochemistry, nucleotides can be Purines
pentose
radiolabeled with radionuclides to yield radionucleotides.
Base

glycosidic bond
Adenine Guanine
OH = ribose
H = deoxyribose Pyrimidines
16.3.1 Structure nucleoside
nucleoside monophosphate
nucleoside diphosphate
R
nucleoside triphosphate Cytosine Uracil Thymine

Structural elements of common nucleic acid constituents. Because

they contain at least one phosphate group, the compounds marked
nucleoside monophosphate, nucleoside diphosphate and nucle-
oside triphosphate are all nucleotides (not simply phosphate-
lacking nucleosides).

16.3.2 Synthesis

Nucleotides can be synthesized by a variety of means both

in vitro and in vivo.
In vivo, nucleotides can be synthesized de novo or
recycled through salvage pathways.[7] The components
used in de novo nucleotide synthesis are derived from
biosynthetic precursors of carbohydrate and amino acid
metabolism, and from ammonia and carbon dioxide. The
liver is the major organ of de novo synthesis of all four nu-
The structure of nucleotide monomers.
cleotides. De novo synthesis of pyrimidines and purines
follows two different pathways. Pyrimidines are synthe-
A nucleotide is made of a nucleobase (also termed a sized first from aspartate and carbamoyl-phosphate in the
nitrogenous base), a five-carbon sugar (either ribose or 2- cytoplasm to the common precursor ring structure orotic
deoxyribose) depending on if it is DNA or RNA, and one acid, onto which a phosphorylated ribosyl unit is cova-
or, depending on the definition, more than one phosphate lently linked. Purines, however, are first synthesized from
groups. Authoritative chemistry sources such as the ACS the sugar template onto which the ring synthesis occurs.
Style Guide[2] and IUPAC Gold Book[3] clearly state that For reference, the syntheses of the purine and pyrimidine
the term nucleotide refers only to a molecule containing nucleotides are carried out by several enzymes in the
one phosphate. However, common usage in molecular cytoplasm of the cell, not within a specific organelle. Nu-
biology textbooks often extends this definition to include cleotides undergo breakdown such that useful parts can be
molecules with two or three phosphate groups.[1][4][5][6] reused in synthesis reactions to create new nucleotides.
Thus, the term “nucleotide” generally refers to a nucleo-
side monophosphate, but a nucleoside diphosphate or nu- In vitro, protecting groups may be used during labora-
cleoside triphosphate could be considered a nucleotide as tory production of nucleotides. A purified nucleoside is
well. protected to create a phosphoramidite, which can then be
used to obtain analogues not found in nature and/or to
Without the phosphate group, the nucleobase and sugar synthesize an oligonucleotide.
compose a nucleoside. The phosphate groups form bonds
with either the 2, 3, or 5-carbon of the sugar, with the
5-carbon site most common. Cyclic nucleotides form Pyrimidine ribonucleotide synthesis
when the phosphate group is bound to two of the sugar’s
hydroxyl groups.[1] Nucleotides contain either a purine Main article: Pyrimidine metabolism
or a pyrimidine base. Ribonucleotides are nucleotides in
which the sugar is ribose. Deoxyribonucleotides are nu- The synthesis of the pyrimidines CTP and UTP oc-
cleotides in which the sugar is deoxyribose. curs in the cytoplasm and starts with the formation of
Nucleic acids are polymeric macromolecules made from carbamoyl phosphate from glutamine and CO2 . Next,
nucleotide monomers. In DNA, the purine bases are aspartate carbamoyltransferase catalyzes a condensation
adenine and guanine, while the pyrimidines are thymine reaction between aspartate and carbamoyl phosphate to
16.3. NUCLEOTIDE 271

CTP is subsequently formed by amination of UTP by the

catalytic activity of CTP synthetase. Glutamine is the
NH3 donor and the reaction is fueled by ATP hydroly-
sis, too:

UTP + Glutamine + ATP + H2 O → CTP +

ADP + Pᵢ

Cytidine monophosphate (CMP) is derived from cyti-

dine triphosphate (CTP) with subsequent loss of two
phosphates.[9] [10]

Purine ribonucleotide synthesis

Main article: Purine metabolism

The atoms which are used to build the purine nucleotides

The synthesis of UMP.
come from a variety of sources:
The color scheme is as follows: enzymes, coenzymes, substrate
names, inorganic molecules

form carbamoyl aspartic acid, which is cyclized into 4,5-

dihydroorotic acid by dihydroorotase. The latter is con-
verted to orotate by dihydroorotate oxidase. The net re-
action is:

(S)-Dihydroorotate + O2 → Orotate + H2 O2

Orotate is covalently linked with a phosphorylated ribo-

syl unit. The covalent linkage between the ribose and
pyrimidine occurs at position C1 [8] of the ribose unit,
which contains a pyrophosphate, and N1 of the pyrim-
idine ring. Orotate phosphoribosyltransferase (PRPP
transferase) catalyzes the net reaction yielding orotidine
monophosphate (OMP): The synthesis of IMP. The color scheme is as follows: enzymes,
coenzymes, substrate names, metal ions, inorganic molecules
Orotate + 5-Phospho-α-D-ribose 1-
The de novo synthesis of purine nucleotides by which
diphosphate (PRPP) → Orotidine 5'-phosphate
these precursors are incorporated into the purine ring pro-
+ Pyrophosphate
ceeds by a 10-step pathway to the branch-point inter-
mediate IMP, the nucleotide of the base hypoxanthine.
Orotidine 5'-monophosphate is decarboxylated by AMP and GMP are subsequently synthesized from this
orotidine-5'-phosphate decarboxylase to form uridine intermediate via separate, two-step pathways. Thus,
monophosphate (UMP). PRPP transferase catalyzes purine moieties are initially formed as part of the
both the ribosylation and decarboxylation reactions, ribonucleotides rather than as free bases.
forming UMP from orotic acid in the presence of PRPP.
It is from UMP that other pyrimidine nucleotides are Six enzymes take part in IMP synthesis. Three of them
derived. UMP is phosphorylated by two kinases to are multifunctional:
uridine triphosphate (UTP) via two sequential reactions
with ATP. First the diphosphate form UDP is produced, • GART (reactions 2, 3, and 5)
which in turn is phosphorylated to UTP. Both steps are • PAICS (reactions 6, and 7)
fueled by ATP hydrolysis:
• ATIC (reactions 9, and 10)
ATP + UMP → ADP + UDP The pathway starts with the formation of PRPP. PRPS1
is the enzyme that activates R5P, which is formed pri-
UDP + ATP → UTP + ADP marily by the pentose phosphate pathway, to PRPP by
272 CHAPTER 16. NITROGEN METABOLISM

reacting it with ATP. The reaction is unusual in that a Hypoxanthine is oxidized to xanthine and finally to uric
pyrophosphoryl group is directly transferred from ATP acid. Instead of uric acid secretion, guanine and IMP can
to C1 of R5P and that the product has the α configura- be used for recycling purposes and nucleic acid synthesis
tion about C1. This reaction is also shared with the path- in the presence of PRPP and aspartate (NH3 donor).
ways for the synthesis of Trp, His, and the pyrimidine
nucleotides. Being on a major metabolic crossroad and
requiring much energy, this reaction is highly regulated.
In the first reaction unique to purine nucleotide biosyn- 16.3.3 Unnatural base pair (UBP)
thesis, PPAT catalyzes the displacement of PRPP's
pyrophosphate group (PPᵢ) by an amide nitrogen donated
Main article: Base pair § Unnatural base pair (UBP)
from either glutamine (N), glycine (N&C), aspartate (N),
folic acid (C1 ), or CO2 . This is the committed step in
purine synthesis. The reaction occurs with the inver- An unnatural base pair (UBP) is a designed subunit (or
sion of configuration about ribose C1 , thereby forming nucleobase) of DNA which is created in a laboratory and
β-5-phosphorybosylamine (5-PRA) and establishing the does not occur in nature. In 2012, a group of American
anomeric form of the future nucleotide. scientists led by Floyd Romesberg, a chemical biologist at
the Scripps Research Institute in San Diego, California,
Next, a glycine is incorporated fueled by ATP hydrolysis
published that his team designed an unnatural base pair
and the carboxyl group forms an amine bond to the NH2
(UBP).[11] The two new artificial nucleotides or Unnat-
previously introduced. A one-carbon unit from folic acid
ural Base Pair (UBP) were named d5SICS and dNaM.
coenzyme N10 -formyl-THF is then added to the amino
More technically, these artificial nucleotides bearing hy-
group of the substituted glycine followed by the closure
drophobic nucleobases, feature two fused aromatic rings
of the imidazole ring. Next, a second NH2 group is trans-
that form a (d5SICS–dNaM) complex or base pair in
ferred from a glutamine to the first carbon of the glycine
DNA.[12][13] In 2014 the same team from the Scripps Re-
unit. A carboxylation of the second carbon of the glycin
search Institute reported that they synthesized a stretch
unit is concomittantly added. This new carbon is modi-
of circular DNA known as a plasmid containing natural
fied by the additional of a third NH2 unit, this time trans-
T-A and C-G base pairs along with the best-performing
ferred from an aspartate residue. Finally, a second one-
UBP Romesberg’s laboratory had designed, and inserted
carbon unit from formyl-THF is added to the nitrogen
it into cells of the common bacterium E. coli that suc-
group and the ring covalently closed to form the common
cessfully replicated the unnatural base pairs through mul-
purine precursor inosine monophosphate (IMP).
tiple generations.[14] This is the first known example of
Inosine monophosphate is converted to adenosine a living organism passing along an expanded genetic
monophosphate in two steps. First, GTP hydrolysis fuels code to subsequent generations.[12][15] This was in part
the addition of aspartate to IMP by adenylosuccinate syn- achieved by the addition of a supportive algal gene that
thase, substituting the carbonyl oxygen for a nitrogen and expresses a nucleotide triphosphate transporter which ef-
forming the intermediate adenylosuccinate. Fumarate ficiently imports the triphosphates of both d5SICSTP and
is then cleaved off forming adenosine monophosphate. dNaMTP into E. coli bacteria.[12] Then, the natural bacte-
This step is catalyzed by adenylosuccinate lyase. rial replication pathways use them to accurately replicate
Inosine monophosphate is converted to guanosine the plasmid containing d5SICS–dNaM.
monophosphate by the oxidation of IMP forming xan- The successful incorporation of a third base pair is a sig-
thylate, followed by the insertion of an amino group at nificant breakthrough toward the goal of greatly expand-
C2 . NAD+ is the electron acceptor in the oxidation reac- ing the number of amino acids which can be encoded
tion. The amide group transfer from glutamine is fueled by DNA, from the existing 20 amino acids to a theoret-
by ATP hydrolysis. ically possible 172, thereby expanding the potential for
living organisms to produce novel proteins.[14] The artifi-
cial strings of DNA do not encode for anything yet, but
Pyrimidine and purine degradation scientists speculate they could be designed to manufac-
ture new proteins which could have industrial or pharma-
In humans, pyrimidine rings (C, T, U) can be degraded ceutical uses.[16]
completely to CO2 and NH3 (urea excretion). That hav-
ing been said, purine rings (G, A) cannot. Instead they
are degraded to the metabolically inert uric acid which is
then excreted from the body. Uric acid is formed when
GMP is split into the base guanine and ribose. Guanine is 16.3.4 Length unit
deaminated to xanthine which in turn is oxidized to uric
acid. This last reaction is irreversible. Similarly, uric acid Nucleotide (abbreviated “nt”) is a common unit of length
can be formed when AMP is deaminated to IMP from for single-stranded nucleic acids, similar to how base pair
which the ribose unit is removed to form hypoxanthine. is a unit of length for double-stranded nucleic acids.
16.3. NUCLEOTIDE 273

16.3.5 Abbreviation codes for degenerate [7] Zaharevitz, DW; Anerson, LW; Manlinowski, NM; Hy-
bases man, R; Strong, JM; Cysyk, RL. “Contribution of de-
novo and salvage synthesis to the uracil nucleotide pool
in mouse tissues and tumors in vivo”.
Main article: Nucleic acid notation
[8] See IUPAC nomenclature of organic chemistry for details
The IUPAC has designated the symbols for on carbon residue numbering
nucleotides.[17] Apart from the five (A, G, C, T/U)
[9] Jones, M. E. (1980). “Pyrimidine nucleotide biosyn-
bases, often degenerate bases are used especially for
thesis in animals: Genes, enzymes, and regulation of
designing PCR primers. These nucleotide codes are UMP biosynthesis”. Ann. Rev. Biochem 49 (1): 253–
listed here. Some primer sequences may also include 79. doi:10.1146/annurev.bi.49.070180.001345. PMID
the character “I”, which codes for the non-standard 6105839.
nucleotide Inosine. Inosine occurs in tRNAs, and will
pair with Adenine, Cytosine, or Thymine. This character [10] McMurry, JE; Begley, TP (2005). The organic chemistry
does not appear in the following table however, because of biological pathways. Roberts & Company. ISBN 978-
it does not represent a degeneracy. While Inosine can 0-9747077-1-6.
serve a similar function as the degeneracy “H”, it is an
actual nucleotide, rather than a representation of a mix [11] Malyshev, Denis A.; Dhami, Kirandeep; Quach, Henry
T.; Lavergne, Thomas; Ordoukhanian, Phillip (24 July
of nucleotides that covers each possible pairing needed.
2012). “Efficient and sequence-independent replica-
tion of DNA containing a third base pair establishes
a functional six-letter genetic alphabet”. Proceedings
16.3.6 See also of the National Academy of Sciences of the United
States of America (PNAS) 109 (30): 12005–12010.
• Biology doi:10.1073/pnas.1205176109. Retrieved 2014-05-11.

• Chromosome [12] Malyshev, Denis A.; Dhami, Kirandeep; Lavergne,

Thomas; Chen, Tingjian; Dai, Nan; Foster, Jeremy M.;
• Gene Corrêa, Ivan R.; Romesberg, Floyd E. (May 7, 2014). “A
semi-synthetic organism with an expanded genetic alpha-
• Genetics bet”. Nature (journal). doi:10.1038/nature13314. Re-
trieved May 7, 2014.
• Nucleic acid analogues
[13] Callaway, Ewan (May 7, 2014). “Scientists Create First
• Nucleobase Living Organism With 'Artificial' DNA”. Nature News
(Huffington Post). Retrieved 8 May 2014.

[14] Fikes, Bradley J. (May 8, 2014). “Life engineered with

16.3.7 References expanded genetic code”. San Diego Union Tribune. Re-
trieved 8 May 2014.
[1] Alberts B, Johnson A, Lewis J, Raff M, Roberts K &
Wlater P (2002). Molecular Biology of the Cell (4th ed.). [15] Sample, Ian (May 7, 2014). “First life forms to pass on ar-
Garland Science. ISBN 0-8153-3218-1. pp. 120–121. tificial DNA engineered by US scientists”. The Guardian.
Retrieved 8 May 2014.
[2] Coghill, Anne M.; Garson, Lorrin R., eds. (2006). The
ACS style guide: effective communication of scientific in- [16] Pollack, Andrew (May 7, 2014). “Scientists Add Letters
formation (3rd ed.). Washington, D.C.: American Chem- to DNA’s Alphabet, Raising Hope and Fear”. New York
ical Society. p. 244. ISBN 978-0-8412-3999-9. Times. Retrieved 8 May 2014.

[3] “Nucleotides”. IUPAC Gold Book. Interna- [17] Nomenclature Committee of the International Union of
tional Union of Pure and Applied Chemists. Biochemistry (NC-IUB) (1984). “Nomenclature for In-
doi:10.1351/goldbook.N04255. Retrieved 30 June completely Specified Bases in Nucleic Acid Sequences”.
2014. Retrieved 2008-02-04.

[4] Lehninger, Albert L. (1975). Biochemistry: the molecular

basis of cell structure and function. New York: Worth
Publishers Inc. doi:10.1002/jobm.19770170116.
16.3.8 External links

[5] Stryer, Lubert (1988). Biochemistry (3rd ed.). New York: • Abbreviations and Symbols for Nucleic Acids,
W. H. Freeman. ISBN 9780716719205. Polynucleotides and their Constituents (IUPAC)

[6] Garrett, Reginald H.; Grisham, Charles M. (2007). Bio- • Provisional Recommendations 2004 (IUPAC)
chemistry (4th ed.). Belmont, California: Brooks/Cole,
Cengage Learning. • Chemistry explanation of nucleotide structure
274 CHAPTER 16. NITROGEN METABOLISM

16.4 Urea cycle

The urea cycle (also known as the ornithine cycle) is a
cycle of biochemical reactions occurring in many animals
that produces urea ((NH2 )2 CO) from ammonia (NH3 ).
This cycle was the first metabolic cycle discovered (Hans
Krebs and Kurt Henseleit, 1932), five years before the
discovery of the TCA cycle. In mammals, the urea cycle
takes place primarily in the liver, and to a lesser extent in
the kidney.

16.4.1 Function

Organisms that cannot easily and quickly remove ammo-

nia usually have to convert it to some other substance, like
urea or uric acid, which are much less toxic. Insufficiency
of the urea cycle occurs in some genetic disorders (inborn
errors of metabolism), and in liver failure. The result of
liver failure is accumulation of nitrogenous waste, mainly
ammonia, which leads to hepatic encephalopathy.

16.4.2 Reactions

The urea cycle consists of five reactions: two

mitochondrial and three cytosolic. The cycle con-
verts two amino groups, one from NH4 + and one from
Asp, and a carbon atom from HCO3 − , to the relatively Since fumarate is obtained by removing NH3 from aspar-
nontoxic excretion product urea at the cost of four tate (by means of reactions 3 and 4), and PPᵢ + H2 O → 2
“high-energy” phosphate bonds (3 ATP hydrolyzed to 2 Pᵢ, the equation can be simplified as follows:
ADP and one AMP). Ornithine is the carrier of these
carbon and nitrogen atoms. • 2 NH3 + CO2 + 3 ATP + H2 O → urea + 2 ADP +
4 Pᵢ + AMP
The reactions of the
urea cycle Note that reactions related to the urea cycle also cause
1 L-ornithine the production of 2 NADH, so the urea cycle releases
2 carbamoyl phosphate slightly more energy than it consumes. These NADH are
3 L-citrulline produced in two ways:
4 argininosuccinate
5 fumarate • One NADH molecule is reduced by the enzyme
6 L-arginine glutamate dehydrogenase in the conversion of gluta-
7 urea mate to ammonium and α-ketoglutarate. Glutamate
L-Asp L-aspartate is the non-toxic carrier of amine groups. This pro-
CPS-1 carbamoyl phosphate synthetase I vides the ammonium ion used in the initial synthesis
OTC Ornithine transcarbamoylase of carbamoyl phosphate.
ASS argininosuccinate synthetase • The fumarate released in the cytosol is converted to
ASL argininosuccinate lyase malate by cytosolic fumarase. This malate is then
ARG1 arginase 1 converted to oxaloacetate by cytosolic malate dehy-
drogenase, generating a reduced NADH in the cy-
In the first reaction, NH4 + + HCO3 − is equivalent to NH3 tosol. Oxaloacetate is one of the keto acids pre-
+ CO2 + H2 O. ferred by transaminases, and so will be recycled to
aspartate, maintaining the flow of nitrogen into the
Thus, the overall equation of the urea cycle is: urea cycle.

• NH3 + CO2 + aspartate + 3 ATP + 2 H2 O → urea The two NADH produced can provide energy for the
+ fumarate + 2 ADP + 2 Pᵢ + AMP + PPᵢ formation of 4 ATP (cytosolic NADH provides only
16.4. UREA CYCLE 275

1.5 ATP due to the glycerol-3-phosphate shuttle who 16.4.4 Pathology

transfers the electrons from cytosolic NADH to FADH2
and that gives 1.5 ATP), a net production of one high- Deficiencies of the various enzymes and transporters in-
energy phosphate bond for the urea cycle. However, volved in the urea cycle can cause urea cycle disorders:
if gluconeogenesis is underway in the cytosol, the latter
reducing equivalent is used to drive the reversal of the • N-Acetylglutamate synthase deficiency
GAPDH step instead of generating ATP.
• Carbamoyl phosphate synthetase deficiency
The fate of oxaloacetate is either to produce as-
partate via transamination or to be converted • Ornithine transcarbamoylase deficiency
to phosphoenolpyruvate, which is a substrate for
gluconeogenesis. • Citrullinemia (Deficiency of argininosuccinic acid
synthase)
• Argininosuccinic aciduria (Deficiency of argini-
nosuccinic acid lyase)
16.4.3 Regulation • Argininemia (Deficiency of arginase)

N-Acetylglutamic acid • Hyperornithinemia, hyperammonemia, ho-

mocitrullinuria syndrome (Deficiency of the
mitochondrial ornithine transporter)
The synthesis of carbamoyl phosphate and the urea cy-
cle are dependent on the presence of NAcGlu, which
allosterically activates CPS1. NAcGlu is an obligate ac- Most urea cycle disorders are associated with
tivator of Carbamoyl phosphate synthase.[1] Synthesis of hyperammonemia, however argininemia and some
NAcGlu by NAGS is stimulated by both Arg, allosteric forms of argininosuccinic aciduria do not present with
stimulator of NAGS, and Glu, a product in the transam- elevated ammonia.
ination reactions and one of NAGS’s substrates, both of
which elevated when free amino acids are elevated. So
16.4.5 Additional images
Glu not only is a substrate for NAGS but also serves as
an activator for the urea cycle. • Urea cycle.
• Urea cycle colored.

Substrate concentrations 16.4.6 References

The remaining enzymes of the cycle are controlled by the [1] Kaplan Medical USMLE Step 1 Biochemistry and Medi-
concentrations of their substrates. Thus, inherited defi- cal Genetics Lecture Notes 2010, page 261
ciencies in cycle enzymes other than ARG1 do not re-
sult in significant decreases in urea production (if any cy-
16.4.7 External links
cle enzyme is entirely missing, death occurs shortly after
birth). Rather, the deficient enzyme’s substrate builds up, • The chemical logic behind the urea cycle
increasing the rate of the deficient reaction to normal.
The anomalous substrate buildup is not without cost, • Basic Neurochemistry - amino acid disorders
however. The substrate concentrations become elevated
all the way back up the cycle to NH4 + , resulting in
hyperammonemia (elevated [NH4 + ]P).
Although the root cause of NH4 + toxicity is not com-
pletely understood, a high [NH4 + ] puts an enormous
strain on the NH4 + -clearing system, especially in the
brain (symptoms of urea cycle enzyme deficiencies in-
clude intellectual disability and lethargy). This clearing
system involves GLUD1 and GLUL, which decrease the
2-oxoglutarate (2OG) and Glu pools. The brain is most
sensitive to the depletion of these pools. Depletion of
2OG decreases the rate of TCAC, whereas Glu is both a
neurotransmitter and a precursor to GABA, another neu-
rotransmitter. (p.734)
Chapter 17

Integration of metabolism

17.1 Hormone lactation, stress, growth and development, movement,

reproduction, and mood.[1][2] Hormones affect distant
cells by binding to specific receptor proteins in the target
cell resulting in a change in cell function. When a hor-
mone binds to the receptor, it results in the activation of
a signal transduction pathway. This may lead to cell type-
specific responses that include rapid non-genomic effects
or slower genomic responses where the hormones acting
through their receptors activate gene transcription result-
ing in increased expression of target proteins.
Hormone synthesis may occur in specific tissues of
endocrine glands or in other specialized cells. Hor-
mone synthesis occurs in response to specific biochem-
ical signals induced by a wide range of regulatory sys-
tems. For instance, ionized calcium concentration af-
fects PTH synthesis, whereas glucose concentration af-
fects insulin synthesis. Regulation of hormone synthesis
of gonadal, adrenal, and thyroid hormones is often de-
pendent on complex sets of direct influence and feedback
interactions involving the hypothalamic-pituitary-adrenal
(HPA), -gonadal (HPG), and -thyroid (HPT) axes.
Upon secretion, certain hormones, including protein hor-
mones and catecholamines, are water-soluble and are
thus readily transported through the circulatory system.
Other hormones, including steroid and thyroid hormones,
Different types of hormones are secreted in the body, with differ- are lipid-soluble; to allow for their widespread distribu-
ent biological roles and functions. tion, these hormones must bond to carrier plasma gly-
coproteins (e.g., thyroxine-binding globulin (TBG)) to
A hormone (from Greek ὁρμή, “impetus”) is any mem- form ligand-protein complexes. Some hormones are
ber of a class of signaling molecules produced by glands completely active when released into the bloodstream
in multicellular organisms that are transported by the (as is the case for insulin and growth hormones), while
circulatory system to target distant organs to regulate others must be activated in specific cells through a se-
physiology and behaviour. Hormones have diverse chem- ries of activation steps that are commonly highly regu-
ical structures including eicosanoids, steroids, amino acid lated. The endocrine system secretes hormones directly
derivatives, peptides, and proteins. The glands that se- into the bloodstream typically into fenestrated capillaries,
crete hormones comprise the endocrine signaling sys- whereas the exocrine system secretes its hormones indi-
tem. The term hormone is sometimes extended to in- rectly using ducts. Hormones with paracrine function dif-
clude chemicals produced by cells that affect the same fuse through the interstitial spaces to nearby target tissue.
cell (autocrine or intracrine signalling) or nearby cells
(paracrine signalling).
Hormones are used to communicate between organs 17.1.1 Overview
and tissues to regulate physiological and behavioral
activities, such as digestion, metabolism, respiration, Further information: Signal transduction
tissue function, sensory perception, sleep, excretion,

276
17.1. HORMONE 277

Hormonal signaling involves the following steps:[3] glands. For example, thyroid-stimulating hormone (TSH)
causes growth and increased activity of another endocrine
1. Biosynthesis of a particular hormone in a particular gland, the thyroid, which increases output of thyroid hor-
tissue mones.
To release active hormones quickly into the circulation,
2. Storage and secretion of the hormone
hormone biosynthetic cells may produce and store bi-
3. Transport of the hormone to the target cell(s) ologically inactive hormones in the form of pre- or
prohormones. These can then be quickly converted into
4. Recognition of the hormone by an associated cell their active hormone form in response to a particular
membrane or intracellular receptor protein stimulus.
5. Relay and amplification of the received hormonal Eicosanoids are considered to act as local hormones.
signal via a signal transduction process: This then
leads to a cellular response. The reaction of the
target cells may then be recognized by the orig- 17.1.3 Receptors
inal hormone-producing cells, leading to a down-
regulation in hormone production. This is an exam- Steroid Hormones
a a
Protein Hormones

ple of a homeostatic negative feedback loop. b 1

1
c
6. Breakdown of the hormone. 2
3
d 2 b c d
Hormone cells are typically of a specialized cell type,
residing within a particular endocrine gland, such as
the thyroid gland, ovaries, and testes. Hormones exit The left diagram shows a steroid (lipid) hormone (1) entering a
cell and (2) binding to a receptor protein in the nucleus, causing
their cell of origin via exocytosis or another means of
(3) mRNA synthesis which is the first step of protein synthesis.
membrane transport. The hierarchical model is an over-
The right side shows protein hormones (1) binding with recep-
simplification of the hormonal signaling process. Cellular tors which (2) begins a transduction pathway. The transduction
recipients of a particular hormonal signal may be one of pathway ends (3) with transcription factors being activated in the
several cell types that reside within a number of different nucleus, and protein synthesis beginning. In both diagrams, a is
tissues, as is the case for insulin, which triggers a diverse the hormone, b is the cell membrane, c is the cytoplasm, and d is
range of systemic physiological effects. Different tissue the nucleus.
types may also respond differently to the same hormonal
signal. Most hormones initiate a cellular response by ini-
tially binding to either cell membrane associated or
intracellular receptors. A cell may have several different
17.1.2 Regulation receptor types that recognize the same hormone but acti-
vate different signal transduction pathways, or a cell may
The rate of hormone biosynthesis and secretion is of- have several different receptors that recognize different
ten regulated by a homeostatic negative feedback con- hormones and activate the same biochemical pathway.
trol mechanism. Such a mechanism depends on factors
Receptors for most peptide as well as many eicosanoid
that influence the metabolism and excretion of hormones.
hormones are embedded in the plasma membrane at the
Thus, higher hormone concentration alone cannot trig-
surface of the cell and the majority of these receptors
ger the negative feedback mechanism. Negative feedback
belong to the G protein-coupled receptor (GPCR) class
must be triggered by overproduction of an “effect” of the
of seven alpha helix transmembrane proteins. The inter-
hormone.
action of hormone and receptor typically triggers a cas-
Hormone secretion can be stimulated and inhibited by: cade of secondary effects within the cytoplasm of the cell,
often involving phosphorylation or dephosphorylation of
• Other hormones (stimulating- or releasing - various other cytoplasmic proteins, changes in ion chan-
hormones) nel permeability, or increased concentrations of intra-
cellular molecules that may act as secondary messengers
• Plasma concentrations of ions or nutrients, as well (e.g., cyclic AMP). Some protein hormones also interact
as binding globulins with intracellular receptors located in the cytoplasm or
nucleus by an intracrine mechanism.
• Neurons and mental activity
For steroid or thyroid hormones, their receptors are lo-
• Environmental changes, e.g., of light or temperature cated inside the cell within the cytoplasm of the target
cell. These receptors belong to the nuclear receptor fam-
One special group of hormones is the tropic hormones ily of ligand-activated transcription factors. To bind their
that stimulate the hormone production of other endocrine receptors, these hormones must first cross the cell mem-
278 CHAPTER 17. INTEGRATION OF METABOLISM

brane. They can do so because they are lipid-soluble. The Animal

combined hormone-receptor complex then moves across
the nuclear membrane into the nucleus of the cell, where Further information: List of human hormones
it binds to specific DNA sequences, regulating the expres-
sion of certain genes, and thereby increasing the levels of Vertebrate hormones fall into four main chemical classes:
the proteins encoded by these genes.[4] However, it has
been shown that not all steroid receptors are located in-
side the cell. Some are associated with the plasma mem- • Amino acid derived – Examples include melatonin
brane. [5] and thyroxine.

• Polypeptide and proteins. – Small peptide hormones

17.1.4 Effects include TRH and vasopressin. Peptides composed
of scores or hundreds of amino acids are referred
A variety of exogenous chemical compounds, both natu- to as proteins. Examples of protein hormones in-
ral and synthetic, have hormone-like effects on both hu- clude insulin and growth hormone. More complex
mans and wildlife. Their interference with the synthe- protein hormones bear carbohydrate side-chains and
sis, secretion, transport, binding, action, or elimination of are called glycoprotein hormones. Luteinizing hor-
natural hormones in the body can change the homeostasis, mone, follicle-stimulating hormone and thyroid-
reproduction, development, and/or behavior, similar to stimulating hormone are examples of glycoprotein
endogenously produced hormones.[6] hormones.

Hormones have the following effects on the body: • Eicosanoids – hormones derive from lipids such as
arachidonic acid, lipoxins and prostaglandins.
• stimulation or inhibition of growth • Steroid – Examples of steroid hormones include the
• wake-sleep cycle and other circadian rhythms sex hormones estradiol and testosterone as well as
the stress hormone cortisol.
• mood swings
Compared with vertebrate, insects and crustaceans pos-
• induction or suppression of apoptosis (programmed
sess a number of structurally unusual hormones such as
cell death)
the juvenile hormone, a sesquiterpenoid.[9]
• activation or inhibition of the immune system

• regulation of metabolism Plant

• preparation of the body for mating, fighting, fleeing, Further information: Plant hormone § Classes of plant
and other activity hormones
• preparation of the body for a new phase of life, such
as puberty, parenting, and menopause Plant hormones include abscisic acid, auxin, cytokinin,
ethylene, and gibberellin.
• control of the reproductive cycle

• hunger cravings 17.1.6 Therapeutic use

• sexual arousal
Many hormones and their analogues are used as
medication. The most commonly prescribed hormones
A hormone may also regulate the production and release are estrogens and progestogens (as methods of hormonal
of other hormones. Hormone signals control the internal contraception and as HRT), thyroxine (as levothyroxine,
environment of the body through homeostasis. for hypothyroidism) and steroids (for autoimmune dis-
eases and several respiratory disorders). Insulin is
used by many diabetics. Local preparations for use in
17.1.5 Chemical classes
otolaryngology often contain pharmacologic equivalents
As hormones are defined functionally, not structurally, of adrenaline, while steroid and vitamin D creams are
they may have diverse chemical structures. Hormones used extensively in dermatological practice.
occur in multicellular organisms (plants, animals, fungi, A “pharmacologic dose” or “supraphysiological dose” of
brown algae and red algae). These compounds occur a hormone is a medical usage referring to an amount of
also in unicellular organisms, and may act as signaling a hormone far greater than naturally occurs in a healthy
molecules,[7][8] but there is no consensus if, in this case, body. The effects of pharmacologic doses of hormones
they can be called hormones. may be different from responses to naturally occurring
17.1. HORMONE 279

amounts and may be therapeutically useful, though not 17.1.9 See also
without potentially adverse side effects. An example is
the ability of pharmacologic doses of glucocorticoids to • Autocrine signaling
suppress inflammation.
• Cytokine
• Endocrine system
17.1.7 Hormone-behavior interactions
• Endocrinology
At the neurological level, behavior can be inferred based
• Growth factor
on: hormone concentrations; hormone-release patterns;
the numbers and locations of hormone receptors; and • Hormone disruptor
the efficiency of hormone receptors for those involved in
gene transcription. Not only do hormones influence be- • Intracrine
havior, but also behavior and the environment influence
• Metabolomics
hormones. Thus, a feedback loop is formed. For exam-
ple, behavior can affect hormones, which in turn can af- • Neuroendocrinology
fect behavior, which in turn can affect hormones, and so
on. • Paracrine signaling
Three broad stages of reasoning may be used when deter- • Plant hormones or plant growth regulators
mining hormone-behavior interactions:
• Semiochemical

• The frequency of occurrence of a hormonally de- • Sexual motivation and hormones

pendent behavior should correspond to that of its
hormonal source
17.1.10 References
• A hormonally dependent behavior is not expected if
the hormonal source (or its types of action) is non- [1] Neave N (2008). Hormones and behaviour: a psychologi-
existent cal approach. Cambridge: Cambridge Univ. Press. ISBN
978-0521692014. Lay summary – Project Muse.
• The reintroduction of a missing behaviorally depen- [2] “Hormones”. MedlinePlus. U.S. National Library of
dent hormonal source (or its types of action) is ex- Medicine.
pected to bring back the absent behavior
[3] Nussey S, Whitehead S (2001). Endocrinology: an in-
tegrated approach. Oxford: Bios Scientific Publ. ISBN
978-1-85996-252-7.
17.1.8 Comparison with neurotransmit-
ters [4] Beato M, Chavez S and Truss M (1996). “Transcrip-
tional regulation by steroid hormones”. Steroids 61 (4):
There are various clear distinctions between hormones 240–251. doi:10.1016/0039-128X(96)00030-X. PMID
and neurotransmitters: 8733009.

[5] Hammes SR (2003). “The further redefining of steroid-

• A hormone can perform functions over a larger spa- mediated signaling”. Proc Natl Acad Sci USA 100
tial and temporal scale than can a neurotransmitter. (5): 21680–2170. doi:10.1073/pnas.0530224100. PMC
151311. PMID 12606724.
• Hormonal signals can travel virtually anywhere in
[6] Crisp TM, Clegg ED, Cooper RL, Wood WP, Anderson
the circulatory system, whereas neural signals are re- DG, Baetcke KP, Hoffmann JL, Morrow MS, Rodier DJ,
stricted to pre-existing nerve tracts Schaeffer JE, Touart LW, Zeeman MG, Patel YM (1998).
“Environmental endocrine disruption: An effects assess-
• Assuming the travel distance is equivalent, neural ment and analysis”. Environ. Health Perspect. 106 (Suppl
signals can be transmitted much more quickly (in 1): 11–56. doi:10.2307/3433911. PMC 1533291. PMID
the range of milliseconds) than can hormonal signals 9539004.
(in the range of seconds, minutes, or hours). Neural
signals can be sent at speeds up to 100 meters per [7] Lenard J (1992). “Mammalian hormones in micro-
bial cells”. Trends Biochem. Sci. 17 (4): 147–50.
second.
doi:10.1016/0968-0004(92)90323-2. PMID 1585458.
• Neural signalling is an all-or-nothing (digital) action, [8] Janssens PM. “Did vertebrate signal transduction mech-
whereas hormonal signalling is an action that can be anisms originate in eukaryotic microbes?". Trends in
continuously variable as dependent upon hormone Biochemical Sciences 12: 456–459. doi:10.1016/0968-
concentration 0004(87)90223-4.
280 CHAPTER 17. INTEGRATION OF METABOLISM

[9] Heyland A, Hodin J, Reitzel AM (2005). “Hor-

mone signaling in evolution and development: a non-
model system approach”. Bioessays 27 (1): 64–75.
doi:10.1002/bies.20136. PMID 15612033.

17.1.11 External links

• The Hormone Foundation

• Article on hormones and their receptors

• HMRbase: A database of hormones and their recep- Occurrence of the term signal transduction in papers since 1977.
tors These figures were derived by an analysis of the papers contained
within the MEDLINE database.
• Hormones at the US National Library of Medicine
Medical Subject Headings (MeSH)
The earliest MEDLINE entry for “signal transduction”
dates from 1972.[6] Some early articles used the terms sig-
17.2 Signal transduction nal transmission and sensory transduction.[7][8] In 2007,
a total of 48,377 scientific papers—including 11,211
review papers—were published on the subject. The term
first appeared in a paper’s title in 1979.[9][10] Widespread
Chemokines,
Hormones,
Survival Factors Transmitters Growth Factors
Extracellular
(e.g., IGF1) (e.g., interleukins, (e.g., TGFα, EGF)

use of the term has been traced to a 1980 review article by

Matrix
serotonin, etc.)

RTK
GPCR
RTK cdc42
Integrins
Wnt
Rodbell:[5][11] Research papers focusing on signal trans-
PLC Grb2/SOS
Fyn/Shc
duction first appeared in large numbers in the late 1980s
Frizzled

PI3K G-Protein Ras FAK Dishevelled

Akt
PKC Adenylate
cyclase
Raf
Src
GSK-3β
Hedgehog
and early 1990s.[12]
Akkα MEK
Cytokine Receptor

NF-κB APC
PKA
Cytokines IκB MEKK MAPK MKK β-catenin
Signal transduction involves the binding of extracellu-
Patched

JAKs
(e.g., EPC)
STAT3,5 TCF

Bcl-xL
Myc: Mad:
Max Max
ERK JNKs

Fos Jun
β-catenin:TCF
lar signalling molecules and ligands to cell-surface re-
SMO

Cytochrome C

Caspase 9
CREB CycID
Rb CDK4
p16
p15
Gli
ceptors that trigger events inside the cell. The combi-
E2F

Caspase 8 Apoptosis
ARF
Gene Regulation
CyclE
CDK2
p27 nation of messenger with receptor causes a change in
the conformation of the receptor, known as receptor ac-
p21
Cell
FADD mdm2
Bcl-2 Proliferation
p53
Bad
Mt Bax
FasR
Abnormality
Sensor Bim tivation. This activation is always the initial step (the
cause) leading to the cell’s ultimate responses (effect) to
Death factors
(e.g. FasL, Tnf)
the messenger. Despite the myriad of these ultimate re-
sponses, they are all directly due to changes in partic-
An overview of major signal transduction pathways in mammals.
ular cell proteins. Intracellular signaling cascades can
be started through cell-substratum interactions; examples
Signal transduction occurs when an extracellular
are the integrin that binds ligands in the extracellular ma-
signaling[1] molecule activates a specific receptor located
trix and steroids.[13] Most steroid hormones have recep-
on the cell surface or inside the cell. In turn, this re-
tors within the cytoplasm and act by stimulating the bind-
ceptor triggers a biochemical chain of events inside the
ing of their receptors to the promoter region of steroid-
cell, creating a response.[2] Depending on the cell, the re-
responsive genes.[14] Examples of signaling molecules in-
sponse alters the cell’s metabolism, shape, gene expres-
clude the hormone melatonin,[15] the neurotransmitter
sion, or ability to divide.[3] The signal can be amplified at
acetylcholine[16] and the cytokine interferon γ.[17]
any step. Thus, one signaling molecule can cause many
responses.[4] The classifications of signalling molecules do not take into
account the molecular nature of each class member; neu-
rotransmitters range in size from small molecules such
17.2.1 History as dopamine[18] to neuropeptides such as endorphins.[19]
Some molecules may fit into more than one class; for ex-
In 1970, Martin Rodbell examined the effects of ample, epinephrine is a neurotransmitter when secreted
glucagon on a rat’s liver cell membrane receptor. He by the central nervous system and a hormone when se-
noted that guanosine triphosphate disassociated glucagon creted by the adrenal medulla.
from this receptor and stimulated the G-protein, which
strongly influenced the cell’s metabolism. Thus, he de-
duced that the G-protein is a transducer that accepts 17.2.2 Environmental stimuli
glucagon molecules and affects the cell.[5] For this, he
shared the 1994 Nobel Prize in Physiology or Medicine With single-celled organisms, the variety of signal trans-
with Alfred G. Gilman. duction processes influence its reaction to its environ-
17.2. SIGNAL TRANSDUCTION 281

ment. With multicellular organisms, numerous processes zymatic activity; examples include tyrosine kinase and
are required for coordinating individual cells to support phosphatases. Some of them create second messengers
the organism as a whole; the complexity of these pro- such as cyclic AMP and IP3 , the latter controlling the re-
cesses tend to increase with the complexity of the or- lease of intracellular calcium stores into the cytoplasm.
ganism. Sensing of environments at the cellular level re- Other activated proteins interact with adaptor proteins
lies on signal transduction; modeling signal transduction that facilitate signalling protein interactions and coordi-
systems as self-organizing allows to explain how equilib- nation of signalling complexes necessary to respond to a
ria are maintained,[20] many disease processes, such as particular stimulus. Enzymes and adaptor proteins are
diabetes and heart disease arise from defects or dysregu- both responsive to various second messenger molecules.
lations in these pathways, highlighting the importance of Many adaptor proteins and enzymes activated as part of
this process in biology and medicine.
signal transduction possess specialized protein domains
Various environmental stimuli exist that initiate signal that bind to specific secondary messenger molecules. For
transmission processes in multicellular organisms; ex- example, calcium ions bind to the EF hand domains of
amples include photons hitting cells in the retina of the calmodulin, allowing it to bind and activate calmodulin-
eye,[21] and odorants binding to odorant receptors in the dependent kinase. PIP3 and other phosphoinositides do
nasal epithelium.[22] Certain microbial molecules, such the same thing to the Pleckstrin homology domains of
as viral nucleotides and protein antigens, can elicit an proteins such as the kinase protein AKT.
immune system response against invading pathogens me-
diated by signal transduction processes. This may occur
independent of signal transduction stimulation by other G protein-coupled Main article: G-protein-coupled
molecules, as is the case for the toll-like receptor. It receptor
may occur with help from stimulatory molecules located
at the cell surface of other cells, as with T-cell receptor G protein-coupled receptors (GPCRs) are a family of in-
signaling. Unicellular organisms may respond to envi- tegral transmembrane proteins that possess seven trans-
ronmental stimuli through the activation of signal trans- membrane domains and are linked to a heterotrimeric
duction pathways. For example, slime molds secrete G protein. Many receptors are in this family, including
cyclic adenosine monophosphate upon starvation, stim- adrenergic receptors and chemokine receptors.
ulating individual cells in the immediate environment to
aggregate,[23] and yeast cells use mating factors to deter- Signal transduction by a GPCR begins with an inactive G
mine the mating types of other cells and to participate in protein coupled to the receptor; it exists as a heterotrimer
sexual reproduction.[24] consisting of Gα, Gβ, and Gγ.[26] Once the GPCR recog-
nizes a ligand, the conformation of the receptor changes
to activate the G protein, causing Gα to bind a molecule
17.2.3 Receptors of GTP and dissociate from the other two G-protein sub-
units. The dissociation exposes sites on the subunits that
Receptors can be roughly divided into two major classes: can interact with other molecules.[27] The activated G
intracellular receptors and extracellular receptors. protein subunits detach from the receptor and initiate
signaling from many downstream effector proteins such
as phospholipases and ion channels, the latter permitting
Extracellular the release of second messenger molecules.[28] The to-
tal strength of signal amplification by a GPCR is deter-
Extracellular receptors are integral transmembrane pro- mined by the lifetimes of the ligand-receptor complex
teins and make up most receptors. They span the plasma and receptor-effector protein complex and the deactiva-
membrane of the cell, with one part of the receptor on tion time of the activated receptor and effectors through
the outside of the cell and the other on the inside. Sig- intrinsic enzymatic activity.
nal transduction occurs as a result of a ligand binding
A study was conducted where a point mutation was in-
to the outside; the molecule does not pass through the
serted into the gene encoding the chemokine receptor
membrane. This binding stimulates a series of events in-
CXCR2; mutated cells underwent a malignant transfor-
side the cell; different types of receptors stimulate differ-
mation due to the expression of CXCR2 in an active
ent responses and receptors typically respond to only the
conformation despite the absence of chemokine-binding.
binding of a specific ligand. Upon binding, the ligand in-
This meant that chemokine receptors can contribute to
duces a change in the conformation of the inside part of
cancer development.[29]
the receptor.[25] These result in either the activation of an
enzyme in the receptor or the exposure of a binding site
for other intracellular signaling proteins within the cell,
Tyrosine and histidine kinase Receptor tyrosine ki-
eventually propagating the signal through the cytoplasm.
nases (RTKs) are transmembrane proteins with an intra-
In eukaryotic cells, most intracellular proteins acti- cellular kinase domain and an extracellular domain that
vated by a ligand/receptor interaction possess an en- binds ligands; examples include growth factor receptors
282 CHAPTER 17. INTEGRATION OF METABOLISM

such as the insulin receptor.[30] To perform signal trans- play a role in cell attachment to other cells and the
duction, RTKs need to form dimers in the plasma mem- extracellular matrix and in the transduction of signals
brane;[31] the dimer is stabilized by ligands binding to from extracellular matrix components such as fibronectin
the receptor. The interaction between the cytoplasmic and collagen. Ligand binding to the extracellular do-
domains stimulates the autophosphorylation of tyrosines main of integrins changes the protein’s conformation,
within the domains of the RTKs, causing conformational clustering it at the cell membrane to initiate signal trans-
changes. Subsequent to this, the receptors’ kinase do- duction. Integrins lack kinase activity; hence, integrin-
mains are activated, initiating phosphorylation signaling mediated signal transduction is achieved through a vari-
cascades of downstream cytoplasmic molecules that facil- ety of intracellular protein kinases and adaptor molecules,
itate various cellular processes such as cell differentiationthe main coordinator being integrin-linked kinase.[34] As
and metabolism.[30] shown in the picture to the right, cooperative integrin-
As is the case with GPCRs, proteins that bind GTP play a RTK signalling determines the timing of cellular survival,
apoptosis, proliferation, and differentiation.
major role in signal transduction from the activated RTK
into the cell. In this case, the G proteins are members of Important differences exist between integrin-signalling in
the Ras, Rho, and Raf families, referred to collectively circulating blood cells and non-circulating cells such as
as small G proteins. They act as molecular switches usu- epithelial cells; integrins of circulating cells are normally
ally tethered to membranes by isoprenyl groups linked to inactive. For example, cell membrane integrins on cir-
their carboxyl ends. Upon activation, they assign proteins culating leukocytes are maintained in an inactive state to
to specific membrane subdomains where they participate avoid epithelial cell attachment; they are activated only
in signaling. Activated RTKs in turn activate small G in response to stimuli such as those received at the site of
proteins that activate guanine nucleotide exchange fac- an inflammatory response. In a similar manner, integrins
tors such as SOS1. Once activated, these exchange fac- at the cell membrane of circulating platelets are normally
tors can activate more small G proteins, thus amplifying kept inactive to avoid thrombosis. Epithelial cells (which
the receptor’s initial signal. The mutation of certain RTK are non-circulating) normally have active integrins at their
genes, as with that of GPCRs, can result in the expression cell membrane, helping maintain their stable adhesion to
of receptors that exist in a constitutively activate state; underlying stromal cells that provide signals to maintain
such mutated genes may act as oncogenes.[32] normal functioning.[35]
Histidine-specific protein kinases are structurally distinct
from other protein kinases and are found in prokaryotes,
Toll gate Main article: Toll-like receptor
fungi, and plants as part of a two-component signal trans-
duction mechanism: a phosphate group from ATP is first
When activated, toll-like receptors (TLRs) take adapter
added to a histidine residue within the kinase, then trans-
ferred to an aspartate residue on a receiver domain on a molecules within the cytoplasm of cells in order to prop-
agate a signal. Four adaptor molecules are known to be
different protein or the kinase itself, thus activating the
aspartate residue.[33] involved in signaling, which are Myd88, TIRAP, TRIF,
and TRAM.[36][37][38] These adapters activate other intra-
cellular molecules such as IRAK1, IRAK4, TBK1, and
IKKi that amplify the signal, eventually leading to the
Integrin Main article: Integrin
induction or suppression of genes that cause certain re-
Integrins are produced by a wide variety of cells; they
sponses. Thousands of genes are activated by TLR sig-
naling, implying that this method constitutes an important
gateway for gene modulation.

Ligand-gated ion channel Main article: Ligand-gated

ion channel

A ligand-gated ion channel, upon binding with a ligand,

changes conformation to open a channel in the cell mem-
brane through which ions relaying signals can pass. An
example of this mechanism is found in the receiving cell
of a neural synapse. The influx of ions that occurs in re-
sponse to the opening of these channels induces action
potentials, such as those that travel along nerves, by de-
polarizing the membrane of post-synaptic cells, resulting
An overview of integrin-mediated signal transduction, adapted in the opening of voltage-gated ion channels.
from Hehlgens et al. (2007).[34] An example of an ion allowed into the cell during a
17.2. SIGNAL TRANSDUCTION 283

ligand-gated ion channel opening is Ca2+ ; it acts as a sec- expression when their transactivation domain is hidden;
ond messenger initiating signal transduction cascades and activity can be enhanced by phosphorylation of serine
altering the physiology of the responding cell. This results residues at their N-terminal as a result of another signal
in amplification of the synapse response between synap- transduction pathway, a process called crosstalk.
tic cells by remodelling the dendritic spines involved in Retinoic acid receptors are another subset of nuclear
the synapse. receptors. They can be activated by an endocrine-
synthesized ligand that entered the cell by diffusion, a
ligand synthesised from a precursor like retinol brought
Intracellular
to the cell through the bloodstream or a completely in-
tracellularly synthesised ligand like prostaglandin. These
Main article: Intracellular receptor
receptors are located in the nucleus and are not accompa-
nied by HSPs; they repress their gene by binding to their
Intracellular receptors, such as nuclear receptors and specific DNA sequence when no ligand binds to them,
cytoplasmic receptors, are soluble proteins localized and vice versa.
within their respective areas. The typical ligands for nu-
Certain intracellular receptors of the immune system
clear receptors are lipophilic hormones like the steroid
are cytoplasmic receptors; recently identified NOD-
hormones testosterone and progesterone and derivatives
like receptors (NLRs) reside in the cytoplasm of some
of vitamins A and D. To initiate signal transduction, the
eukaryotic cells and interact with ligands using a leucine-
ligand must pass through the plasma membrane by pas-
rich repeat (LRR) motif similar to TLRs. Some of these
sive diffusion. On binding with the receptor, the ligands
molecules like NOD2 interact with RIP2 kinase that ac-
pass through the nuclear membrane into the nucleus, en-
tivates NF-κB signaling, whereas others like NALP3 in-
abling gene transcription and protein production.
teract with inflammatory caspases and initiate processing
Activated nuclear receptors attach to the DNA at of particular cytokines like interleukin-1β.[39][40]
receptor-specific hormone-responsive element (HRE) se-
quences, located in the promoter region of the genes ac-
tivated by the hormone-receptor complex. Due to their Second messengers
enabling gene transcription, they are alternatively called
inductors of gene expression. All hormones that act by First messengers are the intercellular chemical
regulation of gene expression have two consequences in messengers (hormones, neurotransmitters, and
their mechanism of action; their effects are produced af- paracrine/autocrine agents) that reach the cell from
ter a characteristically long period of time and their ef- the extracellular fluid and bind to their specific receptors.
fects persist for another long period of time, even after Second messengers are the substances that enter the
their concentration has been reduced to zero, due to a rel- cytoplasm and act within the cell to trigger a response.
atively slow turnover of most enzymes and proteins that In essence, second messengers serve as chemical relays
would either deactivate or terminate ligand binding onto from the plasma membrane to the cytoplasm, thus
the receptor. carrying out intracellular signal transduction.
Signal transduction via these receptors involves little pro-
teins, but the details of gene regulation by this method Calcium
are not well-understood. Nucleic receptors have DNA-
binding domains containing zinc fingers and a ligand- The release of calcium ions from the endoplasmic retic-
binding domain; the zinc fingers stabilize DNA binding ulum into the cytosol results in its binding to signaling
by holding its phosphate backbone. DNA sequences that proteins that are then activated; it is then sequestered in
match the receptor are usually hexameric repeats of any the smooth endoplasmic reticulum and the mitochondria.
kind; the sequences are similar but their orientation and Two combined receptor/ion channel proteins control the
distance differentiate them. The ligand-binding domain transport of calcium: the InsP3 -receptor that transports
is additionally responsible for dimerization of nucleic calcium upon interaction with inositol triphosphate on its
receptors prior to binding and providing structures for cytosolic side; and the ryanodine receptor named after
transactivation used for communication with the transla- the alkaloid ryanodine, similar to the InsP3 receptor but
tional apparatus. having a feedback mechanism that releases more calcium
Steroid receptors are a subclass of nuclear receptors lo- upon binding with it. The nature of calcium in the cytosol
cated primarily within the cytosol; in the absence of means that it is active for only a very short time, meaning
steroids, they cling together in an aporeceptor complex its free state concentration is very low and is mostly bound
containing chaperone or heatshock proteins (HSPs). The to organelle molecules like calreticulin when inactive.
HSPs are necessary to activate the receptor by assisting Calcium is used in many processes including muscle con-
the protein to fold in a way such that the signal sequence traction, neurotransmitter release from nerve endings,
enabling its passage into the nucleus is accessible. Steroid and cell migration. The three main pathways that lead to
receptors, on the other hand, may be repressive on gene its activation are GPCR pathways, RTK pathways, and
284 CHAPTER 17. INTEGRATION OF METABOLISM

gated ion channels; it regulates proteins either directly or multicellular organisms; signal transduction pathways are
by binding to an enzyme. perceived to be so central to biological processes that a
large number of diseases are attributed to their disregu-
lation. Three basic signals determine cellular growth:
Lipophilics
• Stimulatory (growth factors)
Lipophilic second messenger molecules are derived from
lipids residing in cellular membranes; enzymes stimu- • Transcription dependent response
lated by activated receptors activate the lipids by modify- For example steroids act directly as transcrip-
ing them. Examples include diacylglycerol and ceramide, tion factor (gives slow response, as transcrip-
the former required for the activation of protein kinase C. tion factor must bind DNA, which needs to
be transcribed. Produced mRNA needs to be
translated, and the produced protein/peptide
Nitric oxide can undergo Posttranslational_modification
(PMT))
Nitric oxide (NO) acts as a second messenger because
• Transcription independent response
it is a free radical that can diffuse through the plasma
For example epidermal growth factor (EGF)
membrane and affect nearby cells. It is synthesised
binds the epidermal growth factor receptor
from arginine and oxygen by the NO synthase and
(EGFR), which causes dimerization and au-
works through activation of soluble guanylyl cyclase,
tophosphorylation of the EGFR, which in turn
which when activated produces another second messen-
activates the intracellular signaling pathway
ger, cGMP. NO can also act through covalent modifica-
.[45]
tion of proteins or their metal co-factors; some have a
redox mechanism and are reversible. It is toxic in high • Inhibitory (cell-cell contact)
concentrations and causes damage during stroke, but is
the cause of many other functions like relaxation of blood • Permissive (cell-matrix interactions)
vessels, apoptosis, and penile erections.
The combination of these signals are integrated in an al-
tered cytoplasmic machinery which leads to altered cell
Redox signaling behaviour.

In addition to nitric oxide, other electronically activated

species are also signal-transducing agents in a process 17.2.5 Major pathways
called redox signaling. Examples include superoxide,
hydrogen peroxide, carbon monoxide, and hydrogen Following are some major signaling pathways, demon-
sulfide. Redox signaling also includes active modu- strating how ligands binding to their receptors can affect
lation of electronic flows in semiconductive biological second messengers and eventually result in altered cellu-
macromolecules.[41] lar responses.

• MAPK/ERK pathway: A pathway that couples in-

17.2.4 Cellular responses tracellular responses to the binding of growth fac-
tors to cell surface receptors. This pathway is very
Gene activations[42] and metabolism alterations[43] are ex- complex and includes many protein components.[46]
amples of cellular responses to extracellular stimulation In many cell types, activation of this pathway pro-
that require signal transduction. Gene activation leads to motes cell division, and many forms of cancer are
further cellular effects, since the products of responding associated with aberrations in it.[47]
genes include instigators of activation; transcription fac-
tors produced as a result of a signal transduction cascade • cAMP-dependent pathway: In humans, cAMP
can activate even more genes. Hence, an initial stimu- works by activating protein kinase A (PKA, cAMP-
lus can trigger the expression of a large number of genes, dependent protein kinase) (see picture), and, thus,
leading to physiological events like the increased uptake further effects depend mainly on cAMP-dependent
of glucose from the blood stream[43] and the migration protein kinase, which vary based on the type of cell.
of neutrophils to sites of infection. The set of genes and
their activation order to certain stimuli is referred to as a • IP3 /DAG pathway: PLC cleaves the phospholipid
genetic program.[44] phosphatidylinositol 4,5-bisphosphate (PIP2) yield-
Mammalian cells require stimulation for cell division and ing diacyl glycerol (DAG) and inositol 1,4,5-
survival; in the absence of growth factor, apoptosis en- triphosphate (IP3 ). DAG remains bound to the
sues. Such requirements for extracellular stimulation are membrane, and IP3 is released as a soluble struc-
necessary for controlling cell behavior in unicellular and ture into the cytosol. IP3 then diffuses through the
17.2. SIGNAL TRANSDUCTION 285

cytosol to bind to IP3 receptors, particular calcium [9] Hildebrand E. (1977). “What does Halobacterium tell us
channels in the endoplasmic reticulum (ER). These about photoreception?". Biophys. Struct. Mech. 3 (1):
channels are specific to calcium and allow the 69–77. doi:10.1007/BF00536457. PMID 857951.
passage of only calcium to move through. This
[10] Kenny JJ, Martinez-Maza O. et al. (1979). “Lipid synthe-
causes the cytosolic concentration of Calcium to in-
sis: an indicator of antigen-induced signal transduction in
crease, causing a cascade of intracellular changes antigen-binding cells”. J. Immunol. 112 (4): 1278–1284.
and activity.[48] In addition, calcium and DAG to- PMID 376714.
gether works to activate PKC, which goes on to
phosphorylate other molecules, leading to altered [11] Gomperts, BD.; Kramer, IM. Tatham, PER. (2002). Sig-
cellular activity. End-effects include taste, manic nal transduction. Academic Press. ISBN 0-12-289631-9.
depression, tumor promotion, etc.[48]
[12] Vander “et al” (1998). Human Physiology. McGraw-Hill.
p. 159. ISBN 0-07-067065-X.
17.2.6 See also
[13] Beato M, Chavez S and Truss M (1996). “Transcrip-
tional regulation by steroid hormones”. Steroids 61 (4):
• DNA damage checkpoints
240–251. doi:10.1016/0039-128X(96)00030-X. PMID
• Functional selectivity 8733009.

• GTPases [14] Hammes SR (2003). “The further redefining of steroid-

mediated signaling”. Proc Natl Acad Sci USA 100
• Hormones as signals (5): 21680–2170. Bibcode:2003PNAS..100.2168H.
doi:10.1073/pnas.0530224100. PMC 151311. PMID
• Protein phosphatase 12606724.

• Redox signaling [15] Sugden D, Davidson K. et al. (2004). “Melatonin, mela-

tonin receptors and melanophores: a moving story”. Pig-
• Transduction ment Cell Res. 17 (5): 454–460. doi:10.1111/j.1600-
0749.2004.00185.x. PMID 15357831.
• Two-component regulatory system
[16] Kistler J, Stroud RM et al. (1982). “Structure
and function of an acetylcholine receptor”. Biophys.
17.2.7 References J. 37 (1): 371–383. Bibcode:1982BpJ....37..371K.
doi:10.1016/S0006-3495(82)84685-7. PMC 1329155.
[1] http://www.ncbi.nlm.nih.gov/books/NBK21517 PMID 7055628.

[2] Silverthorn (2007). Human Physiology. 4th ed. [17] Schroder et al. (2004). “Interferon-γ an overview of
signals, mechanisms and functions”. Journal of Leuko-
[3] Krauss, Gerhard (2008). Biochemistry of Signal Trans- cyte Biology 75 (2): 163–189. doi:10.1189/jlb.0603252.
duction and Regulation. Wiley-VCH. p. 15. ISBN 978- PMID 14525967.
3527313976.
[18] Missale C, Nash SR. et al. (1998). “Dopamine receptors:
[4] Reece, Jane; Campbell, Neil (2002). Biology. San Fran-
from structure to function”. Physiol. Rev. 78 (1): 189–
cisco: Benjamin Cummings. ISBN 0-8053-6624-5.
225. PMID 9457173.
[5] Rodbell, M. (1980). “The role of hormone receptors and
GTP-regulatory proteins in membrane transduction”. Na- [19] Goldstein, A. (1976). “Opioid peptides endor-
ture 284 (5751): 17–22. Bibcode:1980Natur.284...17R. phins in pituitary and brain”. Science 193 (4258):
doi:10.1038/284017a0. PMID 6101906. 1081–1086. Bibcode:1976Sci...193.1081G.
doi:10.1126/science.959823. PMID 959823.
[6] Rensing, L. (1972). “Periodic geophysical and biological
signals as Zeitgeber and exogenous inducers in animal or- [20] Scheler, G. (2013). “Self-organization of sig-
ganisms”. Int. J. Biometeorol. 16: Suppl:113–125. PMID nal transduction”. F1000research 2 (116).
4621276. doi:10.12688/f1000research.2-116.v1. PMID
25506419.
[7] Tonndorf J. (1975). “Davis-1961 revisited. Sig-
nal transmission in the cochlear hair cell-nerve junc- [21] Burns ME and Arshavsky VY. (2005). “Beyond
tion”. Arch. Otolaryngol. 101 (9): 528–535. counting photons: trials and trends in vertebrate
doi:10.1001/archotol.1975.00780380006002. PMID visual transduction”. Neuron 48 (3): 387–401.
169771. doi:10.1016/j.neuron.2005.10.014. PMID 16269358.

[8] Ashcroft SJ, Crossley JR, Crossley PC. (1976). “The ef- [22] Ronnett GV and Moon C. (2002). “G proteins and olfac-
fect of N-acylglucosamines on the biosynthesis and secre- tory signal transduction”. Annu Rev Physiol 64 (1): 189–
tion of insulin in the rat”. Biochem. J. 154 (3): 701–707. 222. doi:10.1146/annurev.physiol.64.082701.102219.
PMC 1172772. PMID 782447. PMID 11826268.
286 CHAPTER 17. INTEGRATION OF METABOLISM

[23] Hanna MH, Nowicki JJ and Fatone MA (1984). “Extra- Akira S (2003). “Role of adaptor TRIF in the MyD88-
cellular cyclic AMP (cAMP) during development of the independent toll-like receptor signaling pathway”. Sci-
cellular slime mold Polysphondylium violaceum: compar- ence 301 (5633): 640–3. Bibcode:2003Sci...301..640Y.
ison of accumulation in the wild type and an aggregation- doi:10.1126/science.1087262. PMID 12855817.
defective mutant”. J Bacteriol 157 (2): 345–349. PMID
215252. [37] Yamamoto M, Sato S, Hemmi H, Uematsu S, Hoshino
K, Kaisho T, Takeuchi O, Takeda K, Akira S (2003).
[24] Sprague GF Jr. (1991). “Signal transduction in yeast “TRAM is specifically involved in the Toll-like receptor
mating: receptors, transcription factors, and the ki- 4-mediated MyD88-independent signaling pathway”. Nat
nase connection”. Trends Genet 7 (11–12): 393–398. Immunol 4 (11): 1144–50. doi:10.1038/ni986. PMID
doi:10.1016/0168-9525(91)90218-F. PMID 1668192. 14556004.

[25] A molecular model for receptor activation [38] Yamamoto M, Sato S, Hemmi H, Sanjo H, Ue-
matsu S, Kaisho T, Hoshino K, Takeuchi O, Kobayashi
[26] Kou Qin, Chunmin Dong, Guangyu Wu & Nevin A Lam- M, Fujita T, Takeda K, Akira S (2002). “Es-
bert (August 2011). “Inactive-state preassembly of Gq- sential role for TIRAP in activation of the sig-
coupled receptors and Gq heterotrimers”. Nature Chemi- nalling cascade shared by TLR2 and TLR4”. Nature
cal Biology 7 (11): 740–747. doi:10.1038/nchembio.642. 420 (6913): 324–9. Bibcode:2002Natur.420..324Y.
PMC 3177959. PMID 21873996. doi:10.1038/nature01182. PMID 12447441.

[27] Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; Web [39] Delbridge L, O'Riordan M (2007). “Innate recognition of
content by Neil D. Clarke (2002). Biochemistry. San intracellular bacteria”. Curr Opin Immunol 19 (1): 10–6.
Francisco: W.H. Freeman. ISBN 0-7167-4954-8. doi:10.1016/j.coi.2006.11.005. PMID 17126540.

[28] Yang W, Xia S (2006). “Mechanisms of regulation and [40] Vander “et al” (1998). Human Physiology. McGraw-Hill.
function of G-protein-coupled receptor kinases”. World J p. 160. ISBN 0-07-067065-X.
Gastroenterol 12 (48): 7753–7. PMID 17203515.
[41] Forman, H.J., Signal transduction and reactive species.
[29] Burger M, Burger, JA et al. (1999). “Point mutation Free Radic. Biol. Med. 47:1237-1238; 2009
causing constitutive signaling of CXCR2 leads to trans- [42] Lalli E and Sassone-Corsi P (1994). “Signal transduction
forming activity similar to Kaposi’s sarcoma herpesvirus- and gene regulation: the nuclear response to cAMP”. J
G protein-coupled receptor”. J. Immunol. 163 (4): 2017– Biol Chem 269 (26): 17359–17362. PMID 8021233.
2022. PMID 10438939.
[43] Rosen O (1987). “After insulin binds”. Science 237
[30] Li E, Hristova K (2006). “Role of receptor tyrosine ki- (4821): 1452–1458. Bibcode:1987Sci...237.1452R.
nase transmembrane domains in cell signaling and hu- doi:10.1126/science.2442814. PMID 2442814.
man pathologies”. Biochemistry 45 (20): 6241–51.
doi:10.1021/bi060609y. PMID 16700535. [44] Massague J and Gomis RR (2006). “The logic of
TGFbeta signaling”. FEBS Lett 580 (12): 2811–2820.
[31] Schlessinger, J. (1988). “Signal transduction by allosteric doi:10.1016/j.febslet.2006.04.033. PMID 16678165.
receptor oligomerization”. Trends Biochem Sci 13 (11):
443–7. doi:10.1016/0968-0004(88)90219-8. PMID [45] Sako Y, Minoguchi S and Yanagida T (2000). “Single-
3075366. molecule imaging of EGFR signalling on the surface
of living cells”. Nature Cell Biology 2: 168–172.
[32] Roskoski, R, Jr. (2004). “The ErbB/HER re- doi:10.1038/35004044. PMID 10707088.
ceptor protein-tyrosine kinases and cancer”.
Biochem. Biophys. Res. Commun. 319 (1): 1–11. [46] Orton RJ, Sturm OE, Vyshemirsky V, Calder M, Gilbert
doi:10.1016/j.bbrc.2004.04.150. PMID 15158434. DR, Kolch W (Dec 2005). “Computational modelling
of the receptor-tyrosine-kinase-activated MAPK path-
[33] Wolanin PW, Thomason PA, Stock JB (2002). “Histidine way”. The Biochemical journall 392 (Pt 2): 249–
protein kinases: key signal transducers outside the ani- 61. doi:10.1042/BJ20050908. PMC 1316260. PMID
mal kingdom”. Genome Biology 3 (10): reviews3013.1– 16293107.
3013.8. doi:10.1186/gb-2002-3-10-reviews3013. PMC
[47] Vogelstein, B.; Kinzler, K. W. (2004). “Cancer genes and
244915. PMID 12372152.
the pathways they control”. Nature Medicine 10 (8): 789–
[34] Hehlgans, S. Haase, M. and Cordes, N. (2007). “Signaling 799. doi:10.1038/nm1087. PMID 15286780.
via integrins: Implications for cell survival and anticancer
[48] Alberts B, Lewis J, Raff M, Roberts K, Walter P (2002).
strategies”. Biochim. Biophys. Acta. 1775 (1): 163–180.
Molecular biology of the cell (4th ed.). New York: Gar-
doi:10.1016/j.bbcan.2006.09.001. PMID 17084981.
land Science. ISBN 0-8153-3218-1.
[35] Gilcrease MZ. (2006). “Integrin signaling in ep-
ithelial cells”. Cancer Lett. 247 (1): 1–25.
doi:10.1016/j.canlet.2006.03.031. PMID 16725254. 17.2.8 External links
[36] Yamamoto M, Sato S, Hemmi H, Hoshino K, Kaisho T, • Netpath - A curated resource of signal transduction
Sanjo H, Takeuchi O, Sugiyama M, Okabe M, Takeda K, pathways in humans
17.3. DIABETES MELLITUS 287

• Signal Transduction - The Virtual Library of Bio- • Type 2 DM begins with insulin resistance, a con-
chemistry and Cell Biology dition in which cells fail to respond to insulin
properly.[3] As the disease progresses a lack of in-
• TRANSPATH(R) - A database about signal trans-
sulin may also develop.[6] This form was previously
duction pathways
referred to as “non insulin-dependent diabetes mel-
• Science's STKE - Signal Transduction Knowledge litus” (NIDDM) or “adult-onset diabetes”. The pri-
Environment, from the journal Science, published by mary cause is excessive body weight and not enough
AAAS. exercise.[3]

• Signal Transduction at the US National Library of • Gestational diabetes, is the third main form and oc-
Medicine Medical Subject Headings (MeSH) curs when pregnant women without a previous his-
tory of diabetes develop a high blood sugar level.[3]
• UCSD-Nature Signaling Gateway, from Nature
Publishing Group Prevention and treatment involve a healthy diet, physical
• LitInspector - Signal transduction pathway mining in exercise, not using tobacco and being a normal body
PubMed abstracts weight. Blood pressure control and proper foot care are
also important for people with the disease. Type 1 dia-
• Huaxian Chen, et al. A Cell Based Immunocyto- betes must be managed with insulin injections.[3] Type 2
chemical Assay For Monitoring Kinase Signaling diabetes may be treated with medications with or without
Pathways And Drug Efficacy (PDF) Analytical Bio- insulin.[7] Insulin and some oral medications can cause
chemistry 338 (2005) 136-142 low blood sugar.[8] Weight loss surgery in those with
obesity is sometimes an effective measure in those with
• www.Redoxsignaling.com
type 2 DM.[9] Gestational diabetes usually resolves after
• Signaling PAthway Database - Kyushu University the birth of the baby.[10]

• Cell cycle - Homo sapiens (human) - KEGG PATH- As of 2014, an estimated 387 million people have di-
WAY abetes worldwide,[11] with type 2 diabetes making up
about 90% of the cases.[12][13] This represents 8.3% of
• Pathway Interaction Database - NCI the adult population,[13] with equal rates in both women
[14]
• Literature-curated human signaling network, the and men. From 2012 to 2014, diabetes is estimated to
[7][11]
largest human signaling network database have resulted in 1.5 to 4.9 million deaths each year.
Diabetes at least doubles a person’s risk of death.[3] The
number of people with diabetes is expected to rise to 592
million by 2035.[11] The global economic cost of diabetes
17.3 Diabetes mellitus in 2014 was estimated to be $612 billion USD.[15] In the
United States, diabetes cost $245 billion in 2012.[16]
“Diabetes” redirects here. For other uses, see Diabetes
(disambiguation).
17.3.1 Signs and symptoms
Diabetes mellitus (DM), commonly referred to as di-
The classic symptoms of untreated diabetes are weight
abetes, is a group of metabolic diseases in which there
loss, polyuria (increased urination), polydipsia (increased
are high blood sugar levels over a prolonged period.[2]
thirst), and polyphagia (increased hunger).[17] Symptoms
Symptoms of high blood sugar include frequent urination,
may develop rapidly (weeks or months) in type 1 diabetes,
increased thirst, and increased hunger. If left untreated,
while they usually develop much more slowly and may be
diabetes can cause many complications.[3] Acute compli-
subtle or absent in type 2 diabetes.
cations include diabetic ketoacidosis and nonketotic hy-
perosmolar coma.[4] Serious long-term complications in- Several other signs and symptoms can mark the onset of
clude cardiovascular disease, stroke, chronic kidney fail-diabetes, although they are not specific to the disease. In
ure, foot ulcers, and damage to the eyes.[3] addition to the known ones above, they include blurry vi-
sion, headache, fatigue, slow healing of cuts, and itchy
Diabetes is due to either the pancreas not producing
skin. Prolonged high blood glucose can cause glucose ab-
enough insulin or the cells of the body not responding
sorption in the lens of the eye, which leads to changes in
properly to the insulin produced.[5] There are three main
its shape, resulting in vision changes. A number of skin
types of diabetes mellitus:
rashes that can occur in diabetes are collectively known
as diabetic dermadromes.
• Type 1 DM results from the pancreas’ failure to
produce enough insulin. This form was previously
referred to as “insulin-dependent diabetes melli- Diabetic emergencies
tus” (IDDM) or “juvenile diabetes”. The cause is
unknown.[3] Low blood sugar is common in persons with type 1
288 CHAPTER 17. INTEGRATION OF METABOLISM

Main symptoms of
small blood vessels include damage to the eyes, kidneys,
Diabetes and nerves.[23] Damage to the eyes, known as diabetic
blue = more common
Central in Type 1 retinopathy, is caused by damage to the blood vessels
- Polydipsia in the retina of the eye, and can result in gradual vision
- Polyphagia Eyes
- Lethargy - Blurred vision
loss and blindness.[23] Damage to the kidneys, known as
- Stupor diabetic nephropathy, can lead to tissue scarring, urine
protein loss, and eventually chronic kidney disease, some-
Breath
Systemic - Smell of acetone times requiring dialysis or kidney transplant.[23] Damage
- Weight loss
to the nerves of the body, known as diabetic neuropa-
thy, is the most common complication of diabetes.[23]
Gastric
The symptoms can include numbness, tingling, pain, and
Respiratory - Nausea altered pain sensation, which can lead to damage to the
- Kussmaul - Vomiting
breathing - Abdominal
skin. Diabetes-related foot problems (such as diabetic
(hyper- pain foot ulcers) may occur, and can be difficult to treat, oc-
ventilation) casionally requiring amputation. Additionally, proximal
Urinary diabetic neuropathy causes painful muscle wasting and
- Polyuria weakness.
- Glycosuria
There is a link between cognitive deficit and diabetes.
Compared to those without diabetes, those with the dis-
Overview of the most significant symptoms of diabetes
ease have a 1.2 to 1.5-fold greater rate of decline in cog-
nitive function.[24]
and type 2 diabetes. Most cases are mild and are
not considered medical emergencies. Effects can range
from feelings of unease, sweating, trembling, and in-
17.3.2 Causes
creased appetite in mild cases to more serious is-
Diabetes mellitus is classified into four broad categories:
sues such as confusion, changes in behavior, seizures,
type 1, type 2, gestational diabetes, and “other specific
unconsciousness, and (rarely) permanent brain damage or
types”.[5] The “other specific types” are a collection of
death in severe cases.[18][19] Mild cases are self-treated by
a few dozen individual causes.[5] The term “diabetes”,
eating or drinking something high in sugar. Severe cases
without qualification, usually refers to diabetes mellitus.
can lead to unconsciousness and must be treated with in-
travenous glucose or injections with glucagon.
People (usually with type 1 diabetes) may also experience Type 1
episodes of diabetic ketoacidosis, a metabolic disturbance
characterized by nausea, vomiting and abdominal pain, Main article: Diabetes mellitus type 1
the smell of acetone on the breath, deep breathing known
as Kussmaul breathing, and in severe cases a decreased Type 1 diabetes mellitus is characterized by loss of the
level of consciousness.[20] insulin-producing beta cells of the islets of Langerhans
A rare but equally severe possibility is hyperosmolar non- in the pancreas, leading to insulin deficiency. This type
ketotic state, which is more common in type 2 diabetes can be further classified as immune-mediated or idio-
and is mainly the result of dehydration.[20] pathic. The majority of type 1 diabetes is of the immune-
mediated nature, in which a T-cell-mediated autoimmune
attack leads to the loss of beta cells and thus insulin.[26]
Complications It causes approximately 10% of diabetes mellitus cases
in North America and Europe. Most affected people are
Main article: Complications of diabetes mellitus otherwise healthy and of a healthy weight when onset oc-
curs. Sensitivity and responsiveness to insulin are usually
normal, especially in the early stages. Type 1 diabetes
All forms of diabetes increase the risk of long-term com- can affect children or adults, but was traditionally termed
plications. These typically develop after many years (10– “juvenile diabetes” because a majority of these diabetes
20), but may be the first symptom in those who have oth- cases were in children.
erwise not received a diagnosis before that time.
“Brittle” diabetes, also known as unstable diabetes or la-
The major long-term complications relate to damage to bile diabetes, is a term that was traditionally used to de-
blood vessels. Diabetes doubles the risk of cardiovascular
scribe the dramatic and recurrent swings in glucose lev-
disease[21] and about 75% of deaths in diabetics are due
els, often occurring for no apparent reason in insulin-
to coronary artery disease.[22] Other “macrovascular” dis-
dependent diabetes. This term, however, has no biologic
eases are stroke, and peripheral vascular disease. basis and should not be used.[27] Still, type 1 diabetes
The primary complications of diabetes due to damage in can be accompanied by irregular and unpredictable high
17.3. DIABETES MELLITUS 289

blood sugar levels, frequently with ketosis, and some- Gestational diabetes
times with serious low blood sugar levels. Other compli-
cations include an impaired counterregulatory response Main article: Gestational diabetes
to low blood sugar, infection, gastroparesis (which leads
to erratic absorption of dietary carbohydrates), and en-
Gestational diabetes mellitus (GDM) resembles type 2 di-
docrinopathies (e.g., Addison’s disease).[27] These phe-
abetes in several respects, involving a combination of rel-
nomena are believed to occur no more frequently than in
atively inadequate insulin secretion and responsiveness.
1% to 2% of persons with type 1 diabetes.[28]
It occurs in about 2–10% of all pregnancies and may im-
Type 1 diabetes is partly inherited, with multiple genes, prove or disappear after delivery.[34] However, after preg-
including certain HLA genotypes, known to influence the nancy approximately 5–10% of women with gestational
risk of diabetes. In genetically susceptible people, the on- diabetes are found to have diabetes mellitus, most com-
set of diabetes can be triggered by one or more environ- monly type 2.[34] Gestational diabetes is fully treatable,
mental factors, such as a viral infection or diet. There is but requires careful medical supervision throughout the
some evidence that suggests an association between type pregnancy. Management may include dietary changes,
1 diabetes and Coxsackie B4 virus. Unlike type 2 dia- blood glucose monitoring, and in some cases insulin may
betes, the onset of type 1 diabetes is unrelated to lifestyle. be required.
Though it may be transient, untreated gestational diabetes
can damage the health of the fetus or mother. Risks to the
baby include macrosomia (high birth weight), congenital
cardiac and central nervous system anomalies, and skele-
Type 2
tal muscle malformations. Increased fetal insulin may in-
hibit fetal surfactant production and cause respiratory dis-
Main article: Diabetes mellitus type 2 tress syndrome. A high blood bilirubin level may result
from red blood cell destruction. In severe cases, perinatal
death may occur, most commonly as a result of poor pla-
Type 2 diabetes mellitus is characterized by insulin re-
cental perfusion due to vascular impairment. Labor in-
sistance, which may be combined with relatively reduced
duction may be indicated with decreased placental func-
insulin secretion.[5] The defective responsiveness of body
tion. A Caesarean section may be performed if there is
tissues to insulin is believed to involve the insulin recep-
marked fetal distress or an increased risk of injury asso-
tor. However, the specific defects are not known. Dia-
ciated with macrosomia, such as shoulder dystocia.
betes mellitus cases due to a known defect are classified
separately. Type 2 diabetes is the most common type.
In the early stage of type 2, the predominant abnormal- Other types
ity is reduced insulin sensitivity. At this stage, hyper-
glycemia can be reversed by a variety of measures and Prediabetes indicates a condition that occurs when a per-
medications that improve insulin sensitivity or reduce glu- son’s blood glucose levels are higher than normal but not
cose production by the liver. high enough for a diagnosis of type 2 DM. Many peo-
Type 2 diabetes is due primarily to lifestyle factors and ple destined to develop type 2 DM spend many years in a
state of prediabetes.
genetics.[29] A number of lifestyle factors are known to
be important to the development of type 2 diabetes, in- Latent autoimmune diabetes of adults (LADA) is a con-
cluding obesity (defined by a body mass index of greater dition in which type 1 DM develops in adults. Adults
than thirty), lack of physical activity, poor diet, stress, with LADA are frequently initially misdiagnosed as hav-
and urbanization.[12] Excess body fat is associated with ing type 2 DM, based on age rather than etiology.
30% of cases in those of Chinese and Japanese descent, Some cases of diabetes are caused by the body’s tissue
60–80% of cases in those of European and African de- receptors not responding to insulin (even when insulin
scent, and 100% of Pima Indians and Pacific Islanders.[5] levels are normal, which is what separates it from type
Even those who are not obese often have a high waist–hip 2 diabetes); this form is very uncommon. Genetic mu-
ratio.[5] tations (autosomal or mitochondrial) can lead to defects
Dietary factors also influence the risk of developing type in beta cell function. Abnormal insulin action may also
2 diabetes. Consumption of sugar-sweetened drinks have been genetically determined in some cases. Any dis-
in excess is associated with an increased risk.[30][31] ease that causes extensive damage to the pancreas may
The type of fats in the diet is also important, with lead to diabetes (for example, chronic pancreatitis and
saturated fats and trans fatty acids increasing the risk and cystic fibrosis). Diseases associated with excessive se-
polyunsaturated and monounsaturated fat decreasing the cretion of insulin-antagonistic hormones can cause dia-
risk.[29] Eating lots of white rice appears to also play a betes (which is typically resolved once the hormone ex-
role in increasing risk.[32] A lack of exercise is believed cess is removed). Many drugs impair insulin secretion
to cause 7% of cases.[33] and some toxins damage pancreatic beta cells. The ICD-
290 CHAPTER 17. INTEGRATION OF METABOLISM

10 (1992) diagnostic entity, malnutrition-related diabetes The body obtains glucose from three main places: the in-
mellitus (MRDM or MMDM, ICD-10 code E12), was testinal absorption of food, the breakdown of glycogen,
deprecated by the World Health Organization when the the storage form of glucose found in the liver, and
current taxonomy was introduced in 1999.[35] gluconeogenesis, the generation of glucose from non-
Other forms of diabetes mellitus include congenital dia- carbohydrate substrates in the body.[39] Insulin plays a
betes, which is due to genetic defects of insulin secretion, critical role in balancing glucose levels in the body. In-
cystic fibrosis-related diabetes, steroid diabetes induced sulin can inhibit the breakdown of glycogen or the pro-
by high doses of glucocorticoids, and several forms of cess of gluconeogenesis, it can stimulate the transport of
glucose into fat and muscle cells, and it can stimulate the
monogenic diabetes.
storage of glucose in the form of glycogen.[39]
The following is a comprehensive list of other causes of
diabetes:[36] Insulin is released into the blood by beta cells (β-cells),
found in the islets of Langerhans in the pancreas, in re-
sponse to rising levels of blood glucose, typically after
eating. Insulin is used by about two-thirds of the body’s
17.3.3 Pathophysiology cells to absorb glucose from the blood for use as fuel,
for conversion to other needed molecules, or for stor-
age. Lower glucose levels result in decreased insulin re-
lease from the beta cells and in the breakdown of glyco-
gen to glucose. This process is mainly controlled by the
hormone glucagon, which acts in the opposite manner to
insulin.[40]
If the amount of insulin available is insufficient, if cells
respond poorly to the effects of insulin (insulin insensi-
tivity or insulin resistance), or if the insulin itself is de-
fective, then glucose will not be absorbed properly by the
body cells that require it, and it will not be stored appro-
priately in the liver and muscles. The net effect is persis-
tently high levels of blood glucose, poor protein synthesis,
and other metabolic derangements, such as acidosis.[39]
When the glucose concentration in the blood remains
The fluctuation of blood sugar (red) and the sugar-lowering hor-
high over time, the kidneys will reach a threshold of
mone insulin (blue) in humans during the course of a day with
reabsorption, and glucose will be excreted in the urine
three meals — one of the effects of a sugar-rich vs a starch-rich
meal is highlighted. (glycosuria).[41] This increases the osmotic pressure of
the urine and inhibits reabsorption of water by the kidney,
resulting in increased urine production (polyuria) and in-
GLUT 2 K+ATP creased fluid loss. Lost blood volume will be replaced
osmotically from water held in body cells and other body
Respiration ATP:ADP ratio closes
compartments, causing dehydration and increased thirst
Glucose K ATP channel
causing depolarisation (polydipsia).[39]
Voltage
Gated
ATP Ca2+ Ca2+
Channels
Production
17.3.4 Diagnosis
Ca2+ activates insulin gene
expression via CREB (Calcium
Responsive Element Binding Protein) See also: Glycated hemoglobin and Glucose tolerance
test
Exocytosis of stored insulin

Diabetes mellitus is characterized by recurrent or persis-

Mechanism of insulin release in normal pancreatic beta cells — tent high blood sugar, and is diagnosed by demonstrating
insulin production is more or less constant within the beta cells. Its any one of the following:[35]
release is triggered by food, chiefly food containing absorbable
glucose.
• Fasting plasma glucose level ≥ 7.0 mmol/l (126
Insulin is the principal hormone that regulates the uptake mg/dl)
of glucose from the blood into most cells of the body,
especially liver, muscle, and adipose tissue. Therefore, • Plasma glucose ≥ 11.1 mmol/l (200 mg/dl) two
deficiency of insulin or the insensitivity of its receptors hours after a 75 g oral glucose load as in a glucose
plays a central role in all forms of diabetes mellitus.[38] tolerance test
17.3. DIABETES MELLITUS 291

• Symptoms of high blood sugar and casual plasma 17.3.6 Management

glucose ≥ 11.1 mmol/l (200 mg/dl)
Main article: Diabetes management
• Glycated hemoglobin (HbA₁C) ≥ 48 mmol/mol (≥
6.5 DCCT %).[44] Diabetes mellitus is a chronic disease, for which there is
no known cure except in very specific situations.[52] Man-
agement concentrates on keeping blood sugar levels as
A positive result, in the absence of unequivocal high close to normal, without causing low blood sugar. This
blood sugar, should be confirmed by a repeat of any can usually be accomplished with a healthy diet, exercise,
of the above methods on a different day. It is prefer- weight loss, and use of appropriate medications (insulin
able to measure a fasting glucose level because of the in the case of type 1 diabetes; oral medications, as well
ease of measurement and the considerable time commit- as possibly insulin, in type 2 diabetes).
ment of formal glucose tolerance testing, which takes two
Learning about the disease and actively participating in
hours to complete and offers no prognostic advantage
the treatment is important, since complications are far
over the fasting test.[45] According to the current defini-
less common and less severe in people who have well-
tion, two fasting glucose measurements above 126 mg/dl
managed blood sugar levels.[53][54] The goal of treatment
(7.0 mmol/l) is considered diagnostic for diabetes melli-
is an HbA₁C level of 6.5%, but should not be lower than
tus.
that, and may be set higher.[55] Attention is also paid
Per the World Health Organization people with fasting to other health problems that may accelerate the nega-
glucose levels from 6.1 to 6.9 mmol/l (110 to 125 mg/dl) tive effects of diabetes. These include smoking, elevated
are considered to have impaired fasting glucose.[46] peo- cholesterol levels, obesity, high blood pressure, and lack
ple with plasma glucose at or above 7.8 mmol/l (140 of regular exercise.[55] Specialized footwear is widely
mg/dl), but not over 11.1 mmol/l (200 mg/dl), two hours used to reduce the risk of ulceration, or re-ulceration, in
after a 75 g oral glucose load are considered to have at-risk diabetic feet. Evidence for the efficacy of this re-
impaired glucose tolerance. Of these two prediabetic mains equivocal, however.[56]
states, the latter in particular is a major risk factor for
progression to full-blown diabetes mellitus, as well as car-
diovascular disease.[47] The American Diabetes Associ- Lifestyle
ation since 2003 uses a slightly different range for im-
paired fasting glucose of 5.6 to 6.9 mmol/l (100 to 125 See also: Diabetic diet
mg/dl).[48]
Glycated hemoglobin is better than fasting glucose for de- People with diabetes can benefit from education about the
termining risks of cardiovascular disease and death from disease and treatment, good nutrition to achieve a normal
any cause.[49] body weight, and exercise, with the goal of keeping both
short-term and long-term blood glucose levels within ac-
The rare disease diabetes insipidus has similar symptoms ceptable bounds. In addition, given the associated higher
to diabetes mellitus, but without disturbances in the sugar risks of cardiovascular disease, lifestyle modifications are
metabolism (insipidus means “without taste” in Latin) and recommended to control blood pressure.[57]
does not involve the same disease mechanisms. Diabetes
is a part of the wider condition known as metabolic syn-
drome. Medications

See also: Anti-diabetic medication

17.3.5 Prevention
Medications used to treat diabetes do so by lowering
There is no known preventive measure for type 1 blood sugar levels. There are a number of different
diabetes.[3] Type 2 diabetes can often be prevented by classes of anti-diabetic medications. Some are available
a person being a normal body weight, physical exercise, by mouth, such as metformin, while others are only avail-
and following a healthful diet.[3] Dietary changes known able by injection like insulin. Type 1 diabetes can only be
to be effective in helping to prevent diabetes include a treated with insulin, typically with a combination of reg-
diet rich in whole grains and fiber, and choosing good fats, ular and NPH insulin, or synthetic insulin analogs.
such as polyunsaturated fats found in nuts, vegetable oils, Metformin is generally recommended as a first line treat-
and fish.[50] Limiting sugary beverages and eating less red ment for type 2 diabetes, as there is good evidence that it
meat and other sources of saturated fat can also help in the decreases mortality.[58] It works by decreasing production
prevention of diabetes.[50] Active smoking is also associ- of glucose by the liver.[59] Several other groups of drugs,
ated with an increased risk of diabetes, so smoking cessa- mostly given by mouth, may also decrease blood sugar in
tion can be an important preventive measure as well.[51] type II DM. These include agents that increase insulin re-
292 CHAPTER 17. INTEGRATION OF METABOLISM

lease, agents that decrease absorption of sugar from the

intestines, and agents that make the body more sensitive
to insulin.[59] When insulin is used in type 2 diabetes, a
long-acting formulation is usually added initially, while
continuing oral medications.[58] Doses of insulin are then
increased to effect.[58][60]
Since cardiovascular disease is a serious complication
associated with diabetes, some recommend blood pres-
sure levels below 120/80 mmHg;[61][62] however, evi- Prevalence of diabetes worldwide in 2000 (per 1,000 inhabi-
dence only supports less than or equal to somewhere be- tants) — world average was 2.8%.
tween 140/90 mmHg to 160/100 mmHg.[63][64] Amongst
medications that lower blood pressure, angiotensin con-
verting enzyme inhibitors (ACEIs) improve outcomes in
those with DM while the similar medications angiotensin
receptor blockers (ARBs) do not.[65] Aspirin is also
recommended for patient with cardiovascular problems,
however routine use of aspirin has not been found to im-
prove outcomes in uncomplicated diabetes.[66]

Surgery
Disability-adjusted life year for diabetes mellitus per 100,000
A pancreas transplant is occasionally considered for peo- inhabitants in 2004
ple with type 1 diabetes who have severe complications
of their disease, including end stage kidney disease re-
quiring kidney transplantation.[67] In 2014, the International Diabetes Federation (IDF) esti-
Weight loss surgery in those with obesity and type two di- mated that diabetes resulted in 4.9 million deaths.[11] The
abetes is often an effective measure.[68] Many are able to World Health Organization (WHO) estimated that dia-
maintain normal blood sugar levels with little or no med- betes resulted in 1.5 million deaths in 2012, making it the
ications following surgery[69] and long-term mortality is 8th leading cause of death.[7] The discrepancy between
decreased.[70] There however is some short-term mortal- the two estimates is due to the fact that cardiovascular
ity risk of less than 1% from the surgery.[71] The body diseases are often the cause of death for individuals with
mass index cutoffs for when surgery is appropriate are not diabetes; the IDF uses modelling to estimate the amount
yet clear.[70] It is recommended that this option be con- of deaths that could be attributed to diabetes.[15] More
sidered in those who are unable to get both their weight than 80% of diabetic deaths occur in low and middle-
and blood sugar under control.[72] income countries.[74]
Diabetes mellitus occurs throughout the world, but is
more common (especially type 2) in more developed
Support
countries. The greatest increase in rates was expected to
occur in Asia and Africa, where most people with dia-
In countries using a general practitioner system, such as
betes will probably live in 2030.[75] The increase in rates
the United Kingdom, care may take place mainly outside
in developing countries follows the trend of urbanization
hospitals, with hospital-based specialist care used only in
and lifestyle changes, including a “Western-style” diet.
case of complications, difficult blood sugar control, or
This has suggested an environmental (i.e., dietary) effect,
research projects. In other circumstances, general prac-
but there is little understanding of the mechanism(s) at
titioners and specialists share care in a team approach.
present.[75]
Home telehealth support can be an effective management
technique.[73]
17.3.8 History
17.3.7 Epidemiology
Main article: History of diabetes
Main article: Epidemiology of diabetes mellitus
As of 2013, 382 million people have diabetes Diabetes was one of the first diseases described,[76] with
worldwide.[13] Type 2 makes up about 90% of the an Egyptian manuscript from c. 1500 BCE mentioning
cases.[12][14] This is equal to 8.3% of the adult “too great emptying of the urine”.[77] The first described
population[13] with equal rates in both women and cases are believed to be of type 1 diabetes.[77] Indian
men.[14] physicians around the same time identified the disease
17.3. DIABETES MELLITUS 293

and classified it as madhumeha or “honey urine”, not- in 1675 added “mellitus” to the word “diabetes” as a des-
ing the urine would attract ants.[77] The term “diabetes” ignation for the disease, when he noticed the urine of a di-
or “to pass through” was first used in 230 BCE by the abetic had a sweet taste (glycosuria).[81] This sweet taste
Greek Appollonius of Memphis.[77] The disease was con- had been noticed in urine by the ancient Greeks, Chinese,
sidered rare during the time of the Roman empire, with Egyptians, Indians, and Persians.
Galen commenting he had only seen two cases during
his career.[77] This is possibly due the diet and life-style
of the ancient people, or because the clinical symptoms 17.3.9 Society and culture
were observed during the advanced stage of the disease.
Galen named the disease “diarrhea of the urine” (diar- Further information: List of films featuring diabetes
rhea urinosa). The earliest surviving work with a detailed
reference to diabetes is that of Aretaeus of Cappadocia The 1989 "St. Vincent Declaration"[86][87] was the re-
(2nd or early 3rd century CE). He described the symp- sult of international efforts to improve the care ac-
toms and the course of the disease, which he attributed corded to those with diabetes. Doing so is important not
to the moisture and coldness, reflecting the beliefs of the only in terms of quality of life and life expectancy, but
“Pneumatic School”. He hypothesized a correlation of also economically—expenses due to diabetes have been
diabetes with other diseases and he discussed differential shown to be a major drain on health—and productivity-
diagnosis from the snakebite which also provokes exces- related resources for healthcare systems and govern-
sive thirst. His work remained unknown in the West until ments.
the middle of the 16th century when, in 1552, the first
Several countries established more and less successful na-
Latin edition was published in Venice.[78]
tional diabetes programmes to improve treatment of the
Type 1 and type 2 diabetes were identified as separate disease.[88]
conditions for the first time by the Indian physicians
People with diabetes who have neuropathic symptoms
Sushruta and Charaka in 400-500 CE with type 1 asso-
[77] such as numbness or tingling in feet or hands are
ciated with youth and type 2 with being overweight.
twice as likely to be unemployed as those without the
The term “mellitus” or “from honey” was added by the
symptoms.[89]
Briton John Rolle in the late 1700s to separate the con-
dition from diabetes insipidus, which is also associated In 2010, diabetes-related emergency department (ED)
with frequent urination.[77] Effective treatment was not visit rates in the United States were higher among peo-
developed until the early part of the 20th century, when ple from the lowest income communities (526 per 10,000
Canadians Frederick Banting and Charles Herbert Best population) than from the highest income communities
isolated and purified insulin in 1921 and 1922.[77] This (236 per 10,000 population). Approximately 9.4% of
was followed by the development of the long-acting in- diabetes-related ED visits were for the uninsured.[90]
sulin NPH in the 1940s.[77]
Naming
Etymology
The term “type 1 diabetes” has replaced several former
The word diabetes (/ˌdaɪ.əˈbiːtiːz/ or /ˌdaɪ.əˈbiːtɨs/) comes terms, including childhood-onset diabetes, juvenile dia-
from Latin diabētēs, which in turn comes from Ancient betes, and insulin-dependent diabetes mellitus (IDDM).
Greek διαβήτης (diabētēs) which literally means “a Likewise, the term “type 2 diabetes” has replaced several
passer through; a siphon.”[79] Ancient Greek physician former terms, including adult-onset diabetes, obesity-
Aretaeus of Cappadocia (fl. 1st century CE) used that related diabetes, and noninsulin-dependent diabetes mel-
word, with the intended meaning “excessive discharge of litus (NIDDM). Beyond these two types, there is no
urine”, as the name for the disease.[80][81][82] Ultimately, agreed-upon standard nomenclature.
the word comes from Greek διαβαίνειν (diabainein), Diabetes mellitus is also occasionally known as “sugar di-
meaning “to pass through,”[79] which is composed of δια- abetes” to differentiate it from diabetes insipidus.[91]
(dia-), meaning “through” and βαίνειν (bainein), mean-
ing “to go”.[80] The word “diabetes” is first recorded in
English, in the form diabete, in a medical text written 17.3.10 Other animals
around 1425.
The word mellitus (/mɨˈlaɪtəs/ or /ˈmɛlɨtəs/) comes from Main articles: Diabetes in dogs and Diabetes in cats
the classical Latin word mellītus, meaning “mellite”[83]
(i.e. sweetened with honey;[83] honey-sweet[84] ). The In animals, diabetes is most commonly encountered in
Latin word comes from mell-, which comes from mel, dogs and cats. Middle-aged animals are most commonly
meaning “honey";[83][84] sweetness;[84] pleasant thing,[84] affected. Female dogs are twice as likely to be affected
and the suffix -ītus,[83] whose meaning is the same as that as males, while according to some sources, male cats
of the English suffix "-ite”.[85] It was Thomas Willis who are also more prone than females. In both species, all
294 CHAPTER 17. INTEGRATION OF METABOLISM

breeds may be affected, but some small dog breeds are [10] Cash, Jill (2014). Family Practice Guidelines (3rd ed.).
particularly likely to develop diabetes, such as Miniature Springer. p. 396. ISBN 9780826168757.
Poodles.[92] The symptoms may relate to fluid loss and
[11] “Update 2014”. IDF. International Diabetes Federation.
polyuria, but the course may also be insidious. Diabetic
Retrieved 29 November 2014.
animals are more prone to infections. The long-term
complications recognised in humans are much rarer in [12] Williams textbook of endocrinology (12th ed.). Philadel-
animals. The principles of treatment (weight loss, oral phia: Elsevier/Saunders. pp. 1371–1435. ISBN 978-1-
antidiabetics, subcutaneous insulin) and management of 4377-0324-5.
emergencies (e.g. ketoacidosis) are similar to those in
[13] Shi, Yuankai; Hu, Frank B (7 June 2014). “The global
humans.[92] implications of diabetes and cancer”. The Lancet 383
(9933): 1947–8. doi:10.1016/S0140-6736(14)60886-2.
PMID 24910221.
17.3.11 Research
[14] Vos T, Flaxman AD, Naghavi M, Lozano R, Michaud C,
Inhalable insulin has been developed.[93] The origi- Ezzati M, Shibuya K, Salomon JA, Abdalla S, Aboyans
nal products were withdrawn due to side effects.[93] V et al. (Dec 15, 2012). “Years lived with disability
Afrezza, under development by pharmaceuticals com- (YLDs) for 1160 sequelae of 289 diseases and injuries
pany MannKind Corporation, was approved by the FDA 1990–2010: a systematic analysis for the Global Burden
of Disease Study 2010.”. Lancet 380 (9859): 2163–96.
for general sale in June 2014.[94]
doi:10.1016/S0140-6736(12)61729-2. PMID 23245607.
An advantage to inhaled insulin is that it may be more
convenient and easy to use.[95] [15] IDF DIABETES ATLAS (PDF) (6th ed.). International Di-
abetes Federation. 2013. p. 7. ISBN 2930229853.

[16] American Diabetes, Association (Apr 2013). “Economic

17.3.12 References costs of diabetes in the U.S. in 2012.”. Diabetes Care 36
(4): 1033–46. doi:10.2337/dc12-2625. PMC 3609540.
[1] “Diabetes Blue Circle Symbol”. International Diabetes PMID 23468086.
Federation. 17 March 2006.
[17] Cooke DW, Plotnick L (November 2008). “Type 1 dia-
[2] “About diabetes”. World Health Organization. Retrieved betes mellitus in pediatrics”. Pediatr Rev 29 (11): 374–84;
4 April 2014. quiz 385. doi:10.1542/pir.29-11-374. PMID 18977856.
[3] “Diabetes Fact sheet N°312”. WHO. October 2013. Re- [18] Kenny C (April 2014). “When hypoglycemia is not obvi-
trieved 25 March 2014. ous: diagnosing and treating under-recognized and undis-
[4] Kitabchi, AE; Umpierrez, GE; Miles, JM; Fisher, closed hypoglycemia”. Primary care diabetes 8 (1): 3–11.
JN (Jul 2009). “Hyperglycemic crises in adult pa- doi:10.1016/j.pcd.2013.09.002. PMID 24100231.
tients with diabetes.”. Diabetes Care 32 (7): 1335– [19] Verrotti A, Scaparrotta A, Olivieri C, Chiarelli F (Decem-
43. doi:10.2337/dc09-9032. PMC 2699725. PMID ber 2012). “Seizures and type 1 diabetes mellitus: cur-
19564476. rent state of knowledge”. European journal of endocrinol-
[5] Shoback, edited by David G. Gardner, Dolores (2011). ogy 167 (6): 749–58. doi:10.1530/EJE-12-0699. PMID
“Chapter 17”. Greenspan’s basic & clinical endocrinology 22956556.
(9th ed.). New York: McGraw-Hill Medical. ISBN 0-07- [20] Kitabchi AE, Umpierrez GE, Miles JM, Fisher JN
162243-8. (July 2009). “Hyperglycemic crises in adult pa-
[6] RSSDI textbook of diabetes mellitus. (Rev. 2nd ed.). New tients with diabetes”. Diabetes Care 32 (7): 1335–
Delhi: Jaypee Brothers Medical Publishers. 2012. p. 43. doi:10.2337/dc09-9032. PMC 2699725. PMID
235. ISBN 9789350254899. 19564476.

[7] “The top 10 causes of death Fact sheet N°310”. World [21] Sarwar N, Gao P, Seshasai SR, Gobin R, Kaptoge S,
Health Organization. Oct 2013. Di Angelantonio E, Ingelsson E, Lawlor DA, Selvin E,
Stampfer M, Stehouwer CD, Lewington S, Pennells L,
[8] Rippe, edited by Richard S. Irwin, James M. (2010). Thompson A, Sattar N, White IR, Ray KK, Danesh J
Manual of intensive care medicine (5th ed.). Philadelphia: (2010). “Diabetes mellitus, fasting blood glucose concen-
Wolters Kluwer Health/Lippincott Williams & Wilkins. tration, and risk of vascular disease: A collaborative meta-
p. 549. ISBN 9780781799928. analysis of 102 prospective studies”. The Lancet 375
(9733): 2215–22. doi:10.1016/S0140-6736(10)60484-
[9] Picot, J; Jones, J; Colquitt, JL; Gospodarevskaya, E; Love- 9. PMC 2904878. PMID 20609967.
man, E; Baxter, L; Clegg, AJ (September 2009). “The
clinical effectiveness and cost-effectiveness of bariatric [22] O'Gara PT, Kushner FG, Ascheim DD, Casey DE, Chung
(weight loss) surgery for obesity: a systematic review MK, de Lemos JA, Ettinger SM, Fang JC, Fesmire
and economic evaluation”. Health technology assessment FM, Franklin BA, Granger CB, Krumholz HM, Linder-
(Winchester, England) 13 (41): 1–190, 215–357, iii–iv. baum JA, Morrow DA, Newby LK, Ornato JP, Ou N,
doi:10.3310/hta13410. PMID 19726018. Radford MJ, Tamis-Holland JE, Tommaso CL, Tracy
17.3. DIABETES MELLITUS 295

CM, Woo YJ, Zhao DX, Anderson JL, Jacobs AK, (9838): 219–29. doi:10.1016/S0140-6736(12)61031-9.
Halperin JL, Albert NM, Brindis RG, Creager MA, PMC 3645500. PMID 22818936.
DeMets D, Guyton RA, Hochman JS, Kovacs RJ, Kush-
ner FG, Ohman EM, Stevenson WG, Yancy CW (29 [34] “National Diabetes Clearinghouse (NDIC): National Di-
January 2013). “2013 ACCF/AHA guideline for the abetes Statistics 2011”. U.S. Department of Health and
management of ST-elevation myocardial infarction: a re- Human Services. Retrieved 22 April 2014.
port of the American College of Cardiology Founda-
tion/American Heart Association Task Force on Prac- [35] “Definition, Diagnosis and Classification of Diabetes Mel-
tice Guidelines.”. Circulation 127 (4): e362–425. litus and its Complications” (PDF). World Health Organ-
doi:10.1161/CIR.0b013e3182742cf6. PMID 23247304. isation. 1999.

[23] “Diabetes Programme”. World Health Organization. Re- [36] Unless otherwise specified, reference is: Table 20-5 in
trieved 22 April 2014. Mitchell, Richard Sheppard; Kumar, Vinay; Abbas, Abul
K.; Fausto, Nelson. Robbins Basic Pathology (8th ed.).
[24] Cukierman, T (8 Nov 2005). “Cognitive decline and de- Philadelphia: Saunders. ISBN 1-4160-2973-7.
mentia in diabetes—systematic overview of prospective
observational studies”. Springer-Verlag. Retrieved 28 [37] Sattar N, Preiss D, Murray HM, Welsh P, Buckley BM,
Apr 2013. de Craen AJ, Seshasai SR, McMurray JJ, Freeman DJ,
Jukema JW, Macfarlane PW, Packard CJ, Stott DJ, Wes-
[25] Lambert P, Bingley PJ (2002). “What is
tendorp RG, Shepherd J, Davis BR, Pressel SL, Marchi-
Type 1 Diabetes?". Medicine 30: 1–5.
oli R, Marfisi RM, Maggioni AP, Tavazzi L, Tognoni G,
doi:10.1383/medc.30.1.1.28264.
Kjekshus J, Pedersen TR, Cook TJ, Gotto AM, Clearfield
[26] Rother KI (April 2007). “Diabetes treatment—bridging MB, Downs JR, Nakamura H, Ohashi Y, Mizuno K,
the divide”. The New England Journal of Medicine 356 Ray KK, Ford I (February 2010). “Statins and risk of
(15): 1499–501. doi:10.1056/NEJMp078030. PMID incident diabetes: a collaborative meta-analysis of ran-
17429082. domised statin trials”. The Lancet 375 (9716): 735–42.
doi:10.1016/S0140-6736(09)61965-6. PMID 20167359.
[27] “Diabetes Mellitus (DM): Diabetes Mellitus and Disor-
ders of Carbohydrate Metabolism: Merck Manual Profes- [38] “Insulin Basics”. American Diabetes Association. Re-
sional”. Merck Publishing. April 2010. Retrieved 2010- trieved 24 April 2014.
07-30.
[39] Shoback, edited by David G. Gardner, Dolores (2011).
[28] Dorner M, Pinget M, Brogard JM (May 1977). “Essen- Greenspan’s basic & clinical endocrinology (9th ed.). New
tial labile diabetes”. MMW Munch Med Wochenschr (in York: McGraw-Hill Medical. ISBN 9780071622431.
German) 119 (19): 671–4. PMID 406527.
[40] al.], Kim E. Barrett, ... [et (2012). Ganong’s review of
[29] Risérus U, Willett WC, Hu FB (January 2009). medical physiology. (24th ed.). New York: McGraw-Hill
“Dietary fats and prevention of type 2 dia- Medical. ISBN 0071780033.
betes”. Progress in Lipid Research 48 (1): 44–51.
doi:10.1016/j.plipres.2008.10.002. PMC 2654180. [41] al.], Robert K. Murray ... [et (2012). Harper’s illustrated
PMID 19032965. biochemistry (29th ed.). New York: McGraw-Hill Medi-
[30] Malik VS, Popkin BM, Bray GA, Després JP, cal. ISBN 007176576X.
Hu FB (2010-03-23). “Sugar Sweetened Bever-
[42] Definition and diagnosis of diabetes mellitus and interme-
ages, Obesity, Type 2 Diabetes and Cardiovascu-
diate hyperglycemia: report of a WHO/IDF consultation
lar Disease risk”. Circulation 121 (11): 1356–64.
(PDF). Geneva: World Health Organization. 2006. p.
doi:10.1161/CIRCULATIONAHA.109.876185. PMC
21. ISBN 978-92-4-159493-6.
2862465. PMID 20308626.

[31] Malik VS, Popkin BM, Bray GA, Després JP, Willett [43] Vijan, S (March 2010). “Type 2 diabetes”. Annals of
WC, Hu FB (November 2010). “Sugar-Sweetened Bev- Internal Medicine 152 (5): ITC31-15. doi:10.1059/0003-
erages and Risk of Metabolic Syndrome and Type 2 Dia- 4819-152-5-201003020-01003. PMID 20194231.
betes: A meta-analysis”. Diabetes Care 33 (11): 2477–
83. doi:10.2337/dc10-1079. PMC 2963518. PMID [44] ""Diabetes Care” January 2010”. American Diabetes As-
20693348. sociation. Retrieved 2010-01-29.

[32] Hu EA, Pan A, Malik V, Sun Q (2012-03-15). “White [45] Saydah SH, Miret M, Sung J, Varas C, Gause D, Bran-
rice consumption and risk of type 2 diabetes: meta- cati FL (August 2001). “Postchallenge hyperglycemia and
analysis and systematic review”. BMJ (Clinical research mortality in a national sample of U.S. adults”. Diabetes
ed.) 344: e1454. doi:10.1136/bmj.e1454. PMC Care 24 (8): 1397–402. doi:10.2337/diacare.24.8.1397.
3307808. PMID 22422870. PMID 11473076.

[33] Lee IM, Shiroma EJ, Lobelo F, Puska P, Blair SN, Katz- [46] Definition and diagnosis of diabetes mellitus and interme-
marzyk PT (1 July 2012). “Effect of physical inactivity on diate hyperglycemia : report of a WHO/IDF consultation
major non-communicable diseases worldwide: an analysis (PDF). World Health Organization. 2006. p. 21. ISBN
of burden of disease and life expectancy”. The Lancet 380 978-92-4-159493-6.
296 CHAPTER 17. INTEGRATION OF METABOLISM

[47] Santaguida PL, Balion C, Hunt D, Morrison K, Gerstein [59] Krentz, AJ; Bailey, CJ (2005). “Oral antidiabetic
H, Raina P, Booker L, Yazdi H. “Diagnosis, Progno- agents: current role in type 2 diabetes mellitus.”. Drugs
sis, and Treatment of Impaired Glucose Tolerance and 65 (3): 385–411. doi:10.2165/00003495-200565030-
Impaired Fasting Glucose”. Summary of Evidence Re- 00005. PMID 15669880.
port/Technology Assessment, No. 128. Agency for Health-
care Research and Quality. Retrieved 2008-07-20. [60] Consumer Reports; American College of Physicians
(April 2012), “Choosing a type 2 diabetes drug - Why
[48] Bartoli E, Fra GP, Carnevale Schianca GP (Feb 2011). the best first choice is often the oldest drug” (PDF), High
“The oral glucose tolerance test (OGTT) revisited.”. Value Care (Consumer Reports), retrieved August 14,
European journal of internal medicine 22 (1): 8–12. 2012
doi:10.1016/j.ejim.2010.07.008. PMID 21238885.
[61] Nelson, Mark. “Drug treatment of elevated blood pres-
[49] Selvin E, Steffes MW, Zhu H, Matsushita K, Wa- sure”. Australian Prescriber (33): 108–112. Retrieved 11
genknecht L, Pankow J, Coresh J, Brancati FL (2010). August 2010.
“Glycated hemoglobin, diabetes, and cardiovascular risk
in nondiabetic adults”. N. Engl. J. Med. 362 (9): 800–11. [62] Shaw, Gina (2009-03-07). “Prehypertension: Early-stage
doi:10.1056/NEJMoa0908359. PMC 2872990. PMID High Blood Pressure”. WebMD. Retrieved 3 July 2009.
20200384.
[63] Arguedas, JA; Perez, MI; Wright, JM (Jul 8,
[50] “The Nutrition Source”. Harvard School of Public Health. 2009). Arguedas, Jose Agustin, ed. “Treatment
Retrieved 24 April 2014. blood pressure targets for hypertension”. Cochrane
Database of Systematic Reviews (3): CD004349.
[51] Willi C, Bodenmann P, Ghali WA, Faris PD, Cornuz J doi:10.1002/14651858.CD004349.pub2. PMID
(Dec 12, 2007). “Active smoking and the risk of type 2 19588353.
diabetes: a systematic review and meta-analysis.”. JAMA:
the Journal of the American Medical Association 298 [64] Arguedas, JA; Leiva, V; Wright, JM (Oct 30,
(22): 2654–64. doi:10.1001/jama.298.22.2654. PMID 2013). “Blood pressure targets for hypertension
18073361. in people with diabetes mellitus.”. The Cochrane
database of systematic reviews 10: CD008277.
[52] No cure for diabetes (Retrieved May 2015, WebMD web- doi:10.1002/14651858.cd008277.pub2. PMID
site) 24170669.

[53] Nathan DM, Cleary PA, Backlund JY, Genuth SM, [65] Cheng J, Zhang W, Zhang X, Han F, Li X, He
Lachin JM, Orchard TJ, Raskin P, Zinman B (Decem- X, Li Q, Chen J (Mar 31, 2014). “Effect of
ber 2005). “Intensive diabetes treatment and cardio- Angiotensin-Converting Enzyme Inhibitors and
vascular disease in patients with type 1 diabetes”. The Angiotensin II Receptor Blockers on All-Cause
New England Journal of Medicine 353 (25): 2643–53. Mortality, Cardiovascular Deaths, and Cardiovas-
doi:10.1056/NEJMoa052187. PMC 2637991. PMID cular Events in Patients With Diabetes Mellitus: A
16371630. Meta-analysis.”. JAMA internal medicine 174 (5):
773–85. doi:10.1001/jamainternmed.2014.348. PMID
[54] The Diabetes Control and Complications Trial Re- 24687000.
search Group (April 1995). “The effect of inten-
sive diabetes therapy on the development and progres- [66] Pignone M, Alberts MJ, Colwell JA, Cushman M, Inzuc-
sion of neuropathy.”. Annals of Internal Medicine 122 chi SE, Mukherjee D, Rosenson RS, Williams CD, Wil-
(8): 561–8. doi:10.1059/0003-4819-122-8-199504150- son PW, Kirkman MS (June 2010). “Aspirin for primary
00001. PMID 7887548. prevention of cardiovascular events in people with dia-
betes: a position statement of the American Diabetes As-
[55] National Institute for Health and Clinical Excellence. sociation, a scientific statement of the American Heart
Clinical guideline 66: Type 2 diabetes. London, 2008. Association, and an expert consensus document of the
American College of Cardiology Foundation”. Diabetes
[56] Cavanagh PR (2004). “Therapeutic footwear for people Care 33 (6): 1395–402. doi:10.2337/dc10-0555. PMC
with diabetes”. Diabetes Metab. Res. Rev. 20 (Suppl 1): 2875463. PMID 20508233.
S51–5. doi:10.1002/dmrr.435. PMID 15150815.
[67] “Pancreas Transplantation”. American Diabetes Associ-
[57] Adler AI, Stratton IM, Neil HA, Yudkin JS, Matthews ation. Retrieved 9 April 2014.
DR, Cull CA, Wright AD, Turner RC, Holman RR
(August 2000). “Association of systolic blood pres- [68] Picot, J; Jones, J; Colquitt, JL; Gospodarevskaya, E; Love-
sure with macrovascular and microvascular compli- man, E; Baxter, L; Clegg, AJ (September 2009). “The
cations of type 2 diabetes (UKPDS 36): prospec- clinical effectiveness and cost-effectiveness of bariatric
tive observational study”. BMJ 321 (7258): 412–9. (weight loss) surgery for obesity: a systematic review
doi:10.1136/bmj.321.7258.412. PMC 27455. PMID and economic evaluation”. Health technology assessment
10938049. (Winchester, England) 13 (41): 1–190, 215–357, iii–iv.
doi:10.3310/hta13410. PMID 19726018.
[58] Ripsin CM, Kang H, Urban RJ (2009). “Management of
blood glucose in type 2 diabetes mellitus” (PDF). Ameri- [69] Frachetti, KJ; Goldfine, AB (April 2009). “Bariatric
can family physician 79 (1): 29–36. PMID 19145963. surgery for diabetes management”. Current Opinion
17.3. DIABETES MELLITUS 297

in Endocrinology, Diabetes and Obesity 16 (2): 119– [83] Oxford English Dictionary. mellite. Retrieved 2011-06-
24. doi:10.1097/MED.0b013e32832912e7. PMID 10.
19276974.
[84] “MyEtimology. mellitus.". Retrieved 2011-06-10.
[70] Schulman, AP; del Genio, F, Sinha, N, Rubino, F
(September–October 2009). ""Metabolic” surgery for [85] Oxford English Dictionary. -ite. Retrieved 2011-06-10.
treatment of type 2 diabetes mellitus”. Endocrine practice
: official journal of the American College of Endocrinol-
[86] Theodore H. Tulchinsky, Elena A. Varavikova (2008).
ogy and the American Association of Clinical Endocrinolo-
The New Public Health, Second Edition. New York:
gists 15 (6): 624–31. doi:10.4158/EP09170.RAR. PMID
Academic Press. p. 200. ISBN 0-12-370890-7.
19625245.

[71] Colucci, RA (January 2011). “Bariatric surgery [87] Piwernetz K, Home PD, Snorgaard O, Antsiferov M,
in patients with type 2 diabetes: a viable op- Staehr-Johansen K, Krans M (May 1993). “Monitoring
tion”. Postgraduate Medicine 123 (1): 24–33. the targets of the St Vincent Declaration and the imple-
doi:10.3810/pgm.2011.01.2242. PMID 21293081. mentation of quality management in diabetes care: the DI-
ABCARE initiative. The DIABCARE Monitoring Group
[72] Dixon, JB; le Roux, CW; Rubino, F; Zimmet, P (16 June of the St Vincent Declaration Steering Committee”. Di-
2012). “Bariatric surgery for type 2 diabetes”. Lancet 379 abetic Medicine 10 (4): 371–7. doi:10.1111/j.1464-
(9833): 2300–11. doi:10.1016/S0140-6736(12)60401- 5491.1993.tb00083.x. PMID 8508624.
2. PMID 22683132.
[88] Dubois, HFW and Bankauskaite, V (2005). “Type 2 di-
[73] Polisena J, Tran K, Cimon K, Hutton B, McGill S, abetes programmes in Europe” (PDF). Euro Observer 7
Palmer K (2009). “Home telehealth for diabetes man- (2): 5–6.
agement: a systematic review and meta-analysis”. Dia-
betes Obes Metab 11 (10): 913–30. doi:10.1111/j.1463- [89] Stewart WF, Ricci JA, Chee E, Hirsch AG, Branden-
1326.2009.01057.x. PMID 19531058. burg NA (June 2007). “Lost productive time and costs
[74] Mathers CD, Loncar D (November 2006). “Projections due to diabetes and diabetic neuropathic pain in the
of global mortality and burden of disease from US workforce”. J. Occup. Environ. Med. 49 (6):
2002 to 2030”. PLoS Med. 3 (11): e442. 672–9. doi:10.1097/JOM.0b013e318065b83a. PMID
doi:10.1371/journal.pmed.0030442. PMC 1664601. 17563611.
PMID 17132052.
[90] Washington R.E., Andrews R.M., Mutter R.L. (Novem-
[75] Wild S, Roglic G, Green A, Sicree R, King H (2004). ber 2013). “Emergency Department Visits for Adults with
“Global prevalence of diabetes: Estimates for the year Diabetes, 2010”. HCUP Statistical Brief #167. Rockville
2000 and projections for 2030”. Diabetes Care 27 MD: Agency for Healthcare Research and Quality.
(5): 1047–53. doi:10.2337/diacare.27.5.1047. PMID
15111519. [91] Parker, Katrina (2008). Living with diabetes. New York:
Facts On File. p. 143. ISBN 9781438121086.
[76] Ripoll, Brian C. Leutholtz, Ignacio (2011-04-25).
Exercise and disease management (2nd ed.). Boca Raton: [92] “Diabetes mellitus”. Merck Veterinary Manual, 9th edition
CRC Press. p. 25. ISBN 978-1-4398-2759-8. (online version). 2005. Retrieved 2011-10-23.
[77] editor, Leonid Poretsky, (2009). Principles of diabetes
mellitus (2nd ed.). New York: Springer. p. 3. ISBN [93] Maria Rotella C, Pala L, Mannucci E (Summer
978-0-387-09840-1. 2013). “Role of Insulin in the Type 2 Diabetes Ther-
apy: Past, Present and Future.”. International jour-
[78] Laios K, Karamanou M, Saridaki Z, Androutsos G nal of endocrinology and metabolism 11 (3): 137–
(2012). “Aretaeus of Cappadocia and the first descrip- 144. doi:10.5812/ijem.7551. PMC 3860110. PMID
tion of diabetes”. Hormones 11 (1): 109–113. PMID 24348585.
22450352.
[94] http://www.fda.gov/NewsEvents/Newsroom/
[79] Oxford English Dictionary. diabetes. Retrieved 2011-06- PressAnnouncements/ucm403122.htm
10.
[95] “Inhaled Insulin Clears Hurdle Toward F.D.A. Approval”.
[80] Harper, Douglas (2001–2010). “Online Etymology Dic-
New York Times. Retrieved 12 April 2014.
tionary. diabetes.". Retrieved 2011-06-10.

[81] Dallas, John (2011). “Royal College of Physicians of Ed-

inburgh. Diabetes, Doctors and Dogs: An exhibition on 17.3.13 Further reading
Diabetes and Endocrinology by the College Library for
the 43rd St. Andrew’s Day Festival Symposium”.
• Polonsky KS (2012). “The Past 200 Years in Dia-
[82] Aretaeus, De causis et signis acutorum morborum (lib. 2), betes”. New England Journal of Medicine 367 (14):
Κεφ. β. περὶ Διαβήτεω (Chapter 2, On Diabetes, Greek 1332–40. doi:10.1056/NEJMra1110560. PMID
original, on Perseus 23034021.
298 CHAPTER 17. INTEGRATION OF METABOLISM

17.3.14 External links

• Diabetes at the Open Directory Project
• IDF Diabetes Atlas

• National Diabetes Education Program

Chapter 18

Informational Macromolecules

299
Chapter 19

DNA synthesis and repair

19.1 DNA replication biological process occurs in all living organisms and is
the basis for biological inheritance. DNA is made up
of two strands and each strand of the original DNA
molecule serves as a template for the production of
the complementary strand, a process referred to as
G C
semiconservative replication. Cellular proofreading and
error-checking mechanisms ensure near perfect fidelity
C G
for DNA replication.[1][2]
C G
A T In a cell, DNA replication begins at specific locations,
or origins of replication, in the genome.[3] Unwinding of
DNA at the origin and synthesis of new strands results in
G C replication forks growing bidirectional from the origin.
A number of proteins are associated with the replication
T A
fork which helps in terms of the initiation and continu-
T A
ation of DNA synthesis. Most prominently, DNA poly-
C G merase synthesizes the new DNA by adding complemen-
tary nucleotides to the template strand.
A T DNA replication can also be performed in vitro (artifi-
G C cially, outside a cell). DNA polymerases isolated from
A T cells and artificial DNA primers can be used to initiate
G C C DNA synthesis at known sequences in a template DNA
T A T A molecule. The polymerase chain reaction (PCR), a com-
T A T A mon laboratory technique, cyclically applies such artifi-
C C G
cial synthesis to amplify a specific target DNA fragment
C
from a pool of DNA.

G C G
A
T A 19.1.1 Background on DNA structure
A T
A T
A T A T DNA usually exists as a double-stranded structure, with
both strands coiled together to form the characteristic
G C double-helix. Each single strand of DNA is a chain of
G C four types of nucleotides. Nucleotides in DNA con-
A T
A T tain a deoxyribose sugar, a phosphate, and a nucleobase.
T A The four types of nucleotide correspond to the four
T A
G nucleobases adenine, cytosine, guanine, and thymine,
G C
commonly abbreviated as A,C, G and T. Adenine and
guanine are purine bases, while cytosine and thymine
DNA replication. The double helix is unwound and each strand are pyrimidines. These nucleotides form phosphodiester
acts as a template for the next strand. Bases are matched to syn- bonds, creating the phosphate-deoxyribose backbone of
thesize the new partner strands. the DNA double helix with the nucleobases pointing in-
ward. Nucleotides (bases) are matched between strands
DNA replication is the process of producing two iden- through hydrogen bonds to form base pairs. Adenine
tical replicas from one original DNA molecule. This pairs with thymine (two hydrogen bonds), and guanine

300
19.1. DNA REPLICATION 301

pairs with cytosine (stronger: three hydrogen bonds). DNA polymerase P P P

T nucleoside
triphosphate
DNA strands have a directionality, and the different ends
5'
of a single strand are called the “3' (three-prime) end” and P P P P P 3'
T G G A C
the “5' (five-prime) end”. By convention, if the base se-
A P C P C P T G A P C P G P G P
quence of a single strand of DNA is given, the left end of P P P
5'
3'
the sequence is 5' end, while the right end of the sequence
is the 3' end. The strands of the double helix are anti- Extension
parallel with one being 5' to 3', and the opposite strand 3'
P P P
to 5'. These terms refer to the carbon atom in deoxyri- P P
A

bose to which the next phosphate in the chain attaches. 5'

3'
Directionality has consequences in DNA synthesis, be- P
T
P
G
P
G
P
A
P
C
P
T
cause DNA polymerase can synthesize DNA in only one P
A P C P C P T
P
G
P
A P C P G P G P
5'
direction by adding nucleotides to the 3' end of a DNA 3'
strand.
The pairing of complementary bases in DNA through
Extension
hydrogen bonding means that the information contained
P P
(error)
within each strand is redundant. The nucleotides on a 5' 3'
P P P P P P P A
single strand can be used to reconstruct nucleotides on a T G G A C T

newly synthesized partner strand.[4] P

A P C P C P T
P
G
P
A P C P G P G P
5'
3'

19.1.2 DNA polymerase Proofreading

P P P
A P
G
Main article: DNA polymerase
5'
DNA polymerases are a family of enzymes that carry P P P P P P 3'
T G G A C T
out all forms of DNA replication.[6] DNA polymerases in
A P C P C P T G A P C P G P G P
general cannot initiate synthesis of new strands, but can 3'
P P P
5'
only extend an existing DNA or RNA strand paired with
a template strand. To begin synthesis, a short fragment of
DNA, called a primer, must be created and paired with P P
Extension
the template DNA strand. 5'
P P P P P P P 3'
DNA polymerase adds a new strand of DNA by extend- T G G A C T G

ing the 3' end of an existing nucleotide chain, adding P

A P C P C P T
P
G
P
A P C P G P G P
5'
new nucleotides matched to the template strand one at 3'

a time via the creation of phosphodiester bonds. The

energy for this process of DNA polymerization comes DNA polymerases adds nucleotides to the 3' end of a strand of
from hydrolysis of the high-energy phosphate (phospho- DNA.[5] If a mismatch is accidentally incorporated, the poly-
anhydride) bonds between the three phosphates attached merase is inhibited from further extension. Proofreading re-
moves the mismatched nucleotide and extension continues.
to each unincorporated base. (Free bases with their at-
tached phosphate groups are called nucleotides; in par-
ticular, bases with three attached phosphate groups are
called nucleoside triphosphates.) When a nucleotide
is being added to a growing DNA strand, the forma-
tion of a phosphodiester bond between the proximal
phosphate of the nucleotide to the growing chain is ac- mismatch repair mechanisms monitor the DNA for er-
companied by hydrolysis of a high-energy phosphate rors, being capable of distinguishing mismatches in the
bond with release of the two distal phosphates as a newly synthesized DNA strand from the original strand
pyrophosphate. Enzymatic hydrolysis of the resulting py- sequence. Together, these three discrimination steps en-
rophosphate into inorganic phosphate consumes a second able replication fidelity of less than one mistake for every
high-energy phosphate bond and renders the reaction ef- 109 nucleotides added.[7]
fectively irreversible.[Note 1] The rate of DNA replication in a living cell was first mea-
In general, DNA polymerases are highly accurate, with sured as the rate of phage T4 DNA elongation in phage-
an intrinsic error rate of less than one mistake for every infected E. coli.[8] During the period of exponential DNA
107 nucleotides added.[7] In addition, some DNA poly- increase at 37 °C, the rate was 749 nucleotides per sec-
merases also have proofreading ability; they can remove ond. The mutation rate per base pair per replication dur-
nucleotides from the end of a growing strand in order ing phage T4 DNA synthesis is 1.7 per 108 .[9] Thus DNA
to correct mismatched bases. Finally, post-replication replication is both impressively fast and accurate.
302 CHAPTER 19. DNA SYNTHESIS AND REPAIR

19.1.3 Replication process known as "origins", which are targeted by initiator pro-
teins.[3] In E. coli this protein is DnaA; in yeast, this is
Main articles: Prokaryotic DNA replication and the origin recognition complex.[11] Sequences used by ini-
Eukaryotic DNA replication tiator proteins tend to be “AT-rich” (rich in adenine and
thymine bases), because A-T base pairs have two hydro-
DNA Replication, like all biological polymerization pro- gen bonds (rather than the[12] three formed in a C-G pair)
cesses, proceeds in three enzymatically catalyzed and co- which are easier to unzip. Once the origin has been
ordinated steps: initiation, elongation and termination. located, these initiators recruit other proteins and form
the pre-replication complex, which unzips the double-
stranded DNA.
Initiation

Elongation

DNA polymerase has 3'−5' activity. All known DNA

replication systems require a free 3' hydroxyl group be-
fore synthesis can be initiated (Important note: DNA is
read in 3' to 5' direction whereas a new strand is synthe-
sized in the 5' to 3' direction—this is often confused).
Four distinct mechanisms for synthesis are as follows:

1. All cellular life forms and many DNA viruses,

phages and plasmids use a primase to synthesize a
short RNA primer with a free 3' OH group which is
subsequently elongated by a DNA polymerase.

2. The retroelements (including retroviruses) employ a

transfer RNA that primes DNA replication by pro-
viding a free 3′ OH that is used for elongation by the
reverse transcriptase.

3. In the adenoviruses and the φ29 family of

bacteriophages, the 3' OH group is provided by the
side chain of an amino acid of the genome attached
protein (the terminal protein) to which nucleotides
are added by the DNA polymerase to form a new
strand.

4. In the single stranded DNA viruses — a group

that includes the circoviruses, the geminiviruses, the
parvoviruses and others — and also the many phages
and plasmids that use the rolling circle replication
Role of initiators for initiation of DNA replication.
(RCR) mechanism, the RCR endonuclease creates
a nick in the genome strand (single stranded viruses)
or one of the DNA strands (plasmids). The 5′ end of
the nicked strand is transferred to a tyrosine residue
on the nuclease and the free 3′ OH group is then
used by the DNA polymerase to synthesize the new
strand.

The first is the best known of these mechanisms and

is used by the cellular organisms. In this mechanism,
once the two strands are separated, primase adds RNA
primers to the template strands. The leading strand re-
ceives one RNA primer while the lagging strand receives
Formation of pre-replication complex. several. The leading strand is continuously extended from
the primer by a high processivity, replicative DNA poly-
For a cell to divide, it must first replicate its DNA.[10] merase, while the lagging strand is extended discontin-
This process is initiated at particular points in the DNA, uously from each primer, forming Okazaki fragments.
19.1. DNA REPLICATION 303

RNase removes the primer RNA fragments, and a low

processivity DNA polymerase distinct from the replica-
tive polymerase enters to fill the gaps. When this is com-
plete, a single nick on the leading strand and several nicks
on the lagging strand can be found. Ligase works to fill
these nicks in, thus completing the newly replicated DNA
molecule.
The primase used in this process differs significantly
between bacteria and archaea/eukaryotes. Bacteria use
a primase belonging to the DnaG protein superfam-
ily which contains a catalytic domain of the TOPRIM
fold type.[13] The TOPRIM fold contains an α/β core Scheme of the replication fork.
with four conserved strands in a Rossmann-like topol- a: template, b: leading strand, c: lagging strand, d: replication
ogy. This structure is also found in the catalytic domains fork, e: primer, f: Okazaki fragments
of topoisomerase Ia, topoisomerase II, the OLD-family
nucleases and DNA repair proteins related to the RecR DNA-ligase
DNA primase
RNA primer

protein. DNA-Polymerase (Polα)

3’

The primase used by archaea and eukaryotes in contrast Lagging

strand 3’

contains a highly derived version of the RNA recogni- 5’

Okazaki fragment

tion motif (RRM). This primase is structurally similar 5’

Leading
5’
strand
to many viral RNA dependent RNA polymerases, re- 3’
Topoisomerase

DNA Polymerase (Polδ)

verse transcriptases, cyclic nucleotide generating cyclases Helicase
Single strand,
and DNA polymerases of the A/B/Y families that are Binding proteins

involved in DNA replication and repair. In eukaryotic

replication, the primase forms a complex with Pol α.[14] Many enzymes are involved in the DNA replication fork.
Multiple DNA polymerases take on different roles in the
DNA replication process. In E. coli, DNA Pol III is the Replication fork
polymerase enzyme primarily responsible for DNA repli-
cation. It assembles into a replication complex at the The replication fork is a structure that forms within the
replication fork that exhibits extremely high processivity, nucleus during DNA replication. It is created by heli-
remaining intact for the entire replication cycle. In con- cases, which break the hydrogen bonds holding the two
trast, DNA Pol I is the enzyme responsible for replac- DNA strands together. The resulting structure has two
ing RNA primers with DNA. DNA Pol I has a 5' to 3' branching “prongs”, each one made up of a single strand
exonuclease activity in addition to its polymerase activ- of DNA. These two strands serve as the template for
ity, and uses its exonuclease activity to degrade the RNA the leading and lagging strands, which will be created as
primers ahead of it as it extends the DNA strand behind it, DNA polymerase matches complementary nucleotides to
in a process called nick translation. Pol I is much less pro- the templates; the templates may be properly referred to
cessive than Pol III because its primary function in DNA as the leading strand template and the lagging strand tem-
replication is to create many short DNA regions rather plate.
than a few very long regions.
DNA is always synthesized in the 5' to 3' direction.
In eukaryotes, the low-processivity enzyme, Pol α, helps Since the leading and lagging strand templates are ori-
to initiate replication. The high-processivity extension ented in opposite directions at the replication fork, a ma-
enzymes are Pol δ and Pol ε. jor issue is how to achieve synthesis of nascent (new) lag-
As DNA synthesis continues, the original DNA strands ging strand DNA, whose direction of synthesis is opposite
continue to unwind on each side of the bubble, forming to the direction of the growing replication fork.
a replication fork with two prongs. In bacteria, which
have a single origin of replication on their circular chro-
mosome, this process creates a "theta structure" (resem- Leading strand The leading strand is the strand of
bling the Greek letter theta: θ). In contrast, eukaryotes nascent DNA which is being synthesized in the same di-
have longer linear chromosomes and initiate replication rection as the growing replication fork. A polymerase
at multiple origins within these.[15] “reads” the leading strand template and adds complemen-
tary nucleotides to the nascent leading strand on a contin-
uous basis.
The polymerase involved in leading strand synthesis is
DNA polymerase III (DNA Pol III) in prokaryotes and
presumably Pol ε[7][16] in yeasts. In human cells the
304 CHAPTER 19. DNA SYNTHESIS AND REPAIR

leading and lagging strands are synthesized by Pol ε and of the replication fork. Topoisomerases are enzymes that
Pol δ, respectively, within the nucleus and Pol γ in the temporarily break the strands of DNA, relieving the ten-
mitochondria.[17] Pol ε can substitute for Pol δ in special sion caused by unwinding the two strands of the DNA he-
circumstances.[18] lix; topoisomerases (including DNA gyrase) achieve this
by adding negative supercoils to the DNA helix.[22]
Lagging strand The lagging strand is the strand of Bare single-stranded DNA tends to fold back on itself
nascent DNA whose direction of synthesis is opposite to forming secondary structures; these structures can inter-
the direction of the growing replication fork. Because of fere with the movement of DNA polymerase. To prevent
its orientation, replication of the lagging strand is more this, single-strand binding proteins bind to the DNA un-
complicated as compared to that of the leading strand. til a second strand is synthesized, preventing secondary
structure formation.[23]
The lagging strand is synthesized in short, separated seg-
ments. On the lagging strand template, a primase “reads” Clamp proteins form a sliding clamp around DNA, help-
the template DNA and initiates synthesis of a short com- ing the DNA polymerase maintain contact with its tem-
plementary RNA primer. A DNA polymerase extends plate, thereby assisting with processivity. The inner face
the primed segments, forming Okazaki fragments. The of the clamp enables DNA to be threaded through it.
RNA primers are then removed and replaced with DNA, Once the polymerase reaches the end of the template
and the fragments of DNA are joined together by DNA or detects double-stranded DNA, the sliding clamp un-
ligase. dergoes a conformational change that releases the DNA
polymerase. Clamp-loading proteins are used to initially
In eukaryotes, primase is intrinsic to Pol α.[19] DNA load the clamp, recognizing the junction between tem-
polymerase III (in prokaryotes) or Pol δ/Pol ε (in eu- plate and RNA primers.[2]:274-5
karyotes) is/are responsible for extension of the primed
segments. Primer removal in eukaryotes is also per-
formed by Pol δ.[20] In prokaryotes, primer removal is DNA replication proteins
performed by DNA polymerase I, which “reads” the frag-
ments, removes the RNA using its flap endonuclease do- At the replication fork, many replication enzymes assem-
main (RNA primers are removed by 5'−3' exonucle- ble on the DNA into a complex molecular machine called
ase activity of polymerase I, and replaces the RNA nu- the replisome. The following is a list of major DNA repli-
cleotides with DNA nucleotides.) cation enzymes that participate in the replisome:[24]

Replication machinery

Replication machineries consist of factors involved in

DNA replication and appearing on template ssDNAs.
Replication machineries include primosomes also. The
factors are replication enzymes; DNA polymerase, DNA
helicases, DNA clamps and DNA topoisomerases, and
replication proteins; e.g. single-stranded DNA bind-
ing proteins (SSB). In the replication machineries these
components coordinate. In most of the bacteria, all of
the factors involved in DNA replication are located on
replication forks and the complexes stay on the forks
during DNA replication. This replication machineries
are called replisomes or DNA replicase systems, these
terms mean originally a generic term for proteins located
on replication forks. In eukaryotic and some bacterial
cells the replisomes are not formed.
Since replication machineries do not move relatively to
template DNAs such as factories, they are called repli-
cation factory.[26] In an alternative figure, DNA facto-
The assembled human DNA clamp, a trimer of the protein PCNA. ries are similar to projectors and DNAs are like as cin-
ematic films passing constantly into the projectors. In
Dynamics at the replication fork As helicase un- the replication factory model, after both DNA helicases
winds DNA at the replication fork, the DNA ahead is for leading stands and lagging strands are loaded on the
forced to rotate. This process results in a build-up of template DNAs, the helicases run along the DNAs into
twists in the DNA ahead.[21] This build-up forms a tor- each other. The helicases remain associated for the re-
sional resistance that would eventually halt the progress mainder of replication process. Peter Meister et al. ob-
19.1. DNA REPLICATION 305

served directly replication sites in budding yeast by moni- tion of replication occurs when the two replication forks
toring green fluorescent protein(GFP)-tagged DNA poly- meet each other on the opposite end of the parental chro-
merases α. They detected DNA replication of pairs of the mosome. E. coli regulates this process through the use
tagged loci spaced apart symmetrically from a replication of termination sequences that, when bound by the Tus
origin and found that the distance between the pairs de- protein, enable only one direction of replication fork to
creased markedly by time.[27] This finding suggests that pass through. As a result, the replication forks are con-
the mechanism of DNA replication goes with DNA fac- strained to always meet within the termination region of
tories. Suggesting, couples of replication factories are the chromosome.[28]
loaded on replication origins and the factories associated
with each other. Also, template DNAs move into the fac-
tories, which bring extrusion of the template ssDNAs and 19.1.4 Regulation
nascent DNAs. Peter’s finding is the first direct evidence
of replication factory model. By later researches, it is
revealed that DNA helicases form dimers in many eu-
karyotic cells and bacterial replication machineries stay
in single intranuclear location during DNA synthesis.[26]
The replication factories perform disentanglement of sis-
ter chromatids. The disentanglement is essential to dis-
tribute the chromatids into daughter cells after DNA
replication. Because sister chromatids after DNA repli-
cation hold each other by Cohesin rings, there is the only
chance for the disentanglement in DNA replication. Fix-
ing of replication machineries as replication factories can
improve a success rate of DNA replication. If replication
forks move freely in chromosomes, catenation of nuclei
is aggravated and impedes mitotic segregation.[27]

Termination

Eukaryotes initiate DNA replication at multiple points in

the chromosome, so replication forks meet and terminate The cell cycle of eukaryotic cells.
at many points in the chromosome; these are not known
to be regulated in any particular way. Because eukaryotes
have linear chromosomes, DNA replication is unable to Eukaryotes
reach the very end of the chromosomes, but ends at the
telomere region of repetitive DNA close to the end. This Within eukaryotes, DNA replication is controlled within
shortens the telomere of the daughter DNA strand. Short- the context of the cell cycle. As the cell grows and
ening of the telomeres is a normal process in somatic divides, it progresses through stages in the cell cycle;
cells. As a result, cells can only divide a certain num- DNA replication takes place during the S phase (synthe-
ber of times before the DNA loss prevents further divi- sis phase). The progress of the eukaryotic cell through
sion. (This is known as the Hayflick limit.) Within the the cycle is controlled by cell cycle checkpoints. Progres-
germ cell line, which passes DNA to the next generation, sion through checkpoints is controlled through complex
telomerase extends the repetitive sequences of the telom- interactions between various proteins, including cyclins
ere region to prevent degradation. Telomerase can be- and cyclin-dependent kinases.[29]
come mistakenly active in somatic cells, sometimes lead-
ing to cancer formation. Increased telomerase activity is The G1/S checkpoint (or restriction checkpoint) regu-
one of the Hallmarks of cancer. lates whether eukaryotic cells enter the process of DNA
replication and subsequent division. Cells that do not pro-
Termination requires that the progress of the DNA repli- ceed through this checkpoint remain in the G0 stage and
cation fork must stop or be blocked. Termination at a do not replicate their DNA.
specific locus, when it occurs, involves the interaction be-
tween two components: (1) a termination site sequence in Replication of chloroplast and mitochondrial genomes
the DNA, and (2) a protein which binds to this sequence occurs independently of the cell cycle, through the pro-
to physically stop DNA replication. In various bacterial cess of D-loop replication.
species, this is named the DNA replication terminus site-
binding protein, or Ter protein. Replication focus In vertebrate cells, replication sites
Because bacteria have circular chromosomes, termina- concentrate into positions called replication foci.[27]
306 CHAPTER 19. DNA SYNTHESIS AND REPAIR

Replication sites can be detected by immunostaining

daughter strands and replication enzymes and monitor-
ing GFP-tagged replication factors. By these methods it
is found that replication foci of varying size and positions
appear in S phase of cell division and their number per
nucleus is far smaller than the number of genomic repli-
cation forks.
P. Heun et al.(2001) tracked GFP-tagged replication foci
in budding yeast cells and revealed that replication origins
move constantly in G1 and S phase and the dynamics de-
creased significantly in S phase.[27] Traditionally, repli-
cation sites were fixed on spatial structure of chromo-
somes by nuclear matrix or lamins. The Heun’s results
denied the traditional concepts, budding yeasts don't have
lamins, and support that replication origins self-assemble
and form replication foci.
By firing of replication origins, controlled spatially and
temporally, the formation of replication foci is regulated.
D. A. Jackson et al.(1998) revealed that neighboring ori-
gins fire simultaneously in mammalian cells.[27] Spatial
juxtaposition of replication sites brings clustering of
replication forks. The clustering do rescue of stalled
replication forks and favors normal progress of repli-
cation forks. Progress of replication forks is inhibited by
many factors; collision with proteins or with complexes
binding strongly on DNA, deficiency of dNTPs, nicks on
template DNAs and so on. If replication forks stall and
remaining sequences from the stalled forks are not repli-
cated, daughter strands have nick obtained un-replicated
sites. The un-replicated sites on one parents strand hold
other strand together but not daughter strands. There-
fore, resulting sister chromatids cannot separate together
Dam methylates adenine of GATC sites after replication.
and cannot divide into 2 daughter cells. When neighbor-
ing origins fire and a fork from one origin is stalled, fork
from other origin access on an opposite direction of the
tion, DnaA (required for initiation of replication) binds
stalled fork and duplicate the un-replicated sites. As other
less well to hemimethylated DNA. As a result, newly
mechanism of the rescue there is application of dormant
replicated origins are prevented from immediately initi-
replication origins that excess origins don't fire in nor-
ating another round of DNA replication.[31]
mal DNA replication.
ATP builds up when the cell is in a rich medium, trigger-
ing DNA replication once the cell has reached a specific
Bacteria size. ATP competes with ADP to bind to DnaA, and the
DnaA-ATP complex is able to initiate replication. A cer-
tain number of DnaA proteins are also required for DNA
Most bacteria do not go through a well-defined cell cy-
replication — each time the origin is copied, the number
cle but instead continuously copy their DNA; during
of binding sites for DnaA doubles, requiring the synthesis
rapid growth, this can result in the concurrent occur-
[30] of more DnaA to enable another initiation of replication.
rence of multiple rounds of replication. In E. coli, the
best-characterized bacteria, DNA replication is regulated
through several mechanisms, including: the hemimethy-
lation and sequestering of the origin sequence, the ratio of 19.1.5 Polymerase chain reaction
adenosine triphosphate (ATP) to adenosine diphosphate
(ADP), and the levels of protein DnaA. All these control Main article: Polymerase chain reaction
the binding of initiator proteins to the origin sequences.
Because E. coli methylates GATC DNA sequences, DNA Researchers commonly replicate DNA in vitro using the
synthesis results in hemimethylated sequences. This polymerase chain reaction (PCR). PCR uses a pair of
hemimethylated DNA is recognized by the protein SeqA, primers to span a target region in template DNA, and then
which binds and sequesters the origin sequence; in addi- polymerizes partner strands in each direction from these
19.1. DNA REPLICATION 307

primers using a thermostable DNA polymerase. Repeat- [7] McCulloch SD, Kunkel TA (January 2008). “The fi-
ing this process through multiple cycles amplifies the tar- delity of DNA synthesis by eukaryotic replicative and
geted DNA region. At the start of each cycle, the mixture translesion synthesis polymerases”. Cell Research 18 (1):
of template and primers is heated, separating the newly 148–61. doi:10.1038/cr.2008.4. PMC 3639319. PMID
synthesized molecule and template. Then, as the mixture 18166979.
cools, both of these become templates for annealing of [8] McCarthy D, Minner C, Bernstein H, Bernstein C (1976).
new primers, and the polymerase extends from these. As “DNA elongation rates and growing point distributions
a result, the number of copies of the target region doubles of wild-type phage T4 and a DNA-delay amber mu-
each round, increasing exponentially.[32] tant”. J Mol Biol 106 (4): 963–81. doi:10.1016/0022-
2836(76)90346-6. PMID 789903.

19.1.6 Notes [9] Drake JW (1970) The Molecular Basis of Mutation.

Holden-Day, San Francisco ISBN 0816224501 ISBN
[1] The energetics of this process may also help explain the 978-0816224500
directionality of synthesis—if DNA were synthesized in [10] Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Wal-
the 3' to 5' direction, the energy for the process would ter P (2002). Molecular Biology of the Cell. Garland Sci-
come from the 5' end of the growing strand rather than ence. ISBN 0-8153-3218-1. Chapter 5: DNA Replica-
from free nucleotides. The problem is that if the high tion Mechanisms
energy triphosphates were on the growing strand and not
on the free nucleotides, proof-reading by removing a mis- [11] Weigel C, Schmidt A, Rückert B, Lurz R, Messer W
matched terminal nucleotide would be problematic: Once (November 1997). “DnaA protein binding to individ-
a nucleotide is added, the triphosphate is lost and a single ual DnaA boxes in the Escherichia coli replication ori-
phosphate remains on the backbone between the new nu- gin, oriC”. The EMBO Journal 16 (21): 6574–83.
cleotide and the rest of the strand. If the added nucleotide doi:10.1093/emboj/16.21.6574. PMC 1170261. PMID
were mismatched, removal would result in a DNA strand 9351837.
terminated by a monophosphate at the end of the “growing
strand” rather than a high energy triphosphate. So strand [12] Lodish H, Berk A, Zipursky LS, Matsudaira P, Baltimore
would be stuck and wouldn't be able to grow anymore. In D, Darnell J (2000). Molecular Cell Biology. W. H. Free-
actuality, the high energy triphosphates hydrolyzed at each man and Company. ISBN 0-7167-3136-3.12.1. General
step originate from the free nucleotides, not the polymer- Features of Chromosomal Replication: Three Common
ized strand, so this issue does not exist. Features of Replication Origins

[13] Aravind, L.; Leipe, D. D.; Koonin, E. V. (1998).

“Toprim--a conserved catalytic domain in type IA and II
19.1.7 References topoisomerases, DnaG-type primases, OLD family nucle-
ases and RecR proteins”. Nucleic acids research 26 (18):
[1] Imperfect DNA replication results in mutations. Berg JM,
4205–4213. doi:10.1093/nar/26.18.4205. PMC 147817.
Tymoczko JL, Stryer L, Clarke ND (2002). "Chapter
PMID 9722641.
27: DNA Replication, Recombination, and Repair". Bio-
chemistry. W.H. Freeman and Company. ISBN 0-7167- [14] Frick, David; Richardson, Charles (July 2001). “DNA
3051-0. Primases”. Annual Review of Biochemistry 70: 39–
80. doi:10.1146/annurev.biochem.70.1.39. PMID
[2] Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Wal-
11395402.
ter P (2002). "Chapter 5: DNA Replication, Repair, and
Recombination". Molecular Biology of the Cell. Garland [15] Huberman JA, Riggs AD (1968). “On the mecha-
Science. ISBN 0-8153-3218-1. nism of DNA replication in mammalian chromosomes”.
J Mol Biol 32 (2): 327–341. doi:10.1016/0022-
[3] Berg JM, Tymoczko JL, Stryer L, Clarke ND (2002). 2836(68)90013-2. PMID 5689363.
"Chapter 27, Section 4: DNA Replication of Both Strands
Proceeds Rapidly from Specific Start Sites". Biochem- [16] Pursell, Z.F. et al. (2007). “Yeast DNA Polymerase ε Par-
istry. W.H. Freeman and Company. ISBN 0-7167-3051- ticipates in Leading-Strand DNA Replication”. Science
0. 317 (5834): 127–130. doi:10.1126/science.1144067.
PMC 2233713. PMID 17615360.
[4] Alberts, B., et al., Molecular Biology of the Cell, Garland
Science, 4th ed., 2002, pp. 238–240 ISBN 0-8153-3218- [17] Kunkel, Thomas (October 2011). “Balancing eukary-
1 otic replication asymmetry with replication fidelity”. Cur-
rent Opinions in Chemical Biology 15 (5): 620–626.
[5] Allison, Lizabeth A. Fundamental Molecular Biology. doi:10.1016/j.cbpa.2011.07.025.
Blackwell Publishing. 2007. p.112 ISBN 978-1-4051-
0379-4 [18] Hansen, Barbara (2011). Biochemistry and Medical Ge-
netics: Lecture Notes. Kaplan Medical. p. 21.
[6] Berg JM, Tymoczko JL, Stryer L, Clarke ND (2002). Bio-
chemistry. W.H. Freeman and Company. ISBN 0-7167- [19] Elizabeth R. Barry; Stephen D. Bell (December 2006).
3051-0. Chapter 27, Section 2: DNA Polymerases Re- “DNA Replication in the Archaea”. Microbiology
quire a Template and a Primer and Molecular Biology Reviews 70 (4): 876–887.
308 CHAPTER 19. DNA SYNTHESIS AND REPAIR

doi:10.1128/MMBR.00029-06. PMC 1698513. PMID [32] Saiki, RK; Gelfand DH; Stoffel S; Scharf SJ; Higuchi
17158702. R; Horn GT; Mullis KB; Erlich HA (1988). “Primer-
directed enzymatic amplification of DNA with a ther-
[20] Distinguishing the pathways of primer removal during Eu- mostable DNA polymerase”. Science 239 (4839): 487–
karyotic Okazaki fragment maturation Contributor Au- 91. doi:10.1126/science.2448875. PMID 2448875.
thor Rossi, Marie Louise. Date Accessioned: 2009-02-
23T17:05:09Z. Date Available: 2009-02-23T17:05:09Z.
Date Issued: 2009-02-23T17:05:09Z. Identifier Uri: http:
//hdl.handle.net/1802/6537. Description: Dr. Robert A.
19.2 DNA repair
Bambara, Faculty Advisor. Thesis (PhD) – School of
Medicine and Dentistry, University of Rochester. UR For the journal, see DNA Repair (journal).
only until January 2010. UR only until January 2010. DNA repair is a collection of processes by which a
[21] Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter
P (2002). Molecular Biology of the Cell. Garland Sci-
ence. ISBN 0-8153-3218-1. DNA Replication Mech-
anisms: DNA Topoisomerases Prevent DNA Tangling
During Replication

[22] Reece, R. J.; Maxwell, A.; Wang, J. C. (1991). “DNA

Gyrase: Structure and Function”. Critical Reviews in
Biochemistry and Molecular Biology 26 (3–4): 335–375.
doi:10.3109/10409239109114072. PMID 1657531.

[23] Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Wal-

ter P (2002). Molecular Biology of the Cell. Garland Sci-
ence. ISBN 0-8153-3218-1. DNA Replication Mecha-
nisms: Special Proteins Help to Open Up the DNA Dou-
ble Helix in Front of the Replication Fork DNA damage resulting in multiple broken chromosomes

[24] Griffiths A.J.F., Wessler S.R., Lewontin R.C., Carroll S.B. cell identifies and corrects damage to the DNA molecules
(2008). Introduction to Genetic Analysis. W. H. Freeman that encode its genome. In human cells, both normal
and Company. ISBN 0-7167-6887-9.[Chapter 7: DNA: metabolic activities and environmental factors such as
Structure and Replication. pg 283–290]
UV light and radiation can cause DNA damage, result-
[25] “Will the Hayflick limit keep us from living forever?". ing in as many as 1 million individual molecular lesions
Howstuffworks. Retrieved January 20, 2015. per cell per day.[1] Many of these lesions cause structural
damage to the DNA molecule and can alter or eliminate
[26] James D. Watson et al. (2008), “Molecular Biology of the the cell’s ability to transcribe the gene that the affected
gene”, Pearson Education: 237 DNA encodes. Other lesions induce potentially harm-
ful mutations in the cell’s genome, which affect the sur-
[27] Peter Meister, Angela Taddei1, Susan M. Gasser(June
vival of its daughter cells after it undergoes mitosis. As
2006), “In and out of the Replication Factory”, Cell 125
a consequence, the DNA repair process is constantly ac-
(7): 1233–1235
tive as it responds to damage in the DNA structure. When
[28] TA Brown (2002). Genomes. BIOS Scientific Publishers. normal repair processes fail, and when cellular apoptosis
ISBN 1-85996-228-9.13.2.3. Termination of replication does not occur, irreparable DNA damage may occur, in-
cluding double-strand breaks and DNA crosslinkages (in-
[29] Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter terstrand crosslinks or ICLs).[2][3]
P (2002). Molecular Biology of the Cell. Garland Science.
ISBN 0-8153-3218-1. Intracellular Control of Cell-CycleThe rate of DNA repair is dependent on many factors,
Events: S-Phase Cyclin-Cdk Complexes (S-Cdks) Initiate including the cell type, the age of the cell, and the ex-
DNA Replication Once Per Cycle tracellular environment. A cell that has accumulated a
large amount of DNA damage, or one that no longer ef-
[30] Tobiason DM, Seifert HS (2006). “The Obligate Human fectively repairs damage incurred to its DNA, can enter
Pathogen, Neisseria gonorrhoeae, Is Polyploid”. PLoS Bi- one of three possible states:
ology 4 (6): e185. doi:10.1371/journal.pbio.0040185.
PMC 1470461. PMID 16719561. 1. an irreversible state of dormancy, known as
senescence
[31] Slater S, Wold S, Lu M, Boye E, Skarstad K, Kleckner
N (September 1995). “E. coli SeqA protein binds oriC 2. cell suicide, also known as apoptosis or programmed
in two different methyl-modulated reactions appropriate cell death
to its roles in DNA replication initiation and origin se-
questration”. Cell 82 (6): 927–36. doi:10.1016/0092- 3. unregulated cell division, which can lead to the for-
8674(95)90272-4. PMID 7553853. mation of a tumor that is cancerous
19.2. DNA REPAIR 309

The DNA repair ability of a cell is vital to the integrity of The replication of damaged DNA before cell division can
its genome and thus to the normal functionality of that or- lead to the incorporation of wrong bases opposite dam-
ganism. Many genes that were initially shown to influence aged ones. Daughter cells that inherit these wrong bases
life span have turned out to be involved in DNA damage carry mutations from which the original DNA sequence
repair and protection.[4] is unrecoverable (except in the rare case of a back muta-
tion, for example, through gene conversion).

19.2.1 DNA damage

Types of damage
Further information: DNA damage (naturally occurring)
and Free radical damage to DNA There are several types of damage to DNA due to en-
dogenous cellular processes:
DNA damage, due to environmental factors and normal
metabolic processes inside the cell, occurs at a rate of 1. oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine
10,000 to 1,000,000 molecular lesions per cell per day.[1] (8-oxoG)] and generation of DNA strand interrup-
While this constitutes only 0.000165% of the human tions from reactive oxygen species,
genome’s approximately 6 billion bases (3 billion base 2. alkylation of bases (usually methylation), such as
pairs), unrepaired lesions in critical genes (such as tumor formation of 7-methylguanine, 1-methyladenine, 6-
suppressor genes) can impede a cell’s ability to carry out O-Methylguanine
its function and appreciably increase the likelihood of
tumor formation and contribute to tumour heterogeneity. 3. hydrolysis of bases, such as deamination,
depurination, and depyrimidination.
The vast majority of DNA damage affects the primary
structure of the double helix; that is, the bases themselves 4. “bulky adduct formation” (i.e., benzo[a]pyrene diol
are chemically modified. These modifications can in turn epoxide-dG adduct, aristolactam I-dA adduct)
disrupt the molecules’ regular helical structure by intro-
ducing non-native chemical bonds or bulky adducts that 5. mismatch of bases, due to errors in DNA replication,
do not fit in the standard double helix. Unlike proteins and in which the wrong DNA base is stitched into place
RNA, DNA usually lacks tertiary structure and therefore in a newly forming DNA strand, or a DNA base is
damage or disturbance does not occur at that level. DNA skipped over or mistakenly inserted.
is, however, supercoiled and wound around “packaging”
proteins called histones (in eukaryotes), and both super- 6. Monoadduct damage cause by change in single ni-
structures are vulnerable to the effects of DNA damage. trogenous base of DNA

7. Diadduct damage
Sources of damage
Damage caused by exogenous agents comes in many
DNA damage can be subdivided into two main types: forms. Some examples are:

1. endogenous damage such as attack by reactive 1. UV-B light causes crosslinking between adjacent cy-
oxygen species produced from normal metabolic tosine and thymine bases creating pyrimidine dimers.
byproducts (spontaneous mutation), especially the This is called direct DNA damage.
process of oxidative deamination
2. UV-A light creates mostly free radicals. The dam-
(a) also includes replication errors age caused by free radicals is called indirect DNA
damage.
2. exogenous damage caused by external agents such as
3. Ionizing radiation such as that created by radioac-
(a) ultraviolet [UV 200-400 nm] radiation from tive decay or in cosmic rays causes breaks in DNA
the sun strands. Low-level ionizing radiation may induce ir-
(b) other radiation frequencies, including x-rays reparable DNA damage (leading to replicational and
and gamma rays transcriptional errors needed for neoplasia or may
trigger viral interactions) leading to pre-mature ag-
(c) hydrolysis or thermal disruption ing and cancer.
(d) certain plant toxins
4. Thermal disruption at elevated temperature in-
(e) human-made mutagenic chemicals, espe- creases the rate of depurination (loss of purine bases
cially aromatic compounds that act as DNA from the DNA backbone) and single-strand breaks.
intercalating agents For example, hydrolytic depurination is seen in the
(f) viruses[5] thermophilic bacteria, which grow in hot springs at
310 CHAPTER 19. DNA SYNTHESIS AND REPAIR

40-80 °C.[6][7] The rate of depurination (300 purine is required by the organism,[9] which serves as a “last re-
residues per genome per generation) is too high in sort” mechanism to prevent a cell with damaged DNA
these species to be repaired by normal repair ma- from replicating inappropriately in the absence of pro-
chinery, hence a possibility of an adaptive response growth cellular signaling. Unregulated cell division can
cannot be ruled out. lead to the formation of a tumor (see cancer), which is
potentially lethal to an organism. Therefore, the induc-
5. Industrial chemicals such as vinyl chloride and tion of senescence and apoptosis is considered to be part
hydrogen peroxide, and environmental chemicals of a strategy of protection against cancer.[10]
such as polycyclic aromatic hydrocarbons found
in smoke, soot and tar create a huge diversity of
DNA adducts- ethenobases, oxidized bases, alky- DNA damage and mutation
lated phosphotriesters and crosslinking of DNA,
just to name a few. It is important to distinguish between DNA damage
and mutation, the two major types of error in DNA.
UV damage, alkylation/methylation, X-ray damage and DNA damages and mutation are fundamentally dif-
oxidative damage are examples of induced damage. ferent. Damages are physical abnormalities in the
Spontaneous damage can include the loss of a base, DNA, such as single- and double-strand breaks, 8-
deamination, sugar ring puckering and tautomeric shift. hydroxydeoxyguanosine residues, and polycyclic aro-
matic hydrocarbon adducts. DNA damages can be rec-
ognized by enzymes, and, thus, they can be correctly re-
Nuclear versus mitochondrial DNA damage paired if redundant information, such as the undamaged
sequence in the complementary DNA strand or in a ho-
In human cells, and eukaryotic cells in general, DNA mologous chromosome, is available for copying. If a cell
is found in two cellular locations — inside the nucleus retains DNA damage, transcription of a gene can be pre-
and inside the mitochondria. Nuclear DNA (nDNA) ex- vented, and, thus, translation into a protein will also be
ists as chromatin during non-replicative stages of the cell blocked. Replication may also be blocked or the cell may
cycle and is condensed into aggregate structures known die.
as chromosomes during cell division. In either state the In contrast to DNA damage, a mutation is a change in the
DNA is highly compacted and wound up around bead- base sequence of the DNA. A mutation cannot be recog-
like proteins called histones. Whenever a cell needs to nized by enzymes once the base change is present in both
express the genetic information encoded in its nDNA the DNA strands, and, thus, a mutation cannot be repaired.
required chromosomal region is unravelled, genes located At the cellular level, mutations can cause alterations in
therein are expressed, and then the region is condensed protein function and regulation. Mutations are replicated
back to its resting conformation. Mitochondrial DNA when the cell replicates. In a population of cells, mutant
(mtDNA) is located inside mitochondria organelles, ex- cells will increase or decrease in frequency according to
ists in multiple copies, and is also tightly associated with the effects of the mutation on the ability of the cell to sur-
a number of proteins to form a complex known as the vive and reproduce. Although distinctly different from
nucleoid. Inside mitochondria, reactive oxygen species each other, DNA damages and mutations are related be-
(ROS), or free radicals, byproducts of the constant pro- cause DNA damages often cause errors of DNA synthe-
duction of adenosine triphosphate (ATP) via oxidative sis during replication or repair; these errors are a major
phosphorylation, create a highly oxidative environment source of mutation.
that is known to damage mtDNA. A critical enzyme in
counteracting the toxicity of these species is superoxide Given these properties of DNA damage and mutation, it
dismutase, which is present in both the mitochondria and can be seen that DNA damages are a special problem in
cytoplasm of eukaryotic cells. non-dividing or slowly dividing cells, where unrepaired
damages will tend to accumulate over time. On the other
hand, in rapidly dividing cells, unrepaired DNA damages
Senescence and apoptosis that do not kill the cell by blocking replication will tend
to cause replication errors and thus mutation. The great
Senescence, an irreversible process in which the cell no majority of mutations that are not neutral in their effect
longer divides, is a protective response to the shortening are deleterious to a cell’s survival. Thus, in a population
of the chromosome ends. The telomeres are long regions of cells composing a tissue with replicating cells, mutant
of repetitive noncoding DNA that cap chromosomes and cells will tend to be lost. However, infrequent mutations
undergo partial degradation each time a cell undergoes that provide a survival advantage will tend to clonally ex-
division (see Hayflick limit).[8] In contrast, quiescence is pand at the expense of neighboring cells in the tissue.
a reversible state of cellular dormancy that is unrelated This advantage to the cell is disadvantageous to the whole
to genome damage (see cell cycle). Senescence in cells organism, because such mutant cells can give rise to can-
may serve as a functional alternative to apoptosis in cases cer. Thus, DNA damages in frequently dividing cells, be-
where the physical presence of a cell for spatial reasons cause they give rise to mutations, are a prominent cause
19.2. DNA REPAIR 311

of cancer. In contrast, DNA damages in infrequently di-

viding cells are likely a prominent cause of aging.[11]

19.2.2 DNA repair mechanisms

Cells cannot function if DNA damage corrupts the in-

tegrity and accessibility of essential information in the
genome (but cells remain superficially functional when
non-essential genes are missing or damaged). Depending
on the type of damage inflicted on the DNA’s double he-
lical structure, a variety of repair strategies have evolved
to restore lost information. If possible, cells use the un-
modified complementary strand of the DNA or the sister
chromatid as a template to recover the original informa-
tion. Without access to a template, cells use an error-
prone recovery mechanism known as translesion synthe-
sis as a last resort.
Damage to DNA alters the spatial configuration of the he-
lix, and such alterations can be detected by the cell. Once
damage is localized, specific DNA repair molecules bind
at or near the site of damage, inducing other molecules to
bind and form a complex that enables the actual repair to
take place.

Direct reversal

Cells are known to eliminate three types of damage to

their DNA by chemically reversing it. These mechanisms
do not require a template, since the types of damage
they counteract can occur in only one of the four bases.
Such direct reversal mechanisms are specific to the type
of damage incurred and do not involve breakage of the
phosphodiester backbone. The formation of pyrimidine
dimers upon irradiation with UV light results in an abnor-
mal covalent bond between adjacent pyrimidine bases.
The photoreactivation process directly reverses this dam-
age by the action of the enzyme photolyase, whose
activation is obligately dependent on energy absorbed
from blue/UV light (300–500 nm wavelength) to pro-
mote catalysis.[12] Photolyase, an old enzyme present in
bacteria, fungi, and most animals no longer functions in
humans,[13] who instead use nucleotide excision repair
to repair damage from UV irradiation. Another type
of damage, methylation of guanine bases, is directly re-
versed by the protein methyl guanine methyl transferase
(MGMT), the bacterial equivalent of which is called
ogt. This is an expensive process because each MGMT
molecule can be used only once; that is, the reaction
is stoichiometric rather than catalytic.[14] A generalized
response to methylating agents in bacteria is known as Single-strand and double-strand DNA damage
the adaptive response and confers a level of resistance to
alkylating agents upon sustained exposure by upregula-
tion of alkylation repair enzymes.[15] The third type of Single-strand damage
DNA damage reversed by cells is certain methylation of
When only one of the two strands of a double helix has a
the bases cytosine and adenine.
defect, the other strand can be used as a template to guide
312 CHAPTER 19. DNA SYNTHESIS AND REPAIR

of damaged region by an exonuclease, resynthesis

by DNA polymerase, and nick sealing by DNA
ligase.[18]

Double-strand breaks

Double-strand breaks, in which both strands in the dou-

ble helix are severed, are particularly hazardous to the cell
because they can lead to genome rearrangements. Three
mechanisms exist to repair double-strand breaks (DSBs):
non-homologous end joining (NHEJ), microhomology-
mediated end joining (MMEJ), and homologous re-
combination.[14] PVN Acharya noted that double-strand
Structure of the base-excision repair enzyme uracil-DNA glyco-
sylase. The uracil residue is shown in yellow.
breaks and a “cross-linkage joining both strands at the
same point is irreparable because neither strand can then
serve as a template for repair. The cell will die in the next
[2][3]
the correction of the damaged strand. In order to repair mitosis or in some rare instances, mutate.”
damage to one of the two paired molecules of DNA, there
exist a number of excision repair mechanisms that remove
the damaged nucleotide and replace it with an undamaged
nucleotide complementary to that found in the undam-
aged DNA strand.[14]

1. Base excision repair (BER) repairs damage to a sin-

gle nitrogenous base by deploying enzymes called
glycosylases.[16] These enzymes remove a single ni-
trogenous base to create an apurinic or apyrimidnic
site (AP site).[16] Enzymes called AP endonucleases
nick the damaged DNA backbone at the AP site.
DNA polymerase then removes the damaged region
using its 5’ to 3’ exonuclease activity and correctly
synthesizes the new strand using the complementary
strand as a template.[16]

2. Nucleotide excision repair (NER) repairs damaged

DNA which commonly consists of bulky, helix-
distorting damage, such as pyrimidine dimerization
caused by UV light. Damaged regions are removed
in 12-24 nucleotide-long strands in a three-step pro-
cess which consists of recognition of damage, ex-
cision of damaged DNA both upstream and down-
stream of damage by endonucleases, and resysnthe- DNA ligase, shown above repairing chromosomal damage, is an
sis of removed DNA region.[17] NER is a highly evo- enzyme that joins broken nucleotides together by catalyzing the
lutionarily conserved repair mechanism and is used formation of an internucleotide ester bond between the phosphate
in nearly all eukaryotic and prokaryotic cells.[17] In backbone and the deoxyribose nucleotides.
prokaryotes, NER is mediated by Uvr proteins.[17]
In eukaryotes, many more proteins are involved, al- In NHEJ, DNA Ligase IV, a specialized DNA ligase that
though the general strategy is the same.[17] forms a complex with the cofactor XRCC4, directly joins
the two ends.[19] To guide accurate repair, NHEJ relies
3. Mismatch repair systems are present in essentially on short homologous sequences called microhomologies
all cells to correct errors that are not corrected by present on the single-stranded tails of the DNA ends to
proofreading. These systems consist of at least two be joined. If these overhangs are compatible, repair is
proteins. One detects the mismatch, and the other usually accurate.[20][21][22][23] NHEJ can also introduce
recruits an endonuclease that cleaves the newly mutations during repair. Loss of damaged nucleotides
synthesized DNA strand close to the region of at the break site can lead to deletions, and joining of non-
damage. In E. coli , the proteins involved are the matching termini forms translocations. NHEJ is espe-
Mut class proteins. This is followed by removal cially important before the cell has replicated its DNA,
19.2. DNA REPAIR 313

since there is no template available for repair by homol- Translesion synthesis

ogous recombination. There are “backup” NHEJ path-
ways in higher eukaryotes.[24] Besides its role as a genome
Translesion synthesis (TLS) is a DNA damage toler-
caretaker, NHEJ is required for joining hairpin-capped
ance process that allows the DNA replication machinery
double-strand breaks induced during V(D)J recombina-
to replicate past DNA lesions such as thymine dimers
tion, the process that generates diversity in B-cell and T-
or AP sites.[31] It involves switching out regular DNA
cell receptors in the vertebrate immune system.[25]
polymerases for specialized translesion polymerases (i.e.
MMEJ starts with short-range end resection by MRE11 DNA polymerase IV or V, from the Y Polymerase fam-
nuclease on either side of a double-strand break to reveal ily), often with larger active sites that can facilitate the in-
microhomology regions.[26] In further steps,[27] PARP1 sertion of bases opposite damaged nucleotides. The poly-
is required and may be an early step in MMEJ. There merase switching is thought to be mediated by, among
is pairing of microhomology regions followed by recruit- other factors, the post-translational modification of the
ment of flap structure-specific endonuclease 1 ( FEN1) replication processivity factor PCNA. Translesion syn-
to remove overhanging flaps. This is followed by recruit- thesis polymerases often have low fidelity (high propen-
ment of XRCC1–LIG3 to the site for ligating the DNA sity to insert wrong bases) on undamaged templates rel-
ends, leading to an intact DNA. ative to regular polymerases. However, many are ex-
DNA double strand breaks in mammalian cells are pri- tremely efficient at inserting correct bases opposite spe-
marily repaired by homologous recombination (HR) and cific types of damage. For example, Pol η mediates error-
non-homologous end joining (NHEJ).[28] In an in vitro free bypass of lesions induced by UV irradiation, whereas
system, MMEJ occurred in mammalian cells at the lev- Pol ι introduces mutations at these sites. Pol η is known
els of 10–20% of HR when both HR and NHEJ mecha- to add the first adenine across the T^T photodimer using
nisms were also available.[26] MMEJ is always accompa- Watson-Crick base pairing and the second adenine will
nied by a deletion, so that MMEJ is a mutagenic pathway be added in its syn conformation using Hoogsteen base
for DNA repair.[29] pairing. From a cellular perspective, risking the introduc-
tion of point mutations during translesion synthesis may
Homologous recombination requires the presence of an be preferable to resorting to more drastic mechanisms of
identical or nearly identical sequence to be used as a tem- DNA repair, which may cause gross chromosomal aber-
plate for repair of the break. The enzymatic machinery rations or cell death. In short, the process involves spe-
responsible for this repair process is nearly identical to the cialized polymerases either bypassing or repairing lesions
machinery responsible for chromosomal crossover during at locations of stalled DNA replication. For example Hu-
meiosis. This pathway allows a damaged chromosome to man DNA polymerase eta can bypass complex DNA le-
be repaired using a sister chromatid (available in G2 af- sions like guanine-thymine intra-strand crosslink, G[8,5-
ter DNA replication) or a homologous chromosome as Me]T, although can cause targeted and semi-targeted
a template. DSBs caused by the replication machinery mutations.[32] Paromita Raychaudhury and Ashis Basu[33]
attempting to synthesize across a single-strand break or studied the toxicity and mutagenesis of the same le-
unrepaired lesion cause collapse of the replication fork sion in E.coli by replicating a G[8,5-Me]T-modified plas-
and are typically repaired by recombination. mid in Escherichia coli with specific DNA polymerase
Topoisomerases introduce both single- and double-strand knockouts. Viability was very low in a strain lacking
breaks in the course of changing the DNA’s state of pol II, pol IV, and pol V, the three SOS-inducible DNA
supercoiling, which is especially common in regions near polymerases, indicating that translesion synthesis is con-
an open replication fork. Such breaks are not considered ducted primarily by these specialized DNA polymerases.
DNA damage because they are a natural intermediate in A bypass platform is provided to these polymerases by
the topoisomerase biochemical mechanism and are im- Proliferating cell nuclear antigen (PCNA). Under normal
mediately repaired by the enzymes that created them. circumstances, PCNA bound to polymerases replicates
the DNA. At a site of lesion, PCNA is ubiquitinated,
A team of French researchers bombarded Deinococcus
or modified, by the RAD6/RAD18 proteins to provide
radiodurans to study the mechanism of double-strand
a platform for the specialized polymerases to bypass the
break DNA repair in that organism. At least two copies of
lesion and resume DNA replication.[34][35] After transle-
the genome, with random DNA breaks, can form DNA
sion synthesis, extension is required. This extension can
fragments through annealing. Partially overlapping frag-
be carried out by a replicative polymerase if the TLS is
ments are then used for synthesis of homologous regions
error-free, as in the case of Pol η, yet if TLS results in a
through a moving D-loop that can continue extension un-
mismatch, a specialized polymerase is needed to extend
til they find complementary partner strands. In the fi-
it; Pol ζ. Pol ζ is unique in that it can extend terminal mis-
nal step there is crossover by means of RecA-dependent
matches, whereas more processive polymerases cannot.
homologous recombination.[30]
So when a lesion is encountered, the replication fork will
stall, PCNA will switch from a processive polymerase to
a TLS polymerase such as Pol ι to fix the lesion, then
PCNA may switch to Pol ζ to extend the mismatch, and
314 CHAPTER 19. DNA SYNTHESIS AND REPAIR

last PCNA will switch to the processive polymerase to widespread in the Bacteria domain, but it is mostly absent
continue replication. in some bacterial phyla, like the Spirochetes.[42] The most
common cellular signals activating the SOS response are
regions of single-stranded DNA (ssDNA), arising from
19.2.3 Global response to DNA damage stalled replication forks or double-strand breaks, which
are processed by DNA helicase to separate the two DNA
Cells exposed to ionizing radiation, ultraviolet light or strands.[36] In the initiation step, RecA protein binds to
chemicals are prone to acquire multiple sites of bulky ssDNA in an ATP hydrolysis driven reaction creating
DNA lesions and double-strand breaks. Moreover, DNA RecA–ssDNA filaments. RecA–ssDNA filaments acti-
damaging agents can damage other biomolecules such vate LexA autoprotease activity, which ultimately leads
as proteins, carbohydrates, lipids, and RNA. The ac- to cleavage of LexA dimer and subsequent LexA degra-
cumulation of damage, to be specific, double-strand dation. The loss of LexA repressor induces transcription
breaks or adducts stalling the replication forks, are among of the SOS genes and allows for further signal induction,
known stimulation signals for a global response to DNA inhibition of cell division and an increase in levels of pro-
damage.[36] The global response to damage is an act di- teins responsible for damage processing.
rected toward the cells’ own preservation and triggers
multiple pathways of macromolecular repair, lesion by- In Escherichia coli, SOS boxes are 20-nucleotide long se-
pass, tolerance, or apoptosis. The common features of quences near promoters with palindromic structure and
global response are induction of multiple genes, cell cy- a high degree of sequence conservation. In other classes
cle arrest, and inhibition of cell division. and phyla, the sequence of SOS boxes varies consider-
ably, with different length and composition, but it is al-
ways highly conserved and one of the strongest short sig-
DNA damage checkpoints nals in the genome.[42] The high information content of
SOS boxes permits differential binding of LexA to dif-
After DNA damage, cell cycle checkpoints are activated. ferent promoters and allows for timing of the SOS re-
Checkpoint activation pauses the cell cycle and gives the sponse. The lesion repair genes are induced at the be-
cell time to repair the damage before continuing to divide. ginning of SOS response. The error-prone translesion
DNA damage checkpoints occur at the G1/S and G2/M polymerases, for example, UmuCD'2 (also called DNA
boundaries. An intra-S checkpoint also exists. Check- polymerase V), are induced later on as a last resort.[43]
point activation is controlled by two master kinases, ATM Once the DNA damage is repaired or bypassed using
and ATR. ATM responds to DNA double-strand breaks polymerases or through recombination, the amount of
and disruptions in chromatin structure,[37] whereas ATR single-stranded DNA in cells is decreased, lowering the
primarily responds to stalled replication forks. These ki- amounts of RecA filaments decreases cleavage activity
nases phosphorylate downstream targets in a signal trans- of LexA homodimer, which then binds to the SOS boxes
duction cascade, eventually leading to cell cycle arrest. A near promoters and restores normal gene expression.
class of checkpoint mediator proteins including BRCA1,
MDC1, and 53BP1 has also been identified.[38] These
proteins seem to be required for transmitting the check- Eukaryotic transcriptional responses to DNA dam-
point activation signal to downstream proteins. age
An important downstream target of ATM and ATR is
p53, as it is required for inducing apoptosis follow- Eukaryotic cells exposed to DNA damaging agents also
ing DNA damage.[39] The cyclin-dependent kinase in- activate important defensive pathways by inducing mul-
hibitor p21 is induced by both p53-dependent and p53- tiple proteins involved in DNA repair, cell cycle check-
independent mechanisms and can arrest the cell cy- point control, protein trafficking and degradation. Such
cle at the G1/S and G2/M checkpoints by deactivating genome wide transcriptional response is very complex
cyclin/cyclin-dependent kinase complexes.[40] and tightly regulated, thus allowing coordinated global
response to damage. Exposure of yeast Saccharomyces
cerevisiae to DNA damaging agents results in overlapping
The prokaryotic SOS response but distinct transcriptional profiles. Similarities to envi-
ronmental shock response indicates that a general global
The SOS response is the changes in gene expression in stress response pathway exist at the level of transcrip-
Escherichia coli and other bacteria in response to exten- tional activation. In contrast, different human cell types
sive DNA damage. The prokaryotic SOS system is regu- respond to damage differently indicating an absence of a
lated by two key proteins: LexA and RecA. The LexA common global response. The probable explanation for
homodimer is a transcriptional repressor that binds to this difference between yeast and human cells may be
operator sequences commonly referred to as SOS boxes. in the heterogeneity of mammalian cells. In an animal
In Escherichia coli it is known that LexA regulates tran- different types of cells are distributed among different
scription of approximately 48 genes including the lexA organs that have evolved different sensitivities to DNA
and recA genes.[41] The SOS response is known to be damage.[44]
19.2. DNA REPAIR 315

In general global response to DNA damage involves ex- exhibit remarkable resistance to the double-strand break-
pression of multiple genes responsible for postreplication inducing effects of radioactivity, likely due to enhanced
repair, homologous recombination, nucleotide excision efficiency of DNA repair and especially NHEJ.[48]
repair, DNA damage checkpoint, global transcriptional
activation, genes controlling mRNA decay, and many
others. A large amount of damage to a cell leaves it with Longevity and caloric restriction
an important decision: undergo apoptosis and die, or sur-
vive at the cost of living with a modified genome. An in-
crease in tolerance to damage can lead to an increased rate
of survival that will allow a greater accumulation of muta-
tions. Yeast Rev1 and human polymerase η are members
of [Y family translesion DNA polymerases present during
global response to DNA damage and are responsible for
enhanced mutagenesis during a global response to DNA
damage in eukaryotes.[36]

19.2.4 DNA repair and aging

Pathological effects of poor DNA repair

Most life span influencing genes affect the rate of DNA damage

A number of individual genes have been identified as in-

fluencing variations in life span within a population of or-
DNA repair rate is an important determinant of cell pathology
ganisms. The effects of these genes is strongly dependent
Experimental animals with genetic deficiencies in DNA on the environment, in particular, on the organism’s diet.
Caloric restriction reproducibly results in extended lifes-
repair often show decreased life span and increased can-
cer incidence.[11] For example, mice deficient in the dom- pan in a variety of organisms, likely via nutrient sensing
pathways and decreased metabolic rate. The molecular
inant NHEJ pathway and in telomere maintenance mech-
anisms get lymphoma and infections more often, and, mechanisms by which such restriction results in length-
ened lifespan are as yet unclear (see[49] for some discus-
as a consequence, have shorter lifespans than wild-type
mice.[45] In similar manner, mice deficient in a key repair sion); however, the behavior of many genes known to be
involved in DNA repair is altered under conditions of
and transcription protein that unwinds DNA helices have
premature onset of aging-related diseases and consequent caloric restriction.
shortening of lifespan.[46] However, not every DNA re- For example, increasing the gene dosage of the gene
pair deficiency creates exactly the predicted effects; mice SIR-2, which regulates DNA packaging in the nematode
deficient in the NER pathway exhibited shortened life worm Caenorhabditis elegans, can significantly extend
span without correspondingly higher rates of mutation.[47] lifespan.[50] The mammalian homolog of SIR-2 is known
If the rate of DNA damage exceeds the capacity of the to induce downstream DNA repair factors involved in
cell to repair it, the accumulation of errors can overwhelm NHEJ, an activity that is especially promoted under con-
the cell and result in early senescence, apoptosis, or can- ditions of caloric restriction.[51] Caloric restriction has
cer. Inherited diseases associated with faulty DNA repair been closely linked to the rate of base excision repair in
functioning result in premature aging,[11] increased sensi- the nuclear DNA of rodents,[52] although similar effects
tivity to carcinogens, and correspondingly increased can- have not been observed in mitochondrial DNA.[53]
cer risk (see below). On the other hand, organisms with It is interesting to note that the C. elegans gene AGE-1,
enhanced DNA repair systems, such as Deinococcus ra- an upstream effector of DNA repair pathways, confers
diodurans, the most radiation-resistant known organism, dramatically extended life span under free-feeding con-
316 CHAPTER 19. DNA SYNTHESIS AND REPAIR

ditions but leads to a decrease in reproductive fitness un- Hereditary nonpolyposis colorectal cancer (HNPCC) is
der conditions of caloric restriction.[54] This observation strongly associated with specific mutations in the DNA
supports the pleiotropy theory of the biological origins of mismatch repair pathway. BRCA1 and BRCA2, two fa-
aging, which suggests that genes conferring a large sur- mous genes whose mutations confer a hugely increased
vival advantage early in life will be selected for even if risk of breast cancer on carriers, are both associated
they carry a corresponding disadvantage late in life. with a large number of DNA repair pathways, especially
NHEJ and homologous recombination.

19.2.5 Medicine and DNA repair modula- Cancer therapy procedures such as chemotherapy and
radiotherapy work by overwhelming the capacity of the
tion cell to repair DNA damage, resulting in cell death. Cells
that are most rapidly dividing — most typically cancer
Hereditary DNA repair disorders
cells — are preferentially affected. The side-effect is
that other non-cancerous but rapidly dividing cells such
Defects in the NER mechanism are responsible for sev-
as progenitor cells in the gut, skin, and hematopoietic sys-
eral genetic disorders, including:
tem are also affected. Modern cancer treatments attempt
to localize the DNA damage to cells and tissues only as-
• Xeroderma pigmentosum: hypersensitivity to sun- sociated with cancer, either by physical means (concen-
light/UV, resulting in increased skin cancer inci- trating the therapeutic agent in the region of the tumor)
dence and premature aging or by biochemical means (exploiting a feature unique to
cancer cells in the body).
• Cockayne syndrome: hypersensitivity to UV and
chemical agents

• Trichothiodystrophy: sensitive skin, brittle hair and Epigenetic DNA repair defects in cancer
nails
Classically, cancer has been viewed as a set of diseases
that are driven by progressive genetic abnormalities that
Mental retardation often accompanies the latter two dis- include mutations in tumour-suppressor genes and onco-
orders, suggesting increased vulnerability of develop- genes, and chromosomal aberrations. However, it has be-
mental neurons. come apparent that cancer is also driven by epigenetic al-
Other DNA repair disorders include: terations.[57]
Epigenetic alterations refer to functionally relevant modi-
• Werner’s syndrome: premature aging and retarded fications to the genome that do not involve a change in the
growth nucleotide sequence. Examples of such modifications are
changes in DNA methylation (hypermethylation and hy-
• Bloom’s syndrome: sunlight hypersensitivity, high pomethylation) and histone modification,[58] changes in
incidence of malignancies (especially leukemias). chromosomal architecture (caused by inappropriate ex-
[59]
• Ataxia telangiectasia: sensitivity to ionizing radia- pression of proteins such as HMGA2 or HMGA1) and
tion and some chemical agents changes caused by microRNAs. Each of these epigenetic
alterations serves to regulate gene expression without al-
tering the underlying DNA sequence. These changes usu-
All of the above diseases are often called “segmental ally remain through cell divisions, last for multiple cell
progerias" ("accelerated aging diseases") because their generations, and can be considered to be epimutations
victims appear elderly and suffer from aging-related dis- (equivalent to mutations).
eases at an abnormally young age, while not manifesting
all the symptoms of old age. While large numbers of epigenetic alterations are found
in cancers, the epigenetic alterations in DNA repair
Other diseases associated with reduced DNA repair func- genes, causing reduced expression of DNA repair pro-
tion include Fanconi anemia, hereditary breast cancer and teins, appear to be particularly important. Such alter-
hereditary colon cancer. ations are thought to occur early in progression to cancer
and to be a likely cause of the genetic instability charac-
teristic of cancers.[60][61][62][63]
19.2.6 DNA repair and cancer
Reduced expression of DNA repair genes causes defi-
Because of inherent limitations in the DNA repair mech- cient DNA repair. When DNA repair is deficient DNA
anisms, if humans lived long enough, they would all damages remain in cells at a higher than usual level and
eventually develop cancer.[55][56] There are at least 34 these excess damages cause increased frequencies of mu-
Inherited human DNA repair gene mutations that in- tation or epimutation. Mutation rates increase substan-
crease cancer risk. Many of these mutations cause DNA tially in cells defective in DNA mismatch repair[64][65] or
repair to be less effective than normal. In particular, in homologous recombinational repair (HRR).[66] Chro-
19.2. DNA REPAIR 317

mosomal rearrangements and aneuploidy also increase in MGMT expression due to methylation of the MGMT
HRR defective cells.[67] promoter region.[73][74][75][76][77]
Higher levels of DNA damage not only cause increased Similarly, out of 119 cases of mismatch repair-deficient
mutation, but also cause increased epimutation. During colorectal cancers that lacked DNA repair gene PMS2
repair of DNA double strand breaks, or repair of other expression, PMS2 was deficient in 6 due to mutations in
DNA damages, incompletely cleared sites of repair can the PMS2 gene, while in 103 cases PMS2 expression was
cause epigenetic gene silencing.[68][69] deficient because its pairing partner MLH1 was repressed
Deficient expression of DNA repair proteins due to an in- due to promoter methylation (PMS2 protein is unstable in
herited mutation can cause increased risk of cancer. In- the absence of MLH1).[78] In the other 10 cases, loss of
dividuals with an inherited impairment in any of 34 DNA PMS2 expression was likely due to epigenetic overexpres-
repair genes (see article DNA repair-deficiency disorder) sion of the microRNA, miR-155, which down-regulates
have an increased risk of cancer, with some defects caus- MLH1.[79]
ing up to a 100% lifetime chance of cancer (e.g. p53 In further examples [tabulated in the article Epigenetics
mutations).[70] However, such germline mutations (which (see section “DNA repair epigenetics in cancer”)], epi-
cause highly penetrant cancer syndromes) are the cause of genetic defects were found at frequencies of between
only about 1 percent of cancers.[71] 13%−100% for the DNA repair genes BRCA1, WRN,
FANCB, FANCF, MGMT, MLH1, MSH2, MSH4,
ERCC1, XPF, NEIL1 and ATM. These epigenetic de-
Frequencies of epimutations in DNA repair genes fects occurred in various cancers (e.g. breast, ovarian,
colorectal and head and neck). Two or three deficien-
cies in the expression of ERCC1, XPF or PMS2 occur
simultaneously in the majority of the 49 colon cancers
evaluated by Facista et al.[80]
The chart in this section shows some frequent DNA dam-
aging agents, examples of DNA lesions they cause, and
the pathways that deal with these DNA damages. At least
169 enzymes are either directly employed in DNA repair
or influence DNA repair processes.[81] Of these, 83 are
directly employed in the 5 types of DNA repair processes
illustrated in the chart. The more well studied genes cen-
tral to these repair processes are also shown in the chart.
As indicated by the DNA repair genes shown in red, many
of the genes in these repair pathways are regulated by epi-
genetic mechanisms, and these are frequently reduced or
silent in various cancers (marked by an asterisk). Two
review articles,[63][82] and two broad experimental survey
articles[83][84] document most of these epigenetic DNA
repair deficiencies.
It appears that epigenetic alterations in DNA repair genes
are central to carcinogenesis.
A chart of common DNA damaging agents, the lesions they cause
in DNA, the repair pathways utilized to repair these lesions, many
of the genes in those pathways, indication of which genes are reg-
ulated epigenetically, and which of those epigenetically regulated
19.2.7 DNA repair and evolution
genes are found with reduced expression in various cancers.
The basic processes of DNA repair are highly conserved
Deficiencies in DNA repair enzymes are occasionally among both prokaryotes and eukaryotes and even
caused by a newly arising somatic mutation in a DNA among bacteriophage (viruses that infect bacteria); how-
repair gene, but are much more frequently caused by epi- ever, more complex organisms with more complex
genetic alterations that reduce or silence expression of genomes have correspondingly more complex repair
DNA repair genes. For example, when 113 colorec- mechanisms.[85] The ability of a large number of protein
tal cancers were examined in sequence, only four had structural motifs to catalyze relevant chemical reactions
a missense mutation in the DNA repair gene MGMT, has played a significant role in the elaboration of repair
while the majority had reduced MGMT expression due mechanisms during evolution. For an extremely detailed
to methylation of the MGMT promoter region (an epige- review of hypotheses relating to the evolution of DNA
netic alteration).[72] Five different studies found that be- repair, see.[86]
tween 40% and 90% of colorectal cancers have reduced The fossil record indicates that single-cell life began
318 CHAPTER 19. DNA SYNTHESIS AND REPAIR

to proliferate on the planet at some point during the 19.2.9 References

Precambrian period, although exactly when recognizably
modern life first emerged is unclear. Nucleic acids be- [1] Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M,
came the sole and universal means of encoding genetic Scott MP, Zipursky SL, Darnell J. (2004). Molecular Bi-
ology of the Cell, p963. WH Freeman: New York, NY.
information, requiring DNA repair mechanisms that in
5th ed.
their basic form have been inherited by all extant life
forms from their common ancestor. The emergence of [2] Acharya, PV (1971). “The isolation and partial character-
Earth’s oxygen-rich atmosphere (known as the "oxygen ization of age-correlated oligo-deoxyribo-ribonucleotides
catastrophe") due to photosynthetic organisms, as well with covalently linked aspartyl-glutamyl polypeptides.”.
as the presence of potentially damaging free radicals in Johns Hopkins medical journal. Supplement (1): 254–60.
the cell due to oxidative phosphorylation, necessitated PMID 5055816.
the evolution of DNA repair mechanisms that act specifi- [3] Bjorksten, J; Acharya, PV; Ashman, S; Wetlaufer, DB
cally to counter the types of damage induced by oxidative (1971). “Gerogenic fractions in the tritiated rat.”. Journal
stress. of the American Geriatrics Society 19 (7): 561–74. PMID
5106728.

Rate of evolutionary change [4] Browner, WS; Kahn, AJ; Ziv, E; Reiner, AP; Oshima,
J; Cawthon, RM; Hsueh, WC; Cummings, SR. (2004).
On some occasions, DNA damage is not repaired, or is “The genetics of human longevity”. Am J Med 117 (11):
repaired by an error-prone mechanism that results in a 851–60. doi:10.1016/j.amjmed.2004.06.033. PMID
15589490.
change from the original sequence. When this occurs,
mutations may propagate into the genomes of the cell’s [5] Roulston A, Marcellus RC, Branton PE (1999). “Viruses
progeny. Should such an event occur in a germ line cell and apoptosis”. Annu. Rev. Microbiol. 53: 577–628.
that will eventually produce a gamete, the mutation has doi:10.1146/annurev.micro.53.1.577. PMID 10547702.
the potential to be passed on to the organism’s offspring. [6] Madigan MT, Martino JM (2006). Brock Biology of Mi-
The rate of evolution in a particular species (or, in a par- croorganisms (11th ed.). Pearson. p. 136. ISBN 0-13-
ticular gene) is a function of the rate of mutation. As a 196893-9.
consequence, the rate and accuracy of DNA repair mech-
anisms have an influence over the process of evolutionary [7] Ohta, Toshihiro; Shin-ichi, Tokishita; Mochizuki, Kayo;
change.[87] Kawase, Jun; Sakahira, Masahide; Yamagata, Hideo
(2006). “UV Sensitivity and Mutagenesis of the
Extremely Thermophilic Eubacterium Thermus ther-
mophilus HB27”. Genes and Environment 28 (2): 56–61.
19.2.8 See also
doi:10.3123/jemsge.28.56.
• Accelerated aging disease [8] Braig, M; Schmitt, CA. (2006). “Oncogene-induced
senescence: putting the brakes on tumor development”.
• Aging DNA Cancer Res 66 (6): 2881–2884. doi:10.1158/0008-
5472.CAN-05-4006. PMID 16540631.
• Cell cycle
[9] Lynch, MD. (2006). “How does cellular senescence
• DNA damage (naturally occurring) prevent cancer?". DNA Cell Biol 25 (2): 69–78.
doi:10.1089/dna.2006.25.69. PMID 16460230.
• DNA damage theory of aging
[10] Campisi J, d'Adda di Fagagna F (2007). “Cellular senes-
• DNA replication cence: when bad things happen to good cells.”. Rev Mol
• Direct DNA damage Cell Biol. 8 (9): 729–40. doi:10.1038/nrm2233. PMID
17667954.
• Gene therapy
[11] Best, Benjamin P (2009). “Nuclear DNA damage as a di-
• Human mitochondrial genetics rect cause of aging” (PDF). Rejuvenation Research 12 (3):
199–208. doi:10.1089/rej.2009.0847. PMID 19594328.
• Indirect DNA damage
[12] Sancar, A. (2003). “Structure and function of DNA
• Life extension photolyase and cryptochrome blue-light photoreceptors”.
Chem Rev 103 (6): 2203–37. doi:10.1021/cr0204348.
• Progeria PMID 12797829.

• Senescence [13] Michael Lynch, José Ignacio Lucas-Lledó; Lynch, M. (19

February 2009). “Evolution of Mutation Rates: Phyloge-
• SiDNA nomic Analysis of the Photolyase/Cryptochrome Fam-
ily”. Molecular Biology and Evolution 26 (5): 1143–1153.
• The scientific journal DNA Repair under Mutation doi:10.1093/molbev/msp029. PMC 2668831. PMID
Research 19228922.
19.2. DNA REPAIR 319

[14] Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick [26] Truong LN, Li Y, Shi LZ, Hwang PY, He J, Wang H et
R. (2004). Molecular Biology of the Gene. Pearson Ben- al. (2013). “Microhomology-mediated End Joining and
jamin Cummings; CSHL Press. 5th ed., chapters 9 and Homologous Recombination share the initial end resection
10 step to repair DNA double-strand breaks in mammalian
cells”. Proc. Natl. Acad. Sci. U.S.A. 110 (19): 7720–5.
[15] Volkert MR (1988). “Adaptive response of Es- doi:10.1073/pnas.1213431110. PMC 3651503. PMID
cherichia coli to alkylation damage”. Environmen- 23610439.
tal and Molecular Mutagenesis 11 (2): 241–55.
doi:10.1002/em.2850110210. PMID 3278898. [27] Sharma S, Javadekar SM, Pandey M, Srivastava M, Ku-
mari R, Raghavan SC (2015). “Homology and en-
[16] Willey, J; Sherwood, L; Woolverton, C (2014). Prescott’s zymatic requirements of microhomology-dependent al-
Microbiology. New York, New York: McGraw Hill. p. ternative end joining”. Cell Death Dis 6: e1697.
381. ISBN 978-0-07-3402-40-6. doi:10.1038/cddis.2015.58. PMC 4385936. PMID
25789972.
[17] Reardon, J; Sancar, A (2006). “Purification and Charac-
terization of Escherichia coli and Human Nucleotide Ex- [28] Liang L, Deng L, Chen Y, Li GC, Shao C, Tischfield
cision Repair Enzyme Systems”. Methods in Enzymol- JA (2005). “Modulation of DNA end joining by nu-
ogy 408: 189–213. doi:10.1016/S0076-6879(06)08012- clear proteins”. J. Biol. Chem. 280 (36): 31442–9.
8. PMID 16793370. doi:10.1074/jbc.M503776200. PMID 16012167.

[29] Decottignies A (2013). “Alternative end-joining mech-

[18] Berg, M; Tymoczko, J; Stryer, L (2012). Biochemistry
anisms: a historical perspective”. Front Genet 4: 48.
7th edition. New York: W.H. Freeman and Company. p.
doi:10.3389/fgene.2013.00048. PMC 3613618. PMID
840. ISBN 9781429229364.
23565119.
[19] Wilson TE, Grawunder U, Lieber MR (July 1997). “Yeast [30] Zahradka K, Slade D, Bailone A et al. (October
DNA ligase IV mediates non-homologous DNA end join- 2006). “Reassembly of shattered chromosomes in
ing”. Nature 388 (6641): 495–8. doi:10.1038/41365. Deinococcus radiodurans”. Nature 443 (7111): 569–73.
PMID 9242411. doi:10.1038/nature05160. PMID 17006450.
[20] Moore JK, Haber JE (May 1996). “Cell cycle and genetic [31] Waters LS, Minesinger BK, Wiltrout ME, D'Souza S,
requirements of two pathways of nonhomologous end- Woodruff RV, Walker GC (March 2009). “Eukaryotic
joining repair of double-strand breaks in Saccharomyces Translesion Polymerases and Their Roles and Regulation
cerevisiae”. Molecular and Cellular Biology 16 (5): 2164– in DNA Damage Tolerance”. Microbiol. Mol. Biol. Rev.
73. PMC 231204. PMID 8628283. 73 (1): 134–54. doi:10.1128/MMBR.00034-08. PMC
2650891. PMID 19258535.
[21] Boulton SJ, Jackson SP (September 1996).
“Saccharomyces cerevisiae Ku70 potentiates illegit- [32] LC Colis, P Raychaudhury, AK Basu (2008). “Mutational
imate DNA double-strand break repair and serves as specificity of gamma-radiation-induced guanine-thymine
a barrier to error-prone DNA repair pathways”. The and thymine-guanine intrastrand cross-links in mam-
EMBO Journal 15 (18): 5093–103. PMC 452249. PMID malian cells and translesion synthesis past the guanine-
8890183. thymine lesion by human DNA polymerase eta”. Bio-
chemistry 47 (6): 8070–8079. doi:10.1021/bi800529f.
[22] Wilson TE, Lieber MR (August 1999). “Efficient pro- PMID 18616294.
cessing of DNA ends during yeast nonhomologous end
joining. Evidence for a DNA polymerase beta (Pol4)- [33] P Raychaudhury; Basu, Ashis K. (2011). “Genetic re-
dependent pathway”. The Journal of Biological Chemistry quirement for mutagenesis of the G[8,5-Me]T cross-link
274 (33): 23599–609. doi:10.1074/jbc.274.33.23599. in Escherichia coli: DNA polymerases IV and V compete
PMID 10438542. for error-prone bypass”. Biochemistry 50 (12): 2330–
2338. doi:10.1021/bi102064z. PMID 21302943.
[23] Budman J, Chu G (February 2005). “Processing
of DNA for nonhomologous end-joining by cell-free [34] “Translesion Synthesis”. Research.chem.psu.edu. Re-
extract”. The EMBO Journal 24 (4): 849–60. trieved 2012-08-14.
doi:10.1038/sj.emboj.7600563. PMC 549622. PMID [35] Wang, Z (2001). “Translesion synthesis by the UmuC
15692565. family of DNA polymerases”. Mutat. Res. 486 (2):
59–70. doi:10.1016/S0921-8777(01)00089-1. PMID
[24] Wang H, Perrault AR, Takeda Y, Qin W, Wang H, Ili-
11425512.
akis G (September 2003). “Biochemical evidence for Ku-
independent backup pathways of NHEJ”. Nucleic Acids [36] Friedberg EC, Walker GC, Siede W, Wood RD, Schultz
Research 31 (18): 5377–88. doi:10.1093/nar/gkg728. RA, Ellenberger T. (2006). DNA Repair and Mutagene-
PMC 203313. PMID 12954774. sis, part 3. ASM Press. 2nd ed.

[25] Jung D, Alt FW (January 2004). “Unraveling V(D)J re- [37] Bakkenist CJ, Kastan MB (January 2003). “DNA damage
combination; insights into gene regulation”. Cell 116 (2): activates ATM through intermolecular autophosphoryla-
299–311. doi:10.1016/S0092-8674(04)00039-X. PMID tion and dimer dissociation”. Nature 421 (6922): 499–
14744439. 506. doi:10.1038/nature01368. PMID 12556884.
320 CHAPTER 19. DNA SYNTHESIS AND REPAIR

[38] Wei, Qingyi; Lei Li; David Chen (2007). DNA Repair, [51] Cohen, HY; Miller, C; Bitterman, KJ; Wall, NR; Hekking,
Genetic Instability, and Cancer. World Scientific. ISBN B; Kessler, B; Howitz, KT; Gorospe, M et al. (2004).
981-270-014-5. “Calorie restriction promotes mammalian cell survival by
inducing the SIRT1 deacetylase”. Science 305 (5682):
[39] Schonthal, Axel H. (2004). Checkpoint Controls and Can- 390–2. doi:10.1126/science.1099196. PMID 15205477.
cer. Humana Press. ISBN 1-58829-500-1.
[52] Cabelof, DC; Yanamadala, S; Raffoul, JJ; Guo, Z; Soofi,
[40] Gartel AL, Tyner AL (June 2002). “The role of the cyclin- A; Heydari, AR. (2003). “Caloric restriction promotes
dependent kinase inhibitor p21 in apoptosis”. Molecular genomic stability by induction of base excision repair and
Cancer Therapeutics 1 (8): 639–49. PMID 12479224. reversal of its age-related decline”. DNA Repair (Amst.)
2 (3): 295–307. doi:10.1016/S1568-7864(02)00219-7.
[41] Janion, C. (2001). “Some aspects of the SOS response PMID 12547392.
system-a critical survey”. Acta Biochim Pol. 48 (3): 599–
610. PMID 11833768. [53] Stuart, JA; Karahalil, B; Hogue, BA; Souza-Pinto, NC;
Bohr, VA. (2004). “Mitochondrial and nuclear DNA
[42] Erill, I; Campoy, S; Barbé, J (2007). “Aeons of base excision repair are affected differently by caloric re-
distress: an evolutionary perspective on the bacterial striction”. FASEB J 18 (3): 595–7. doi:10.1096/fj.03-
SOS response”. FEMS Microbiol Rev. 31 (6): 637– 0890fje. PMID 14734635.
656. doi:10.1111/j.1574-6976.2007.00082.x. PMID
17883408. [54] Walker, DW; McColl, G; Jenkins, NL; Harris, J; Lithgow,
GJ. (2000). “Evolution of lifespan in C. elegans”. Na-
[43] Schlacher, K; Pham, P; Cox, MM; Goodman, MF. ture 405 (6784): 296–7. doi:10.1038/35012693. PMID
(2006). “Roles of DNA Polymerase V and RecA Protein 10830948.
in SOS Damage-Induced Mutation”. Chem. Rev 106 (2):
406–419. doi:10.1021/cr0404951. PMID 16464012. [55] Johnson, George (28 December 2010). “Unearthing Pre-
historic Tumors, and Debate”. The New York Times. If we
[44] Fry RC, Begley TJ, Samson LD. (2004). Genome-wide lived long enough, sooner or later we all would get cancer.
responses to DNA-damaging agents. Annu Rev Microbiol.
[56] Alberts, B, Johnson A, Lewis J et al. (2002). “The Pre-
59 pp 357–77
ventable Causes of Cancer”. Molecular biology of the cell
[45] Espejel, S; Martin, M; Klatt, P; Martin-Caballero, J; (4th ed.). New York: Garland Science. ISBN 0-8153-
Flores, JM; Blasco, MA. (2004). “Shorter telom- 4072-9. A certain irreducible background incidence of
eres, accelerated ageing and increased lymphoma in cancer is to be expected regardless of circumstances: mu-
DNA-PKcs-deficient mice”. EMBO Rep 5 (5): 503–9. tations can never be absolutely avoided, because they are
doi:10.1038/sj.embor.7400127. PMC 1299048. PMID an inescapable consequence of fundamental limitations on
15105825. the accuracy of DNA replication, as discussed in Chapter
5. If a human could live long enough, it is inevitable that
[46] De Boer, J; Andressoo, JO; De Wit, J; Huijmans, J; at least one of his or her cells would eventually accumulate
Beems, RB; Van Steeg, H; Weeda, G; Van Der Horst, GT a set of mutations sufficient for cancer to develop.
et al. (2002). “Premature aging in mice deficient in DNA
[57] Baylin SB; Ohm, Joyce E. (February 2006). “Epigenetic
repair and transcription”. Science 296 (5571): 1276–9.
gene silencing in cancer - a mechanism for early oncogenic
doi:10.1126/science.1070174. PMID 11950998.
pathway addiction?". Nat. Rev. Cancer 6 (2): 107–16.
doi:10.1038/nrc1799. PMID 16491070.
[47] Dolle, ME; Busuttil, RA; Garcia, AM; Wijnhoven, S; van
Drunen, E; Niedernhofer, LJ; der Horst, G; Hoeijmak- [58] Kanwal R, Gupta S (April 2012). “Epigenetic modifi-
ers, JH et al. (2006). “Increased genomic instability is cations in cancer”. Clinical Genetics 81 (4): 303–11.
not a prerequisite for shortened life span in DNA repair doi:10.1111/j.1399-0004.2011.01809.x. PMC 3590802.
deficient mice”. Mutation Research 596 (1–2): 22–35. PMID 22082348.
doi:10.1016/j.mrfmmm.2005.11.008. PMID 16472827.
[59] Baldassarre G, Battista S, Belletti B et al. (April
[48] Kobayashi, Y; Narumi, I; Satoh, K; Funayama, T; 2003). “Negative regulation of BRCA1 gene ex-
Kikuchi, M; Kitayama, S; Watanabe, H. (2004). “Radia- pression by HMGA1 proteins accounts for the re-
tion response mechanisms of the extremely radioresistant duced BRCA1 protein levels in sporadic breast carci-
bacterium Deinococcus radiodurans”. Biol Sci Space 18 noma”. Molecular and Cellular Biology 23 (7): 2225–38.
(3): 134–5. PMID 15858357. doi:10.1128/MCB.23.7.2225-2238.2003. PMC 150734.
PMID 12640109.
[49] Spindler, SR. (2005). “Rapid and reversible induc-
tion of the longevity, anticancer and genomic effects of [60] Jacinto FV, Esteller M; Esteller, M. (July 2007).
caloric restriction”. Mech Ageing Dev 126 (9): 960–6. “Mutator pathways unleashed by epigenetic silencing
doi:10.1016/j.mad.2005.03.016. PMID 15927235. in human cancer”. Mutagenesis 22 (4): 247–53.
doi:10.1093/mutage/gem009. PMID 17412712.
[50] Tissenbaum, HA; Guarente, L. (2001). “In-
creased dosage of a sir-2 gene extends life span in [61] Lahtz C; Pfeifer, G. P. (February 2011). “Epigenetic
Caenorhabditis elegans”. Nature 410 (6825): 227–30. changes of DNA repair genes in cancer”. J Mol Cell
doi:10.1038/35065638. PMID 11242085. Biol 3 (1): 51–8. doi:10.1093/jmcb/mjq053. PMC
19.2. DNA REPAIR 321

3030973. PMID 21278452. http://jmcb.oxfordjournals. colorectal cancers: detection of mutations, loss of expres-
org/content/3/1/51.long sion, and weak association with G:C>A:T transitions”.
Gut 54 (6): 797–802. doi:10.1136/gut.2004.059535.
[62] Bernstein C, Nfonsam V, Prasad AR, Bernstein H PMC 1774551. PMID 15888787.
(March 2013). “Epigenetic field defects in progression
to cancer”. World J Gastrointest Oncol 5 (3): 43– [73] Shen L, Kondo Y, Rosner GL et al. (September 2005).
9. doi:10.4251/wjgo.v5.i3.43. PMC 3648662. PMID “MGMT promoter methylation and field defect in spo-
23671730. radic colorectal cancer”. Journal of the National Can-
cer Institute 97 (18): 1330–8. doi:10.1093/jnci/dji275.
[63] Bernstein C, Prasad AR, Nfonsam V, Bernstein H. (2013). PMID 16174854.
"Chapter 16: DNA Damage, DNA Repair and Cancer",
New Research Directions in DNA Repair, Prof. Clark [74] Psofaki V, Kalogera C, Tzambouras N et al. (July
Chen (Ed.), ISBN 978-953-51-1114-6, InTech. 2010). “Promoter methylation status of hMLH1,
MGMT, and CDKN2A/p16 in colorectal adenomas”.
[64] Narayanan L, Fritzell JA, Baker SM, Liskay RM, Glazer World Journal of Gastroenterology 16 (28): 3553–60.
PM (April 1997). “Elevated levels of mutation in mul- doi:10.3748/wjg.v16.i28.3553. PMC 2909555. PMID
tiple tissues of mice deficient in the DNA mismatch re- 20653064.
pair gene Pms2”. Proceedings of the National Academy of
Sciences of the United States of America 94 (7): 3122– [75] Lee KH, Lee JS, Nam JH et al. (October 2011).
7. doi:10.1073/pnas.94.7.3122. PMC 20332. PMID “Promoter methylation status of hMLH1, hMSH2, and
9096356. MGMT genes in colorectal cancer associated with
adenoma-carcinoma sequence”. Langenbeck’s Archives
[65] Hegan DC, Narayanan L, Jirik FR, Edelmann W, Liskay of Surgery 396 (7): 1017–26. doi:10.1007/s00423-011-
RM, Glazer PM (December 2006). “Differing patterns of 0812-9. PMID 21706233.
genetic instability in mice deficient in the mismatch repair
genes Pms2, Mlh1, Msh2, Msh3 and Msh6”. Carcinogen- [76] Amatu A, Sartore-Bianchi A, Moutinho C et al. (April
esis 27 (12): 2402–8. doi:10.1093/carcin/bgl079. PMC 2013). “Promoter CpG island hypermethylation of the
2612936. PMID 16728433. DNA repair enzyme MGMT predicts clinical response to
dacarbazine in a phase II study for metastatic colorec-
[66] Tutt AN, van Oostrom CT, Ross GM, van Steeg H, tal cancer”. Clinical Cancer Research 19 (8): 2265–
Ashworth A (March 2002). “Disruption of Brca2 in- 72. doi:10.1158/1078-0432.CCR-12-3518. PMID
creases the spontaneous mutation rate in vivo: synergism 23422094.
with ionizing radiation”. EMBO Reports 3 (3): 255–
60. doi:10.1093/embo-reports/kvf037. PMC 1084010. [77] Mokarram P, Zamani M, Kavousipour S et al. (May
PMID 11850397. 2013). “Different patterns of DNA methylation of the two
distinct O6-methylguanine-DNA methyltransferase (O6-
[67] German J (March 1969). “Bloom’s syndrome. I. Ge- MGMT) promoter regions in colorectal cancer”. Molecu-
netical and clinical observations in the first twenty-seven lar Biology Reports 40 (5): 3851–7. doi:10.1007/s11033-
patients”. American Journal of Human Genetics 21 (2): 012-2465-3. PMID 23271133.
196–227. PMC 1706430. PMID 5770175.
[78] Truninger K, Menigatti M, Luz J et al. (May 2005).
[68] O'Hagan HM, Mohammad HP, Baylin SB (2008). “Immunohistochemical analysis reveals high frequency of
“Double strand breaks can initiate gene silencing and PMS2 defects in colorectal cancer”. Gastroenterology 128
SIRT1-dependent onset of DNA methylation in an ex- (5): 1160–71. doi:10.1053/j.gastro.2005.01.056. PMID
ogenous promoter CpG island”. PLoS Genetics 4 (8): 15887099.
e1000155. doi:10.1371/journal.pgen.1000155. PMC
2491723. PMID 18704159. [79] Valeri N, Gasparini P, Fabbri M et al. (April 2010).
“Modulation of mismatch repair and genomic stability by
[69] Cuozzo C, Porcellini A, Angrisano T et al. (July miR-155”. Proceedings of the National Academy of Sci-
2007). “DNA damage, homology-directed repair, and ences of the United States of America 107 (15): 6982–7.
DNA methylation”. PLoS Genetics 3 (7): e110. doi:10.1073/pnas.1002472107. PMC 2872463. PMID
doi:10.1371/journal.pgen.0030110. PMC 1913100. 20351277.
PMID 17616978.
[80] Facista A, Nguyen H, Lewis C et al. (2012). “Deficient
[70] Malkin D (April 2011). “Li-fraumeni syn- expression of DNA repair enzymes in early progression
drome”. Genes & Cancer 2 (4): 475–84. to sporadic colon cancer”. Genome Integrity 3 (1): 3.
doi:10.1177/1947601911413466. PMC 3135649. doi:10.1186/2041-9414-3-3. PMC 3351028. PMID
PMID 21779515. 22494821.

[71] Fearon ER (November 1997). “Human can- [81] Human DNA Repair Genes, 15 April 2014, MD Ander-
cer syndromes: clues to the origin and na- son Cancer Center, University of Texas
ture of cancer”. Science 278 (5340): 1043–50.
doi:10.1126/science.278.5340.1043. PMID 9353177. [82] Xinrong Chen and Tao Chen (2011). "Chapter 18: Roles
of MicroRNA in DNA Damage and Repair", DNA Re-
[72] Halford S, Rowan A, Sawyer E, Talbot I, Tomlinson I pair, Dr. Inna Kruman (Ed.), ISBN 978-953-307-697-3,
(June 2005). “O(6)-methylguanine methyltransferase in InTech.
322 CHAPTER 19. DNA SYNTHESIS AND REPAIR

[83] Krishnan K, Steptoe AL, Martin HC et al. (Febru-

ary 2013). “MicroRNA-182-5p targets a network of
genes involved in DNA repair”. RNA 19 (2): 230–42.
doi:10.1261/rna.034926.112. PMC 3543090. PMID
23249749.

[84] Chaisaingmongkol J, Popanda O, Warta R et al. (De-

cember 2012). “Epigenetic screen of human DNA repair
genes identifies aberrant promoter methylation of NEIL1
in head and neck squamous cell carcinoma”. Oncogene
31 (49): 5108–16. doi:10.1038/onc.2011.660. PMID
22286769.

[85] Cromie, GA; Connelly, JC; Leach, DR (2001). “Recom-

bination at double-strand breaks and DNA ends: con- Illustration of how a normal cell is converted to a cancer cell,
served mechanisms from phage to humans”. Mol Cell. when an oncogene becomes activated
8 (6): 1163–74. doi:10.1016/S1097-2765(01)00419-1.
PMID 11779493.

[86] O'Brien, PJ. (2006). “Catalytic promiscuity and the diver- dozens of oncogenes have been identified in human can-
gent evolution of DNA repair enzymes”. Chem Rev 106 cer. Many cancer drugs target the proteins encoded by
(2): 720–52. doi:10.1021/cr040481v. PMID 16464022. oncogenes.[2][4][5][6]

[87] Maresca, B; Schwartz, JH (2006). “Sudden origins: a gen-

eral mechanism of evolution based on stress protein con- 19.3.1 History
centration and rapid environmental change”. Anat Rec
B New Anat. 289 (1): 38–46. doi:10.1002/ar.b.20089.
The first theory of oncogenes were provided around 1950
PMID 16437551.
by Niels Henrik Arley, a danish physicist (1938-40 sci-
entific private secretary for Niels Bohr. 1947-53 head of
19.2.10 External links Copenhagen University geophysics research.) At a time
where it was considered nonsense. Later the term “onco-
• Roswell Park Cancer Institute DNA Repair Lectures gene” was rediscovered in 1969 by National Cancer In-
stitute scientists, George Todaro and Robert Heubner.[7]
• A comprehensive list of Human DNA Repair Genes
The first confirmed oncogene was discovered in 1970 and
• 3D structures of some DNA repair enzymes was termed src (pronounced sarc as in sarcoma). Src
was in fact first discovered as an oncogene in a chicken
• Human DNA repair diseases retrovirus. Experiments performed by Dr. G. Steve Mar-
• DNA repair special interest group tin of the University of California, Berkeley demonstrated
that the Src was indeed the oncogene of the virus.[8] The
• DNA Repair first nucleotide sequence of v-src was sequenced in 1980
by A.P. Czernilofsky et al.[9]
• DNA Damage and DNA Repair
In 1976 Drs. Dominique Stehelin, J. Michael Bishop and
• Segmental Progeria Harold E. Varmus of the University of California, San
Francisco demonstrated that oncogenes were activated
• DNA-damage repair; the good, the bad, and the ugly
proto-oncogenes, found in many organisms including hu-
mans. For this discovery, proving Todaro and Heubner’s
“oncogene theory”, Bishop and Varmus were awarded the
19.3 Oncogenes Nobel Prize in Physiology or Medicine in 1989.[10]
Oncoproteins are any proteins coded by an oncogene and
For the journal, see Oncogene (journal). they play an important role in the regulation or synthe-
An oncogene is a gene that has the potential to cause sis of proteins linked to tumorigenic cell growth. Some
cancer.[1] In tumor cells, they are often mutated or ex- oncoproteins are accepted and used as tumor markers
pressed at high levels.[2]
Most normal cells will undergo a programmed form of
rapid cell death (apoptosis) when critical functions are 19.3.2 Proto-oncogene
altered. Activated oncogenes can cause those cells des-
ignated for apoptosis to survive and proliferate instead.[3] A proto-oncogene is a normal gene that can become
Most oncogenes require an additional step, such as mu- an oncogene due to mutations or increased expression.
tations in another gene, or environmental factors, such The resultant protein encoded by an oncogene is termed
as viral infection, to cause cancer. Since the 1970s, oncoprotein.[11] Proto-oncogenes code for proteins that
19.3. ONCOGENES 323

help to regulate cell growth and differentiation. Proto- 3. A chromosomal translocation (another type of
oncogenes are often involved in signal transduction and chromosome abnormality)
execution of mitogenic signals, usually through their
protein products. Upon activation, a proto-oncogene • There are 2 different types of chromosomal
(or its product) becomes a tumor-inducing agent, an translocations that can occur:
oncogene.[12] Examples of proto-oncogenes include RAS,
(a) translocation events which relocate a proto-
WNT, MYC, ERK, and TRK. The MYC gene is im-
oncogene to a new chromosomal site that leads
plicated in Burkitt’s Lymphoma, which starts when a
to higher expression
chromosomal translocation moves an enhancer sequence
within the vicinity of the MYC gene. The MYC gene (b) translocation events that lead to a fusion be-
codes for widely used transcription factors. When the tween a proto-oncogene and a 2nd gene (this
enhancer sequence is wrongly placed, these transcription creates a fusion protein with increased cancer-
factors are produced at much higher rates. Another ex- ous/oncogenic activity)
ample of an oncogene is the Bcr-Abl gene found on the • the expression of a constitutively active
Philadelphia Chromosome, a piece of genetic material hybrid protein. This type of mutation in
seen in Chronic Myelogenous Leukemia caused by the a dividing stem cell in the bone marrow
translocation of pieces from chromosomes 9 and 22. Bcr- leads to adult leukemia
Abl codes for a receptor tyrosine kinase, which is consti-
• Philadelphia Chromosome is an example
tutively active, leading to uncontrolled cell proliferation.
of this type of translocation event. This
(More information about the Philadelphia Chromosome
chromosome was discovered in 1960 by
below)
Peter Nowell and David Hungerford, and
it is a fusion of parts of DNA from chro-
Activation mosome 22 and chromosome 9. The bro-
ken end of chromosome 22 contains the
proto-oncogene “BCR” gene, which fuses with a frag-
deletion or point mutation
ment of chromosome 9 that contains the
gene amplification chromosome rearrangement
in coding sequence

or
"ABL1" gene. When these two chromo-
DNA
some fragments fuse the genes also fuse
RNA creating a new gene: “BCR-ABL”. This
a hypeactive protein a normal protein nearby regulatory fusion to actively
fused gene encodes for a protein that dis-
is produced
in normal amounts
is overexpressed sequence causes
normal protein
to be overexpressed
transcribed gene
overexpresses
fusion protein;
plays high protein tyrosine kinase activity
or fusion protein
is hyperactive
(this activity is due to the “ABL1” half
(A) (B) (C1) (C2)
of the protein). The unregulated expres-
sion of this protein activates other pro-
From proto-oncogene to oncogene
teins that are involved in cell cycle and
cell division which can cause a cell to
The proto-oncogene can become an oncogene by a rela- grow and divide uncontrollably (the cell
tively small modification of its original function. There becomes cancerous). As a result, the
are three basic methods of activation: Philadelphia Chromosome is associated
with Chronic Myelogenous Leukemia (as
1. A mutation within a proto-oncogene, or within a reg- mentioned before) as well as other forms
ulatory region (for example the promoter region), of Leukemia.[13]
can cause a change in the protein structure, causing

• an increase in protein (enzyme) activity The expression of oncogenes can be regulated by

microRNAs (miRNAs), small RNAs 21-25 nucleotides
• a loss of regulation in length that control gene expression by downregulating
them.[14] Mutations in such microRNAs (known as
2. An increase in the amount of a certain protein (pro-
oncomirs) can lead to activation of oncogenes.[15]
tein concentration), caused by
Antisense messenger RNAs could theoretically be used
• an increase of protein expression (through to block the effects of oncogenes.
misregulation)
• an increase of protein (mRNA) stability, pro- 19.3.3 Classification
longing its existence and thus its activity in the
cell There are several systems for classifying
• gene duplication (one type of chromosome ab- oncogenes,[16][17] but there is not yet a widely ac-
normality), resulting in an increased amount of cepted standard. They are sometimes grouped both
protein in the cell spatially (moving from outside the cell inwards) and
324 CHAPTER 19. DNA SYNTHESIS AND REPAIR

chronologically (parallelling the “normal” process of 19.3.4 See also

signal transduction). There are several categories that
are commonly used: • Oncogenomics
More detailed information for the above Table: • Tumor suppressor gene

• Oncovirus

• Growth factors are usually • Genetic predisposition

secreted by either specialized
or not specialized cells to • Quantitative trait locus
induce cell proliferation in
• Genetic susceptibility
themselves, nearby cells, or
distant cells. An oncogene
may cause a cell to secrete
19.3.5 References
growth factors even though it
does not normally do so. It will [1] Wilbur, Beth, editor. The World of the Cell, Becker,
thereby induce its own uncon- W.M., et al., 7th ed. San Francisco, CA; 2009.
trolled proliferation (autocrine
loop), and proliferation of [2] Kimball’s Biology Pages. “Oncogenes” Free full text
neighboring cells. It may also
cause production of growth [3] The Nobel Prize in Physiology or Medicine 2002. Illus-
trated presentation.
hormones in other parts of the
body. [4] Croce CM (Jan 2008). “Oncogenes and cancer”. N Engl
J Med. 358 (5): 502–11. doi:10.1056/NEJMra072367.
• Receptor Tyrosine kinases add PMID 18234754.
phosphate groups to other pro-
teins to turn them on or off. [5] Yokota J (Mar 2000). “Tumor progression and
Receptor kinases add phos- metastasis”. Carcinogenesis. 21 (3): 497–503.
phate groups to receptor pro- doi:10.1093/carcin/21.3.497. PMID 10688870.
teins at the surface of the cell
[6] The Nobel Prize in Physiology or Medicine 1989 to J.
(which receive protein signals
Michael Bishop and Harold E. Varmus for their discov-
from outside the cell and trans-
ery of “the cellular origin of retroviral oncogenes”.
mit them to the inside of the
cell). Tyrosine kinases add [7] The Emperor of All Maladies, Siddhartha Mukherjee,
phosphate groups to the amino 2011, p. 363, endnote.
acid tyrosine in the target pro-
tein. They can cause cancer [8] The Hunting of the Src, G. Steven Martin, Nature Reviews
Molecular Cell Biology 2: 467 (2001)
by turning the receptor perma-
nently on (constitutively), even [9] (A.P. Czernilofsky et al., 1980, Nature Vol 287, pp 198-
without signals from outside 203).
the cell.
[10] Nobel Prize in Physiology or Medicine for 1989 jointly to
• Ras is a small GTPase that J. Michael Bishop and Harold E. Varmus for their discov-
hydrolyses GTP into GDP ery of “the cellular origin of retroviral oncogenes”. Press
and phosphate. Ras is ac- Release.
tivated by growth factor sig-
naling (i.e., EGF, TGFbeta) [11] Chapter 20 - NEOPLASMS OF THE THYROID - in:
Mitchell, Richard Sheppard; Kumar, Vinay; Abbas, Abul
and acting like a binary switch
K.; Fausto, Nelson. Robbins Basic Pathology. Philadel-
(on/off) in growth signaling phia: Saunders. ISBN 1-4160-2973-7. 8th edition.
pathways. Downstream ef-
fectors of Ras include three [12] Todd R, Wong DT; Wong (1999). “Oncogenes”. Anti-
mitogen-activated protein ki- cancer Res. 19 (6A): 4729–46. PMID 10697588.
nases Raf a MAP Kinase
Kinase Kinase (MAPKKK), [13] Chial, H (2008). “Proto-oncogenes to Oncogenes to Can-
cer”. Nature Education 1 (1).
MEK a MAP Kinase Kinase
(MAPKK), and ERK a MAP [14] Negrini M, Ferracin M, Sabbioni S, Croce CM; Ferracin;
Kinase(MAPK), which in turn Sabbioni; Croce (Jun 2007). “MicroRNAs in human can-
regulate genes that mediate cer: from research to therapy”. J Cell Sci. 120 (Pt 11):
cell proliferation. 1833–40. doi:10.1242/jcs.03450. PMID 17515481.
19.3. ONCOGENES 325

[15] Esquela-Kerscher A, Slack FJ; Slack (Apr 2006). “On-

comirs - microRNAs with a role in cancer”. Nat Rev
Cancer 6 (4): 259–69. doi:10.1038/nrc1840. PMID
16557279.

[16] THE Medical Biochemistry Page

[17] Classification of Oncogene Function

[18] Press, Richard; Anita Misra; Glenda Gillaspy; David

Samols; David A. Goldthwait2 (June 1, 1989). “Control
of the Expression of c-sis mRNA in Human Glioblastoma
Cells by Phorbol Ester and Transforming Growth Factor
ß1”. Cancer Research (49): 2914–2920.

[19] Gschwind, Andreas; Fischer, Oliver M.; Ullrich, Axel

(May 2004). “Timeline: The discovery of receptor tyro-
sine kinases: targets for cancer therapy”. Nature Reviews
Cancer 4 (5): 361–370. doi:10.1038/nrc1360. PMID
15122207.

[20] Summy, Justin M.; Gallick, GE (1 January 2003).

“Src family kinases in tumor progression and metasta-
sis”. Cancer and Metastasis Reviews 22 (4): 337–358.
doi:10.1023/A:1023772912750. PMID 12884910.

[21] Thomas, Sheila M.; Brugge, Joan S. (1 November

1997). “CELLULAR FUNCTIONS REGULATED
BY SRC FAMILY KINASES”. Annual Review of
Cell and Developmental Biology 13 (1): 513–609.
doi:10.1146/annurev.cellbio.13.1.513. PMID 9442882.

[22] Garnett, Mathew J.; Marais, Richard (1 October 2004).

“Guilty as charged: B-RAF is a human oncogene”. Can-
cer Cell 6 (4): 313–319. doi:10.1016/j.ccr.2004.09.022.
PMID 15488754.

[23] Leicht, D; Vitaly Balan; Alexander Kaplun; Vinita Singh-

Gupta; Ludmila Kaplun; Melissa Dobson; Guri Tzivion
(August 2007). “Rafkinases: Function, regulation and
role in human cancer”. Biochimica et Biophysica Acta
(BBA) - Molecular Cell Research 1773 (8): 1196–1212.
doi:10.1016/j.bbamcr.2007.05.001.

[24] Bos, JL (Sep 1, 1989). “ras oncogenes in human can-

cer: a review”. Cancer Research 49 (17): 4682–9. PMID
2547513.

[25] Hilgenfeld, Rolf (1 December 1995). “Regulatory GT-

Pases”. Current Opinion in Structural Biology 5 (6):
810–817. doi:10.1016/0959-440X(95)80015-8. PMID
8749370.

[26] Felsher, Dean W.; Bishop, J.Michael (August 1999).

“Reversible Tumorigenesis by MYC in Hematopoi-
etic Lineages”. Molecular Cell 4 (2): 199–207.
doi:10.1016/S1097-2765(00)80367-6. PMID 10488335.

19.3.6 External links

• Drosophila Oncogenes and Tumor Suppressors -
The Interactive Fly
Chapter 20

RNA synthesis and processing

20.1 Transcription This is done by breaking the hydrogen bonds be-

tween complementary DNA nucleotides.
This article is about a genetic process. For other uses, see
Transcription. 3. RNA polymerase adds matching RNA nucleotides
Transcription is the first step of gene expression, in to the complementary nucleotides of one DNA
strand.

4. RNA sugar-phosphate backbone forms with assis-

tance from RNA polymerase to form an RNA
strand.

5. Hydrogen bonds of the untwisted RNA-DNA helix

break, freeing the newly synthesized RNA strand.

6. If the cell has a nucleus, the RNA may be fur-

ther processed. This may include polyadenylation,
capping, and splicing.

7. The RNA may remain in the nucleus or exit to the

cytoplasm through the nuclear pore complex.

The stretch of DNA transcribed into an RNA molecule is

Simplified diagram of mRNA synthesis and processing. Enzymes called a transcription unit and encodes at least one gene. If
not shown. the gene transcribed encodes a protein, messenger RNA
(mRNA) will be transcribed; the mRNA will in turn
which a particular segment of DNA is copied into RNA serve as a template for the protein’s synthesis through
(mRNA) by the enzyme RNA polymerase. translation. Alternatively, the transcribed gene may en-
Both RNA and DNA are nucleic acids, which use base code for either non-coding RNA (such as microRNA),
pairs of nucleotides as a complementary language. The ribosomal RNA (rRNA), transfer RNA (tRNA), or other
two can be converted back and forth from DNA to RNA enzymatic RNA molecules called ribozymes.[1] Overall,
by the action of the correct enzymes. During tran- RNA helps synthesize, regulate, and process proteins; it
scription, a DNA sequence is read by an RNA poly- therefore plays a fundamental role in performing func-
merase, which produces a complementary, antiparallel tions within a cell.
RNA strand called a primary transcript. In virology, the term may also be used when referring
Transcription proceeds in the following general steps: to mRNA synthesis from an RNA molecule (i.e., RNA
replication). For instance, the genome of a negative-
1. One or more sigma factor protein binds to the sense single-stranded RNA (ssRNA -) virus may be tem-
RNA polymerase holoenzyme, allowing it to bind plate for a positive-sense single-stranded RNA (ssRNA
to promoter DNA. +). This is because the positive-sense strand contains the
information needed to translate the viral proteins for viral
2. RNA polymerase creates a transcription bubble, replication afterwards. This process is catalysed by a vi-
which separates the two strands of the DNA helix. ral RNA replicase.[2]

326
20.1. TRANSCRIPTION 327

20.1.1 Background found 25-30 base pairs upstream from the TSS.[4] The
TATA box, as a core promoter, is the binding site for
A DNA transcription unit encoding for a protein may a transcription factor known as TATA-binding protein
contain both a coding sequence, which will translated into (TBP), which is itself a subunit of another transcrip-
the protein, and regulatory sequences, which direct and tion factor, called Transcription Factor II D (TFIID).
regulate the synthesis of that protein. The regulatory se- After TFIID binds to the TATA box via the TBP, five
quence before ("upstream" from) the coding sequence is more transcription factors and RNA polymerase com-
called the five prime untranslated region (5'UTR); the se- bine around the TATA box in a series of stages to
quence after ("downstream" from) the coding sequence form a preinitiation complex. One transcription fac-
is called the three prime untranslated region (3'UTR).[1] tor, Transcription factor II H, has two components with
As opposed to DNA replication, transcription results in helicase activity and so is involved in the separating of op-
an RNA complement that includes the nucleotide uracil posing strands of double-stranded DNA to form the ini-
(U) in all instances where thymine (T) would have oc- tial transcription bubble. However, only a low, or basal,
curred in a DNA complement. rate of transcription is driven by the preinitiation complex
alone. Other proteins known as activators and repressors,
Only one of the two DNA strands serve as a template along with any associated coactivators or corepressors,
for transcription. The antisense strand of DNA is read are responsible for modulating transcription rate.[4]
by RNA polymerase from the 3' end to the 5' end dur-
ing transcription (3' → 5'). The complementary RNA is Thus, preinitiation complex contains:.
created in the opposite direction, in the 5' → 3' direction,
matching the sequence of the sense strand with the excep- 1. Core Promoter Sequence
tion of switching uracil for thymine. This directionality is
2. Transcription Factors
because RNA polymerase can only add nucleotides to the
3' end of the growing mRNA chain. This use of only the 3. RNA Polymerase
3' → 5' DNA strand eliminates the need for the Okazaki
fragments that are seen in DNA replication.[1] This re- 4. Activators and Repressors.
moves the need for an RNA primer to initiate RNA syn-
thesis, as is the case in DNA replication. The transcription preinitiation in archaea is, in essence,
The non-template sense strand of DNA is called the homologous [5]
to that of eukaryotes, but is much less
coding strand, because its sequence is the same as the complex. The archaeal preinitiation complex assem-
newly created RNA transcript (except for the substitu- bles at a TATA-box binding site; however, in archaea,
tion of uracil for thymine). This is the strand that is used this complex is composed of only RNA polymerase II,
by convention when presenting a DNA sequence. TBP, and TFB (the archaeal homologue of eukaryotic
transcription factor II B (TFIIB)).[6][7]
Transcription has some proofreading mechanisms, but
they are fewer and less effective than the controls for
copying DNA; therefore, transcription has a lower copy- Initiation
ing fidelity than DNA replication.[3]
RNAP

20.1.2 Major steps Coding

Strand
5' 3'
Transcription is divided into pre-initiation, initiation, pro- 3'
Template
5'

moter clearance, elongation and termination.[1] Gene Strand

Simple diagram of transcription initiation. RNAP = RNA poly-

Pre-initiation merase

In eukaryotes, RNA polymerase, and therefore the ini- In bacteria, transcription begins with the binding of
tiation of transcription, requires the presence of a core RNA polymerase to the promoter in DNA. RNA poly-
promoter sequence in the DNA. Promoters are regions merase is a core enzyme consisting of five subunits: 2 α
of DNA that promote transcription and, in eukaryotes, subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. At
are found at −30, −75, and −90 base pairs upstream the start of initiation, the core enzyme is associated with
from the transcription start site (abbreviated to TSS). a sigma factor that aids in finding the appropriate −35
Transcription factors are proteins that bind to these and −10 base pairs upstream of promoter sequences.[8]
promoter sequences and facilitate the binding of RNA When the sigma factor and RNA polymerase combine,
Polymerase.[4] they form a holoenzyme.
The most characterized type of core promoter in eukary- Transcription initiation is more complex in eukaryotes.
otes is a short DNA sequence known as a TATA box, Eukaryotic RNA polymerase does not directly recognize
328 CHAPTER 20. RNA SYNTHESIS AND PROCESSING

the core promoter sequences. Instead, a collection of pro- mRNA transcription can involve multiple RNA poly-
teins called transcription factors mediate the binding of merases on a single DNA template and multiple rounds
RNA polymerase and the initiation of transcription. Only of transcription (amplification of particular mRNA), so
after certain transcription factors are attached to the pro- many mRNA molecules can be rapidly produced from a
moter does the RNA polymerase bind to it. The com- single copy of a gene.
pleted assembly of transcription factors and RNA poly- Elongation also involves a proofreading mechanism that
merase bind to the promoter, forming a transcription ini- can replace incorrectly incorporated bases. In eukary-
tiation complex. Transcription in the archaea domain is otes, this may correspond with short pauses during tran-
similar to transcription in eukaryotes.[9]
scription that allow appropriate RNA editing factors to
bind. These pauses may be intrinsic to the RNA poly-
Promoter clearance merase or due to chromatin structure.

After the first bond is synthesized, the RNA polymerase

must clear the promoter. During this time there is a ten- Termination
dency to release the RNA transcript and produce trun-
cated transcripts. This is called abortive initiation and is Main article: Terminator (genetics)
common for both eukaryotes and prokaryotes.[10]
In prokaryotes, abortive initiation continues to occur Bacteria use two different strategies for transcription
until an RNA product of a threshold length of approx- termination - Rho-independent termination and Rho-
imately 10 nucleotides is synthesized, at which point pro- dependent termination. In Rho-independent transcrip-
moter escape occurs and a transcription elongation com- tion termination, also called intrinsic termination, RNA
plex is formed. The σ factor is released according to transcription stops when the newly synthesized RNA
a stochastic model.[11] Mechanistically, promoter escape molecule forms a G-C-rich hairpin loop followed by a
occurs through a scrunching mechanism, where the en- run of Us. When the hairpin forms, the mechanical stress
ergy built up by DNA scrunching provides the energy breaks the weak rU-dA bonds, now filling the DNA-RNA
needed to break interactions between RNA polymerase hybrid. This pulls the poly-U transcript out of the ac-
holoenzyme and the promoter.[12] tive site of the RNA polymerase, in effect, terminating
transcription. In the “Rho-dependent” type of termina-
In eukaryotes, after several rounds of 10nt abortive ini- tion, a protein factor called "Rho" destabilizes the in-
tiation, promoter clearance coincides with the TFIIH’s teraction between the template and the mRNA, thus re-
phosphorylation of serine 5 on the carboxy terminal do- leasing the newly synthesized mRNA from the elongation
main of RNAP II, leading to the recruitment of capping complex.[15]
enzyme (CE).[13][14] The exact mechanism of how CE in-
duces promoter clearance in eukaryotes is not yet known. Transcription termination in eukaryotes is less under-
stood but involves cleavage of the new transcript followed
by template-independent addition of adenines at its new
Elongation 3' end, in a process called polyadenylation.[16]

Coding
5' RNAP
Strand
3' 20.1.3 Inhibitors
3' 5'
Template
5'
Strand
Transcription inhibitors can be used as antibiotics against,
for example, pathogenic bacteria (antibacterials) and
Simple diagram of transcription elongation
fungi (antifungals). An example of such an an-
tibacterial is rifampicin, which inhibits prokaryotic
One strand of the DNA, the template strand (or noncod-
DNA transcription into mRNA by inhibiting DNA-
ing strand), is used as a template for RNA synthesis. As
dependent RNA polymerase by binding its beta-
transcription proceeds, RNA polymerase traverses the
subunit. 8-Hydroxyquinoline is an antifungal transcrip-
template strand and uses base pairing complementarity
tion inhibitor.[17] The effects of histone methylation may
with the DNA template to create an RNA copy. Although
also work to inhibit the action of transcription.
RNA polymerase traverses the template strand from 3' →
5', the coding (non-template) strand and newly formed
RNA can also be used as reference points, so transcrip-
tion can be described as occurring 5' → 3'. This pro-
20.1.4 Transcription factories
duces an RNA molecule from 5' → 3', an exact copy of
the coding strand (except that thymines are replaced with Main article: Transcription factories
uracils, and the nucleotides are composed of a ribose (5-
carbon) sugar where DNA has deoxyribose (one fewer Active transcription units are clustered in the nu-
oxygen atom) in its sugar-phosphate backbone). cleus, in discrete sites called transcription factories or
20.1. TRANSCRIPTION 329

euchromatin. Such sites can be visualized by allowing

engaged polymerases to extend their transcripts in tagged
precursors (Br-UTP or Br-U) and immuno-labeling the
tagged nascent RNA. Transcription factories can also
be localized using fluorescence in situ hybridization
or marked by antibodies directed against polymerases.
There are ~10,000 factories in the nucleoplasm of a HeLa
cell, among which are ~8,000 polymerase II factories
and ~2,000 polymerase III factories. Each polymerase
II factory contains ~8 polymerases. As most active tran-
scription units are associated with only one polymerase,
each factory usually contains ~8 different transcription
units. These units might be associated through promot-
ers and/or enhancers, with loops forming a ‘cloud’ around
the factor.[18]

20.1.5 History
A molecule that allows the genetic material to be real-
ized as a protein was first hypothesized by François Jacob
and Jacques Monod. Severo Ochoa won a Nobel Prize
in Physiology or Medicine in 1959 for developing a pro- Electron micrograph of transcription of ribosomal RNA. The
cess for synthesizing RNA in vitro with polynucleotide forming ribosomal RNA strands are visible as branches from the
phosphorylase, which was useful for cracking the genetic main DNA strand.
code. RNA synthesis by RNA polymerase was estab-
lished in vitro by several laboratories by 1965; how-
• MS2 tagging: by incorporating RNA stem loops,
ever, the RNA synthesized by these enzymes had prop-
such as MS2, into a gene, these become incorpo-
erties that suggested the existence of an additional factor
rated into newly synthesized RNA. The stem loops
needed to terminate transcription correctly.
can then be detected using a fusion of GFP and
In 1972, Walter Fiers became the first person to actually the MS2 coat protein, which has a high affinity,
prove the existence of the terminating enzyme. sequence-specific interaction with the MS2 stem
Roger D. Kornberg won the 2006 Nobel Prize in Chem- loops. The recruitment of GFP to the site of
istry “for his studies of the molecular basis of eukaryotic transcription is visualised as a single fluorescent
transcription”.[19] spot. This new approach has revealed that transcrip-
tion occurs in discontinuous bursts, or pulses (see
Transcriptional bursting). With the notable excep-
20.1.6 Measuring and detecting transcrip- tion of in situ techniques, most other methods pro-
tion vide cell population averages, and are not capable of
detecting this fundamental property of genes.[20]
Transcription can be measured and detected in a variety
• Northern blot: the traditional method, and until the
of ways:
advent of RNA-Seq, the most quantitative

• Nuclear Run-on assay: measures the relative abun- • RNA-Seq: applies next-generation sequencing tech-
dance of newly formed transcripts niques to sequence whole transcriptomes, which
allows the measurement of relative abundance of
• RNase protection assay and ChIP-Chip of RNAP: RNA, as well as the detection of additional varia-
detect active transcription sites tions such as fusion genes, post-transcriptional edits
and novel splice sites
• RT-PCR: measures the absolute abundance of total
or nuclear RNA levels, which may however differ
from transcription rates 20.1.7 Reverse transcription
• DNA microarrays: measures the relative abundance
of the global total or nuclear RNA levels; however, Some viruses (such as HIV, the cause of AIDS), have the
these may differ from transcription rates ability to transcribe RNA into DNA. HIV has an RNA
genome that is reverse transcribed into DNA. The result-
• In situ hybridization: detects the presence of a tran- ing DNA can be merged with the DNA genome of the
script host cell. The main enzyme responsible for synthesis of
330 CHAPTER 20. RNA SYNTHESIS AND PROCESSING

20.1.8 See also

• Crick’s central dogma - DNA is transcribed to RNA,
which is translated to polypeptides (polypeptides
cannot “reverse translate” into RNA or DNA)

• Eukaryotic transcription

• Gene regulation

• Bacterial transcription

• RNA Polymerase

• Reverse transcription - process viruses use to make

DNA from RNA
Scheme of reverse transcription
• Splicing - process of removing introns from precur-
sor messenger RNA (pre-mRNA) to make messen-
ger RNA (mRNA)

• Translation - process of decoding RNA to form

DNA from an RNA template is called reverse transcrip-
polypeptides
tase.
In the case of HIV, reverse transcriptase is responsible • Transcription factor
for synthesizing a complementary DNA strand (cDNA)
to the viral RNA genome. The enzyme ribonuclease
H then digests the RNA strand, and reverse transcrip-
20.1.9 References
tase synthesises a complementary strand of DNA to form [1] Eldra P. Solomon, Linda R. Berg, Diana W. Martin. Biol-
a double helix DNA structure (“cDNA”). The cDNA ogy, 8th Edition, International Student Edition. Thomson
is integrated into the host cell’s genome by the enzyme Brooks/Cole. ISBN 978-0495317142
integrase, which causes the host cell to generate viral pro-
teins that reassemble into new viral particles. In HIV, [2] “Tentative identification of RNA-dependent RNA poly-
subsequent to this, the host cell undergoes programmed merases of dsRNA viruses and their relationship to pos-
cell death, or apoptosis of T cells. [21]
However, in other itive strand RNA viral polymerases”. FEBS Letters 252:
42–46. doi:10.1016/0014-5793(89)80886-5.
retroviruses, the host cell remains intact as the virus buds
out of the cell. [3] Berg J, Tymoczko JL, Stryer L (2006). Biochemistry (6th
Some eukaryotic cells contain an enzyme with reverse ed.). San Francisco: W. H. Freeman. ISBN 0-7167-
8724-5.
transcription activity called telomerase. Telomerase is
a reverse transcriptase that lengthens the ends of lin- [4] Basic Medical Biochemistry, 4th edition, Marks. Chapter
ear chromosomes. Telomerase carries an RNA template 14
from which it synthesizes a repeating sequence of DNA,
or “junk” DNA. This repeated sequence of DNA is called [5] Littlefield, O., Korkhin, Y., and Sigler, P.B. (1999).
a telomere and can be thought of as a “cap” for a chromo- “The structural basis for the oriented assembly of a
TBP/TFB/promoter complex”. PNAS 96 (24): 13668–
some. It is important because every time a linear chro-
13673. doi:10.1073/pnas.96.24.13668. PMC 24122.
mosome is duplicated, it is shortened. With this “junk”
PMID 10570130.
DNA or “cap” at the ends of chromosomes, the short-
ening eliminates some of the non-essential, repeated se- [6] Hausner, W., Michael Thomm, M. (2001). “Events
quence rather than the protein-encoding DNA sequence, during Initiation of Archaeal Transcription: Open
that is farther away from the chromosome end. Complex Formation and DNA-Protein Interac-
tions”. Journal of Bacteriology 183 (10): 3025–3031.
Telomerase is often activated in cancer cells to enable doi:10.1128/JB.183.10.3025-3031.2001. PMC 95201.
cancer cells to duplicate their genomes indefinitely with- PMID 11325929.
out losing important protein-coding DNA sequence. Ac-
tivation of telomerase could be part of the process that [7] Qureshi, SA; Bell, SD; Jackson, SP (1997). “Factor
allows cancer cells to become immortal. The immortal- requirements for transcription in the archaeon Sul-
izing factor of cancer via telomere lengthening due to folobus shibatae”. EMBO Journal 16 (10): 2927–2936.
doi:10.1093/emboj/16.10.2927. PMC 1169900. PMID
telomerase has been proven to occur in 90% of all car-
9184236.
cinogenic tumors in vivo with the remaining 10% using
an alternative telomere maintenance route called ALT or [8] Raven, Peter H. (2011). Biology (9th ed.). New York:
Alternative Lengthening of Telomeres.[22] McGraw-Hill. pp. 278–301. ISBN 978-0-07-353222-6.
20.2. REGULATION OF GENE EXPRESSION 331

[9] Mohamed Ouhammouch, Robert E. Dewhurst, Win- [22] ALT and Telomerase from Nature. Retrieved May 2010
fried Hausner, Michael Thomm, and E. Peter Gei-
duschek (2003). “Activation of archaeal transcrip-
tion by recruitment of the TATA-binding protein”. 20.1.10 External links
Proceedings of the National Academy of Sciences of
the United States of America 100 (9): 5097–5102. • Interactive Java simulation of transcription initia-
doi:10.1073/pnas.0837150100. PMC 154304. PMID tion. From Center for Models of Life at the Niels
12692306. Bohr Institute.
[10] Goldman, S.; Ebright, R.; Nickels, B. (May
• Interactive Java simulation of transcription
2009). “Direct detection of abortive RNA tran-
scripts in vivo”. Science 324 (5929): 927–928.
interference--a game of promoter dominance in
doi:10.1126/science.1169237. PMC 2718712. PMID bacterial virus. From Center for Models of Life at
19443781. the Niels Bohr Institute.

[11] Raffaelle, M.; Kanin, E. I.; Vogt, J.; Burgess, R. R.; • Biology animations about this topic under Chapter
Ansari, A. Z. (2005). “Holoenzyme Switching and 15 and Chapter 18
Stochastic Release of Sigma Factors from RNA Poly-
merase in Vivo”. Molecular Cell 20 (3): 357–366. • Virtual Cell Animation Collection, Introducing
doi:10.1016/j.molcel.2005.10.011. PMID 16285918. Transcription
[12] Revyakin, A.; Liu, C.; Ebright, R.; Strick, T. (2006). • Easy to use DNA transcription site
“Abortive initiation and productive initiation by RNA
polymerase involve DNA scrunching”. Science 314
(5802): 1139–1143. doi:10.1126/science.1131398.
PMC 2754787. PMID 17110577. 20.2 Regulation of gene expression
[13] Mandal, S. S.; Chu, C.; Wada, T.; Handa, H.; Shatkin, Gene modulation redirects here. For informa-
A. J.; Reinberg, D. (2004). “Functional interactions of
tion on therapeutic regulation of gene expres-
RNA-capping enzyme with factors that positively and
negatively regulate promoter escape by RNA polymerase
sion, see therapeutic gene modulation.
II”. Proceedings of the National Academy of Sciences 101 For vocabulary, see Glossary of gene expression
(20): 7572–7577. doi:10.1073/pnas.0401493101. PMC terms
419647. PMID 15136722.

[14] Goodrich, J. A.; Tjian, R. (1994). “Transcription factors

IIE and IIH and ATP hydrolysis direct promoter clear-
ance by RNA polymerase II”. Cell 77 (1): 145–156.
doi:10.1016/0092-8674(94)90242-9. PMID 8156590.

[15] Richardson, J (2002). “Rho-dependent termination and

ATPases in transcript termination”. Biochimica et Bio-
physica Acta 1577 (2): 251–260. doi:10.1016/S0167-
4781(02)00456-6.

[16] Lykke-Andersen, S; Jensen, TH (2007). “Over-

lapping pathways dictate termination of RNA poly-
merase II transcription”. Biochimie 89 (10): 1177–82.
doi:10.1016/j.biochi.2007.05.007.

[17] 8-Hydroxyquinoline info from SIGMA-ALDRICH. Re-

trieved Feb 2012 Diagram showing at which stages in the DNA-mRNA-protein
[18] Papantonis, A (2012-10-26). “TNFα signals through spe- pathway expression can be controlled
cialized factories where responsive coding and miRNA
genes are transcribed”. Nature EMBO J. Regulation of gene expression includes a wide range
of mechanisms that are used by cells to increase or de-
[19] “Chemistry 2006”. Nobel Foundation. Retrieved March
29, 2007.
crease the production of specific gene products (protein
or RNA), and is informally termed gene regulation. So-
[20] Raj, A.; van Oudenaarden, A. (2008). “Na- phisticated programs of gene expression are widely ob-
ture, nurture, or chance: stochastic gene expres- served in biology, for example to trigger developmental
sion and its consequences”. Cell 135: 216–26. pathways, respond to environmental stimuli, or adapt to
doi:10.1016/j.cell.2008.09.050. new food sources. Virtually any step of gene expression
[21] Kolesnikova I. N. (2000). “Some patterns of apoptosis can be modulated, from transcriptional initiation, to RNA
mechanism during HIV-infection”. Dissertation (in Rus- processing, and to the post-translational modification of
sian). Retrieved February 20, 2011. a protein.
332 CHAPTER 20. RNA SYNTHESIS AND PROCESSING

Gene regulation is essential for viruses, prokaryotes and Structural

eukaryotes as it increases the versatility and adaptabil-
ity of an organism by allowing the cell to express pro- Transcription of DNA is dictated by its structure. In gen-
tein when needed. Although as early as 1951 Barbara eral, the density of its packing is indicative of the fre-
McClintock showed interaction between two genetic loci, quency of transcription. Octameric protein complexes
Activator (Ac) and Dissociator (Ds), in the color forma- called nucleosomes are responsible for the amount of
tion of maize seeds, the first discovery of a gene regula- supercoiling of DNA, and these complexes can be tem-
tion system is widely considered to be the identification in porarily modified by processes such as phosphorylation
1961 of the lac operon, discovered by Jacques Monod, in or more permanently modified by processes such as
which some enzymes involved in lactose metabolism are methylation. Such modifications are considered to be re-
expressed by the genome of E. coli only in the presence sponsible for more or less permanent changes in gene ex-
of lactose and absence of glucose. pression levels.[2]
Furthermore, in multicellular organisms, gene regula-
tion drives the processes of cellular differentiation and Chemical
morphogenesis, leading to the creation of different cell
types that possess different gene expression profiles, and Methylation of DNA is a common method of gene si-
hence produce different proteins/have different ultra- lencing. DNA is typically methylated by methyltrans-
structures that suit them to their functions (though they ferase enzymes on cytosine nucleotides in a CpG din-
all possess the genotype, which follows the same genome ucleotide sequence (also called "CpG islands" when
sequence). densely clustered). Analysis of the pattern of methy-
The initiating event leading to a change in gene ex- lation in a given region of DNA (which can be a pro-
pression include activation or deactivation of receptors. moter) can be achieved through a method called bisulfite
Also, there is evidence that changes in a cell’s choice of mapping. Methylated cytosine residues are unchanged by
catabolism leads to altered gene expressions.[1] the treatment, whereas unmethylated ones are changed to
uracil. The differences are analyzed by DNA sequenc-
ing or by methods developed to quantify SNPs, such
20.2.1 Regulated stages of gene expression as Pyrosequencing (Biotage) or MassArray (Sequenom),
measuring the relative amounts of C/T at the CG dinu-
cleotide. Abnormal methylation patterns are thought to
Any step of gene expression may be modulated, from the
be involved in oncogenesis.[3]
DNA-RNA transcription step to post-translational mod-
ification of a protein. The following is a list of stages Histone acetylation is also an important process in tran-
where gene expression is regulated, the most extensively scription. Histone acetyltransferase enzymes (HATs)
utilised point is Transcription Initiation: such as CREB-binding protein also dissociate the DNA
from the histone complex, allowing transcription to pro-
ceed. Often, DNA methylation and histone deacetylation
• Chromatin domains
work together in gene silencing. The combination of the
two seems to be a signal for DNA to be packed more
• Transcription
densely, lowering gene expression.
• Post-transcriptional modification
20.2.3 Regulation of transcription
• RNA transport
Main article: Transcriptional regulation
• Translation Regulation of transcription thus controls when transcrip-
tion occurs and how much RNA is created. Transcription
• mRNA degradation of a gene by RNA polymerase can be regulated by at least
five mechanisms:

20.2.2 Modification of DNA • Specificity factors alter the specificity of RNA

polymerase for a given promoter or set of promoters,
In eukaryotes, the accessibility of large regions of DNA making it more or less likely to bind to them (i.e.,
can depend on its chromatin structure, which can be al- sigma factors used in prokaryotic transcription).
tered as a result of histone modifications directed by
DNA methylation, ncRNA, or DNA-binding protein. • Repressors bind to the Operator, coding se-
Hence these modifications may up or down regulate the quences on the DNA strand that are close to or over-
expression of a gene. Some of these modifications that lapping the promoter region, impeding RNA poly-
regulate gene expression are inheritable and are referred merase’s progress along the strand, thus impeding
to as epigenetic regulation. the expression of the gene.The image to the right
20.2. REGULATION OF GENE EXPRESSION 333

mRNA is translated into proteins. Cells do this by mod-

ulating the capping, splicing, addition of a Poly(A) Tail,
the sequence-specific nuclear export rates, and, in several
contexts, sequestration of the RNA transcript. These pro-
cesses occur in eukaryotes but not in prokaryotes. This
modulation is a result of a protein or transcript that, in
turn, is regulated and may have an affinity for certain se-
quences.

20.2.5 Regulation of translation

Main article: Translational regulation

1: RNA Polymerase, 2: Repressor, 3: Promoter, 4: Operator, The translation of mRNA can also be controlled by a
5: Lactose, 6: lacZ, 7: lacY, 8: lacA. Top: The gene is es-
number of mechanisms, mostly at the level of initiation.
sentially turned off. There is no lactose to inhibit the repressor,
so the repressor binds to the operator, which obstructs the RNA
Recruitment of the small ribosomal subunit can indeed
polymerase from binding to the promoter and making lactase. be modulated by mRNA secondary structure, antisense
Bottom: The gene is turned on. Lactose is inhibiting the repres- RNA binding, or protein binding. In both prokaryotes
sor, allowing the RNA polymerase to bind with the promoter, and and eukaryotes, a large number of RNA binding proteins
express the genes, which synthesize lactase. Eventually, the lac- exist, which often are directed to their target sequence
tase will digest all of the lactose, until there is none to bind to the by the secondary structure of the transcript, which may
repressor. The repressor will then bind to the operator, stopping change depending on certain conditions, such as temper-
the manufacture of lactase. ature or presence of a ligand (aptamer). Some transcripts
act as ribozymes and self-regulate their expression.
demonstrates regulation by a repressor in the lac
operon.
20.2.6 Examples of gene regulation
• General transcription factors position RNA poly-
merase at the start of a protein-coding sequence • Enzyme induction is a process in which a molecule
and then release the polymerase to transcribe the (e.g., a drug) induces (i.e., initiates or enhances) the
mRNA. expression of an enzyme.

• Activators enhance the interaction between RNA • The induction of heat shock proteins in the fruit fly
polymerase and a particular promoter, encourag- Drosophila melanogaster.
ing the expression of the gene. Activators do this
by increasing the attraction of RNA polymerase for • The Lac operon is an interesting example of how
the promoter, through interactions with subunits of gene expression can be regulated.
the RNA polymerase or indirectly by changing the
• Viruses, despite having only a few genes, possess
structure of the DNA.
mechanisms to regulate their gene expression, typi-
• Enhancers are sites on the DNA helix that are cally into an early and late phase, using collinear sys-
bound by activators in order to loop the DNA bring- tems regulated by anti-terminators (lambda phage)
ing a specific promoter to the initiation complex. or splicing modulators (HIV).
Enhancers are much more common in eukaryotes
than prokaryotes, where only a few examples exist • GAL4 is a transcriptional activator that controls the
(to date).[4] expression of GAL1, GAL7, and GAL10 (all of
which code for the metabolic of galactose in yeast).
• Silencers are regions of DNA sequences that, when The GAL4/UAS system has been used in a vari-
bound by particular transcription factors, can silence ety of organisms across various phyla to study gene
expression of the gene. expression.[5]

20.2.4 Post-transcriptional regulation Developmental biology

Main article: Post-transcriptional regulation Main article: morphogen

After the DNA is transcribed and mRNA is formed, A large number of studied regulatory systems come from
there must be some sort of regulation on how much the developmental biology. Examples include:
334 CHAPTER 20. RNA SYNTHESIS AND PROCESSING

• The colinearity of the Hox gene cluster with their Inducible vs. repressible systems
nested antero-posterior patterning
Gene Regulation can be summarized by the response of
• It has been speculated that pattern generation of the respective system:
the hand (digits - interdigits) The gradient of Sonic
hedgehog (secreted inducing factor) from the zone • Inducible systems - An inducible system is off un-
of polarizing activity in the limb, which creates a less there is the presence of some molecule (called
gradient of active Gli3, which activates Gremlin, an inducer) that allows for gene expression. The
which inhibits BMPs also secreted in the limb, re- molecule is said to “induce expression”. The manner
sulting in the formation of an alternating pattern of by which this happens is dependent on the control
activity as a result of this reaction-diffusion system. mechanisms as well as differences between prokary-
otic and eukaryotic cells.
• Somitogenesis is the creation of segments (somites)
from a uniform tissue (Pre-somitic Mesoderm,
PSM). They are formed sequentially from anterior • Repressible systems - A repressible system is on
to posterior. This is achieved in amniotes possibly except in the presence of some molecule (called a
by means of two opposing gradients, Retinoic acid corepressor) that suppresses gene expression. The
in the anterior (wavefront) and Wnt and Fgf in the molecule is said to “repress expression”. The man-
posterior, coupled to an oscillating pattern (segmen- ner by which this happens is dependent on the
tation clock) composed of FGF + Notch and Wnt in control mechanisms as well as differences between
antiphase.[6] prokaryotic and eukaryotic cells.

• Sex determination in the soma of a Drosophila re- The GAL4/UAS system is an example of both an in-
quires the sensing of the ratio of autosomal genes ducible and repressible system. GAL4 binds an up-
to sex chromosome-encoded genes, which results in stream activation sequence (UAS) to activate the tran-
the production of sexless splicing factor in females, scription of the GAL1/GAL7/GAL10 cassette. On the
resulting in the female isoform of doublesex.[7] other hand, a MIG1 response to the presence of glucose
can inhibit GAL4 and therefore stop the expression of the
GAL1/GAL7/GAL10 cassette.[8]
20.2.7 Circuitry

Main article: Gene regulatory network Theoretical circuits

• Repressor/Inducer: an activation of a sensor results

in the change of expression of a gene
Up-regulation and down-regulation
• negative feedback: the gene product downregulates
Up-regulation is a process that occurs within a cell trig- its own production directly or indirectly, which can
gered by a signal (originating internal or external to the result in
cell), which results in increased expression of one or more
• keeping transcript levels constant/proportional
genes and as a result the protein(s) encoded by those
to a factor
genes. On the converse, down-regulation is a process
resulting in decreased gene and corresponding protein ex- • inhibition of run-away reactions when coupled
pression. with a positive feedback loop
• creating an oscillator by taking advantage in
• Up-regulation occurs, for example, when a cell is de- the time delay of transcription and translation,
ficient in some kind of receptor. In this case, more given that the mRNA and protein half-life is
receptor protein is synthesized and transported to shorter
the membrane of the cell and, thus, the sensitivity
of the cell is brought back to normal, reestablishing • positive feedback: the gene product upregulates its
homeostasis. own production directly or indirectly, which can re-
sult in

• Down-regulation occurs, for example, when a cell is • signal amplification

overstimulated by a neurotransmitter, hormone, or
• bistable switches when two genes inhibit each
drug for a prolonged period of time, and the expres-
other and both have positive feedback
sion of the receptor protein is decreased in order to
protect the cell (see also tachyphylaxis). • pattern generation
20.2. REGULATION OF GENE EXPRESSION 335

20.2.8 Study methods (actinomycin D or α-amanitin) or translation

inhibitors (Cycloheximide), respectively.
For DNA and RNA methods, see nucleic acid methods.
For protein methods, see protein methods.
20.2.9 See also
In general, most experiments investigating differential
• Enhancer (genetics)
expression used whole cell extracts of RNA, called
steady-state levels, to determine which genes changed and • Artificial transcription factors (small molecules that
by how much they did. These are, however, not infor- mimic transcription factor protein)
mative of where the regulation has occurred and may
actually mask conflicting regulatory processes (see post- • Cellular model
transcriptional regulation), but it is still the most com-
monly analysed (quantitative PCR and DNA microarray). • Conserved non-coding DNA sequence
When studying gene expression, there are several meth- • Spatiotemporal gene expression
ods to look at the various stages. In eukaryotes these in-
clude:
20.2.10 Notes and references
• The local chromatin environment of the region can
be determined by ChIP-chip analysis by pulling [1] Pereira, S. L.; Rodrigues, A. S.; Sousa, M. I.; Correia,
down RNA Polymerase II, Histone 3 modifications, M.; Perestrelo, T.; Ramalho-Santos, J. (2014). “From ga-
Trithorax-group protein, Polycomb-group protein, metogenesis and stem cells to cancer: common metabolic
or any other DNA-binding element to which a good themes”. Human Reproduction Update 20 (6): 924–943.
antibody is available. doi:10.1093/humupd/dmu034. ISSN 1355-4786.

• Epistatic interactions can be investigated by [2] Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R,
synthetic genetic array analysis Degner JF, Gilad Y, Pritchard JK (2011). “DNA methy-
lation patterns associate with genetic and gene expression
• Due to post-transcriptional regulation, transcription variation in HapMap cell lines”. Genome Biology 12 (1):
rates and total RNA levels differ significantly. To R10. doi:10.1186/gb-2011-12-1-r10. PMC 3091299.
measure the transcription rates nuclear run-on as- PMID 21251332.
says can be done and newer high-throughput meth- [3] Vertino PM, Spillare EA, Harris CC, Baylin SB (April
ods are being developed, using thiol labelling instead 1993). “Altered chromosomal methylation patterns ac-
of radioactivity.[9] company oncogene-induced transformation of human
bronchial epithelial cells” (PDF). Cancer Res. 53 (7):
• Only 5% of the RNA polymerised in the nucleus
1684–9. PMID 8453642.
actually exits,[10] and not only introns, abortive
products, and non-sense transcripts are degradated. [4] Austin S, Dixon R (June 1992). “The prokaryotic en-
Therefore, the differences in nuclear and cytoplas- hancer binding protein NTRC has an ATPase activity
mic levels can be see by separating the two fractions which is phosphorylation and DNA dependent”. EMBO
by gentle lysis.[11] J. 11 (6): 2219–28. PMC 556689. PMID 1534752.

• Alternative splicing can be analysed with a splicing [5] Barnett, J. A. (2004), A history of research on yeasts 7:
array or with a tiling array (see DNA microarray). enzymic adaptation and regulation. Yeast, 21: 703–746.
doi: 10.1002/yea.1113
• All in vivo RNA is complexed as RNPs. The quan-
tity of transcripts bound to specific protein can be [6] Dequéant ML, Pourquié O. Segmental patterning of the
also analysed by RIP-Chip. For example, DCP2 will vertebrate embryonic axis. Nat Rev Genet. 2008
give an indication of sequestered protein; ribosome- May;9(5):370-82. PMID 18414404
bound gives and indication of transcripts active in
[7] Gilbert SF (2003). Developmental biology, 7th ed., Sun-
transcription (although it should be noted that a derland, Mass: Sinauer Associates, 65–6. ISBN 0-87893-
more dated method, called polysome fractionation, 258-5.
is still popular in some labs)
[8] PMCID: PMC453065
• Protein levels can be analysed by Mass spectrom-
etry, which can be compared only to quantitative [9] Cheadle C, Fan J, Cho-Chung YS, Werner T, Ray J,
PCR data, as microarray data is relative and not ab- Do L, Gorospe M, Becker KG (2005). “Control of
solute. gene expression during T cell activation: alternate regula-
tion of mRNA transcription and mRNA stability”. BMC
• RNA and protein degradation rates are mea- Genomics 6: 75. doi:10.1186/1471-2164-6-75. PMC
sured by means of transcription inhibitors 1156890. PMID 15907206.
336 CHAPTER 20. RNA SYNTHESIS AND PROCESSING

[10] Jackson DA, Pombo A, Iborra F (2000). “The bal-

ance sheet for transcription: an analysis of nuclear RNA
metabolism in mammalian cells”. FASEB J. 14 (2): 242–
54. PMID 10657981.

[11] Schwanekamp JA, Sartor MA, Karyala S, Halbleib

D, Medvedovic M, Tomlinson CR (2006). “Genome-
wide analyses show that nuclear and cytoplasmic
RNA levels are differentially affected by dioxin”.
Biochim. Biophys. Acta 1759 (8–9): 388–402.
doi:10.1016/j.bbaexp.2006.07.005. PMID 16962184.

20.2.11 Bibliography
• Latchman, David S. (2005). Gene regulation: a eu-
karyotic perspective. Psychology Press. ISBN 978-
0-415-36510-9.

20.2.12 External links

Regulation of Gene Expression at the US National Li-
brary of Medicine Medical Subject Headings (MeSH)

• Cellular Darwinism
Chapter 21

Protein synthesis and modifications

21.1 Translation In translation, messenger RNA (mRNA)—produced by

transcription from DNA—is decoded by a ribosome to
produce a specific amino acid chain, or polypeptide. The
polypeptide later folds into an active protein and per-
forms its functions in the cell. The ribosome facili-
tates decoding by inducing the binding of complementary
tRNA anticodon sequences to mRNA codons. The tR-
NAs carry specific amino acids that are chained together
into a polypeptide as the mRNA passes through and is
“read” by the ribosome. The entire process is a part of
gene expression.
In brief, translation proceeds in four phases:

1. Initiation: The ribosome assembles around the tar-

get mRNA. The first tRNA is attached at the start
codon.
2. Elongation: The tRNA transfers an amino acid to
the tRNA corresponding to the next codon.
3. Translocation:The ribosome then moves (translo-
cates) to the next mRNA codon to continue the pro-
cess, creating an amino acid chain.
4. Termination: When a stop codon is reached, the
Overview of the translation of eukaryotic messenger RNA
ribosome releases the polypeptide.

In bacteria, translation occurs in the cell’s cytoplasm,

where the large and small subunits of the ribosome bind
to the mRNA. In eukaryotes, translation occurs in the
cytosol or across the membrane of the endoplasmic retic-
ulum in a process called vectorial synthesis. In many
instances, the entire ribosome/mRNA complex binds to
the outer membrane of the rough endoplasmic reticulum
(ER); the newly created polypeptide is stored inside the
ER for later vesicle transport and secretion outside of the
cell.
Many types of transcribed RNA, such as transfer RNA,
ribosomal RNA, and small nuclear RNA, do not undergo
translation into proteins.
Diagram showing the translation of mRNA and the synthesis of
A number of antibiotics act by inhibiting transla-
proteins by a ribosome tion. These include anisomycin, cycloheximide,
chloramphenicol, tetracycline, streptomycin,
In molecular biology and genetics, translation is the pro- erythromycin, and puromycin. Prokaryotic ribo-
cess in which cellular ribosomes create proteins. somes have a different structure from that of eukaryotic

337
338 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

ribosomes, and thus antibiotics can specifically target molecule. Each amino acid added is matched to a
bacterial infections without any harm to a eukaryotic three nucleotide subsequence of the mRNA. For each
host’s cells. such triplet possible, the corresponding amino acid is
accepted. The successive amino acids added to the
chain are matched to successive nucleotide triplets in the
21.1.1 Basic mechanisms mRNA. In this way the sequence of nucleotides in the
template mRNA chain determines the sequence of amino
Further information: Prokaryotic translation and acids in the generated amino acid chain.[1] Addition of
Eukaryotic translation an amino acid occurs at the C-terminus of the peptide
The basic process of protein production is addition of and thus translation is said to be amino-to-carboxyl
directed.[2]
The mRNA carries genetic information encoded as a ri-
bonucleotide sequence from the chromosomes to the ri-
bosomes. The ribonucleotides are “read” by translational
machinery in a sequence of nucleotide triplets called
codons. Each of those triplets codes for a specific amino
acid.
The ribosome molecules translate this code to a spe-
cific sequence of amino acids. The ribosome is a mul-
tisubunit structure containing rRNA and proteins. It is
the “factory” where amino acids are assembled into pro-
teins. tRNAs are small noncoding RNA chains (74-93
nucleotides) that transport amino acids to the ribosome.
tRNAs have a site for amino acid attachment, and a site
called an anticodon. The anticodon is an RNA triplet
complementary to the mRNA triplet that codes for their
cargo amino acid.
Aminoacyl tRNA synthetases (enzymes) catalyze the
A ribosome translating a protein that is secreted into the bonding between specific tRNAs and the amino acids that
endoplasmic reticulum. tRNAs are colored dark blue. their anticodon sequences call for. The product of this
reaction is an aminoacyl-tRNA. This aminoacyl-tRNA is
carried to the ribosome by EF-Tu, where mRNA codons
are matched through complementary base pairing to spe-
cific tRNA anticodons. Aminoacyl-tRNA synthetases
that mispair tRNAs with the wrong amino acids can pro-
duce mischarged aminoacyl-tRNAs, which can result in
inappropriate amino acids at the respective position in
protein. This “mistranslation”[3] of the genetic code nat-
urally occurs at low levels in most organisms, but cer-
tain cellular environments cause an increase in permissive
mRNA decoding, sometimes to the benefit of the cell.
The ribosome has three sites for tRNA to bind. They
are the aminoacyl site (abbreviated A), the peptidyl site
(abbreviated P) and the exit site (abbreviated E). With
respect to the mRNA, the three sites are oriented 5’ to
3’ E-P-A, because ribosomes move toward the 3' end
of mRNA. The A site binds the incoming tRNA with
the complementary codon on the mRNA. The P site
holds the tRNA with the growing polypeptide chain. The
E site holds the tRNA without its amino acid. When
Tertiary structure of tRNA. CCA tail in orange, Acceptor stem an aminoacyl-tRNA initially binds to its corresponding
in purple, D arm in red, Anticodon arm in blue with Anticodon codon on the mRNA, it is in the A site. Then, a peptide
in black, T arm in green. bond forms between the amino acid of the tRNA in the
A site and the amino acid of the charged tRNA in the P
one amino acid at a time to the end of a protein. This site. The growing polypeptide chain is transferred to the
operation is performed by a ribosome. The choice of tRNA in the A site. Translocation occurs, moving the
amino acid type to add is determined by an mRNA
21.1. TRANSLATION 339

tRNA in the P site, now without an amino acid, to the E rare alternative start codon CTG codes for Methionine
site; the tRNA that was in the A site, now charged with when used as a start codon, and for Leucine in all other
the polypeptide chain, is moved to the P site. The tRNA positions.
in the E site leaves and another aminoacyl-tRNA enters Example: Condensed translation table for the Standard
the A site to repeat the process.[4] Genetic Code (from the NCBI Taxonomy webpage).
After the new amino acid is added to the chain, and after AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKK
the mRNA is released out of the nucleus and into the ri-
Starts = ---M---------------M-----------
bosome’s core, the energy provided by the hydrolysis of ----M---------------------------- Base1 =
a GTP bound to the translocase EF-G (in prokaryotes) TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCC-
and eEF-2 (in eukaryotes) moves the ribosome down one CAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
codon towards the 3' end. The energy required for trans- Base2 = TTTTCCCCAAAAGGGGTTTTC-
lation of proteins is significant. For a protein containing n CCCAAAAGGGGTTTTCCC-
amino acids, the number of high-energy phosphate bonds CAAAAGGGGTTTTCCCCAAAAGGGG Base3 =
required to translate it is 4n−1 . The rate of translation TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
varies; it is significantly higher in prokaryotic cells (up to
17-21 amino acid residues per second) than in eukaryotic
cells (up to 6-9 amino acid residues per second).[5] Translation tables
In activation, the correct amino acid is covalently bonded
to the correct transfer RNA (tRNA). The amino acid is Even when working with ordinary eukaryotic sequences
joined by its carboxyl group to the 3' OH of the tRNA by such as the Yeast genome, it is often desired to be able
an ester bond. When the tRNA has an amino acid linked to use alternative translation tables—namely for transla-
to it, it is termed “charged”. Initiation involves the small tion of the mitochondrial genes. Currently the follow-
subunit of the ribosome binding to the 5' end of mRNA ing translation tables are defined by the NCBI Taxonomy
with the help of initiation factors (IF). Termination of Group for the translation of the sequences in GenBank:
the polypeptide happens when the A site of the ribosome 1: The Standard 2: The Vertebrate Mitochondrial
faces a stop codon (UAA, UAG, or UGA). No tRNA Code 3: The Yeast Mitochondrial Code 4: The Mold,
can recognize or bind to this codon. Instead, the stop Protozoan, and Coelenterate Mitochondrial Code and
codon induces the binding of a release factor protein thatthe Mycoplasma/Spiroplasma Code 5: The Invertebrate
prompts the disassembly of the entire ribosome/mRNA Mitochondrial Code 6: The Ciliate, Dasycladacean
complex. and Hexamita Nuclear Code 9: The Echinoderm and
The process of translation proceeds in a fashion reminis- Flatworm Mitochondrial Code 10: The Euplotid Nu-
cent to that of a stock ticker and ticker tape. clear Code 11: The Bacterial and Plant Plastid Code 12:
The Alternative Yeast Nuclear Code 13: The Ascidian
Mitochondrial Code 14: The Alternative Flatworm Mi-
21.1.2 Genetic code tochondrial Code 15: Blepharisma Nuclear Code 16:
Chlorophycean Mitochondrial Code 21: Trematode Mi-
Main article: Genetic code tochondrial Code 22: Scenedesmus obliquus mitochon-
drial Code 23: Thraustochytrium Mitochondrial Code

Whereas other aspects such as the 3D structure, called

tertiary structure, of protein can only be predicted using 21.1.3 See also
sophisticated algorithms, the amino acid sequence, called
primary structure, can be determined solely from the nu- • DNA codon table
cleic acid sequence with the aid of a translation table.
• Expanded genetic code
This approach may not give the correct amino acid com-
position of the protein, in particular if unconventional • Protein methods
amino acids such as selenocysteine are incorporated into
the protein, which is coded for by a conventional stop • Start codon
codon in combination with a downstream hairpin (SE-
lenoCysteine Insertion Sequence, or SECIS).
There are many computer programs capable of translat- 21.1.4 References
ing a DNA/RNA sequence into a protein sequence. Nor-
[1] Neill, Campbell (1996). Biology; Fourth edition. The
mally this is performed using the Standard Genetic Code;
Benjamin/Cummings Publishing Company. p. 309,310.
many bioinformaticians have written at least one such ISBN 0-8053-1940-9.
program at some point in their education. However, few
programs can handle all the “special” cases, such as the [2] Stryer, Lubert (2002). Biochemistry; Fifth edition. W. H.
use of the alternative initiation codons. For instance, the Freeman and Company. p. 826. ISBN 0-7167-4684-0.
340 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

[3] Moghal, A., Mohler, K., and Ibba, M. (September 2014).

“Mistranslation of the genetic code.”. FEBS Letters 588: key
ribosome signal peptide
4305–10. doi:10.1016/j.febslet.2014.08.035. PMID B-chain peptide
dibasic cleavage peptides
C peptide
25220850. se
c6 A-chain peptide
1
tr
an
sl
[4] Griffiths, Anthony (2008). “9”. Introduction to Genetic oc
on 1. translation
Analysis (9th ed.). New York: W.H. Freeman and Com- and translocation
pany. pp. 335–339. ISBN 978-0-7167-6887-6. cytosol
2. folding, oxidation
and signal peptide
[5] Ross JF, Orlowski M (February 1982). “Growth-rate- cleavage
1
dependent adjustment of ribosome function in chemostat- se
c1

grown cells of the fungus Mucor racemosus". J. Bacteriol.

149 (2): 650–3. PMC 216554. PMID 6799491. ER lumen

21.1.5 Further reading 3. ER export, Golgi

transport, vesicle
• Champe, Pamela C; Harvey, Richard A; Ferrier, packaging Golgi

Denise R (2004). Lippincott’s Illustrated Reviews: 4.protease cleavage

liberates C-peptide
Biochemistry (3rd ed.). Hagerstwon, MD: Lippin- secretory vesicle
PC 1/3
PC
cott Williams & Wilkins. ISBN 0-7817-2265-9. 2

• Cox, Michael; Nelson, David R.; Lehninger, Albert

L (2005). Lehninger principles of biochemistry (4th

cp
5. carboxypeptidase E

E
ed.). San Francisco...: W.H. Freeman. ISBN 0- produces mature insulin
7167-4339-6.

• Malys N, McCarthy JEG (2010). “Translation ini-

tiation: variations in the mechanism can be antic- Post-translational modification of insulin. At the top, the ribo-
ipated”. Cellular and Molecular Life Sciences 68 some translates a mRNA sequence into a protein, insulin, and
(6): 991–1003. doi:10.1007/s00018-010-0588-z. passes the protein through the endoplasmic reticulum, where it is
PMID 21076851. cut, folded and held in shape by disulfide (-S-S-) bonds. Then the
protein passes through the golgi apparatus, where it is packaged
into a vesicle. In the vesicle, more parts are cut off, and it turns
21.1.6 External links into mature insulin.

• Virtual Cell Animation Collection: Introducing

Translation eukaryotic proteins also have carbohydrate molecules at-
tached to them in a process called glycosylation, which
• Translate tool (from DNA or RNA sequence) can promote protein folding and improve stability as
well as serving regulatory functions. Attachment of lipid
molecules, known as lipidation, often targets a protein or
21.2 Posttranslational modifica- part of a protein to the cell membrane.
tion Other forms of post-translational modification consist of
cleaving peptide bonds, as in processing a propeptide
to a mature form or removing the initiator methionine
Post-translational modification (PTM) refers to the
covalent and generally enzymatic modification of proteins residue. The formation of disulfide bonds from cysteine
during or after protein biosynthesis. Proteins are synthe- residues may also be referred to as a post-translational
sized by ribosomes translating mRNA into polypeptide modification.[3]:17.6 For instance, the peptide hormone
chains, which may then undergo PTM to form the ma- insulin is cut twice after disulfide bonds are formed, and
ture protein product. PTMs are important components a propeptide is removed from the middle of the chain;
in cell signaling. the resulting protein consists of two polypeptide chains
connected by disulfide bonds.
Post-translational modifications can occur on the amino
acid side chains or at the protein’s C- or N- termini.[1] Some types of post-translational modification are conse-
They can extend the chemical repertoire of the 20 stan- quences of oxidative stress. Carbonylation is one example
dard amino acids by introducing new functional groups that targets the modified protein for degradation and can
such as phosphate, acetate, amide groups, or methyl result in the formation of protein aggregates.[4][5] Specific
groups. Phosphorylation is a very common mecha- amino acid modifications can be used as biomarkers in-
nism for regulating the activity of enzymes and is the dicating oxidative damage.[6]
most common post-translational modification.[2] Many Sites that often undergo post-translational modification
21.2. POSTTRANSLATIONAL MODIFICATION 341

are those that have a functional group that can serve as a • farnesylation
nucleophile in the reaction: the hydroxyl groups of serine, • geranylgeranylation
threonine, and tyrosine have hydroxyl groups; the amine
forms of lysine, arginine, and histidine; the thiolate anion • glypiation, glycosylphosphatidylinositol (GPI) an-
of cysteine; the carboxylates of aspartate and glutamate; chor formation via an amide bond to C-terminal tail
and the N- and C-termini. In addition, although the
amides of asparagine and glutamine are weak nucle-
ophiles, both can serve as attachment points for glycans. Cofactors for enhanced enzymatic activity
Rarer modifications can occur at oxidized methionines
and at some methylenes in side chains.[7]:12-14 • lipoylation, attachment of a lipoate (C8 ) functional
Post-translational modification of proteins can be exper- group
imentally detected by a variety of techniques, including
• flavin moiety (FMN or FAD) may be covalently at-
mass spectrometry, Eastern blotting, and Western blot-
tached
ting.
• heme C attachment via thioether bonds with cysteins
21.2.1 PTMs involving addition of func- • phosphopantetheinylation, the addition of a 4'-
tional groups phosphopantetheinyl moiety from coenzyme A, as
in fatty acid, polyketide, non-ribosomal peptide and
H2N O leucine biosynthesis
amino acid

H2N O Basic
H2N O
Acidic
Polar
OH Nonpolar

• retinylidene Schiff base formation

OH OH H2N O (hydrophobic)
M
O
H3C E Essential
pKa 4.1 Glycine
OH
Gly Phenylalanine OH Modification
Glutamic acid
Phe S- Sumo
Glu E H3C
M- Methyl
H2N O Leucine P- Phospho
M
O Leu H2N O U- Ubiquitin
nM - N-Methyl
E
P OH
P oG

HO OH
oG - O-glycosyl
nG - N-glycosyl Modifications of translation factors
HO pKa 3.9
Aspartic acid Serine
Asp Ser H2N O

• diphthamide formation (on a histidine found in

H2N O P oG

HO OH
H3C OH
Alanine
Ala 75.07 165.19
131.18
pKa 10.5
Tyrosine
eEF2)
H2N O
147.13
Tyr H2N O
133.11 G F L 105.09
E S
D U CA G UC A G U
• ethanolamine phosphoglycerol attachment (on glu-
181.19
H3C OH
Valine
89.09
AG CA Stop HS OH
Val A UC
U
G Y Cysteine
pKa 8.4
CH3 E AG C Cys O
G U C
tamate found in eEF1α)[9]
C A
U A G 121.16 H2N
G C A U C
Arginine 117.15
V A
C
C
A
Stop
Arg U G U G OH
H2N O U
G
1st position 2nd 3rd
G
U
W 204.23
Tryptophan
NH
R A G A C U C
P Serine 174.20
C A L Trp
• hypusine formation (on conserved lysine of eIF5A
A C G
HO OH
Ser S U
G U
131.18 E
105.09 A C A
K C U G AC
U
GA U
G P
nM 146.19
N AC H2N O
nG
H2N O
Lysine
Lys
132.12
CU
T
G A C U GA CU G
Q
H 115.13 Leucine
Leu H3C (eukaryotic) and aIF5A (archaeal))
U 119.12
M I R 155.16
OH
OH E 146.15
a

131.18 174.20
21 D

S Proline H3C
Pro
149.

H2N pKa 10.5 How to Use This Chart:

O
=

This chart will enable you to identify an amino acid from

MW

Asparagine a single codon. Begin in the center with the first nucleotide G

Asn NH
Smaller chemical groups
of the codon and work your way out. For example, to translate
CAU, use the first position nucleotide (C) to identify the correct
quadrant of the center circle. Next, find the second position
nucleotide in the first ring surrounding the center (A), which is at
OH
H2N O five o'clock. Finally, locate the third nucleotide (U) in the second
Isoleucine ring from the center (five o'clock). Follow the segment outward to
O
Ile the next ring, where you will find the single-letter code for
the amino acid (H). By following the color-coded section
Histidine
nG OH
E His
outward, you will find structural information and related

• acylation, e.g. O-acylation (esters), N-acylation

post-translational modifications.
E H2N O
H2N O
H2N pKa 6.0
Threonine
Arginine N
Thr Arg OH
H2N O
E

H3C CH3
OH

H2N
E
O
NH
P nM
(amides), S-acylation (thioesters)
P oG
Methionine
Glutamine
HO OH Met Gln H2N O

• acetylation, the addition of an acetyl group, ei-

E OH
CH3 H2N O
nM NH
OH

ther at the N-terminus [10] of the protein or

HN nM
OH nM
O
H3C S
pKa12.5 NH2

at lysine residues.[11] See also histone acetyla-

NH2

tion.[12][13] The reverse is called deacetylation.

The genetic code diagram[8] showing the amino acid residues as
target of modification. • formylation

• alkylation, the addition of an alkyl group, e.g.

Addition by an enzyme in vivo methyl, ethyl

Hydrophobic groups for membrane localization • methylation the addition of a methyl group,
usually at lysine or arginine residues. The re-
• myristoylation, attachment of myristate, a C14 satu- verse is called demethylation.
rated acid
• amide bond formation
• palmitoylation, attachment of palmitate, a C16 satu-
rated acid • amidation at C-terminus

• isoprenylation or prenylation, the addition of an • amino acid addition

isoprenoid group (e.g. farnesol and geranylgeraniol) • arginylation, a tRNA-mediation addition
342 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

• polyglutamylation, covalent linkage of 21.2.2 Other proteins or peptides

glutamic acid residues to the N-terminus
of tubulin and some other proteins.[14] • ISGylation, the covalent linkage to the ISG15 pro-
(See tubulin polyglutamylase) tein (Interferon-Stimulated Gene 15)[16]
• polyglycylation, covalent linkage of one • SUMOylation, the covalent linkage to the SUMO
to more than 40 glycine residues to the protein (Small Ubiquitin-related MOdifier)[17]
tubulin C-terminal tail
• ubiquitination, the covalent linkage to the protein
• butyrylation ubiquitin.
• gamma-carboxylation dependent on Vitamin K [15]
• Neddylation, the covalent linkage to Nedd
• glycosylation, the addition of a glycosyl group to ei-
• Pupylation, the covalent linkage to the Prokaryotic
ther arginine, asparagine, cysteine, hydroxylysine,
ubiquitin-like protein
serine, threonine, tyrosine, or tryptophan resulting
in a glycoprotein. Distinct from glycation, which is
regarded as a nonenzymatic attachment of sugars. 21.2.3 Chemical modification of amino
• polysialylation, addition of polysialic acid, acids
PSA, to NCAM
• citrullination, or deimination, the conversion of
• malonylation arginine to citrulline
• hydroxylation • deamidation, the conversion of glutamine to
glutamic acid or asparagine to aspartic acid
• iodination (e.g. of thyroglobulin)
• eliminylation, the conversion to an alkene
• nucleotide addition such as ADP-ribosylation
by beta-elimination of phosphothreonine and
• oxidation phosphoserine, or dehydration of threonine and
serine, as well as by decarboxylation of cysteine [18]
• phosphate ester (O-linked) or phosphoramidate (N-
linked) formation • carbamylation, the conversion of lysine to
homocitrulline [19]
• phosphorylation, the addition of a phosphate
group, usually to serine, threonine, and
tyrosine (O-linked), or histidine (N-linked) 21.2.4 Structural changes
• adenylylation, the addition of an adenylyl moi-
ety, usually to tyrosine (O-linked), or histidine • disulfide bridges, the covalent linkage of two
and lysine (N-linked) cysteine amino acids

• propionylation • proteolytic cleavage, cleavage of a protein at a pep-

tide bond
• pyroglutamate formation
• racemization
• S-glutathionylation
• of proline by prolyl isomerase
• S-nitrosylation
• of serine by protein-serine epimerase
• succinylation addition of a succinyl group to lysine • of alanine in dermorphin, a frog opioid peptide
• sulfation, the addition of a sulfate group to a • of methionine in deltorphin, also a frog opioid
tyrosine. peptide
• protein splicing, self-catalytic removal of inteins
Non-enzymatic additions in vivo analogous to mRNA processing

• glycation, the addition of a sugar molecule to a pro-

tein without the controlling action of an enzyme. 21.2.5 Post-translational modification
statistics
Non-enzymatic additions in vitro
Recently, statistics of each post-translational modifica-
tion experimentally and putatively detected have been
• biotinylation, acylation of conserved lysine residues
compiled using proteome-wide information from the
with a biotin appendage
Swiss-Prot database.[20] These statistics can be found at
• pegylation http://selene.princeton.edu/PTMCuration/.
21.2. POSTTRANSLATIONAL MODIFICATION 343

21.2.6 Case examples [5] Grimsrud, P. A.; Xie, H.; Griffin, T. J.; Bern-
lohr, D. A. (2008). “Oxidative Stress and Cova-
• Cleavage and formation of disulfide bridges during lent Modification of Protein with Bioactive Aldehydes”.
the production of insulin Journal of Biological Chemistry 283 (32): 21837–41.
doi:10.1074/jbc.R700019200. PMC 2494933. PMID
• PTM of histones as regulation of transcription: 18445586.
RNA polymerase control by chromatin structure
[6] Gianazza, E; Crawford, J; Miller, I (July 2007). “De-
• PTM of RNA polymerase II as regulation of tran- tecting oxidative post-translational modifications in pro-
scription teins.”. Amino acids 33 (1): 51–6. PMID 17021655.

• Cleavage of polypeptide chains as crucial for lectin [7] Walsh,, Christopher T. (2006). Posttranslational modifi-
cation of proteins : expanding nature’s inventory. Engle-
specificity
wood: Roberts and Co. Publ. ISBN 9780974707730.

[8] Gramatikoff K. in Abgent Catalog (2004-5) p.263

21.2.7 See also
[9] Whiteheart SW, Shenbagamurthi P, Chen L et al.
• Protein targeting (1989). “Murine elongation factor 1 alpha (EF-1 al-
pha) is posttranslationally modified by novel amide-linked
ethanolamine-phosphoglycerol moieties. Addition of
21.2.8 External links ethanolamine-phosphoglycerol to specific glutamic acid
residues on EF-1 alpha”. J. Biol. Chem. 264 (24): 14334–
• dbPTM - database of protein post-translational 41. PMID 2569467.
modifications [10] Polevoda B, Sherman F; Sherman (2003). “N-terminal
acetyltransferases and sequence requirements for N-
• List of posttranslational modifications in ExPASy
terminal acetylation of eukaryotic proteins”. J Mol Biol
• Browse SCOP domains by PTM — from the dcGO 325 (4): 595–622. doi:10.1016/S0022-2836(02)01269-
database X. PMID 12507466.

[11] Yang XJ, Seto E; Seto (2008). “Lysine acetyla-

• Statistics of each post-translational modification
tion: codified crosstalk with other posttransla-
from the Swiss-Prot database tional modifications”. Mol Cell 31 (4): 449–61.
• AutoMotif Server - A Computational Protocol for doi:10.1016/j.molcel.2008.07.002. PMC 2551738.
PMID 18722172.
Identification of Post-Translational Modifications in
Protein Sequences [12] Bártová E, Krejcí J, Harnicarová A, Galiová G, Kozubek
S; Krejcí; Harnicarová; Galiová; Kozubek (2008).
• Functional analyses for site-specific phosphorylation “Histone modifications and nuclear architecture: a
of a target protein in cells review”. J Histochem Cytochem 56 (8): 711–21.
doi:10.1369/jhc.2008.951251. PMC 2443610. PMID
• Detection of Post-Translational Modifications after 18474937.
high-accuracy MSMS
[13] Glozak MA, Sengupta N, Zhang X, Seto E; Sen-
gupta; Zhang; Seto (2005). “Acetylation and deacety-
21.2.9 References lation of non-histone proteins”. Gene 363: 15–23.
doi:10.1016/j.gene.2005.09.010. PMID 16289629.
[1] Pratt, Donald Voet; Judith G. Voet; Charlotte W. (2006).
Fundamentals of biochemistry : life at the molecular level [14] Eddé B, Rossier J, Le Caer JP, Desbruyères E,
(2. ed. ed.). Hoboken, NJ: Wiley. ISBN 0-471-21495-7. Gros F, Denoulet P; Rossier; Le Caer; Des-
bruyères; Gros; Denoulet (1990). “Posttransla-
[2] Khoury, GA; Baliban, RC; Floudas, CA (13 September tional glutamylation of alpha-tubulin”. Science
2011). “Proteome-wide post-translational modification 247 (4938): 83–5. Bibcode:1990Sci...247...83E.
statistics: frequency analysis and curation of the swiss- doi:10.1126/science.1967194. PMID 1967194.
prot database.”. Scientific reports 1. PMID 22034591.
[15] Walker CS, Shetty RP, Clark K et al. (2001). “On a
[3] al.], Harvey Lodish ... [et (2000). Molecular cell biology potential global role for vitamin K-dependent gamma-
(4th ed. ed.). New York: Scientific American Books. carboxylation in animal systems. Animals can expe-
ISBN 0-7167-3136-3. rience subvaginal hemototitis as a result of this link-
age. Evidence for a gamma-glutamyl carboxylase in
[4] Dalle-Donne, Isabella; Aldini, Giancarlo; Carini, Ma- Drosophila”. J. Biol. Chem. 276 (11): 7769–74.
rina; Colombo, Roberto; Rossi, Ranieri; Milzani, Aldo doi:10.1074/jbc.M009576200. PMID 11110799.
(2006). “Protein carbonylation, cellular dysfunction, and
disease progression”. Journal of Cellular and Molec- [16] Malakhova, Oxana A.; Yan, Ming; Malakhov, Michael
ular Medicine 10 (2): 389–406. doi:10.1111/j.1582- P.; Yuan, Youzhong; Ritchie, Kenneth J.; Kim, Keun
4934.2006.tb00407.x. PMID 16796807. Il; Peterson, Luke F.; Shuai, Ke; and Dong-Er Zhang
344 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

(2003). “Protein ISGylation modulates the JAK-STAT (N-acetylglucosamine or N-acetylgalactosamine) along

signaling pathway”. Genes & Development 17 (4): 455– with a uronic sugar (glucuronic acid or iduronic acid) or
60. doi:10.1101/gad.1056303. PMC 195994. PMID galactose.[3] Glycosaminoglycans are highly polar and at-
12600939. tract water. They are therefore useful to the body as a
[17] Van G. Wilson (Ed.) (2004). Sumoylation: Molecular Bi- lubricant or as a shock absorber.
ology and Biochemistry. Horizon Bioscience. ISBN 0-
9545232-8-8.

[18] Brennan DF, Barford D; Barford (2009). “Eliminyla-

21.3.1 Production
tion: a post-translational modification catalyzed by phos-
phothreonine lyases”. Trends in Biochemical Sciences 34 Glycosaminoglycans have high degrees of heterogeneity
(3): 108–114. doi:10.1016/j.tibs.2008.11.005. PMID with regards to molecular mass, disaccharide construc-
19233656. tion, and sulfation due to the fact that GAG synthesis,
unlike proteins or nucleic acids, is not template driven,
[19] Piotr Mydel, Zeneng Wang, Mikael Brisslert, Annelie and dynamically modulated by processing enzymes.[4]
Hellvard, Leif E. Dahlberg, Stanley L. Hazen and Maria
Bokarewa (2010). “Carbamylation-dependent activa- Based on core disaccharide structures, GAGs are classi-
tion of T cells: a novel mechanism in the pathogene- fied into four groups.[5] Heparin/heparan sulfate (HS-
sis of autoimmune arthritis”. Journal of Immunology GAGs) and chondroitin sulfate/dermatan sulfate (CS-
184 (12): 6882–6890. doi:10.4049/jimmunol.1000075. GAGs) are synthesized in the Golgi apparatus, where
PMC 2925534. PMID 20488785. protein cores made in the rough endoplasmic reticu-
[20] Khoury, George A.; Baliban, Richard C.; and Christodou- lum are posttranslationally modified with O-linked glyco-
los A. Floudas (2011). “Proteome-wide post-translational sylations by glycosyltransferases forming proteoglycans.
modification statistics: frequency analysis and curation of Keratan sulfate may modify core proteins through N-
the swiss-prot database”. Scientific Reports 1 (90): 90. linked glycosylation or O-linked glycosylation of the pro-
Bibcode:2011NatSR...1E..90K. doi:10.1038/srep00090. teoglycan. The fourth class of GAG, hyaluronic acid, is
not synthesized by the Golgi, but rather by integral mem-
brane synthases which immediately secrete the dynami-
21.3 Glycosaminoglycans cally elongated disaccharide chain.
HSGAG and CSGAG modified proteoglycans first begin
“GAGs” redirects here. For other uses of GAGs, see Gag with a consensus Ser-Gly/Ala-X-Gly motif in the core
(disambiguation). protein. Construction of a tetrasaccharide linker that
Glycosaminoglycans[1] (GAGs) or mucopolysaccha- consists of -GlcAβ1–3Galβ1–3Galβ1–4Xylβ1-O-(Ser)-
, where xylosyltransferase, β4-galactosyl transferase
(GalTI),β3-galactosyl transferase (GalT-II), and β3-
GlcA transferase (GlcAT-I) transfer the four monosac-
charides, begins synthesis of the GAG modified protein.
The first modification of the tetrasaccharide linker deter-
mines whether the HSGAGs or CSGAGs will be added.
Addition of a GlcNAc promotes the addition of HSGAGs
while addition of GalNAc to the tetrasaccharide linker
promotoes CSGAG development.[5] GlcNAcT-I trans-
fers GlcNAc to the tetrasaccahride linker, which is dis-
Chondroitin sulfate
tinct from glycosyltransferase GlcNAcT-II, the enzyme
that is utilized to build HSGAGs. Interestingly, EXTL2
and EXTL3, two genes in the EXT tumor suppressor fam-
ily, have been shown to have GlcNAcT-I activity. Con-
versely, GalNAc is transferred to the linker by the en-
zyme GalNAcT to initiate synthesis of CSGAGs, an en-
zyme which may or may not have distinct activity com-
pared to the GalNAc transferase activity of chondroitin
synthase.[5]
With regards to HSGAGs, a multimeric enzyme en-
coded by EXT1 and EXT2 of the EXT family of genes,
Hyaluronan (−4GlcUAβ1-3GlcNAcβ1-)n transfers both GlcNAc and GlcA for HSGAG chain
elongation. While elongating, the HSGAG is dynami-
rides[2] are long unbranched polysaccharides consist- cally modified, first by N-deacetylase, N-sulfotransferase
ing of a repeating disaccharide unit. The repeating (NDST1), which is a bifunctional enyzme that cleaves the
unit (except for keratan) consists of an amino sugar N-acetyl group from GlcNAc and subsequently sulfates
21.3. GLYCOSAMINOGLYCANS 345

the N-position. Next, C-5 uronyl epimerase coverts d- smaller sizes of HA are synthesized by HAS1 and HAS3.
GlcA to l-IdoA followed by 2-O sulfation of the uronic While each HAS isoform catalyzes the same biosynthetic
acid sugar by 2-O sulfotransferase (Heparan sulfate 2-O- reaction, each HAS isoform is independently active. HAS
sulfotransferase). Finally, the 6-O and 3-O positions of isoforms have also been shown to have differing K val-
GlcNAc moities are sulfated by 6-O (Heparan sulfate 6- ues for UDP-GlcA and UDPGlcNAc.[11] It is believed
O-sulfotransferase) and 3-O (3-OST) sulfotransferases. that through differences in enzyme activity and expres-
Chondroitin sulfate and dermatan sulfate, which comprise sion, the wide spectrum of biological functions mediated
CSGAGs, are differentiated from each other by the pres- by HA can be regulated.
ence of GlcA and IdoA epimers respectively. Similar to
the production of HSGAGs, C-5 uronyl epimerase con-
verts d-GlcA to l-IdoA to synthesize dermatan sulfate. 21.3.2 Function
Three sulfation events of the CSGAG chains occur: 4-
O and/or 6-O sulfation of GalNAc and 2-O sulfation of Endogenous heparin is localized and stored in secretory
uronic acid. Four isoforms of the 4-O GalNAc sulfo- granules of mast cells. Histamine that is present within
2+
transferases (C4ST-1, C4ST-2, C4ST-3, and D4ST-1) the granules is protonated (H2 A ) at pH within granules
and three isoforms of the GalNAc 6-O sulfotransferases (5.2-6.0), thus it is believed that heparin, which is highly
(C6ST, C6ST-2, and GalNAc4S-6ST) are responsible for negatively charged, functions to electrostatically retain
the sulfation of GalNAc.[6] and store histamine.[12] In the clinic, heparin is admin-
istered as an anticoagulant and is also the first line choice
Unlike HSGAGs and CSGAGs, the third class of GAGs,
for thromboembolic diseases.[13][14] Heparan sulfate (HS)
those belonging to keratan sulfate types, are driven to-
has numerous biological activities and functions, includ-
wards biosynthesis through particular protein sequence
ing cell adhesion, regulation of cell growth and prolifer-
motifs. For example, in the cornea and cartilage, the
ation, developmental processes, cell surface binding of
keratan sulfate domain of aggrecan consists of a se-
lipoprotein lipase and other proteins, angiogenesis, viral
ries of tandemly repeated hexapeptides with a consen-
[7] invasion, and tumor metastasis.[12]
sus sequence of E(E/L)PFPS. Additionally, for three
other keratan sulfated proteoglycans, lumican, keratocan, CSGAGs interact with heparin binding proteins, specifi-
and mimecan (OGN), the consensus sequence NX(T/S) cally dermatan sulfate interactions with fibroblast growth
along with protein secondary structure was determined factor FGF-2 and FGF-7 have been implicated in cellu-
[15]
to be involved in N-linked oligosaccharide extension lar proliferation and wound repair while interactions
with keratan sulfate. Keratan sulfate elongation be- with hepatic growth factor/scatter factor (HGF/SF) acti-
[7]

gins at the nonreducing ends of three linkage oligosac- vate the HGF/SF signaling pathway (c-Met) through its
charides, which define the three classes of keratan sul- receptor. Other biological functions for which CSGAGs
fate. Keratan sulfate I (KSI) is N -linked via a high are known to play critical functions in include inhibi-
mannose type precursor oligosaccharide. Keratan sul- tion of axonal growth and regeneration in CNS develop-
fate II (KSII) and keratan sulfate III (KSIII) are O- ment, roles in brain development, neuritogenic activity,
[16]
linked, with KSII linkages identical to that of mucin core and pathogen infection.
structure, and KSIII linked to a 2-O mannose. Elon- One of the main functions of the third class of GAGs,
gation of the keratan sulfate polymer occurs through keratan sulfates, is the maintenance of tissue hydration.
the glycosyltransferase addition of Gal and GlcNAc. Within the normal cornea, dermatan sulfate is fully hy-
Galactose addition occurs primarily through the β−1,4- drated whereas keratan sulfate is only partially hydrated
galactosyltransferase enzyme (β4Gal-T1) while the en- suggesting that keratan sulfate may behave as a dynami-
zymes responsible for β−3-Nacetylglucosamine have not cally controlled buffer for hydration.[17] In disease states
been clearly identified. Finally, sulfation of the polymer such as macular corneal dystrophy, in which GAGs lev-
occurs at the 6-position of both sugar residues. The en- els such as KS are altered, loss of hydration within the
zyme KS-Gal6ST (CHST1) transfers sulfate groups to corneal stroma is believed to be the cause of corneal haze,
galactose while N-acetylglucosaminyl-6-sulfotransferase thus supporting the long held hypothesis that corneal
(GlcNAc6ST) (CHST2) transfers sulfate groups to termi- transparency is a dependent on proper levels of ker-
nal GlcNAc in keratan sulfate.[8] atan sulfate. Keratan sulfate GAGs are found in many
The fourth class of GAG, hyaluronic acid, is syn- other tissues besides the cornea, where they are known
thesized by three transmembrane synthase proteins to regulate macrophage adhesion, form barriers to neu-
HAS1, HAS2, and HAS3. HA, a linear polysac- rite growth, regulate embryo implantation in the endome-
charide, is composed of repeating disaccharide units trial uterine lining during menstrual cycles, and affect the
of →4)GlcAβ(1→3)GlcNAcβ(1→ and has a very high motility of corneal endothelial cells.[17] In summary, KS
molecular mass, ranging from 105 to 107 Da. Each HAS plays an anti-adhesive role, which suggests very important
enzyme is capable of transglycosylation when supplied functions of KS in cell motility and attachment as well as
with UDP-GlcA and UDP-GlcNAc.[9][10] HAS2 is re- other potential biological processes.
sponsible for very large hyaluronic acid polymers, while Hyaluronic acid is a major component of synovial tis-
346 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

sues and fluid, as well as other soft tissues, and endows • IdoUA = α-L-iduronic acid
their environments with remarkable rheological proper-
ties. For example, solutions of hyaluronic acid are known • IdoUA(2S) = 2-O-sulfo-α-L-iduronic acid
to be viscoelastic, and viscosity changes with shear stress.
At low shear stress, a solution of 10 g/L of hyaluronic • Gal = β-D-galactose
6
acid may have a viscosity 10 times the viscosity of the • Gal(6S) = 6-O-sulfo-β-D-galactose
solvent, while under high shear stress, viscosity may drop
by as much as 103 times.[18] The aforementioned rheo- • GalNAc = β-D-N-acetylgalactosamine
logical properties of solutions of hyaluronic acid make it
ideal for lubricating joints and surfaces that move along • GalNAc(4S) = β-D-N-acetylgalactosamine-4-O-
each other, such as cartilage. In vivo, hyaluronic acid sulfate
forms hydrated coils that form randomly kinked coils
that entangle to form a network. Hyaluronan networks • GalNAc(6S) = β-D-N-acetylgalactosamine-6-O-
retard diffusion and form a diffusion barrier that regu- sulfate
lates transport of substances through intercellular spaces.
For example, hyaluronan takes part in the partitioning • GalNAc(4S,6S) = β-D-N-acetylgalactosamine-4-
of plasma proteins between vascular and extravascular O, 6-O-sulfate
spaces, and it is this excluded volume phenomenon that • GlcNAc = α-D-N-acetylglucosamine
affects solubility of macromolecules in the interstitium,
changes chemical equilibria, and stabilizes the struc- • GlcNS = α-D-N-sulfoglucosamine
ture of collagen fibers.[18] Other functions include ma-
trix interactions with hyaluronan binding proteins such • GlcNS(6S) = α-D-N-sulfoglucosamine-6-O-sulfate
as hyaluronectin, glial hyaluronan binding protein, brain
enriched hyaluronan binding protein, collagen VI, TSG-
6, and inter-alpha-trypsin inhibitor. Cell surface inter- 21.3.4 See also
actions involving hyaluronan are its well-known coupling
with CD44, which may be related to tumor progression, • Mucopolysaccharidosis (lysosomal storage diseases)
and also with RHAMM (Hyaluronan-mediated motility
receptor), which has been implicated in developmen- • Lipopolysaccharide
tal processes, tumor metastasis, and pathological repara-
tive processes. Fibroblasts, mesothelial cells, and certain
types of stem cells surround themselves in a pericellular 21.3.5 References
“coat”, part of which is constructed from hyaluronan, in
order to shield themselves from bacteria, red blood cells, [1] "glycosaminoglycan" at Dorland’s Medical Dictionary
or other matrix molecules. For example, with regards [2] "mucopolysaccharide" at Dorland’s Medical Dictionary
to stem cells, hyaluronan, along with chondroitin sulfate,
helps to form the stem cell niche. Stem cells are protected [3] Esko, Jeffrey D; Kimata, Koji; Lindahl, Ulf (2009).
from the effects of growth factors by a shield of hyaluro- “Chapter 16: Proteoglycans and Sulfated Glycosamino-
nan and minimally sulfated chondroitin sulfate. During glycans”. Essentials of Glycobiology. Cold Spring Harbor
progenitor division, the daughter cell moves outside of Laboratory Press. ISBN 0879695595.
this pericellular shield where it can then be influenced by
[4] Caligur, Vicki (2008). “Glycosaminoglycan Sulfation and
growth factors to differentiate even further. Signaling”. Retrieved 25 November 2012.

[5] Sasisekharan, Ram; Raman, Rahul; Prabhakar, Vikas

21.3.3 Classification (August 2006). “GLYCOMICS APPROACH TO
STRUCTURE-FUNCTION RELATIONSHIPS
Members of the glycosaminoglycan family vary in the OF GLYCOSAMINOGLYCANS”. Annual Re-
type of hexosamine, hexose or hexuronic acid unit they view of Biomedical Engineering 8 (1): 181–231.
contain (e.g. glucuronic acid, iduronic acid, galactose, doi:10.1146/annurev.bioeng.8.061505.095745. Re-
galactosamine, glucosamine). trieved 12 December 2014.

They also vary in the geometry of the glycosidic linkage. [6] Kusche-Gullberg M, Kjellén L. (2003).
Examples of GAGs include: “Sulfotransferases in glycosaminoglycan biosynthesis.”.
Current Opinion in Structural Biology 13 (5): 605–11.
doi:10.1016/j.sbi.2003.08.002. PMID 14568616.
Abbreviations
[7] Funderburgh JL. (2002). “Keratan sulfate
• GlcUA = β-D-glucuronic acid biosynthesis.”. IUBMB Life 54 (4): 187–94.
doi:10.1080/15216540214932. PMC 2874674.
• GlcUA(2S) = 2-O-sulfo-β-D-glucuronic acid PMID 12512857.
21.4. PROTEOLYSIS 347

[8] Yamamoto Y, Takahashi I, Ogata N, Nakazawa K. [20] Gallagher, J.T., Lyon, M. (2000). “Molecular structure of
(2001). “Purification and characterization of N- Heparan Sulfate and interactions with growth factors and
acetylglucosaminyl sulfotransferase from chick corneas.”. morphogens”. In Iozzo, M, V. Proteoglycans: structure,
Archives of Biochemistry and Biophysics 392 (1): 87–92. biology and molecular interactions. Marcel Dekker Inc.
doi:10.1006/abbi.2001.2422. PMID 11469798. New York, New York. pp. 27–59. ISBN 978-0-8247-
0334-9.
[9] Yoshida M, Itano N, Yamada Y, Kimata K. (2000).
“In vitro synthesis of hyaluronan by a single protein de-
rived from mouse HAS1 gene and characterization of
amino acid residues essential for the activity.”. The 21.3.6 External links
Journal of Biological Chemistry 275 (1): 497–506.
doi:10.1074/jbc.275.1.497. PMID 10617644. • King M. 2005. Glycosaminoglycans. Indiana Uni-
[10] DeAngelis PL, and Weigel PH (1994). “Immunochem-
versity School of Medicine Accessed December 31,
ical confirmation of the primary structure of streptococ- 2006.
cal hyaluronan synthase and synthesis of high molecular
weight product by the recombinant enzyme.”. Biochem- • Glycosaminoglycans at the US National Library of
istry 33 (31): 9033–9039. doi:10.1021/bi00197a001. Medicine Medical Subject Headings (MeSH)
PMID 8049203.

[11] Itano N, Sawai T, Yoshida M, Lenas P, Yamada Y, • MRI evaluation of glycosaminoglycan loss (dGEM-
Imagawa M, Shinomura T, Hamaguchi M., Yoshida Y, RIC evaluation)
Ohnuki Y, Miyauchi S, Spicer AP, McDonald JA, and
Kimata K. (1999). “Three isoforms of mammalian
hyaluronan synthases have distinct enzymatic properties.”.
Journal of Biological Chemistry 274 (35): 25085–92. 21.4 Proteolysis
doi:10.1074/jbc.274.35.25085. PMID 10455188.

[12] Rabenstein DL. (2002). “Heparin and heparan sulfate:

Proteolysis is the breakdown of proteins into smaller
structure and function”. Natural Products Reports 19: polypeptides or amino acids. In general, this occurs by
312–331. doi:10.1039/B100916H. PMID 12137280. the hydrolysis of the peptide bond, and is most commonly
achieved by cellular enzymes called proteases, but may
[13] Jin L, Abrahams JP, Skinner R, Petitou M, Pike RN, also occur by intramolecular digestion, as well as by non-
Carrell RW. (1997). “The anticoagulant activation of enzymatic methods such as the action of mineral acids
antithrombin by heparin.”. Proceedings of the National and heat.
Academy of Sciences of the United States of America 94
(26): 14683–8. doi:10.1073/pnas.94.26.14683. PMC Proteolysis in organisms serves many purposes; for ex-
25092. PMID 9405673. ample, digestive enzymes break down proteins in food to
provide amino acids for the organism, while proteolytic
[14] Rodén, L. (1989). Lane, DA, ed. Heparin: Chemical and processing of polypeptide chain after its synthesis may
Biological Properties, ClinicalApplications. CRC Press,
be necessary for the production of an active protein. It
Inc. p. 1.
is also important in the regulation of some physiological
[15] Trowbridge JM, Gallo RL. (2002). “Dermatan sulfate: and cellular processes, as well as preventing the accumu-
new functions from an old glycosaminoglycan”. Glyco- lation of unwanted or abnormal proteins in cells.
biology 12 (9): 117R–125R. doi:10.1093/glycob/cwf066.
PMID 12213784.

[16] Sugahara K, Mikami T, Uyama T, Mizuguchi S, Nomura 21.4.1 Post-translational proteolytic pro-
K, Kitagawa H. (2003). “Recent advances in the struc- cessing
tural biology of chondroitin sulfate and dermatan sulfate.”.
Current Opinion in Structural Biology 13 (5): 612–620. Limited proteolysis of a polypeptide during or after
doi:10.1016/j.sbi.2003.09.011. PMID 14568617. translation in protein synthesis often occurs for many
[17] Funderburgh, JL. (2000). “Keratan sulfate: structure, proteins. This may involve removal of the N-terminal
biosynthesis, and function.”. Glycobiology 10 (10): 951– methionine, signal peptide, and/or the conversion of an
8. doi:10.1093/glycob/10.10.951. PMID 11030741. inactive or non-functional protein to an active one. The
precursor to the final functional form of protein is termed
[18] Laurent TC, Laurent UB, Fraser JR. (1996). proprotein, and these proproteins may be first synthesized
“The structure and function of hyaluronan: An as preproprotein. For example, albumin is first synthe-
overview.”. Immunology and Cell Biology 74 (2): A1–7.
sized as preproalbumin and contains an uncleaved signal
doi:10.1038/icb.1996.32. PMID 8724014.
peptide. This forms the proalbumin after the signal pep-
[19] Funderburgh JL. (2000). “Keratan sulfate: structure, tide is cleaved, and a further processing to remove the
biosynthesis, and function”. Glycobiology 10 (10): 951– N-terminal 6-residue propeptide yields the mature form
958. doi:10.1093/glycob/10.10.951. PMID 11030741. of the protein.[1]
348 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

Removal of N-terminal methionine ple, when trypsinogen is cleaved to form trypsin, a slight
rearrangement of the protein structure that completes the
The initiating methionine (and, in prokaryotes, fMet) active site of the protease occurs, thereby activating the
may be removed during translation of the nascent pro- protein.
tein. For E. coli, fMet is efficiently removed if the sec-
Proteolysis can, therefore, be a method of regulating bi-
ond residue is small and uncharged, but not if the second
ological processes by turning inactive proteins into ac-
residue is bulky and charged.[2] In both prokaryotes and
tive ones. A good example is the blood clotting cascade
eukaryotes, the exposed N-terminal residue may deter-
whereby an initial event triggers a cascade of sequential
mine the half-life of the protein according to the N-end
proteolytic activation of many specific proteases, result-
rule.
ing in blood coagulation. The complement system of the
immune response also involves a complex sequential pro-
Removal of the signal sequence teolytic activation and interaction that result in an attack
on invading pathogens.
Proteins that are to be targeted to a particular organelle
or for secretion have an N-terminal signal peptide that
directs the protein to its final destination. This signal 21.4.2 Protein degradation
peptide is removed by proteolysis after their transport
through a membrane. Protein degradation may take place intracellularly or ex-
tracellularly. In digestion of food, digestive enzymes may
be released into the environment for extracellular diges-
Cleavage of polyprotein tion whereby proteolytic cleavage breaks down proteins
into smaller peptides and amino acids so that they may be
Some proteins and most eukaryotic polypeptide hor- absorbed and used by an organism. In animals the food
mones are synthesized as a large precursor polypep- may be processed extracellularly in specialized digestive
tide known as polyprotein that require proteolytic organs or guts, but in many bacteria the food may be in-
cleavage into individual smaller polypeptide chains. ternalized into the cell via phagocytosis. Microbial degra-
The polyprotein pro-opiomelanocortin (POMC) contains dation of protein in the environment can be regulated by
many polypeptide hormones. The cleavage pattern of nutrient availability. For example, limitation for major
POMC, however, may vary between different tissues, elements in proteins (carbon, nitrogen, and sulfur) has
yielding different sets of polypeptide hormones from the been shown to induce proteolytic activity in the fungus
same polyprotein. Neurospora crassa[3] as well as in whole communities of
[4]
Many viruses also produce their proteins initially as a soil organisms.
single polypeptide chain that were translated from a Proteins in cells are also constantly being broken down
polycistronic mRNA. This polypeptide is subsequently into amino acids. This intracellular degradation of pro-
cleaved into individual polypeptide chains.[1] tein serves a number of functions: It removes damaged
and abnormal protein and prevent their accumulation, and
it also serves to regulate cellular processes by remov-
Cleavage of precursor proteins ing enzymes and regulatory proteins that are no longer
needed. The amino acids may then be reused for protein
Many proteins and hormones are synthesized in the
synthesis.
form of their precursors - zymogens, proenzymes, and
prehormones. These proteins are cleaved to form their fi-
nal active structures. Insulin, for example, is synthesized Lysosome and proteasome
as preproinsulin, which yields proinsulin after the signal
peptide has been cleaved. To form the mature insulin, The intracellular degradation of protein may be achieved
the proinsulin is then cleaved at two positions to yield two in two ways - proteolysis in lysosome, or a ubiquitin-
polypeptide chains linked by 2 disulphide bonds. Proin- dependent process that targets unwanted proteins to
sulin is necessary for the folding of the polypeptide chain, proteasome. The autophagy-lysosomal pathway is nor-
as the 2 polypeptide chains of insulin may not correctly mally a non-selective process, but it may become selec-
assemble into the correct form, whereas its precursor tive upon starvation whereby proteins with peptide se-
proinsulin does. quence KFERQ or similar are selectively broken down.
Proteases in particular are synthesized in the inactive The lysosome contains a large number of proteases such
form so that they may be safely stored in cells, and ready as cathepsins.
for release in sufficient quantity when required. This is The ubiquitin-mediated process is selective. Proteins
to ensure that the protease is activated only in the correct marked for degradation are covalently linked to ubiqui-
location or context, as inappropriate activation of these tin. Many molecules of ubiquitin may be linked in tan-
proteases can be very destructive for an organism. Prote- dem to a protein destined for degradation. The polyu-
olysis of the zymogen yields an active protein; for exam- biquinated protein is targeted to an ATP-dependent pro-
21.4. PROTEOLYSIS 349

iological conditions. One of the most rapidly degraded

proteins is ornithine decarboxylase, which has a half-
life of 11 minutes. In contrast, other proteins like actin
and myosin have half-life of a month or more, while,
in essence, haemoglobin lasts for the entire life-time of
erythrocyte.[5]
The N-end rule may partially determine the half-life of
a protein, and proteins with segments rich in proline,
glutamic acid, serine, and threonine (the so-called PEST
proteins) have short half-life.[6] Other factors suspected
to affect degradation rate include the rate deamination
of glutamine and asparagine and oxidation of cystein,
histidine, and methionine, the absence of stabilizing lig-
ands, the presence of attached carbohydrate or phosphate
groups, the presence of free α-amino group, the negative
charge of protein, and the flexibility and stability of the
protein.[5]
The rate of proteolysis may also depend on the physiolog-
ical state of the cell, such as its hormonal state as well as
nutritional status. In time of starvation, the rate of protein
degradation increases.

Digestion

In human digestion, proteins in food are broken

down into smaller peptide chains by digestive enzymes
such as pepsin, trypsin, chymotrypsin, and elastase,
and into amino acids by various enzymes such as
carboxypeptidase, aminopeptidase, and dipeptidase. It
is necessary to break down proteins into small pep-
tides (tripeptides and dipeptides) and amino acids so
they can be absorbed by the intestines, and the ab-
sorbed tripeptides and dipeptides are also further bro-
ken into amino acids intracellularly before they enter the
bloodstream.[7] Different enzymes have different speci-
ficity for their substrate; trypsin, for example, cleaves the
peptide bond after a positively charged residue (arginine
and lysine); chymotrypsin cleaves the bond after an aro-
matic residue (phenylalanine, tyrosine, and tryptophan);
elastase cleaves the bond after a small non-polar residue
such as alanine or glycine.
Structure of a proteasome. Its active sites are inside the tube (blue) In order to prevent inappropriate or premature activation
where proteins are degraded. of the digestive enzymes (they may, for example, trigger
pancreatic self-digestion causing pancreatitis), these en-
zymes are secreted as inactive zymogen. The precursor
tease complex, the proteasome. The ubiquitin is released
of pepsin, pepsinogen, is secreted by the stomach, and is
and reused, while the targeted protein is degraded.
activated only in the acidic environment found in stom-
ach. The pancreas secretes the precursors of a number of
Rate of intracellular protein degradation proteases such as trypsin and chymotrypsin. The zymo-
gen of trypsin is trypsinogen, which is activated by a very
Different proteins are degraded at different rate. Abnor- specific protease, enterokinase, secreted by the mucosa
mal proteins are quickly degraded, whereas the rate of of the duodenum. The trypsin, once activated, can also
degradation of normal proteins may vary widely depend- cleave other trypsinogens as well as the precursors of
ing on their functions. Enzymes at important metabolic other proteases such as chymotrypsin and carboxypepti-
control points may be degraded much faster than those dase to activate them.
enzymes whose activity is largely constant under all phys- In bacteria, a similar strategy of employing an inactive
350 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

zymogen or prezymogen is used. Subtilisin, which is pro- may have increased lysosomal activity and the degrada-
duced by Bacillus subtilis, is produced as preprosubtilisin, tion of some proteins can increase significantly. Chronic
and is released only if the signal peptide is cleaved and inflammatory diseases such as rheumatoid arthritis may
autocatalytic proteolytic activation has occurred. involve the release of lysosomal enzymes into extracel-
lular space that break down surrounding tissues. Abnor-
mal proteolysis and generation of peptides that aggregate
21.4.3 Proteolysis in cellular regulation in cells and their ineffective removal may result in many
age-related neurological diseases such as Alzheimer's.[12]
Proteolysis is also involved in the regulation of many
Proteases may be regulated by antiproteases or protease
cellular processes by activating or deactivating enzymes,
inhibitors, and imbalance between proteases and antipro-
transcription factors, and receptors, for example in the
teases can result in diseases, for example, in the de-
biosynthesis of cholesterol,[8] or the mediation of throm-
struction of lung tissues in emphysema brought on by
bin signalling through protease-activated receptors.[9]
smoking tobacco. Smoking is thought to increase the
Some enzymes at important metabolic control points such neutrophils and macrophages in the lung which release
as ornithine decarboxylase is regulated entirely by its rate excessive amount of proteolytic enzymes such as elastase,
of synthesis and its rate of degradation. Other rapidly such that they can no longer be inhibited by serpins such
degraded proteins include the protein products of proto- as α1 -antitrypsin, thereby resulting in the breaking down
oncogenes, which play central roles in the regulation of of connective tissues in the lung. Other proteases and
cell growth. their inhibitors may also be involved in this disease, for
example matrix metalloproteinases (MMPs) and tissue
inhibitors of metalloproteinases (TIMPs).[13]
Cell cycle regulation
Other diseases linked to aberrant proteolysis include
Cyclins are a group of proteins that activate kinases in- muscular dystrophy, degenerative skin disorders, respi-
volved in cell division. The degradation of cyclins is the ratory and gastrointestinal diseases, and malignancy.
key step that governs the exit from mitosis and progress
into the next cell cycle.[10] Cyclins accumulate in the
course the cell cycle, then abruptly disappear just before 21.4.6 Non-enzymatic proteolysis
the anaphase of mitosis. The cyclins are removed via a
ubiquitin-mediated proteolytic pathway. Chemicals may be used in laboratory to target specific
residues and cleave its peptide bond so that protein may
be broken down into smaller polypeptides for analysis.[14]
Apoptosis
Cyanogen bromide is often used to cleave the peptide
bond after a methionine. Other methods may be used to
Caspases are an important group of proteases involved in
specifically cleave tryptophanyl, aspartyl, cysteinyl, and
apoptosis. The precursors of caspase, procaspase, may
asparaginyl peptide bonds. Acids such as trifluoroacetic
be activated by proteolysis through its association with a
acid and formic acid may also be used.
protein complex that forms apoptosome, or by granzyme
B, or via the death receptor pathways. Strong mineral acids can readily hydrolyse the peptide
bonds in a protein. However, some proteins are remark-
ably resistant to hydrolysis. One well-known example is
21.4.4 Regulatory domains in proteolysis ribonuclease A, and one method for its purification in-
volves treatment of crude extracts with hot sulphuric acid
Protease may have one or more regulatory domains - so that other proteins become degraded while ribonucle-
ase A is left intact.[15]
• Calcium-binding domain - e.g., prothrombin, factor
IX, X, VII, protein C in blood clotting cascade,
calpain. 21.4.7 Laboratory applications
• Kringle domain - e.g., in prothrombin it keeps the Proteolysis is also used in research and diagnostic appli-
protease inactive. cations:

21.4.5 Proteolysis and diseases • Cleavage of fusion protein so that the fusion part-
ner and protein tag used in protein expression and
Abnormal proteolytic activity are associated with many purification may be removed. The proteases used
diseases.[11] In pancreatitis, leakage of proteases and their have high degree of specificity, such as thrombin,
premature activation in the pancreas results in the self- enterokinase, and TEV protease, so that only the tar-
digestion of the pancreas. People with diabetes mellitus geted sequence may be cleaved.
21.4. PROTEOLYSIS 351

• Complete inactivation of undesirable enzymatic ac- 21.4.10 References

tivity or removal of unwanted proteins. For exam-
ple, proteinase K, a broad-spectrum proteinase sta- [1] Thomas E Creighton (1993). Proteins: Structures and
ble in urea and SDS, is often used in the preparation Molecular Properties (2nd ed.). W H Freeman and Com-
of nucleic acids to remove unwanted nuclease con- pany. pp. 78–86. ISBN 0-7167-2317-4.
taminants that may otherwise degrade the DNA or
[2] P H Hirel, M J Schmitter, P Dessen, G Fayat, and
RNA.[16]
S Blanquet (1989). “Extent of N-terminal methio-
nine excision from Escherichia coli proteins is gov-
• Partial inactivation, or changing the functionality, of
erned by the side-chain length of the penultimate amino
specific protein. For example, treatment of DNA
acid”. Proc Natl Acad Sci U S A 86 (21): 8247–51.
polymerase I with subtilisin yields the Klenow frag- doi:10.1073/pnas.86.21.8247. PMC 298257. PMID
ment, which retains its polymerase function but 2682640.
lacks 5'-exonuclease activity.[17]
[3] Hanson, M.A., Marzluf, G.A., 1975. Control of the syn-
• Digestion of proteins in solution for proteome anal- thesis of a single enzyme by multiple regulatory circuits
ysis by liquid chromatography-mass spectrometry in Neurospora crassa. Proc. Natl. Acad. Sci. U.S.A. 72,
(LC-MS). This may also be done by in-gel diges- 1240–1244.
tion of proteins after separation by gel electrophore-
sis for the identification by mass spectrometry. [4] Sims, G. K., and M. M. Wander. 2002. Proteolytic ac-
tivity under nitrogen or sulfur limitation. Appl. Soil Ecol.
• Analysis of the stability of folded domain under a 568:1-5.
wide range of conditions.[18]
[5] Thomas E Creighton (1993). “Chapter 10 - Degradation”.
• Increasing success rate of crystallisation projects [19] Proteins: Structures and Molecular Properties (2nd ed.). W
H Freeman and Company. pp. 463–473. ISBN 0-7167-
• Commonly in microbiology as a source of digested 2317-4.
protein to support bacterial reproduction, and to in-
[6] Voet & Voet (1995). Biochemisty (2nd ed.). John Wiley
directly culture viruses, e.g. tryptone in Lysogeny & Sons. pp. 1010–1014. ISBN 0-471-58651-X.
Broth.
[7] Silk DB (1974). “Progress report. Peptide absorption in
man”. Gut 15 (6): 494–501. doi:10.1136/gut.15.6.494.
21.4.8 Venoms PMC 1413009. PMID 4604970.

Certain types of venom, such as those produced by ven- [8] Michael S. Brown and Joseph L. Goldstein (May
omous snakes, can also cause proteolysis. These venoms 1997). “The SREBP Pathway: Regulation of Choles-
terol Metabolism by Proteolysis of a Membrane-
are, in fact, complex digestive fluids that begin their work
Bound Transcription Factor”. Cell 89 (3): 331–340.
outside of the body. Proteolytic venoms cause a wide
doi:10.1016/S0092-8674(00)80213-5. PMID 9150132.
range of toxic effects,[20] including effects that are:
[9] Shaun R. Coughlin (2000). “Thrombin signalling and
• cytotoxic (cell-destroying) protease-activated receptors”. Nature 407 (6801): 258–
264. doi:10.1038/35025229. PMID 11001069.
• hemotoxic (blood-destroying)
[10] Glotzer M, Murray AW, Kirschner MW (1991). “Cyclin
• myotoxic (muscle-destroying) is degraded by the ubiquitin pathway”. Nature 349 (6305):
132–8. doi:10.1038/349132a0. PMID 1846030.
• hemorrhagic (bleeding)
[11] Kathleen M. Sakamoto (2002). “Ubiquitin-dependent
proteolysis: its role in human diseases and the de-
sign of therapeutic strategies” (PDF). Molecular Genetics
21.4.9 See also and Metabolism 77 (1–2): 44–56. doi:10.1016/S1096-
7192(02)00146-4. PMID 12359129.
• Proteolytic enzyme
[12] De Strooper B. (2010). “Proteases and proteolysis in
• The Proteolysis Map Alzheimer disease: a multifactorial view on the dis-
ease process”. Physiological Reviews 90 (2): 465–94.
• PROTOMAP a proteomic technology for identify- doi:10.1152/physrev.00023.2009. PMID 20393191
ing proteolytic substrates
[13] Abboud RT1, Vimalanathan S (2008). “Pathogenesis of
• Proteasome COPD. Part I. The role of protease-antiprotease imbal-
ance in emphysema”. International Journal of Tuberculo-
• In-gel digestion sis and Lung Diseases 12 (4): 361–7. PMID 18371259.
352 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

[14] Bryan John Smith (2002). “Chapter 71-75”. In John M.

Walker. The Protein Protocols Handbook (2 ed.). Humana
Press. pp. 485–510. doi:10.1385/1592591698. ISBN
978-0-89603-940-7.

[15] “Ribonuclease A”. Protein Data Bank.

[16] Hilz H, Wiegers U, Adamietz P (1975). “Stimulation

of Proteinase K action by denaturing agents: applica-
tion to the isolation of nucleic acids and the degra-
dation of 'masked' proteins”. European Journal of
Biochemistry 56 (1): 103–108. doi:10.1111/j.1432-
1033.1975.tb02211.x. PMID 1236799.

[17] Klenow H and Henningsen I (1970). “Selective Elimina-

tion of the Exonuclease Activity of the Deoxyribonucleic
Acid Polymerase from Escherichia coli B by Limited Pro-
teolysis”. Proc. Natl. Acad. Sci. USA 65 (1): 168–
175. doi:10.1073/pnas.65.1.168. PMC 286206. PMID
4905667.

[18] Minde DP; Maurice, Madelon M.; Rüdiger, Stefan G.

D. (2012). Uversky, Vladimir N, ed. “Determining
biophysical protein stability in lysates by a fast prote-
olysis assay, FASTpp”. PLoS ONE 7 (10): e46147.
doi:10.1371/journal.pone.0046147. PMC 3463568.
PMID 23056252.

[19] Wernimont, A; Edwards, A (2009). Song, Hai-

wei, ed. “In situ proteolysis to generate crystals for
structure determination: An update”. PLoS ONE 4
(4): e5094. doi:10.1371/journal.pone.0005094. PMC
2661377. PMID 19352432.

[20] Hayes WK. 2005. Research on Biological Roles and Vari-

ation of Snake Venoms. Loma Linda University.

21.4.11 Further reading

• Thomas E Creighton (1993). Proteins: Structures
and Molecular Properties (2nd ed.). W H Freeman
and Company. ISBN 0-7167-2317-4.

21.4.12 External links

• The Journal of Proteolysis is an open access jour-
nal that provides an international forum for the elec-
Cartoon representation of a proteasome. Its active sites are shel-
tronic publication of the whole spectrum of high-
tered inside the tube (blue). The caps (red; in this case, 11S reg-
quality articles and reviews in all areas of proteolysis ulatory particles) on the ends regulate entry into the destruction
and proteolytic pathways. chamber, where the protein is degraded.
• Proteolysis MAP from Center on Proteolytic Path-
ways
21.5.1 Overview

Proteasomes are protein complexes inside all eukaryotes

21.5 Proteasome and archaea, and in some bacteria. In eukaryotes, they
are located in the nucleus and the cytoplasm.[1] The main
Proteasomes are protein complexes inside all eukaryotes function of the proteasome is to degrade unneeded or
and archaea, and in some bacteria. The main function damaged proteins by proteolysis, a chemical reaction that
of the proteasome is to degrade unneeded or damaged breaks peptide bonds. Enzymes that help such reac-
proteins by proteolysis, a chemical reaction that breaks tions are called proteases. Proteasomes are part of a ma-
peptide bonds. jor mechanism by which cells regulate the concentration
21.5. PROTEASOME 353

Chemistry to Aaron Ciechanover, Avram Hershko and

Irwin Rose.[3]

21.5.2 Discovery
Before the discovery of the ubiquitin proteasome system,
protein degradation in cells was thought to rely mainly on
lysosomes, membrane-bound organelles with acidic and
protease-filled interiors that can degrade and then recycle
exogenous proteins and aged or damaged organelles.[2]
However, work by Alfred Goldberg in 1977 on ATP-
dependent protein degradation in reticulocytes, which
lack lysosomes, suggested the presence of a second in-
tracellular degradation mechanism.[4] This was shown in
1978 to be composed of several distinct protein chains,
a novelty among proteases at the time.[5] Later work on
modification of histones led to the identification of an
unexpected covalent modification of the histone protein
by a bond between a lysine side chain of the histone
and the C-terminal glycine residue of ubiquitin, a pro-
tein that had no known function.[6] It was then discovered
Top view of the proteasome above. that a previously identified protein associated with prote-
olytic degradation, known as ATP-dependent proteolysis
factor 1 (APF-1), was the same protein as ubiquitin.[7]
of particular proteins and degrade misfolded proteins. The proteolytic activities of this system was isolated
The degradation process yields peptides of about seven as a multi-protein complex originally called the multi-
to eight amino acids long, which can then be further catalytic proteinase complex by Sherwin Wilk and Mar-
degraded into shorter amino acid sequences and used ion Orlowski.[8] Later, the ATP-dependent proteolytic
in synthesizing new proteins.[2] Proteins are tagged for complex that was responsible for ubiquitin-dependent
degradation with a small protein called ubiquitin. The protein degradation was discovered and was called the
tagging reaction is catalyzed by enzymes called ubiquitin 26S proteasome.[9][10]
ligases. Once a protein is tagged with a single ubiquitin
Much of the early work leading up to the discovery of the
molecule, this is a signal to other ligases to attach addi-
ubiquitin proteasome system occurred in the late 1970s
tional ubiquitin molecules. The result is a polyubiquitin
and early 1980s at the Technion in the laboratory of
chain that is bound by the proteasome, allowing it to de-
Avram Hershko, where Aaron Ciechanover worked as a
grade the tagged protein.[2]
graduate student. Hershko’s year-long sabbatical in the
In structure, the proteasome is a cylindrical complex con- laboratory of Irwin Rose at the Fox Chase Cancer Cen-
taining a “core” of four stacked rings forming a central ter provided key conceptual insights, though Rose later
pore. Each ring is composed of seven individual pro- downplayed his role in the discovery.[11] The three shared
teins. The inner two rings are made of seven β subunits the 2004 Nobel Prize in Chemistry for their work in dis-
that contain three to seven protease active sites. These covering this system.[3]
sites are located on the interior surface of the rings, so
Although electron microscopy data revealing the stacked-
that the target protein must enter the central pore before
ring structure of the proteasome became available in the
it is degraded. The outer two rings each contain seven
mid-1980s,[12] the first structure of the proteasome core
α subunits whose function is to maintain a “gate” through
particle was not solved by X-ray crystallography until
which proteins enter the barrel. These α subunits are con-
1994.[13]
trolled by binding to “cap” structures or regulatory parti-
cles that recognize polyubiquitin tags attached to protein
substrates and initiate the degradation process. The over-
21.5.3 Structure and organization
all system of ubiquitination and proteasomal degradation
is known as the ubiquitin-proteasome system. The proteasome subcomponents are often referred to
The proteasomal degradation pathway is essential for by their Svedberg sedimentation coefficient (denoted
many cellular processes, including the cell cycle, the reg- S). The proteasome most exclusively used in mammals
ulation of gene expression, and responses to oxidative is the cytosolic 26S proteasome, which is about 2000
stress. The importance of proteolytic degradation inside kilodaltons (kDa) in molecular mass containing one 20S
cells and the role of ubiquitin in proteolytic pathways was protein subunit and two 19S regulatory cap subunits. The
acknowledged in the award of the 2004 Nobel Prize in core is hollow and provides an enclosed cavity in which
354 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

protease active sites that perform the proteolysis reac-

tions. Three distinct catalytic activities were identified
in the purified complex: chymotrypsin-like, trypsin-like
and peptidylglutamyl-peptide hydrolyzing.[16] The size of
the proteasome is relatively conserved and is about 150
angstroms (Å) by 115 Å. The interior chamber is at most
53 Å wide, though the entrance can be as narrow as 13 Å,
suggesting that substrate proteins must be at least partially
unfolded to enter.[17]
In archaea such as Thermoplasma acidophilum, all the
α and all the β subunits are identical, whereas eukary-
otic proteasomes such as those in yeast contain seven dis-
tinct types of each subunit. In mammals, the β1, β2,
and β5 subunits are catalytic; although they share a com-
mon mechanism, they have three distinct substrate speci-
ficities considered chymotrypsin-like, trypsin-like, and
peptidyl-glutamyl peptide-hydrolyzing (PHGH).[18] Al-
ternative β forms denoted β1i, β2i, and β5i can be ex-
pressed in hematopoietic cells in response to exposure to
pro-inflammatory signals such as cytokines, in particular,
interferon gamma. The proteasome assembled with these
alternative subunits is known as the immunoproteasome,
whose substrate specificity is altered relative to the nor-
mal proteasome.[17]
A schematic diagram of the proteasome 20S core particle viewed
from one side. The α subunits that make up the outer two rings
are shown in green, and the β subunits that make up the inner 19S regulatory particle
two rings are shown in blue.
The 19S particle in eukaryotes consists of 19 individ-
ual proteins and is divisible into two subassemblies, a
proteins are degraded; openings at the two ends of the 9-subunit base that binds directly to the α ring of the
core allow the target protein to enter. Each end of the core 20S core particle, and a 10-subunit lid. Six of the
particle associates with a 19S regulatory subunit that con- nine base proteins are ATPase subunits from the AAA
tains multiple ATPase active sites and ubiquitin binding Family, and an evolutionary homolog of these ATPases
sites; it is this structure that recognizes polyubiquitinated exists in archaea, called PAN (Proteasome-Activating
proteins and transfers them to the catalytic core. An alter- Nucleotidase).[19] The association of the 19S and 20S
native form of regulatory subunit called the 11S particle particles requires the binding of ATP to the 19S ATPase
can associate with the core in essentially the same manner subunits, and ATP hydrolysis is required for the assem-
as the 19S particle; the 11S may play a role in degradation bled complex to degrade folded and ubiquitinated pro-
of foreign peptides such as those produced after infection teins. Note that only the step of substrate unfolding re-
by a virus.[14] quires energy from ATP hydrolysis, while ATP-binding
alone can support all the other steps required for pro-
20S core particle tein degradation (e.g., complex assembly, gate opening,
translocation, and proteolysis).[20][21] In fact, ATP bind-
The number and diversity of subunits contained in the ing to the ATPases by itself supports the rapid degra-
20S core particle depends on the organism; the number dation of unfolded proteins. However, while ATP hy-
of distinct and specialized subunits is larger in multicel- drolysis is required for unfolding only, it is not yet clear
lular than unicellular organisms and larger in eukaryotes whether this energy may be used in the coupling of some
than in prokaryotes. All 20S particles consist of four of these steps.[21][22]
stacked heptameric ring structures that are themselves In 2012, two independent efforts have elucidated the
composed of two different types of subunits; α subunits molecular architecture of the 26S proteasome by single
are structural in nature, whereas β subunits are predom- particle electron microscopy.[24][25] More recently, a
inantly catalytic. The outer two rings in the stack con- pseudo-atomic atomic model has been built, again us-
sist of seven α subunits each, which serve as docking ing cryo-EM.[23] In the heart of the 19S, directly adja-
domains for the regulatory particles and the alpha sub- cent to the 20S, are the AAA-ATPases (AAA proteins)
units N-termini form a gate that blocks unregulated ac- that assemble to a heterohexameric ring of the order
cess of substrates to the interior cavity.[15] The inner two Rpt1/Rpt2/Rpt6/Rpt3/Rpt4/Rpt5. This ring is a trimer
rings each consist of seven β subunits and contain the of dimers: Rpt1/Rpt2, Rpt6/Rpt3, and Rpt4/Rpt5 dimer-
21.5. PROTEASOME 355

Conformational changes of 19S

The 19S regulatory particle has been observed in three

strongly differing conformational states to date.[26] Real-
ization of all these three conformational states is likely
necessary for accomplishing substrate recognition and
degradation (see below). A hallmark of the AAA-
ATPase configuration in this predominant low-energy
state is a staircase- or lockwasher-like arrangement of
the AAA-domains.[23][24] Also in the presence of ATP
but absence of substrate an alternative, less abundant
conformation of the 19S is adopted primarily differing
in the positioning of the lid with respect to the AAA-
ATPase module.[26] In the presence of ATP-gammaS or
a substrate (stabilized in a 26S mutant with defective
Rpn11) a third conformation has been observed display-
ing a dramatic structural change of the AAA-ATPase
module.[27][28]

Three distinct conformational states of the 26S proteasome.[26]

The conformations are hypothesized to be responsible for recruit-
ment of the substrate, its irreversible commitment, and finally
Cartoon representation of the 26S proteasome.[23] processing and translocation into the core particle, where degra-
dation occurs.

Regulation of the 20S by the 19S

ize via their N-terminal coiled-coils. These coiled-coils
protrude from the hexameric ring. The largest regulatory The 19S regulatory particle is responsible for stimulating
particle non-ATPases Rpn1 and Rpn2 bind to the tips of the 20S to degrade proteins. A primary function of the
Rpt1/2 and Rpt6/3, respectively. The ubiquitin recep- 19S regulatory ATPases is to open the gate in the 20S
tor Rpn13 binds to Rpn2 and completes the base cub- that blocks the entry of substrates into the degradation
complex. The lid covers one half of the AAA-ATPase chamber.[29] The mechanism by which the proteasomal
hexamer (Rpt6/Rpt3/Rpt4) and, unexpectedly, directly ATPase open this gate has been recently elucidated.[15]
contacts the 20S via Rpn6 and to lesser extent Rpn5. The 20S gate opening, and thus substrate degradation, re-
subunits Rpn9, Rpn5, Rpn6, Rpn7, Rpn3, and Rpn12, quires the C-termini of the proteasomal ATPases, which
which are structurally related among themselves and to contains a specific motif (i.e., HbYX motif). The AT-
subunits of the COP9 complex and the Eukaryotic initi- Pases C-termini bind into pockets in the top of the 20S,
ation factor 3 (hence called PCI subunits) assemble to a and tether the ATPase complex to the 20S proteolytic
horseshoe-like structure enclosing the Rpn8/Rpn11 het- complex, thus joining the substrate unfolding equipment
erodimer. Rpn11, the deubiquinating enzyme, is placed with the 20S degradation machinery. Binding of these C-
at the mouth of the AAA-ATPase hexamer, ideally posi- termini into these 20S pockets by themselves stimulates
tioned to remove ubiquitin moieties immediately before opening of the gate in the 20S in much the same way that
translocation of substrates into the 20S. The second ubiq- a “key-in-a-lock” opens a door.[15] The precise mecha-
uitin receptor identified to date, Rpn10, is positioned at nism by which this “key-in-a-lock” mechanism functions
the periphery of the lid, near subunits Rpn8 and Rpn9. has been structurally elucidated.[30]
356 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

11S regulatory particle 21.5.5 The protein degradation process

20S proteasomes can also associate with a second type

of regulatory particle, the 11S regulatory particle, a hep-
tameric structure that does not contain any ATPases and
can promote the degradation of short peptides but not of
complete proteins. It is presumed that this is because the
complex cannot unfold larger substrates. This structure is
also known as PA28 or REG. The mechanisms by which
it binds to the core particle through the C-terminal tails
of its subunits and induces α-ring conformational changes
to open the 20S gate suggest a similar mechanism for the
19S particle.[31] The expression of the 11S particle is in-
duced by interferon gamma and is responsible, in con-
junction with the immunoproteasome β subunits, for the
generation of peptides that bind to the major histocom-
patibility complex.[14] Ribbon diagram of ubiquitin, the highly conserved protein that
serves as a molecular tag targeting proteins for degradation by
the proteasome

21.5.4 Assembly

The assembly of the proteasome is a complex process due Ubiquitination and targeting
to the number of subunits that must associate to form an
active complex. The β subunits are synthesized with N- Proteins are targeted for degradation by the proteasome
terminal “propeptides” that are post-translationally mod- with covalent modification of a lysine residue that re-
ified during the assembly of the 20S particle to expose quires the coordinated reactions of three enzymes. In the
the proteolytic active site. The 20S particle is assem- first step, a ubiquitin-activating enzyme (known as E1)
bled from two half-proteasomes, each of which consists hydrolyzes ATP and adenylylates a ubiquitin molecule.
of a seven-membered pro-β ring attached to a seven- This is then transferred to E1’s active-site cysteine residue
membered α ring. The association of the β rings of in concert with the adenylylation of a second ubiquitin.[37]
the two half-proteasomes triggers threonine-dependent This adenylylated ubiquitin is then transferred to a cys-
autolysis of the propeptides to expose the active site. teine of a second enzyme, ubiquitin-conjugating enzyme
These β interactions are mediated mainly by salt bridges (E2). In the last step, a member of a highly diverse class
and hydrophobic interactions between conserved alpha of enzymes known as ubiquitin ligases (E3) recognizes
helices whose disruption by mutation damages the protea- the specific protein to be ubiquitinated and catalyzes the
some’s ability to assemble.[32] The assembly of the half- transfer of ubiquitin from E2 to this target protein. A
proteasomes, in turn, is initiated by the assembly of the target protein must be labeled with at least four ubiquitin
monomers (in the form of a polyubiquitin chain) before it
α subunits into their heptameric ring, forming a template
for the association of the corresponding pro-β ring. The is recognized by the proteasome lid.[38] It is therefore the
E3 that confers substrate specificity to this system.[39] The
assembly of α subunits has not been characterized.[33]
number of E1, E2, and E3 proteins expressed depends on
Only recently, the assembly process of the 19S regu- the organism and cell type, but there are many different
latory particle has been elucidated to considerable ex- E3 enzymes present in humans, indicating that there is a
tent. The 19S regulatory particle assembles as two dis- huge number of targets for the ubiquitin proteasome sys-
tinct subcomponents, the base and the lid. Assem- tem.
bly of the base complex is facilitated by four assembly
chaperones, Hsm3/S5b, Nas2/p27, Rpn14/PAAF1, and The mechanism by which a polyubiquitinated pro-
Nas6/gankyrin (names for yeast/mammals).[34] These as- tein is targeted to the proteasome is not fully under-
sembly chaperones bind to the AAA-ATPase subunits stood. Ubiquitin-receptor proteins have an N-terminal
and their main function seems to be to ensure proper as- ubiquitin-like (UBL) domain and one or more ubiquitin-
sembly of the heterohexameric AAA-ATPase ring. To associated (UBA) domains. The UBL domains are rec-
date it is still under debate whether the base complex ognized by the 19S proteasome caps and the UBA do-
assembles separately, whether the assembly is templated mains bind ubiquitin via three-helix bundles. These re-
by the 20S core particle, or whether alternative assembly ceptor proteins may escort polyubiquitinated proteins to
pathways exist. In addition to the four assembly chaper- the proteasome, though the specifics of this interaction
ones, the deubiquitinating enzyme Ubp6/Usp14 also pro- and its regulation are unclear.[40]
motes base assembly, but it is not essential.[35] The lid as- The ubiquitin protein itself is 76 amino acids long and
sembles separately in a specific order and does not require was named due to its ubiquitous nature, as it has a
assembly chaperones.[36] highly conserved sequence and is found in all known eu-
21.5. PROTEASOME 357

karyotic organisms.[41] The genes encoding ubiquitin in hydrolysis is used for substrate unfolding.[20] Passage of
eukaryotes are arranged in tandem repeats, possibly due the unfolded substrate through the opened gate occurs via
to the heavy transcription demands on these genes to pro- facilitated diffusion if the 19S cap is in the ATP-bound
duce enough ubiquitin for the cell. It has been proposed state.[48]
that ubiquitin is the slowest-evolving protein identified to The mechanism for unfolding of globular proteins is nec-
date.[42] Ubiquitin contains seven lysine residues to which essarily general, but somewhat dependent on the amino
another ubiquitin can be ligated, resulting in different acid sequence. Long sequences of alternating glycine and
types of polyubiquitin chains.[43] Chains in which each alanine have been shown to inhibit substrate unfolding,
additional ubiquitin is linked to lysine 48 of the previous
decreasing the efficiency of proteasomal degradation; this
ubiquitin have a role in proteasome targeting, while other results in the release of partially degraded byproducts,
types of chains may be involved in other processes.[44][45]
possibly due to the decoupling of the ATP hydrolysis and
unfolding steps.[49] Such glycine-alanine repeats are also
found in nature, for example in silk fibroin; in particular,
certain Epstein-Barr virus gene products bearing this se-
quence can stall the proteasome, helping the virus propa-
gate by preventing antigen presentation on the major his-
tocompatibility complex.[50]

The ubiquitination pathway

Unfolding and translocation

After a protein has been ubiquitinated, it is recognized by

the 19S regulatory particle in an ATP-dependent binding
step.[21] The substrate protein must then enter the interior
of the 20S particle to come in contact with the proteolytic
active sites. Because the 20S particle’s central channel is
narrow and gated by the N-terminal tails of the α ring
subunits, the substrates must be at least partially unfolded
before they enter the core. The passage of the unfolded
substrate into the core is called translocation and neces-
sarily occurs after deubiquitination.[21] However, the or-
der in which substrates are deubiquitinated and unfolded
is not yet clear.[46] Which of these processes is the rate-
A cutaway view of the proteasome 20S core particle illustrating
limiting step in the overall proteolysis reaction depends
the locations of the active sites. The α subunits are represented as
on the specific substrate; for some proteins, the unfold- green spheres and the β subunits as protein backbones colored by
ing process is rate-limiting, while deubiquitination is the individual polypeptide chain. The small pink spheres represent
slowest step for other proteins.[20] The extent to which the location of the active-site threonine residue in each subunit.
substrates must be unfolded before translocation is not Light blue chemical structures are the inhibitor bortezomib bound
known, but substantial tertiary structure, and in particu- to the active sites.
lar nonlocal interactions such as disulfide bonds, are suf-
ficient to inhibit degradation.[47]
The gate formed by the α subunits prevents peptides Proteolysis
longer than about four residues from entering the interior
of the 20S particle. The ATP molecules bound before the See also: threonine protease § mechanism
initial recognition step are hydrolyzed before transloca-
tion. While energy is needed for substrate unfolding, it is The mechanism of proteolysis by the β subunits of
not required for translocation.[20][21] The assembled 26S the 20S core particle is through a threonine-dependent
proteasome can degrade unfolded proteins in the pres- nucleophilic attack. This mechanism may depend on an
ence of a non-hydrolyzable ATP analog, but cannot de- associated water molecule for deprotonation of the reac-
grade folded proteins, indicating that energy from ATP tive threonine hydroxyl. Degradation occurs within the
358 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

central chamber formed by the association of the two

β rings and normally does not release partially degraded
products, instead reducing the substrate to short polypep-
tides typically 7–9 residues long, though they can range
from 4 to 25 residues, depending on the organism and
substrate. The biochemical mechanism that determines
product length is not fully characterized.[51] Although
the three catalytic β subunits have a common mecha-
nism, they have slightly different substrate specificities,
which are considered chymotrypsin-like, trypsin-like,
and peptidyl-glutamyl peptide-hydrolyzing (PHGH)-like.
These variations in specificity are the result of interatomic
contacts with local residues near the active sites of each
subunit. Each catalytic β subunit also possesses a con-
served lysine residue required for proteolysis.[18]
Although the proteasome normally produces very short
peptide fragments, in some cases these products are
themselves biologically active and functional molecules.
Certain transcription factors regulating the expression of The assembled complex of hslV (blue) and hslU (red) from E.
specific genes, including one component of the mam- coli. This complex of heat shock proteins is thought to resemble
malian complex NF-κB, are synthesized as inactive pre- the ancestor of the modern proteasome.
cursors whose ubiquitination and subsequent proteasomal
degradation converts them to an active form. Such activ-
21.5.6 Evolution
ity requires the proteasome to cleave the substrate protein
internally, rather than processively degrading it from one
The 20S proteasome is both ubiquitous and essential in
terminus. It has been suggested that long loops on these
eukaryotes. Some prokaryotes, including many archaea
proteins’ surfaces serve as the proteasomal substrates and
and the bacterial order Actinomycetales also share ho-
enter the central cavity, while the majority of the protein
mologs of the 20S proteasome, whereas most bacteria
remains outside.[52] Similar effects have been observed in
possess heat shock genes hslV and hslU, whose gene
yeast proteins; this mechanism of selective degradation is
products are a multimeric protease arranged in a two-
known as regulated ubiquitin/proteasome dependent pro-
layered ring and an ATPase.[58] The hslV protein has been
cessing (RUP).[53]
hypothesized to resemble the likely ancestor of the 20S
proteasome.[59] In general, HslV is not essential in bacte-
ria, and not all bacteria possess it, whereas some protists
possess both the 20S and the hslV systems.[58] Many bac-
teria also possess other homologs of the proteasome and
an associated ATPase, most notably ClpP and ClpX. This
Ubiquitin-independent degradation redundancy explains why the HslUV system is not essen-
tial.
Although most proteasomal substrates must be ubiquiti- Sequence analysis suggests that the catalytic β subunits di-
nated before being degraded, there are some exceptions verged earlier in evolution than the predominantly struc-
to this general rule, especially when the proteasome plays tural α subunits. In bacteria that express a 20S protea-
a normal role in the post-translational processing of the some, the β subunits have high sequence identity to ar-
protein. The proteasomal activation of NF-κB by pro- chaeal and eukaryotic β subunits, whereas the α sequence
cessing p105 into p50 via internal proteolysis is one ma- identity is much lower. The presence of 20S proteasomes
jor example.[52] Some proteins that are hypothesized to in bacteria may result from lateral gene transfer, while the
be unstable due to intrinsically unstructured regions,[54] diversification of subunits among eukaryotes is ascribed
are degraded in a ubiquitin-independent manner. The to multiple gene duplication events.[58]
most well-known example of a ubiquitin-independent
proteasome substrate is the enzyme ornithine decar-
boxylase.[55] Ubiquitin-independent mechanisms target- 21.5.7 Cell cycle control
ing key cell cycle regulators such as p53 have also
been reported, although p53 is also subject to ubiquitin- Cell cycle progression is controlled by ordered action of
dependent degradation.[56] Finally, structurally abnormal, cyclin-dependent kinases (CDKs), activated by specific
misfolded, or highly oxidized proteins are also subject to cyclins that demarcate phases of the cell cycle. Mitotic
ubiquitin-independent and 19S-independent degradation cyclins, which persist in the cell for only a few minutes,
under conditions of cellular stress.[57] have one of the shortest life spans of all intracellular
21.5. PROTEASOME 359

proteins.[2] After a CDK-cyclin complex has performed protein ubiquitination, and of E1, E2, and E3 enzymes
its function, the associated cyclin is polyubiquitinated and that is observed well in advance of apoptosis.[67][68][69]
destroyed by the proteasome, which provides directional- During apoptosis, proteasomes localized to the nucleus
ity for the cell cycle. In particular, exit from mitosis re- have also been observed to translocate to outer membrane
quires the proteasome-dependent dissociation of the reg- blebs characteristic of apoptosis.[70]
ulatory component cyclin B from the mitosis promoting Proteasome inhibition has different effects on apoptosis
factor complex.[60] In vertebrate cells, “slippage” through induction in different cell types. In general, the protea-
the mitotic checkpoint leading to premature M phase exit some is not required for apoptosis, although inhibiting it
can occur despite the delay of this exit by the spindle
is pro-apoptotic in most cell types that have been studied.
checkpoint.[61] Apoptosis is mediated through disrupting the regulated
Earlier cell cycle checkpoints such as post-restriction degradation of pro-growth cell cycle proteins.[71] How-
point check between G1 phase and S phase similarly in- ever, some cell lines — in particular, primary cultures of
volve proteasomal degradation of cyclin A, whose ubiq- quiescent and differentiated cells such as thymocytes and
uitination is promoted by the anaphase promoting com- neurons — are prevented from undergoing apoptosis on
plex (APC), an E3 ubiquitin ligase.[62] The APC and the exposure to proteasome inhibitors. The mechanism for
Skp1/Cul1/F-box protein complex (SCF complex) are this effect is not clear, but is hypothesized to be specific to
the two key regulators of cyclin degradation and check- cells in quiescent states, or to result from the differential
point control; the SCF itself is regulated by the APC via activity of the pro-apoptotic kinase JNK.[72] The ability
ubiquitination of the adaptor protein, Skp2, which pre- of proteasome inhibitors to induce apoptosis in rapidly
vents SCF activity before the G1-S transition.[63] dividing cells has been exploited in several recently de-
Individual components of the 19S particle have their veloped chemotherapy agents such as bortezomib and
own regulatory roles. Gankyrin, a recently identified salinosporamide A.
oncoprotein, is one of the 19S subcomponents that also
tightly binds the cyclin-dependent kinase CDK4 and
plays a key role in recognizing ubiquitinated p53, via 21.5.8 Response to cellular stress
its affinity for the ubiquitin ligase MDM2. Gankyrin is
anti-apoptotic and has been shown to be overexpressed In response to cellular stresses – such as infection, heat
in some tumor cell types such as hepatocellular carci- shock, or oxidative damage – heat shock proteins that
noma.[64] identify misfolded or unfolded proteins and target them
for proteasomal degradation are expressed. Both Hsp27
and Hsp90—chaperone proteins have been implicated
Regulation of plant growth in increasing the activity of the ubiquitin-proteasome
system, though they are not direct participants in the
In plants, signaling by auxins, or phytohormones that or- process.[73] Hsp70, on the other hand, binds exposed
der the direction and tropism of plant growth, induces hydrophobic patches on the surface of misfolded proteins
the targeting of a class of transcription factor repressors and recruits E3 ubiquitin ligases such as CHIP to tag the
known as Aux/IAA proteins for proteasomal degradation. proteins for proteasomal degradation.[74] The CHIP pro-
These proteins are ubiquitinated by SCFTIR1, or SCF in tein (carboxyl terminus of Hsp70-interacting protein) is
complex with the auxin receptor TIR1. Degradation of itself regulated via inhibition of interactions between the
Aux/IAA proteins derepresses transcription factors in the E3 enzyme CHIP and its E2 binding partner.[75]
auxin-response factor (ARF) family and induces ARF-
Similar mechanisms exist to promote the degradation
directed gene expression.[65] The cellular consequences
of oxidatively damaged proteins via the proteasome sys-
of ARF activation depend on the plant type and devel-
tem. In particular, proteasomes localized to the nucleus
opmental stage, but are involved in directing growth in
are regulated by PARP and actively degrade inappropri-
roots and leaf veins. The specific response to ARF dere-
ately oxidized histones.[76] Oxidized proteins, which of-
pression is thought to be mediated by specificity in the
ten form large amorphous aggregates in the cell, can be
pairing of individual ARF and Aux/IAA proteins.[66]
degraded directly by the 20S core particle without the 19S
regulatory cap and do not require ATP hydrolysis or tag-
Apoptosis ging with ubiquitin.[57] However, high levels of oxidative
damage increases the degree of cross-linking between
Both internal and external signals can lead to the induc- protein fragments, rendering the aggregates resistant to
tion of apoptosis, or programmed cell death. The result- proteolysis. Larger numbers and sizes of such [77]
highly ox-
ing deconstruction of cellular components is primarily idized aggregates are associated with aging.
carried out by specialized proteases known as caspases, Dysregulation of the ubiquitin proteasome system may
but the proteasome also plays important and diverse roles contribute to several neural diseases. It may lead to brain
in the apoptotic process. The involvement of the protea- tumors such as astrocytomas.[78] In some of the late-onset
some in this process is indicated by both the increase in neurodegenerative diseases that share aggregation of mis-
360 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

folded proteins as a common feature, such as Parkinson’s tite motif family) binds with immunoglobulin G to direct
disease and Alzheimer’s disease, large insoluble aggre- the virion to the proteasome where it is degraded.[83]
gates of misfolded proteins can form and then result in
neurotoxicity, through mechanisms that are not yet well
understood. Decreased proteasome activity has been sug- 21.5.10 Proteasome inhibitors
gested as a cause of aggregation and Lewy body formation
in Parkinson’s.[79] This hypothesis is supported by the ob- Main article: Proteasome inhibitor
servation that yeast models of Parkinson’s are more sus- Proteasome inhibitors have effective anti-tumor activity
ceptible to toxicity from α-synuclein, the major protein
component of Lewy bodies, under conditions of low pro-
teasome activity.[80] Impaired proteasomal activity may
underlie cognitive disorders such as the autism spectrum
disorders, and muscle and nerve diseases such as inclusion
body myopathy.[78]

21.5.9 Role in the immune system

The proteasome plays a straightforward but critical role

in the function of the adaptive immune system. Peptide
antigens are displayed by the major histocompatibility
complex class I (MHC) proteins on the surface of antigen- Chemical structure of bortezomib, a proteasome inhibitor used
presenting cells. These peptides are products of protea- in chemotherapy that is particularly effective against multiple
somal degradation of proteins originated by the invad- myeloma
ing pathogen. Although constitutively expressed protea-
somes can participate in this process, a specialized com-
plex composed of proteins, whose expression is induced
by interferon gamma, are the primary producers of pep-
tides which are optimal in size and composition for MHC
binding. These proteins whose expression increases dur-
ing the immune response include the 11S regulatory par-
ticle, whose main known biological role is regulating the
production of MHC ligands, and specialized β subunits
called β1i, β2i, and β5i with altered substrate specificity.
The complex formed with the specialized β subunits is
known as the immunoproteasome.[14] Another β5i vari-
ant subunit, β5t, is expressed in the thymus, leading to a
thymus-specific “thymoproteasome” whose function is as
yet unclear.[81]
The strength of MHC class I ligand binding is depen-
dent on the composition of the ligand C-terminus, as pep-
tides bind by hydrogen bonding and by close contacts Bortezomib bound to the core particle in a yeast proteasome. The
with a region called the “B pocket” on the MHC surface. bortezomib molecule is in the center colored by atom type (carbon
Many MHC class I alleles prefer hydrophobic C-terminal = pink, nitrogen = blue, oxygen = red, boron = yellow), sur-
residues, and the immunoproteasome complex is more rounded by the local protein surface. The blue patch is the cat-
alytic threonine residue whose activity is blocked by the presence
likely to generate hydrophobic C-termini.[82]
of bortezomib.
Due to its role in generating the activated form of NF-
κB, an anti-apoptotic and pro-inflammatory regulator of in cell culture, inducing apoptosis by disrupting the reg-
cytokine expression, proteasomal activity has been linked ulated degradation of pro-growth cell cycle proteins.[71]
to inflammatory and autoimmune diseases. Increased lev- This approach of selectively inducing apoptosis in tumor
els of proteasome activity correlate with disease activity cells has proven effective in animal models and human
and have been implicated in autoimmune diseases includ- trials.
ing systemic lupus erythematosus and rheumatoid arthri- Lactacystin, a natural product synthesized by
tis.[14] Streptomyces bacteria, was the first non-peptidic
The proteasome is also involved in Intracellular antibody- proteasome inhibitor discovered[84] and is widely used
mediated proteolysis of antibody-bound virions. In this as a research tool in biochemistry and cell biology.
neutralisation pathway, TRIM21 (a protein of the tripar- Lactacystin was licensed to Myogenics/Proscript, which
21.5. PROTEASOME 361

was acquired by Millennium Pharmaceuticals, now part been made to consider the proteasome for the develop-
of Takeda Pharmaceuticals. Lactacystin covalently ment of novel diagnostic markers and strategies. An im-
modifies the amino-terminal threonine of catalytic β proved and comprehensive understanding of the patho-
subunits of the proteasome, particularly the β5 subunit physiology of the proteasome should lead to clinical ap-
responsible for the proteasome’s chymotrypsin-like plications in the future.
activity. This discovery helped to establish the protea- The proteasomes form a pivotal component for the
some as a mechanistically novel class of protease: an Ubiquitin-Proteasome System (UPS) [99] and corre-
amino-terminal threonine protease. sponding cellular Protein Quality Control (PQC). Pro-
Bortezomib, a molecule developed by Millennium Phar- tein ubiquitination and subsequent proteolysis and degra-
maceuticals and marketed as Velcade, is the first protea- dation by the proteasome are important mechanisms in
some inhibitor to reach clinical use as a chemotherapy the regulation of the cell cycle, cell growth and dif-
agent.[85] Bortezomib is used in the treatment of multiple ferentiation, gene transcription, signal transduction and
myeloma.[86] Notably, multiple myeloma has been ob- apoptosis.[100] Subsequently, a compromised proteasome
served to result in increased proteasome-derived peptide complex assembly and function lead to reduced prote-
levels in blood serum that decrease to normal levels in re- olytic activities and the accumulation of damaged or mis-
sponse to successful chemotherapy.[87] Studies in animals folded protein species. Such protein accumulation may
have indicated that bortezomib may also have clinically contribute to the pathogenesis and phenotypic character-
significant effects in pancreatic cancer.[88][89] Preclinical istics in neurodegenerative diseases,[101][102] cardiovascu-
and early clinical studies have been started to examine lar diseases,[103][104][105] inflammatory responses and au-
bortezomib’s effectiveness in treating other B-cell-related toimmune diseases,[106] and systemic DNA damage re-
cancers,[90] particularly some types of non-Hodgkin’s sponses leading to malignancies.[107]
lymphoma.[91] Clinical results also seem to justify use of Several experimental and clinical studies have indicated
proteasome inhibitor combined with chemotherapy, for that aberrations and deregulations of the UPS contribute
B-cell acute lymphoblastic leukemia [92] Proteasome in- to the pathogenesis of several neurodegenerative and
hibitor can kill some types of cultured leukemia cells that myodegenerative disorders, including Alzheimer’s dis-
are resistant to glucocorticoid.[93] ease,[108] Parkinson’s disease[109] and Pick’s disease,[110]
The molecule ritonavir, marketed as Norvir, was devel- Amyotrophic lateral sclerosis (ALS),[110] Huntington’s
oped as a protease inhibitor and used to target HIV infec- disease,[109] Creutzfeldt-Jacob disease,[111] and mo-
tion. However, it has been shown to inhibit proteasomes tor neuron diseases, polyglutamine (PolyQ) diseases,
as well as free proteases; to be specific, the chymotrypsin- Muscular dystrophies[112] and several rare forms of neu-
like activity of the proteasome is inhibited by ritonavir, rodegenerative diseases associated with dementia.[113] As
while the trypsin-like activity is somewhat enhanced.[94] part of the Ubiquitin-Proteasome System (UPS), the pro-
Studies in animal models suggest that ritonavir may have teasome maintains cardiac protein homeostasis and thus
inhibitory effects on the growth of glioma cells.[95] plays a significant role in cardiac Ischemic injury,[114]
Proteasome inhibitors have also shown promise in treat- ventricular hypertrophy[115] and Heart failure.[116] Ad-
ing autoimmune diseases in animal models. For example, ditionally, evidence is accumulating that the UPS plays
studies in mice bearing human skin grafts found a reduc- an essential role in malignant transformation. UPS pro-
tion in the size of lesions from psoriasis after treatment teolysis plays a major role in responses of cancer cells
with a proteasome inhibitor.[96] Inhibitors also show pos- to stimulatory signals that are critical for the develop-
itive effects in rodent models of asthma.[97] ment of cancer. Accordingly, gene expression by degra-
dation of transcription factors, such as p53, c-Jun, c-
Labeling and inhibition of the proteasome is also of inter- Fos, NF-κB, c-Myc, HIF-1α, MATα2, STAT3, sterol-
est in laboratory settings for both in vitro and in vivo study regulated element-binding proteins and androgen recep-
of proteasomal activity in cells. The most commonly used tors are all controlled by the UPS and thus involved
laboratory inhibitors are lactacystin and the peptide alde- in the development of various malignancies.[117] More-
hyde MG132. Fluorescent inhibitors have also been de- over, the UPS regulates the degradation of tumor sup-
veloped to specifically label the active sites of the assem- pressor gene products such as adenomatous polyposis
bled proteasome.[98] coli (APC) in colorectal cancer, retinoblastoma (Rb).
and von Hippel-Lindau tumor suppressor (VHL), as well
as a number of proto-oncogenes (Raf, Myc, Myb, Rel,
21.5.11 Clinical significance Src, Mos, Abl).The UPS is also involved in the regu-
lation of inflammatory responses. This activity is usu-
The Proteasome and its subunits are of clinical signifi- ally attributed to the role of proteasomes in the acti-
cance for at least two reasons: (1) a compromised com- vation of NF-κB which further regulates the expression
plex assembly or a dysfunctional proteasome can be as- of pro inflammatory cytokines such as TNF-α, IL-β,
sociated with the underlying pathophysiology of specific IL-8, adhesion molecules (ICAM-1, VCAM-1, P selec-
diseases, and (2) they can be exploited as drug targets for tine) and prostaglandins and nitric oxide (NO).[118] Ad-
therapeutic interventions. More recently, more effort has
362 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

ditionally, the UPS also plays a role in inflammatory re- [8] Wilk S, Orlowski M (Nov 1980). “Cation-sensitive neu-
sponses as regulators of leukocyte proliferation, mainly tral endopeptidase: isolation and specificity of the bovine
through proteolysis of cyclines and the degradation of pituitary enzyme”. Journal of Neurochemistry 35 (5):
CDK inhibitors.[119] Lastly, autoimmune disease patients 1172–82. doi:10.1111/j.1471-4159.1980.tb07873.x.
with SLE, Sjogren’s syndrome and rheumatoid arthri- PMID 6778972.
tis (RA) predominantly exhibit circulating proteasomes [9] Tanaka K, Waxman L, Goldberg AL (Jun 1983). “ATP
which can be applied as clinical biomarkers.[120] serves two distinct roles in protein degradation in retic-
ulocytes, one requiring and one independent of ubiq-
uitin”. The Journal of Cell Biology 96 (6): 1580–
21.5.12 See also 5. doi:10.1083/jcb.96.6.1580. PMC 2112434. PMID
6304111.
• The Proteolysis Map
[10] Hough R, Pratt G, Rechsteiner M (Jun 1987).
“Purification of two high molecular weight proteases
• Exosome
from rabbit reticulocyte lysate”. The Journal of Biological
Chemistry 262 (17): 8303–13. PMID 3298229.
• Endoplasmic reticulum-associated protein degrada-
tion [11] Hershko A (Sep 2005). “Early work on the ubiqui-
tin proteasome system, an interview with Avram Her-
• JUNQ and IPOD shko. Interview by CDD”. Cell Death and Differentiation
12 (9): 1158–61. doi:10.1038/sj.cdd.4401709. PMID
16094391.
21.5.13 References
[12] Kopp F, Steiner R, Dahlmann B, Kuehn L, Reinauer
[1] Peters JM, Franke WW, Kleinschmidt JA (Mar 1994). H (Aug 1986). “Size and shape of the multicatalytic
“Distinct 19 S and 20 S subcomplexes of the 26 S pro- proteinase from rat skeletal muscle”. Biochimica Et
teasome and their distribution in the nucleus and the cy- Biophysica Acta 872 (3): 253–60. doi:10.1016/0167-
toplasm”. The Journal of Biological Chemistry 269 (10): 4838(86)90278-5. PMID 3524688.
7709–18. PMID 8125997.
[13] Löwe J, Stock D, Jap B, Zwickl P, Baumeister W,
Huber R (Apr 1995). “Crystal structure of the
[2] Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M,
20S proteasome from the archaeon T. acidophilum
Scott MP, Zipursky SL, Darnell J (2004). “3”. Molecular
at 3.4 A resolution”. Science 268 (5210): 533–9.
cell biology (5th ed.). New York: W.H. Freeman and CO.
doi:10.1126/science.7725097. PMID 7725097.
pp. 66–72. ISBN 978-0-7167-4366-8.
[14] Wang J, Maldonado MA (Aug 2006). “The ubiquitin-
[3] Nobel Prize Committee (2004). “Nobel Prize Awardees proteasome system and its role in inflammatory and au-
in Chemistry, 2004”. Retrieved 2006-12-11. toimmune diseases”. Cellular & Molecular Immunology 3
(4): 255–61. PMID 16978533.
[4] Etlinger JD, Goldberg AL (Jan 1977). “A soluble ATP-
dependent proteolytic system responsible for the degrada- [15] Smith DM, Chang SC, Park S, Finley D, Cheng Y, Gold-
tion of abnormal proteins in reticulocytes”. Proceedings of berg AL (Sep 2007). “Docking of the proteasomal AT-
the National Academy of Sciences of the United States of Pases’ carboxyl termini in the 20S proteasome’s alpha ring
America 74 (1): 54–8. doi:10.1073/pnas.74.1.54. PMC opens the gate for substrate entry”. Molecular Cell 27
393195. PMID 264694. (5): 731–44. doi:10.1016/j.molcel.2007.06.033. PMC
2083707. PMID 17803938.
[5] Ciehanover A, Hod Y, Hershko A (Apr 1978). “A heat-
stable polypeptide component of an ATP-dependent pro- [16] Wilk S, Orlowski M (Mar 1983). “Evidence that pitu-
teolytic system from reticulocytes”. Biochemical and itary cation-sensitive neutral endopeptidase is a multicat-
Biophysical Research Communications 81 (4): 1100–5. alytic protease complex”. Journal of Neurochemistry 40
doi:10.1016/0006-291X(78)91249-4. PMID 666810. (3): 842–9. doi:10.1111/j.1471-4159.1983.tb08056.x.
PMID 6338156.
[6] Goldknopf IL, Busch H (Mar 1977). “Isopeptide linkage
between nonhistone and histone 2A polypeptides of chro- [17] Nandi D, Tahiliani P, Kumar A, Chandu D (Mar 2006).
mosomal conjugate-protein A24”. Proceedings of the Na- “The ubiquitin-proteasome system”. Journal of Bio-
tional Academy of Sciences of the United States of Amer- sciences 31 (1): 137–55. doi:10.1007/BF02705243.
ica 74 (3): 864–8. doi:10.1073/pnas.74.3.864. PMC PMID 16595883.
430507. PMID 265581.
[18] Heinemeyer W, Fischer M, Krimmer T, Stachon U, Wolf
[7] Ciechanover A (Sep 2005). “Early work on the ubiquitin DH (Oct 1997). “The active sites of the eukaryotic 20
proteasome system, an interview with Aaron Ciechanover. S proteasome and their involvement in subunit precur-
Interview by CDD”. Cell Death and Differentiation sor processing”. The Journal of Biological Chemistry 272
12 (9): 1167–77. doi:10.1038/sj.cdd.4401691. PMID (40): 25200–9. doi:10.1074/jbc.272.40.25200. PMID
16094393. 9312134.
21.5. PROTEASOME 363

[19] Zwickl P, Ng D, Woo KM, Klenk HP, Goldberg AL [29] Köhler A, Cascio P, Leggett DS, Woo KM, Goldberg
(Sep 1999). “An archaebacterial ATPase, homologous AL, Finley D (Jun 2001). “The axial channel of the
to ATPases in the eukaryotic 26 S proteasome, acti- proteasome core particle is gated by the Rpt2 ATPase
vates protein breakdown by 20 S proteasomes”. The and controls both substrate entry and product release”.
Journal of Biological Chemistry 274 (37): 26008–14. Molecular Cell 7 (6): 1143–52. doi:10.1016/S1097-
doi:10.1074/jbc.274.37.26008. PMID 10473546. 2765(01)00274-X. PMID 11430818.

[20] Smith DM, Kafri G, Cheng Y, Ng D, Walz T, Gold- [30] Rabl J, Smith DM, Yu Y, Chang SC, Goldberg AL, Cheng
berg AL (Dec 2005). “ATP binding to PAN or Y (May 2008). “Mechanism of gate opening in the 20S
the 26S ATPases causes association with the 20S proteasome by the proteasomal ATPases”. Molecular Cell
proteasome, gate opening, and translocation of un- 30 (3): 360–8. doi:10.1016/j.molcel.2008.03.004. PMC
folded proteins”. Molecular Cell 20 (5): 687–98. 4141531. PMID 18471981.
doi:10.1016/j.molcel.2005.10.019. PMID 16337593.
[31] Förster A, Masters EI, Whitby FG, Robinson H, Hill CP
[21] Liu CW, Li X, Thompson D, Wooding K, Chang (May 2005). “The 1.9 A structure of a proteasome-
TL, Tang Z et al. (Oct 2006). “ATP binding and 11S activator complex and implications for proteasome-
ATP hydrolysis play distinct roles in the function of PAN/PA700 interactions”. Molecular Cell 18 (5):
26S proteasome”. Molecular Cell 24 (1): 39–50. 589–99. doi:10.1016/j.molcel.2005.04.016. PMID
doi:10.1016/j.molcel.2006.08.025. PMID 17018291. 15916965.

[22] Lam YA, Lawson TG, Velayutham M, Zweier JL, Pickart [32] Witt S, Kwon YD, Sharon M, Felderer K, Beut-
CM (Apr 2002). “A proteasomal ATPase subunit recog- tler M, Robinson CV et al. (Jul 2006). “Pro-
nizes the polyubiquitin degradation signal”. Nature 416 teasome assembly triggers a switch required for
(6882): 763–7. doi:10.1038/416763a. PMID 11961560. active-site maturation”. Structure 14 (7): 1179–88.
doi:10.1016/j.str.2006.05.019. PMID 16843899.
[23] Beck F, Unverdorben P, Bohn S, Schweitzer A, Pfeifer
G, Sakata E et al. (Sep 2012). “Near-atomic reso- [33] Krüger E, Kloetzel PM, Enenkel C (2001). “20S
lution structural model of the yeast 26S proteasome”. proteasome biogenesis”. Biochimie 83 (3-4): 289–
Proceedings of the National Academy of Sciences of 93. doi:10.1016/S0300-9084(01)01241-X. PMID
the United States of America 109 (37): 14870–5. 11295488.
doi:10.1073/pnas.1213333109. PMID 22927375.
[34] Murata S, Yashiroda H, Tanaka K (Feb 2009). “Molec-
ular mechanisms of proteasome assembly”. Nature
[24] Lander GC, Estrin E, Matyskiela ME, Bashore C, Nogales
Reviews. Molecular Cell Biology 10 (2): 104–115.
E, Martin A (Feb 2012). “Complete subunit architec-
doi:10.1038/nrm2630. PMID 19165213.
ture of the proteasome regulatory particle”. Nature 482
(7384). doi:10.1038/nature10774. PMID 22237024. [35] Sakata E, Stengel F, Fukunaga K, Zhou M, Saeki Y,
Förster F et al. (Jun 2011). “The catalytic activity
[25] Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Un-
of Ubp6 enhances maturation of the proteasomal reg-
verdorben P et al. (Jan 2012). “Molecular architecture of
ulatory particle”. Molecular Cell 42 (5): 637–649.
the 26S proteasome holocomplex determined by an inte-
doi:10.1016/j.molcel.2011.04.021. PMID 21658604.
grative approach”. Proceedings of the National Academy
of Sciences of the United States of America 109 (5): 1380– [36] Fukunaga K, Kudo T, Toh-e A, Tanaka K, Saeki Y (Jun
7. doi:10.1073/pnas.1120559109. PMID 22307589. 2010). “Dissection of the assembly pathway of the pro-
teasome lid in Saccharomyces cerevisiae”. Biochemi-
[26] Unverdorben P, Beck F, Śledź P, Schweitzer A, Pfeifer cal and Biophysical Research Communications 396 (4):
G, Plitzko JM et al. (Apr 2014). “Deep classification of 1048–1053. doi:10.1016/j.bbrc.2010.05.061. PMID
a large cryo-EM dataset defines the conformational land- 20471955.
scape of the 26S proteasome”. Proceedings of the Na-
tional Academy of Sciences of the United States of America [37] Haas AL, Warms JV, Hershko A, Rose IA (Mar 1982).
111 (15): 5544–9. doi:10.1073/pnas.1403409111. PMC “Ubiquitin-activating enzyme. Mechanism and role in
3992697. PMID 24706844. protein-ubiquitin conjugation”. The Journal of Biological
Chemistry 257 (5): 2543–8. PMID 6277905.
[27] Śledź P, Unverdorben P, Beck F, Pfeifer G, Schweitzer
A, Förster F et al. (Apr 2013). “Structure of the 26S [38] Thrower JS, Hoffman L, Rechsteiner M, Pickart CM
proteasome with ATP-γS bound provides insights into the (Jan 2000). “Recognition of the polyubiquitin prote-
mechanism of nucleotide-dependent substrate transloca- olytic signal”. The EMBO Journal 19 (1): 94–102.
tion”. Proceedings of the National Academy of Sciences doi:10.1093/emboj/19.1.94. PMC 1171781. PMID
of the United States of America 110 (18): 7264–7269. 10619848.
doi:10.1073/pnas.1305782110. PMID 23589842.
[39] Risseeuw EP, Daskalchuk TE, Banks TW, Liu E, Cote-
[28] Matyskiela ME, Lander GC, Martin A (Jul 2013). “Con- lesage J, Hellmann H et al. (Jun 2003). “Protein in-
formational switching of the 26S proteasome enables sub- teraction analysis of SCF ubiquitin E3 ligase subunits
strate degradation”. Nature Structural & Molecular Biol- from Arabidopsis”. The Plant Journal 34 (6): 753–
ogy 20 (7): 781–788. doi:10.1038/nsmb.2616. PMID 67. doi:10.1046/j.1365-313X.2003.01768.x. PMID
23770819. 12795696.
364 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

[40] Elsasser S, Finley D (Aug 2005). “Delivery of ubiqui- [52] Rape M, Jentsch S (May 2002). “Taking a bite: proteaso-
tinated substrates to protein-unfolding machines”. Na- mal protein processing”. Nature Cell Biology 4 (5): E113–
ture Cell Biology 7 (8): 742–9. doi:10.1038/ncb0805-742. 6. doi:10.1038/ncb0502-e113. PMID 11988749.
PMID 16056265.
[53] Rape M, Jentsch S (Nov 2004). “Productive RUPture:
[41] Sadanandom A, Bailey M, Ewan R, Lee J, Nelis S (Oct activation of transcription factors by proteasomal process-
2012). “The ubiquitin-proteasome system: central mod- ing”. Biochimica Et Biophysica Acta 1695 (1-3): 209–13.
ifier of plant signalling”. The New Phytologist 196 (1): doi:10.1016/j.bbamcr.2004.09.022. PMID 15571816.
13–28. doi:10.1111/j.1469-8137.2012.04266.x. PMID
[54] Asher G, Reuven N, Shaul Y (Aug 2006). “20S pro-
22897362.
teasomes and protein degradation “by default"". BioEs-
[42] Sharp PM, Li WH (1987). “Ubiquitin genes as says 28 (8): 844–9. doi:10.1002/bies.20447. PMID
a paradigm of concerted evolution of tandem re- 16927316.
peats”. Journal of Molecular Evolution 25 (1): 58–64. [55] Zhang M, Pickart CM, Coffino P (Apr 2003).
doi:10.1007/BF02100041. PMID 3041010. “Determinants of proteasome recognition of or-
nithine decarboxylase, a ubiquitin-independent
[43] Pickart CM, Fushman D (Dec 2004). “Polyubiq-
substrate”. The EMBO Journal 22 (7): 1488–96.
uitin chains: polymeric protein signals”. Cur-
doi:10.1093/emboj/cdg158. PMC 152902. PMID
rent Opinion in Chemical Biology 8 (6): 610–16.
12660156.
doi:10.1016/j.cbpa.2004.09.009. PMID 15556404.
[56] Asher G, Shaul Y (Aug 2005). “p53 proteasomal degra-
[44] Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, dation: poly-ubiquitination is not the whole story”. Cell
Robert J et al. (Apr 2009). “Quantitative proteomics Cycle 4 (8): 1015–8. doi:10.4161/cc.4.8.1900. PMID
reveals the function of unconventional ubiquitin chains 16082197.
in proteasomal degradation”. Cell 137 (1): 133–45.
doi:10.1016/j.cell.2009.01.041. PMC 2668214. PMID [57] Shringarpure R, Grune T, Mehlhase J, Davies KJ (Jan
19345192. 2003). “Ubiquitin conjugation is not required for
the degradation of oxidized proteins by proteasome”.
[45] Pickart CM (Nov 2000). “Ubiquitin in chains”. The Journal of Biological Chemistry 278 (1): 311–8.
Trends in Biochemical Sciences 25 (11): 544–8. doi:10.1074/jbc.M206279200. PMID 12401807.
doi:10.1016/S0968-0004(00)01681-9. PMID 11084366.
[58] Gille C, Goede A, Schlöetelburg C, Preissner R, Kloetzel
[46] Zhu Q, Wani G, Wang QE, El-mahdy M, Snapka RM, PM, Göbel UB et al. (Mar 2003). “A comprehensive view
Wani AA (Jul 2005). “Deubiquitination by proteasome on proteasomal sequences: implications for the evolution
is coordinated with substrate translocation for proteolysis of the proteasome”. Journal of Molecular Biology 326 (5):
in vivo”. Experimental Cell Research 307 (2): 436–51. 1437–48. doi:10.1016/S0022-2836(02)01470-5. PMID
doi:10.1016/j.yexcr.2005.03.031. PMID 15950624. 12595256.

[47] Wenzel T, Baumeister W (Mar 1995). “Conforma- [59] Bochtler M, Ditzel L, Groll M, Hartmann C, Huber
tional constraints in protein degradation by the 20S pro- R (1999). “The proteasome”. Annual Review of
teasome”. Nature Structural Biology 2 (3): 199–204. Biophysics and Biomolecular Structure 28 (1): 295–
doi:10.1038/nsb0395-199. PMID 7773788. 317. doi:10.1146/annurev.biophys.28.1.295. PMID
10410804.
[48] Smith DM, Benaroudj N, Goldberg A (Oct 2006). “Pro-
[60] Chesnel F, Bazile F, Pascal A, Kubiak JZ (Aug 2006).
teasomes and their associated ATPases: a destructive
“Cyclin B dissociation from CDK1 precedes its degra-
combination”. Journal of Structural Biology 156 (1): 72–
dation upon MPF inactivation in mitotic extracts of
83. doi:10.1016/j.jsb.2006.04.012. PMID 16919475.
Xenopus laevis embryos”. Cell Cycle 5 (15): 1687–98.
[49] Hoyt MA, Zich J, Takeuchi J, Zhang M, Gov- doi:10.4161/cc.5.15.3123. PMID 16921258.
aerts C, Coffino P (Apr 2006). “Glycine-alanine re- [61] Brito DA, Rieder CL (Jun 2006). “Mitotic checkpoint
peats impair proper substrate unfolding by the pro- slippage in humans occurs via cyclin B destruction in the
teasome”. The EMBO Journal 25 (8): 1720–9. presence of an active checkpoint”. Current Biology 16
doi:10.1038/sj.emboj.7601058. PMC 1440830. PMID (12): 1194–200. doi:10.1016/j.cub.2006.04.043. PMC
16601692. 2749311. PMID 16782009.
[50] Zhang M, Coffino P (Mar 2004). “Repeat sequence [62] Havens CG, Ho A, Yoshioka N, Dowdy SF (Jun 2006).
of Epstein-Barr virus-encoded nuclear antigen 1 pro- “Regulation of late G1/S phase transition and APC Cdh1
tein interrupts proteasome substrate processing”. The by reactive oxygen species”. Molecular and Cellular Bi-
Journal of Biological Chemistry 279 (10): 8635–41. ology 26 (12): 4701–11. doi:10.1128/MCB.00303-06.
doi:10.1074/jbc.M310449200. PMID 14688254. PMC 1489138. PMID 16738333.
[51] Voges D, Zwickl P, Baumeister W (1999). “The 26S [63] Bashir T, Dorrello NV, Amador V, Guardavaccaro D,
proteasome: a molecular machine designed for con- Pagano M (Mar 2004). “Control of the SCF(Skp2-Cks1)
trolled proteolysis”. Annual Review of Biochemistry 68 ubiquitin ligase by the APC/C(Cdh1) ubiquitin ligase”.
(1): 1015–68. doi:10.1146/annurev.biochem.68.1.1015. Nature 428 (6979): 190–3. doi:10.1038/nature02330.
PMID 10872471. PMID 15014502.
21.5. PROTEASOME 365

[64] Higashitsuji H, Liu Y, Mayer RJ, Fujita J (Oct 2005). [75] Dai Q, Qian SB, Li HH, McDonough H, Borchers C,
“The oncoprotein gankyrin negatively regulates both p53 Huang D et al. (Nov 2005). “Regulation of the cy-
and RB by enhancing proteasomal degradation”. Cell Cy- toplasmic quality control protein degradation pathway
cle 4 (10): 1335–7. doi:10.4161/cc.4.10.2107. PMID by BAG2”. The Journal of Biological Chemistry 280
16177571. (46): 38673–81. doi:10.1074/jbc.M507986200. PMID
16169850.
[65] Dharmasiri S, Estelle M (2002). “The role
of regulated protein degradation in auxin re- [76] Bader N, Grune T (2006). “Protein oxidation and pro-
sponse”. Plant Molecular Biology 49 (3-4): 401–9. teolysis”. Biological Chemistry 387 (10-11): 1351–5.
doi:10.1023/A:1015203013208. PMID 12036263. doi:10.1515/BC.2006.169. PMID 17081106.
[66] Weijers D, Benkova E, Jäger KE, Schlereth A, Hamann [77] Davies KJ (2003). “Degradation of oxidized proteins
T, Kientz M et al. (May 2005). “Developmental by the 20S proteasome”. Biochimie 83 (3-4): 301–10.
specificity of auxin response by pairs of ARF and doi:10.1016/S0300-9084(01)01250-0. PMID 11295490.
Aux/IAA transcriptional regulators”. The EMBO Journal
24 (10): 1874–85. doi:10.1038/sj.emboj.7600659. PMC [78] Lehman NL (Sep 2009). “The ubiquitin proteasome
1142592. PMID 15889151. system in neuropathology”. Acta Neuropathologica 118
(3): 329–47. doi:10.1007/s00401-009-0560-x. PMC
[67] Haas AL, Baboshina O, Williams B, Schwartz LM 2716447. PMID 19597829.
(Apr 1995). “Coordinated induction of the ubiqui-
tin conjugation pathway accompanies the developmen- [79] McNaught KS, Jackson T, JnoBaptiste R, Kapustin A,
tally programmed death of insect skeletal muscle”. The Olanow CW (May 2006). “Proteasomal dysfunction in
Journal of Biological Chemistry 270 (16): 9407–12. sporadic Parkinson’s disease”. Neurology 66 (10 Suppl
doi:10.1074/jbc.270.16.9407. PMID 7721865. 4): S37–49. doi:10.1212/01.wnl.0000221745.58886.2e.
PMID 16717251.
[68] Schwartz LM, Myer A, Kosz L, Engelstein M, Maier C
(Oct 1990). “Activation of polyubiquitin gene expression [80] Sharma N, Brandis KA, Herrera SK, Johnson BE, Vaidya
during developmentally programmed cell death”. Neu- T, Shrestha R et al. (2006). “alpha-Synuclein budding
ron 5 (4): 411–9. doi:10.1016/0896-6273(90)90080-Y. yeast model: toxicity enhanced by impaired proteasome
PMID 2169771. and oxidative stress”. Journal of Molecular Neuroscience
[69] Löw P, Bussell K, Dawson SP, Billett MA, Mayer RJ, 28 (2): 161–78. doi:10.1385/JMN:28:2:161. PMID
Reynolds SE (Jan 1997). “Expression of a 26S pro- 16679556.
teasome ATPase subunit, MS73, in muscles that un- [81] Murata S, Sasaki K, Kishimoto T, Niwa S, Hayashi
dergo developmentally programmed cell death, and its H, Takahama Y et al. (Jun 2007). “Regulation
control by ecdysteroid hormones in the insect Manduca of CD8+ T cell development by thymus-specific
sexta”. FEBS Letters 400 (3): 345–9. doi:10.1016/S0014- proteasomes”. Science 316 (5829): 1349–53.
5793(96)01413-5. PMID 9009228. doi:10.1126/science.1141915. PMID 17540904.
[70] Pitzer F, Dantes A, Fuchs T, Baumeister W, Amsterdam
[82] Cascio P, Hilton C, Kisselev AF, Rock KL, Goldberg
A (Sep 1996). “Removal of proteasomes from the nu-
AL (May 2001). “26S proteasomes and immunoprotea-
cleus and their accumulation in apoptotic blebs during
somes produce mainly N-extended versions of an anti-
programmed cell death”. FEBS Letters 394 (1): 47–50.
genic peptide”. The EMBO Journal 20 (10): 2357–66.
doi:10.1016/0014-5793(96)00920-9. PMID 8925925.
doi:10.1093/emboj/20.10.2357. PMC 125470. PMID
[71] Adams J, Palombella VJ, Sausville EA, Johnson J, Destree 11350924.
A, Lazarus DD et al. (Jun 1999). “Proteasome inhibitors:
a novel class of potent and effective antitumor agents”. [83] Mallery DL, McEwan WA, Bidgood SR, Towers GJ,
Cancer Research 59 (11): 2615–22. PMID 10363983. Johnson CM, James LC (Nov 2010). “Antibodies mediate
intracellular immunity through tripartite motif-containing
[72] Orlowski RZ (Apr 1999). “The role of the ubiquitin- 21 (TRIM21)". Proceedings of the National Academy of
proteasome pathway in apoptosis”. Cell Death and Dif- Sciences of the United States of America 107 (46): 19985–
ferentiation 6 (4): 303–13. doi:10.1038/sj.cdd.4400505. 19990. doi:10.1073/pnas.1014074107. PMC 2993423.
PMID 10381632. PMID 21045130.
[73] Garrido C, Brunet M, Didelot C, Zermati Y, Schmitt E, [84] Fenteany G, Standaert RF, Lane WS, Choi S, Corey EJ,
Kroemer G (Nov 2006). “Heat shock proteins 27 and Schreiber SL (May 1995). “Inhibition of proteasome
70: anti-apoptotic proteins with tumorigenic properties”. activities and subunit-specific amino-terminal threonine
Cell Cycle 5 (22): 2592–601. doi:10.4161/cc.5.22.3448. modification by lactacystin”. Science 268 (5211): 726–
PMID 17106261. 31. doi:10.1126/science.7732382. PMID 7732382.
[74] Park SH, Bolender N, Eisele F, Kostova Z, Takeuchi J, [85] United States Food and Drug Administration press release
Coffino P et al. (Jan 2007). “The cytoplasmic Hsp70 13 May 2003. Access date 29 December 2006. See also
chaperone machinery subjects misfolded and endoplas- FDA Velcade information page.
mic reticulum import-incompetent proteins to degrada-
tion via the ubiquitin-proteasome system”. Molecular Bi- [86] Fisher RI, Bernstein SH, Kahl BS, Djulbegovic B, Robert-
ology of the Cell 18 (1): 153–65. doi:10.1091/mbc.E06- son MJ, de Vos S et al. (Oct 2006). “Multicenter phase II
04-0338. PMC 1751312. PMID 17065559. study of bortezomib in patients with relapsed or refractory
366 CHAPTER 21. PROTEIN SYNTHESIS AND MODIFICATIONS

mantle cell lymphoma”. Journal of Clinical Oncology 24 and the severity of psoriasis in a SCID-hu model”.
(30): 4867–74. doi:10.1200/JCO.2006.07.9665. PMID The Journal of Clinical Investigation 109 (5): 671–9.
17001068. doi:10.1172/JCI12736. PMC 150886. PMID 11877475.

[87] Jakob C, Egerer K, Liebisch P, Türkmen S, Zavrski I, [97] Elliott PJ, Pien CS, McCormack TA, Chapman ID,
Kuckelkorn U et al. (Mar 2007). “Circulating protea- Adams J (Aug 1999). “Proteasome inhibition: A novel
some levels are an independent prognostic factor for sur- mechanism to combat asthma”. The Journal of Al-
vival in multiple myeloma”. Blood 109 (5): 2100–5. lergy and Clinical Immunology 104 (2 Pt 1): 294–300.
doi:10.1182/blood-2006-04-016360. PMID 17095627. doi:10.1016/S0091-6749(99)70369-6. PMID 10452747.

[88] Shah SA, Potter MW, McDade TP, Ricciardi R, Perugini [98] Verdoes M, Florea BI, Menendez-Benito V, Maynard CJ,
RA, Elliott PJ et al. (2001). “26S proteasome inhibition Witte MD, van der Linden WA et al. (Nov 2006). “A fluo-
induces apoptosis and limits growth of human pancreatic rescent broad-spectrum proteasome inhibitor for labeling
cancer”. Journal of Cellular Biochemistry 82 (1): 110–22. proteasomes in vitro and in vivo”. Chemistry & Biology
doi:10.1002/jcb.1150. PMID 11400168. 13 (11): 1217–26. doi:10.1016/j.chembiol.2006.09.013.
PMID 17114003.
[89] Nawrocki ST, Sweeney-Gotsch B, Takamori R, Mc-
Conkey DJ (Jan 2004). “The proteasome inhibitor borte- [99] Kleiger G, Mayor T (Jun 2014). “Perilous journey: a
zomib enhances the activity of docetaxel in orthotopic tour of the ubiquitin-proteasome system”. Trends in Cell
human pancreatic tumor xenografts”. Molecular Cancer Biology 24 (6): 352–9. doi:10.1016/j.tcb.2013.12.003.
Therapeutics 3 (1): 59–70. PMID 14749476. PMID 24457024.

[90] Schenkein D (Jun 2002). “Proteasome inhibitors in the [100] Goldberg AL, Stein R, Adams J (Aug 1995). “New in-
treatment of B-cell malignancies”. Clinical Lymphoma sights into proteasome function: from archaebacteria to
3 (1): 49–55. doi:10.3816/CLM.2002.n.011. PMID drug development”. Chemistry & Biology 2 (8): 503–8.
12141956. PMID 9383453.

[91] O'Connor OA, Wright J, Moskowitz C, Muzzy J, [101] Sulistio YA, Heese K (Jan 2015). “The Ubiquitin-
MacGregor-Cortelli B, Stubblefield M et al. (Feb Proteasome System and Molecular Chaperone Deregu-
2005). “Phase II clinical experience with the novel lation in Alzheimer’s Disease”. Molecular Neurobiology.
proteasome inhibitor bortezomib in patients with in- doi:10.1007/s12035-014-9063-4. PMID 25561438.
dolent non-Hodgkin’s lymphoma and mantle cell lym-
[102] Ortega Z, Lucas JJ (2014). “Ubiquitin-proteasome system
phoma”. Journal of Clinical Oncology 23 (4): 676–84.
involvement in Huntington’s disease”. Frontiers in Molec-
doi:10.1200/JCO.2005.02.050. PMID 15613699.
ular Neuroscience 7: 77. doi:10.3389/fnmol.2014.00077.
[92] Messinger YH, Gaynon PS, Sposto R, van der Giessen PMID 25324717.
J, Eckroth E, Malvar J et al. (Jul 2012). “Borte-
[103] Sandri M, Robbins J (Jun 2014). “Proteotoxicity: an
zomib with chemotherapy is highly active in advanced
underappreciated pathology in cardiac disease”. Jour-
B-precursor acute lymphoblastic leukemia: Therapeutic
nal of Molecular and Cellular Cardiology 71: 3–10.
Advances in Childhood Leukemia & Lymphoma (TACL)
doi:10.1016/j.yjmcc.2013.12.015. PMID 24380730.
Study”. Blood 120 (2): 285–90. doi:10.1182/blood-
2012-04-418640. PMID 22653976. [104] Drews O, Taegtmeyer H (Dec 2014). “Targeting the
ubiquitin-proteasome system in heart disease: the basis
[93] Lambrou GI, Papadimitriou L, Chrousos GP, Vlahopou- for new therapeutic strategies”. Antioxidants & Redox
los SA (Apr 2012). “Glucocorticoid and proteasome Signaling 21 (17): 2322–43. doi:10.1089/ars.2013.5823.
inhibitor impact on the leukemic lymphoblast: multi- PMID 25133688.
ple, diverse signals converging on a few key downstream
regulators”. Molecular and Cellular Endocrinology 351 [105] Wang ZV, Hill JA (Feb 2015). “Protein qual-
(2): 142–51. doi:10.1016/j.mce.2012.01.003. PMID ity control and metabolism: bidirectional control
22273806. in the heart”. Cell Metabolism 21 (2): 215–26.
doi:10.1016/j.cmet.2015.01.016. PMID 25651176.
[94] Schmidtke G, Holzhütter HG, Bogyo M, Kairies N, Groll
M, de Giuli R et al. (Dec 1999). “How an inhibitor [106] Karin M, Delhase M (Feb 2000). “The I kappa B kinase
of the HIV-I protease modulates proteasome activity”. (IKK) and NF-kappa B: key elements of proinflamma-
The Journal of Biological Chemistry 274 (50): 35734–40. tory signalling”. Seminars in Immunology 12 (1): 85–98.
doi:10.1074/jbc.274.50.35734. PMID 10585454. doi:10.1006/smim.2000.0210. PMID 10723801.

[95] Laurent N, de Boüard S, Guillamo JS, Christov C, Zini [107] Ermolaeva MA, Dakhovnik A, Schumacher B (Jan 2015).
R, Jouault H et al. (Feb 2004). “Effects of the protea- “Quality control mechanisms in cellular and systemic
some inhibitor ritonavir on glioma growth in vitro and DNA damage responses”. Ageing Research Reviews.
in vivo”. Molecular Cancer Therapeutics 3 (2): 129–36. doi:10.1016/j.arr.2014.12.009. PMID 25560147.
PMID 14985453.
[108] Checler F, da Costa CA, Ancolio K, Chevallier N, Lopez-
[96] Zollner TM, Podda M, Pien C, Elliott PJ, Kaufmann Perez E, Marambaud P (Jul 2000). “Role of the protea-
R, Boehncke WH (Mar 2002). “Proteasome inhi- some in Alzheimer’s disease”. Biochimica Et Biophysica
bition reduces superantigen-mediated T cell activation Acta 1502 (1): 133–8. PMID 10899438.
 21.5. PROTEASOME 367

[109] Chung KK, Dawson VL, Dawson TM (Nov 2001). “The 21.5.14 Further reading
role of the ubiquitin-proteasomal pathway in Parkinson’s
disease and other neurodegenerative disorders”. Trends in • Glickman MH, Adir N (Jan 2004). “The protea-
Neurosciences 24 (11 Suppl): S7–14. PMID 11881748. some and the delicate balance between destruc-
tion and rescue”. PLoS Biology 2 (1): e13.
[110] Ikeda K, Akiyama H, Arai T, Ueno H, Tsuchiya K, doi:10.1371/journal.pbio.0020013. PMC 314468.
Kosaka K (Jul 2002). “Morphometrical reappraisal of PMID 14737189.
motor neuron system of Pick’s disease and amyotrophic
lateral sclerosis with dementia”. Acta Neuropathologica • The Yeast 26S Proteasome with list of subunits and
104 (1): 21–8. doi:10.1007/s00401-001-0513-5. PMID pictures
12070660.
• Ciechanover A (Sep 2005). “Early work on
[111] Manaka H, Kato T, Kurita K, Katagiri T, Shikama Y, Ku- the ubiquitin proteasome system, an interview
jirai K et al. (May 1992). “Marked increase in cere- with Aaron Ciechanover. Interview by CDD”.
brospinal fluid ubiquitin in Creutzfeldt-Jakob disease”. Cell Death and Differentiation 12 (9): 1167–77.
Neuroscience Letters 139 (1): 47–9. PMID 1328965. doi:10.1038/sj.cdd.4401691. PMID 16094393.

[112] Mathews KD, Moore SA (Jan 2003). “Limb-girdle mus- • Hershko A (Sep 2005). “Early work on the
cular dystrophy”. Current Neurology and Neuroscience Re- ubiquitin proteasome system, an interview with
ports 3 (1): 78–85. PMID 12507416. Avram Hershko. Interview by CDD”. Cell
Death and Differentiation 12 (9): 1158–61.
[113] Mayer RJ (Mar 2003). “From neurodegeneration to neu- doi:10.1038/sj.cdd.4401709. PMID 16094391.
rohomeostasis: the role of ubiquitin”. Drug News & Per-
spectives 16 (2): 103–8. PMID 12792671. • Rose I (Sep 2005). “Early work on the ubiquitin pro-
teasome system, an interview with Irwin Rose. In-
[114] Calise J, Powell SR (Feb 2013). “The ubiquitin protea- terview by CDD”. Cell Death and Differentiation 12
some system and myocardial ischemia”. American Jour- (9): 1162–6. doi:10.1038/sj.cdd.4401700. PMID
nal of Physiology. Heart and Circulatory Physiology 304 16094392.
(3): H337–49. doi:10.1152/ajpheart.00604.2012. PMC
3774499. PMID 23220331. • Cvek B, Dvorak Z (2007). “Targeting of nu-
clear factor-kappaB and proteasome by dithio-
[115] Predmore JM, Wang P, Davis F, Bartolone S, West- carbamate complexes with metals”. Current
fall MV, Dyke DB et al. (Mar 2010). “Ubiquitin Pharmaceutical Design 13 (30): 3155–67.
proteasome dysfunction in human hypertrophic and di- doi:10.2174/138161207782110390. PMID
lated cardiomyopathies”. Circulation 121 (8): 997–1004. 17979756.
doi:10.1161/CIRCULATIONAHA.109.904557. PMC
2857348. PMID 20159828.
21.5.15 External links
[116] Powell SR (Jul 2006). “The ubiquitin-proteasome system
in cardiac physiology and pathology”. American Jour- • Proteasome subunit nomenclature guide
nal of Physiology. Heart and Circulatory Physiology 291
(1): H1–H19. doi:10.1152/ajpheart.00062.2006. PMID • 3D proteasome structures in the EM Data
16501026. Bank(EMDB)

[117] Adams J (Apr 2003). “Potential for proteasome inhibition

in the treatment of cancer”. Drug Discovery Today 8 (7):
307–15. PMID 12654543.

[118] Karin M, Delhase M (Feb 2000). “The I kappa B kinase

(IKK) and NF-kappa B: key elements of proinflamma-
tory signalling”. Seminars in Immunology 12 (1): 85–98.
doi:10.1006/smim.2000.0210. PMID 10723801.

[119] Ben-Neriah Y (Jan 2002). “Regulatory functions of ubiq-

uitination in the immune system”. Nature Immunology 3
(1): 20–6. doi:10.1038/ni0102-20. PMID 11753406.

[120] Egerer K, Kuckelkorn U, Rudolph PE, Rückert JC,

Dörner T, Burmester GR et al. (Oct 2002). “Circulat-
ing proteasomes are markers of cell damage and immuno-
logic activity in autoimmune diseases”. The Journal of
Rheumatology 29 (10): 2045–52. PMID 12375310.
Chapter 22

Text and image sources, contributors, and

licenses

22.1 Text
• Biochemistry Source: https://en.wikipedia.org/wiki/Biochemistry?oldid=671860807 Contributors: AxelBoldt, Tobias Hoevekamp, Mag-
nus Manske, Marj Tiefert, Mav, Bryan Derksen, Tarquin, Andre Engels, Enchanter, Deb, Peterlin~enwiki, AdamRetchless, Heron,
Youandme, Someone else, Dwmyers, D, Booyabazooka, Lexor, Card~enwiki, 168..., Ellywa, Ahoerstemeier, Cyp, Mac, Александър,
Glenn, º¡º, Rob Hooft, Tobias Conradi, Mxn, Vivin, Lfh, Selket, Steinsky, DJ Clayworth, Paul-L~enwiki, Samsara, Vincent kraeutler, Doug
swisher, Donarreiskoffer, Gentgeen, Robbot, Jotomicron, Kowey, Mayooranathan, Stewartadcock, Blainster, Mendalus~enwiki, Wikibot,
Fuelbottle, Quadalpha, Diberri, Giftlite, Mikez, Netoholic, Curps, Dmb000006, Bensaccount, Andris, Guanaco, Kandar, OldakQuill,
Knutux, Antandrus, Beland, Karol Langner, APH, H Padleckas, Bornslippy, Gscshoyru, Ben Zealley, Kevyn, Bluemask, Ornil, Discospin-
ster, Vsmith, Notinasnaid, Mani1, Bender235, El C, Bobo192, Smalljim, Maurreen, Arcadian, Jag123, Giraffedata, Pschemp, Haham
hanuka, Krellis, HasharBot~enwiki, Passw0rd, Jumbuck, Danski14, Alansohn, Etxrge, Arthena, Wouterstomp, Kocio, Alex '05, Om-
budsman, ClockworkSoul, Knowledge Seeker, Bsadowski1, Alai, Mattbrundage, Dan East, HenryLi, Ceyockey, Boothy443, Linnea,
TigerShark, YannisKollias, JeremyA, Bennetto, JRHorse, TheAlphaWolf, MarcoTolo, Halcatalyst, Palica, Marskell, Chun-hian, Kb-
dank71, Jclemens, Techneaux, Mayumashu, Alcarreau, Mike Peel, ScottJ, FlaBot, RexNL, Tedder, Chobot, WriterHound, YurikBot,
Wavelength, Mushin, RobotE, RussBot, J. M., Splette, Stephenb, CambridgeBayWeather, Doctorbruno, Wimt, NawlinWiki, Grafen, Ori-
oneight, Gareth Jones, Ragesoss, Gadget850, Bota47, Trainra, Wknight94, Occhanikov, Djramone, Arthur Rubin, Josh3580, JeramieHicks,
LeonardoRob0t, Katieh5584, GrinBot~enwiki, Luk, Itub, SmackBot, Looper5920, Espresso Addict, Hydrogen Iodide, McGeddon, Pgk,
KocjoBot~enwiki, AndreasJS, Eskimbot, Kjaergaard, Edgar181, Zephyris, M stone, Gilliam, Cabe6403, Chris the speller, Jethero, Per-
sian Poet Gal, Bduke, Rich.buckman, MalafayaBot, Go for it!, DHN-bot~enwiki, Sbharris, Darth Panda, MyNameIsVlad, Snowmanradio,
Rrburke, COMPFUNK2, Chris jf, Flyguy649, Dreadstar, Richard001, Drphilharmonic, DMacks, Lineweaver~enwiki, Sadi Carnot, Sasha-
toBot, Serein (renamed because of SUL), Kuru, J. Finkelstein, Kipala, IronGargoyle, Tarcieri, Mets501, Sasata, Andreworkney, Quaeler,
J Di, Twas Now, Chika11, Courcelles, Tawkerbot2, K.murphy, Pi, Firewall62, CmdrObot, Ale jrb, Moreschi, Cydebot, MC10, Rifleman
82, Neuroticopia, Carstensen, Shirulashem, Christian75, Anpetu-We, John Lake, Epbr123, Headbomb, X201, Defeatedfear, Escarbot,
I already forgot, Thomaswgc, AntiVandalBot, Majorly, Luna Santin, Quintote, TimVickers, Qwerty Binary, Figma, JAnDbot, MER-C,
The Transhumanist, Justacontributor, Jhay116, BenB4, Zeb edee, GoodDamon, Magioladitis, Staib, Pedro, VoABot II, Confiteordeo,
Mah159, Bubba hotep, Mikhail Garouznov, Allstarecho, DerHexer, Gludwiczak, Squidonius, DGG, Gwern, Pvosta, MartinBot, ChemN-
erd, Rettetast, Winkel111, N4nojohn, J.delanoy, TimBuck2, Mikael Häggström, Coppertwig, Chriswiki, Loohcsnuf, The Transhumanist
(AWB), Rominandreu, Tanaats, Bob, Cometstyles, Tiggerjay, Potaaatos, 52G, Bonadea, Squids and Chips, Remi0o, Deor, VolkovBot,
Jeff G., Alexandria, Philip Trueman, TXiKiBoT, Caltechdoc, Amaher, Leafyplant, Ermysted’s school, Jackfork, Brandonrush, United-
Statesian, Untitled300, Mishlai, Jaqen, Loka1282, RaseaC, Spinningspark, Monty845, HiDrNick, AlleborgoBot, EmxBot, Deafgirl, Nssr
84, SieBot, Logan baum, Calliopejen1, Tiddly Tom, Graham Beards, Caulde, WereSpielChequers, Gerakibot, Keilana, Dramagirlforje-
sus, Jcsvarela, Oxymoron83, Scorpion451, Lightmouse, Pmrich, Superbeecat, Into The Fray, Naturespace, WikipedianMarlith, Pscott22,
Loren.wilton, ClueBot, Avenged Eightfold, PipepBot, The Thing That Should Not Be, Stupid2, Yikrazuul, Arakunem, Drmies, Rebel-
Bodhi, Neverquick, ChandlerMapBot, Promage281, DragonBot, Excirial, Sarakoth, Cbailey7, Sun Creator, 2pac 2007, Jotterbot, KLas-
setter, Dekisugi, Tbeyett, Bald Zebra, N8mills, Jamesscottbrown, XLinkBot, Fastily, Jytdog, Jovianeye, DPistotallyawesome, Willisis2,
Basilicofresco, DOI bot, Tcncv, CanadianLinuxUser, MrOllie, Favonian, SamatBot, Numbo3-bot, Tide rolls, Vicki breazeale, Legobot,
Luckas-bot, Yobot, Themfromspace, Ptbotgourou, TaBOT-zerem, Salvaje20, Mauler90, Essam Sharaf, Explosivedeath7, Washburnmav,
AnomieBOT, Jim1138, Templatehater, Materialscientist, Stevendboy, Qwertyman33, Citation bot, Lil’swallowtail, Frankenpuppy, Lil-
Helpa, Xqbot, Zad68, Timir2, The Banner, Capricorn42, Jburlinson, P99am, Fakih1234, Paulkappelle, BostonBiochem, ThyCantabrigde,
RibotBOT, Barefootguy, Doulos Christos, Shadowjams, PiFanatic, PM800, Erik9, StevieNic, A.amitkumar, Gumball456, FrescoBot, To-
bby72, Jobseeker-us, Theruchet, Pinethicket, I dream of horses, Abductive, A8UDI, Ntropy25, Alaadabarita, Jauhienij, Gamewizard71,
Wotnow, Vanished user kiij3irj4tihns, Kiwakwok, Jeffrd10, Canuckian89, Weewengweng, Riomack, TjBot, Sdneidich, Ash421, Skame-
crazy123, Applepie390, EmausBot, H.tjerns, GoingBatty, Babyboy004, Neilmitch02, K6ka, Lucas Thoms, Thecheesykid, JSquish, John
Cline, Lalsingh, Jenvargas93, Ohsoserious, Tom the biochemist, Kelly222, Jesanj, L Kensington, Donner60, DASHBotAV, 28bot, Clue-
Bot NG, Rodelapa, Jdcollins13, Frietjes, Widr, EtherROR, Krist Wood, Wertyu739, Curb Chain, Arifur6051, Nighttoy, Piguy101, Mark
Arsten, Amitashsam, MrBill3, YVSREDDY, Joud98, Fathimaazara, ChrisGualtieri, GoShow, Saltwolf, Fvandrog, JYBot, Webclient101,
Marywhi, CaSJer, Frosty, SFK2, David P Minde, Aftabbanoori, Epicgenius, Shafiq.sims, Jamesmcmahon0, AmaryllisGardener, American-
Lemming, Mrs.Stewart, Tony johnsong, Rjdodger, David246, Ugog Nizdast, Rahul and Atasi, Ginsuloft, Lizia7, Nazia Singh, Sirisindhu,
DrFGWöhler, Crisur, Jasonbourn2, Sixtyn, Ped92man, Shaneandlauren, LaughableStand, Hypervalentanion, Biochemistry&Love, Wis-

368
22.1. TEXT 369

coeditor, Eatmyjorts, Mintosh Kumar, Lol235689, KasparBot and Anonymous: 594

• Cell (biology) Source: https://en.wikipedia.org/wiki/Cell_(biology)?oldid=671896243 Contributors: AxelBoldt, Magnus Manske, Joao,

Kpjas, Brion VIBBER, Mav, Bryan Derksen, Taw, Malcolm Farmer, RK, BenBaker, Andre Engels, LA2, Josh Grosse, Christian List,
William Avery, Anthere, AdamRetchless, Heron, Icarus~enwiki, Patrick, Olrick, D, Michael Hardy, Zocky, Lexor, Gabbe, Ixfd64, Lquilter,
GTBacchus, Dori, Kosebamse, 168..., Ahoerstemeier, Theresa knott, JWSchmidt, Julesd, Glenn, Andres, Evercat, Cherkash, Rob Hooft,
Mxn, Smack, Jengod, Emperorbma, Ec5618, RodC, Timwi, Wikiborg, Selket, Steinsky, Tpbradbury, Marshman, Morwen, Itai, Omega-
tron, Thue, Quoth-22, Topbanana, Bjarki S, Renato Caniatti~enwiki, Raul654, Doug swisher, DougS, Bcorr, Camerong, Francs2000,
Shantavira, Rogper~enwiki, Donarreiskoffer, Robbot, Josh Cherry, Sander123, Vyasa, Romanm, Caknuck, Moink, Hadal, Fuelbottle,
Pengo, Dina, Adam78, Mdmcginn, Alan Liefting, Fabiform, Giftlite, Christopher Parham, Crimson30, Nmg20, Wikilibrarian, Kim Brun-
ing, Ævar Arnfjörð Bjarmason, Netoholic, Bradeos Graphon, Average Earthman, Everyking, Michael Devore, Bensaccount, Gareth Wyn,
Hugh2414, Sietse, Siroxo, Kandar, Wmahan, Adenosine, Gadfium, Andycjp, Pcarbonn, Antandrus, GeneMosher, Williamb, Onco p53,
OverlordQ, PDH, Sean Heron, Vina, MacGyverMagic, Brian Brondel, Rdsmith4, Sam Hocevar, Vogon77, Gscshoyru, Creidieki, Kevin
Rector, Deglr6328, Grunt, SYSS Mouse, Possession, ClockworkTroll, Discospinster, Zaheen, Rich Farmbrough, KillerChihuahua, Gua-
nabot, Lejean2000, Kdammers, Vsmith, CrisDias, 1pezguy, Mani1, Dmr2, Yersinia~enwiki, Bender235, ESkog, Kbh3rd, Kaisershatner,
Violetriga, Pusher, Eric Forste, Pofkezas, Syp, Kaszeta, CanisRufus, Charm, Illumynite, Anphanax, Lycurgus, Skeppy, Koenige, Shanes,
Art LaPella, RoyBoy, CDN99, Gyll, Bobo192, Whosyourjudas, .:Ajvol:., Mytildebang, Arcadian, Jag123, Dennis Valeev, Joe Jarvis, Man
vyi, MPerel, Hagerman, EricAir, Orangemarlin, Ranveig, Jumbuck, Danski14, Bob rulz, Alansohn, Mo0, Jared81, Tek022, Wouterstomp,
Scarecroe, Lightdarkness, Fawcett5, Bart133, Snowolf, ClockworkSoul, Tycho, Cburnett, TenOfAllTrades, Sciurinæ, Charlie123, Meme-
nen, Iustinus, Oleg Alexandrov, Rorschach, 2004-12-29T22:45Z, Rocastelo, Mark K. Jensen, Yuubinbako, WadeSimMiser, JeremyA,
MONGO, CiTrusD, Kmg90, LadyofHats, MarcoTolo, Palica, Tslocum, SqueakBox, Justin Bailey, BD2412, Chun-hian, FreplySpang,
Vvuppala, DePiep, Icey, BorgHunter, Edison, Sjakkalle, Rjwilmsi, Harry491, SMC, Mitul0520, Nneonneo, Kalogeropoulos, ScottJ, Oliv-
erkeenan, Matt Deres, Sango123, Yamamoto Ichiro, Ravidreams, Titoxd, Nihiltres, Crazycomputers, RexNL, Gurch, Jrtayloriv, R Lee E,
TeaDrinker, Terrx, Nabarry, NetAddict, BradBeattie, Chris is me, Chobot, WriterHound, Whosasking, Kjlewis, YurikBot, Wavelength,
TexasAndroid, Pile0nades, Icedemon, Phantomsteve, RussBot, Sputnikcccp, Reo On, Hydrargyrum, Stephenb, Emmanuelm, Gaius Cor-
nelius, Yyy, Rsrikanth05, Pseudomonas, Wimt, NawlinWiki, Misos, Wiki alf, Astral, Jaxl, Justin Eiler, Chunky Rice, Joelr31, Irishguy,
PeepP, Froth, Hv, Misza13, Chichui, Zwobot, Samir, Mysid, Jhinman, FF2010, 2over0, Zzuuzz, Lt-wiki-bot, Uartseieu, Imaninjapirate,
Warfreak, Squeedlyspooch, Smoggyrob, Theda, Closedmouth, Jwissick, Јованвб, Pb30, Kris33, BorgQueen, Amren, Anclation~enwiki,
Jaranda, Cjfsyntropy, Katieh5584, NeilN, GrinBot~enwiki, DVD R W, Dposse, Snalwibma, Hughitt1, Crystallina, KnightRider~enwiki,
SmackBot, MattieTK, Moeron, Arti Sahajpal, TestPilot, Unyoyega, Blue520, KocjoBot~enwiki, Stepa, Vanished user 3dk2049pot4, Tim-
otheus Canens, CuriousOliver, Zephyris, Pathless, Gilliam, Rickpearce, Ohnoitsjamie, Betacommand, Bluebot, Persian Poet Gal, NCurse,
MK8, Sirex98, Master of Puppets, Oli Filth, IanBailey, Miquonranger03, SchfiftyThree, Akanemoto, Adamstevenson, Onkelschark, Darth
Panda, Gracenotes, Nick Bond, Can't sleep, clown will eat me, TheRaven7, Shalom Yechiel, Snowmanradio, JonHarder, Andy120290,
Threeafterthree, Dharmabum420, Krich, Flyguy649, Nakon, Jiddisch~enwiki, Funky Monkey, Dacoutts, Weregerbil, Iridescence, Zzorse,
Andrew4010, Pilotguy, FelisLeo, Wikier.ko, Nmnogueira, The undertow, SashatoBot, EMan32x, Nishkid64, GiollaUidir, ArglebargleIV,
Mouse Nightshirt, Zahid Abdassabur, Kuru, Scientizzle, Kipala, Epingchris, Sir Nicholas de Mimsy-Porpington, James.S, Chodorkovskiy,
JorisvS, Accurizer, Goodnightmush, Mr. Lefty, Cielomobile, Extremophile, Jaredhelfer, 041744, Ckatz, Grumpyyoungman01, Slakr,
Avs5221, The Missing Hour, Brazucs, Childzy, Spook`, Ryulong, Citicat, Elb2000, Nbhatla, LaMenta3, Darry2385, DabMachine, Nat-
pal, BranStark, WahreJakob, Nehrams2020, Mario2000, Delta x, Imad marie, Matzman, Tawkerbot2, Timrem, Chris55, The Haunted
Angel, JForget, CmdrObot, Ale jrb, Scohoust, SupaStarGirl, Ninetyone, Nunquam Dormio, Kylu, N2e, Istrancis, Yarnalgo, Fletcher,
Bbasen, Peripitus, Reywas92, Gogo Dodo, Was a bee, JFreeman, ST47, Julian Mendez, Tawkerbot4, DumbBOT, Narayanese, Kozuch,
JayW, Greeneto, Woland37, Rjm656s, Thijs!bot, Epbr123, Afctenfour, Opabinia regalis, N5iln, Anupam, Headbomb, Marek69, Peter Zna-
menskiy, John254, A3RO, PaperTruths, James086, Zé da Silva, MesserWoland, Dgies, Thedarkestshadow, Dawnseeker2000, Hempfel,
Escarbot, Ju66l3r, David D., AntiVandalBot, Yomamais, Konman72, Luna Santin, Akradecki, Quintote, Jesse dudezx, TimVickers,
Smartse, PhilipWest, Farosdaughter, Alvarogonzalezsotillo, Figma, Phil153, Res2216firestar, DCincarnate, JAnDbot, AOB, Leuko, Hu-
sond, MER-C, Plantsurfer, The Transhumanist, WikipedianProlific, Hello32020, Db099221, Owenozier, Chizeng, Andonic, Noobeditor,
Hut 8.5, BrotherE, Bearly541, Jarkeld, .anacondabot, Acroterion, Bencherlite, FaerieInGrey, Magioladitis, Canjth, Bongwarrior, VoABot
II, Brunoman1990, AuburnPilot, Tatwell, Wikidudeman, Jnb, CTF83!, Prestonmcconkie, Avicennasis, Catgut, Animum, Shim'on, Allstare-
cho, Spellmaster, DerHexer, JaGa, Linuxcity, Squidonius, SquidSK, Darthtire, Rustyfence, Hdt83, MartinBot, Gasheadsteve, Dietzel65,
Arjun01, Robin63, Tuganax~enwiki, Rettetast, Tholly, R'n'B, Kateshortforbob, CommonsDelinker, AlexiusHoratius, LedgendGamer,
J.delanoy, Pharaoh of the Wizards, CFCF, Bogey97, Nbauman, Hans Dunkelberg, Uncle Dick, A:f6, Ccwoo, Eliz81, Extransit, Jerry, Ot-
toMäkelä, Phatdan46, Keesiewonder, Acalamari, Katalaveno, Kangie, BMBTHC, CountZepplin, TomasBat, NewEnglandYankee, Raichu
Trainer, Charmander trainer, 83d40m, Cackerman, FJPB, 2help, Juliancolton, Cometstyles, SlightlyMad, Erick.Antezana, Khargas, Ja 62,
Ministry of truth 02, Useight, Magoscope, Idioma-bot, Kay for kate, Wikieditor06, Deor, VolkovBot, Lordmontu, Spancakes2, Flyingid-
iot, Adapter~enwiki, Jeff G., Lia Todua, HJ32, Philip Trueman, Drunkenmonkey, Jhon montes24, TXiKiBoT, Gato340, Susan Walton,
Miranda, Ogger181, Wxyz999a, Anonymous Dissident, Qxz, Littlealien182, Anna Lincoln, Walteryoo93, Leafyplant, Sanfranman59, Ab-
dullais4u, LeaveSleaves, Sc0ttkclark, Hobbit13, Earthdirt, SpecMode, Brainmuncher, Adam.J.W.C., Richwil, Synthebot, Strangerer, Duck-
ttape17, Enviroboy, RaseaC, Brianga, Northfox, AlleborgoBot, Kehrbykid, NorbertR, Readthesign, NHRHS2010, Ivanivanovich, Demmy,
GirasoleDE, SieBot, Funkamatic, ThomasTenCate, Restre419, Graham Beards, Danimsturr, BotMultichill, Jauerback, Gerakibot, West-
errer, Dawn Bard, Caltas, Jasujas0, Xymmax, TheScotsman1987, Out slide, Oxymoron83, Byrialbot, Xelaw, Rpgch, Lightmouse, Merce-
nario97, BenoniBot~enwiki, Paully111, Sunrise, Rewdewa, Robert W. A., Stfg, CryoSagittarius, Jmameren, Anchor Link Bot, Crazydoc-
tor, Bhartta, Hamiltondaniel, Ascidian, Lloydpick, Micheb, Troy 07, WikipedianMarlith, WakingLili, ClueBot, PipepBot, The Thing That
Should Not Be, Zfc89, Cheapshots, Blogeswar, Cryptographic hash, Uncle Milty, SuperHamster, Boing! said Zebedee, CounterVandalism-
Bot, Woodardc, Blanchardb, Jordin986, Dylan620, Fatsamsgrandslam, Riccomario96, Aua, DragonBot, Jusdafax, Calimo, Nudve, KC109,
Chance Jeong, Shinkolobwe, Jdmirfer, MacedonianBoy, Tyler, NuclearWarfare, Lunchscale, Sbfw, Feeuoo, Razorflame, NoriMori, Muro
Bot, Cloning jedi, Aitias, Versus22, Timshiels, Johnuniq, SoxBot III, Psymier, DumZiBoT, XLinkBot, Soccerstar132, Pichpich, Pseu-
doOne, Rror, Koolokamba, Dylandugan, Crowbarthe1337h4x0r, Nepenthes, Little Mountain 5, Treesoulja, NellieBly, Mifter, Ianbecerro,
Poopybutts, JinJian, ZooFari, Kittymew1, Mowgali, Bookgeek10, Thatguyflint, MACHINAENIX, Addbot, Xp54321, Salwateama2008,
DOI bot, Thecorduroysuit, PaterMcFly, GSMR, Ronhjones, Fieldday-sunday, CanadianLinuxUser, Tedmund, Looie496, MrOllie, Down-
load, LaaknorBot, Duckdude, Bernstein0275, Debresser, Dr. Universe, LinkFA-Bot, West.andrew.g, Numbo3-bot, Zachary Murray,
Carbon arka, Bradht2710, Erutuon, Tide rolls, Krano, Ramsis II, Gail, Xenobot, Jarble, Kelseyking, Ettrig, Jim, Luckas-bot, Biji123,
Yobot, 2D, Ptbotgourou, Les boys, II MusLiM HyBRiD II, Testaccount rrrr, Medical geneticist, Ajh16, THEN WHO WAS PHONE?,
Nallimbot, KamikazeBot, AnakngAraw, Eric-Wester, Magog the Ogre, Bility, Backslash Forwardslash, AnomieBOT, Galoubet, Savedhe-
wadgh, Piano non troppo, AdjustShift, Kingpin13, EryZ, Bodiejnr, Materialscientist, Dracopacoboy, Socrates321, The High Fin Sperm
370 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

Whale, Citation bot, Hatesschool, ArthurBot, Szxd, Xqbot, SciGuy013, Timir2, Jeffrey Mall, Gensanders, Wyklety, Tennispro427, Trivelt,
GrouchoBot, DerryTaylor, Shirik, Mark Schierbecker, Gott wisst, Doulos Christos, IShadowed, Natural Cut, Shadowjams, Methcub, Van-
ished user giiw8u4ikmfw823foinc2, Erik9, Swimmrfrend97, Dougofborg, Mikesta2, Alisonthegreat, Sugarrush100, Sterimmer, Clearrise,
GT5162, Bookwormlady1100, FrescoBot, Yssha, LucienBOT, Pepper, Wikipe-tan, Galorr, Goodbye Galaxy, D'ohBot, Cargoking, Alx-
eedo, HJ Mitchell, DivineAlpha, Stephen Morley, HamburgerRadio, Sarpelia, Pinethicket, HRoestBot, PrincessofLlyr, LinDrug, Hamtech-
person, A8UDI, Zaluzar, MastiBot, Pertusaria, IP69.226.103.13, SpaceFlight89, Σ, Meaghan, Merlion444, KnowledgeRequire, Jeangabin,
Gamewizard71, FoxBot, TobeBot, Trappist the monk, Hippy Sorix, DragonofFire, January, WeiAMS426, Gaby97123, Toejam1101,
Wsander, Najzeko, JoshHoward77, Specs112, ShyHinaHyuga, Tbhotch, Reach Out to the Truth, Flatulent tube, Blackdeath15, DARTH
SIDIOUS 2, Difu Wu, ScienceFreakGeek, Andrea105, 1tinyboo, Jacyanda9, TjBot, Popular97, Kezari, NerdyScienceDude, Nd State As-
sosiation, Mandolinface, Leroylevine, DASHBot, EmausBot, Acather96, WikitanvirBot, Ajraddatz, Heracles31, Ndkl, Suh004757, ME
IS NINJA, I be awsome, Wright496, Bruceplayzwow, NoisyJinx, The Last Kilroy, Jake, MrTranscript, Usama042, Abbypettis, Wak 999,
Ren799, Madmaxz, Acer al2017, Werieth, ZéroBot, Josve05a, Aeonx, Sky380, Demiurge1000, L Kensington, Lawstubes, ChuispastonBot,
Juanjosegreen2, Snehalshekatkar, Pooja raveendran, Шиманський Василь, Frietjes, Ww12, Helpful Pixie Bot, BG19bot, Mohamed CJ,
KingMunch, Cadiomals, Ahora, NotWith, Deuterostome, Bourgeb, Gladissk, MMA rox, Miszatomic, Jimw338, ChrisGualtieri, Danthe-
man4297, InsaneInnerMembrane, Davidlwinkler, Kelvinsong, Dexbot, Randomizer3, Jcardazzi, Royroydeb, FallingGravity, Iztwoz, Wik-
iuser13, Jwratner1, BruceBlaus, MBproj, Ttlaz123, Mahusha, Monkbot, Rakeshyashroy, Trackteur, Arvind asia, TypingAway, KasparBot
and Anonymous: 1247

• Water Source: https://en.wikipedia.org/wiki/Water?oldid=672245225 Contributors: Damian Yerrick, AxelBoldt, Kpjas, Marj Tiefert,
WojPob, Calypso, Sodium, Mav, Wesley, Bryan Derksen, The Anome, Tarquin, Stephen Gilbert, Malcolm Farmer, Higbvuyb, Wayne
Hardman, Andre Engels, Sandos, XJaM, Rmhermen, PierreAbbat, William Avery, Roadrunner, Ben-Zin~enwiki, Jdpipe, Heron, Jinian,
Icarus~enwiki, Montrealais, Ewen, Rickyrab, MimirZero, AntonioMartin, Edward, Dwmyers, Bdesham, K.lee, Lir, Patrick, Infrogmation,
Michael Hardy, Tim Starling, Booyabazooka, Llywrch, Fred Bauder, BrianHansen~enwiki, Oliver Pereira, Lexor, Shellreef, Kku, Liftarn,
Jketola, Tannin, Ixfd64, Eric119, Iluvcapra, Tregoweth, CesarB, Egil, Looxix~enwiki, Ihcoyc, Ahoerstemeier, DavidWBrooks, Mac, Ronz,
Dgaubin, William M. Connolley, Angela, Jebba, Jdforrester, Александър, Julesd, GoGi, Cgs, Stefan-S, Poor Yorick, Nikai, Cimon Avaro,
Smicke~enwiki, Evercat, Jedidan747, Cherkash, Edaelon, Mxn, Smack, Pizza Puzzle, Ffransoo, RadarCzar, Charles Matthews, Timwi,
Dcoetzee, Reddi, Dysprosia, Rednblu, Doradus, Piolinfax, Greenrd, Wik, Birkett, Tpbradbury, Marshman, Furrykef, Morwen, ErikDun-
sing, Saltine, Nv8200pa, Alight, Jnc, SEWilco, Ed g2s, Samsara, Traroth, Shizhao, Bjarki S, Fvw, CW, AnonMoos, Pstudier, Pakaran,
Finlay McWalter, Mrdice, Denelson83, PuzzletChung, Donarreiskoffer, Gentgeen, Robbot, Paranoid, Sander123, Astronautics~enwiki,
ChrisO~enwiki, Jakohn, Fredrik, Chris 73, Schutz, Gak, RedWolf, ZimZalaBim, Naddy, Arkuat, Lowellian, Plasmaroo, Ashley Y, Sver-
drup, Nach0king, Flauto Dolce, Texture, Timrollpickering, Hadal, UtherSRG, Saforrest, Wereon, Alistair b, Ruakh, Pengo, Cutler, Per
Abrahamsen, SpellBott, Alan Liefting, Enochlau, Matthew Stannard, Alerante, Centrx, Giftlite, Smjg, Bob Palin, MPF, Marnanel, Isam,
Elf, Oberiko, Mousomer, BenFrantzDale, Geeoharee, Ævar Arnfjörð Bjarmason, Meursault2004, Ferkelparade, Herbee, Spencer195, Pe-
ruvianllama, Everyking, No Guru, Gus Polly, Moyogo, Curps, NeoJustin, Alison, Aoi, Eric Harris-Braun, Revth, H-2-O, Sludtke42, Dsmd-
gold, Hugh2414, Guanaco, Zinnmann, Zhen Lin, Sundar, Mboverload, Eequor, The zoro, Darrien, SWAdair, Glengarry, Bobblewik, Delta
G, William Ashe, Geni, J~enwiki, R. fiend, CryptoDerk, Screetchy cello, Yath, Sonjaaa, Danny Rathjens, Pcarbonn, Quadell, Selva, An-
tandrus, HorsePunchKid, BozMo, IdahoEv, Beland, Onco p53, Kusunose, Lesgles, Eregli bob, G3pro, PDH, Jossi, Sambostock, Wikimol,
DanielCohen, Rdsmith4, Johnflux, Kevin B12, Dikaiopolis, Deewiant, Creidieki, Neutrality, Urhixidur, Joyous!, Jh51681, Syvanen, Gerrit,
Grm wnr, Deglr6328, Patrick ns, Dpen2000, Zondor, Adashiel, Trevor MacInnis, Avatar, Mike Rosoft, Dr.frog, D6, Ouro, Xrchz, Ta bu shi
da yu, Freakofnurture, Heegoop, Poccil, JTN, Indosauros, NathanHurst, Rich Farmbrough, Guanabot, Cacycle, TomPreuss, Rama, Vsmith,
HeikoEvermann, Autiger, Chad okere, MeltBanana, Roodog2k, Ashwatham, Pavel Vozenilek, GregBenson, SpookyMulder, Bender235,
ESkog, Android79, Sum0, Kbh3rd, FrankCostanza, Tarndt, Petersam, Brian0918, Pmcm, Publicenemy, MisterSheik, CanisRufus, Mr. Bil-
lion, El C, Phrozenfire, Cherry blossom tree, Lankiveil, Kwamikagami, Shanes, Susvolans, SS~enwiki, Sietse Snel, Art LaPella, RoyBoy, Jp-
gordon, Bill Thayer, Causa sui, Bobo192, Fir0002, BrokenSegue, Duk, Viriditas, Vortexrealm, Johnteslade, Foobaz, Davelane, L33tminion,
I9Q79oL78KiL0QTFHgyc, Pokrajac, Giraffedata, Aquillion, Man vyi, La goutte de pluie, Jojit fb, TheProject, Pflodo, Deryck Chan,
BW52, Minghong, Idleguy, Haham hanuka, Jonathunder, Tos~enwiki, Willard, Illegal, Mareino, Merope, Knucmo2, Ranveig, Jumbuck,
Mikeshk, Alansohn, Anthony Appleyard, Polarscribe, Eric Kvaalen, Rd232, Carbon Caryatid, ExpatEgghead, Andrewpmk, Hagnat, Riana,
AzaToth, Ahruman, Psychofox, Lightdarkness, Viridian, Mace, Mac Davis, Walkerma, Gblaz, Cdc, Wdfarmer, Nitrogenx, Hu, Malo, Av-
enue, Hohum, Mbimmler, Shinjiman, Dschwen, Velella, Super-Magician, Wtshymanski, Proton, Cburnett, Stephan Leeds, Evil Monkey,
Howard scott, Randy Johnston, Shoefly, Pethr, Vuo, H2g2bob, Gearspring, Skatebiker, EventHorizon, Qooth, DV8 2XL, Gene Nygaard,
Klparrot, DarrenBaker, Feline1, Johntex, Dan100, Galaxiaad, Kenyon, Stephen, Empoor, LARS, Feezo, Gmaxwell, Weyes, Boothy443,
OwenX, Woohookitty, DavidK93, Vanished User 3388458, TigerShark, Camw, Daniel Case, StradivariusTV, Jonathan de Boyne Pol-
lard, Arnomane, Madchester, Kzollman, Before My Ken, Fbv65edel, WadeSimMiser, JeremyA, MONGO, Eleassar777, Tabletop, Sholtar,
Jleon, Bbatsell, Lol~enwiki, Terence, Mangojuice, Sengkang, GregorB, D0t, Wayward, MarcoTolo, Stevey7788, Dysepsion, Emerson7,
Paxsimius, SqueakBox, Ashmoo, EgonWillighagen, Graham87, Magister Mathematicae, Zeromaru, Raivein, BD2412, Kbdank71, Fre-
plySpang, Icey, Drbogdan, Rjwilmsi, Mayumashu, Tizio, Tim!, Virtualphtn, WCFrancis, Collins.mc, Vary, Strait, BadCRC, Jeftrokat,
PinchasC, Quiddity, Teklund, Tangotango, Tawker, Crazynas, HappyCamper, Ligulem, NeonMerlin, Bedrupsbaneman, Daniel Collins,
Brighterorange, Bhadani, GeorgeBills, Bratch, Matt Deres, FlavrSavr, Sango123, Watcharakorn, Yamamoto Ichiro, Dracontes, Leithp, Ya-
gagakhee, FayssalF, Titoxd, Jamesmusik, DDerby, RobertG, Windchaser, Old Moonraker, Doc glasgow, Nihiltres, Alhutch, GnuDoyng,
Sanbeg, Nivix, Chanting Fox, Dsdhall, Celestianpower, Ayumbhara, RexNL, Ewlyahoocom, Gurch, Pcj, Wars, Vilcxjo, Drumguy8800,
TeaDrinker, Bmicomp, Tysto, Zotel, Knoma Tsujmai, Nor-dakota, Chobot, Elpaw, Sherool, Antilived, Visor, HKT, Bornhj, Korg, Igorde-
braga, 334a, Digitalme, Markmichaelh, Simesa, Gwernol, Banaticus, Elfguy, The Rambling Man, Siddhant, Mercury McKinnon, Wave-
length, TexasAndroid, Rmo13, Sceptre, Gavrilis, Huw Powell, Jimp, Brandmeister (old), Phantomsteve, RussBot, Red Slash, Jtkiefer,
Postglock, Anonymous editor, Diliff, Conscious, Kevs, Splash, Jengelh, Bergsten, SpuriousQ, Hellbus, Hydrargyrum, Stephenb, David
Woodward, Gaius Cornelius, CambridgeBayWeather, Shaddack, Rsrikanth05, Pseudomonas, Wimt, GeeJo, RadioKirk, TheMandarin,
NormalAsylum, NawlinWiki, Wiki alf, Wiktionary4Prez!, Astral, Snek01, Janke, Grafen, Escheffel, Gamerider, Jaxl, Johann Wolfgang,
SivaKumar, Snowfalcon, Nick, Banes, Cholmes75, Ianleow7, DAJF, Daniel Mietchen, InvaderJim42, PhilipO, Kwh, Misza13, Killdevil,
Semperf, Chichui, Ospalh, DGJM, Xompanthy, Samir, BOT-Superzerocool, Khonsali, Mysid, Olleicua, PS2pcGAMER, Psy guy, Colin-
Fine, Derek.cashman, Mistercow, Brisvegas, Phenz, User27091, Nick123, Max Schwarz, Wknight94, TouN~enwiki, FF2010, Sandstein,
Vpendse, Getcrunk, Zzuuzz, Djramone, StuRat, Tom Sponheim, Huangcjz, Trismc, Pb30, Canley, JuJube, Petri Krohn, GraemeL, JoanneB,
Symon, RajbirParmar, Chriswaterguy, Carabinieri, Fram, HereToHelp, Jaranda, PGleick, Ilmari Karonen, MagneticFlux, Kungfuadam,
Meegs, MasterXiam, NeilN, Philip Stevens, Star trooper man, Pentasyllabic, Serendipodous, DVD R W, Bonnie91, Tobyk777, That Guy,
From That Show!, robot, Luk, The Wookieepedian, Itub, SpLoT, Lviatour, Yvwv, Sardanaphalus, Crystallina, Hl540511, SmackBot,
Mwazzap, YellowMonkey, TomGreen, Ashenai, Acatkiller, Terrancommander, Moeron, EJVargas, Rex the first, Rishabhgupta, Knowled-
22.1. TEXT 371

geOfSelf, Royalguard11, Bigbluefish, RevolverOcelot~enwiki, Fdt, Pgk, Proficient, C.Fred, Blue520, Jacek Kendysz, Immanuel goldstein,
Verne Equinox, Ifnord, Wolf ODonnell, Anastrophe, Jrockley, Delldot, Mdd4696, Fnfd, Edgar181, HalfShadow, Alex earlier account,
DarkTurtle, Commander Keane bot, Xaosflux, Yamaguchi , Aksi great, Macintosh User, Peter Isotalo, Gilliam, Ohnoitsjamie, Hmains,
Jushi, Ppntori, Carl.bunderson, ERcheck, JMiall, Andy M. Wang, Airplanedude550, Saros136, Chris the speller, Keegan, Quinsareth,
Jprg1966, B00P, DroEsperanto, Japaa, Gil mo, Elagatis, MalafayaBot, Khobler, Hibernian, Deli nk, Achristl, Bob the ducq, CSWarren,
Baronnet, DHN-bot~enwiki, Kabri, Zven, Konstable, Hallenrm, Rlevse, Gracenotes, Vinmax, John Reaves, RuudVisser, Sanshore, Au-
driusa, Tacceber, Cyberninja49, Can't sleep, clown will eat me, Catalyst37, Jon Nevill, White Wolf, DLand, Ultra-Loser, Chlewbot, Min-
uteHand, OrphanBot, TheKMan, TonySt, Homestarmy, Xyzzyplugh, Bolivian Unicyclist, Midnightcomm, Grover cleveland, Hobbes3k,
Khoikhoi, Krich, Kthxhax, Silverjonny, Makemi, Nakon, Savidan, Aranmore, Cubbi, Richard001, Eran of Arcadia, Brucer42, Invinci-
ble Ninja, IrisKawling, Monsterboy, Derek R Bullamore, Sokolesq, DMacks, Omnijohn, Xiutwel, Antipode, Kkmd, Mion, Richard0612,
Springnuts, Rodeosmurf, Vina-iwbot~enwiki, DKEdwards, Pilotguy, Kukini, Circumspice, Drunken Pirate, Ohconfucius, Will Beback,
Xezlec, SashatoBot, Lambiam, Ashvidia, Rory096, Swatjester, Quendus, Harryboyles, Anlace, Attys, JzG, Dbtfz, Kuru, John, AmiDaniel,
Jidanni, Drahcir, So9q, J 1982, Tazmaniacs, Heimstern, SilkTork, Disavian, Nathanww, Lloydwatkins, Fev, Sir Nicholas de Mimsy-
Porpington, A.b.s, EA Kok~enwiki, Linnell, Coredesat, Hemmingsen, Peterlewis, Zpop101, Ocatecir, IronGargoyle, Beefball, Ckatz,
Dilcoe, CPAScott, White.matthew.09, Chuck Simmons, Stefo~enwiki, Stupid Corn, Andypandy.UK, Slakr, Special-T, Rob Shanahan,
Beetstra, Childzy, Santa Sangre, Bendzh, RyJones, Waggers, Mets501, Mattabat, Whomp, NJA, Mintchocolatebear, RichardF, Peter Horn,
AEMoreira042281, Jose77, Galactor213, Mzuo, KJS77, Hu12, DabMachine, Ginkgo100, OnBeyondZebrax, Nehrams2020, Wizard191,
Echofloripa, Cry baby99, Polymerbringer, Paul venter, Markan~enwiki, JoeBot, Basicdesign, Walton One, Muéro, J Di, Honorkell, Tony
Fox, Dp462090, Heshelm, Maelor, Civil Engineer III, Supertigerman, Az1568, Adambiswanger1, Courcelles, Anger22, Jlove13, Coffee
Atoms, Fdp, Tawkerbot2, MarylandArtLover, Alegoo92, Daniel5127, Ouishoebean, The Letter J, Eastlaw, SkyWalker, Cromas, JForget,
Stifynsemons, Cacahueten, Safewater, WCar1930, Sam giles2001, CmdrObot, Antelopotamus, Shyland, Zarex, Unionhawk, GeraldH, Sco-
houst, Aherunar, BennyD, SupaStarGirl, W guice, Brownings, Nunquam Dormio, Vinty, GHe, Exhummerdude, Argon233, Ballajames33,
MarsRover, Mattcordle, WeggeBot, ONUnicorn, Grj23, Ispy1981, Samuella99, RobertLovesPi, MrFish, Fordmadoxfraud, GCRaya, Coun-
terfit, Kelly elf, The Enslaver, Qrc2006, Samdawg84, Mryakima, Cydebot, Peripitus, Avigdor6, Slayerhk47, Rifleman 82, Gogo Dodo,
Jkokavec, A Softer Answer, Rracecarr, Ritujith, Julian Mendez, Acs4b, Tawkerbot4, Kevin Kidd, Chrislk02, Johnfn, Pakada, Robowurmz,
Inkington, Blindman shady, Ebyabe, The Lizard Wizard, Sabertooth, Connorh90803, JodyB, Matwilko, Daniel Olsen, UberScienceNerd,
Gungaden, Richhoncho, JohnInDC, FrancoGG, Malleus Fatuorum, Thijs!bot, Epbr123, Bladechampion~enwiki, SinisterLemon, Eric-
stoesser, Mbell, Ucanlookitup, Asweni, Some Guy !@$, N5iln, Nonagonal Spider, Moondigger, Yzmo, Marek69, John254, Electron9,
James086, Zé da Silva, Patchiemoo, Weasel5i2, Miller17CU94, Dfrg.msc, Pantallica00, Qarel, Pcbene, Dgies, CharlotteWebb, Sikkema,
MichaelMaggs, Uruiamme, Fiber-optics, Sean William, Haha169, Natalie Erin, Denverjeffrey, Berethor222, Mmelgar, Dane13, JE-
Brown87544, KrakatoaKatie, AntiVandalBot, Majorly, Yonatan, Luna Santin, Seaphoto, Opelio, Steve Zissou, Just Chilling, Dashboardy,
Isilanes, Rhinoracer, Davken1102, Danger, Tuor~enwiki, Istartfires, Gregorof, Altamel, Elaragirl, Manu bcn, Myanw, Canadian-Bacon,
Cherylyoung, Tomertomer, Mikenorton, JAnDbot, Husond, Barek, MER-C, Matthew Fennell, Jonemerson, Silenius~enwiki, Hello32020,
Db099221, Symode09, Andonic, Tiddlywinks, Savant13, Kirrages, Joshua, LittleOldMe, SiobhanHansa, Acroterion, Angelofdeath275,
Penubag, Magioladitis, Karlhahn, Pedro, Pzone, Bongwarrior, VoABot II, Mredheffer, MartinDK, Dekimasu, Nyourhead, Alexultima,
Yandman, Michael Stangeland, Amkozmo10, CattleGirl, Vernon39, Think outside the box, Disconformist, SineWave, Soulbot, Rich257,
Landart222, Avicennasis, Midgrid, GroovySandwich, BrianGV, Jimjamjak, Destroyer000, Animum, Maryilang, Woodcore, JJ Harrison,
Trisar, LorenzoB, P.B. Pilhet, Bigbobc293, Vssun, Glen, DerHexer, JaGa, Jahangard, Pan Dan, Nevit, Calltech, Lord Of The Crayons, I
B Wright, Arnesh, Mschiffler, GSGSGSG, Chris.matt, Lswinger, Aliendude5300, Jerem43, Hdt83, MartinBot, Kjhf, Charlie MacKenzie,
Cutesybuttons295, Jackfrondas74, Arjun01, ChemNerd, Kaarthick, Theultimatejoeshmo, Rettetast, Ultraviolet scissor flame, M.suresh,
Thejazzcaveman, Penikett, Luis731, Fallen angel88, TheEgyptian, Absolwent, R'n'B, CommonsDelinker, AlexiusHoratius, Lilreefer420,
Tiger swimmer09, Nathan J. Hamilton, Hawkhockey, PrestonH, Senthryl, Smokizzy, Marco Alfarrobinha, LedgendGamer, Tgeairn, Ed-
ward Blaze, Exarion, Thirdeyeavatar, J.delanoy, Lophoole, Pharaoh of the Wizards, Nev1, ABlake, Jmehu.123, Walsh family, Bogey97,
Silverxxx, Hwaqar, MrBell, Eliz81, John Mack, Thaurisil, Murmurr, Hodja Nasreddin, Murphy ernsdorff, There are unused icons on your
desktop, Bob billydoe joe, Galanskov, Loonitreefrog, Gzkn, Acalamari, Littleghostboo, Aqwis, MR.Nicholson, Davidm617617, Muzza2,
DragonDance, Katalaveno, AmandaFraser, Amiruka, LordAnubisBOT, Thomas Larsen, Jeepday, Mikael Häggström, L'Aquatique, Xyza-
xis, Bladesofblood112, Leefatting, Monkey.choker, Jiu9, Tsuite, Ejhoekstra, AntiSpamBot, Info bunny, Berserkerz Crit, Umbrah, Warut,
Belovedfreak, Ryanscool55, NewEnglandYankee, Abarton777, Cadwaladr, Nwbeeson, SJP, Railcgun, MKoltnow, Farbror Erik~enwiki,
Tigerlisa, Lincoln187, Shoessss, Crash nitro cart, BookSquirrel, Enix150, Dhaluza, Bennelliott, Cometstyles, Tatortats21, Micah2012,
Mrguy753, Tbhartman, SBKT, Gwen Gale, Meganerdtron, Csavoia, Bcnof, Mike V, Natl1, Thecanadiankid, Roberto Fiadone, Black
Walnut, Nscott.odi, Jarry1250, Adsomvilay, Andy Marchbanks, Speedreed, Jelani94, Zeosurfer, DASonnenfeld, Samsw2, Jedawson2000,
Scud12343219, SoCalSuperEagle, Xiahou, Squids and Chips, Muchclag, Liop666, JonathanFish, Idioma-bot, Highfields, CaptainFire, Cac-
tus Guru, Lights, Snakehr3, DerekSmalls~enwiki, Fbffe, VolkovBot, Hyper Ferret, Sethant, Type-R-Avatar, Nick245, Alexandria, Katy-
didit, Fences and windows, Philip Trueman, Marekzp, Sweetness46, Glamourgirl33, TXiKiBoT, Alesnormales, Angelclown3, Blah63,
Jacob Lundberg, Malinaccier, Java7837, Muro de Aguas, LLroxsox, Xerxesnine, Miranda, Rei-bot, Ann Stouter, Z.E.R.O., Zurishaddai,
Anonymous Dissident, Afluent Rider, Njd11, Lampshade7, Fillupboy, Someguy1221, Vanished user ikijeirw34iuaeolaseriffic, Oxfordwang,
Anna Lincoln, Estrieluv, Qyt, SHARU(ja), DennyColt, Martin451, JhsBot, Leafyplant, Don4of4, K193, Xavier13~enwiki, ClarkKent13,
Abdullais4u, Canaima, Psyche825, Gettingcrossnow, Cremepuff222, Waterwise, Xcryoftheafflictedx, Deipnosopher, Telecineguy, Mad-
whizzer, Rolphing, Ashlopedia, Justiceleegealiancejla, Colocomp~enwiki, Wiggdaddy, Smetje, Tj84, Comrade Tux, Gillyweed, Carine-
mily, Synthebot, Strangerer, Falcon8765, Enviroboy, Coolio1125, Burntsauce, MCTales, Master of the Oríchalcos, WatermelonPotion,
Nssbm117, Nibios, Brianga, Monty845, Twooars, Codairem, AlleborgoBot, Thunderbird2, Closenplay, Shadow2598, Corneliusdenali,
NHRHS2010, Sources said, EmxBot, KyleCon, D. Recorder, Givegains, Arush79, Kbrose, Beryish mourner, Santabunny, Newbyguesses,
SieBot, StAnselm, Poip2, Rhydon, Cha ching24, Michiavelli, Augustus Rookwood, Calliopejen1, Nubiatech, PlanetStar, Champ wwe john-
cena, Moonriddengirl, Kkcoolz, BotMultichill, ToePeu.bot, The silent assasin, Ori, Matttttttador, Sakkura, Vandaliz3, Master 999uk, Mbz1,
Xfinnegan3x, Caltas, Popithelf, Kinkwan, Strayan, Hyper year, Striowski, GomersallT, Metallicradiation428, Andrewjlockley, Cm3942,
Barliner, Nbowers10, Vandill 01, Morrrrrrrada, Purbo T, Warhammer 8, Jarood, Keilana, Cincydude55, Aillema, AnneDELS, T weiss9910,
Elementx03, Plmnbvc, Kristinwt, Aravindk editing, Oda Mari, Canned Fruit, Everybeaned, Nopetro, JetLover, Mimihitam, Gilmiciak,
Turtle123, Oxymoron83, AngelOfSadness, Lightmouse, Laurence35, Manway, AWeishaupt, Pediainsight, The Hemp Necktie, Correogsk,
Spartan-James, Wyroba, Acspsg, Kopid03, Mike2vil, X2Xnorris, Hamiltondaniel, Realm of Shadows, Acceptable, Dabomb87, Wahrmund,
Kalidasa 777, Marlajim, Finetooth, BlogforHealth, Singmarlasing, Marons34, WordyGirl90, Pursanova, Meleeboy, WikipedianMarlith,
Pigwig, ClueBot, Mc2000, GorillaWarfare, PipepBot, Snigbrook, Badger Drink, Deeper Black, The Thing That Should Not Be, Coca-
colaisthebest, Vkap, Keeper76, Realitytvlover, Taquito1, ImperfectlyInformed, CooPs89, Fiet Nam, Oddtail, Polyamorph, Niceguyedc,
Blanchardb, Athomsfere, Piledhigheranddeeper, Fgasber, Adampantha, Auntof6, Pointillist, DragonBot, Deadgnome, Zombie621, Aw-
372 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

ickert, Drewster1829, Excirial, Alexbot, CrazyChemGuy, Talizadeh, Resoru, Winston365, Rct36, Christainthomas, Waterairfirearth,
Stealth500, Vanderz, Cenarium, Jotterbot, RC-0722, Guild2, Onesilentlight, Warrior4321, Lowetta, Waqqasd, Chewy1993, Alloquep,
Plasmic Physics, Dziewa, CoolNew, Nancygirl199, Jupiter849, Ps07swt, DumZiBoT, Darkicebot, BarretB, Nathan Johnson, James Kanjo,
Sanjay517, DaL33T, MD.Brian, WikHead, Martin Chaplin, Rounddot5827, Goolizap, Stormcloud51090, Thatguyflint, Falconkhe, Asd-
ofindia, The Tutor, Addbot, Cxz111, Roentgenium111, Mattguzy, Surfman23, DOI bot, FlowRate, JeremyBiggs, Binary TSO, M.nelson,
Prerna.pooja, Mergim321, Totakeke423, Fieldday-sunday, Ashton1983, Leszek Jańczuk, Fluffernutter, Richmond96, Cst17, MrOllie,
Download, Proxima Centauri, LaaknorBot, Chamal N, Jgmikulay, Glane23, Casperdc, Debresser, Fires64, LinkFA-Bot, 5 albert square,
TheFreeloader, Brian Laishes, Quasidan, Numbo3-bot, Tide rolls, Verbal, MuZemike, Arbitrarily0, Ettrig, CountryBot, Megaman en m,
Ben Ben, Legobot, Luckas-bot, Yobot, Ptbotgourou, TaBOT-zerem, Newportm, II MusLiM HyBRiD II, KamikazeBot, ChildSurvival,
Rock pillow, South Bay, Backtothemacman32, AnomieBOT, John Holmes II, Sanfy, Daniele Pugliesi, Killiondude, Galoubet, Royote,
Short Brigade Harvester Boris, JackieBot, AdjustShift, Dalcanale, Materialscientist, Danno uk, Citation bot, Waterjuice, Flipping Mackerel,
Xqbot, Gopal81, JimVC3, Renaissancee, Jeffrey Mall, Nasnema, Herr Mlinka, Wikify567, P99am, Star Trek enthusiast, Anna Frodesiak,
J04n, GrouchoBot, Ataleh, RibotBOT, SassoBot, Bahahs, PeanutMeh, Medicuspetrus, GhalyBot, MerlLinkBot, Shadowjams, Pakpoom da,
Universalss, SchnitzelMannGreek, Whatnwas, Thefloogadooga, Nicholasphilipov, Zachnobob, FrescoBot, Phasertype3, Zachalope, Paine
Ellsworth, Pepper, Sky Attacker, Ironboy11, Goodbye Galaxy, I42, Pgh2738, HJ Mitchell, Joplin127, Citation bot 1, Galmicmi, Launch-
baller, Jakob Russian, Shanghainese.ua, AstaBOTh15, Windsor Help Desk, DrilBot, Luebuwei~enwiki, Pinethicket, HRoestBot, Edderso,
Miguelaaron, Jonesey95, Alltat, A8UDI, RedBot, Lars Washington, Kuru500, Cullen12, Hallred, Rotorcowboy, Fsafnmoisbnacj, Attack
2400, ChiSoxFan93, Savemaxim, Violabiola, Shahzeb1119, Wikimann132, Mikespedia, Harry362, Gamescreator, Anqdrew, GoneIn60,
Shadow grunt, MikeJR0509, Angelatheaven, KnowledgeRequire, Zaheermerali, IVAN3MAN, Iris92, Awesomeman7788, Jamesm199,
Wikiwhoodi, CrowzRSA, Fallingwaffl3z, Bullybum1, FoxBot, 11nniuq, TobeBot, Declan Clam, Aceofhearts157, Ilovefuckingeverything,
Ticklewickleukulele, TheCollectorz, Lotje, Vrenator, Suomi Finland 2009, Extra999, Begoon, Jookie444, Gogored, Ohdam, 1qaz!QAZ,
Sarahmann2009, Samjohn95, WaterCommunicator, Diannaa, Stephen MUFC, Unrulyevil, Jynto, Sirkablaam, Tbhotch, DARTH SIDIOUS
2, TjBot, VernoWhitney, Harrypotter90, ElPeste, Spatel333, Toasters34, Ionut Cojocaru, Narayanan20092009, Chris Rocen, Rv3016,
Chicco3, Paul24112, Riley vb, Awesomeness37, Mr. Anon515, EmausBot, Orphan Wiki, WikitanvirBot, Qurq, Surlyduff50, Gfoley4,
Bowei Huang 1, ScottyBerg, Ncsr11, Candyisdandy, GoingBatty, Thywob, 19maxx, Rajkiandris, Jmencisom, Slightsmile, Tommy2010,
Wikipelli, Savh, JSquish, Reyndeer, ZéroBot, Pooky199610, Ashtonrocksmysox, Informatus, Mamtapednekar, Unessacary cencorship,
Fæ, Asephei, Askedonty, Xabier Armendaritz, Beddowve, Magasjukur, Jncheese, Jrmarsico, Wayne Slam, Arman Cagle, Brandmeister,
Al Adriance, Voltronladiesman, L Kensington, Kranix, Fagopyrum, Scientific29, Puffin, EvenGreenerFish, Nickwaz98, Defeater982, As-
mah01, ChuispastonBot, Thiagoreis leon, Elayne123, Unholydoom99, Epic ninja, Shawnee6677, ClueBot NG, Irfanazam7, NGMan62,
CocuBot, Aligalal, Justinarmas2009, Monsoon Waves, Rezabot, Pluma, Helpful Pixie Bot, Barrodrajesh, Victor.reznov, Calabe1992,
Gob Lofa, Bibcode Bot, BG19bot, Hz.tiang, Eric567, PhnomPencil, Hallows AG, BDasher, Nick2crosby, JohnChrysostom, Amp71,
StuGeiger, DarkThunder42069, AvatarNavi, Delgadoj33, BML0309, Mypooster, AwamerT, Whatnotwhat, Josh Du Toit, Onewhohelps,
Josephlee94, Ajayupai95, Lovebugeater, Ilovemarcusfarnham, DeerKiller54321, Lolololol020863, Jikepaddy, Ross ucowr, Eagle479, Cool
chic 101, Lolilikecats, Lolilikecats123, Darkjudah, Stradiot, Saintbobbyvinton, Saintbobdylan, Berkleejean, Hurricanefan24, JSWHU,
Sheldon Kepler, Wuebker04, ES123, Youssef1110, Darkwolf2230, Boonezoore, Sharkboyjake, Aljohnson2000, JZCL, Ibrandjews5,
Nitrobutane, Jonadin93, Justincheng12345-bot, Judiakok1985, HueSatLum, Arcandam, Soulparadox, JYBot, Dwindu, Dexbot, Mende-
zlover69, Ump786, Reatlas, VanishedUser 2313214sad1, Mr. Railroader, JPaestpreornJeolhlna, Praemonitus, Kuyi123w, Jwratner1, W.
P. Uzer, Kind Tennis Fan, Climate123, Kinglycitrus, Nahnah4, Lagoset, Monkbot, Cityrailsaints, Jh1234l, Trackteur, Vanished user
9j34rnfjemnrjnasj4, Hillysilly, Mooresteve76, Oiyarbepsy, Mario Castelán Castro, Qzekrom, Ostrichyearning, 2TonyTony, KasparBot,
Echeranay and Anonymous: 1753
• Nucleic acid Source: https://en.wikipedia.org/wiki/Nucleic_acid?oldid=668101236 Contributors: AxelBoldt, Kpjas, Mav, Ed Poor, An-
dre Engels, Josh Grosse, Anthere, Ellmist, Graft, Hephaestos, Lir, Lexor, Egil, 168..., Ellywa, Snoyes, Angela, Julesd, Ugen64, Cyan,
Smack, Adam Bishop, Lfh, Dysprosia, Ngourlie, Pakaran, Gentgeen, Josh Cherry, Astronautics~enwiki, Stewartadcock, Giftlite, Aoi,
Bensaccount, Kandar, Leonard Vertighel, Pgan002, Onco p53, G3pro, Ukexpat, Trevor MacInnis, Mike Rosoft, Discospinster, Cacycle,
Narsil, Violetriga, Joanjoc~enwiki, Laurascudder, CDN99, Bobo192, Wisdom89, Dungodung, La goutte de pluie, Nk, Pschemp, Van-
ished user 19794758563875, Kierano, HasharBot~enwiki, Jumbuck, Alansohn, Kocio, Hu, Sciurinæ, Ceyockey, Miaow Miaow, Marudub-
shinki, SqueakBox, BD2412, Kbdank71, FreplySpang, Mendaliv, Sjö, Rjwilmsi, Vary, MZMcBride, JonMoulton, The wub, FlaBot,
Gurch, Str1977, Chobot, Bgwhite, Gwernol, YurikBot, Wavelength, Hede2000, Beethoven’s DNA, LyXX, Wimt, GeeJo, NawlinWiki,
Astral, Xdenizen, Mlouns, Misza13, Alex43223, JHCaufield, Derek.cashman, CLW, Kkmurray, Lt-wiki-bot, GraemeL, Anclation~enwiki,
Mikegrant, Dposse, SmackBot, Hydrogen Iodide, W3bj3d1, Gilliam, Skizzik, Ppntori, Keegan, Liamdaly620, MalafayaBot, OrangeDog,
DHN-bot~enwiki, Acelgoyobis~enwiki, Can't sleep, clown will eat me, Rrburke, Addshore, Salamurai, Scharks, SashatoBot, Beetstra, Wag-
gers, MTSbot~enwiki, BranStark, J Di, Courcelles, Ziusudra, Polypipe Wrangler, Tawkerbot2, Daniel5127, ChrisCork, JForget, Agath-
man, BeenAroundAWhile, TheTito, Araucaria, Maxxicum, Ppgardne, 2 of 8, Rifleman 82, Gogo Dodo, Narayanese, Omicronpersei8,
John R Murray, Barticus88, Kablammo, Simeon H, James086, OrenBochman, AntiVandalBot, Luna Santin, Widefox, ShellCoder, Rcej,
DarkAudit, TimVickers, Res2216firestar, Bongwarrior, VoABot II, A4, Careless hx, Nposs, Emw, User A1, Chanoyu, Talon Artaine,
DerHexer, Squidonius, Seba5618, ChaosR, Tuganax~enwiki, Strathallen, M80forYOU, J.delanoy, Pharaoh of the Wizards, Hellowhy,
Rhinestone K, Uncle Dick, Maurice Carbonaro, Hellow yo, Reedy Bot, It Is Me Here, DarkFalls, NewEnglandYankee, Antony-22, SJP,
Cmichael, U.S.A.U.S.A.U.S.A., Treisijs, Wikipedia addict101, VIOLENTRULER, VolkovBot, Philip Trueman, TXiKiBoT, Jhannah, Sin-
taku, BotKung, Bobchicken9, Chillowack, Yk Yk Yk, AlleborgoBot, Petergans, SieBot, Sonicology, RJaguar3, Antzervos, Stephen5406,
Oxymoron83, Smaug123, OKBot, Mygerardromance, Hamiltondaniel, Forluvoft, ClueBot, LAX, The Thing That Should Not Be, K3f3rn,
Unbuttered Parsnip, Gaia Octavia Agrippa, Wysprgr2005, Arakunem, Grunty Thraveswain, Abrech, SpikeToronto, NuclearWarfare, Royal-
mate1, ChrisHodgesUK, Thehelpfulone, Thingg, Versus22, Hyperliner, Alboyle, Stickee, Avoided, NellieBly, Alexius08, Pobregatita, Sgp-
saros, Addbot, Yoenit, CL, Ronhjones, Looie496, EconoPhysicist, Armin Straub, Tide rolls, Preston.hussey, Teles, Zorrobot, Arbitrarily0,
Yobot, Yngvadottir, Ciphers, Rubinbot, Piano non troppo, Yachtsman1, Magog the Ogre 2, Citation bot, Frankenpuppy, MauritsBot,
Xqbot, Schmutz MDPI, Babyranks17, Tad Lincoln, P99am, Almabot, ChristopherKingChemist, Ianis G. Vasilev, FrescoBot, LucienBOT,
Tobby72, Arjen IF, TimonyCrickets, Nirmos, SixPurpleFish, Pinethicket, I dream of horses, Desireader, Jauhienij, Tim1357, Double
sharp, TobeBot, Kalaiarasy, Vrenator, Kyle 290, Reenus, DARTH SIDIOUS 2, Dng267, Salvio giuliano, DASHBot, Franz Bryan, Emaus-
Bot, Cpeditorial, Tommy2010, JSquish, John Cline, Shuipzv3, John Mackenzie Burke, Wayne Slam, Tolly4bolly, GeorgeBarnick, Don-
ner60, Inka 888, ChuispastonBot, JMBurke1791, DASHBotAV, 28bot, JonRichfield, Petrb, ClueBot NG, O.Koslowski, Widr, Bibcode
Bot, BG19bot, MusikAnimal, Amp71, Cadiomals, Ornithodiez, Glacialfox, Achowat, ChrisGualtieri, GoShow, BrightStarSky, Bulba2036,
Frosty, Ruby Murray, Tentinator, BSBxObsession, Glaisher, AnahiSantiago, Meteor sandwich yum, Word ynopeau, Heartbreaker1247,
2016pearsoow, Acagastya, Ulfat baig, Adityanarayan1412, ChamithN, KasparBot and Anonymous: 498
• RNA Source: https://en.wikipedia.org/wiki/RNA?oldid=672354821 Contributors: AxelBoldt, Magnus Manske, Marj Tiefert, Derek Ross,
22.1. TEXT 373

Sodium, Bryan Derksen, The Anome, Malcolm Farmer, Andre Engels, PierreAbbat, Deb, SimonP, AdamRetchless, Graft, Bdesham,
Lir, Spring~enwiki, Zashaw, BrianHansen~enwiki, Lexor, Gdarin, Ixfd64, Sannse, TakuyaMurata, Ahoerstemeier, ZoeB, Glenn, Andres,
Hashar, Dino, RickK, Selket, Shizhao, Elwoz, PuzzletChung, Robbot, Josh Cherry, Astronautics~enwiki, Vespristiano, Romanm, Sver-
drup, Flauto Dolce, Hadal, Fuelbottle, Diberri, GreatWhiteNortherner, Dina, Giftlite, Gamaliel, Bensaccount, Unconcerned, Duncharris,
Pascal666, Delta G, Adenosine, Gadfium, Andycjp, Slowking Man, Mr d logan, Beland, Onco p53, PDH, Jossi, Maximaximax, Bumm13,
Icairns, Chadernook, KeithTyler, Jh51681, Alikhtarov, Thorwald, Mattman723, Indosauros, A-giau, Discospinster, Rich Farmbrough, Ca-
cycle, Vsmith, SpookyMulder, Bender235, Neko-chan, Violetriga, RoyBoy, Perfecto, Cyc~enwiki, Bobo192, Longhair, W8TVI, Smalljim,
Arcadian, Sriram sh, Pschemp, Srlasky, Sam Korn, HasharBot~enwiki, Jumbuck, Alansohn, Anthony Appleyard, Chino, Arthena, Calton,
Kocio, Denniss, Gsandi, Velella, KingTT, Suruena, Alsager boy, Yurivict, Zntrip, Natarajanganesan, Woohookitty, Kurzon, Ruud Koot,
The Wordsmith, Duncan.france, Firien, MarcoTolo, Palica, Mandarax, Graham87, Magister Mathematicae, Li-sung, Edison, Drbogdan,
Jorunn, Rjwilmsi, Kinu, Jmcc150, Westcairo, JonMoulton, Sjlegg, FlaBot, Nihiltres, RexNL, Vossman, Bmicomp, Chobot, Bornhj, Writer-
Hound, Whosasking, YurikBot, Wavelength, Xuul, Jtkiefer, Beethoven’s DNA, Splette, RadioFan2 (usurped), Gaius Cornelius, Eleassar,
Shanel, Exir Kamalabadi, Dureo, Kabewm, Multichill, Misza13, Alex43223, Olleicua, Derek.cashman, DRosenbach, Wknight94, Ke6jjj,
Zzuuzz, Lt-wiki-bot, Jules.LT, Closedmouth, Anclation~enwiki, GrinBot~enwiki, Evolver, DVD R W, CIreland, Veinor, SmackBot, Tinz,
KnowledgeOfSelf, TestPilot, Pgk, KocjoBot~enwiki, ZerodEgo, Eupedia, Debatebob, Gilliam, Chaojoker, Crimsonfox, Trampikey, Algu-
macoisaqq~enwiki, Jprg1966, Tree Biting Conspiracy, Liamdaly620, Hichris, MalafayaBot, Davidmpye, Goldfinger820, Uthbrian, Ctbolt,
Can't sleep, clown will eat me, Usna~enwiki, Scray, SundarBot, Richard001, Ekirth, Drphilharmonic, Ollj, SashatoBot, Nishkid64, Kuru,
John, Scientizzle, Tim bates, Tktktk, MichaelHa, Cmh, Ben Moore, Munita Prasad, Alethiophile, Kyoko, Darth Smith, Hu12, ChazYork,
JMK, Shoeofdeath, Courcelles, Tawkerbot2, Harold f, CmdrObot, Ale jrb, Agathman, MrZap, Drmed36, JanDaMan, Ppgardne, WillowW,
Fedra, Was a bee, Smelissali, Codetiger, DumbBOT, Sazzlysarah, Chrislk02, Narayanese, Daniel Olsen, Mauroesguerroto, Crum375,
Casliber, Eubulide, Thijs!bot, NorwegianBlue, Escarbot, Eleuther, AntiVandalBot, Seaphoto, Rcej, Prolog, Dfrendewey, TimVickers,
Deflective, Leuko, MER-C, Plantsurfer, Jonemerson, Dave101, PhilKnight, MSBOT, LittleOldMe, Acroterion, Yahel Guhan, TransCon-
trol, Sangak, Bongwarrior, VoABot II, JNW, Rallyemax, Voloshinov, Roadsoap, Fabrictramp, Nposs, 28421u2232nfenfcenc, Allstarecho,
Macboots, Squidonius, Arnesh, Jleecole, Pvosta, Joker99352, Yobol, MartinBot, ChemNerd, Jay Litman, Neoguy999115, El0i, Wmoss2,
Sunny876, J.delanoy, Trusilver, Abbhinand, Umirox, Indiealtphreak, WarthogDemon, Ian.thomson, OttoMäkelä, Keesiewonder, Mikael
Häggström, Sephirothjms, Rnaactivation, DogcatcherDrew, Wavemaster447, Deadfishstyx, STBotD, Dr.Kerr, BENWD33333, Aa bat-
tery2003, CardinalDan, Speciate, Wikieditor06, X!, Deor, VolkovBot, TreasuryTag, AlnoktaBOT, CART fan, TXiKiBoT, Anonymous
Dissident, GcSwRhIc, Littlealien182, MarvPaule, Alexbateman, Aron.Foster, Synthebot, Lova Falk, Falcon8765, Enviroboy, Aaronatwpi,
Northfox, AlleborgoBot, Logan, NHRHS2010, EmxBot, SieBot, Tresiden, Graham Beards, Scarian, BotMultichill, Rob.bastholm, Toddst1,
Oda Mari, Ipodamos, Boppet, BenoniBot~enwiki, OKBot, Pediainsight, Mike2vil, Sardaukar Blackfang, Anchor Link Bot, Lascorz, Ex-
plicit, Forluvoft, Touchstone42, DeYoung9, Animeronin, ClueBot, The Thing That Should Not Be, Yikrazuul, Wysprgr2005, Neverquick,
DragonBot, Excirial, Jusdafax, Gtstricky, Anoop2000, Black88rabbit, Unmerklich, Bald Zebra, Nimavojdani, 9Nak, Jadeddissonance,
Aitias, Jonverve, 7, Versus22, Johnuniq, SoxBot III, Apparition11, RMFan1, Jmanigold, Bondrake, BodhisattvaBot, Allikendr1, Tegiap,
Vojtěch Dostál, Anturiaethwr, WikHead, Doc9871, 2013schwarzkopfn, Ihavewon, Addbot, Arlindos, Some jerk on the Internet, DOI bot,
Guoguo12, Vishnava, Cst17, Download, Glane23, LinkFA-Bot, Tide rolls, Teles, Gail, Legobot, Luckas-bot, Yobot, EdwardLane, Pt-
botgourou, TaBOT-zerem, Cflm001, II MusLiM HyBRiD II, KamikazeBot, AnomieBOT, AdjustShift, Nemadude, Materialscientist, The
High Fin Sperm Whale, Citation bot, MauritsBot, Xqbot, MAKSIMYUSHKOV, GkiwiPD, P99am, NFD9001, Almabot, Daddyerinenoch,
Bear15987, Mathonius, N419BH, Miyagawa, Jearbear34, , Tobby72, King of the Court, HJ Mitchell, Tegel, Citation bot 1, Citation
bot 4, Pinethicket, I dream of horses, Jonesey95, Tom.Reding, RedBot, Jauhienij, Madurai1982, Trappist the monk, Jordgette, Jonkerz,
Vrenator, LilyKitty, Davish Krail, Gold Five, Greengiant9875, Butterball888, Jcorry10, Tbhotch, MirankerAD, Jesse V., SimpsonMA,
RoseAE, DARTH SIDIOUS 2, Andrea105, Lbarquist, Ripchip Bot, NerdyScienceDude, Salvio giuliano, Mashin6, EmausBot, Wikitan-
virBot, Immunize, Ibbn, Djaboube, Sponk, Marcos canbeiro, Wikipelli, K6ka, ZéroBot, Fæ, Zotti6464, Davykamanzi, Natseea, The Nut,
John Mackenzie Burke, EWikist, Rcsprinter123, JoeSperrazza, Hccc, L Kensington, JMBurke1791, Woodsrock, ClueBot NG, Gareth
Griffith-Jones, Bilrand, HaveAHappyJBDay, Millermk, Mastrnacho9, Helpful Pixie Bot, පසිඳු කාවින්ද, Bibcode Bot, Saflksahfdl, 4chanb,
Syeda Hassan Rabia, Glevum, Bbrucebaker, BattyBot, Biosthmors, ThatBrownLady, Hsp90, Saltwolf, Aliwal2012, Wdrp8b, Compsim,
Dexbot, KWiki, Lugia2453, Szeherezadess, Frosty, UntouchableTRAMP, ComfyKem, Wywin, Fjozk, Keiyashi, SnauilHD, John54100,
296.x, Faskal, My name is not dave, BruceBlaus, Chrilli, Elizabeth sunny, Slj758, Rocker2064, Giancarlobasile, Monkbot, Acagastya,
Entitymasterblaster, Amortias, Crystallizedcarbon, Bhootrina, Ggabriel5899, Craftwerker, KasparBot, JJMC89, Jtune19 and Anonymous:
700

• DNA Source: https://en.wikipedia.org/wiki/DNA?oldid=672203416 Contributors: AxelBoldt, Magnus Manske, Peter Winnberg, Marj
Tiefert, Lee Daniel Crocker, Eloquence, Mav, Bryan Derksen, Slrubenstein, RK, Andre Engels, Fnielsen, Ted Longstaffe, LA2, Danny,
Aldie, Unukorno, Toby Bartels, PierreAbbat, Ortolan88, Ben-Zin~enwiki, Anthere, Ellmist, Graft, Heron, Hephaestos, Someone else,
Stevertigo, Spiff~enwiki, Lir, Erik Zachte, Lexor, Wwwwolf, Ixfd64, Fruge~enwiki, TakuyaMurata, (, Pde, Pcb21, Goatasaur, Egil, 168...,
Looxix~enwiki, Ellywa, Mortene, Ahoerstemeier, Fcrick, Mac, Docu, Snoyes, CatherineMunro, JWSchmidt, Kingturtle, Glenn, Cyan,
Poor Yorick, Kwekubo, Rotem Dan, Llull, Samuel~enwiki, Mxn, Raven in Orbit, Quickbeam, Hashar, Mulad, Crusadeonilliteracy, Adam
Bishop, Timwi, Dcoetzee, Nohat, Wikiborg, Reddi, Lfh, Jwrosenzweig, Gutza, Rednblu, Wik, Zoicon5, Steinsky, Patrick0Moran, Tp-
bradbury, Tom Allen, Samsara, Thue, Bevo, Shizhao, Dbabbitt, Raul654, Gakrivas, Bcorr, Pakaran, Jerzy, Lumos3, Donarreiskoffer,
Robbot, Astronautics~enwiki, Chris 73, Schutz, Vyasa, Peak, Stewartadcock, Sverdrup, Academic Challenger, Timrollpickering, Bkell,
Factual, Moink, Hadal, Jstech, Anthony, Neckro, Pifactorial, Diberri, Cyrius, Dmn, Dina, Ancheta Wis, Giftlite, JamesMLane, Graeme
Bartlett, DocWatson42, Nunh-huh, Kapow, Netoholic, Fastfission, MSGJ, Obli, Everyking, No Guru, Dratman, Curps, Michael Devore,
Bensaccount, Guanaco, Jorge Stolfi, Pascal666, Horatio, Luigi30, Solipsist, Ojl, Avala, SWAdair, Bobblewik, Alan Au, Delta G, Wma-
han, Stevietheman, Adenosine, Utcursch, Pgan002, Andycjp, Dullhunk, CryptoDerk, Gazibara, Kums, Antandrus, Onco p53, MisfitToys,
G3pro, PDH, Jossi, Rdsmith4, Mikko Paananen, OwenBlacker, Kevin B12, PFHLai, Magadan, Icairns, Troels Arvin, Figure, Asbestos,
Neutrality, Golnazfotohabadi, JohnArmagh, Jh51681, Sonett72, Adashiel, Thorwald, Mike Rosoft, Alkivar, D6, Freakofnurture, Rdb,
A-giau, William Pietri, ElTyrant, Rich Farmbrough, Guanabot, Ffirehorse, Cacycle, Qutezuce, Vsmith, EliasAlucard, Mgtoohey, Mjpi-
eters, Zazou, Bender235, ESkog, Kbh3rd, Swid, Loren36, Danny B-), Brian0918, Charm, Ben Webber, Kwamikagami, Mwanner, Phoenix
Hacker, Aude, Shanes, Susvolans, RoyBoy, EurekaLott, Andreww, Causa sui, Bobo192, Kghose, Infocidal, R. S. Shaw, Brim, Dungodung,
Arcadian, Redquark, Timl, Tomgally, La goutte de pluie, Jojit fb, Malcolm rowe, Vanished user 19794758563875, Kierano, Hagerman,
Bijee~enwiki, HasharBot~enwiki, Sam Burne James, Emoticon, Jumbuck, Danski14, Mithent, Gary, Anthony Appleyard, Chino, Boris-
blue, Atlant, SemperBlotto, Ricky81682, Loris, Benjah-bmm27, Wouterstomp, AzaToth, Yamla, Water Bottle, Echuck215, Seans Potato
Business, Kocio, InShaneee, Hu, Malo, VladimirKorablin, Snowolf, PaePae, Melaen, Schapel, BaronLarf, ClockworkSoul, Unconven-
tional, KingTT, Knowledge Seeker, Cburnett, Evil Monkey, Cal 1234, Max Naylor, CloudNine, TenOfAllTrades, Sciurinæ, Inge-Lyubov,
Lerdsuwa, LFaraone, Gene Nygaard, Alai, Mattbrundage, Netkinetic, Johntex, Kitch, Adrian.benko, RyanGerbil10, Falcorian, Tariqab-
374 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

jotu, Ashujo, DeAceShooter, Stemonitis, Natarajanganesan, Gmaxwell, Zanaq, Kelly Martin, OwenX, Woohookitty, Mindmatrix, Kat-
yare, TigerShark, Yansa, Rocastelo, Carcharoth, Nitecrawler, Lincher, Colorajo, JeremyA, Duncan.france, MONGO, Nirajrm, Astrowob,
Eleassar777, Bbatsell, GregorB, SCEhardt, TheAlphaWolf, Junes, Palica, Turnstep, Marudubshinki, Mandarax, Frostyservant, Squeak-
Box, Yasha~enwiki, Graham87, Deltabeignet, Magister Mathematicae, 168.., 169, GoldRingChip, Buxtehude, BD2412, Patrick2480, Fre-
plySpang, Lion Wilson, Yurik, RxS, Effeietsanders, Whoutz, Crzrussian, Drbogdan, Rjwilmsi, Biriwilg, Koavf, Virtualphtn, Collins.mc,
Vary, JHMM13, Bruce1ee, Jmcc150, Salix alba, JonMoulton, Oblivious, DonSiano, Ligulem, Gjuggler, SeanMack, Bubba73, Brighteror-
ange, Bhadani, Ucucha, AySz88, Sango123, Yamamoto Ichiro, Kevmitch, Wobble, Ravidreams, FlaBot, Tufflaw, RobertG, Latka, Nihiltres,
Crazycomputers, Chanting Fox, Chill Pill Bill, RexNL, Takometer, Karrmann, Jrtayloriv, DevastatorIIC, Wikipedia Administration, ZS-
cout370, Alphachimp, McDogm, Daycd, BMF81, GordonWatts, Smithbrenon, Mstroeck, King of Hearts, Chobot, Nauseam, Antilived,
Bornhj, Bjwebb, Mhking, Digitalme, Whosasking, The Rambling Man, Wavelength, Cathalgarvey, Sceptre, WAvegetarian, Jumbo Snails,
Spaully, DNA EDIT WAR, Editing DNA, Anarchy on DNA, DNA is shyt, I hate DNA, Zell Miller’s DNA, Trent Lott’s DNA, RJC,
Pigman, Bernie Sanders’ DNA, Orrin Hatch’s DNA, Bill Nelson’s DNA, Tom Harkin’s DNA, Chuck Grassley’s DNA, Richard Durbin’s
DNA, Max Baucus’ DNA, Splette, SpuriousQ, Stephenb, Wimt, GeeJo, Tavilis, Anomalocaris, Canadaduane, Alcides, Sentausa, Fabhcún,
EWS23, Alzhaid~enwiki, Dysmorodrepanis~enwiki, Wiki alf, Chick Bowen, Jaxl, Tmueck, Psora, Taco325i, Djm1279, Ragesoss, Re-
tired username, Sangwine, Robdurbar, Bert Macklin, PhilipO, Misza13, Grafikm fr, Fs, Tony1, Dbfirs, Lockesdonkey, Roy Brumback,
DeadEyeArrow, Bota47, Biolinker, Cosmotron, Supspirit, Scope creep, Caerwine, Chris84~enwiki, Somoza, Wknight94, Leptictidium,
WAS 4.250, FF2010, Alarob, Calaschysm, 2over0, Theodolite, BenBildstein, Theda, Spondoolicks, Hurricanehink, Jolt76, GraemeL,
Acer, JoanneB, Heathhunnicutt, Zahiri, ArielGold, Curpsbot-unicodify, Michigan user, RunOrDie, Stuhacking, Kungfuadam, Banus, Air-
conswitch, Samuel Blanning, BiH, DVD R W, Jer ome, Luk, RichG, Blastwizard, Itub, Twilight Realm, A bit iffy, SmackBot, Epero-
tao, Spongebobsqpants, Tarret, Chodges, Prodego, KnowledgeOfSelf, TestPilot, Royalguard11, Martin.Budden, Melchoir, Nitramrekcap,
Shoy, Joconnol, Jacek Kendysz, Pkirlin, Delldot, Blondtraillite, Zephyris, Yamaguchi , Cool3, Aksi great, Peter Isotalo, Gilliam, Julian
Diamond, Chaojoker, Jimwong, ERcheck, Carbon-16, Yaser al-Nabriss, Kazkaskazkasako, Izehar, Unint, Keegan, Persian Poet Gal, RD-
Brown, MidgleyDJ, Uthbrian, Adamstevenson, Dlohcierekim’s sock, DHN-bot~enwiki, Terraguy, Zven, Darth Panda, Firetrap9254, Gra-
cenotes, Lightspeedchick, Mikker, Hgrosser, Zsinj, Can't sleep, clown will eat me, Jorvik, Danielkueh, Snowmanradio, OOODDD, Road-
nottaken, TheKMan, Anita1988, GVnayR, Grover cleveland, Aldaron, NoIdeaNick, Spectrogram, Iapetus, Nakon, Savidan, Ne0Freedom,
Jiddisch~enwiki, Rezecib, RandomP, Smokefoot, SteveHopson, Drphilharmonic, Portugue6927, Fagstein, Kendrick7, Where, Jls043, Pi-
lotguy, Madeleine Price Ball, SashatoBot, Nishkid64, Visium, Rory096, Zahid Abdassabur, Kuru, Tazmaniacs, Kahlfin~enwiki, Epingchris,
Statsone, Shadowlynk, AstroChemist, JoshuaZ, Edwy, Coredesat, Mgiganteus1, MichaelHa, IronGargoyle, Fernando S. Aldado~enwiki,
The Man in Question, Loadmaster, Digger3000, Alexandremas~enwiki, Hvn0413, Mantissa128, Echo park00, Munita Prasad, Mr Stephen,
Dicklyon, Serephine, 4u1e, SandyGeorgia, Sir.Loin, Midnightblueowl, Ryulong, Elb2000, Carlo.milanesi, Squirepants101, RoyLaurie, Au-
tonova, Glen Hunt’s DNA, PaulGS, SimonD, Vanished user, Paul venter, Ariel Pontes, Younusporteous, Paul Foxworthy, ScottBS, Esurnir,
Adambiswanger1, Tawkerbot2, Alegoo92, Ouishoebean, Davidbspalding, Redneckjimmy, Fvasconcellos, Switchercat, JForget, RSido,
Friendly Neighbour, Gatortpk, CmdrObot, Mattbr, Wafulz, Zarex, Lavateraguy, SupaStarGirl, Leevanjackson, CWY2190, GHe, STAN
SWANSON, Mintman16, Outriggr, Cerberus lord, Logical2u, Nthornberry, Moorice~enwiki, RoddyYoung, GeoMor, Sopoforic, A D 13,
WillowW, Bryan, Steel, YanWong~enwiki, Michaelas10, Gogo Dodo, Travelbird, Red Director, Trd300gt, Hughdbrown, Sloth monkey,
Studerby, Shekharsuman, B, Tawkerbot4, Carstensen, Doug Weller, DumbBOT, Narayanese, ErrantX, Omicronpersei8, Daniel Olsen,
Gimmetrow, Casliber, Sabbre, Thijs!bot, Bloger, Opabinia regalis, Ante Aikio, Russ47025, Headbomb, West Brom 4ever, Norwegian-
Blue, Tellyaddict, Peter K., GAThrawn22, EdJohnston, Eddycrai, Nick Number, S77914767, Sean William, Natalie Erin, Escarbot, David
D., KrakatoaKatie, Cyclonenim, Ialsoagree, Mattjblythe, AntiVandalBot, Mr Bungle, Ty146Ty146, Majorly, Luna Santin, Jeka911, Why
My Fleece?, Opelio, Jayron32, 17Drew, Pro crast in a tor, TimVickers, Isilanes, Darklilac, Davegrupp, Storkk, Sjollema, Lklundin, Figma,
Canadian-Bacon, JAnDbot, Deflective, Leuko, MER-C, Janejellyroll, DigitalGhost, Db099221, Alpinu, Andonic, Hut 8.5, Tstrobaugh,
Clivedelmonte, Yahel Guhan, Efbfweborg, Sangak, Magioladitis, Pigmietheclub, WolfmanSF, Pedro, Bongwarrior, Hb2019, Carlwev,
NighthawkJ, Bhar100101, Hullaballoo Wolfowitz, Jlh29, CattleGirl, Docjames, Scincesociety, GODhack~enwiki, Tobogganoggin, Tho-
Hug, Avicennasis, WhatamIdoing, BatteryIncluded, Torchiest, David Eppstein, Emw, Gurko, Doctor Faust, Mr Meow Meow, Mika293,
TheRanger, Stolsvik, Squidonius, Patstuart, E. Wayne, NatureA16, PsyMar, Yobol, MartinBot, NochnoiDozor, Sjjupadhyay~enwiki,
ShaunL, Jonrunles, Pierceno, Dudewheresmywallet, Motley Crue Rocks, Rettetast, Fishingpal99, Zouavman Le Zouave, R'n'B, Test100000,
CommonsDelinker, Nono64, Armored Ear, Impamiizgraa, Hairchrm, Fconaway, Jarhed, WelshMatt, Grandegrandegrande, 3dscience,
Cinnamon colbert, DrKiernan, Trusilver, Nate1028, Spathaky, UBeR, Nbauman, Boghog, Shmee47, Maurice Carbonaro, Vandelizer,
WarthogDemon, Tdadamemd, Andrew wilson, BikA06, Ellis O'Neill, TheChrisD, Bmtbomb, DJRafe, Tonyrenploki, Nemo bis, Dr d12,
MrErku, Lhenslee, Kemyou, Pyrospirit, (jarbarf), WHeimbigner, Aquaplus, NewEnglandYankee, Antony-22, SmilesALot, ArazZeynili,
Master dingley, Touch Of Light, MKoltnow, Aatomic1, Potatoswatter, Scoterican, Cornacchia123, FOTEMEH, Aj123456, WJBscribe,
YOUR DNA, Mleefs7, Dr.Kerr, Cainer91, Treisijs, Vaernnond, Etanol~enwiki, Idioma-bot, Hammersoft, VolkovBot, Preston47, DrMi-
cro, Seldon1, Midoriko, Coolawesome~enwiki, Mstislavl, Daniel987600, Hersfold, Orthologist, Lia Todua, AlnoktaBOT, Fences and win-
dows, The WikiWhippet, Loginbuddy, Philip Trueman, Director, TXiKiBoT, Muro de Aguas, Billmcgn189, CupOBeans, ElinorD, Qxz,
Ocolon, Harianto, Sintaku, Michael H 34, Toninu, Chanora, Seb az86556, Ilia Kr., UnitedStatesian, Pristontale111, Chuck02, Luuva, Jo-
hanvs, Hockey21dude, DJAX, Nighthawk380, Rajwiki123, Gilisa, Hannes Röst, Gwsrinme, Mentalmaniac07, MarvPaule, Flavaflav1005,
Yomama9753, Madhero88, Amboo85, Ashnard, JamesMt1984, Usergreatpower, Synthebot, CephasE, Northfox, AlleborgoBot, Sly G,
Timewatcher, Pediaknowledge, Isis07, EmxBot, Gustav von Humpelschmumpel, Kbrose, Safwan40, SieBot, Cubskrazy29, Tiddly Tom,
Graham Beards, BotMultichill, Sakkura, Gerakibot, Dawn Bard, Cwkmail, RJaguar3, Triwbe, Brockett, Execvator, Keilana, Aaaxlp,
Crowstar, Prestonmag, Hzh, Artoasis, Lightmouse, Nanettea, Escape Artist Swyer, Hairwheel, BenoniBot~enwiki, Cradlelover123, Diego
Grez, Vividonset, Juneythomas, Andrij Kursetsky, Taulant23, Bogwhistle, Randomblue, Paulinho28, Florentino floro, Lascorz, Forluvoft,
SallyForth123, Stuart7m, Jimriz, ClueBot, GorillaWarfare, Artichoker, Wikievil666, Yikrazuul, Ewawer, TobyWilson1992, Niceguyedc,
GoEThe, Llongland, DragonBot, Excirial, Alexbot, Pumpkingrower05, Gulmammad, ThreeDaysGraceFan101, Estirabot, Coinmanj, Nu-
clearWarfare, Jotterbot, Medos2, Highfly3442, Jackrm, OekelWm, Heyheyhack, Br shadow, Ardyn, Muro Bot, Gaara san, Aitias, Jon-
verve, Versus22, Josq, Johnuniq, Wnt, Wkboonec, Psymier, Rishi.bedi, DumZiBoT, Jetsetpainter, Mandyj61596, Simultaneous, Silvo-
nenBot, Priscilla 95925, Lemchesvej, Addbot, Giftiger wunsch, DOI bot, Medessec, TutterMouse, OBloodyHell, Low-frequency internal,
Keepweek~enwiki, NjardarBot, Bernstein0275, DFS454, LinkFA-Bot, Kisbesbot, 84user, Numbo3-bot, Tide rolls, Luckas Blade, Zor-
robot, WikiDreamer Bot, Ettrig, Legobot, Drpickem, Luckas-bot, Yobot, Marcus.aerlous, Aquilla34, Nallimbot, KamikazeBot, LightFlare,
AnomieBOT, Tryptofish, 1exec1, Jim1138, Galoubet, JWSurf, Mahmudmasri, Materialscientist, Citation bot, Bci2, ArthurBot, Quebec99,
Xqbot, Sciencechick, Chaboura, Timir2, Kholdstare99, Khajidha, JWBE, P99am, GrouchoBot, Ute in DC, Wizardist, RibotBOT, Wiki
emma johnson, 7434be, Briland, GhalyBot, AustralianRupert, Hersfold tool account, Jack B108, Legobot III, FrescoBot, Paine Ellsworth,
Dogposter, Rohitsuratekar, Jc3s5h, KerryO77, HJ Mitchell, Steve Quinn, Citation bot 1, SebastianHawes, Scarce, Javert, Chenopodia-
ceous, Redrose64, DrilBot, Pinethicket, I dream of horses, HRoestBot, Jonesey95, Tom.Reding, Supreme Deliciousness, RedBot, Curehd,
22.1. TEXT 375

Jujutacular, DixonDBot, Jann, Dinamik-bot, Clarkcj12, Sgt. R.K. Blue, HayleyJohnson21, Jynto, Tbhotch, Jesse V., Minimac, DARTH
SIDIOUS 2, Mean as custard, RjwilmsiBot, Cloakedyoshi, Salvio giuliano, Mandolinface, Toto Azéro, Mashin6, EmausBot, Orphan Wiki,
Acather96, WikitanvirBot, Never give in, Jodon1971, Joeywallace9, GoingBatty, Black Yoshi, Winner 42, Dcirovic, TeleComNasSprVen,
Hhhippo, JSquish, Otterinfo, Empty Buffer, Dffgd, John Mackenzie Burke, SporkBot, AManWithNoPlan, Ocaasi, Thine Antique Pen,
Hccc, JZuehlke, Brandmeister, Pkank, L Kensington, Perseus, Son of Zeus, Rr2wiki, Donner60, Dnacond, Nanodance, Scientific29, Puffin,
Nofatlandshark, LikeLakers2, Davidartois, Woodsrock, Mikhail Ryazanov, Will Beback Auto, ClueBot NG, Jnorton7558, Ds2207, Mel-
bourneStar, Prathfig, Kaushlendratripathi, Zynwyx, O.Koslowski, Argionember, Username 772, Theopolisme, Vogel2014, Helpful Pixie
Bot, Iyentra Rasonica, Calabe1992, Bibcode Bot, Lowercase sigmabot, BOK602, Piguy101, Midnight Green, Astpurcell, JasonK33, Jaz-
zlw, Min.neel, Snow Blizzard, Uluru345, Achowat, Djihinne1, AndroidOS, Biosthmors, TuringMachine17, Stigmatella aurantiaca, Chris-
Gualtieri, Saxophilist, Khazar2, IjonTichyIjonTichy, Dexbot, Webclient101, Mogism, Oliverrichardson, Laxative Brownies, THFC1996,
Fox2k11, Zziccardi, Hopefuldonor, Mshamza112, Phil2793, Fjozk, RandomLittleHelper, Cor Ferrum, Joeinwiki, ProDawg5, 9FireStar,
Diegomanzana, Keiyashi, Dbzhero5000, IncredibleWondersYes1, Youngdro2, ManofQueens, Bever, BruceBlaus, Anrnusna, Meteor sand-
wich yum, Andrewmhhs, Abitslow, Csutric, Chaya5260, Zettek95, Giancarlobasile, Monkbot, Virion123, Owais Khursheed, Acagastya,
Entitymasterblaster, Cyntiamaspian, KH-1, Bhootrina, Soldier of the Empire, MicroPaLeo, Jensberzelius, Forscienceonly, Azealia911,
Craftwerker, ABCDEFAD, COOL ANKUR CHOUDHURY, Unmaterial scientist, MANEVIL 187, Rrwanga17, Maddog9962002, Chris-
tianmorasco, Underlyingboss3, CAPTAIN RAJU, S281305, Nn9888 and Anonymous: 999

• Protein Source: https://en.wikipedia.org/wiki/Protein?oldid=671296889 Contributors: AxelBoldt, Magnus Manske, Marj Tiefert, Mav,
Bryan Derksen, Tarquin, Taw, Malcolm Farmer, Andre Engels, Toby Bartels, PierreAbbat, Karen Johnson, Ben-Zin~enwiki, Robert Foley,
AdamRetchless, Netesq, Mbecker, DennisDaniels, Spiff~enwiki, Dwmyers, Lir, Michael Hardy, Erik Zachte, Lexor, Ixfd64, Fruge~enwiki,
Cyde, 168..., Ams80, Ahoerstemeier, Mac, Snoyes, Msablic, JWSchmidt, Darkwind, Glenn, Whkoh, Aragorn2, Mxn, Zarius, Lfh, Ike9898,
StAkAr Karnak, Tpbradbury, Taxman, Taoster, Samsara, Shizhao, Jecar, Bloodshedder, Carl Caputo, Jusjih, Donarreiskoffer, Robbot,
Josh Cherry, Altenmann, Peak, Romanm, Arkuat, Stewartadcock, Merovingian, Sunray, Hadal, Isopropyl, Anthony, Holeung, Lupo, Dina,
Mattwolf7, Centrx, Giftlite, Christopher Parham, Andries, Mikez, Wolfkeeper, Netoholic, Doctorcherokee, Peruvianllama, Everyking,
Subsolar, Curps, Alison, Dmb000006, Bensaccount, Eequor, Alvestrand, Jackol, Delta G, Neilc, OldakQuill, Adenosine, ChicXulub, Doc-
Sigma, Jonathan Grynspan, Knutux, Antandrus, Onco p53, G3pro, PDH, Karol Langner, H Padleckas, Bumm13, Tsemii, JohnArmagh,
Jh51681, I b pip, Jake11, Ivo, Adashiel, Corti, Sysy, Indosauros, A-giau, Johan Elisson, Diagonalfish, Discospinster, Rich Farmbrough,
Guanabot, Cacycle, Wk muriithi, Bishonen, Bibble, Bender235, ESkog, Cyclopia, Kbh3rd, Richard Taylor, Eric Forste, MBisanz, El
C, Rgdboer, Gilgamesh he, Susvolans, RoyBoy, Perfecto, RTucker, Bobo192, Jasonzhuocn, Cmdrjameson, R. S. Shaw, Polluks, Pass-
word~enwiki, Arcadian, Joe Jarvis, Jerryseinfeld, Jojit fb, NickSchweitzer, Banks, BW52, Haham hanuka, Hangjian, Benbread, Es-
poo, Siim, Alansohn, JYolkowski, Chino, Tpikonen, Interiot, Andrewpmk, SlimVirgin, Kocio, Mailer diablo, ClockworkSoul, Super-
Magician, Knowledge Seeker, Cburnett, LFaraone, Gene Nygaard, Redvers, Bookandcoffee, BadSeed, Kznf, RyanGerbil10, Ron Ritzman,
Megan1967, Roland2~enwiki, Angr, Richard Arthur Norton (1958- ), Pekinensis, Woohookitty, TigerShark, Jpers36, Benbest, JeremyA,
Miss Madeline, Sir Lewk, Fenteany, Steinbach, M412k, Wayward, Essjay, Turnstep, Dysepsion, Matturn, SqueakBox, Magister Mathemati-
cae, V8rik, BorisTM, RxS, Sjakkalle, Rjwilmsi, Tizio, Tawker, Yamamoto Ichiro, FuelWagon, Titoxd, FlaBot, Ageo020, Yanggers, RexNL,
Gurch, Alexjohnc3, Fresheneesz, Alphachimp, Chobot, Moocha, Bornhj, Korg, Bubbachuck, The Rambling Man, YurikBot, Wavelength,
Sceptre, Reo On, Jtkiefer, Zafiroblue05, Chuck Carroll, Splette, SpuriousQ, Rada, Derezo, CanadianCaesar, Stephenb, Gaius Cornelius,
CambridgeBayWeather, Yyy, Ihope127, Cryptic, Cpuwhiz11, Wimt, The Hokkaido Crow, Annabel, Sentausa, Shanel, NawlinWiki, Wiki
alf, UCaetano, BigCow, Exir Kamalabadi, Dureo, Mccready, Irishguy, Shinmawa, Banes, Matticus78, Rmky87, Raven4x4x, Khooly59,
Neil.steiner, Misza13, Tony1, Bucketsofg, Dbfirs, Aaron Schulz, BOT-Superzerocool, DeadEyeArrow, Bota47, Kkmurray, Brisvegas,
Mr.Bip, Wknight94, Trigger hippie77, Astrojan~enwiki, Tetracube, Holderca1, Phgao, Zzuuzz, Closedmouth, Dspradau, Pookythegreat,
GraemeL, JoanneB, CWenger, Anclation~enwiki, Staxringold, Banus, AssistantX, GrinBot~enwiki, 8472, DVD R W, CIreland, That Guy,
From That Show!, Eog1916, Wikimercenary, AndrewWTaylor, Sardanaphalus, Twilight Realm, Crystallina, Scolaire, SmackBot, Focal-
Point, Zenchu, Paranthaman, Slashme, TestPilot, Pgk, Bomac, Davewild, Delldot, AnOddName, RobotJcb, Edgar181, Zephyris, Xaosflux,
Gilliam, Ppntori, Richfife, Malatesta, NickGarvey, ERcheck, JSpudeman, Tyciol, Bluebot, Dbarker348, Persian Poet Gal, Ben.c.roberts,
Stubblyhead, Elagatis, MalafayaBot, Moshe Constantine Hassan Al-Silverburg, Deli nk, Rama’s Arrow, Zsinj, Can't sleep, clown will eat
me, Keith Lehwald, DéRahier, Fjool, Onorem, Snowmanradio, Yidisheryid, EvelinaB, Rrburke, Mr.Z-man, SundarBot, NewtN, Nibuod,
Nakon, Drdozer, MEJ119, Smokefoot, Drphilharmonic, Wisco, Wybot, DMacks, PandaDB, Jls043, Mikewall, Kukini, Clicketyclack,
Derekwriter, EMan32x, Rockvee, Akubra, J. Finkelstein, Euchiasmus, Timdownie, Soumyasch, AstroChemist, Hemmingsen, Accurizer,
Kyawtun, Mr. Lefty, IronGargoyle, The Man in Question, MarkSutton, Bhulsepga, Special-T, Munita Prasad, Beetstra, Muadd, Rick-
ert, Bendzh, Aarktica, Johnchiu, Shella, Sijo Ripa, Citicat, Jose77, Sasata, ShakingSpirit, BranStark, Iridescent, Electrified mocha chin-
chilla, Lakers, JoeBot, Wjejskenewr, Tawkerbot2, Dlohcierekim, Bioinformin, MightyWarrior, Jman5, Fvasconcellos, SkyWalker, JFor-
get, GeneralIroh, Porterjoh, Ale jrb, Dread Specter, Insanephantom, Satyrium, Dycedarg, Scohoust, Makeemlighter, Picaroon, KyraV-
ixen, DSachan, CWY2190, Nadyes, THF, Outriggr, ONUnicorn, Icek~enwiki, WillowW, MC10, Michaelas10, Gogo Dodo, Eric Martz,
Ttiotsw, Chasingsol, Studerby, Tawkerbot4, Carstensen, Christian75, Narayanese, Btharper1221, Omicronpersei8, Nugneant, Gimmetrow,
Thijs!bot, Epbr123, Barticus88, StuartF, Opabinia regalis, Sid 3050, Mojo Hand, Headbomb, Marek69, John254, Folantin, James086,
Tellyaddict, Miller17CU94, Dgies, Tim2027uk, Escarbot, Ileresolu, AntiVandalBot, Galilee12, Luna Santin, Settersr, BenJWoodcroft,
AaronY, Jj137, TimVickers, Priscus~enwiki, Sprite89, MECU, JAnDbot, Deflective, Husond, MER-C, Janejellyroll, Andonic, OllyG,
Lawilkin, Acroterion, Magioladitis, Henning Blatt, Karlhahn, Bongwarrior, VoABot II, AuburnPilot, Hasek is the best, Think outside
the box, Roadsoap, Srice13, Stelligent, Eldumpo, Mkdw, Emw, User A1, Lafw, Glen, Rajpaj, DerHexer, JaGa, Megalodon99, Khalid
Mahmood, WLU, Wayne Miller, Squidonius, Seba5618, Hdt83, MartinBot, Kenshealth, Meduban, Dan Gagnon, R'n'B, Player 03, Led-
gendGamer, Paranomia, J.delanoy, Pharaoh of the Wizards, CFCF, Hans Dunkelberg, Boghog, Uncle Dick, Public Menace, Pipe34,
WarthogDemon, Hodja Nasreddin, G. Campbell, Lantonov, Tylerhammond2, LordAnubisBOT, Ignatzmice, Dthzip, Coppertwig, Py-
rospirit, Belovedfreak, GBoran, SJP, AA, Touch Of Light, Shoessss, Juliancolton, Bogdan~enwiki, Burzmali, Jamesontai, Natl1, Winter-
Spw, Pdcook, Kalyandchakravarthy, Mlsquirrel, CardinalDan, Idioma-bot, Montchav, Carl jr., King Lopez, VolkovBot, IWhisky, Mstislavl,
ABF, Ashdog137, Leebo, AlnoktaBOT, VasilievVV, Tiberti, Philip Trueman, TXiKiBoT, Oshwah, Tameeria, JesseOjala, Sam1001,
A4bot, Guillaume2303, Nitin77, Xavierschmit~enwiki, Qxz, Clarince63, Melsaran, Martin451, Leafyplant, LeaveSleaves, Mkv22, Seb
az86556, Fitnesseducation, Mkubica, Sirsanjuro, Hannes Röst, Naturedude858, Spiral5800, Hedgehog33, Pierpunk, Amb sib, Synthe-
bot, Wilbur2012, Falcon8765, Duckttape17, Enviroboy, Vector Potential, Kingjalis3, Brigand dog, Doc James, AlleborgoBot, Kehrbykid,
Gangsta4lif, Frank 212121, Zoeiscow, EmxBot, ThinkerThoughts, Masterofsuspense3, Christoph.gille, SieBot, Graham Beards, Moonrid-
dengirl, Work permit, Sharpvisuals, Winchelsea, Caltas, Iwearsox21, Jipan, Triwbe, Manojdhawade, Yintan, Agesworth, Mfickes, Eganio,
Keilana, Shura58, Radon210, Editore99, Oda Mari, Grimey109, Danizdeman, Paolo.dL, Thishumorcake, Jlaudiow713, Oxymoron83, Nut-
tycoconut, Chenmengen, Jdaloner, Poindexter Propellerhead, Lordfeepness, Fratrep, Maelgwnbot, N96, StaticGull, Mike2vil, Wuhwuzdat,
Mygerardromance, Hamiltondaniel, Ascidian, Dabomb87, Superbeecat, Agilemolecule, Ayleuss, TwinnedChimera, AutoFire, Asher196,
376 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

Lascorz, Tatterfly, Naturespace, Amotz, WikipedianMarlith, Seaniemaster, De728631, ClueBot, The Thing That Should Not Be, Rodhul-
landemu, Plankwalking, Arakunem, Mild Bill Hiccup, Coookeee crisp, CounterVandalismBot, Niceguyedc, Spritegenie, Peteruetz, Chan-
dlerMapBot, NClement, Wardface, DragonBot, Douglasmtaylor, Alexbot, Jusdafax, Jordell 000, Mike713, OpinionPerson, CupOfRoses,
NuclearWarfare, Cenarium, Lunchscale, Jotterbot, Achilles.g, Aitias, Versus22, NERIC-Security, Thinking Stone, ClanCC, Tprentice,
XLinkBot, Ivan Akira, Rror, Capitana, Mifter, Samwebstah, Michael.J.Goydich, Noctibus, Jbeans, ZooFari, Frictionary, Sgpsaros, Doctor
Knoooow, Champ0815, Lemchesvej, HexaChord, Addbot, Some jerk on the Internet, DOI bot, Landon1980, SunDragon34, Ronhjones,
TutterMouse, Fieldday-sunday, Cuaxdon, Nick Van Ni, Cst17, Mentisock, CarsracBot, EconoPhysicist, Mai-tai-guy, Glane23, Anders-
Bot, Omnipedian, Debresser, LinkFA-Bot, RoadieRich, Tassedethe, Numbo3-bot, OffsBlink, Tide rolls, James42.5, Gail, Ettrig, Swarm,
Javanbakht, A K AnkushKumar, Luckas-bot, Yobot, II MusLiM HyBRiD II, Minorfixer, Eric-Wester, Tempodivalse, AnomieBOT, Itln
boy, Xelixed, Galoubet, Piano non troppo, AdjustShift, VK3, Kingpin13, RandomAct, Sonic h, Materialscientist, Yurilinda, Citation bot,
Knightdude99, Neurolysis, Aspenandgwen, LilHelpa, Xqbot, Timir2, Capricorn42, Bihco, Tchussle, Tad Lincoln, Flavonoid, P99am, Ten-
nispro427, Almabot, 200itlove, GrouchoBot, Laxman12, Abce2, Aznnerd123, Omnipaedista, HernanQB, RibotBOT, Pravinhiwale, Al-
truistic Egotist, GhalyBot, Miyagawa, Captain-n00dle, FrescoBot, Tobby72, This doesnt help at all, Citation bot 1, Pinethicket, Bernarddb,
HRoestBot, Katherine Folsom, Jstraining, Curehd, Ascha, My very best wishes, Jauhienij, ActivExpression, Cnwilliams, Tim1357, Mis-
sellyah, FoxBot, TobeBot, Sweet xx, Lotje, Ndkartik, January, Max Janu, Duckyinc2, Specs112, Brian the Editor, Suffusion of Yellow,
Tbhotch, Jesse V., Minimac, DARTH SIDIOUS 2, Usmanmyname, Ripchip Bot, Agent Smith (The Matrix), DASHBot, EmausBot, Cped-
itorial, WikitanvirBot, Immunize, Snow storm in Eastern Asia, 021-adilk, JonReader, Clarker1, ScottyBerg, Joeywallace9, GoingBatty,
Minimac’s Clone, RenamedUser01302013, Hous21, Wikipelli, Commanderigg, SRMN2, Meruem, JSquish, HiW-Bot, Traxs7, Hesham-
science, Futureworldconqueror, Alpha Quadrant, John Mackenzie Burke, AvicAWB, Elektrik Shoos, Bamyers99, H3llBot, Zap Rowsdower,
RODSHEL, Imnoteditinganything, Rajatgaur, Richardmnewton, Codahawk, Wstraub, Hylian Auree, Petrb, Teaktl17, ClueBot NG, East-
ewart2010, Pisaadvocate, Helpful Pixie Bot, Bibcode Bot, BG19bot, Gautehuus, Edward Gordon Gey, Gupta.udatha, Protein Chemist,
NotWith, Smettems, Prof. Squirrel, Smileguy91, Fma69, Dexbot, Wimblecf, Joeinwiki, David P Minde, Evolution and evolvability,
Prokaryotes, Kirtimaansyal, Anrnusna, Monkbot, KasparBot and Anonymous: 1184

• Amino acid Source: https://en.wikipedia.org/wiki/Amino_acid?oldid=672189882 Contributors: AxelBoldt, Tobias Hoevekamp, Magnus

Manske, Kpjas, General Wesc, Marj Tiefert, Mav, Bryan Derksen, Andre Engels, Josh Grosse, Unukorno, Enchanter, PierreAbbat, Fubar
Obfusco, William Avery, Roadrunner, SimonP, Ben-Zin~enwiki, Olivier, Edward, Dwmyers, Lexor, Ixfd64, Looxix~enwiki, Ahoerste-
meier, Glenn, Habj, Llull, Andres, Tristanb, Evercat, Harris7, Ww, Stone, Lfh, Stismail, Stephentaylor, Zoicon5, Selket, Tpbradbury,
Omegatron, Tonderai, MD87, Lumos3, Donarreiskoffer, Gentgeen, Robbot, LuckyWizard, Josh Cherry, Peak, Switchsonic, Stewartad-
cock, Hadal, Wikibot, Diberri, Giftlite, Wizzy, Everyking, Dmb000006, Bensaccount, Jfdwolff, Soren.harward, Eequor, Delta G, Kandar,
Utcursch, Pgan002, Knutux, Antandrus, Onco p53, Xinit, G3pro, Vina, MacGyverMagic, Maximaximax, Advanet, Sam Hocevar, Atem-
perman, Karl Dickman, M1ss1ontomars2k4, Qef, Adashiel, Archer3, Discospinster, Rich Farmbrough, Guanabot, Cacycle, Naive cynic,
Mani1, Billfred, Bender235, El C, Shanes, RoyBoy, ~K, Bobo192, Truthflux, Dungodung, Arcadian, La goutte de pluie, Kjkolb, Tha-
seint, Obradovic Goran, HasharBot~enwiki, Jumbuck, Alansohn, Chino, Oasisbob, Don Reba, Sheehan, Keenan Pepper, Benjah-bmm27,
ABCD, AzaToth, Fritzpoll, Seans Potato Business, Sligocki, Jaw959, BernardH, Stillnotelf, Wtmitchell, ClockworkSoul, Kijitah, Comput-
erjoe, Pauli133, Versageek, Oystertoadfish, Duplode, Ceyockey, Trlblzr, Richard Arthur Norton (1958- ), Borb, JeremyA, Eleassar777,
Joe Beaudoin Jr., Turnstep, Dysepsion, Graham87, Magister Mathematicae, BD2412, BorisTM, DePiep, Sjö, Sjakkalle, Rjwilmsi, Leeyc0,
Moryoav~enwiki, Nandesuka, Molybdenumblue, Yamamoto Ichiro, FlaBot, Cless Alvein, Ausinha, Nihiltres, Crazycomputers, RexNL,
Gurch, Rlee1185, Physchim62, Smithbrenon, Chobot, Chessercat2003, SirGrant, Krishnavedala, Rewster, Bornhj, JesseGarrett, FeldBum,
Antiuser, Bgwhite, WriterHound, JimJ, YurikBot, Wavelength, Mushin, Wolfmankurd, BruceDLimber, Serinde, Chris Capoccia, Rada,
Matteo2000, Yosef1987, Matt Fitzpatrick, Yyy, Shaddack, Ihope127, Maartend8, Wimt, Grafen, Shadowfax0, Yoasif, Khooly59, Dan
Wylie-Sears, Tony1, Ectropist, Nlu, Lt-wiki-bot, KGasso, Cobblet, GraemeL, JeramieHicks, TBadger, CWenger, Tarawneh, Smurrayinch-
ester, Anclation~enwiki, Kubra, Archer7, Maxamegalon2000, GrinBot~enwiki, DVD R W, ViolentRage, Itub, SpLoT, SmackBot, Jedi-
Bookworm, Prodego, McGeddon, Tuckerekcut, Bomac, KocjoBot~enwiki, End3rtheThird, EncycloPetey, Delldot, BiT, Edgar181, Peter-
Symonds, Gilliam, Hmains, Rmosler2100, Master gopher, Kazkaskazkasako, Chris the speller, Dreg743, MalafayaBot, Dabigkid, Deli nk,
Baa, DHN-bot~enwiki, Colonies Chris, Darth Panda, Galizur, Can't sleep, clown will eat me, Snowmanradio, Bisected8, Nuklear, Robma,
Fullstop, James McNally, Richard001, IrisKawling, Smokefoot, Drphilharmonic, Eynar, DMacks, Vina-iwbot~enwiki, Clicketyclack,
Ohconfucius, SashatoBot, Rory096, Harryboyles, Kuru, John, J. Finkelstein, Zaphraud, FrozenMan, Gobonobo, Geoffreynham, Breno,
Coredesat, Pansi gupta, Majorclanger, Blacksmith tb, White.matthew.09, Beetstra, Bendzh, Shinryuu, Optakeover, Ravi12346, Elb2000,
BranStark, Grothmag, Kaarel, Wwallacee, Tawkerbot2, Daniel5127, Orangutan, JForget, CmdrObot, Fedir, Tjodonnell, WeggeBot, Al-
chemistmatt, Nilfanion, Crookshankz227, Ppgardne, Slp1, WillowW, Skoddet, Rifleman 82, Corpx, Shekharsuman, Carstensen, Chris-
tian75, Narayanese, Eribro, Crum375, Amdk8800, Mattisse, Thijs!bot, Epbr123, Hybrid04, Opabinia regalis, TonyTheTiger, Superarthur,
Memty Bot, N5iln, Headbomb, Donjavi, Marek69, WVhybrid, Brichcja, FelixP~enwiki, Aboveleft, Dfrg.msc, FreeKresge, Sikkema, Tran-
shumanist, Natalie Erin, Openlander, Escarbot, Cyclonenim, AntiVandalBot, Luna Santin, Seaphoto, Opelio, Memset, Pro crast in a tor,
TimVickers, North Shoreman, Myanw, Res2216firestar, JAnDbot, Sydney naturopath, Deflective, Aardtek, MER-C, Andonic, TAnthony,
AOL account, .anacondabot, Acroterion, Magioladitis, Bongwarrior, VoABot II, JNW, DWIII, Ling.Nut, Roadsoap, Otivaeey, Animum,
Nucleophilic, Antorjal, Emw, User A1, Cpl Syx, Lvwarren, Kammler1, Fmandog85, Squidonius, Whittlewiki, Patstuart, Monurkar~enwiki,
Cliff smith, MartinBot, XoiiLov3Youuxo55, Tremello, Ustye, Anaxial, Kostisl, CommonsDelinker, Nono64, Captain panda, Berkzafer, Es-
capingLife, Nbauman, Hans Dunkelberg, Boghog, Maurice Carbonaro, HoergerJ, Slow Riot, Hodja Nasreddin, G. Campbell, Gzkn, It Is
Me Here, Toyz, Austin512, Jeepday, Mikael Häggström, Tarotcards, Coppertwig, Toon05, SriMesh, Prilla, Fylwind, Cbeau (usurped),
KylieTastic, Cometstyles, Nikki311, Tiggerjay, Ja 62, CardinalDan, Lights, VolkovBot, LeilaniLad, Philip Trueman, TXiKiBoT, Malljaja,
Rei-bot, Ask123, Qxz, Trevor Wennblom, Rich Janis, JhsBot, Bcharles, Dprust, Knivusa, AgentCDE, !dea4u, AlleborgoBot, NHRHS2010,
EmxBot, Lesterama, SieBot, Ttony21, Graham Beards, Apodtele, Sakkura, Winchelsea, Gerakibot, Stormhawk~enwiki, Matthew Yea-
ger, God Emperor, Alexbook, Andrewjlockley, Keilana, Flyer22, Radon210, Paolo.dL, Hzh, Faradayplank, Eggwadi, Vanished user
oij8h435jweih3, Mayalld, Dr CareBear, Mike2vil, Dabomb87, Azzamsyr, Denisarona, Chem-awb, Naturespace, Sfan00 IMG, Elassint,
ClueBot, Jbening, The Thing That Should Not Be, YassineMrabet~enwiki, Arakunem, Blanchardb, Ajoykt, Excirial, Alexbot, Encyclo-
pedia77, Heckledpie, Tyler, Cenarium, Lovey73, Hsn mhd, Thehelpfulone, GFHandel, Chirpy7, Aitias, Jamil17, Berean Hunter, Wnt,
XLinkBot, Avoided, SilvonenBot, Coolesthunk, RyanCross, LikeHolyWater, Addbot, Proofreader77, Bennnh, DOI bot, Wickey-nl, Bet-
terusername, Otisjimmy1, Kengo1040, Yobmod, Nomad2u001, Jncraton, Leszek Jańczuk, Fluffernutter, Bettingr, MrOllie, EconoPhysi-
cist, Jomunro, Phorbol, AtheWeatherman, Jasper Deng, Quercus solaris, Tide rolls, Teles, Zorrobot, Legobot, Luckas-bot, Yobot, Kartano,
II MusLiM HyBRiD II, The Earwig, KamikazeBot, IW.HG, AnomieBOT, Astronomicalunit, Tryptofish, IRP, AdjustShift, Kingpin13,
Wiki007wiki, Mahmudmasri, Materialscientist, Citation bot, E2eamon, Bellemonde, Elbodno, Jock Boy, Rittard, LilHelpa, FreeRange-
Frog, Ultimate sickness, Xqbot, Sionus, Khajidha, Jeffrey Mall, JWBE, DSisyphBot, Uttam Pal, Teddks, Almabot, J04n, Vandalism
destroyer, ProtectionTaggingBot, ShadowBlade1000, RibotBOT, Amaury, Safiel, L-Tyrosine, Miyagawa, Methcub, SchnitzelMannGreek,
22.1. TEXT 377

A.amitkumar, Legobot III, FrescoBot, Dogposter, Citation bot 1, Javert, Pinethicket, Rushbugled13, RedBot, SpaceFlight89, LosDorks,
Kevinallencrittenden, Jauhienij, TobeBot, Trappist the monk, ‫کاشف عقیل‬, Xook1kai Choa6aur, Vrenator, Diannaa, Weedwhacker128,
Jesse V., Hornlitz, DARTH SIDIOUS 2, EngineerFromVega, Dancojocari, Hajatvrc, NerdyScienceDude, DASHBot, EmausBot, Cpedi-
torial, WikitanvirBot, Immunize, Amenray, GoingBatty, Wrstroud, RenamedUser01302013, Umleashuh, Erickulcyk, TuHan-Bot, K6ka,
AvicBot, JSquish, Fæ, Bollyjeff, Nevin Janzen, Finemann, Bahudhara, Access Denied, A930913, RE73, CountMacula, Llightex, 28bot,
Teaktl17, ClueBot NG, Adamrce, Soks1, Baseball Watcher, Millermk, Kaushlendratripathi, Widr, Helpful Pixie Bot, Ajt496, Bibcode Bot,
Lowercase sigmabot, Wasbeer, Woodoome, Mark Arsten, Dmcarey1, NVCRalston, Hwang hongjoo, 1tennisstar15, Roleren, Shisha-Tom,
Geneticcuckoo, BeachDonkey, LHcheM, Ivan trus, Ducknish, BrendonWSmith, Hannahashley9998, IceMan23is1, James 173, Pwijesek,
Ekips39, CsDix, Sameemian, NinjaSaysPoo, DavidLeighEllis, Bighitters202, Ketabejame, Thanguhs, Jwratner1, Jianhui67, TCMemoire,
Brainiacal, Btheils, Anrnusna, Stamptrader, Kizza1500, TogTMdubs, Ferromagnetic Super-Otter, Jesseh2323, Monkbot, Thetruthanal-
ized, Imdrathlir343, BlueFenixReborn, Great liar, Esquivalience, XxMD95340xX, Rj98743, KasparBot, Irene1840 and Anonymous: 850
• Proteinogenic amino acid Source: https://en.wikipedia.org/wiki/Proteinogenic_amino_acid?oldid=671554011 Contributors: Selket, Rob-
bot, Chris Roy, Nagelfar, Pgan002, Kaldari, Rich Farmbrough, Cacycle, Phoenix Hacker, Arcadian, Keenan Pepper, BrentN, Mindma-
trix, Qchristensen, Rjwilmsi, Gurch, Takometer, Benlisquare, Kkmurray, Leptictidium, ChipperGuy, Itub, SmackBot, Edgar181, Eloil,
Kazkaskazkasako, Chris the speller, Hichris, Uthbrian, Radagast83, Smokefoot, Drphilharmonic, DMacks, Grothmag, Fat64~enwiki, Sti-
fynsemons, Kupirijo, Christian75, Thijs!bot, Erechtheus, BenJWoodcroft, TimVickers, Xact, Squidonius, Mikael Häggström, Phlounder,
Cpt ricard, TXiKiBoT, Kumorifox, Gregogil, Zoasterboy, Agur bar Jacé, Myceteae, Mlaffs, MystBot, Addbot, Willking1979, Tanhabot,
Flakinho, Luckas-bot, Amirobot, Microball, Carolina wren, Wiki007wiki, Citation bot, Xqbot, Capricorn42, Aa77zz, RibotBOT, L-
Tyrosine, Jackroven, Scoutfreak, RjwilmsiBot, Dancojocari, EmausBot, Dcirovic, MRandazzUCSD, GenyAncalagon, Whoop whoop pull
up, Teaktl17, Lanthanum-138, Frietjes, HPBiochemie, ChrisGualtieri, Ivan trus, SophieAthena, Hieu nguyentrung12, CsDix, Doniitoo,
Monkbot, WamSam, MGaloni and Anonymous: 57
• Myoglobin Source: https://en.wikipedia.org/wiki/Myoglobin?oldid=668907862 Contributors: Magnus Manske, Marj Tiefert, Mav, Bryan
Derksen, Alex.tan, Dwmyers, JWSchmidt, Habj, Phil Boswell, Robbot, Marc Venot, Jfdwolff, Revth, Antandrus, Rich Farmbrough, El C,
Wisdom89, Arcadian, Giraffedata, Samulili, Alansohn, Etxrge, Atlant, Mr Adequate, ClockworkSoul, Cburnett, Memenen, BerserkerBen,
Rjwilmsi, FlaBot, Vossman, The Rambling Man, YurikBot, Wavelength, Metalloid, Bhny, Splette, Shell Kinney, Tavilis, Herbertxu, Lt-
wiki-bot, SV Resolution, Digfarenough, That Guy, From That Show!, SmackBot, Liaocyed, Gilliam, RDBrown, The Rogue Penguin,
Smokefoot, Clicketyclack, Spiritia, John, Mgiganteus1, Atakdoug, Fvasconcellos, MaerlynsRainbow, Rifleman 82, Anonymi, Blindman
shady, Thijs!bot, Epbr123, BokicaK, Yongrenjie, TimVickers, Soulbot, Glacian79, Shu99, Adrian J. Hunter, DerHexer, Mmoneypenny,
CommonsDelinker, Nono64, Erexeisen, Boghog, Inslid, Pdcook, Cmastris, VolkovBot, Andrew Su, Vipinhari, A4bot, Shureg, Zybez,
Twooars, ProteinBoxBot, SieBot, Bob98133, C'est moi, Bogwhistle, AnteaterZot, Entropic existence, CounterVandalismBot, Excirial,
Noca2plus, Stenzela, Polly, Tangpoet, Aitias, XLinkBot, Forbes72, MystBot, SkyLined, Addbot, DOI bot, Luckas-bot, Kingpin13, Citation
bot, Jonowen008, CRaines, Br77rino, RibotBOT, Mattis, Some standardized rigour, Jack B108, FrescoBot, Wikipe-tan, D'ohBot, Citation
bot 1, Yahia.barie, ResearchProteins1, SporkBot, Wayne Slam, Kelly222, Donner60, ChuispastonBot, ClueBot NG, Rezabot, Helpful Pixie
Bot, Curb Chain, Bibcode Bot, Jadram2011, Gibbja, Jimw338, Thucyx, JYBot, Liyue2011, Ny5128a, Glaisher, Joseph M. Steinberger,
Monkbot, KasparBot and Anonymous: 114
• Hemoglobin Source: https://en.wikipedia.org/wiki/Hemoglobin?oldid=667511588 Contributors: AxelBoldt, Magnus Manske, Kpjas, Mav,
Taw, Alex.tan, Youssefsan, Christian List, Heron, Jaknouse, Stevertigo, Dwmyers, D, Pathew, Kku, Ixfd64, Ahoerstemeier, Jebba, Julesd,
Habj, Andres, Tristanb, Vivin, Greatpatton, Jay, Tarosan~enwiki, Abscissa, Taxman, Topbanana, Prisonblues, GPHemsley, Donarreiskof-
fer, Robbot, Gak, Academic Challenger, Bkell, Fuelbottle, SoLando, Cek, Diberri, Giftlite, DocWatson42, Pretzelpaws, Alison, Ben-
saccount, Nick04, Ramsus, Jfdwolff, Gilgamesh~enwiki, Kandar, Christopherlin, Alanl, Pgan002, Calm, Onco p53, PDH, Maximaxi-
max, H Padleckas, Zfr, Sam Hocevar, Hellisp, Joyous!, JohnArmagh, Fabrício Kury, Davidfraser, Mike Rosoft, Jkl, Discospinster, Rich
Farmbrough, Ivan Bajlo, Xiggelee, Bender235, Rubicon, Kbh3rd, ReallyNiceGuy, Geoking66, Pinzo, Kwamikagami, Edward Z. Yang,
Shanes, Sietse Snel, Bobo192, Lenov, Elipongo, Dungodung, Arcadian, Ziggurat, Darwinek, Orangemarlin, Jumbuck, Alansohn, Atlant,
Riana, Mac Davis, Bucephalus, ClockworkSoul, TaintedMustard, RJFJR, BerserkerBen, Dejvid, Stemonitis, Unixer, Robert K S, Qad-
dosh, Schzmo, Canderson7, Rjwilmsi, Koavf, Vary, Bruce1ee, Arisa, FlaBot, Doc glasgow, Ysangkok, New299, Nivix, Gurch, Fresh-
eneesz, Rrenner, Silivrenion, Imnotminkus, Silversmith, Phoenix2~enwiki, Mark Yen, Chobot, Hitokirishinji, Peterl, YurikBot, Wave-
length, Matthias.hilty, Whoisjohngalt, RobotE, Sceptre, Hairy Dude, Metalloid, Petiatil, Spaully, SpuriousQ, Hellbus, Eleassar, Pseu-
domonas, Draeco, NawlinWiki, Snek01, Kirika, Natkeeran, Benamies, BOT-Superzerocool, Bota47, DRosenbach, Zzuuzz, Lt-wiki-bot,
KGasso, DGaw, Allens, Jonathan.s.kt, Airconswitch, Zvika, DVD R W, CIreland, Aragan Jarosalam, Luk, SmackBot, Saravask, Triggtay,
Pgk, Blue520, Chairman S., Saxonwhittle, BiT, Edgar181, Alsandro, Srnec, Lukas.S, Zephyris, Gilliam, Eug, Bluebot, Persian Poet Gal,
Master of Puppets, MalafayaBot, Lennert B, Miguel Andrade, DHN-bot~enwiki, Sbharris, Nixeagle, Snowmanradio, Sephirothrr, KevM,
EvelinaB, TonySt, Flyguy649, Radagast83, Nibuod, Pwjb, Smokefoot, Drphilharmonic, A. Rad, Bob Castle, Cottingham, Midorilily,
SashatoBot, Sbmehta, ZenSaohu, Gobonobo, Epingchris, Tillalb, Green Giant, Triacylglyceride, Rmessenger, Kyoko, Cajolingwilhelm,
InedibleHulk, Perditor, Pedrora, Lunajurai, Dan Gluck, TwistOfCain, Iepeulas, Taucetiman, Wwallacee, MottyGlix, Polypipe Wrangler,
PaddyM, Tawkerbot2, Ouishoebean, Fvasconcellos, Sir Vicious, Silversink, JohnCD, Avablass, OMGsplosion, ShelfSkewed, WeggeBot,
TheTito, Funnyfarmofdoom, Pseudo clever, Icek~enwiki, A876, Rifleman 82, Gogo Dodo, Was a bee, Jared Wilmoth, Carstensen, Sep-
tagram, Aldis90, PKT, Thijs!bot, Epbr123, Peter morrell, ChunkySoup, Opabinia regalis, LeeG, Andrewko, Teh tennisman, Hazmat2,
Mojo Hand, Cwtyler, Moulder, DmitTrix, West Brom 4ever, Doyley, Nick Number, Anatoly IVANOV, Charles Brooking, Mentifisto,
AntiVandalBot, Crabula, TimVickers, Tjmayerinsf, Darklilac, Blu3d, Fallendarling, JAnDbot, Deflective, MER-C, Dannyt101, Ph.eyes,
Savant13, Perlygatekeeper, Magioladitis, WolfmanSF, Aneurysmal, VoABot II, Myxoma, Fallon Turner, Appraiser, JRamlow, Twsx,
CS46, WhatamIdoing, Loonymonkey, Adrian J. Hunter, Ym3, Scottalter, FisherQueen, MartinBot, Mmoneypenny, STBot, BetBot~enwiki,
CommonsDelinker, Nono64, Leyo, Sherybatta, Pdeitiker, Nieren, Pinot, J.delanoy, Bogey97, Hans Dunkelberg, Boghog, RebootThal-
heimer, Bombhead, Gzkn, Wouterblox, Mikael Häggström, LittleHow, Belovedfreak, NewEnglandYankee, Vainamainien, Treisijs, Lex-
oka, X!, VolkovBot, Man12345, VasilievVV, Philip Trueman, TXiKiBoT, Mogsmar5, Miranda, Sk741~enwiki, Csv028, Richthewitch,
Martin451, Headleyp, BotKung, Madhero88, Beepu, Brian Huffman, Michaeldsuarez, Carlosisgay, Amb sib, Synthebot, Ziphon, Cmcni-
coll, AdrianaW, Temporaluser, Northfox, Qworty, Twooars, AlleborgoBot, Mah131, TheAlmightyEgg, Petergans, EmxBot, Muzzypatmn,
Ramrajesh, SieBot, BotMultichill, Platinumbuddha, Gerakibot, Dawn Bard, LeadSongDog, Julianva, Momo san, Oxymoron83, Nutty-
coconut, EMSPhydeaux, Lightmouse, Macy, Jojocurler, Spartan-James, Mike2vil, Hamiltondaniel, Maralia, Rabend, Dereck poliink, Si-
tush, Escape Orbit, Naturespace, ImageRemovalBot, Forluvoft, WikipedianMarlith, ClueBot, Master of darkness 666, The Thing That
Should Not Be, Isaac.holeman, Yikrazuul, SuperHamster, CounterVandalismBot, LizardJr8, DragonBot, Excirial, Heathmoor, Jusdafax,
Three-quarter-ten, Funkadan, Winston365, Pmm530, Vgree 01, Beachbutt66, Valpe, Sharksoup, DumZiBoT, LostLucidity, SwirlBoy39,
Mitch Ames, WikHead, Vianello, Lemchesvej, HexaChord, Anticipation of a New Lover’s Arrival, The, CalumH93, BlackBeast, Addbot,
378 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

Freakmighty, DOI bot, Neptunecradle, Wickey-nl, Friginator, Rhiani-ani-on, OmgItsTheSmartGuy, Helios87, MartinezMD, Zaheer12a,
Low-frequency internal, CanadianLinuxUser, Diptanshu.D, Hroychow, LinkFA-Bot, Quercus solaris, Kisbesbot, Numbo3-bot, Tide rolls,
Notcart, Ettrig, Legobot, Chaldor, Luckas-bot, Yobot, Scientificone, El piel, AnomieBOT, Master of Pies, Macquaire, Jim1138, Galou-
bet, Kingpin13, Sz-iwbot, Materialscientist, Citation bot, Aleph Infinity, Reyps, Xqbot, Quazgaa, Kisher07, DSisyphBot, GrouchoBot,
Melman14, Shirik, GorgeCustersSabre, Alvin Seville, Sercretions101, Rainald62, Shadowjams, Erik9, Some standardized rigour, Jack
B108, Joeshmoe123123123, FrescoBot, Tobby72, Uazikoff, Commit charge, Atlantia, Citation bot 1, Natisto, Pinethicket, I dream of
horses, Recipe For Hate, Achaemenes, Codwiki, Ezhuttukari, Kinberg1, Corinne68, TobeBot, ZarathustraD, Black Cat Claws, Kalaiarasy,
Vrenator, Reaper Eternal, Leonid 2, Dusty777, King of the Eagles, Gator0929, Difu Wu, Shawthorn, Mean as custard, RjwilmsiBot,
Doc.mari, Phlegat, Priyankadaga, Chad.burrus, EmausBot, John of Reading, Orphan Wiki, Immunize, Solarra, The Mysterious El Willstro,
Tommy2010, Wikipelli, Baron von Zandt, JSquish, Deviceauthor1, Aka ninja69, Fæ, Josve05a, Lateg, Emil Teofanov, IGeMiNix, Brand-
meister, Coasterlover1994, L Kensington, Correctaboot, Donner60, Kittenono, Smodtactical, Staticd, Will Beback Auto, ClueBot NG,
Ccevo2010, Bhca, GolfYankee, Rainbowwrasse, Snotbot, Braincricket, Jordanmif, Widr, Helpful Pixie Bot, Heli1062, Jylothr, BG19bot,
Alain.michalowicz, Mynameisnoted, Neøn, AhMedRMaaty, Dan653, Mark Arsten, Becksdrake, CitationCleanerBot, Hurricanefan24,
Mejoribus, Jamessmith2011, AWeenie, Yosaphbridge, Gladissk, Tutelary, JGM73, Testem, ChrisGualtieri, GoShow, JesseAlanGordon,
MadGuy7023, Dexbot, HerbVick, Wimblecf, Wywin, Guidemodel, Darthredpen, Ekips39, Mstb42, Vgriffeth, Tentinator, Jakec, Anan-
thkamath1995, Evolution and evolvability, Boopoodoo, VeryCrocker, JaconaFrere, More.suraj33, Dodgeb2, Monkbot, MikeTheEditor104,
Mattythefatty123, NewEnglandDr, BethNaught, CanadianJane, Amortias, Yestefanov, Mahnifez, IAmAwesomeAndTheCoolestPersonEv-
err, Ah91086, Orduin, KcBessy, KasparBot and Anonymous: 736
• Enzyme catalysis Source: https://en.wikipedia.org/wiki/Enzyme_catalysis?oldid=668859109 Contributors: Alan Liefting, Dratman,
Clemwang, Rich Farmbrough, Arcadian, Ceyockey, Woohookitty, Rjwilmsi, Icelight, Daniel Mietchen, Banus, Bomac, Zephyris, Hmains,
Colonies Chris, Rrburke, Mion, Ben Moore, Simon12, Rifleman 82, Hughdbrown, Thijs!bot, Opabinia regalis, NorwegianBlue, TimVick-
ers, Wikidudeman, Emw, Squidonius, R'n'B, Leyo, BigrTex, Perkinsonj, LordAnubisBOT, KylieTastic, Pdcook, Jamiejoseph, Broadbot,
HiDrNick, Kosigrim, ClueBot, Niceguyedc, Jkhwang, Vanisheduser12345, Dthomsen8, Addbot, Jacopo Werther, DOI bot, Arbitrarily0,
AnomieBOT, Citation bot, Bci2, GrouchoBot, RibotBOT, Citation bot 1, Citation bot 4, Stefano Garibaldi, RjwilmsiBot, John of Reading,
Dcirovic, Dspoel, Beta cafe, RockMagnetist, Peter Karlsen, ClueBot NG, Antiqueight, Curb Chain, Bibcode Bot, BattyBot, ChrisGualtieri,
Parker.deWaal, Cerabot~enwiki, A. Foigel, Evolution and evolvability, Jwratner1, Monkbot, Sayarizwan, Pitchcapper and Anonymous: 46
• Enzyme kinetics Source: https://en.wikipedia.org/wiki/Enzyme_kinetics?oldid=669761825 Contributors: Graft, Michael Hardy, Shyamal,
SebastianHelm, Samsara, Raul654, Diberri, Alan Liefting, Giftlite, Adenosine, Sonjaaa, Ukexpat, Clemwang, Qef, Poccil, Rich Farm-
brough, Cacycle, ESkog, Bobo192, R. S. Shaw, Brim, Arcadian, Storm Rider, Alansohn, SnowFire, Stillnotelf, ClockworkSoul, Suruena,
Cmprince, Gene Nygaard, Kmg90, Dmol, Bbatsell, Karam.Anthony.K, V8rik, Kane5187, Rjwilmsi, Koavf, Rschen7754, Brighterorange,
RobertG, Sodin, OpenToppedBus, YurikBot, Hede2000, Chaser, Rsrikanth05, Kimchi.sg, Wknight94, Mastercampbell, AndrewWTay-
lor, Itub, KnightRider~enwiki, SmackBot, Espresso Addict, Saravask, Slashme, Kjaergaard, TheTweaker, Yaser al-Nabriss, Chris the
speller, RDBrown, Moonsword, Flyguy649, Xcomradex, Richard001, Mion, Vina-iwbot~enwiki, Scientizzle, Mgiganteus1, Knights who
say ni, Kyoko, SandyGeorgia, Domitori, Outriggr, Pro bug catcher, Dr Zak, WillowW, Carstensen, Kozuch, Thijs!bot, Opabinia regalis,
Java13690, BokicaK, Luna Santin, TimVickers, Gökhan, Igodard, DRHagen, WolfmanSF, Jeff Dahl, Shauun, Economo, Adrian J. Hunter,
MartinBot, R'n'B, Leyo, RockMFR, Spidrak, Nigholith, Chymo72, JoNo67, BanjoCam, Xiahou, VolkovBot, Alexandria, Hannes Röst,
CarinaT, Jacobandrew2012, Wabaman44, Sxenko, Britzingen, SieBot, The Parsnip!, Oda Mari, Lightmouse, BecR, A2a2a2, Forluvoft,
ClueBot, Snigbrook, The Thing That Should Not Be, Spoladore, Blanchardb, Tom Doniphon, ToNToNi, Joshwa-hayswa, Davo22, Fourth-
hour, Xijkix, Dasdasdase, Manysplintered, Legalvoice123, Rasikraj, I need a game, Ruute, NuclearWarfare, Muro Bot, Dana boomer,
Wnt, Addbot, DOI bot, Laurinavicius, MrOllie, Download, CountryBot, Luckas-bot, Yobot, AnomieBOT, Materialscientist, Citation bot,
Angmar09, Xqbot, 08cflin, Rhodydog, Some standardized rigour, FrescoBot, Citation bot 1, Evenap, Stefano Garibaldi, Mauegd, Tbhotch,
Onel5969, Eskeptic, RjwilmsiBot, Todd40324, Oliverlyc, Tommy2010, Tolly4bolly, JanVerstraete, ClueBot NG, Michael A. Wilkins, Sa-
vantas83, TheoThompson, Helpful Pixie Bot, Leonxlin, Anylai, NotWith, C.Rose.Kennedy.2, Dlituiev, Joannatrykowska, ChrisGualtieri,
Dexbot, DionT71, 069952497a, Evolution and evolvability, Monkbot, Chaan19881, Pratyay Seth, Finagle29, Simon kinyanjui and Anony-
mous: 134
• Lipid Source: https://en.wikipedia.org/wiki/Lipid?oldid=671519742 Contributors: Magnus Manske, Marj Tiefert, Sodium, Mav, Stephen
Gilbert, Ubiquity, Lir, Patrick, Ixfd64, Karada, 168..., Ellywa, Ahoerstemeier, Mac, JWSchmidt, Nikai, Jedidan747, Mxn, HolIgor,
Dcoetzee, Tb, Saltine, Bevo, Lunchboxhero, Donarreiskoffer, Robbot, Mayooranathan, Stewartadcock, HaeB, Dina, DarkHorizon, Dave6,
Marc Venot, Giftlite, Nunh-huh, Everyking, Michael Devore, Bensaccount, Jfdwolff, SWAdair, Edcolins, Kandar, Utcursch, Andycjp,
Toytoy, Cckkab, Quadell, Antandrus, Alteripse, Karol Langner, Neutrality, Mike Rosoft, Felix Wan, Rich Farmbrough, Mani1, Hap-
siainen, Sten, Joanjoc~enwiki, RoyBoy, Adambro, Stesmo, Orbst, Shenme, Arcadian, Giraffedata, Physicistjedi, Daf, Pschemp, Sam
Korn, Haham hanuka, Pearle, Ranveig, Jumbuck, Alansohn, Etxrge, Arthena, Walkerma, Velella, ClockworkSoul, Cburnett, Garzo, Cey-
ockey, Cimex, Mivadar, Cruccone, Eleassar777, Fenteany, Schzmo, Plw, Marudubshinki, GFP~enwiki, Graham87, V8rik, BorisTM,
Sjakkalle, Rjwilmsi, JHMM13, Tangotango, MZMcBride, Crazynas, Yamamoto Ichiro, FlaBot, RobertG, Nivix, RexNL, Gurch, Jrtay-
loriv, Travis.Thurston, Chobot, Gwernol, The Rambling Man, YurikBot, Wavelength, Borgx, Ashleyisachild, Dannyhoffman, Matanya
(renamed), Sceptre, Reo On, Shaddack, Pseudomonas, Gustavb, Wiki alf, ViperBite, AeonicOmega, Tjarrett, Bobak, Syrthiss, Dead-
EyeArrow, Bota47, Derek.cashman, Elkman, Nlu, FF2010, Zzuuzz, Lt-wiki-bot, DVD R W, Eog1916, Sardanaphalus, Dybdahl, Smack-
Bot, Ashill, TestPilot, Ikip, Bomac, Thunderboltz, Chairman S., S charette, Leptonsoup337, Edgar181, Zephyris, Gilliam, Quidam65,
Bluebot, NCurse, Tree Biting Conspiracy, Lennert B, Octahedron80, DHN-bot~enwiki, Darth Panda, Enigma55, Myrryam, Can't sleep,
clown will eat me, Roadnottaken, VMS Mosaic, Addshore, Nakon, Richard001, Drphilharmonic, Doodle77, Where, Richard0612, Click-
etyclack, Bioashok, Visium, Platonides, Mouse Nightshirt, Kuru, Andymc, Mgiganteus1, Mr. Lefty, Special-T, Spook`, ElBeeroMan,
Sasata, Esoltas, Iridescent, Harvy2004, JoeBot, Kelly Katula, Courcelles, Daniel5127, CalebNoble, JForget, CmdrObot, Aherunar, Woud-
loper, Hardrada, Casper2k3, TheTito, Kupirijo, Reywas92, Rifleman 82, Wildnox, Tawkerbot4, Shirulashem, Christian75, Chrislk02,
Narayanese, Krylonblue83, Epbr123, Redwullf, Headbomb, Miller17CU94, CharlotteWebb, AntiVandalBot, Why My Fleece?, KP Botany,
Autocracy, TimVickers, Darklilac, Fireice, AubreyEllenShomo, Myanw, Dan4636, JAnDbot, Husond, MER-C, FaerieInGrey, Sangak, Pe-
dro, Bongwarrior, VoABot II, Kajasudhakarababu, Bulbeck, Lunkwill42, User A1, Gomm, DerHexer, WLU, Olegkolesnikov, MartinBot,
NochnoiDozor, 52 Pickup, Anaxial, Mschel, Ryanreednro, TLF1981, Captain panda, Pharaoh of the Wizards, Trusilver, EscapingLife,
Peter Chastain, Hodja Nasreddin, SubwayEater, Jadeogle, Squeezeweasel, TheUnionBlood, Mikael Häggström, Coppertwig, Pyrospirit,
AntiSpamBot, Fylwind, KylieTastic, ThePointblank, Idioma-bot, Deor, MEHMEHMEHMEH, EchoBravo, Quentonamos, Philip True-
man, TXiKiBoT, Oshwah, BuickCenturyDriver, Showjumpersam, Rei-bot, Qxz, Big Papa 13, JhsBot, LeaveSleaves, Vgranucci, King003,
Jdude89, Madhero88, Chaffers, Burntsauce, Quantpole, Sfmammamia, NHRHS2010, Steven Weston, D. Recorder, SieBot, Sakkura,
Nathan, Keilana, Bentogoa, Flyer22, Qst, Oiws, Pradilla94, Maryrebecca, Hiei-Touya-icedemon, Mike2vil, SallyForth123, Wikipedian-
Marlith, Vreezkid, Loren.wilton, ClueBot, Artichoker, Jvcallaway, The Thing That Should Not Be, Taroaldo, Compaddict11, MchRj2,
22.1. TEXT 379

Michaplot, WiseManOnTheMountain, Nikolaevna, Boosmith, Excirial, Eeekster, Vaz222, Rubylover234, Cenarium, Bergamo~enwiki,
Thingg, Aitias, Kruusamägi, Lmaps, Dakilla15, XLinkBot, Tullywinters, Knopfkind, Bagelboi, Actam, Avoided, NellieBly, Mifter, Jin-
Jian, Lemchesvej, Yelsaimery, Addbot, DOI bot, Wickey-nl, Ronhjones, Fieldday-sunday, Download, EconoPhysicist, Glane23, Tahmmo,
DubaiTerminator, Tide rolls, Quantumobserver, Albert galiza, Javanbakht, आशीष भटनागर, Luckas-bot, Nlaeditor, Fraggle81, P1ayer,
R500Mom, Tempodivalse, 61 88 131 149a, AnomieBOT, Choij, Hughesdavidw, Giants27, Materialscientist, Citation bot, Frankenpuppy,
Muffinman123123, Carturo222, Xqbot, Hoops32, Addihockey10, JimVC3, Capricorn42, GrouchoBot, RibotBOT, Eboireau, Markaco-
hen, Miyagawa, Bekus, Sphinxlipos, LucienBOT, 27 Juni, Curiousgeorgethemonkey, Madfalcon108, Citation bot 1, Niazac, Pinethicket, I
dream of horses, Boulaur, Jonesey95, Nanominori, AmphBot, A8UDI, OrcaMorgan, Ezhuttukari, SpaceFlight89, Pbsouthwood, Medicin-
eMan555, Jauhienij, Tim1357, FoxBot, ‫کاشف عقیل‬, Musselboy, JimBrownish, SeoMac, Katgabrielle, Tbhotch, Jesse V., Andrewx96,
DARTH SIDIOUS 2, Mrsmosher, RjwilmsiBot, Sion55, Alice Davidson, Daniel Cliff, Immunize, Costas78~enwiki, Dewritech, Primefac,
Jax0527, Tommy2010, Wikipelli, We hope, SporkBot, Wayne Slam, Ocaasi, Rcsprinter123, NYMets2000, MonoAV, ChuispastonBot,
DASHBotAV, ClueBot NG, Widr, CasualVisitor, Helpful Pixie Bot, Nothing98765432154, NotWith, Vanischenu, Shisha-Tom, Neu-
labs, Mitality, Prof. Squirrel, Khazar2, Illia Connell, BrightStarSky, TwoTwoHello, Logan.Phospholipid, Keroru, Epicgenius, Tentinator,
Wuerzele, Ginsuloft, AddWittyNameHere, Huscarlkarl, Anrnusna, Nothingserious, Monkbot, BethNaught, Rakeshyashroy, Jonoallen22,
Blazer32100, Gingee41100, Physicsmathftw, Davidparklee, Johnbender01, Forscienceonly, Aaqib mohiuddin and Anonymous: 651
• Biological membrane Source: https://en.wikipedia.org/wiki/Biological_membrane?oldid=663048466 Contributors: Magnus Manske,
Marj Tiefert, SimonP, Lexor, 168..., Naddy, Alan Liefting, Gtrmp, Bensaccount, JuanitaJP, Karol Langner, Adashiel, CALR, R. S.
Shaw, Arcadian, La goutte de pluie, Pschemp, Alansohn, RyanGerbil10, LadyofHats, BorisTM, FlaBot, Margosbot~enwiki, Nihiltres,
RobyWayne, YurikBot, Reo On, Sjb90, Spike Wilbury, Bota47, WAS 4.250, SmackBot, Apers0n, Bluebot, TimBentley, RDBrown,
Drphilharmonic, Lunarbunny, Sadalmelik, Chrisahn, Icek~enwiki, Skittleys, AntiVandalBot, Widefox, Smartse, JAnDbot, PhilKnight,
Adrian J. Hunter, User A1, Squidonius, Rosentod, Hodja Nasreddin, Cmichael, Dabombg, Zidonuke, Jvbishop, Shanata, TCO, JerrySteal,
Thorncrag, Elassint, Animeronin, NERIC-Security, Jytdog, Aceofhearts1968, LaaknorBot, EconoPhysicist, Tide rolls, Jarble, Legobot,
Yobot, AnomieBOT, Madman Ven Colt II, Citation bot, ArthurBot, Biophysik, FrescoBot, Brghntr, Lotje, Vrenator, 777sms, GhiathKhlif,
RA0808, JSquish, ZéroBot, JS Hoyer, Alpha Quadrant (alt), Wayne Slam, Δ, ClueBot NG, Aejohnst, Fylbecatulous, Kjmarjun, Eorkfl102,
Mark viking, Hastings biology, Monkbot, LordKevinReuter, NewEnglandDr, Rakeshyashroy, MandanaM, KasparBot and Anonymous: 41
• Membrane protein Source: https://en.wikipedia.org/wiki/Membrane_protein?oldid=668602679 Contributors: Magnus Manske, Lexor,
Ixfd64, 168..., JWSchmidt, Lfh, Grendelkhan, Stewartadcock, Michael Devore, Jfdwolff, Neutrality, El C, Arcadian, Jag123, Pschemp,
Alansohn, Fritzpoll, Graham87, Rjwilmsi, Yamamoto Ichiro, Gurch, Chobot, ShaiM, SmackBot, Stepa, Bluebot, Baronnet, Robomaey-
hem, FrozenMan, Sasata, Gosolowe, Cydebot, Road Wizard, Asymptote, Thijs!bot, Connormah, VoABot II, DerHexer, R'n'B, Com-
monsDelinker, Hodja Nasreddin, D Wells, Pdcook, AlnoktaBOT, Tameeria, Meters, Snapouse, AlleborgoBot, SieBot, YonaBot, OKBot,
Kmcallenberg, Boobermonkey, ClueBot, NickCT, Drmies, Niceguyedc, Kcgi, Peteruetz, DragonBot, Jusdafax, Thingg, Namenotek, Vo-
jtěch Dostál, NellieBly, CalumH93, Addbot, Bjørn P Pedersen, Luckas-bot, Yobot, Ramamoor, IW.HG, AnomieBOT, BIONICLE233,
GrouchoBot, FrescoBot, Citation bot 1, MastiBot, My very best wishes, Ripchip Bot, Gould363, Dcirovic, Mike of Wikiworld, RockMag-
netist, ClueBot NG, A09147801, Dtroestler, Radowell, Helpful Pixie Bot, Lalehkam, BG19bot, CatPath, Ksalcines, Rumadatme, Vish-
nukaranayil, Bradastaley, InsaneInnerMembrane, Grzegorznadolski, Kfh123, Mark viking, Evolution and evolvability, Monkbot, NewEng-
landDr, Rakeshyashroy, Carolinegreen26 and Anonymous: 58
• Cell membrane Source: https://en.wikipedia.org/wiki/Cell_membrane?oldid=668915488 Contributors: Magnus Manske, Joao, Sodium,
Mav, Bryan Derksen, Peterlin~enwiki, Heron, Stevertigo, DennisDaniels, Frecklefoot, Dwmyers, Lir, Zocky, Ixfd64, Tregoweth, 168...,
Ellywa, Elano, Jebba, JWSchmidt, Habj, Andres, Evercat, Selket, Saltine, Samsara, Shizhao, Bjarki S, Stormie, Johnleemk, Robbot, Chris
73, Akajune, Naddy, Academic Challenger, Jondel, JesseW, HaeB, Diberri, Tobias Bergemann, Giftlite, Jyril, Tom harrison, Ferkelpa-
rade, HangingCurve, Peruvianllama, Everyking, No Guru, Bensaccount, Jfdwolff, Saaga, Luigi30, Jackol, Kandar, Adenosine, Pgan002,
Antandrus, Onco p53, Phe, Ian Yorston, G3pro, PDH, Jossi, Karol Langner, PFHLai, Dcandeto, Fermion, Trevor MacInnis, Mike Rosoft,
Freakofnurture, ClockworkTroll, DanielCD, Chris j wood, Discospinster, Rich Farmbrough, Xxlitleonexx, Mani1, Zenohockey, Shanes,
Art LaPella, Adambro, Bobo192, Truthflux, Smalljim, Jeppelbaum, Wisdom89, Elementalish, Arcadian, Kjkolb, Pschemp, Nhandler,
Axyjo, Krellis, Nsaa, Ruwan~enwiki, Luckyluke, Jumbuck, Zachlipton, Alansohn, Mrees1997, Jared81, Arthena, Riana, Lectonar, Mac
Davis, Jaw959, Mrholybrain, Bart133, Velella, ClockworkSoul, Tycho, Mcmillin24, Redvers, Ringbang, Tainter, Ceyockey, Harvestdancer,
Adrian.benko, Yousaf465, Rvlaw, Isfisk, Firsfron, Woohookitty, Quadduc, John Cardinal, JeremyA, MONGO, Eleassar777, Fenteany,
Andrea.gf, LadyofHats, MarcoTolo, Zpb52, Tslocum, Graham87, BorisTM, RxS, Canderson7, Drbogdan, Rjwilmsi, Vary, SMC, Thisis-
mikesother, HappyCamper, Fred Bradstadt, Maxim Razin, FlaBot, Windchaser, SouthernNights, Andy85719, RexNL, Gurch, Chobot,
DVdm, Skela, Bgwhite, NSR, Gwernol, Cornellrockey, Banaticus, MatthiasG, YurikBot, Wavelength, Reo On, Laserion, Epolk, Spuri-
ousQ, Stephenb, Rainbowjinjo, Gaius Cornelius, Eleassar, Chaos, Pseudomonas, Wimt, Tavilis, Thane, Draeco, Sentausa, NawlinWiki,
Wiki alf, Grafen, NickBush24, Brauigja, Nick, Tony1, Somoza, Wknight94, TheSeer, Phgao, Lt-wiki-bot, Closedmouth, Pb30, Nemu,
ZabMilenko, BorgQueen, JoanneB, Levil, CWenger, LeonardoRob0t, JLaTondre, Kubra, Katieh5584, Some guy, DVD R W, SpLoT,
Amalthea, SmackBot, ThreeDee912, Incnis Mrsi, Thunderboltz, WookieInHeat, Delldot, Jab843, Flying Canuck, Knute1232001, Half-
Shadow, Lukas.S, Gaff, Müslimix, Yamaguchi , Gilliam, NickGarvey, JSpudeman, Radcen, Seto Kaiba~enwiki, Wigren, Chris the
speller, RDBrown, SMP, Jprg1966, Deli nk, Akanemoto, Emperor Banh, Tripledot, J. Spencer, Darth Panda, MaxSem, Can't sleep, clown
will eat me, Fat Ted~enwiki, EvelinaB, Claire van der Meer, Echtoran, Khukri, Nakon, John D. Croft, Richard001, Drphilharmonic, Rex1
Wiki*, Jóna Þórunn, Kukini, Ged UK, Visium, Krashlandon, AThing, DO11.10, Soap, Kuru, Soumyasch, JoshuaZ, Hannah14, Mr. Lefty,
Ben Moore, A. Parrot, MarkSutton, Slakr, Stwalkerster, Munita Prasad, Hoobajube, Bendzh, Serephine, Citicat, Zapvet, Sasata, Wahre-
Jakob, BananaFiend, Iridescent, TwistOfCain, Blehfu, Adambiswanger1, Courcelles, Gornly, PaddyM, Tawkerbot2, Lahiru k, JForget,
Ale jrb, WeggeBot, Moreschi, Dss971, Darrentcook, Yaris678, Gogo Dodo, Corpx, Tawkerbot4, DumbBOT, Chrislk02, Crana, Viridae,
Thijs!bot, Epbr123, Qwyrxian, Xcfrommars, N5iln, JohnstonDJ, Marek69, Frank, CharlotteWebb, Sean William, Natalie Erin, Eleuther,
Cyclonenim, AntiVandalBot, JordanDeLong, Luna Santin, Seaphoto, Prolog, TimVickers, Smartse, Dylan Lake, Chill doubt, Myanw,
Joehall45, Res2216firestar, IrishFBall32, JAnDbot, MER-C, Hut 8.5, Wasnik, LittleOldMe, Bencherlite, WolfmanSF, Schmackity, Bong-
warrior, VoABot II, Think outside the box, Twsx, Foochar, Catgut, BatteryIncluded, ArmadilloFromHell, Wesleywillis, DerHexer, Evy
Surender, WLU, Gludwiczak, Patstuart, Jonomacdrones, Erpbridge, MartinBot, Arjun01, GillPer, Bissinger, Howl5, Anaxial, AlexiusHor-
atius, Nono64, Tgeairn, J.delanoy, Pharaoh of the Wizards, Trusilver, Carre, Bogey97, Nbauman, Xcompton, Hodja Nasreddin, Fire-
brother, Faradan, Darkmanx806, Ncmvocalist, McSly, Mikael Häggström, ROFLCOPTERone1!, SteveChervitzTrutane, Chiswick Chap,
NewEnglandYankee, Kavanagh21, Phizit, EMT1871, Gffkr, KylieTastic, Juliancolton, Burzmali, Alan012, Pdcook, Ray Glock-Grueneich,
Ronbo76, E-lord, Aliyarockzharder, Cedmudowicz, Spellcast, Lights, VolkovBot, 6osama9, ABF, Temporarily Insane, Thisisborin9, Doc-
torkismet, The Duke of Waltham, Jeff G., Indubitably, HeckXX, Keelan1993, Soliloquial, Philip Trueman, Chiros Sunrider, TXiKi-
BoT, Java7837, Hqb, Porkrind, Crohnie, Qxz, Someguy1221, Jackfork, LeaveSleaves, Jvbishop, BotKung, Wingedsubmariner, Maxim,
380 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

Shanata, Lerdthenerd, Gen. von Klinkerhoffen, Ziphon, Enviroboy, Vector Potential, Burntsauce, Lagatapirata, RaseaC, Watermelon-
Potion, Novadeath69, Logan, PGWG, NHRHS2010, Gaelen S., Akap007, SieBot, Ttony21, Nawlinsprincess, Gerakibot, Hacker312,
LeadSongDog, Ygramul, GlassCobra, Keilana, Flyer22, Terper, Sovbeos, Dhatfield, ScAvenger lv, JSpung, Oxymoron83, Nuttycoconut,
Kochipoik, Elmyr, OKBot, Maelgwnbot, Torchwoodwho, Mygerardromance, PerryTachett, Joshwalker, Troy 07, Explicit, Ytraere, Mar-
tarius, Sfan00 IMG, Tanvir Ahmmed, Elassint, ClueBot, GorillaWarfare, The Thing That Should Not Be, Wwheaton, Mild Bill Hiccup,
Neffyring, Uncle Milty, Boing! said Zebedee, WDM27, Willybobbyjimbob, Masterpiece2000, Catfish Jim and the soapdish, Excirial,
Deino Wanthers, NuclearWarfare, Arjayay, Honkbird, Thingg, Rswarbrick, Ranjithsutari, SoxBot III, Apparition11, XLinkBot, Stickee,
Rror, Little Mountain 5, Avoided, SilvonenBot, Mifter, Noctibus, Daughter of Mímir, Addbot, Willking1979, Tsealy6, Some jerk on
the Internet, Atethnekos, Friginator, Ronhjones, Fieldday-sunday, Cira030, Sleepaholic, Kcox101, Anchit virmani, LAAFan, Glane23,
Bassbonerocks, Debresser, Pigglesworth, LinkFA-Bot, West.andrew.g, Briannna21a, Itfc+canes=me, Dick Mcgee, Tide rolls, Bfigura’s
puppy, Chronus1029, AlexJFox, LuK3, Jackelfive, Chaldor, Luckas-bot, Yobot, Tohd8BohaithuGh1, Fraggle81, Disturbedling, Medical
geneticist, Gg4u, AnomieBOT, Andrewrp, Exp HP, Fatal!ty, 1exec1, Piano non troppo, Glagolev, BlahSpecialK, Giants27, Materialscien-
tist, I.am.not.communist, Citation bot, E2eamon, Radicalrad44, RenesmeeEmilyCullen, GB fan, Biophysik, Tamil94, Xqbot, Eastssideboy,
Nasnema, Sellyme, NFD9001, The Evil IP address, Gd231, GrouchoBot, Abce2, ProtectionTaggingBot, Mathonius, Doulos Christos, Iced-
Nut, Howard McCay, A.amitkumar, Legobot III, FrescoBot, HJ Mitchell, Wifione, BitingHobo, Gene-va, ClickRick, Pe-Jo, Pinethicket,
10metreh, LinDrug, Ultimatewall5, Meaghan, My very best wishes, Reconsider the static, FoxBot, Tubarun, Villatorresronaldo, ItsZippy,
Vrenator, Tomnewman12345, JohnFFields, Amkilpatrick, Merlinsorca, Diannaa, Tbhotch, Lee726, DARTH SIDIOUS 2, Obankston,
Tidema, Uanfala, HotBabyBoy31097, Pinkbeast, EmausBot, Domesticenginerd, Immunize, Ajraddatz, Nuujinn, GoingBatty, RA0808,
RenamedUser01302013, NotAnonymous0, Slightsmile, Tommy2010, JSquish, The Irish Mule, Pewnedtotal, Access Denied, Collector-
ben, Wayne Slam, Ocaasi, Mnlkpoq, GeorgeBarnick, Brandmeister, L Kensington, Coolidays, Donner60, Wannabekiller, RockMagnetist,
Matthewrbowker, Peter Karlsen, JYoung130, VNonesuch, LikeLakers2, DASHBotAV, 7cg43m, 28bot, Leilimo, Petrb, Xanchester, Clue-
Bot NG, Lightbulb500, Gareth Griffith-Jones, Jugyhng, Mbtran, Racush, Satellizer, Joseph Rudolf, Dudelock24, Urmomhaha21, RockSu-
perStar12, Vacation9, Delusion23, Curiouscorey, Avagad2, O.Koslowski, JohnnyTehUnicorn, Rezabot, Widr, Marcus.brenneman, Helpful
Pixie Bot, Titodutta, Lowercase sigmabot, Walrus068, I7988414, Raitul hasan nibir, Dootv.tv, Northamerica1000, MusikAnimal, Amp71,
GKFX, Zipzip50, Gautehuus, Mark Arsten, Merovigla, GClugo, HrishikeshSarode, Theboss9921, Snow Blizzard, Fern91, Nategraves,
Fylbecatulous, EricEnfermero, BattyBot, Pratyya Ghosh, Mrt3366, Yanthran, EuroCarGT, MadGuy7023, Kelvinsong, Tow, Dexbot,
Snowdootle, Webclient101, Lugia2453, CaSJer, Membrane-biologist, Spamer2000, Carpy singer, Wywin, Taylordavison, BrooksMaxwell,
Faizan, Epicgenius, Nnszhdm, Missionedit, Trudeau97, Jledgren, I am One of Many, Mudit7, Iztwoz, Eyesnore, Stegmeister99, Redditor69,
Tentinator, Ananthkamath1995, Tmmordret, Tripleshame, Zairen99, DavidLeighEllis, Sladeb, Elia-thomas-zard, Iburk, Ontilu, Prokary-
otes, Noob244, BobbyBoy69, BruceBlaus, Jianhui67, 2sharkalh, Lialono, Csutric, Goldmask99, Monkbot, Bobwhitehammer, C1776M,
Rakeshyashroy, Cc028152, Bhargawanan, Jason 201168, Spencer23moore1010, Midrastogi, KasparBot and Anonymous: 1283
• Carbohydrate Source: https://en.wikipedia.org/wiki/Carbohydrate?oldid=671871366 Contributors: Magnus Manske, Marj Tiefert,
Sodium, Bryan Derksen, Zundark, Tarquin, Taw, Josh Grosse, Youssefsan, Toby Bartels, William Avery, Anthere, Robert Foley, Heron,
DennisDaniels, Ubiquity, Lir, Wshun, Booyabazooka, Ixfd64, Sheldon Rampton, Cyde, GTBacchus, Tregoweth, Looxix~enwiki, El-
lywa, Ahoerstemeier, Mac, Jebba, Ojs, Julesd, Ugen64, Glenn, Tristanb, Palfrey, Evercat, Jedidan747, Mxn, Hashar, Charles Matthews,
Ww, Steinsky, Tero~enwiki, Carbuncle, Donarreiskoffer, Gentgeen, Robbot, Josh Cherry, Tomchiukc, Mayooranathan, Stewartadcock,
Pingveno, Academic Challenger, AaronS, HaeB, Tobias Bergemann, Centrx, Giftlite, DocWatson42, Lupin, Everyking, Dratman, Ben-
saccount, Digital infinity, Jfdwolff, Guanaco, Jorge Stolfi, Eequor, SWAdair, Kandar, Christopherlin, Decoy, Knutux, Sonjaaa, Antan-
drus, Onco p53, OverlordQ, G3pro, Jossi, H Padleckas, Neutrality, Imjustmatthew, Chmod007, Generic Player, Mike Rosoft, Kingal86,
Shipmaster, Discospinster, Cacycle, Vsmith, Kennnesbitt, Mani1, Martpol, Aardark, Bender235, ESkog, Geoking66, Hritcu, MisterSheik,
Joanjoc~enwiki, Kwamikagami, Mwanner, Shanes, Matteh, Adambro, Causa sui, Bobo192, Dungodung, Arcadian, Jag123, Avitek~enwiki,
Shambler1, La goutte de pluie, Sasquatch, Cjb88, XDarklytez, Krellis, Jjron, Mareino, Lunigma, Jumbuck, Alansohn, Gary, Elpincha,
Patrick Bernier, Arthena, Bart133, Melaen, Bucephalus, ClockworkSoul, Evil Monkey, Shoefly, Bsadowski1, Redvers, Bookandcoffee,
Antifamilymang, BadSeed, Kenyon, OwenX, Lkjhgfdsa, Macaddct1984, GraemeLeggett, Christopher Thomas, Slgrandson, GFP~enwiki,
Graham87, V8rik, FreplySpang, BorisTM, RxS, Tabercil, Rjwilmsi, Coemgenus, Bfigura, Fish and karate, Redecke~enwiki, FlaBot,
RobertG, Mishuletz, Nihiltres, Who, DuckLionDog, Karrmann, McDogm, Chobot, DVdm, Wasted Time R, Elfguy, YurikBot, Wavelength,
Muchness, Kirill Lokshin, Stephenb, Bill52270, Pseudomonas, NawlinWiki, Wiki alf, Grafen, Erielhonan, Deskana, RazorICE, Thiseye,
Ezberry, Boobytrapped, Irishguy, Raven4x4x, Khooly59, Nick C, DeadEyeArrow, Tetracube, Silverchemist, Kriskhaira, 21655, Zzuuzz,
Theda, Closedmouth, Jwissick, GraemeL, CWenger, WILLY-MART, Afn, HereToHelp, Katieh5584, Diablo Rojo, GrinBot~enwiki, DVD
R W, Kf4bdy, Tirronan, That Guy, From That Show!, Sardanaphalus, Vanka5, Veinor, Crystallina, SmackBot, Skaijo, MattieTK, Ter-
rancommander, Saravask, ThreeDee912, JK23, Hydrogen Iodide, Blue520, Bomac, KocjoBot~enwiki, Anastrophe, Delldot, Zephyris,
Gilliam, Ohnoitsjamie, Skizzik, Chaojoker, ERcheck, Tyciol, Kurykh, Persian Poet Gal, Jprg1966, MalafayaBot, Deli nk, Nbarth, DHN-
bot~enwiki, Gruzd, Philip Howard, Darth Panda, Brinerustle, CharonM72, Can't sleep, clown will eat me, Frap, TheKMan, Addshore, Flub-
bit, Stevenmitchell, Richard001, Drphilharmonic, DMacks, Where, Kuzaar, DJIndica, SashatoBot, Lasindi, Dbtfz, Soap, Kuru, Vaterlo,
Kipala, DrNixon, Gobonobo, Perfectblue97, Aleenf1, IronGargoyle, Mr. Vernon, A. Parrot, Hootforum, Mr Stephen, Ryulong, MTS-
bot~enwiki, Hetar, BranStark, Iridescent, Az1568, Tawkerbot2, Curtmack, Google20, AlbertChesterMan, Daedalus969, JForget, Cac-
ahueten, Andrew nixon, Deon, Ale jrb, Robotsintrouble, Scohoust, The Font, JohnCD, WillowW, SyntaxError55, Gogo Dodo, Anthony-
hcole, Pascal.Tesson, Tawkerbot4, Christian75, DumbBOT, Chrislk02, Omicronpersei8, Robert.Allen, Grant M, Gimmetrow, JamesAM,
Thijs!bot, Epbr123, Pstanton, Following specific instructions whispered by a mysterious cat, N5iln, Mojo Hand, Marek69, WVhybrid,
Mbrutus, Hermioneelovesron, Leon7, Miller17CU94, Eleuther, LachlanA, David D., AntiVandalBot, Swac, Gioto, Settersr, Seaphoto,
Opelio, QuiteUnusual, TimVickers, Smartse, Danger, MECU, Spencer, DarthShrine, Eleos, Gökhan, Yancyfry jr, JAnDbot, Deflective,
Husond, MER-C, Mcorazao, Sanchom, Xeno, Hut 8.5, Makron1n, Kirrages, Geniac, Connormah, Bongwarrior, VoABot II, Plusik~enwiki,
Densan98, Equinexus, JamesBWatson, CTF83!, Bubba hotep, Srice13, 28421u2232nfenfcenc, Lilmisshawna, NicD, Cpl Syx, Just James,
DerHexer, Esanchez7587, TheRanger, Yobol, MartinBot, STBot, CliffC, EyeSerene, Spencerw, Bushwacker1, Arjun01, Kiore, Clientele,
Killakiwi, R'n'B, Ash, J.delanoy, Pharaoh of the Wizards, Trusilver, Bogey97, Herbythyme, Peter Chastain, Hans Dunkelberg, Yonidebot,
Rod57, TheChrisD, Jeffrey Rollins, Xdamagedx, Coppertwig, HiLo48, Loperg, Belovedfreak, NewEnglandYankee, Jenrose, Touch Of
Light, Jmcw37, Auuman Anubis, KylieTastic, Thygan, Jamesontai, Vanished user 39948282, Brvman, Microbrain, Black Kite, Aznskill101,
Deor, VolkovBot, ABF, Indubitably, VasilievVV, Wolfnix, Philip Trueman, TXiKiBoT, OverSS, Juniperusjosh, Qxz, Someguy1221,
Littlealien182, Lradrama, Martin451, JhsBot, Buddhipriya, LeaveSleaves, Ffinder, Rjm at sleepers, Wingedsubmariner, RadiantRay,
Lerdthenerd, Itzchink, Enviroboy, Vector Potential, Spinningspark, Newsaholic, Ronmore, AlleborgoBot, Logan, EmxBot, Boloneyboy is
awsome, Joshua Rambajue, Quietbritishjim, SieBot, Lazarevski, BotMultichill, Krawi, Gerakibot, Rockstone35, Caltas, RJaguar3, Yintan,
Xkfusionxk, Hxhbot, Nuttycoconut, Recursiveblue, Tombomp, Drywontonmee, StaticGull, Leetuser, WikiLaurent, Pinkadelica, Ainlina,
WikipedianMarlith, Loren.wilton, ClueBot, The Thing That Should Not Be, Arakunem, Reeceyyyy15, Drmies, Razimantv, The determi-
22.1. TEXT 381

nator, Healthynutrition, Paradox pioneer, Uncle Milty, Joao Xavier, Michaplot, ChandlerMapBot, Phenylalanine, VIC&EM, DragonBot,
Excirial, Alexbot, Jusdafax, Pwgman14, PixelBot, OpinionPerson, CupOfRoses, NuclearWarfare, Peter.C, TheRedPenOfDoom, Tnx-
man307, Albla.rocks.u.251, BOTarate, La Pianista, Unmerklich, Thingg, Vegetator, Aitias, Scalhotrod, Versus22, DumZiBoT, Forged-
bliss, InternetMeme, XLinkBot, Mjharrison, Spitfire, Little Mountain 5, Avoided, SilvonenBot, NellieBly, PL290, Frood, Thatguyflint,
Benjaminruggill, Addbot, Willking1979, Some jerk on the Internet, Thomas888b, Ronhjones, TutterMouse, Fieldday-sunday, GD 6041,
Jasonbholden, CanadianLinuxUser, Fluffernutter, Diptanshu.D, NjardarBot, Morning277, EconoPhysicist, Glane23, Energie energie, Favo-
nian, Tide rolls, Verbal, Czar Brodie, Teles, Alamgir, Swarm, Legobot, Luckas-bot, Yobot, Tohd8BohaithuGh1, Berkay0652, II Mus-
LiM HyBRiD II, Nallimbot, IW.HG, Beavs, Backslash Forwardslash, AnomieBOT, Rubinbot, 1exec1, Jim1138, Pyrrhus16, AdjustShift,
Caca21he, Materialscientist, Kasper90, Citation bot, Erlendaakre, Vuerqex, Steven10000bca, Frankenpuppy, Nifky?, Xqbot, Tinucherian-
Bot II, Addihockey10, Gigemag76, Nasnema, XZeroBot, Tad Lincoln, D2earth, Biggieyankfan, GrouchoBot, Abce2, Frankie0607, Ribot-
BOT, Amaury, Glycoform, 78.26, Shadowjams, Dr. Klim, Jotade11, Thomas Hoglund, FrescoBot, Vinithehat, Oldlaptop321, 24ten, The-
owoo, HJ Mitchell, Billtkd, Iqinn, DivineAlpha, Biker Biker, Pinethicket, I dream of horses, Trvb, Triplestop, A8UDI, Impala2009, Space-
Flight89, Mikespedia, Mary Ann N. Magallen, MrTobias, Bgpaulus, Jauhienij, Sultan11, Cancerquest, TobeBot, ‫کاشف عقیل‬, Yunshui,
ItsZippy, Sumone10154, Callanecc, Vrenator, Clarkcj12, Diannaa, Suffusion of Yellow, Sirkablaam, Reach Out to the Truth, Minimac,
Skmacksler, Marie Poise, Andrea105, Mean as custard, Toliseju, RjwilmsiBot, Vokes1, Jakebedard, DASHBot, EmausBot, Acather96,
WikitanvirBot, Immunize, Ajraddatz, Broflowsky, Razor2988, RaoInWiki, Ben salvatori, Tommy2010, Winner 42, Ingridcool1193,
Wikipelli, K6ka, Shadowhunter177, Kriskbunch, Hbuschman, Melissa1995, Cjbe2, AvicBot, JSquish, Barfonyourface, Fæ, Julius00007,
ThecarterV, Wayne Slam, Tolly4bolly, Erianna, Mayur, Donner60, Kriders54, Carmichael, ChuispastonBot, Peter Karlsen, Leoj83, TYel-
liot, DASHBotAV, Sonicyouth86, Dakilla55, Will Beback Auto, ClueBot NG, Iiii I I I, MelbourneStar, This lousy T-shirt, NTTGermania,
Escapepea, O.Koslowski, Castncoot, Widr, Gelainest, HMSSolent, Calabe1992, WNYY98, Gamye387, Lowercase sigmabot, NZLS11,
Catherine garnsey, MusikAnimal, AvocatoBot, Metricopolus, Now Look What You've Done, Mark Arsten, D Namtar, 96smidge, The-
Brandon1099, 4001001A, Jeuce6, Jackie0711, Zujua, Keturys, Swyilk, Davos1423, 4Jays1034, Johnmichaeloliver, Biosthmors, Riley
Huntley, Pratyya Ghosh, Boboshowme, W.D., T0M80Y, Cyberbot II, ChrisGualtieri, Mediran, AlchemistOfJoy, JYBot, Dexbot, Web-
client101, Islander007, Lugia2453, Hair, Penguin112, Little green rosetta, Sowlos, Whynotlamacha, Jumpingwhiskers, ZX95, Legalus452,
Nhathuyenle, Mbeavers13, Kimberly.zimmel, Epicgenius, Nicevilleangel, Puffin2012, Iztwoz, Eyesnore, UnluckyJohnThomas, Jstacy1,
EvergreenFir, Фил Тоукач, DavidLeighEllis, Zenibus, Stefangv123, Iwantfreebooks, Miscellaneous131, Addishamsi, Donjoe, Manul,
Tkyles1009, Abineish, Meteor sandwich yum, Crazy131, Monkbot, TheBigtobia, Chocolatte123456789, Scarlettail, Trackteur, Bade-
noch13, Shiva Kant Gautam, Mr.Nukem, Bicepeddie, Y-S.Ko, Jonathan is dumb, StewdioMACK, Papasotevergotas42, Govindaharihari,
Jerry09baddog, Ternary.pulsar, Cflynnbraves, Lucasjackson00, Infinite0694, KasparBot, Cheekyskrub and Anonymous: 1195
• Polysaccharide Source: https://en.wikipedia.org/wiki/Polysaccharide?oldid=671621914 Contributors: Marj Tiefert, Bryan Derksen,
Chuq, Lir, Tenbaset, Rhys~enwiki, Donarreiskoffer, Robbot, Pfortuny, Fredrik, Baldhur, Securiger, Stewartadcock, Rfc1394, Hadal, Fu-
elbottle, DocWatson42, BenFrantzDale, Bensaccount, Kandar, Andycjp, G3pro, The MoUsY spell-checker, H Padleckas, Semenko, Gsc-
shoyru, Tsemii, The number c, EugeneZelenko, Discospinster, Cfailde, El C, Imoen, Sietse Snel, ~K, Bobo192, SpeedyGonsales, Cjb88,
Ardric47, Passw0rd, SemperBlotto, Theodore Kloba, Velella, HenkvD, Versageek, Kenyon, Woohookitty, Pol098, GregorB, Eras-mus,
Palica, Jimrharvey, Magister Mathematicae, RxS, Sango123, FlaBot, Gurch, Iridos~enwiki, DaGizza, Bgwhite, Roboto de Ajvol, Yurik-
Bot, NTBot~enwiki, Kirill Lokshin, Sentausa, NickBush24, Nephron, Gabix, Phgao, Ghazer~enwiki, SmackBot, David Shear, Blue520,
Skizzik, Hugo-cs, Persian Poet Gal, Androsyn, Richard001, Paroxysm, Vina-iwbot~enwiki, Kukini, Swatjester, Kuru, John, Dr.saptarshi,
Mr. Vernon, Dhp1080, Esoltas, Irvinefan, Farglator, Sir Vicious, Insanephantom, Orayzio, Hardrada, Kupirijo, Kanags, Anthonyhcole,
Christian75, Thijs!bot, Nonagonal Spider, LachlanA, Mentifisto, AntiVandalBot, TimVickers, Glennwells, Res2216firestar, JAnDbot,
MER-C, Owenozier, Fragmaroom, .anacondabot, 28421u2232nfenfcenc, MartinBot, Kostisl, Kaveish, Architpuri, J.delanoy, Adifeldman,
Numbo3, Boghog, Dai mingjie, Mikael Häggström, Lbthrice, KangAK, Funandtrvl, VolkovBot, Zctglassman83, Jazz man jeans, Jeff
G., TXiKiBoT, Chimpex, Broadbot, Eubulides, Yk Yk Yk, HiDrNick, SieBot, Mikemoral, Oz Spinner, Da Joe, Flyer22, KoshVorlon,
Ks0stm, OKBot, Ptr123, Denisarona, WikipedianMarlith, Touchstone42, Vuts, ClueBot, Gits (Neo), Hyalite, Harland1, SamuelTheGhost,
CrazyChemGuy, PixelBot, Melintelinas, Gwguffey, Markgriz, Iohannes Animosus, 7, Silence of the Yams, SilvonenBot, Kal-El-Bot,
Alexius08, Addbot, DOI bot, Fieldday-sunday, CanadianLinuxUser, West.andrew.g, Tide rolls, Ettrig, Luckas-bot, Yobot, Anypodetos,
Eric-Wester, AnomieBOT, Adeliine, IRP, Piano non troppo, Materialscientist, Citation bot, Xqbot, Br77rino, RibotBOT, Glycoform,
Guillaume Ponchel, OlaIsacsson, FrescoBot, IO Device, Jatlas, Citation bot 1, Nirmos, Pinethicket, Jschnur, Robo Cop, FoxBot, Trappist
the monk, Throwaway85, 777sms, Kobeisbeast, Drthomasj, Jynto, EmausBot, RaoInWiki, JSquish, Wayne Slam, JoeSperrazza, L Kens-
ington, Kleopatra, E. Fokker, Imichigan2, ClueBot NG, Jack Greenmaven, Chemicus 234, Seancasey00, Helpful Pixie Bot, Calabe1992,
CatPath, Altaïr, Glacialfox, Vanischenu, Unto Caesar, Jimw338, ChrisGualtieri, YFdyh-bot, Bfedward13, Little green rosetta, Joeinwiki,
DavidLeighEllis, The Herald, Crow, Monkbot, Acagastya, KasparBot, TMA-1701, 4 and Anonymous: 264
• Metabolism Source: https://en.wikipedia.org/wiki/Metabolism?oldid=671733473 Contributors: Magnus Manske, Kpjas, Bryan Derksen,
Taw, Enchanter, R Lowry, Lir, Michael Hardy, Booyabazooka, Lexor, Looxix~enwiki, Ahoerstemeier, Mac, Docu, JWSchmidt, Glenn,
TonyClarke, Rob Hooft, Mxn, Ellenshuman, Shizhao, Wetman, Jusjih, PuzzletChung, Robbot, Pigsonthewing, Fredrik, Pingveno, Diberri,
Vacuum, Alan Liefting, Marc Venot, Giftlite, The sanch, Bensaccount, Alan Au, Kandar, Antandrus, Onco p53, OverlordQ, PDH, Jossi,
M.e, Sleepygreen~enwiki, Fanghong~enwiki, Monkeyman, Discospinster, Rich Farmbrough, Thematicunity, Cacycle, Vsmith, Bob horn,
El C, Buxtor, Art LaPella, RoyBoy, Deanos, Femto, LeonardoGregianin, .:Ajvol:., Arcadian, Giraffedata, Nk, John Fader, MPerel, Mdd, Io-
lar~enwiki, Etxrge, Arthena, Kocio, Batmanand, Caesura, Macowell, Zantastik, Alai, HenryLi, Y0u, Stemonitis, Simetrical, LOL, WadeS-
imMiser, Fenteany, Palica, Graham87, Marskell, BD2412, Keamari, Sjakkalle, Rjwilmsi, Smithfarm, Brighterorange, FlaBot, RobertG,
Vietbio~enwiki, Margosbot~enwiki, Winhunter, Thndr333, Imnotminkus, Chobot, YurikBot, Wavelength, Ashleyisachild, RobotE, Rus-
soc4, Sentausa, NawlinWiki, Snek01, NickBush24, Tony1, User27091, 21655, Closedmouth, Colin, BorgQueen, Carabinieri, Willtron,
ArielGold, Vanished user 99034jfoiasjq2oirhsf3, DVD R W, SmackBot, McGeddon, Jagged 85, AndreasJS, Jfurr1981, Zephyris, Gilliam,
Eug, RDBrown, MK8, Algumacoisaqq~enwiki, DHN-bot~enwiki, Colonies Chris, Hallenrm, Gracenotes, NYKevin, MyNameIsVlad, Van-
ished User 0001, Zirconscot, Smooth O, Khukri, Richard001, Sporkot, DMacks, Skinnyweed, Madeleine Price Ball, SashatoBot, Harry-
boyles, Adam Hasheesh, Ampersand777, IronGargoyle, A. Parrot, Munita Prasad, Beetstra, Mr Stephen, SandyGeorgia, Citicat, Pedrora,
Pqrstuv, Sahuagin, Jhayes94, Tawkerbot2, Yashgaroth, Dto, Rozzychan~enwiki, Fvasconcellos, Patho~enwiki, Robotsintrouble, KyraV-
ixen, Nunquam Dormio, AshLin, Outriggr, Agentilini, JFreeman, XcepticZP, DumbBOT, Dipics, Hubba, Epbr123, Opabinia regalis,
Headbomb, Marek69, Brichcja, Mmortal03, David D., AntiVandalBot, Yonatan, TimVickers, Alphachimpbot, MikeLynch, Mikenor-
ton, JAnDbot, Ericoides, J-stan, RebelRobot, Xact, Acroterion, WolfmanSF, Bongwarrior, VoABot II, CattleGirl, Cheklevara, Adrian J.
Hunter, Allstarecho, Emw, Spellmaster, Vssun, WLU, Gjd001, Philg 124, STBot, Anaxial, R'n'B, CommonsDelinker, Leyo, Fconaway,
Lilac Soul, J.delanoy, Unauthorised Immunophysicist, LordAnubisBOT, McSly, Mikael Häggström, Mcat2, Nwbeeson, Cheeserules214,
Geekdiva, Bonadea, Useight, VolkovBot, DSRH, AlnoktaBOT, Philip Trueman, TXiKiBoT, Tameeria, A4bot, Miranda, Jurock, Anna
Lincoln, Una Smith, Amaher, Rexeken, Sanfranman59, Jackfork, LeaveSleaves, Eubulides, Enigmaman, Yk Yk Yk, Lamro, Realer, Tur-
382 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

gan, CephasE, Spinningspark, AlleborgoBot, Petergans, H.kittredge, Valce, Kaseydahne, SieBot, Caltas, Lhasalisa, Flyer22, Tiptoety,
Arbor to SJ, Yerpo, Infohut, Oxymoron83, Kochipoik, Lightmouse, Alex.muller, Jack the Stripper, Kumioko (renamed), Mygerardro-
mance, Dabomb87, Hordaland, SallyForth123, Touchstone42, Ababababa1, ClueBot, The Thing That Should Not Be, Rodhullandemu,
Xerj, Cryptographic hash, Uncle Milty, S22544, Piledhigheranddeeper, Diagramma Della Verita, Esbboston, NuclearWarfare, Linusgreen,
Thehelpfulone, Carnage49, Secret, Aitias, Versus22, Meske, BarretB, XLinkBot, Tony K10, Kitfox.it, Subversive.sound, FireBrandon,
HexaChord, Addbot, AVand, DOI bot, Element16, Landon1980, Jncraton, MrOllie, Klowe01, RTG, PranksterTurtle, AndersBot, Favo-
nian, LinkFA-Bot, Numbo3-bot, Tide rolls, Teles, WikiDreamer Bot, HerculeBot, Krukouski, Legobot, Tjorgensen, Luckas-bot, Vedran12,
Yobot, EdwardLane, Ptbotgourou, Gambori, THEN WHO WAS PHONE?, Gunnar Hendrich, IW.HG, AnomieBOT, Rubinbot, Jim1138,
JackieBot, AdjustShift, Mahmudmasri, Materialscientist, Citation bot, Kalamkaar, ArthurBot, Xqbot, Timir2, Plumpurple, Capricorn42,
DSisyphBot, - ), GrouchoBot, Omnipaedista, Uloggonitor, GNRY09, Smallman12q, Mclal1pt1, Paine Ellsworth, Tobby72, Aaaaaactually,
Recognizance, HJ Mitchell, Citation bot 1, Winterst, Pinethicket, Edderso, 10metreh, Jstraining, A8UDI, Ezhuttukari, SpaceFlight89,
Pbsouthwood, Jauhienij, Spandyp190, Kolay123, Callanecc, VNNS, Rats8888, LawBot, Tbhotch, Jesse V., DARTH SIDIOUS 2, Rjwilm-
siBot, Mntdooking, Androstachys, EmausBot, Gohornets23, Siden, Dcirovic, JSquish, John Cline, John Mackenzie Burke, Meddoc13,
Imnoteditinganything, Donner60, Drwickerson, ChuispastonBot, Mr. Igra, Aacac, 28bot, Blah1285348, Roro2011, Liuthar, ClueBot
NG, Cwilcox1976, Alpha1337Saint, Widr, Helpful Pixie Bot, Excerpted31, Bibcode Bot, The ReadC, BG19bot, MusikAnimal, Snow
Rise, Jobin RV, Mark Arsten, Thelastredshirt, Queen of Awesome, Zach Vega, Hurriquake, Tottosel, Dos Perros Estupidos, Wordqex-
pert, Mot3rgl4d, Min.neel, Id 1948, Zedshort, Georgesource1, MahdiBot, Mrt3366, Andrew6906, Dexbot, SantoshBot, Cwn rui, Mogism,
Dede1996, Bdj22, Globalbluebird, Prokaryotes, Ginsuloft, Isaachughen, Thephil12312, Jkirby754, MegaAlex, Monkbot, AlexanderGWC,
Alrich44, Nicoleandrew.btc, ScrapIronIV, Dorion1999, Paris1207, KasparBot and Anonymous: 506
• Glycolysis Source: https://en.wikipedia.org/wiki/Glycolysis?oldid=672394250 Contributors: AxelBoldt, Magnus Manske, Marj Tiefert,
Bryan Derksen, Malcolm Farmer, Andre Engels, AlexCruise, Dan Koehl, JWSchmidt, Andres, Zoicon5, Selket, Pakaran, Robbot, Josh
Cherry, Jotomicron, Hadal, Fuelbottle, Diberri, Giftlite, Everyking, Bensaccount, JuanitaJP, Munkee, Delta G, Kandar, Gyrofrog, Dull-
hunk, Alteripse, Williamb, DevilsAdvocate, G3pro, Maximaximax, Fuzlyssa, Iwilcox, Kramtark, JTN, Discospinster, Michall~enwiki,
Geoking66, CanisRufus, Triona, Bobo192, Meggar, Arcadian, Jag123, Jojit fb, Etxrge, Arthena, Andrewpmk, Cburnett, RainbowOfLight,
Naveen57, Dan100, Ceyockey, RyanGerbil10, Marcelo1229, Richard Arthur Norton (1958- ), Mindmatrix, Recnilgiarc, Kirez, Mpatel,
Tabletop, Fenteany, SCEhardt, Isnow, Plrk, Cyberman, Gimboid13, Graham87, Magister Mathematicae, FreplySpang, BorisTM, Rjwilmsi,
Demian12358, OliAtlason, Soakologist, Mohawkjohn, Yamamoto Ichiro, FlaBot, SouthernNights, Gurch, Daycd, Gurubrahma, Chobot,
Krishnavedala, DVdm, The Rambling Man, YurikBot, Marc Isaacs, Darsie, Sasuke Sarutobi, Gaius Cornelius, Abarry, Ekton, Wimt,
SEWilcoBot, Wiki alf, Gareth Jones, JDoorjam, Anetode, Bucketsofg, Rhodekyll, Wknight94, Zargulon, Svetlana Miljkovic~enwiki,
Colin, JeramieHicks, Niccus, SmackBot, Elonka, Saravask, Reedy, Slashme, Stepa, Jrockley, Delldot, Kjaergaard, Zephyris, Elronxenu,
Gilliam, Eug, Chris the speller, Bluebot, Tito4000, TsunadeSama, Miquonranger03, Ctbolt, Oatmeal batman, Ravnoor, Scwlong, Can't
sleep, clown will eat me, Shalom Yechiel, HoodedMan, Chlewbot, Smooth O, Richard001, Drphilharmonic, Ligulembot, Clicketyclack,
Dono, ArglebargleIV, J. Finkelstein, Paulwithap, IronGargoyle, JHunterJ, Meco, Cheez277, Kaarel, Shoeofdeath, Amdurbin, Polypipe
Wrangler, Rozzychan~enwiki, Fvasconcellos, JForget, CmdrObot, Ilphin, Robotsintrouble, Scohoust, Lentower, TicketMan, Narayanese,
Krylonblue83, Epbr123, Barticus88, Kubanczyk, Opabinia regalis, N5iln, Sfxdude, Laportechicago, CTZMSC3, Northumbrian, Nav-
dar, David D., AntiVandalBot, Seaphoto, TimVickers, PloniAlmoni, Evergreen vsh007, AubreyEllenShomo, Joehall45, Deadbeef, JAnD-
bot, Gcm, Superdoggy, Registrar, Magioladitis, Bongwarrior, VoABot II, Aka042, D-rew, Adrian J. Hunter, Allstarecho, JaGa, Phi-
lANThropiSt, Spencerw, Lexivore, CommonsDelinker, Leyo, CBSB, Lilac Soul, Ryanreednro, Manticore, AlphaEta, J.delanoy, Yraser,
Bogey97, NightFalcon90909, Khullah~enwiki, DD2K, Ibrmrn3000, Bot-Schafter, Mikael Häggström, Screensaver7, Igotlotsaquarters, Su-
per tom2, Alnokta, Uhai, Use the force, Jmauser, Yuorme, Microbrain, Wikieditor06, VolkovBot, Pelirojopajaro, Agpetern, Jeff G.,
Soliloquial, TXiKiBoT, Dburson, Una Smith, Pedvi, Nuttcrakerr, BotKung, Roland Kaufmann, Jonas094, Enviroboy, Wolfinbm, Logan,
MicroProf, Pred7799, G00nsf, Alhead, Dmdukes, SieBot, Brenont, Tiddly Tom, Spamburgler, Lucasbfrbot, Jack.schonbrun, Buttholation-
szee, K. Hiippari, Yerpo, Lightmouse, KathrynLybarger, Miguel.mateo, Jack the Stripper, Sunrise, Anchor Link Bot, Sitush, Righthing,
Sfan00 IMG, ClueBot, The Thing That Should Not Be, Yikrazuul, YassineMrabet~enwiki, KristinaHanspers, EconomicsGuy, OccamzRa-
zor, Puchiko, Speshuldusty, Gtstricky, Lartoven, Jakob Theorell, GraybeardBiochemist, Vin268, Thehelpfulone, MelonBot, XLinkBot,
Mifter, Jimhsu77479, Dnvrfantj, SchwarzeMelancholie, HexaChord, Addbot, DOI bot, Element16, Friginator, Ronhjones, TutterMouse,
Glane23, Exor674, LinkFA-Bot, Numbo3-bot, HerculeBot, Alex F., Luckas-bot, Yobot, JohnnyCalifornia, AnomieBOT, Rubinbot, Choij,
Mplona, Jim1138, Materialscientist, Citation bot, Jmarchn, Tekks, Szxd, Xqbot, J G Campbell, Addihockey10, DSisyphBot, Harbinary, -
), GrouchoBot, ChristopherKingChemist, Markacohen, RetiredWikipedian789, FrescoBot, Nicolas Perrault III, Z0OMD, Citation bot 1,
Ruzha, Pinethicket, Pmokeefe, Jusses2, RedBot, Dude1818, Jauhienij, Trappist the monk, Amkilpatrick, Yappy2bhere, Onel5969, Mean
as custard, Bento00, Reverus, EmausBot, The Mysterious El Willstro, AvicBot, Dempsey1717, Erianna, RaptureBot, EricWesBrown, Seat-
tle, Alice.odin, Donner60, DASHBotAV, 28bot, ClueBot NG, Satellizer, Rainbowwrasse, Frietjes, Widr, Swmmr1928, Helpful Pixie Bot,
BG19bot, Arnavchaudhary, Jeffscott007, Prav001, EmadIV, YodaRULZ, MrBill3, Trnoriega, JonathonSimister, Mikechul, ChrisGualtieri,
Laurenferruccio, LHcheM, Jonsprofile, JohnyAbb, BrightStarSky, Dexbot, Ranze, Lugia2453, Cuculus, Jeremy.d.morgan, Boytae, Joein-
wiki, AmericanLemming, Anawesomeperson1000, OdentheGray, Evolution and evolvability, Poolic, Courserepjoe, Asamos47, Tonyest,
JaconaFrere, Csutric, JoeNRG, Monkbot, AvishekDas123, VeenM64, Stavroskg, KasparBot, Animalshaver, Cruithne9 and Anonymous:
463
• Gluconeogenesis Source: https://en.wikipedia.org/wiki/Gluconeogenesis?oldid=669601577 Contributors: Taral, Rsabbatini, AlexCruise,
Zanimum, Nerd~enwiki, Tristanb, Finlay McWalter, Diberri, Jyril, OverlordQ, Chao, Michall~enwiki, El C, CDN99, Jeppelbaum, Ar-
cadian, Jag123, La goutte de pluie, Axl, Crux, ScottDavis, SCEhardt, Isnow, Grammarbot, Rjwilmsi, YurikBot, RobotE, Turgonml,
Barefootmatt, Leptictidium, Sandstein, Scoutersig, SmackBot, Slashme, Bomac, Edgar181, Ohnoitsjamie, Bluebot, Uthbrian, Tsca.bot,
Can't sleep, clown will eat me, Richard001, Drphilharmonic, DMacks, Clicketyclack, FrozenMan, Gobonobo, Accurizer, Anand Karia,
Pedrora, Wafulz, Mcstrother, Ruslik0, WeggeBot, Neelix, Calvero JP, Kubanczyk, Pro crast in a tor, TimVickers, Grammerking97,
Gökhan, Someone87, Bubba hotep, Dbrouse, JaGa, Mikr18, Wolingfeng, Boghog, Cmghim925, Ibrmrn3000, Rod57, It Is Me Here,
Mikael Häggström, Jelipon86, TXiKiBoT, A4bot, Malljaja, Una Smith, Molkhal, Kawta maderchoud55, Lova Falk, OKBot, Waves00,
ClueBot, Avenged Eightfold, Unused0026, Michaplot, GraybeardBiochemist, BVBede, Mjharrison, Vojtěch Dostál, TFOWR, PL290, Ad-
dbot, Jojhutton, Shahriyar alavi, Diptanshu.D, Download, Zorrobot, Yobot, Ptbotgourou, Citation bot, Jmarchn, Obersachsebot, Skaaii,
GrouchoBot, CompliantDrone, Captain-n00dle, FrescoBot, OgreBot, Citation bot 1, RedBot, Wimjongman, AhsenM, Nxl256, Reach Out
to the Truth, RjwilmsiBot, EmausBot, WikitanvirBot, Seren-dipper, Dcirovic, ChuispastonBot, Iknewwhereelectricitycomesfrom, Lligh-
tex, ClueBot NG, Jack Greenmaven, PinchTheBear, Gilderien, Frietjes, Helpful Pixie Bot, Vokesk, Yale2013, MStorey582, Schafhirt,
LHcheM, YFdyh-bot, Ulupoi, Adgjl1357, JYBot, Kenneth.jh.han, Tsangpakho, Hieu nguyentrung12, Iztwoz, Tchouvek, Elephantsofearth,
Monkbot, RayIndo, Stavroskg and Anonymous: 152
• Glycogen Source: https://en.wikipedia.org/wiki/Glycogen?oldid=667334305 Contributors: Magnus Manske, Bryan Derksen, The Anome,
22.1. TEXT 383

Rsabbatini, Edward, Looxix~enwiki, Michael Shields, Ww, Renato Caniatti~enwiki, Carbuncle, Robbot, Securiger, Rfc1394, Hadal, Fuel-
bottle, Mushroom, Giftlite, DocWatson42, The sanch, Ahltorp, Bensaccount, Digital infinity, Delta G, Sonjaaa, Alteripse, PDH, Cederal,
Mike Rosoft, Zombiejesus, Eric Shalov, Imoen, ~K, CDN99, Shenme, Arcadian, Jag123, Jjron, Jumbuck, Jjayson, Arthena, GJeffery,
Mattbrundage, Dan100, SietskeEN, Benbest, Bunchofgrapes, BorisTM, Sjö, Sjakkalle, Rjwilmsi, Bhadani, FlaBot, Margosbot~enwiki,
Nihiltres, RexNL, McDogm, Physchim62, DVdm, WriterHound, Whosasking, YurikBot, Chris Capoccia, Akamad, Lijealso, Icy bot,
Zwobot, Bota47, JustAddPeter, Sandstein, Banus, Cecilyen, SmackBot, Bomac, KocjoBot~enwiki, Liaocyed, Gilliam, Ohnoitsjamie,
Skizzik, Stubblyhead, Darth Panda, Richard001, Drphilharmonic, Drc79, BRSM, XxNeXuSxX, Ahda, AThing, John, Taishaku, JorisvS,
BillFlis, Agathoclea, Beetstra, MTSbot~enwiki, BranStark, Courcelles, Shrimp wong, Ale jrb, Sir Vicious, Fedir, Robotsintrouble, Poktir-
ity, P.s. hua, Kanags, Solidpoint, Narayanese, Lewisskinner, JamesAM, Epbr123, Tonyle, Peter K., Mmortal03, Pro crast in a tor, Darklilac,
JAnDbot, Bencherlite, Magioladitis, VoABot II, TARBOT, 28421u2232nfenfcenc, Allstarecho, Hbent, Spencerw, BetBot~enwiki, Com-
monsDelinker, Akxcskier, Thegreenj, LordAnubisBOT, Adamcieslicki, Mikael Häggström, Idioma-bot, Funandtrvl, Hchoe, Xenonice,
Firebird84, Dqeswn, AlnoktaBOT, TXiKiBoT, A4bot, Ng.j, Kawta maderchoud556, Enviroboy, EJF, SieBot, Phe-bot, LeadSongDog,
Flyer22, OKBot, Hamiltondaniel, Chem-awb, WikipedianMarlith, DanCAK, ClueBot, GorillaWarfare, MR Deidra, Michał Sobkowski,
DragonBot, Excirial, Alexbot, Jusdafax, Tnxman307, PCHS-NJROTC, Crazy Boris with a red beard, Mjharrison, Georgehead, Freestyle-
69, Addbot, Wickey-nl, Tmcclell, Ronhjones, Sethkatz, NjardarBot, AndersBot, SamatBot, Numbo3-bot, Craigsjones, Tminus65, ,
Arbitrarily0, Ettrig, Legobot, Luckas-bot, Vedran12, Yobot, AnomieBOT, Nutriveg, Jambobambo, Materialscientist, Citation bot, Xqbot,
Copperman2011, Wikiwooroo, CeresVesta, Hongsy, Zuma212, WATerian, Girlwithgreeneyes, Aldousari, Nirmos, Pinethicket, Recon-
sider the static, Mj455972007, Trappist the monk, LogAntiLog, Ben Thuronyi, Vrenator, Cyanophycean314, Nxl256, Jmun7616, Rjwilm-
siBot, EmausBot, JSquish, ArthurCammers, ClueBot NG, Gilderien, Zynwyx, Kingzwest, Helpful Pixie Bot, BG19bot, Fedor Babkin,
XxClayTheBossxX, CitationCleanerBot, WiseUmos, Zedshort, Vanischenu, Jeanloujustine, Jimw338, IronHokie, PreCambrianBunny,
Nic.anfernee, Elephantsofearth, Monkbot, ZhongtheRetard, Biologybadlad, KasparBot, Thepilotusa, Ryanspanier-uh and Anonymous:
253
• Pentose phosphate pathway Source: https://en.wikipedia.org/wiki/Pentose_phosphate_pathway?oldid=655883810 Contributors: Bryan
Derksen, Gabbe, Steinsky, Giftlite, Tagishsimon, Adenosine, Nina Gerlach, El C, Arcadian, Jag123, Isnow, Eras-mus, Anneli1, Bgwhite,
YurikBot, Ge Tianfang, Edgar181, Eug, Kazkaskazkasako, Bluebot, Chtit draco, Drphilharmonic, Horiavulpe, Shoeofdeath, Fvascon-
cellos, Robotsintrouble, John Riemann Soong, Runningonbrains, Gpalchik, Kupirijo, Narayanese, Thijs!bot, CopperKettle, Nonagonal
Spider, TimVickers, .anacondabot, Acroterion, MiPe, Adrian J. Hunter, -VL-, R'n'B, PatríciaR, Xris0, Lrunge, Pelirojopajaro, Pcampeau,
Dhorspool, Doc James, AlleborgoBot, Cj1340, ClueBot, Yikrazuul, Cepheus 5, PixelBot, GraybeardBiochemist, SkyMaja, DumZiBoT,
Addbot, Shahriyar alavi, Tahmmo, Luckas-bot, Yobot, Ptbotgourou, AnomieBOT, Materialscientist, GrouchoBot, Citation bot 1, Time9,
Jffre, EmausBot, ZéroBot, GdenBesten, 28bot, ClueBot NG, BG19bot, Neøn, Mmhrmhrm, AhMedRMaaty, YFdyh-bot, Davidlwinkler,
Matxjos, Elephantsofearth, Monkbot, Geekytux and Anonymous: 77
• Citric acid cycle Source: https://en.wikipedia.org/wiki/Citric_acid_cycle?oldid=670345723 Contributors: AxelBoldt, Magnus Manske,
Mav, Bryan Derksen, Tarquin, Charleschuck, Vanderesch, AdamRetchless, Dwmyers, Bdesham, Lir, Lexor, Mkweise, Ugen64, Michael
Shields, Jiang, Rob Hooft, Wik, Selket, Jose Ramos, Shizhao, Josh Cherry, Peak, Stewartadcock, Nilmerg, Mark Patterson, Catbar, Alba,
Profoss, Fuelbottle, Giftlite, Christopher Parham, Jyril, Kim Bruning, Everyking, Dratman, Bensaccount, JuanitaJP, Jfdwolff, Guanaco,
Jorge Stolfi, Delta G, Kandar, Christopherlin, Adenosine, Antandrus, Onco p53, OwenBlacker, H Padleckas, Julianonions, Ultratomio,
Discospinster, Rich Farmbrough, Guanabot, Slipstream, Nchaimov, ESkog, Brian0918, CDN99, Semper discens, Stesmo, Arcadian,
Jag123, Jojit fb, Pschemp, Unused000701, Haham hanuka, Alansohn, Andrewpmk, Craigy144, Tokhtuev, Pion, ClockworkSoul, Docboat,
Bsadowski1, Dan100, Dennis Bratland, Isfisk, Mpatel, Kmg90, Contele de Grozavesti, Cyberman, Gimboid13, Dysepsion, BorisTM,
Rjwilmsi, Mohawkjohn, Nihiltres, Daycd, Chobot, DVdm, Dj Capricorn, WriterHound, Gwernol, YurikBot, Wavelength, Mushin, Darsie,
Spaully, DVirus101, Cquan, Zarel, Chakazul, Nucleusboy, Zwobot, DeadEyeArrow, Kelovy, CaitlinG, Imaninjapirate, CharlesHBennett,
LeonardoRob0t, A bit iffy, SmackBot, YellowMonkey, Sardino, Zephyris, Elronxenu, Yamaguchi , Gilliam, Bluebot, Jprg1966, DHN-
bot~enwiki, Oatmeal batman, Madeinsane, Aldaron, Ghettobrown, John D. Croft, Barney Stratford, Richard001, Ggpauly, Drphilharmonic,
Scattered Lights, Vina-iwbot~enwiki, Clicketyclack, CoeurDeLion, SashatoBot, Serein (renamed because of SUL), FrozenMan, Žiga,
Curtholr, DrNixon, Epingchris, Mgiganteus1, Djmccoul, AdultSwim, DarkoV~enwiki, Iridescent, Bernlomnty, Scigatt, Orangutan, Shrimp
wong, SkyWalker, JForget, Robotsintrouble, Jiwhit01, Jesse Viviano, Johner, Marqueed, Tawkerbot4, Narayanese, Crana, John Lake, La-
choy11, Thijs!bot, Eviternity, Luigifan, Marek69, The Hybrid, Eleuther, David D., AntiVandalBot, Seaphoto, TimVickers, Bluedustmite,
JAnDbot, Davewho2, MER-C, Weird Bird, DRHagen, VoABot II, Cadsuane Melaidhrin, Rivertorch, Animum, Castiron, DGG, Mart-
inBot, Leyo, Ryanreednro, J.delanoy, MercuryBlue, Nbauman, Boghog, Ashcraft, Ryan Postlethwaite, Qcomplex5, KrebsCycle, Nwbee-
son, SJP, Student7, BrettAllen, CardinalDan, Idioma-bot, Microbrain, Deor, VolkovBot, Butwhatdoiknow, Philip Trueman, Katoa, Gwib,
Technopat, Malljaja, Shureg, Drestros power, BotKung, Kawta maderchoud, Chibibrain, Enviroboy, Thatother1dude, SieBot, Da Joe, Dawn
Bard, ScAvenger lv, Baxter9, Mátyás, Dlrohrer2003, Laburke, LikeFunYouAre, ClueBot, PipepBot, Jackollie, Spoladore, YassineMra-
bet~enwiki, AlexanderPico, Arakunem, Uncle Milty, CounterVandalismBot, Niceguyedc, Thegeneralguy, PixelBot, GraybeardBiochemist,
Kaidenet, Sbfw, Basicsharingwatuknow!, VsevolodKrolikov, Rdphair, Zeeroid, 1029x, Plasmic Physics, Versus22, AC+79 3888, Dthom-
sen8, Dnvrfantj, Addbot, Dryphi, Some jerk on the Internet, Freakmighty, DOI bot, Shahriyar alavi, Ronhjones, Nomad2u001, NjardarBot,
Numbo3-bot, Tide rolls, Ettrig, Legobot, Luckas-bot, Yobot, THEN WHO WAS PHONE?, AnomieBOT, Nike tick, Piano non troppo,
Materialscientist, Bballbackus, Citation bot, Jlsmaddden, Xqbot, Capricorn42, Pontificalibus, Magicxcian, Aa77zz, ODoyle040, Citation
bot 1, Pinethicket, Arctic Night, RedBot, My very best wishes, FoxBot, ToematoeAdmn, Sojoho09, Andrea105, RjwilmsiBot, EmausBot,
Rcaspi, Ajraddatz, AManWithNoPlan, MisterDub, L Kensington, RedSoxFan274, Donner60, JG1440, ClamDip, Turmerick, ClueBot
NG, Tknight1011, Rhino8, ProfessorAM, CocuBot, KoleTang, O.Koslowski, Widr, Helpful Pixie Bot, Tdimhcs, Calabe1992, Chemistry
phd, CityOfSilver, Skeksys, Dan653, Zedshort, Newmanrs, Trnoriega, Dexbot, Nilyaa, Lugia2453, Frosty, Jaiweb, Jan1swag2, Falling-
Gravity, Dillyswag, Thebiocriic, Jono2013, Mlacount82891, Spyglasses, Monkbot, Jelly Bean MD, Griffindoc, Geldingwelding, Stavroskg,
KasparBot, Cruithne9 and Anonymous: 403
• Oxidative phosphorylation Source: https://en.wikipedia.org/wiki/Oxidative_phosphorylation?oldid=672262382 Contributors: Marj
Tiefert, Bryan Derksen, Danny, Dwmyers, JWSchmidt, Habj, DJ Clayworth, IKenny, Chris Rodgers, Robbot, Josh Cherry, Stewartad-
cock, Fuelbottle, Alan Liefting, Michael Devore, Bensaccount, Adenosine, Julianonions, Imjustmatthew, Jpg, Rich Farmbrough, El C,
Art LaPella, Bobo192, Arcadian, Jag123, ParticleMan, Nhandler, Abstraktn, Etxrge, Macowell, Suruena, Ttownfeen, StradivariusTV,
Graham87, BD2412, BorisTM, Rjwilmsi, Brighterorange, Crazycomputers, Slowpokeiv, Dj Capricorn, WriterHound, YurikBot, Wave-
length, Borgx, Gaius Cornelius, El Cazangero, Leptictidium, Nikkimaria, Smurrayinchester, Semitallsmalls, SmackBot, Espresso Addict,
Stepa, Zephyris, Persian Poet Gal, RDBrown, Gsp8181, Simpsons contributor, Can't sleep, clown will eat me, Richard001, Smokefoot,
Drphilharmonic, DMacks, Richard0612, Clicketyclack, Harryboyles, Attys, SandyGeorgia, Fvasconcellos, CmdrObot, AshLin, Rakwiki,
Narayanese, Eribro, Kakli, Kozuch, Epbr123, CopperKettle, Escarbot, David D., AntiVandalBot, TimVickers, Bahar, WolfmanSF, An-
telan, MartinBot, CommonsDelinker, Nono64, Leyo, Lilac Soul, LedgendGamer, Ulisse0, DogNewTricks, J.delanoy, MITBeaverRocks,
384 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

DrKiernan, Boghog, Hodja Nasreddin, Ijustam, Mikael Häggström, Nwbeeson, Alnokta, Treisijs, Lrunge, Tameeria, Plugs0, BotKung,
Eubulides, Anton Gutsunaev, EerieNight, Brenont, Philgoetz, Gerakibot, Wmpearl, Nuttycoconut, StaticGull, Pinkadelica, ClueBot,
Niceguyedc, Piledhigheranddeeper, Leonard^Bloom, GraybeardBiochemist, MystBot, Addbot, Xp54321, Some jerk on the Internet, DOI
bot, Shahriyar alavi, Mwucherer, Cst17, ‫נטע‬, Tedtoal, Yobot, Davaith, Laurip, IRP, Materialscientist, Citation bot, Faramir333, Some
standardized rigour, Citation bot 1, Jamouse, Trappist the monk, Jesse V., RjwilmsiBot, EmausBot, Lesviolonsdautomne, Dcirovic, Maxim
Gavrilyuk, K Y Nelson, Yangfl, Jarodalien, Jwollbold, Verticalstall, ClueBot NG, LightBringer, MerlIwBot, Helpful Pixie Bot, Bibcode
Bot, BG19bot, Iamozy, Dexbot, 2Plus2Is4, Brunei, Margaretabuttery, Anrnusna, Monkbot, Dahal narzary and Anonymous: 137

• Photosynthesis Source: https://en.wikipedia.org/wiki/Photosynthesis?oldid=664587752 Contributors: AxelBoldt, Magnus Manske, Marj

Tiefert, Mav, Bryan Derksen, Tarquin, Malcolm Farmer, -- April, Josh Grosse, Rgamble, William Avery, Chlor~enwiki, Ben-Zin~enwiki,
Heron, Jaknouse, Ram-Man, Spiff~enwiki, Dwmyers, Michael Hardy, Modster, Jtdirl, Ixfd64, Cyde, Sannse, GTBacchus, Dori, Sebastian-
Helm, Looxix~enwiki, Ahoerstemeier, DavidWBrooks, Angela, JWSchmidt, Glenn, Ciphergoth, Tristanb, Evercat, Rob Hooft, Ghewgill,
Selket, Hao2lian, Tpbradbury, Tero~enwiki, Nv8200pa, Larryorr, Samsara, Traroth, Jecar, Elwoz, Fvw, AnonMoos, Jusjih, Shafei, An-
thonyQBachler, Jeffq, Jni, Robbot, Fredrik, Modulatum, Postdlf, Academic Challenger, Jondel, Hadal, Fuelbottle, Cyrius, Pengo, Dina,
ManuelGR, Alan Liefting, Giftlite, Dbenbenn, Ryanrs, MPF, Mat-C, Kim Bruning, Lupin, Peruvianllama, Everyking, NeoJustin, An-
dris, Ans, Patrickdavidson, Sundar, Mboverload, Delta G, SonicAD, Adenosine, Gadfium, Dullhunk, Antandrus, Onco p53, OverlordQ,
PDH, Bodnotbod, Zfr, Feniouk, Talrias, Mrrhum, Creidieki, Chao, Fermion, Sonett72, Kevyn, Demiurge, Adashiel, Aut1221, Chepry,
Canterbury Tail, Clubjuggle, Shotwell, Atrian, Perey, Freakofnurture, ClockworkTroll, DanielCD, RedWordSmith, Discospinster, Rich
Farmbrough, Cacycle, Vsmith, Wk muriithi, Xezbeth, Mani1, Pavel Vozenilek, Paul August, ESkog, Kbh3rd, Danny B-), Neko-chan,
RJHall, Germen, *drew, Pinzo, Joanjoc~enwiki, Phoenix Hacker, Art LaPella, RoyBoy, Plociam, Guettarda, Causa sui, Bobo192, Whosy-
ourjudas, Shenme, Cmdrjameson, Vortexrealm, Cohesion, Dungodung, Arcadian, Cayte, SpeedyGonsales, La goutte de pluie, Xoddam,
Hi112233, Rje, Burnhamd, Brainy J, Haham hanuka, Iolar~enwiki, HasharBot~enwiki, Tra, Red Winged Duck, Alansohn, Gary, JY-
olkowski, Etxrge, Nik42, Eric Kvaalen, Valérie75, JoaoRicardo, R Calvete, SlimVirgin, Mlessard, Hgrenbor, Malo, PaePae, BanyanTree,
ClockworkSoul, Dbrett480, Evil Monkey, Amorymeltzer, ComCat, Gene Nygaard, Bookandcoffee, Kazvorpal, Michael Ward, Ceyockey,
Tchaika, Feezo, Nuno Tavares, Angr, OwenX, Woohookitty, Henrik, Cimex, TigerShark, Etacar11, Camw, LOL, Consequencefree, Dandv,
PoccilScript, TheArmadillo, Schlice, Mooinglemur, Username314, Fenteany, Bbatsell, Optichan, Sengkang, Jugger90, Xiong Chiamiov,
MassGalactusUniversum, Magister Mathematicae, BD2412, Li-sung, Tradnor, Chun-hian, Lanoitarus, FreplySpang, Swmcd, Lord.lucan,
Pentawing, Search4Lancer, Sjakkalle, Rjwilmsi, Commander, Vary, Quiddity, Sdornan, Tawker, CQJ, The wub, Bhadani, Dar-Ape, Gre-
gAsche, Sango123, Molybdenumblue, Yamamoto Ichiro, Red Herring, FlaBot, Ian Pitchford, Nivix, Elmer Clark, RexNL, Jrtayloriv, KFP,
Miketam, Srleffler, Daycd, Procrastinator~enwiki, Nsteinberg, King of Hearts, Nicholasink, Chobot, DaGizza, Mhking, Korg, Dj Capri-
corn, WriterHound, Gwernol, Cassius987, YurikBot, Wavelength, TexasAndroid, Hawaiian717, JDnCoke, Vuvar1, Sceptre, Jlittlet, Peti-
atil, Crazytales, Postglock, Acefox, Bergsten, SpuriousQ, Okedem, Gaius Cornelius, Eleassar, Ihope127, Salsb, Wimt, GeeJo, Herbertxu,
Jrbouldin, Shanel, Wiki alf, Jaxl, Johann Wolfgang, Długosz, Robchurch, Apokryltaros, Irishguy, Nick, Raven4x4x, Epipelagic, Pier-
pontpaul2351, FF2010, Lt-wiki-bot, Bayerischermann, U.S.Vevek, Closedmouth, Studentne, KGasso, Fram, Katieh5584, Kungfuadam,
The Catfish, DVD R W, Quadpus, David Wahler, Crystallina, SmackBot, FocalPoint, MattieTK, Dweller, Malkinann, Tarret, Slashme,
Prodego, TestPilot, Hydrogen Iodide, Melchoir, K-UNIT, Unyoyega, Pgk, AndyZ, Jfg284, Davewild, Matthuxtable, Alksub, EncycloPetey,
Hardyplants, Frymaster, RobotJcb, HalfShadow, Gaff, Yamaguchi , ITOD, Samballance, Gilliam, Ohnoitsjamie, Hmains, Skizzik,
Rmosler2100, Amatulic, Master Jay, Persian Poet Gal, Rmstock, Tito4000, Dreg743, Tree Biting Conspiracy, SchfiftyThree, Tetraglot,
Funper, EScribe, Kungming2, Munyanah, Gruzd, Sbharris, Polyhedron, Sunholm, Reaper X, Simpsons contributor, Veggies, Myrryam,
Xchbla423, Lawrenceuniversity1, Can't sleep, clown will eat me, OrphanBot, Init~enwiki, Rrburke, Kcordina, Wine Guy, Celarnor,
SundarBot, Stevenmitchell, Iapetus, Decltype, Makemi, Bowlhover, Nakon, TedE, Nick125, Dreadstar, Crittens, Drphilharmonic, Jk-
lin, ATMarsden, Mion, InNuce, Clicketyclack, SashatoBot, Nisadaninisa, Kuru, John, AmiDaniel, Soumyasch, JoshuaZ, Chodorkovskiy,
JorisvS, Tim Q. Wells, Minna Sora no Shita, Teh wise one, Mgiganteus1, Zarniwoot, Tikoo, Ocatecir, Eaglestrike117, Saseigel, Ckatz,
White.matthew.09, Smith609, Munita Prasad, Beetstra, Bendzh, Waggers, ASKingquestions, Funnybunny, Ryulong, Condem, Gregturn,
Zepheus, Hu12, CerealKiller~enwiki, Ginkgo100, Ramcy~enwiki, Vanished user, Nehrams2020, Iridescent, Pipedreambomb, Cheesy
Yeast, Melnicki, NativeForeigner, Mrg024, Hipporoo, Cbrown1023, SweetNeo85, Blehfu, Marysunshine, Color probe, Daharde, Cour-
celles, Tawkerbot2, Daniel5127, Ouishoebean, Vices, Meltzerju, Rozzychan~enwiki, JForget, Toadams, Mattbr, Van helsing, Agathman,
Shorespirit, Scohoust, Woudloper, Riader0, CWY2190, Hometown, GHe, Pajast, TheTito, Z 153, Fox6453, Kupirijo, MC10, 678910,
BGFMSM, Govindjee, Pontifex101, Anonymi, B820, Chasingsol, Michael C Price, DumbBOT, Chrislk02, Robertinventor, Narayanese,
NMChico24, HBNayr, GeeOh, Thijs!bot, Epbr123, Dsinghs, Pajz, Kamal Chid, Kablammo, Angam~enwiki, Nonagonal Spider, John254,
Kathovo, Tellyaddict, Uiteoi, GregMinton, Dfrg.msc, Pkpat2011, Wikidenizen, Natalie Erin, Drdaveng, Escarbot, Darekun, David D.,
AntiVandalBot, Kylemcinnes, Abu-Fool Danyal ibn Amir al-Makhiri, Luna Santin, Prince Godfather, EarthPerson, Quintote, Pro crast
in a tor, TimVickers, Peipei, Smartse, Darklilac, Malcolm, Zedla, Imogen89, Storkk, Ed, Incredio, Trappist, Deflective, MER-C, Kaabi,
Sanchom, Hello32020, Db099221, Mwarren us, Johna100, Bencherlite, Robsavoie, Gekedo, Connormah, Bongwarrior, VoABot II, Vol-
comRUXC, Wikidudeman, Aeioun, SparrowsWing, Avicennasis, Qwerqwerqwer, Indon, 28421u2232nfenfcenc, User A1, Laur2ro, Der-
Hexer, Stephenchou0722, Hdt83, MartinBot, Unclepea, Arjun01, MNAdam, Anaxial, Sarin123, CommonsDelinker, Leyo, Joshjoshjosh1,
Jamib0y, Pekaje, WelshMatt, Smokizzy, J.delanoy, Pkoden, Blahed768, Ali, Bogey97, Nbauman, Name b, Hans Dunkelberg, Boghog,
Usdi, Uncle Dick, Interplanet Janet, Icseaturtles, NinaStarry, McSly, RTBoyce, Mikael Häggström, L'Aquatique, (jarbarf), Exdejesus,
NewEnglandYankee, Domminico, Fullmetal123321, Rhysboy, Dienamight, Dacrycarpus, DorganBot, Treisijs, King Toadsworth, Bonadea,
JamesR777, Goatman12, Ali salter, Darklich14, P a k 2, AJRM, Cdorman2, Iron Dragon91, Bertiethecat, CardinalDan, RJASE1, Idioma-
bot, Nonluddite, Lights, Deor, VolkovBot, Clyde10race, OMGHeHasAGun, Indubitably, AlnoktaBOT, Philip Trueman, TXiKiBoT, Ram-
batino, Kww, Tameeria, Malljaja, Norrello, SueHay, Hpfreak26, Qxz, Someguy1221, HLHJ, Steven J. Anderson, Martin451, JhsBot,
Juhwade, Raymondwinn, Ilyushka88, Duncan.Hull, Maxim, Coching, Synthebot, @pple, Turgan, Likeabird, Bateman1234, Thanatos666,
PoeticX, WatermelonPotion, Lily15, Delfigolo, AlleborgoBot, Imi2012, Logan, Pcruce, Rock2e, EmxBot, Neyne, Bailey654, Lord 1284,
SieBot, Jwray, Primal400, Scarian, ToePeu.bot, Caltas, Randomnotice, Hunrizzo8, Keilana, Yon Yonson, Collegedegree, Momo san,
Samtux~enwiki, Oiws, Yerpo, Mimihitam, Oxymoron83, Jasonphollinger, Steven Zhang, Lightmouse, Towerofthunder, Dr. Mandellez,
Sunrise, Maelgwnbot, Viper777~enwiki, Spartan-James, Kopid03, Thatotherdude, Mygerardromance, WikiLaurent, Pinkadelica, Horda-
land, Troy 07, WikipedianMarlith, Touchstone42, Bfahome, Faithlessthewonderboy, ClueBot, Snigbrook, Foxj, Stoic Squirrel, The Thing
That Should Not Be, Jan1nad, Yikrazuul, Nsk92, Shark96z, Wutsje, Skäpperöd, Boing! said Zebedee, Malomaboy06, Dasyornis, Progu-
itarboy, DragonBot, Excirial, Eeekster, Estirabot, Silasmellor, Mdavies 965, Dekisugi, Muro Bot, Ottawa4ever, ChrisHodgesUK, Thingg,
Chirpy7, Aitias, SoxBot III, Tdslk, DumZiBoT, RMFan1, Jamesscottbrown, Eik Corell, Nnewton, Jovianeye, WikHead, Daleks Rule, Alex-
ius08, Torahjerus14, ZooFari, Gggh, Lemchesvej, Surtsicna, CalumH93, Gacha1, Addbot, CurtisSwain, DOI bot, Guoguo12, Oliverc1991,
Theleftorium, Upeksha112, C3r4, Nuvitauy07, Tattoo275, Ronhjones, CanadianLinuxUser, Jpoelma13, Download, Morning277, Chamal
N, EconoPhysicist, Demi s96, Debresser, Doniago, LinkFA-Bot, 5 albert square, Imanoob69, Brainmachine, Numbo3-bot, Bluedeed,
22.1. TEXT 385

Tide rolls, Ettrig, Math Champion, Luckas-bot, Yobot, TaBOT-zerem, II MusLiM HyBRiD II, The Earwig, THEN WHO WAS PHONE?,
, Szajci, YouAreNotReadingThis, AnomieBOT, 1exec1, Accuruss, JackieBot, Oggie boggie in the loo, 9258fahsflkh917fas, Piano
non troppo, Fahadsadah, Kingpin13, Nibls, Ulric1313, EryZ, Materialscientist, Kasper90, Citation bot, ArthurBot, Xqbot, The sock that
should not be, Gigemag76, Corrigen, Tomaschwutz, Call me Bubba, Twirligig, EqualMusic, Tackyleprechaun, Antony2, Dinsdalea, Me big
fishy, Jazzy211, Eumeng.chong, Prunesqualer, Oxnora2012, Mrmonsterman, Ryantoh wiki, Shadowjams, Racknack7824, Samwb123, Gli-
derMaven, FrescoBot, DavidDidwin, LucienBOT, Paine Ellsworth, Tobby72, Wikipe-tan, Oldlaptop321, Staccatoque, D'ohBot, Dirty MF
Harry, Crazychinchilla, Fgbhrgthnrtgnb, Citation bot 1, Citation bot 4, Shiningstarr1997, Daniel233, Intelligentsium, Pinethicket, P00100p,
HRoestBot, Edderso, Watplay, Abductive, Jonesey95, Sdittami, RedBot, DotComCairney, Thinking of England, SpaceFlight89, NarSak-
SasLee, Barras, Wejer, SW3 5DL, Jauhienij, Mj455972007, TobeBot, Sweet xx, NYMFan69-86, Lotje, NMFA Northern Eagle, Vrenator,
Zvn, LilyKitty, Jackgeddes1234, Eddturtle, Amkilpatrick, Weedwhacker128, Amercer09, Tbhotch, Stroppolo, Reach Out to the Truth,
Minimac, Sd card, Tastycheeze, Mikimickz, DARTH SIDIOUS 2, RjwilmsiBot, Bento00, DrMtl, Gould363, Billare, Grondemar, DASH-
Bot, EmausBot, John of Reading, O le gend, Ohyeahbabe, Tommy2010, Platoface, Rachelpurdon, Sergey WereWolf, Starzjake, Stevead-
cuk, Nickresch, Pvgetsome, Wiitennisxd, Zap Rowsdower, Jay-Sebastos, L Kensington, ChuispastonBot, Cman12345657578, Saif11, Iam
angryrawr, Staticd, Mrwarriorman, LikeLakers2, JonRichfield, ClueBot NG, Cwmhiraeth, Gilderien, Zxoxm, Devil42400, ScottSteiner,
Helpful Pixie Bot, Calabe1992, Bibcode Bot, CatPath, AvocatoBot, Davidiad, Weblars, Tom Pippens, Exercisephys, Aranea Mortem, Gle-
vum, Robert Thyder, Derekrhu, Jacob635, Aidentbrown, At09kg, Minsbot, Jonadin93, Kc kennylau, Jack No1, ChrisGualtieri, Tn4196,
JYBot, BrightStarSky, Dexbot, Mogism, Abotan, Kylcon2, FallingGravity, Zorahia, JPaestpreornJeolhlna, NHCLS, Eunkyoon, Csutric,
PaulGWiki, Monkbot, Somepics, D. Cordoba-Bahle, Trackteur, Manaiak31, Nmcke1, Felipe Jo, IMcBeats, VeenM64, KasparBot and
Anonymous: 1376
• Fatty acid synthesis Source: https://en.wikipedia.org/wiki/Fatty_acid_synthesis?oldid=671188415 Contributors: Fizzyfifi, D6, Cow2001,
Arcadian, Giraffedata, Zachlipton, Contele de Grozavesti, Rjwilmsi, Bgwhite, Ojii-san, Itub, SmackBot, Yamaguchi , Drphilharmonic,
Clicketyclack, Dl2000, Harej bot, Hubba, Kubanczyk, Pro crast in a tor, Magioladitis, Adrian J. Hunter, Mtuttle, Pelirojopajaro, Leafyplant,
SieBot, Azo bob, Dakinijones, Yikrazuul, AlexanderPico, Porcofederal, Panoramix303, GraybeardBiochemist, SkyMaja, SchreiberBike,
Knopfkind, Ctrlaltdelete200390, Colinc719, Addbot, Jacopo Werther, Diptanshu.D, Citation bot, Skaaii, GrouchoBot, Chodid~enwiki,
LucienBOT, NikeTenis, RShorty30, Suffusion of Yellow, RjwilmsiBot, John of Reading, Rcaspi, Tommy2010, Dcirovic, OG Clriley,
AvicAWB, Jaypg, RE73, Teaktl17, Bganong, JohnSRoberts99, Bochyboch, LHcheM, YFdyh-bot, Monkbot, Beanstash and Anonymous:
39
• Lipogenesis Source: https://en.wikipedia.org/wiki/Lipogenesis?oldid=655306182 Contributors: Rich Farmbrough, Paul August, Arcadian,
Unused000701, Keenan Pepper, Speedevil, Leptictidium, SmackBot, Bluebot, RDBrown, Drphilharmonic, Shrimp wong, CmdrObot,
Harej bot, LittleT889, Mark Gobbin, Christian75, BetacommandBot, Kubanczyk, Plico, Gökhan, Ksero, Pelirojopajaro, Amog, Lamro,
Helenabella, Ctrlaltdelete200390, Colinc719, Addbot, Luckas-bot, Gensanders, Chodid~enwiki, DrilBot, RedBot, Jujutacular, Rjwilmsi-
Bot, Falconerd, Ponydepression, Ed7654, Fdc210, Dermoid, Monkbot and Anonymous: 48
• Acetyl-CoA carboxylase Source: https://en.wikipedia.org/wiki/Acetyl-CoA_carboxylase?oldid=665448420 Contributors: SimonP, Ed-
ward, Tom harrison, Arcadian, Woohookitty, BorisTM, Rjwilmsi, The wub, RainR, Mushin, SmackBot, Waldroplab, Sbmehta, Saxbryn,
Shrimp wong, Robotsintrouble, Im.a.lumberjack, M gehrig2000, Magioladitis, EagleFan, Leyo, Boghog, Xris0, Mikael Häggström, Al-
nokta, Alexhlau, VolkovBot, Luuva, Adeez, Bfx0, Slaporte, Rb1248, Muhandes, GraybeardBiochemist, Rdphair, AngelHerraez, WikHead,
Jimhsu77479, MystBot, Addbot, DOI bot, AkhtaBot, Luckas-bot, Yobot, Citation bot, Xqbot, J G Campbell, Bear919506, SassoBot, Ci-
tation bot 1, Yottie, RedBot, Trappist the monk, Reaper Eternal, Nw.NPC, DASHBotAV, Whoop whoop pull up, Frietjes, Helpful Pixie
Bot, NotWith, Monkbot and Anonymous: 23
• Fatty acid degradation Source: https://en.wikipedia.org/wiki/Fatty_acid_degradation?oldid=669489400 Contributors: Rich Farm-
brough, Arcadian, Walkerma, Richard001, Clicketyclack, Kubanczyk, Nick Number, WolfmanSF, Nyttend, Leyo, Mikael Häggström,
ThinkerThoughts, Wmpearl, Haripandit, Clayt85, SoxBot, Diptanshu.D, Synchronism, Erik9bot, Δ, ClueBot NG, Enigmaticfool,
HoorayFerSocks, Faizan, Fregersonman101, Ameyadravid and Anonymous: 7
• Beta oxidation Source: https://en.wikipedia.org/wiki/Beta_oxidation?oldid=671390518 Contributors: Bogdangiusca, Semenko, Abdull,
Mike Rosoft, Arcadian, Velella, ClockworkSoul, Natarajanganesan, V8rik, Rjwilmsi, Physchim62, YurikBot, Mushin, Grafen, Dawhit-
field, SmackBot, Drocra, InverseHypercube, Aurista25, C.Fred, Stepa, Paxse, Jstanley~enwiki, Drphilharmonic, Henning Makholm,
Clicketyclack, Dono, Seven of Nine, Kupirijo, Christian75, Krylonblue83, Thijs!bot, Mastee, Dawkeye, Zink53, TimVickers, Darklilac,
Oddity-, LinkinPark, NEUROtiker, Dmanagadze, Nyttend, -VL-, Su-no-G, Riccardobot, Owl9, Jeyradan, STBotD, Nitroblu, VolkovBot,
DrMicro, LoneSeeker, Chibibrain, HkCaGu, Wmpearl, Coolstoryhansel, Haripandit, Tomifly, Abrech, GraybeardBiochemist, Zerkalox,
AC+79 3888, Vojtěch Dostál, Lemchesvej, Addbot, Luckas-bot, Bunnyhop11, Ptbotgourou, Magairlin, Langthorne, AnomieBOT, Taskual-
ads, Obersachsebot, Silkblackrose, Almabot, Vivekanand23, Eumeng.chong, Spongefrog, FrescoBot, Louperibot, RShorty30, Narfaniel,
EmausBot, Dr. Ambitious, Dcirovic, Lecj77, Hyalos, Meaganrock, Whoop whoop pull up, ClueBot NG, Zoidbergness, Beamoflaser,
Meph636, MauchoEagle, BG19bot, Pompay, Justincheng12345-bot, Ossip Groth, YFdyh-bot, Iamozy, SZhangJerry, Frickson, DR.CROT,
Nehcttocs, Elephantsofearth, RingPie, Pramit57, Hajime7basketball, SongofSol, Jelly Bean MD and Anonymous: 91
• Nitrogen fixation Source: https://en.wikipedia.org/wiki/Nitrogen_fixation?oldid=670710396 Contributors: Bryan Derksen, Malcolm
Farmer, Ortolan88, SimonP, Quercusrobur, Michael Hardy, Stan Shebs, Smack, Stone, Marshman, Topbanana, WormRunner, Securiger,
Devtrash, Alan Liefting, DocWatson42, MPF, FrYGuY, Manuel Anastácio, Beland, Onco p53, Sonett72, Rich Farmbrough, Cacycle,
Zombiejesus, Vsmith, Notinasnaid, Yersinia~enwiki, Bender235, Kbh3rd, CanisRufus, Tigerente, C S, Kappa, A2Kafir, Quintucket, Alan-
sohn, Keenan Pepper, Paleorthid, Monado, Melaen, Velella, Kazvorpal, Woohookitty, LOL, Macaddct1984, MarcoTolo, Marudubshinki,
Ashmoo, V8rik, Drbogdan, Rjwilmsi, Mork the delayer, Dougluce, RobertG, Nihiltres, Chobot, Frappyjohn, Bgwhite, Dj Capricorn, Yurik-
Bot, Wavelength, RobotE, Huw Powell, Butterflied~enwiki, Callior, Pseudomonas, Anomalocaris, NawlinWiki, Dysmorodrepanis~enwiki,
Veledan, Brian Crawford, Tetracube, True Pagan Warrior, SmackBot, PipOC, Keegan, Nazzy, Sbharris, Snowmanradio, NoahElhardt, Ran-
domP, Smokefoot, Drphilharmonic, Dvorak729, Clicketyclack, Mouse Nightshirt, Bendzh, RyJones, TimTL, JForget, Satyrium, Kupir-
ijo, Michael C Price, Christian75, Rosser1954, Thijs!bot, Epbr123, Headbomb, M uzair, OrenBochman, KrakatoaKatie, AntiVandalBot,
DarkAudit, Mary Mark Ockerbloom, TimVickers, Smartse, Bakabaka, Spencer, Alphachimpbot, Midnightdreary, Igodard, PhilKnight,
Daxdigital, VoABot II, JamesBWatson, Bkurl, Mapetite526, Sabedon, Yobol, MartinBot, Nono64, J.delanoy, Pharaoh of the Wizards,
Gareth.randall, Katalaveno, Tsugasdad, Idioma-bot, Andrewlevy, Soliloquial, Katoa, Charfroman, Seraphim, Ilyushka88, Wingedsub-
mariner, Ashnard, Ninjatacoshell, Haikon, Why Not A Duck, RHaden, Atubeileh, Petergans, SieBot, BotMultichill, Caltas, RucasHost,
AnonGuy, Touchstone42, MenoBot, Church, Elassint, ClueBot, HujiBot, Hysocc, Drmies, Mild Bill Hiccup, Shinpah1, Alandmanson,
Puppy8800, Thomasn1, Mspraveen, Ekawolfram, DragonBot, Excirial, Heathmoor, Jusdafax, Shinkolobwe, BOTarate, Lab-oratory, Ad-
dbot, SchoonerGuy, CanadianLinuxUser, CarsracBot, XRK, Tide rolls, Jarble, Zazil, Luckas-bot, 2D, Fraggle81, PMLawrence, CinchBug,
386 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

Avinashraut, AnomieBOT, 1exec1, Citation bot, Bob Burkhardt, ArthurBot, Xqbot, Weetziekat, Fancy steve, Br77rino, J04n, RibotBOT,
Prari, FrescoBot, Smurfsahoy, Paine Ellsworth, Riventree, Citation bot 4, Pinethicket, Fumitol, Utility Monster, Russot1, Mjs1991, Parisoil,
Innotata, DARTH SIDIOUS 2, RjwilmsiBot, EmausBot, Dewritech, Slightsmile, Wikipelli, Auró, Wackywace, Andyman1125, AMan-
WithNoPlan, L Kensington, Mountainninja, 28bot, Sonicyouth86, Xanchester, ClueBot NG, Jmreinhart, Mollydb, Chester Markel, Tylko,
Tideflat, ScottSteiner, DBigXray, BG19bot, Zollo9999, Guaráwolf, CatPath, MusikAnimal, Frze, Tom Pippens, Meocjt, Heterotheca, Par-
vathisri, NotWith, Marcjarod, YodaWhat, Darorcilmir, Darylgolden, YFdyh-bot, ImWhotto, MichaelKhadavi, Epicgenius, Zorahia, James-
Moose, Churchgrim, Stamptrader, Uhrakajar, Wiki at Royal Society John, Bettadr, Jgjgvjgfduiggd, KasparBot, Delorend and Anonymous:
251
• Amino acid synthesis Source: https://en.wikipedia.org/wiki/Amino_acid_synthesis?oldid=660113595 Contributors: Alan Liefting,
Giftlite, Zeimusu, Rich Farmbrough, Arcadian, Keenan Pepper, Dan East, Woohookitty, BD2412, John Baez, Welsh, Leptictidium, Elonka,
Pedro-kun, Edgar181, Zephyris, Chris the speller, Drphilharmonic, Avs5221, Shrimp wong, AntiVandalBot, CommonsDelinker, Boghog,
Phlounder, VolkovBot, Littlealien182, Michael H 34, Wingedsubmariner, Rockfang, Diderot’s dreams, Addbot, Redheylin, Luckas-bot,
Fraggle81, Mirabellen, AnomieBOT, Nutriveg, Hairhorn, Lightlowemon, Trappist the monk, Nxl256, EdoBot, Conifer, Anluwust, EricEn-
fermero, Testem, MIP443.2012, SkilletIsMyLife, Lawrie-ashton, Buffbills7701, Monkbot, Tilifa Ocaufa and Anonymous: 23
• Nucleotide Source: https://en.wikipedia.org/wiki/Nucleotide?oldid=670153456 Contributors: Marj Tiefert, Bryan Derksen, Andre En-
gels, Youssefsan, AdamRetchless, Michael Hardy, Lexor, Gdarin, Docu, Rl, Tobias Conradi, Matdaddy, Stone, Markhurd, Grendelkhan,
Stormie, Robbot, Stewartadcock, Ojigiri~enwiki, Giftlite, Kim Bruning, Brona, Horatio, Christopherlin, Adenosine, Utcursch, John-
Armagh, ELApro, Rich Farmbrough, Cacycle, Vsmith, Andrejj, Kbh3rd, Dpotter, Bobo192, Wisdom89, Arcadian, Jag123, Jerrysein-
feld, Haham hanuka, Storm Rider, Kocio, Garfield226, Bart133, Velella, ClockworkSoul, Amorymeltzer, Dzordzm, Triddle, Slgrandson,
BorisTM, FlaBot, RexNL, M7bot, Chobot, Krishnavedala, Bornhj, YurikBot, Wavelength, X42bn6, Dnik, Wimt, Mysid, DeadEyeArrow,
Wknight94, Calaschysm, CWenger, HereToHelp, Banus, GrinBot~enwiki, DVD R W, SmackBot, KnowledgeOfSelf, Hydrogen Iodide,
Bomac, KocjoBot~enwiki, Eskimbot, Edgar181, Gilliam, Chris the speller, Miquonranger03, MalafayaBot, Baa, Nmacpherson, Can't sleep,
clown will eat me, Soosed, KnowBuddy, Radagast83, TedE, Drphilharmonic, DMacks, Henning Makholm, FrozenMan, Heimstern, Breno,
Lim Wei Quan, 2T, Joseph Solis in Australia, Vermiculus, Tawkerbot2, Flubeca, Harold f, Myncknm, JForget, Wafulz, Agathman, Ma-
keemlighter, Kupirijo, Dr. Ransom, Crossmr, Travelbird, Narayanese, Epbr123, Mojo Hand, Marek69, West Brom 4ever, AntiVandalBot,
Jj137, TimVickers, Alphachimpbot, OrinR, JAnDbot, Dcooper, Noobeditor, Hut 8.5, VoABot II, Cypher056E, Rivertorch, Roadsoap, Bat-
teryIncluded, Adrian J. Hunter, Emw, Cpl Syx, DerHexer, WLU, Squidonius, NunoAgostinho, MartinBot, Lisamh, Strathallen, Jonathan
Hall, Nono64, Leyo, Mehul trivedi, J.delanoy, Numbo3, Rhinestone K, Antony-22, Ontarioboy, DorganBot, CardinalDan, VolkovBot,
Lia Todua, TXiKiBoT, Una Smith, Jackfork, Gbaor, Aliasd, Yk Yk Yk, EerieNight, Legoktm, ThinkerThoughts, SieBot, ToePeu.bot,
Ipodamos, Chirigami, Sbowers3, Oxymoron83, Denisarona, Forluvoft, ClueBot, Isaac.holeman, Unused0026, Joaopaulopontes, Excirial,
Muhandes, Jonverve, Johnuniq, SoxBot III, DumZiBoT, Kuzzy68, Gonzonoir, Gigapede, Yossarian og, Addbot, Legosock, Download, Laa-
knorBot, PranksterTurtle, Favonian, BrianKnez, Megaman en m, MissAlyx, Legobot, Tedtoal, Luckas-bot, Yobot, Gbobrt, QueenCake,
Eric-Wester, LLDMart, DemocraticLuntz, IRP, Piano non troppo, HappyTesting, Materialscientist, Citation bot, Obersachsebot, Xqbot,
Capricorn42, Mononomic, GrouchoBot, RibotBOT, Natural Cut, Prari, FrescoBot, Citation bot 1, Þjóðólfr, Nirmos, Tom.Reding, Masti-
Bot, Brettyfxu, Vrenator, Nemesis of Reason, Minimac, TjBot, VDanger, EmausBot, Racerx11, JSquish, Ronk01, Shshr, John Macken-
zie Burke, Access Denied, Scientistview, Donner60, Petrzak, Woodsrock, ClueBot NG, Horoporo, Rezabot, Widr, Helpful Pixie Bot,
Uniquenick, AdventurousSquirrel, Blakethegundork, TuringMachine17, Suizei, Khazar2, Leilimosa, Kelvinsong, EagerToddler39, An-
drewrgross, Eyesnore, Everymorning, BruceBlaus, Bilorv, Monkbot, Acagastya, Jdvalencia, Medgirl131, Kaseypeesho, Pinnate foliage,
KasparBot and Anonymous: 308
• Urea cycle Source: https://en.wikipedia.org/wiki/Urea_cycle?oldid=672054091 Contributors: AxelBoldt, Bryan Derksen, Andre Engels,
Dwmyers, Elano, Tristanb, Selket, Stewartadcock, Jfdwolff, Onco p53, PDH, Quirk, Cacycle, Brim, Arcadian, La goutte de pluie, Wouter-
stomp, Ceyockey, Dennis Bratland, Nuno Tavares, Mindmatrix, Dolfrog, Jugger90, BorisTM, Brighterorange, Physchim62, YurikBot,
Gaius Cornelius, Nicke L, Ritchy, User27091, Svetlana Miljkovic~enwiki, Linkminer, Imz, Giraldusfaber, KocjoBot~enwiki, Stepa,
Edgar181, Zephyris, Bluebot, Drphilharmonic, Clicketyclack, SashatoBot, Pedrora, Andreas Rejbrand, Patho~enwiki, Robotsintrou-
ble, JohnCD, Maadal, Miller17CU94, TimVickers, MiPe, Gludwiczak, Squidonius, R'n'B, PietjeK, Nono64, Dennis Myts, Geraki-
bot, Paolo.dL, Moletrouser, Sfan00 IMG, PipepBot, Yikrazuul, GraybeardBiochemist, Doprendek, Addbot, Wickey-nl, Shahriyar alavi,
AkhtaBot, Legobot, Luckas-bot, Yobot, Fraggle81, JackieBot, Materialscientist, ArthurBot, Xqbot, Vadha, Pinethicket, Paulrutten2,
Ripchip Bot, Canada Hky, EmausBot, WikitanvirBot, ChuispastonBot, Whoop whoop pull up, ClueBot NG, Widr, Mira.juanc, Snow
Blizzard, Rfxor2002, Ossip Groth, MichaelUyeda, EtymAesthete and Anonymous: 78
• Hormone Source: https://en.wikipedia.org/wiki/Hormone?oldid=669895217 Contributors: Magnus Manske, Kpjas, Lee Daniel Crocker,
Mav, Andre Engels, Youssefsan, Vanderesch, Karen Johnson, Ben-Zin~enwiki, Netesq, Youandme, Someone else, Stevertigo, Edward,
Michael Hardy, Lexor, Nixdorf, Ixfd64, MichaelJanich, Ahoerstemeier, Zannah, Glenn, Tristanb, Dcoetzee, Dysprosia, Toreau, Carbun-
cle, Rhys~enwiki, Robbot, Sander123, RedWolf, Romanm, Nadia1717, Fuelbottle, Diberri, Dina, Marc Venot, Giftlite, Smjg, Pretzel-
paws, Alison, Bensaccount, Jfdwolff, Ravn, Naufana, Foobar, Erich gasboy, Knutux, Alteripse, Chiu frederick, G3pro, PFHLai, Zfr,
Dutai68, Mike Rosoft, Freakofnurture, Discospinster, Cacycle, Vsmith, LindsayH, Notinasnaid, Brian0918, Sfahey, Kwamikagami, Nick-
Gorton~enwiki, Easyer, Bobo192, Smalljim, Evolauxia, Brim, Arcadian, Stephen Bain, A2Kafir, Ranveig, Jumbuck, Alansohn, Free Bear,
Arthena, Kurieeto, SidP, RainbowOfLight, Mikeo, Deathphoenix, Dan East, Stemonitis, Woohookitty, Barrylb, Macronyx~enwiki, Blue-
moose, SDC, Paxsimius, Graham87, Col.Kiwi, Sjakkalle, Rjwilmsi, Biochemza, FlaBot, RobertG, JRice, Nihiltres, Chobot, DVdm,
VolatileChemical, Bgwhite, Dj Capricorn, WriterHound, YurikBot, Wavelength, RobotE, Rxnd, Petiatil, Reo On, Spaully, Stephenb,
Raven4x4x, Bota47, Richardcavell, Closedmouth, Pb30, MrTroy, Banus, Lyrl, GrinBot~enwiki, Tom Morris, Luk, SmackBot, Haza-
w, KocjoBot~enwiki, Edgar181, Gilliam, Ohnoitsjamie, Ppntori, Durova, Chris the speller, Keegan, Fuzzform, MalafayaBot, Deli nk,
Kungming2, Can't sleep, clown will eat me, Snowmanradio, Vnadorable, Parent5446, Celarnor, Stevenmitchell, Rastik~enwiki, T-borg,
Jdlambert, Artie p, Drphilharmonic, Acdx, Horiavulpe, SashatoBot, AThing, John, Xornok, Gleng, JoshuaZ, Mgiganteus1, Aleenf1, Iron-
Gargoyle, Filippowiki, Dilcoe, Munita Prasad, Beetstra, Mrhurtin, Dicklyon, Matatigre36, Samarat, Michaelbusch, StuHarris, Kaarel,
Muéro, Octane, CapitalR, Tawkerbot2, K.murphy, JForget, SammB, N2e, Alexamies, Cydebot, Travelbird, Llort, Julian Mendez, Roberta
F., Ebyabe, Lo2u, PKT, Thijs!bot, Epbr123, TheFearow, S Marshall, Luigifan, Vala M, Mentifisto, Cyclonenim, AntiVandalBot, Luna
Santin, Christian15213, Jj137, TimVickers, Maork, Chill doubt, Lfstevens, Hoffmeier, JAnDbot, Kaobear, MER-C, PhilKnight, Ja-
hoe, Miracle Five, Bongwarrior, VoABot II, Jomacajo, Dbrouse, Ciar, 28421u2232nfenfcenc, MartinBot, ChemNerd, WelshMatt, Led-
gendGamer, Tgeairn, HEL, RockMFR, Pharaoh of the Wizards, CFCF, Numbo3, Boghog, Eliz81, Hodja Nasreddin, Homerdomes, Kata-
laveno, Mrs.meganmmc, Mikael Häggström, Belovedfreak, Sir Claws, X990, Verklighet, Useight, ELLusKa 86, Idioma-bot, VolkovBot,
Luisen~enwiki, Indubitably, Lia Todua, AlnoktaBOT, Philip Trueman, DoorsAjar, TXiKiBoT, JenniferFisher, Captain Wikify, Broadbot,
Raymondwinn, W12phaeton, Earthdirt, Suriel1981, Synthebot, Lova Falk, Falcon8765, Enviroboy, Godspet, Temporaluser, 613 The Evil,
22.1. TEXT 387

Countincr, AlleborgoBot, Adeez, Seventynine, SieBot, Turnaround3, Sonicology, Temujin108, Euryalus, VVVBot, Krawi, Matthew Yea-
ger, Flyer22, Wombatcat, Oxymoron83, Fratrep, Correogsk, Kas-nik, Sloane77, Iushad, Troop350, Escape Orbit, Loren.wilton, ClueBot,
LAX, The Thing That Should Not Be, Wysprgr2005, RYNORT, Neverquick, Barney-12-3, Excirial, Ffsgoogle, Vivio Testarossa, Zelfver-
wijzing, The Red, Pythrion, BOTarate, Bobsmith040689, Jensta, Thingg, Versus22, Pirags, DumZiBoT, XLinkBot, JenningsLA, Andruxo,
Noctibus, HexaChord, Addbot, DOI bot, Betterusername, Montgomery '39, Moosehadley, SpillingBot, Juan During, Download, Hroy-
chow, West.andrew.g, 5 albert square, Numbo3-bot, Tide rolls, Gail, Zorrobot, Jarble, Legobot, Luckas-bot, Yobot, Fraggle81, Cflm001,
ArchonMagnus, Imtechchd, AnomieBOT, Rubinbot, Jim1138, Piano non troppo, Collieuk, Pishaww, Materialscientist, Rtyq2, Danno uk,
Citation bot, Neurolysis, ArthurBot, Gsmgm, Xqbot, JoshGrosse, Jeffrey Mall, Mononomic, 661kts, NFD9001, Almabot, GrouchoBot,
Zefr, Ervance, PM800, TJmax5000, Haeinous, Stephen Morley, Pinethicket, I dream of horses, NoFlyingCars, A8UDI, Serols, Grendel12,
Jujutacular, Jauhienij, Mj455972007, FoxBot, Ale And Quail, Javierito92, Vrenator, Dc987, DadOfBeanAndBug, Amkilpatrick, Mini-
mac, Jfmantis, Sting7969, Onel5969, Mean as custard, Ripchip Bot, Mandolinface, DASHBot, EmausBot, Orphan Wiki, WikitanvirBot,
Candicell, Hreid11, Monkeyqt093, Xlilmelly32x, Racerx11, Seren-dipper, L235, Tommy2010, Wikipelli, Traxs7, Sokeater, WeigelaPen,
Feral mage, ChuispastonBot, DASHBotAV, Signalizing, ClueBot NG, Millermk, Frietjes, Muon, Kjytt0, North Atlanticist Usonian, Vas-
silios de Veritas, Arthur Swift, Calabe1992, Foxbat21, BG19bot, Bmusician, Jakeathome, Davidiad, ManyueGPH, Mark Arsten, Min.neel,
PwilliamQ99, Kreamie, Shaunagm, Juliecarver, ChrisGualtieri, Swanonator, TylerDurden8823, BrightStarSky, Hardaf, Tommie43, Zo-
rahia, Amy styles69, DavidLeighEllis, Doweexist42, Jwratner1, Sam Sailor, Crystaljeth12, SJ Defender, Gcanny, Niga22918, HiYahh-
Friend, SuleeeOuh, AntyJusteen, SpanglishArmado, Scarlettail, Mykerobinson, Kingdomkeyblade, Medgirl131, Jonnybravo5, Juna-tun,
Iamrightfuckyou, Ginamaree, Newspringmd7789, Mr.fixer17, KasparBot and Anonymous: 523
• Signal transduction Source: https://en.wikipedia.org/wiki/Signal_transduction?oldid=647836167 Contributors: AxelBoldt, Magnus
Manske, Derek Ross, Mav, Malcolm Farmer, Andre Engels, LA2, Deb, Someone else, Deejoe, Erik Zachte, Lexor, 168..., JWSchmidt,
Darkwind, Tristanb, Sjoerd de Vries, Charles Matthews, Greenrd, Samsara, Aliekens, Robbot, RedWolf, Peak, Hideshi, Sternthinker,
Jfdwolff, OldakQuill, ChicXulub, Andycjp, Mr d logan, Williamb, MacGyverMagic, PFHLai, Poccil, Rich Farmbrough, Cacycle, Nina
Gerlach, CanisRufus, Pabloes, Wisdom89, R. S. Shaw, Arcadian, ClockworkSoul, Danhash, RainbowOfLight, Kusma, Woohookitty,
MarcoTolo, D.Holt, Graham87, Rjwilmsi, Biochemza, Arnero, Alberrosidus, Whosasking, YurikBot, Wavelength, Eleassar, NawlinWiki,
Pproctor, Daniel Mietchen, Supten, PGPirate, Tevildo, Banus, JDspeeder1, SmackBot, Slashme, Rokfaith, AndreasJS, Edgar181, Durova,
Master gopher, David.Throop, Bluebot, Droll, Gracenotes, Wynand.winterbach, Roadnottaken, Drphilharmonic, Clicketyclack, Ohconfu-
cius, Suaudeau, Jagowins, DabMachine, K.murphy, CmdrObot, Gogo Dodo, Skittleys, Christian75, Freak in the bunnysuit, Rocket000,
Thijs!bot, Holopoj, Peter Znamenskiy, AntiVandalBot, Alisonchilla@yahoo.com, TimVickers, Erxnmedia, Dpryan, ElComandanteChe,
Ph.eyes, NickOsborn, NighthawkJ, Nucleophilic, Ciar, Emw, Vaultdoor, Ekotkie, Drjem3, CommonsDelinker, Nono64, J.delanoy, Nbau-
man, Boghog, Yonidebot, Scidem, Hodja Nasreddin, Johnbod, Cessagian, Mikael Häggström, NewEnglandYankee, AndreasJSbot, Spell-
cast, Barbaking, Adapter~enwiki, AlnoktaBOT, TXiKiBoT, Andrew Su, Remindmelater, Biologos, Technopat, Ychastnik APL, Locogato,
TaintedCherub, Hedgehog33, Yk Yk Yk, Lova Falk, Cseoighe, Sapphic, SieBot, Mikemoral, Sakkura, Mangostar, Genalipsis, GaryCole-
manFan, Correogsk, Motyka, Slaporte, Forluvoft, Loren.wilton, ClueBot, Gracejc25, Auntof6, PL290, Addbot, DOI bot, Redheylin, Light-
bot, Luckas-bot, Yobot, AnomieBOT, Rubinbot, Law, Citation bot, Lapabc, LilHelpa, Itskkumaran, GrouchoBot, REACHist, Howard
McCay, FrescoBot, Citation bot 1, Y4tell, Fgibson30, Bisc import, Hypermagus, Rnakatsuji, Jonkerz, Amkilpatrick, Suffusion of Yel-
low, RjwilmsiBot, Mandolinface, EmausBot, WikitanvirBot, Tiny cookie ninja, Dcirovic, Warkocur, MacDaid, Sjiang11, Orange Suede
Sofa, ChuispastonBot, 28bot, SamBouwer, Esotera~enwiki, Minnsurfur2, ClueBot NG, Parcly Taxel, CaesarAugustus7791, Bibcode Bot,
BG19bot, CatPath, Katemend, ShoziKT, Sue Larson, Sordner, Mohsinpk95, Rob Hurt, Toddly9464, Johnathon Trimbole, Pratyya Ghosh,
Samina gull, Lyonsk, Travisjamison, Pyr0gel, Agreezy12, Otony, Cerabot~enwiki, Frosty, Luchenry, Tmehlman, Brainiacal, Monkbot,
GinAndChronically, Compbiol and Anonymous: 160
• Diabetes mellitus Source: https://en.wikipedia.org/wiki/Diabetes_mellitus?oldid=670646549 Contributors: AxelBoldt, Kpjas, Marj
Tiefert, Mav, Bryan Derksen, The Anome, Alex.tan, Andre Engels, Redmist, Christian List, PierreAbbat, Karen Johnson, William Av-
ery, SimonP, Ben-Zin~enwiki, Montrealais, Bernfarr, Ram-Man, AntonioMartin, Steverapaport, Frecklefoot, Patrick, Gabbe, Gaurav,
Paul Benjamin Austin, GTBacchus, Karada, Minesweeper, Ahoerstemeier, Kricxjo, Mac, Jpatokal, Zannah, Baylink, Susan Mason, An-
gela, Statkit1, JWSchmidt, Александър, Julesd, Stefan-S, Netsnipe, Andres, Silverfish, Richard Avery, Jengod, Ww, Jitse Niesen, Tp-
bradbury, Maximus Rex, Furrykef, Phoebe, Jeeves, Topbanana, Prisonblues, Olathe, Pakaran, Jamesday, Shantavira, Donarreiskoffer,
Gentgeen, Robbot, Michael Schubart~enwiki, Josh Cherry, 01214410, Gak, Kristof vt, Donreed, Kowey, Psychonaut, JosephBarillari,
Modulatum, Nilmerg, Clngre, Rholton, Rasmus Faber, Hadal, Mushroom, Diberri, Xanzzibar, Tobias Bergemann, Bavaro47, Giftlite,
DocWatson42, Pmaguire, Techelf, MPF, Nmg20, Elf, Nunh-huh, Bork, Lupin, Zigger, Robodoc.at, Kelp, Everyking, Michael Devore,
Pashute, Jgritz, Jfdwolff, Al-khowarizmi, AlistairMcMillan, WinterWolf, Ianmc, Jackol, SWAdair, Pne, Bobblewik, Wmahan, Rainman,
Erich gasboy, Chowbok, Gadfium, Alexf, LiDaobing, Antandrus, Alteripse, OverlordQ, PDH, RichardAmes, Exigentsky, 1297, Carib-
Digita, Zfr, Sam Hocevar, J0m1eisler, Mschlindwein, Ukexpat, SousaFan88, Marine 69-71, DMG413, GreenReaper, Trevor MacInnis,
Eridanis, Grstain, Mike Rosoft, Jwdietrich2, DanielCD, Mongrel 8, Discospinster, Rich Farmbrough, Reallycoolguy, Drgnu23, MAlvis,
Mani1, Bender235, ESkog, Cyclopia, Kbh3rd, Ground, Petersam, Sgeo, Hfs, Charm, Lankiveil, Joanjoc~enwiki, Kwamikagami, Nick-
Gorton~enwiki, Mwanner, Spearhead, RoyBoy, Triona, Bookofjude, The Noodle Incident, CDN99, Thu, Bobo192, Truthflux, Smalljim,
Bollar, Rhaas, Davidruben, Duk, PeteThePill, ZayZayEM, Arcadian, Guiltyspark, Nk, Microtony, MARQUIS111, Slipperyweasel, Pdb,
Idleguy, Sam Korn, Haham hanuka, Nsaa, Matti Koskimies, Googie man, Espoo, Ranveig, LibraryLion, Alansohn, Duffman~enwiki, Eric
Kvaalen, Arthena, Mykej, Wouterstomp, Lectonar, Axl, Seans Potato Business, QBaz, Naomit, Snowolf, Bucephalus, Erik II, Nikuku,
Cburnett, Docboat, Knutties, Sciurinæ, Metju~enwiki, VoluntarySlave, Boyd Steere, Versageek, SteinbDJ, Gene Nygaard, Ghirlandajo,
Dan100, Ceyockey, DeAceShooter, Smark33021, Richard Arthur Norton (1958- ), Kelly Martin, Simetrical, Woohookitty, TigerShark,
Camw, Pol098, ^demon, Jeff3000, Tabletop, Samprs, Astanhope, GregorB, Yakobbokay, Wayward, Gimboid13, Essjay, Geoff Wing,
Dysepsion, Graham87, Grundle, Magister Mathematicae, FreplySpang, Search4Lancer, Canderson7, Sjö, Jorunn, Rjwilmsi, Seidenstud,
Nightscream, Coro, Jivecat, PinchasC, JHMM13, Nneonneo, Mdanciu, Mexaguil, SeanMack, StephanieM, Brighterorange, Concordia,
DoubleBlue, Williamborg, GregAsche, Gozar, FlaBot, RobertG, Windchaser, AED, Nihiltres, Crazycomputers, Remember.pol, RexNL,
Gurch, Leonardwee, Travis.Thurston, Diza, Compotatoj, Bmicomp, David H Braun (1964), Introvert, King of Hearts, Chobot, Maltese-
dog, Theo Pardilla, Sharkface217, Nagytibi, Gwernol, RandyRhoadsRonnieDio, Wiserd911, The Rambling Man, Cuahl, YurikBot, Wave-
length, Bmichel, Koveras, Hairy Dude, Malfidus, Midgley, RussBot, Crazytales, Bhny, Pigman, Chris Capoccia, Groogle, SpuriousQ,
Chaser, CanadianCaesar, Moshe777, Ori Livneh, Chensiyuan, Stephenb, Manop, CambridgeBayWeather, Theelf29, Rsrikanth05, Var-
nav, Wimt, Irrevenant, NawlinWiki, WulfTheSaxon, Wiki alf, Bachrach44, Marinadedave, BaldMonkey, Tetsuo, Btnheazy03, Rjensen,
Manuelhp42, Wagginpitbull, Nephron, Veracious Rey, Bobak, ScottyWZ, Rmky87, Bl00mie, Ezeu, Froth, Misza13, Supten, Nate1481,
Bucketsofg, Dbfirs, Seigneur101, Zirland, DeadEyeArrow, Tealpetunia, Andrewr47, DRosenbach, Haemo, Nlu, Dv82matt, Light cur-
rent, Zzuuzz, Agapetos angel, Cybergoth, Bayerischermann, Theda, Shashikiranu, Colin, GraemeL, Badgettrg, Willtron, ArielGold, AG-
Toth, Rathfelder, Schubatis1, Kungfuadam, Junglecat, Woodmang, Mdwyer, Tzepish, Maxamegalon2000, Andrew73, Bibliomaniac15,
388 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

That Guy, From That Show!, Eog1916, Luk, Aschmidt, Crystallina, A bit iffy, Vvill, True Pagan Warrior, SmackBot, FocalPoint,
Alexlinsker@gmail.com, Anarchist42, KnowledgeOfSelf, TracerBuIIet, FloNight, David.Mestel, NorthernFire, Unyoyega, Goldfishbutt,
InvictaHOG, Jagged 85, AndreasJS, Finavon, KVDP, Delldot, Arny, Sonaljhuj, Edgar181, Ultnet, Shai-kun, Tocotrienols, Gaff, Gilliam,
Ohnoitsjamie, Folajimi, Choalbaton, Jcarroll, ERcheck, Rmosler2100, Drn8, Kurykh, MikeSy, Agateller, Persian Poet Gal, RDBrown,
Ian13, Salvor, MalafayaBot, Deli nk, AnimalMother, Baa, DHN-bot~enwiki, Da Vynci, Toughpigs, Darth Panda, CJGB, Zsinj, Can't
sleep, clown will eat me, Jahiegel, BuckeyeRowe, Richlumaui, Onorem, Lanfire~enwiki, Snowmanradio, JonHarder, Yidisheryid, Mooterj,
Rrburke, Krsont, Niels Olson, JakartaDean, Daydreamer302000, RedHillian, Celarnor, SundarBot, Artephius, PetterBudt, Khukri, Nibuod,
Mailachang, Nakon, Auslander99, Richard001, A.R., Tmkain, Only, DMacks, HDow, Shushruth, Er Komandante, Andrewpayneaqa,
Kukini, Clicketyclack, Supaplex~enwiki, SashatoBot, G-Bot~enwiki, ArglebargleIV, Rklawton, Anlace, Drawat123, Richard L. Peter-
son, Markdr, Scientizzle, Treyt021, Lllk, Kipala, Jeff Nobles, Gobonobo, Lazylaces, This user has left wikipedia, Piplicus, Mogtheman,
DianaCouture, Ocatecir, Scetoaux, Aleenf1, Ian Dalziel, Jellyfishcom, Slakr, Xaura, Beetstra, Mr Stephen, Tengsoon, Rock4arolla, Stained-
glasscurtain, InedibleHulk, Rockpickle85, AdultSwim, Iansmcl, Ryulong, Fluppy, Novangelis, Elb2000, Daviddaniel37, Peyre, Thatcher,
Blasikov, KJS77, Hu12, Ginkgo100, Ardo191, Emx~enwiki, Tiim, Iridescent, MFago, Alchav, Electrified mocha chinchilla, Fmitchell2,
Tony Fox, Sahuagin, Beno1000, Kirk.wolfe, Ellis2ca, Az1568, Courcelles, Wyrmfire, Frank Lofaro Jr., Tawkerbot2, Travisl, Cryptic C62,
IronChris, Solled1, JForget, Matt Pullen, Infidelmatt, VoxLuna, CmdrObot, W guice, KyraVixen, Kormerant, DSachan, Kiswanson, GHe,
N2e, Jaxad0127, Ch.norn, Mpmcrd, Lokal Profil, Karenjc, MrFish, AndrewHowse, Cydebot, Island Dave, 2 of 8, Rifleman 82, Gogo
Dodo, Red Director, Sloth monkey, JuliaHavey, Wildnox, Dancter, Tawkerbot4, Dragomiloff, Juansempere, NEtReVoLuTiOn, Energetic
is francine@yahoo.com, Roberta F., DumbBOT, RoboNerd, Emmett5, Omicronpersei8, Mark7211, Krylonblue83, Itsme2003, FrancoGG,
Thijs!bot, Gacggt, Epbr123, Barticus88, Biruitorul, Opabinia regalis, Voltaic, CopperKettle, Mechcozmo, Hcberkowitz, Tmguchi, He-
lix589, Headbomb, Jojan, Marek69, NorwegianBlue, Leon7, CharlotteWebb, The Hybrid, Davisxa, Zdli005, Tidusx145, Natalie Erin,
Steven25615, Jmc wiki, Mentifisto, Jorian-Kell, Calaka, AntiVandalBot, Jalan z, Fru1tbat, Tjmayerinsf, LibLord, Felishumanus, Mestre,
Falconleaf, Charantea, Storkk, Ironiridis, NorthOfTheCity, Joehall45, Res2216firestar, Cdrikari, Annekcm, Deflective, Kaobear, Pen-
twirler, Barek, Downstrike, MER-C, Xemxija, Instinct, Janejellyroll, MelanieN, OhanaUnited, Greensburger, Rok Bura, Job314, John-
Murphy, Stronbull, Andreas Toth, Magioladitis, Rbwilson, Parsecboy, VoABot II, LogicUser, Tripbeetle, AuburnPilot, MastCell, Jdlankin,
EOBeav, JDRF, Npang, HHggff, Iftt~enwiki, Dr.Gangino, Richardtc, Sstrumello, DB specialist, NLLIC, Compact105, Catgut, WhatamI-
doing, Animum, Nposs, Wikiak, Loonymonkey, 28421u2232nfenfcenc, Afaprof01, Allstarecho, Sapnafive, Glen, DerHexer, Hansr8,
SparkyLee, Robkeenan11, WLU, Patstuart, War wizard90, Monagc, AliaGemma, Danielcrockett, S3000, Yobol, MartinBot, Dsloct2691,
CliffC, Jeendan, Ncurrier, Arjun01, Poeloq, Greekfever, C.brian.taylor@gmail.com, Chickenboner, Anaxial, Jack007, Mschel, Murray-
huntington, Ayotte, Lightwt, Pekaje, Oopie, Ash, Jeremygentles, Ingleopard~enwiki, Cyrus Andiron, BGOATDoughnut, Cubetriangle,
Paranomia, J.delanoy, Pharaoh of the Wizards, Nev1, Deedeedum, Benny 142, DrKiernan, Ezzsakr, Bogey97, Nbauman, Peter Chastain,
TyrS, Dcaronejr, Boghog, Maurice Carbonaro, Gogglebum, Aetkin, Feegit, Pharmassist, Bellthorpe, Aaron Simon, Sharlene Thompson,
Bizflyer, Faldizzle, Gobawoo, Shauna 1200, Shawn in Montreal, Katalaveno, DarkFalls, Povertycat, OldRoy, Jeepday, Naniwako, Mikael
Häggström, Donaldtrumalumpy, Gurchzilla, Mbbradford, WebHamster, Rocket71048576, AntiSpamBot, Ltlioe, Vitanova, BoredTerry,
HealthiNation LLC, Plasticup, Es uomikim, Mary Edward, NewEnglandYankee, SJP, JenC2, Jasanchez, T3hllama, Ljgua124, Bigdumb-
dinosaur, Sangriademuertos, Sunderland06, MetsFan76, Wuzzybaba, Enix150, Shshshsh, WJBscribe, Senthilvelsp, Remember the dot,
Anonymous251, Whodondon, Blue42andredflag99, Potaco99, JavierMC, Jtdaugir, ELLusKa 86, Xiahou, Fappy, DRAJ 25, Filthy mank-
ins, Idioma-bot, TNTfan101, Signalhead, Fr33kman, Sooner Dave, Wikieditor06, Gogobera, X!, My Core Competency is Competency,
HamatoKameko, Deor, VolkovBot, UKMatt123, ABF, Ankabout, Petersonbill64, Sbyhre, Cazarooni, Macedonian, Nickmattress, Jeff G.,
Alexandria, VasilievVV, Philip Trueman, Koda2828, TXiKiBoT, Mitsver, BuickCenturyDriver, Irberry, Jere123 9, Dockarenf, Emeiste,
Jlanier, A4bot, NipokNek, Joehall219, Youni43, Ann Stouter, Tarrom, Cashpotato, The promise1010, Bob103051, Gekritzl, Donimo,
Cochan, Bahruth, Cool moe dee 345, Frankortmann, Jackfork, LeaveSleaves, Optigan13, Monkeynoze, Cnyh, BearGuard, Benebenbike,
Quindraco, Rumiton, ACEOREVIVED, Fuzzywallaby, Wilsonfosho, CO, Zain Ebrahim111, Roland Kaufmann, Stevey101, Wiki is my
homepage, Constantine Gorov, Egyptian lion, Doom2k6, Snash13, Synthebot, Ziphon, Enviroboy, RL123, Sonichypr4, Seresin, Insanity
Incarnate, Chenzw, Northfox, Countincr, Palaeovia, Doc James, AlleborgoBot, Peterpickle, ClintMalpaso, Me020, Me202, JENNAJOE,
Cbanks88, Abellina, Lindakenny, Macanima, Peter Fleet, SieBot, SirLeopold, 4wajzkd02, Ødipus sic, Sav vas, Danushk1, YourEyesOnly,
Josconklin, Dawn Bard, Gobbly2100, Viskonsas, Caltas, Xymmax, RJaguar3, Triwbe, Reuqr, AlcheMister, Mr smith87, Keilana, Tiptoety,
Alexbrn, Kristinwt, Oda Mari, Jpala, JSpung, JuanFox, BlueCerinthe, Oxymoron83, Ioverka, Antonio Lopez, Rhcastilhos, KPH2293,
Kochipoik, Lightmouse, Ufinne, Sinkwa, Rlewinson, Johndheathcote, Wiki-ny-2007, Spitfire19, Mike2vil, Jacob.jose, Meowist, Realm
of Shadows, Maralia, Ianupright, Imathiotis, Richard David Ramsey, Jl1995, Tatterfly, Troy 07, Gibbzmann, Invertzoo, Prof. Campbell,
WikipedianMarlith, Martarius, Elassint, ClueBot, Rumping, GorillaWarfare, PipepBot, Ideal gas equation, The Thing That Should Not
Be, Seth3481, Librarian2, Ewawer, Drmies, Sanjeev.singh3, CounterVandalismBot, Jamistic, Mrchadsexington, Otolemur crassicaudatus,
Wsbsteven, Internetking, Neverquick, Auntof6, DragonBot, Hard rock hurricane, Excirial, Krishnan2424, Gnome de plume, Stuatskool,
Likeacupatea30, Davegomes, Erebus Morgaine, Eeekster, Skypen, Lartoven, Bertrus, AnthroGael, Tyler, Yim00, Sepeople, Cenarium,
Samarsyed, Peter.C, Jotterbot, Kingskid 727, Promethean, Putrid76, Kaiba, Razorflame, Mikaey, SchreiberBike, Muro Bot, Discover-
Worlds, Stepheng3, Unmerklich, Thingg, 1ForTheMoney, Aitias, DoctorEric, Zig-Zag Zig-Zag, SeanCastillo, Barrymahon, Fantus 8,
Gogebic, Wilford Brimley’s Diabeetus, Bücherwürmlein, Hyoshida, Shoteh, DumZiBoT, RexxS, Burelom, Havenoterty, InternetMeme,
Pinkelk, XLinkBot, Unidoctor, Jytdog, Jbmweb1, Dthomsen8, ThujaSol, Adambigmac, Drmanukrishnan, Skarebo, SilvonenBot, Rais-
inbreadwithapplesauce, Mifter, Alexius08, Arunjithp, Smileh, TamePhysician, Matrixhealth, Good Olfactory, VMKiller, Thatguyflint,
HexaChord, Eshubn, Addbot, Willking1979, MrZoolook, Matt641, DOI bot, Shawisland, Bristlenosecat, Joeybleach72, Binary TSO,
HateThePolice329, Nora nettlerash, NoNoonNo, Antnoah, Anjik, Parkicar, Me Three, Fieldday-sunday, BF2MCplaya4life, Ldchalem,
Sixuntilme, Leszek Jańczuk, Blappen, Diptanshu.D, MrOllie, Soxfan1112, Download, LaaknorBot, Chamal N, Meddance, Ccacsmss,
Glane23, Imfatx, Kknd123, Nerdwienerpig, Debresser, Quercus solaris, Renatokeshet, Numbo3-bot, Tide rolls, ScAvenger, Ivancurtisivan-
curtis, Ettrig, JSR, Legobot, Luckas-bot, Wooblz!, Yobot, Kartano, Dooste, Legobot II, Dsmorton, Nirvana888, Mmxx, Wilmar ArthurB,
D.3emad, Farloth, IW.HG, Cm3208708, Eric-Wester, Watchmann1, N1RK4UDSK714, AnomieBOT, Nutriveg, Letuño, Katheryne S,
Krisandie, Areyouinparis, IRP, Piano non troppo, Chuckiesdad, Kingpin13, Flewis, Materialscientist, Imkool93, Rantwell, Rtyq2, Citation
bot, OllieFury, Maxis ftw, Ouroboros726, Ferrari lobby, Madsaw332, Nthoang1039, Xqbot, BruceMiller, Dzotx, Capricorn42, Gigemag76,
Wperdue, GatorInCary, A455bcd9, Gilo1969, InternationalDiabetesFederation, Grim23, Teamjenn, Jmundo, Thiruvelan, Anna Frodesiak,
Locos epraix, Zip0777, Cheesewheelz, Even Adam1000, JCrue, Maddie!, Thorn breaker, Almabot, Anonymous from the 21st century,
Luvhawtpink, GrouchoBot, Annalise, Wiki emma johnson, Trafford09, Sophus Bie, GhalyBot, Smallman12q, Verbum Veritas, Shad-
owjams, Aaron Kauppi, Bcd760, Tannim101, AJCham, Gcjblack, Dougofborg, Parchbold, Mymommytime, Gmonari, Alexander0884,
CSyver, Depictionimage, FrescoBot, Tangent747, Vchavez1984, Doctor Incarnate6, Paine Ellsworth, Kehelm, Jatlas, Tobby72, Saintge-
orge2, Doctor Incarnate62, LuisArmandoRasteletti, Laurel7000, TimonyCrickets, Nisavid, Apeplinskie, Contentmaven, Nightrunner10,
Rkr1991, Plowsie, Danhomer, Criticalsoul, Cannolis, Citation bot 1, FYWassignment, Wuthering123, Javert, Mintsmike, Hiholetsgow, I
22.1. TEXT 389

dream of horses, Elockid, Mrwick1, Jmadhura, Wikispaceman, Jackrace, KeithBeltham, A8UDI, Sealpoint33, Tyrfan, RedBot, Ant62493,
Cheekychappiecharlie, E36613, Thecurran91, MedicineMan555, Brndlnbs, Jauhienij, Zinbarg, Lightlowemon, FoxBot, Lando Calrissian,
TobeBot, Trappist the monk, Aytrus, Etincelles, Carrrrrnez, Lotje, SciCorrector, Steelerdon, Dinamik-bot, Connormilton, Thedentistmod,
Lemonpeiman, David Hedlund, ReidpBoJangles, Testosterone vs diabetes, SmozBleda, The Pink Oboe, Aniten21, Ryanv.hockey, Rjwilm-
siBot, Aidan Kehoe, TjBot, RepliCarter, Abaute, DentalSchoolProfessor, Whywhenwhohow, EmausBot, WikitanvirBot, Stemscientist,
Heimoma, Everybear, Diabetes666, Eetom, Mktgguest1, We hope, Springerkup, H3llBot, Jonathansammy, AManWithNoPlan, Point-
less.FF59F5C9, Jesanj, Brandmeister, Euzen, Gsarwa, The Fourth Dimension, Jabaway, Alcazar84, L1ght5h0w, Teaktl17, ClueBot NG,
Cuddyer55, Theaitetos, Khangrah, Kevin Gorman, Chonchonr, JTT Young, Ryan Vesey, Jrobin08, Helpful Pixie Bot, Regulov, Lowercase
sigmabot, Moscone, Umar farooq miana, Socialmaven1, Je.rrt, Tomcorsonknowles, May Prumar, 14940674md, Fuse809, Lmlmss44, Bat-
tyBot, Biosthmors, Piers126, Toneda, ChrisGualtieri, TylerDurden8823, Ajv39, BrightStarSky, Ravidhruv04, Dexbot, FoCuSandLeArN,
Morrowfolk, RachulAdmas, KhryssoHeart, Monticores, SolubleAtoms, CorinneSD, Lucid3D, Ibn Ridwan, Vaughn88, Robertprowser72,
Alexd1010101, Binko100, BruceBlaus, Alice Person, Darkesthoursoflife, Igoody, Chemistry74, JEMZ1995, Giancarlobasile, Monkbot,
Luigi Albert Maria, Rakeshyashroy, UCSFrb1983, Thechirogarage, EditorAliShah, John Buller, KasparBot, Ruftas and Anonymous: 1699
• DNA replication Source: https://en.wikipedia.org/wiki/DNA_replication?oldid=671555954 Contributors: AxelBoldt, The Anome, Van-
deresch, Graft, Heron, Lexor, Skysmith, Alfio, Ahoerstemeier, Habj, Samuel~enwiki, Fibonacci, Robbot, Baldhur, ZimZalaBim,
Whiteniko, Hadal, Lupo, Oddharmonic, Giftlite, Bensaccount, FriedMilk, Adenosine, Pgan002, GD~enwiki, Jossi, Taka, Ary29, Neutral-
ity, Julianonions, Imjustmatthew, Mike Rosoft, Rich Farmbrough, Guanabot, Vsmith, Xezbeth, Bender235, Kaisershatner, El C, RoyBoy,
Adambro, Bobo192, Stesmo, Whosyourjudas, Smalljim, Cmdrjameson, Arcadian, Timl, Dennis Valeev, La goutte de pluie, Nhandler,
Nsaa, Alansohn, Arthena, Wouterstomp, Stillnotelf, Snowolf, Ravenhull, Velella, ClockworkSoul, Tycho, Netkinetic, RyanGerbil10, Jack-
hynes, Before My Ken, Fbv65edel, MONGO, LadyofHats, Plrk, Dysepsion, Snafflekid, Rjwilmsi, SMC, Thisismikesother, Alveolate, The
wub, Mortice, FlaBot, Cless Alvein, RobertG, Nihiltres, Alphachimp, BradBeattie, Chobot, Whosasking, YurikBot, Borgx, WAvegetarian,
Chris Capoccia, GLaDOS, SpuriousQ, Thiseye, Malcolma, Daniel Mietchen, Jpbowen, InvaderJim42, Raven4x4x, RUL3R, Wangi, Jhin-
man, Closedmouth, Maristoddard, Pb30, Xaxafrad, Svetlana Miljkovic~enwiki, Mfedder, JoanneB, CIreland, Rystic, SmackBot, Andthen-
dougsaid, Ariliand, InverseHypercube, KnowledgeOfSelf, Royalguard11, Bomac, Stepa, Eskimbot, CapitalSasha, Bozartas, Edgar181,
Blondtraillite, Zephyris, Ashermadan, Freddy S., Gilliam, DividedByNegativeZero, Skizzik, ERcheck, Andy M. Wang, Bluebot, Persian
Poet Gal, JDCMAN, Tree Biting Conspiracy, Hichris, MalafayaBot, Celarnor, Zrulli, Bowlhover, Richard001, Drphilharmonic, Madeleine
Price Ball, SashatoBot, Harryboyles, Scientizzle, Gobonobo, JulianBlow, Thegathering, Edwy, Steipe, Mgiganteus1, MichaelHa, Pseudo-
Sudo, A. Parrot, Stwalkerster, Noah Salzman, Wrlampe, Romanticcynic, TastyPoutine, Artman40, Sasata, Hu12, Dan Gluck, JayZ, Twas
Now, Igoldste, Yukaxu, Pranay Biswas, Tawkerbot2, Dave Runger, Yashgaroth, Falconus, Jpeguero, Superandomness, JForget, CmdrObot,
Agathman, Harej bot, AKaK, Dgw, Tex, Tomjc, Ppgardne, Meno25, RelentlessRecusant, Was a bee, Macduy, Narayanese, Biomedeng,
Thijs!bot, Epbr123, Pstanton, Ucanlookitup, Nonagonal Spider, Marek69, Crazysunshineboy, Sturm55, Pfranson, CTZMSC3, Danthe-
man531, Mentifisto, David D., AntiVandalBot, Majorly, BokicaK, TimVickers, Shajilvt, TexMurphy, Tlabshier, Farosdaughter, Bio-queen,
Instinct, Jonemerson, Hello32020, Jullag, Tstrobaugh, MSBOT, Freedomlinux, VoABot II, Sedmic, Arthmelow, SparrowsWing, Midgrid,
Olavrg, Catgut, Cyktsui, Emw, DerHexer, Squidonius, MartinBot, STBot, Rettetast, Anaxial, CommonsDelinker, Player 03, Victor Bla-
cus, Exarion, J.delanoy, Harsha112, Maurice Carbonaro, Captain Infinity, Ignacio Icke, MrErku, Mikael Häggström, WebHamster, Jcwf,
Omes, NewEnglandYankee, Firelement85, Mufka, Hanacy, Iduggin, MishaPan, Useight, VolkovBot, DrMicro, AlnoktaBOT, Pkakaris, So-
liloquial, Aesopos, Philip Trueman, Tameeria, A4bot, Monkey Bounce, JhsBot, Leafyplant, Im emo tastic, Archdevil75, LoneSeeker, Dr.
Anton Funk PhD, Sylent, Guelphie, Twooars, Guelphie85, PGWG, Sandymit, Rafis v, Nubiatech, Work permit, BotMultichill, ToePeu.bot,
Sakkura, Eganio, Radon210, Yerpo, Oxymoron83, Erick880, Faradayplank, Nancy, BSoD, Capitalismojo, Mygerardromance, Ucphilsc,
Gloss, Nornour, ClueBot, Mstuddert, Medfreak, The Thing That Should Not Be, Voxpuppet, Unbuttered Parsnip, Kusb, Blanchardb, Nev-
erquick, Cirt, Arunsingh16, Canis Lupus, Alexbot, Cookatoo.ergo.ZooM, Tassos Kan., Gregoots, Duxenaz, 101louise101, Kakofonous,
Aitias, ForestDim, Burner0718, Johnuniq, DumZiBoT, Residenthalo, Jovianeye, Vojtěch Dostál, SilvonenBot, Jimhsu77479, Jadtnr1, Cal-
ito00000001, Addbot, DOI bot, Chasturn, CanadianLinuxUser, Ka Faraq Gatri, Download, LaaknorBot, Coveman999, Bernstein0275,
Debresser, Favonian, LinkFA-Bot, Rtz-bot, Numbo3-bot, Tide rolls, Gail, Megaman en m, Legobot, Luckas-bot, Yobot, Andreasmperu,
Nallimbot, Azcolvin429, AnomieBOT, LLDMart, Nutriveg, EryZ, Bluerasberry, FangedFaerie, Citation bot, ArthurBot, Xqbot, JimVC3,
RibotBOT, WaysToEscape, Brianwatson94, Media1312, AstaBOTh15, Pinethicket, I dream of horses, 10metreh, Robinhaw, Σ, Emply
shell China dry, Dac04, Saintonge235, Trappist the monk, Jonkerz, TBloemink, DragonofFire, Reaper Eternal, Skakkle, Kidwet, Jessi bob,
DARTH SIDIOUS 2, Whisky drinker, RjwilmsiBot, DASHBot, Immunize, Lotez, Bob100077, Golfandme, Wikipelli, Dusanman1, PJin-
Boston, JSquish, Access Denied, OnePt618, Cyberdog958, Flightx52, Scientific29, Puffin, Ego White Tray, Orange Suede Sofa, Demon-
icPartyHat, Chatmonregina, Petrb, ClueBot NG, Dwc89, Rsc227, Mesoderm, Widr, Bosborne21212, Theopolisme, Wbm1058, BG19bot,
Joydeep, Syeda Hassan Rabia, NotWith, Smettems, Lsanman, Shaun, Thermodynamic, BattyBot, Zhaofeng Li, Stigmatella aurantiaca, Rin-
kle gorge, Deathlasersonline, Ricochet Jones, Dexbot, Saba irshad, Mohamed 151995, YurTru, Kfh123, Everything Is Numbers, Churn
and change, Kevin12xd, GabeIglesia, Epicgenius, FallingGravity, U1012738, Melonkelon, Tentinator, Epic123456789, MedicalStuden-
tOxford, Triolysat, Jlmalcos, JaconaFrere, Bonob, Stormmeteo, Monkbot, Vieque, Freddieyao167, AmericanSocialist, Paul Badillo, Dai
Pritchard, RationalBlasphemist, Manal Adil, KasparBot and Anonymous: 745
• DNA repair Source: https://en.wikipedia.org/wiki/DNA_repair?oldid=663011058 Contributors: Fnielsen, JDG, Stormwriter, Lexor,
Ixfd64, Angela, JWSchmidt, Schneelocke, Quizkajer, Ec5618, Steinsky, Samsara, Dbabbitt, Raul654, Pir, Stephan Schulz, Tualha, Yosri,
Hadal, Bhuvanesh aravind, Giftlite, Nunh-huh, Herbee, Duncharris, Eequor, Solipsist, Edcolins, ALargeElk, PhiloVivero, Utcursch, Shib-
boleth, PDH, Jimaginator, Monkeyman, Discospinster, Nina Gerlach, Kenb215, Prometheus1~enwiki, Fenice, Brian0918, MisterSheik,
Autrijus, Jon the Geek, Arcadian, Harvestgalaxy, Martinmmc, Giraffedata, La goutte de pluie, Athf1234, Pschemp, Abstraktn, Chfosli,
Alansohn, Gargaj, Wouterstomp, Axl, Dark Shikari, Emvee~enwiki, LukeSurl, Mindmatrix, Benbest, Harrison35, Grammarbot, Rjwilmsi,
Angusmclellan, Oblivious, Brighterorange, Pruneau, RobertG, Ali Raza, Tone, Wavelength, Mushin, Splintercellguy, Zafiroblue05, Chris
Capoccia, Rintrah, Tavilis, NawlinWiki, Aeusoes1, Welsh, Yoninah, Wknight94, Leptictidium, Deville, Nikkimaria, Allens, RG2, Alex-
trevelian 006, SmackBot, Ariliand, Foosh, Mdd4696, Edgar181, PiKeeper, Kazkaskazkasako, Chris the speller, Cadmium, Deli nk, Ikiroid,
Marcosantezana, Superdix, JonHarder, GVnayR, Roncalli, Smokefoot, Drphilharmonic, Clicketyclack, Ching-3, DO11.10, Aleenf1,
Smith609, Mr Stephen, Serephine, SandyGeorgia, Ginkgo100, Grasshoppa, Agathman, Ninetyone, Jimktrains, Cydebot, Gogo Dodo, Red
Director, Bavan Palasanthiran, Christian75, Asenine, Thijs!bot, Opabinia regalis, CaMpixx, Amazinglarry, Headbomb, TimVickers, Jay
Gatsby, Mr. Blackout, RebekahThorn, WhatamIdoing, Cyktsui, Asbhagwat, Emw, JoergenB, DerHexer, Patstuart, Otvaltak, FisherQueen,
MartinBot, PAK Man, DrKiernan, Umarekawaru, Arup Acharjee, NYC-METS, Alnokta, Juliancolton, Uhai, Treisijs, Auk nambiar2002,
VolkovBot, Deepa.kushwaha, Radowayne, Rei-bot, Wikiisawesome, Eugeneltc, Amboo85, Bruno in Columbus, CephasE, Trilateral comm,
HaHa AI, SieBot, Graham Beards, Lightmouse, Mike2vil, Maralia, Forluvoft, ClueBot, HujiBot, Scientist101, 718 Bot, Gerriet42, Nucle-
arWarfare, Jonverve, ForestDim, LostLucidity, PervyPirate, Vojtěch Dostál, Snapperman2, Addbot, DOI bot, Bernstein0275, Tornsubject,
LinkFA-Bot, Kurtz22, Verbal, Synthetase, Tedtoal, Luckas-bot, Yobot, Amirobot, AnomieBOT, Nutriveg, Materialscientist, Bhyun5, Ci-
390 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

tation bot, TheAMmollusc, TinucherianBot II, Capricorn42, Firassalim, Tyrol5, RibotBOT, Methcub, FrescoBot, Gnomehacker, Citation
bot 1, Lagnajeet, MolBioMan, Robinhaw, Wigbold, Mr a retha, Tim1357, Trappist the monk, Reaper Eternal, Kiko0610, Tbhotch, Jesse
V., El Mayimbe, RjwilmsiBot, Tumadre36, Dcirovic, A2soup, Clementine2009, Itizen, Kittenono, Bulwersator, Puffin, ChuispastonBot,
ClueBot NG, Kaushlendratripathi, Frietjes, Theopolisme, AvocatoBot, CitationCleanerBot, Biosthmors, Amnot Areso, Mohammid, Jion-
pedia, Dexbot, FishingKing, Saba irshad, Lone boatman, Everything Is Numbers, Joeinwiki, Melonkelon, DavidLeighEllis, Stevia badger,
Triolysat, Chaya5260, Alex Childs, Monkbot, Sjones008, Χρυσάνθη Λυκούση, DaveJones2, Talha9977, Anitasimha, JamDeliSoup007
and Anonymous: 176
• Oncogene Source: https://en.wikipedia.org/wiki/Oncogene?oldid=671724157 Contributors: Magnus Manske, Bryan Derksen, Taw, Mal-
colm Farmer, Ed Poor, Zashaw, Skysmith, Kricxjo, JWSchmidt, Charles Matthews, Jaimeglz, Robbot, Electric goat, HorsePunchKid,
Immunoboy, PFHLai, Jigorou, Brim, Arcadian, Oncogene, Matani2005~enwiki, Wouterstomp, Pen1234567, Axl, Tomythius, TenOfAll-
Trades, Jackhynes, CyrilleDunant, EnSamulili, Palica, Graham87, Rjwilmsi, FlaBot, Margosbot~enwiki, Terrace4, Dj Capricorn, Bub-
bachuck, YurikBot, Wavelength, Gaius Cornelius, Rmky87, JHCaufield, Bota47, Pb30, Dr.alf, Xanin, GrinBot~enwiki, AndyZ, RobotJcb,
Picobyte~enwiki, Bluebot, RDBrown, Not Sure, Miguel Andrade, Anabus, NicolasStransky, David cameron, Drphilharmonic, Nishkid64,
IsaacD, Kyoko, JoeBot, Trialsanderrors, Raetzsch, CmdrObot, Yoni bhonker, Robinatron, RelentlessRecusant, Thijs!bot, Opabinia regalis,
CopperKettle, Headbomb, AntiVandalBot, JAnDbot, Quentar~enwiki, Instinct, Maias, .anacondabot, Sedmic, LedgendGamer, J.delanoy,
Nbauman, Hakushu8, Rod57, Mikael Häggström, Tmarshll, Tarotcards, EquationDoc, Cometstyles, Cmastris, Idioma-bot, VolkovBot,
Philip Trueman, TXiKiBoT, Rei-bot, Porsch1909, UnitedStatesian, Dr.michael.benjamin, Bfpage, SieBot, Bform, Z3n0s, ClueBot, BO-
Tarate, Banano03, DumZiBoT, XLinkBot, Jytdog, Deepfreeze63, Addbot, Salwateama2008, DOI bot, Tanhabot, Numbo3-bot, Tide rolls,
Lightbot, ‫ماني‬, Luckas-bot, Yobot, Materialscientist, Citation bot, Analphabot, Gumruch, Peter Beattie, Rezarj, FrescoBot, Amkilpatrick,
RjwilmsiBot, TjBot, EmausBot, XinaNicole, Brodyt66, Dcirovic, Savh, ZéroBot, Jhnson134, Minnsurfur2, Will Beback Auto, ClueBot
NG, Ejgx93, Wthanassi, Chester Markel, Jpgill86, Czernilofsky, P'tit Pierre, Msozmen2, BattyBot, Luckydhaliwal, ChrisGualtieri, Fred-
diecrane1, Saltwolf, SFK2, Haywardlc, Phupe1, Rjdodger, Ginsuloft, Monkbot, HopeBinns, KasparBot and Anonymous: 108
• Transcription (genetics) Source: https://en.wikipedia.org/wiki/Transcription_(genetics)?oldid=672143886 Contributors: Mav, The
Anome, Michael Hardy, Zashaw, Lexor, Kku, Menchi, Ronz, JWSchmidt, Александър, Mxn, Ec5618, Fuzheado, Steinsky, Phil Boswell,
Kzhr, Timemutt, VanishedUser kfljdfjsg33k, Giftlite, Michael Devore, Bensaccount, Duncharris, Antandrus, G3pro, Oneiros, PFHLai,
Grunt, Archer3, DanielCD, Discospinster, Mgtoohey, Pabloes, Perfecto, AKGhetto, Tmh, Arcadian, Sriram sh, Srlasky, Haham hanuka,
Alansohn, Terrycojones, Sl, Wouterstomp, Riana, Seans Potato Business, Batmanand, Helixblue, Tycho, Amorymeltzer, GabrielF, Cey-
ockey, RyanGerbil10, Brookie, Woohookitty, Mindmatrix, EnSamulili, Fbv65edel, Mms, Jclemens, Dpv, Sjakkalle, Rjwilmsi, FlaBot, Mar-
gosbot~enwiki, Vossman, Fenoxielo, Roboto de Ajvol, Wavelength, Postglock, WAvegetarian, Hede2000, Rosieredfield, Shanel, Rmky87,
Bucketsofg, WAS 4.250, JoanneB, Curpsbot-unicodify, Teply, Mengxu, Hughitt1, SmackBot, TestPilot, Martin.Budden, Hydrogen Iodide,
Geno-Supremo, Apers0n, Zephyris, Yamaguchi , Gilliam, BrotherGeorge, Kazkaskazkasako, Evandrix, Aaadddaaammm, MalafayaBot,
Uthbrian, Oxhop, Miguel Andrade, DHN-bot~enwiki, Ribrob, Vidric, Khoikhoi, Totophe64~enwiki, Richard001, Drphilharmonic, Kshieh,
Ifan160, Kukini, CoeurDeLion, The undertow, Nishkid64, ArglebargleIV, AThing, Kuru, Epingchris, Bloodpack, Ben Moore, Mark-
Sutton, Slakr, Noah Salzman, Iridescent, Gentlemaan, Peter M Dodge, Kaarel, Cph3992, JForget, Liam Skoda, CmdrObot, Overlord-
Kain, Bonás, Agathman, Sameerbau, Spottydog3, Neelix, Opus118, Yided, Tomjc, Nuplex, Nick.wiebe, RelentlessRecusant, Was a bee,
Corpx, Smelissali, Narayanese, Vanished User jdksfajlasd, Phi*n!x, Thijs!bot, Opabinia regalis, Mojo Hand, John254, NERIUM, Kick-
assso, AntiVandalBot, MoogleDan, BokicaK, Eltanin, NightwolfAA2k5, TimVickers, Smartse, MDG38, Neur0X, Legolost, Kswenson,
Dcooper, Jullag, Greensburger, .anacondabot, VoABot II, LeaHazel, Antorjal, Squidonius, NunoAgostinho, MartinBot, Cvd5012, Rettetast,
Anaxial, R'n'B, Qrex123, Huzzlet the bot, HoergerJ, SU Linguist, Lantonov, Rod57, KDSKDS, Jmajeremy, Mikael Häggström, Martyn
Axon, Antony-22, Vanished user 39948282, Useight, Zamftb, Llorenzi, G. Völcker, Hammersoft, Saurabh523, Nburden, AlnoktaBOT,
Scresawn, Philip Trueman, Segabud, Z.E.R.O., Ilia Kr., Mishlai, Furfurfur, Gillyweed, Enviroboy, Jcdietz03, RaseaC, Pjoef, Allebor-
goBot, Kehrbykid, PGWG, ASDZXCQWE, SieBot, Nubiatech, Sophos II, Sakkura, Lucasbfrbot, Flyer22, Teethies563, Yerpo, Sunrise,
Iknowyourider, DaDrought3, Altzinn, Neta90, Brettbarbaro, Forluvoft, ClueBot, Binksternet, Paulabek, DragonBot, Excirial, PixelBot,
Skyuppercutt, Cbailey7, Sydney3803, Frigginacky, SchreiberBike, LeighClesterMolar, Thingg, BVBede, Qwfp, Johnuniq, Local hero,
XLinkBot, LostLucidity, Feinoha, Vojtěch Dostál, WikHead, Yvorez1274, Drosilia, Hilwhale, Alohascott, Geir.overland, Addbot, DOI bot,
CanadianLinuxUser, R-skin, Lehtv, ChenzwBot, Tide rolls, Gail, Tedtoal, Luckas-bot, Yobot, Ptbotgourou, Berkay0652, TaBOT-zerem,
Amirobot, KamikazeBot, The Flying Spaghetti Monster, Legendre17, AnomieBOT, Kerfuffler, Jim1138, Kingpin13, Hpswimmer, Citation
bot, Maxis ftw, Quebec99, Marshallsumter, Xqbot, GrouchoBot, Brandon5485, Vikky2904, E0steven, Thehelpfulbot, Rgocs, FrescoBot,
Brianwatson94, S73v3n, Citation bot 1, I dream of horses, Foureyes915, Flecha2, A8UDI, RedBot, Mexican9493, Orenburg1, Bursting74,
Περίεργος, Ferrari430man, Amkilpatrick, Jcorry10, Gamingmaster125, Tbhotch, Jesse V., Galneon23, RjwilmsiBot, Pjshort42, J36miles,
EmausBot, WikitanvirBot, RA0808, Transitiveinstance, Wikipelli, K6ka, 20Lukianto, Grunny, John Mackenzie Burke, EWikist, Wayne
Slam, Tropicalpurplekitty, Donner60, BioPupil, Theislikerice, ChuispastonBot, Jeffpkamp, AnnaJune, ClueBot NG, This lousy T-shirt,
Rida97, Liney22, Alex-engraver, Mesoderm, Jogmiers, Brynedal, Ajdavis5, Yasmeh, Jacobso4, Helpful Pixie Bot, Miguelferig, BG19bot,
Bths83Cu87Aiu06, CatPath, Dhp4, MusikAnimal, Cncmaster, Mdebortoli, Barton1234, Cmcclean22, Lolzpvp, Roleren, Klilidiplomus,
SIMONCOHEN, BattyBot, TuringMachine17, Jimw338, Sermadison, Iamozy, Kelvinsong, Saba irshad, Mohamed 151995, Avijitarya64,
Guma44, Dreesem, Xxkitsune, Limelightmk, FallingGravity, Lemnaminor, Melonkelon, Aadharm, Wally 84, MopSeeker, Quenhitran,
APsCollegeEditor, Slj758, ChelseaE, Mjt3727, Wikicology, Iwilsonp, Rai hamid raza kharal, Cyrej, Zhirzh, Mmm053, KasparBot and
Anonymous: 508
• Regulation of gene expression Source: https://en.wikipedia.org/wiki/Regulation_of_gene_expression?oldid=657002314 Contributors:
AxelBoldt, Magnus Manske, Michael Hardy, Booyabazooka, Lexor, Kku, Darkwind, Pengo, Bensaccount, Jfdwolff, Fjarlq, Garrett~enwiki,
Onco p53, PDH, Mike Storm, Nina Gerlach, Arcadian, Pearle, Alansohn, Wouterstomp, Seans Potato Business, Melaen, Woohookitty,
VoltairesBastard, Rjwilmsi, Quale, Stevenfruitsmaak, Sceptre, Gaius Cornelius, Kkmurray, Turan~enwiki, Mahdim, Tevildo, Allens,
SmackBot, TestPilot, AndreasJS, ElAmericano, Jethero, JonHarder, TedE, Drphilharmonic, Clicketyclack, Chenli, Ale jrb, Agathman,
Narayanese, Smartse, Mr mutwil, Ph.eyes, Greensburger, Gomm, Squidonius, Jasonmbechtel, Nono64, Trusilver, Boghog, Yonidebot,
Chopin-Ate-Liszt!, Mikael Häggström, SteveChervitzTrutane, STBotD, Emmertjp, X!, Annatyler23, TXiKiBoT, Jgreally, Antoni Ba-
rau, Rei-bot, Nassirys, ‫כל יכול‬, AlleborgoBot, Active contributor, Aarre, Jwclement, Mauritsmaartendejong, Mike2vil, Forluvoft, Dan-
CAK, ClueBot, Tomas e, Arjayay, Ngebendi, Kembangraps, Addbot, Diuturno, DOI bot, Jimbothegreek, Mrs Often, Luckas-bot, Yobot,
AnomieBOT, Eahd201, Templatehater, MauritsBot, Xqbot, Capricorn42, Unscented, Bluemonkey33, Fdardel, FrescoBot, Mamaberry11,
Hosszuka, HJ Mitchell, Citation bot 1, LittleWink, Amkilpatrick, Jesse V., EmausBot, John of Reading, WikitanvirBot, Ikerus, Dcirovic,
Serketan, John Mackenzie Burke, Gongoozler123, ClueBot NG, Msks, Froggermaster96, Ayush girish nagar, DS Belgium, Mesoderm, Joel
B. Lewis, Waterlae, Helpful Pixie Bot, Monolemma, Paul Kemp~enwiki, Neuroschizl, Duxwing, ChrisGualtieri, Iamozy, Kirill Tsukanov,
Apynekeeper, Clucaj, Tfrand, Hatagalow, Seamsurgegen, Mon3oturf, Monkbot, Gschliss and Anonymous: 97
22.2. IMAGES 391

• Translation (biology) Source: https://en.wikipedia.org/wiki/Translation_(biology)?oldid=667059560 Contributors: The Anome, SimonP,

Graft, Lexor, MichaelJanich, JWSchmidt, MichaK, Timwi, Taoster, Robbot, Josh Cherry, Rolando, Peak, Modulatum, Sverdrup, Timemutt,
Giftlite, Kim Bruning, Bensaccount, JuanitaJP, Gadfium, Dan aka jack, Phe, G3pro, PDH, PFHLai, M1ss1ontomars2k4, Duja, Nina
Gerlach, ESkog, Chewie, CanisRufus, MBisanz, Irrbloss, Arcadian, Fotinakis, Alansohn, Chino, TenOfAllTrades, Kazvorpal, Gccwang,
Dzordzm, Achim Raschka, Unfortunate, Rjwilmsi, JHMM13, Thisismikesother, The wub, Mohawkjohn, FlaBot, Margosbot~enwiki, Voss-
man, Trinit, Chobot, Bgwhite, YurikBot, Wavelength, Kazulanth, CharlesZ, Sjdk13, Mr. Know-It-All, Closedmouth, Fortunecookie289,
Allens, SmackBot, Haza-w, InverseHypercube, Martin.Budden, Bomac, Zephyris, Gilliam, Bluebot, RDBrown, Kostmo, Uncle-P, Jbhood,
Sord halo, James McNally, Mrpark01, Salt Yeung, ZayFoTT~enwiki, Saippuakauppias, FrozenMan, Hackwrth, Neokamek, Ammonfife,
MBob, Kaarel, Yashgaroth, Bioinformin, Agathman, Pro bug catcher, Bobmarley1987, Was a bee, HilJackson, Christian75, Crum375,
SomethingCatchy, Thijs!bot, Epbr123, Rasmusw, Marek69, Pupunwiki, Orionus, Lgin, Yontally, Superdoggy, MSBOT, Alexandre Vas-
salotti, TransControl, VoABot II, Appraiser, BernardP, Antorjal, Squidonius, MartinBot, Connacht~enwiki, Yasingam, Nbauman, Gin-
sengbomb, Lantonov, ThsTorturedSoul, Mikael Häggström, Dexter prog, NewEnglandYankee, Antony-22, Nwbeeson, Alnokta, STBotD,
Xiahou, VolkovBot, OtakuNOVAkun, CrzyMke, AlnoktaBOT, TXiKiBoT, Donimo, Gabby8228, Thanatopoeia, Northfox, Lando5, Kegs-
cm13sx, Caulde, Psbsub, Cookey118, Sunrise, Forluvoft, Elassint, ClueBot, Peteruetz, Uraza, Sanbioinfo, Oldekop, Saffi2k7, Cunard,
Addbot, DB au, Wickey-nl, Jncraton, Shadowelve11, Secundus Zephyrus, Gail, Ettrig, Luckas-bot, Yobot, Intropy, Citation bot, Whang-
hansong, MauritsBot, Xqbot, YaacovCR, DSisyphBot, XZeroBot, GrouchoBot, SassoBot, Brianwatson94, Michael93555, D'ohBot, Red-
Bot, LukeGoodsell, Franckperez, Robo Cop, Stroppolo, EmausBot, WikitanvirBot, Immunize, Dewritech, RenamedUser01302013, K6ka,
ZéroBot, Matthews31, John Mackenzie Burke, DASHBotAV, Teaktl17, ClueBot NG, Mesoderm, Yasmeh, Helpful Pixie Bot, Monolemma,
AvocatoBot, Ianian123, Jzinskie, Hamish59, Kelvinsong, Lugia2453, FallingGravity, Babitaarora, Doughtar, Wall-ski, Swissactionhero,
Ryan115, Monkbot and Anonymous: 262
• Posttranslational modification Source: https://en.wikipedia.org/wiki/Post-translational_modification?oldid=667324406 Contributors:
Magnus Manske, Bryan Derksen, MarXidad, SimonP, Graft, Julesd, Jni, Stewartadcock, Bensaccount, Jfdwolff, Xwu, Pgan002, PFH-
Lai, Arminius, Rich Farmbrough, Arcadian, La goutte de pluie, Stillnotelf, Bsadowski1, Ceyockey, Tuomas Hätinen~enwiki, Reinoutr,
Woohookitty, Rjwilmsi, YurikBot, Kkmurray, Kawika, Mike Serfas, Banus, SmackBot, Edgar181, Zephyris, Clicketyclack, Madeleine
Price Ball, Epingchris, Kaarel, Vermiculus, Geobacter~enwiki, Kupirijo, A876, WillowW, ‫הסרפד‬, Thijs!bot, Opabinia regalis, GATh-
rawn22, Social tamarisk, Nbauman, Hodja Nasreddin, Bdekker, VolkovBot, Amikake3, Shuvaev, Aquaphobic, Kosigrim, SieBot, Silly
shrimp, Wmpearl, Sunrise, DragonBot, PixelBot, Thewildtype, Lemchesvej, C31004, Addbot, Bromomir, LaaknorBot, Glane23, Luckas-
bot, Yobot, Ptbotgourou, Citation bot, Eumolpo, ArthurBot, Jolivio, Citation bot 1, Mintsmike, I dream of horses, MastiBot, Jonkerz,
Dimethylformamide, Yyadam7, RjwilmsiBot, WikitanvirBot, Dcirovic, KuduIO, Minnsurfur2, Teaktl17, Yyocean, Bibcode Bot, Alon
Gabbay, Yudem, Hsp90, YFdyh-bot, Hfang bristol, Naikymen and Anonymous: 65
• Glycosaminoglycans Source: https://en.wikipedia.org/wiki/Glycosaminoglycan?oldid=664073335 Contributors: AxelBoldt, Diberri, Ar-
cadian, ClockworkSoul, RainbowOfLight, Bluemoose, Palica, Rjwilmsi, MicroBio Hawk, Bgwhite, WriterHound, Eleassar, 2over0, Stepa,
Delldot, Edgar181, David.Throop, MichaelBillington, Drphilharmonic, Beetstra, Aldert, Joseph Solis in Australia, Avac, K.murphy, Cop-
perKettle, Hoffmeier, JAnDbot, Pagz9, JNW, Indon, MiPe, Rod57, Biotechbuff, Barbaking, VolkovBot, Lyonsbane, Pedvi, Caps tiki,
SieBot, PatientAdvocateBJD, ClueBot, PixelBot, Burfine, Teutonic Tamer, Websight1, Addbot, DOI bot, Element16, Zorrobot, Luckas-
bot, Berkay0652, KamikazeBot, Rubinbot, IRP, Citation bot, Xqbot, Gonn, Captain-n00dle, Nirmos, RedBot, Full-date unlinking bot,
TobeBot, Zanhe, Symbic, Miracle Pen, Dcirovic, Llightex, BG19bot, Vokesk, Illia Connell, Cwobeel, Kenneth.jh.han, ImDiene, Ele-
phantsofearth, Victor puma, Sadegh76, KasparBot, Me Telioses and Anonymous: 42
• Proteolysis Source: https://en.wikipedia.org/wiki/Proteolysis?oldid=660761520 Contributors: Marj Tiefert, Bryan Derksen, SimonP, Ed-
ward, JohnOwens, Michael Hardy, Habj, Jotomicron, Nina Gerlach, Arcadian, Jwinius, Rjwilmsi, YurikBot, Chris Capoccia, Maxamega-
lon2000, Stepa, Algont, Roadnottaken, Clicketyclack, Svartkell, Martious, PaddyM, WillowW, Rcej, Magioladitis, Nono64, Actarux,
Hirokun, Almazi, TXiKiBoT, A4bot, Kosigrim, PhD Dre, Hzh, Champ0815, Addbot, Download, Yobot, EdwardLane, Citation bot,
ArthurBot, Xqbot, RibotBOT, LucienBOT, EmausBot, ZéroBot, A930913, Cognitive teacher, NotWith, Webclient101, Lugia2453, Hero
of Ludi, David P Minde, Brainiacal and Anonymous: 34
• Proteasome Source: https://en.wikipedia.org/wiki/Proteasome?oldid=663525024 Contributors: Magnus Manske, Marj Tiefert, Bryan
Derksen, Taw, Vanderesch, AdamRetchless, Michael Hardy, Lexor, JWSchmidt, Raven in Orbit, Stone, Shizhao, PuzzletChung, Rob-
bot, Fredrik, Romanm, Hadal, Giftlite, Michael Devore, Bobblewik, Thorwald, Rich Farmbrough, Guanabot, YUL89YYZ, Bender235,
CDN99, Longhair, Alansohn, Pspealman, Wouterstomp, ClockworkSoul, Tycho, Alai, Ceyockey, Japanese Searobin, Reinoutr, Marudub-
shinki, Graham87, BD2412, Rjwilmsi, Biochemza, Quiddity, Brighterorange, Ucucha, Lilious~enwiki, FlaBot, Whosasking, YurikBot,
Wavelength, Iayork, Chris Capoccia, Splette, Gaius Cornelius, Eleassar, Daniel Mietchen, JHCaufield, DeadEyeArrow, SmackBot, One-
bravemonkey, Kazkaskazkasako, RDBrown, BloodIce, Snowmanradio, Drphilharmonic, Serephine, Elb2000, Sasata, Martious, Fvascon-
cellos, Biogvk, The ed17, CBM, Smably, Bobmarley1987, Maxxicum, Lucadino, Cydebot, WillowW, Michaelas10, Anthonyhcole, JodyB,
Pustelnik, Thijs!bot, Gacggt, Barticus88, Opabinia regalis, Headbomb, Neil916, TimVickers, Smartse, Alphachimpbot, ThomasO1989,
Ph0987, Sangak, JPG-GR, WhatamIdoing, S3000, R'n'B, CommonsDelinker, DrKiernan, Boghog, Rod57, Treisijs, Tomas.Persson,
Idioma-bot, VasilievVV, A4bot, Broadbot, Eubulides, Oncogenes, Kosigrim, ThinkerThoughts, SieBot, Graham Beards, Winchelsea,
Revent, Editore99, Lightmouse, Kenmcl2, Naturespace, Webridge, Separa, ClueBot, Niceguyedc, Piledhigheranddeeper, Excirial, ToN-
ToNi, NuclearWarfare, Dekisugi, Vojtěch Dostál, Addbot, DOI bot, Ashanda, Chzz, 5 albert square, BCvek, CountryBot, Luckas-bot,
Yobot, Ptbotgourou, Berkay0652, AnomieBOT, Rubinbot, Hunter3316, Citation bot, LilHelpa, Aa77zz, NocturneNoir, BostonBiochem,
CaC, Howard McCay, Wikipism, RGlasser, Citation bot 2, Citation bot 1, Time9, Tbhotch, EmausBot, Dcirovic, Orange Suede Sofa,
TYelliot, Minnsurfur2, Will Beback Auto, ClueBot NG, Grife, Weird Black Lady 4 U, SentientSystem, Miguelferig, BG19bot, Cyanoir,
DPL bot, NotWith, Hamish59, Biosthmors, YFdyh-bot, Dexbot, Proteinfolder, Tom Toyosaki, Electronsaregreen, Koszik, Maximus155,
BreCaitlin, Flemingrjf, MChapman5, FridoFoe, Evolution and evolvability, Ubiquitintools, Anrnusna, Monkbot, Aceestrin1, Arosowsky,
Heartbd2k DavidLiem and Anonymous: 69

22.2 Images
• File:0322_DNA_Nucleotides.jpg Source: https://upload.wikimedia.org/wikipedia/commons/d/d3/0322_DNA_Nucleotides.jpg License:
CC BY 3.0 Contributors: Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013. Original artist:
OpenStax College
392 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:1,3-bisphospho-D-glycerate.png Source: https://upload.wikimedia.org/wikipedia/commons/1/16/1%

2C3-bisphospho-D-glycerate.png License: CC BY-SA 3.0 Contributors: Amwhynot Original artist: Amwhynot
• File:1,3-bisphospho-D-glycerate.svg Source: https://upload.wikimedia.org/wikipedia/commons/7/75/1%
2C3-bisphospho-D-glycerate.svg License: CC BY-SA 3.0 Contributors: Own work Original artist: Panoramix303
• File:11-cyclohexyludencanioc_acid.png Source: https://upload.wikimedia.org/wikipedia/commons/e/e8/11-cyclohexyludencanioc_
acid.png License: CC0 Contributors: Own work Original artist: Bochyboch
• File:1802_Examples_of_Amine_Peptide_Protein_and_Steroid_Hormone_Structure.jpg Source: https://upload.wikimedia.org/
wikipedia/commons/e/ea/1802_Examples_of_Amine_Peptide_Protein_and_Steroid_Hormone_Structure.jpg License: CC BY 3.0 Con-
tributors: Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013. Original artist: OpenStax
College
• File:1G0U_subunits_sideview.png Source: https://upload.wikimedia.org/wikipedia/commons/5/5b/1G0U_subunits_sideview.png Li-
cense: CC-BY-SA-3.0 Contributors: ? Original artist: ?
• File:1GZX_Haemoglobin.png Source: https://upload.wikimedia.org/wikipedia/commons/3/3d/1GZX_Haemoglobin.png License: CC-
BY-SA-3.0 Contributors: Transferred from en.wikipedia to Commons. Original artist: Zephyris at English Wikipedia
• File:1axc_tricolor.png Source: https://upload.wikimedia.org/wikipedia/commons/6/61/1axc_tricolor.png License: CC-BY-SA-3.0
Contributors: Self created from PDB entry 1AXC using the freely available visualization and analysis package VMD

Credits (as required by the license):

Original artist: Opabinia regalis
• File:2-oxoglutarate_wpmp.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/d9/2-oxoglutarate_wpmp.svg License:
Public domain Contributors: en:Image:2-oxoglutarate_wpmp.svg Original artist: Richard Wheeler (Zephyris)
• File:2-phospho-D-glycerate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/2/28/2-phospho-D-glycerate_
wpmp.png License: Public domain Contributors: en:Image:2-phospho-D-glycerate wpmp.png Original artist: Richard Wheeler (Zephyris)
• File:2-phospho-D-glycerate_wpmp.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/2a/2-phospho-D-glycerate_
wpmp.svg License: Public domain Contributors: Own work Original artist: Krishnavedala
• File:200407-sandouping-sanxiadaba-4.med.jpg Source: https://upload.wikimedia.org/wikipedia/commons/9/95/
200407-sandouping-sanxiadaba-4.med.jpg License: CC-BY-SA-3.0 Contributors: ? Original artist: ?
• File:2006_Global_Water_Availability.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/80/2006_Global_Water_
Availability.svg License: CC BY-SA 3.0 Contributors: Own work Original artist: OmnipotentArchetype0309
• File:225_Peptide_Bond-01.jpg Source: https://upload.wikimedia.org/wikipedia/commons/2/26/225_Peptide_Bond-01.jpg License: CC
BY 3.0 Contributors: Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013. Original artist:
OpenStax College
• File:26S_proteasome_structure.jpg Source: https://upload.wikimedia.org/wikipedia/commons/d/d5/26S_proteasome_structure.jpg Li-
cense: CC BY-SA 3.0 Contributors: Cartoon rendering in UCSF Chimera Original artist: FridoFoe
• File:2f16_bortezomib_pink.png Source: https://upload.wikimedia.org/wikipedia/commons/9/93/2f16_bortezomib_pink.png License:
CC-BY-SA-3.0 Contributors: Self-created using PyMOL v0.99 from PDB ID 2F16. Original artist: Opabinia regalis
• File:2r9r_opm.png Source: https://upload.wikimedia.org/wikipedia/commons/0/02/2r9r_opm.png License: CC-BY-SA-3.0 Contributors:
Own work Original artist: Andrei Lomize
• File:3-hydroxyacyl-ACP_dehydrase.png Source: https://upload.wikimedia.org/wikipedia/commons/f/f5/3-hydroxyacyl-ACP_
dehydrase.png License: CC0 Contributors: Own work Original artist: Bochyboch
• File:3-ketoactl-ACP_synthetase.png Source: https://upload.wikimedia.org/wikipedia/commons/f/fd/3-ketoactl-ACP_synthetase.png
License: CC0 Contributors: Own work Original artist: Bochyboch
• File:3-ketoacyl-ACP_reductase.png Source: https://upload.wikimedia.org/wikipedia/commons/9/9e/3-ketoacyl-ACP_reductase.png
License: CC0 Contributors: Own work Original artist: Bochyboch
• File:3-phospho-D-glycerate.svg Source: https://upload.wikimedia.org/wikipedia/commons/9/99/3-phospho-D-glycerate.svg License:
CC BY-SA 3.0 Contributors: Own work Original artist: Panoramix303
• File:3-phospho-D-glycerate_trulyglycerate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/c/c3/
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• 3-phospho-D-glycerate_wpmp.png Original artist: 3-phospho-D-glycerate_wpmp.png: Richard Wheeler (Zephyris)
• File:3D_model_hydrogen_bonds_in_water.svg Source: https://upload.wikimedia.org/wikipedia/commons/c/c6/3D_model_hydrogen_
bonds_in_water.svg License: CC BY-SA 3.0 Contributors: File:3D model hydrogen bonds in water.jpg Original artist: User Qwerter at
Czech wikipedia: Qwerter. Transferred from cs.wikipedia; Transfer was stated to be made by User:sevela.p. Translated to english by by
Michal Maňas (User:snek01). Vectorized by Magasjukur2
• File:3_conformational_states_of_26S_proteasome.jpg Source: https://upload.wikimedia.org/wikipedia/commons/7/7e/3_
conformational_states_of_26S_proteasome.jpg License: CC BY-SA 3.0 Contributors: Rendered using Chimera Original artist:
FridoFoe
• File:3d_tRNA.png Source: https://upload.wikimedia.org/wikipedia/commons/f/f1/3d_tRNA.png License: CC BY-SA 3.0 Contributors:
Own work Original artist: Vossman
• File:5-Methylcytosine.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/3a/5-Methylcytosine.svg License: Public do-
main Contributors: Own work Original artist: Yikrazuul (<a href='//commons.wikimedia.org/wiki/User_talk:Yikrazuul' title='User talk:
Yikrazuul'>talk</a>)
• File:50S-subunit_of_the_ribosome_3CC2.png Source: https://upload.wikimedia.org/wikipedia/commons/e/e4/50S-subunit_of_the_
ribosome_3CC2.png License: CC BY-SA 3.0 Contributors: Own work Original artist: Yikrazuul
22.2. IMAGES 393

• File:A-DNA,_B-DNA_and_Z-DNA.png Source: https://upload.wikimedia.org/wikipedia/commons/b/b1/A-DNA%2C_B-DNA_and_

Z-DNA.png License: GFDL Contributors: Originally from en.wikipedia; description page is/was here. Original artist: Original uploader
was Richard Wheeler (Zephyris) at en.wikipedia
• File:ACAC_mechanism.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a1/ACAC_mechanism.png License: Public
domain Contributors: Transferred from en.wikipedia; transfer was stated to be made by User:xvazquez. Original artist: Original uploader
was BorisTM at en.wikipedia
• File:ADN_animation.gif Source: https://upload.wikimedia.org/wikipedia/commons/8/81/ADN_animation.gif License: Public domain
Contributors: Own work Original artist: brian0918™
• File:ATP-3D-vdW.png Source: https://upload.wikimedia.org/wikipedia/commons/2/22/ATP-3D-vdW.png License: Public domain Con-
tributors: ? Original artist: ?
• File:ATPsyn.gif Source: https://upload.wikimedia.org/wikipedia/commons/6/62/ATPsyn.gif License: Public domain Contributors:
Transferred from en.wikipedia; Transfer was stated to be made by User:wiseman25. Original artist: Original uploader was TimVickers
at en.wikipedia
• File:A_sectioned_alder_root_nodule_gall.JPG Source: https://upload.wikimedia.org/wikipedia/commons/8/82/A_sectioned_alder_
root_nodule_gall.JPG License: Public domain Contributors: self-made - Roger Griffith Original artist: Rosser1954
• File:A_thaliana_metabolic_network.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a0/A_thaliana_metabolic_
network.png License: Public domain Contributors: Transferred from en.wikipedia to Commons. Original artist: TimVickers at English
Wikipedia
• File:Access_to_drinking_water_in_third_world.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/34/Access_to_
drinking_water_in_third_world.svg License: Public domain Contributors: Vectorised from File:Access to drinking water in third
world.GIF. Original artist: Jynto
• File:Acety-CoA_ACP_transacylase.png Source: https://upload.wikimedia.org/wikipedia/commons/d/dc/Acety-CoA_ACP_
transacylase.png License: CC0 Contributors: Own work Original artist: Bochyboch
• File:Acetyl-CoA-2D.svg Source: https://upload.wikimedia.org/wikipedia/commons/e/ea/Acetyl-CoA-2D.svg License: Public domain
Contributors: Own work Original artist: User:Bryan Derksen
• File:Acetyl_co-A_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/e/ed/Acetyl_co-A_wpmp.png License: Public
domain Contributors: Own work Original artist: DMacks (<a href='//commons.wikimedia.org/wiki/User_talk:DMacks' title='User talk:
DMacks'>talk</a>)
• File:Activation2_updated.svg Source: https://upload.wikimedia.org/wikipedia/commons/e/e3/Activation2_updated.svg License: CC-
BY-SA-3.0 Contributors: en:Image:Activation2.png Original artist: Originally uploaded by Jerry Crimson Mann, vectorized by Tutmosis,
corrected by Fvasconcellos
• File:Aegopodium_podagraria1_ies.jpg Source: https://upload.wikimedia.org/wikipedia/commons/b/bf/Aegopodium_podagraria1_ies.
jpg License: CC-BY-SA-3.0 Contributors: Own work Original artist: Frank Vincentz
• File:Aerobic_desaturation.png Source: https://upload.wikimedia.org/wikipedia/commons/6/6a/Aerobic_desaturation.png License:
CC0 Contributors: ? Original artist: ?
• File:Allosteric_v_by_S_curve.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/44/Allosteric_v_by_S_curve.svg Li-
cense: Copyrighted free use Contributors: from en.wiki [1] Original artist: by TimVickers.
• File:Alpha-D-glucopyranose-2D-skeletal.png Source: https://upload.wikimedia.org/wikipedia/commons/4/48/
Alpha-D-glucopyranose-2D-skeletal.png License: Public domain Contributors: ? Original artist: ?
• File:Alpha-D-glucose-6-phosphate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/c/ca/
Alpha-D-glucose-6-phosphate_wpmp.png License: Public domain Contributors: en:Image:Alpha-D-glucose-6-phosphate wpmp.png
Original artist: Richard Wheeler (Zephyris)
• File:Alpha-D-glucose-6-phosphate_wpmp.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/80/
Alpha-D-glucose-6-phosphate_wpmp.svg License: Public domain Contributors: Own work Original artist: Krishnavedala
• File:Alpha_Intercalated_Cell_Cartoon.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/38/Alpha_Intercalated_Cell_
Cartoon.svg License: CC BY 3.0 Contributors: Own work, based on en.wikipedia.org’s Alpha_Intercalated_Cell_Cartoon.jpg. Original
artist: Rswarbrick
• File:Ambox_important.svg Source: https://upload.wikimedia.org/wikipedia/commons/b/b4/Ambox_important.svg License: Public do-
main Contributors: Own work, based off of Image:Ambox scales.svg Original artist: Dsmurat (talk · contribs)
• File:AminoAcidball.svg Source: https://upload.wikimedia.org/wikipedia/commons/c/ce/AminoAcidball.svg License: Public domain
Contributors: Own work Original artist: This vector image was created with Inkscape.
• File:Amino_Acid_Titration_Curves_By_Side_Chain.png Source: https://upload.wikimedia.org/wikipedia/commons/1/16/Amino_
Acid_Titration_Curves_By_Side_Chain.png License: CC BY-SA 3.0 Contributors: Own work Original artist: L. Van Warren
• File:Amino_Acids.svg Source: https://upload.wikimedia.org/wikipedia/commons/a/a9/Amino_Acids.svg License: CC BY-SA 3.0 Con-
tributors:
Print It Here
Original artist: Dancojocari
• File:Amino_acid_catabolism_revised.png Source: https://upload.wikimedia.org/wikipedia/commons/1/16/Amino_acid_catabolism_
revised.png License: CC0 Contributors: http://commons.wikimedia.org/wiki/File:Amino_acid_catabolism.png Original artist: Mikael Häg-
gström
• File:Amino_acid_zwitterions.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/de/Amino_acid_zwitterions.svg License:
CC BY 3.0 Contributors: from Amino acid zwitterions.png made by TimVickers. Original artist: TimVickers
• File:Amino_acids_1.png Source: https://upload.wikimedia.org/wikipedia/commons/8/82/Amino_acids_1.png License: CC-BY-SA-3.0
Contributors: ? Original artist: ?
394 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Amylose_3Dprojection.corrected.png Source: https://upload.wikimedia.org/wikipedia/commons/7/71/Amylose_3Dprojection.

corrected.png License: Public domain Contributors: Own work Original artist: glycoform
• File:Anaerobic_desaturation.png Source: https://upload.wikimedia.org/wikipedia/commons/c/c5/Anaerobic_desaturation.png License:
CC0 Contributors: Own work Original artist: Bochyboch
• File:Animal_cell_structure_en.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/48/Animal_cell_structure_en.svg Li-
cense: Public domain Contributors: Own work using Adobe Illustrator. Image renamed from Image:Animal cell structure.svg Original
artist: LadyofHats (Mariana Ruiz)
• File:Auto-and_heterotrophs.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/2f/Auto-and_heterotrophs.svg License:
CC BY-SA 3.0 Contributors: Images used:

• <a href='//commons.wikimedia.org/wiki/File:Alpha-D-glucose-3D-balls.png' class='image'><img alt='' src='https:

//upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Alpha-D-glucose-3D-balls.png/108px-Alpha-D-glucose-3D-balls.png'
width='108' height='120' srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/Alpha-D-glucose-3D-balls.
png/163px-Alpha-D-glucose-3D-balls.png 1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/6/6a/
Alpha-D-glucose-3D-balls.png/217px-Alpha-D-glucose-3D-balls.png 2x' data-file-width='994' data-file-height='1100' /></a>

Glucose
• <a href='//commons.wikimedia.org/wiki/File:Animaldiversity.jpg' class='image'><img alt='' src='https://upload.
wikimedia.org/wikipedia/commons/thumb/f/fd/Animaldiversity.jpg/120px-Animaldiversity.jpg' width='120' height='72'
srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Animaldiversity.jpg/180px-Animaldiversity.jpg 1.5x,
https://upload.wikimedia.org/wikipedia/commons/thumb/f/fd/Animaldiversity.jpg/240px-Animaldiversity.jpg 2x' data-file-
width='1079' data-file-height='648' /></a>

Animals
• <a href='//commons.wikimedia.org/wiki/File:Carbon-dioxide-3D-vdW.svg' class='image'><img alt='' src='https:
//upload.wikimedia.org/wikipedia/commons/thumb/a/af/Carbon-dioxide-3D-vdW.svg/120px-Carbon-dioxide-3D-vdW.svg.png'
width='120' height='79' srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/a/af/Carbon-dioxide-3D-vdW.
svg/180px-Carbon-dioxide-3D-vdW.svg.png 1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/a/af/
Carbon-dioxide-3D-vdW.svg/240px-Carbon-dioxide-3D-vdW.svg.png 2x' data-file-width='1100' data-file-height='723'
/></a>

Carbon dioxide
• <a href='//commons.wikimedia.org/wiki/File:D-glucose-chain-3D-balls.png' class='image'><img alt='' src='https:
//upload.wikimedia.org/wikipedia/commons/thumb/5/5a/D-glucose-chain-3D-balls.png/120px-D-glucose-chain-3D-balls.png'
width='120' height='67' srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/5/5a/D-glucose-chain-3D-balls.
png/180px-D-glucose-chain-3D-balls.png 1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/5/5a/
D-glucose-chain-3D-balls.png/240px-D-glucose-chain-3D-balls.png 2x' data-file-width='1100' data-file-height='611' /></a>

Glucose (open form)

• <a href='//commons.wikimedia.org/wiki/File:Dioxygen-3D-vdW.png' class='image'><img alt='' src='https://upload.wikimedia.
org/wikipedia/commons/thumb/c/c9/Dioxygen-3D-vdW.png/120px-Dioxygen-3D-vdW.png' width='120' height='89'
srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Dioxygen-3D-vdW.png/180px-Dioxygen-3D-vdW.png
1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Dioxygen-3D-vdW.png/240px-Dioxygen-3D-vdW.png 2x'
data-file-width='1100' data-file-height='813' /></a>

Oxygen
• <a href='//commons.wikimedia.org/wiki/File:Diversity_of_plants.png' class='image'><img alt='' src='https://upload.wikimedia.
org/wikipedia/commons/thumb/9/98/Diversity_of_plants.png/120px-Diversity_of_plants.png' width='120' height='81'
srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/9/98/Diversity_of_plants.png/180px-Diversity_of_plants.png
1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/9/98/Diversity_of_plants.png/240px-Diversity_of_plants.png 2x'
data-file-width='453' data-file-height='304' /></a>

Plants
• <a href='//commons.wikimedia.org/wiki/File:Fungi_collage.jpg' class='image'><img alt='' src='https://upload.
wikimedia.org/wikipedia/commons/thumb/f/fc/Fungi_collage.jpg/120px-Fungi_collage.jpg' width='120' height='104'
srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/f/fc/Fungi_collage.jpg/180px-Fungi_collage.jpg 1.5x,
https://upload.wikimedia.org/wikipedia/commons/thumb/f/fc/Fungi_collage.jpg/240px-Fungi_collage.jpg 2x' data-file-
width='1220' data-file-height='1062' /></a>

Fungi
• <a href='//commons.wikimedia.org/wiki/File:Starch_helix.jpg' class='image'><img alt='' src='https://upload.wikimedia.
org/wikipedia/commons/thumb/0/0f/Starch_helix.jpg/35px-Starch_helix.jpg' width='35' height='120' srcset='https:
//upload.wikimedia.org/wikipedia/commons/thumb/0/0f/Starch_helix.jpg/52px-Starch_helix.jpg 1.5x, https://upload.wikimedia.
org/wikipedia/commons/thumb/0/0f/Starch_helix.jpg/69px-Starch_helix.jpg 2x' data-file-width='247' data-file-height='850'
/></a>

Starch
22.2. IMAGES 395

• <a href='//commons.wikimedia.org/wiki/File:Water_molecule_3D.svg' class='image'><img alt='' src='https://upload.wikimedia.

org/wikipedia/commons/thumb/1/1c/Water_molecule_3D.svg/120px-Water_molecule_3D.svg.png' width='120' height='103'
srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/1/1c/Water_molecule_3D.svg/180px-Water_molecule_3D.svg.
png 1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/1/1c/Water_molecule_3D.svg/240px-Water_molecule_3D.
svg.png 2x' data-file-width='1100' data-file-height='945' /></a>

Water
• <a href='//commons.wikimedia.org/wiki/File:Anterior_view_of_female_upper_body,_retouched_-_transparent.png'
class='image'><img alt='' src='https://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Anterior_view_of_female_upper_
body%2C_retouched_-_transparent.png/103px-Anterior_view_of_female_upper_body%2C_retouched_-_transparent.png'
width='103' height='120' srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Anterior_view_of_female_upper_
body%2C_retouched_-_transparent.png/155px-Anterior_view_of_female_upper_body%2C_retouched_-_transparent.png 1.5x,
https://upload.wikimedia.org/wikipedia/commons/thumb/c/c9/Anterior_view_of_female_upper_body%2C_retouched_-_
transparent.png/206px-Anterior_view_of_female_upper_body%2C_retouched_-_transparent.png 2x' data-file-width='1850'
data-file-height='2152' /></a>

Human
Original artist: Mikael Häggström
• File:Average_prokaryote_cell-_en.svg Source: https://upload.wikimedia.org/wikipedia/commons/5/5a/Average_prokaryote_cell-_en.
svg License: Public domain Contributors: Own work (Source: Typical prokaryotic cell, Chapter 4: Mutagenicity of alkyl N-
acetoxybenzohydroxamates, Concept 1: Common Features of All Cells, Cells - Structure and Function) Original artist: Mariana Ruiz
Villarreal, LadyofHats
• File:BCCP.png Source: https://upload.wikimedia.org/wikipedia/commons/0/05/BCCP.png License: CC0 Contributors: Own work Origi-
nal artist: Nw.NPC
• File:Band_5_ALMA_receiver.jpg Source: https://upload.wikimedia.org/wikipedia/commons/c/c3/Band_5_ALMA_receiver.jpg Li-
cense: CC BY 4.0 Contributors: http://www.eso.org/public/images/ann15059a/ Original artist: ALMA (ESO/NAOJ/NRAO), N. Tabilo
• File:Base_pair_AT.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/db/Base_pair_AT.svg License: Public domain Con-
tributors: Own work Original artist: Yikrazuul
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• File:Bay_of_Fundy_High_Tide.jpg Source: https://upload.wikimedia.org/wikipedia/commons/7/76/Bay_of_Fundy_High_Tide.jpg Li-
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• File:Bay_of_Fundy_Low_Tide.jpg Source: https://upload.wikimedia.org/wikipedia/commons/c/cf/Bay_of_Fundy_Low_Tide.jpg Li-
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• File:Benzopyrene_DNA_adduct_1JDG.png Source: https://upload.wikimedia.org/wikipedia/commons/d/d8/Benzopyrene_DNA_
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• File:Beta-D-Glucose.svg Source: https://upload.wikimedia.org/wikipedia/commons/b/bb/Beta-D-Glucose.svg License: Public domain
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• File:Beta-D-fructose-1,6-bisphosphate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/9/95/
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wpmp.png Original artist: Richard Wheeler (Zephyris)
• File:Beta-D-fructose-1,6-bisphosphate_wpmp.svg Source: https://upload.wikimedia.org/wikipedia/commons/7/7d/
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Original artist: Richard Wheeler (Zephyris)
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• File:Beta-D-glucopyranose-2D-skeletal.png Source: https://upload.wikimedia.org/wikipedia/commons/6/60/
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• File:Beta_alanine_comparison.svg Source: https://upload.wikimedia.org/wikipedia/commons/9/92/Beta_alanine_comparison.svg Li-
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396 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Biochem_reaction_arrow_forward_NYNN_horiz_med.png Source: https://upload.wikimedia.org/wikipedia/commons/d/d3/

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Biochem_reaction_arrow_forward_YNNN_horiz_med.png License: CC-BY-SA-3.0 Contributors: Unknown Original artist: By Richard
Wheeler (Zephyris) 2006.
• File:Biochem_reaction_arrow_forward_YYNN_horiz_med.png Source: https://upload.wikimedia.org/wikipedia/commons/5/5f/
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YYNN horiz med.png Original artist: Richard Wheeler (Zephyris)
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Image:Biochem reaction arrow foward YYNN horiz med.png, by Richard Wheeler (Zephyris) Original artist: User:Superm401, based on
work by Richard Wheeler (Zephyris)
• File:Biochem_reaction_arrow_reverse_NNYN_horiz_med.png Source: https://upload.wikimedia.org/wikipedia/commons/d/d5/
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• File:Biochem_reaction_arrow_reversible_NNNN_horiz_med.svg Source: https://upload.wikimedia.org/wikipedia/commons/7/70/
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• File:Biochem_reaction_arrow_reversible_NYYN_horiz_med.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a9/
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reversible_NYYN_horiz_med.png Original artist: Richard Wheeler (Zephyris)
• File:Biochem_reaction_arrow_reversible_NYYN_horiz_med.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/86/
Biochem_reaction_arrow_reversible_NYYN_horiz_med.svg License: CC-BY-SA-3.0 Contributors: Own work Original artist: Malcolm
Gin
• File:Biochem_reaction_arrow_reversible_YYYY_horiz_med.png Source: https://upload.wikimedia.org/wikipedia/commons/6/64/
Biochem_reaction_arrow_reversible_YYYY_horiz_med.png License: CC-BY-SA-3.0 Contributors: en:Image:Biochem_reaction_arrow_
reversible_YYYY_horiz_med.png Original artist: Richard Wheeler (Zephyris)
• File:Biochem_reaction_arrow_reversible_YYYY_horiz_med.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/19/
Biochem_reaction_arrow_reversible_YYYY_horiz_med.svg License: CC-BY-SA-3.0 Contributors: Own work Original artist: Malcolm
Gin
• File:Biochem_reaction_arrow_special_1.png Source: https://upload.wikimedia.org/wikipedia/commons/c/cc/Biochem_reaction_
arrow_special_1.png License: CC-BY-SA-3.0 Contributors: Unknown Original artist: By Richard Wheeler (Zephyris) 2006.
• File:Biochem_reaction_arrow_special_2.png Source: https://upload.wikimedia.org/wikipedia/commons/4/43/Biochem_reaction_
arrow_special_2.png License: CC-BY-SA-3.0 Contributors: en:Image:Biochem_reaction_arrow_special_2.png Original artist: Richard
Wheeler (Zephyris)
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arrow_special_3.png License: CC-BY-SA-3.0 Contributors: Transferred from en.wikipedia to Commons by Sfan00_IMG using
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arrow_special_5.png License: CC-BY-SA-3.0 Contributors: Transferred from en.wikipedia to Commons. Original artist: Zephyris at
English Wikipedia
• File:Biotin_carboxylase_rainbow.png Source: https://upload.wikimedia.org/wikipedia/commons/4/49/Biotin_carboxylase_rainbow.
png License: CC0 Contributors: Own work Original artist: Nw.NPC
• File:Blausen_0208_CellAnatomy.png Source: https://upload.wikimedia.org/wikipedia/commons/4/4e/Blausen_0208_CellAnatomy.
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nal sources it can be cited as:
• File:Blausen_0773_RNA.png Source: https://upload.wikimedia.org/wikipedia/commons/9/98/Blausen_0773_RNA.png License: CC
BY 3.0 Contributors: Own work Original artist: BruceBlaus. When using this image in external sources it can be cited as:
• File:Blue_Linckia_Starfish.JPG Source: https://upload.wikimedia.org/wikipedia/commons/7/76/Blue_Linckia_Starfish.JPG License:
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• File:Bortezomib.svg Source: https://upload.wikimedia.org/wikipedia/commons/e/ea/Bortezomib.svg License: Public domain Contribu-
tors: Own work, after World Health Organization (2003). "International Nonproprietary Names for Pharmaceutical Substances (INN).
Recommended INN: List 50". WHO Drug Information 21 (4): 273. Original artist: Fvasconcellos (talk · contribs)
• File:Branch-DNA-multiple.svg Source: https://upload.wikimedia.org/wikipedia/commons/0/08/Branch-DNA-multiple.svg License:
CC BY-SA 3.0 Contributors: This vector image was created with Inkscape, and then manually replaced. Original artist: Otterinfo
22.2. IMAGES 397

• File:Branch-dna-single.svg Source: https://upload.wikimedia.org/wikipedia/commons/5/54/Branch-dna-single.svg License: CC BY-SA

3.0 Contributors: This vector image was created with Inkscape, and then manually replaced. Original artist: Otterinfo
• File:Branched_fatty_acid_synthesis-isoleucine.png Source: https://upload.wikimedia.org/wikipedia/commons/7/7e/Branched_fatty_
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• File:Branched_fatty_acid_synthesis-leucine.png Source: https://upload.wikimedia.org/wikipedia/commons/4/4f/Branched_fatty_
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• File:Branched_fatty_acid_synthesis-valine.png Source: https://upload.wikimedia.org/wikipedia/commons/2/28/Branched_fatty_
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• File:Brokechromo.jpg Source: https://upload.wikimedia.org/wikipedia/commons/b/b2/Brokechromo.jpg License: CC-BY-SA-3.0 Con-
tributors: ? Original artist: ?
• File:Buckminsterfullerene-perspective-3D-balls.png Source: https://upload.wikimedia.org/wikipedia/commons/0/0f/
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• File:Burst_phase.svg Source: https://upload.wikimedia.org/wikipedia/commons/a/ab/Burst_phase.svg License: Public domain Con-
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TimVickers, SVG version traced over it in Inkscape by Qef.
• File:C_elegans_stained.jpg Source: https://upload.wikimedia.org/wikipedia/commons/7/77/C_elegans_stained.jpg License: CC BY 2.5
Contributors: ? Original artist: ?
• File:Calvin-cycle4.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/8e/Calvin-cycle4.svg License: CC BY-SA 3.0 Con-
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• File:Capillarity.svg Source: https://upload.wikimedia.org/wikipedia/commons/6/64/Capillarity.svg License: CC-BY-SA-3.0 Contribu-
tors: own work created in Inkscape, based on the graphics by Daniel Stiefelmaier Original artist: MesserWoland
• File:Carbamoylphosphat_deprotoniert.svg Source: https://upload.wikimedia.org/wikipedia/commons/9/94/Carbamoylphosphat_
deprotoniert.svg License: Public domain Contributors: Own work Original artist: NEUROtiker
• File:Carboxypeptidase_catalysis.png Source: https://upload.wikimedia.org/wikipedia/commons/4/4e/Carboxypeptidase_catalysis.png
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• File:Carboxytransferase_2F9Y_E-Coli.png Source: https://upload.wikimedia.org/wikipedia/commons/0/07/Carboxytransferase_
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• File:Carson_Fall_Mt_Kinabalu.jpg Source: https://upload.wikimedia.org/wikipedia/commons/5/57/Carson_Fall_Mt_Kinabalu.jpg Li-
cense: CC BY-SA 3.0 Contributors: Own work Original artist: Sze Sze SOO
• File:Catabolism_schematic.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/11/Catabolism_schematic.svg License:
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• File:Cell_Cycle_2.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/d0/Cell_Cycle_2.svg License: CC-BY-SA-3.0 Con-
tributors:
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• File:Cell_membrane_detailed_diagram_4.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/3a/Cell_membrane_
detailed_diagram_4.svg License: CC BY-SA 3.0 Contributors:
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• derivative work: Dhatfield (talk)
• File:Cell_membrane_detailed_diagram_en.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/da/Cell_membrane_
detailed_diagram_en.svg License: Public domain Contributors: Own work. Image renamed from File:Cell membrane detailed diagram.svg
Original artist: LadyofHats Mariana Ruiz
• File:Celltypes.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/83/Celltypes.svg License: Public domain Contributors:
SVG version of Image:Celltypes.png. Original artist: Science Primer (National Center for Biotechnology Information). Vectorized by
Mortadelo2005.
• File:Cellulose-2D-skeletal.png Source: https://upload.wikimedia.org/wikipedia/commons/3/3e/Cellulose-2D-skeletal.png License:
Public domain Contributors: ? Original artist: ?
• File:Cellulose-Ibeta-from-xtal-2002-3D-balls.png Source: https://upload.wikimedia.org/wikipedia/commons/f/f9/
Cellulose-Ibeta-from-xtal-2002-3D-balls.png License: Public domain Contributors: Own work Original artist: Ben Mills
• File:Ch1-oncogene.svg Source: https://upload.wikimedia.org/wikipedia/commons/c/c1/Ch1-oncogene.svg License: CC BY-SA 3.0 Con-
tributors: Emmanuel Barillot, Laurence Calzone, Philippe Hupé, Jean-Philippe Vert, Andrei Zinovyev, Computational Systems Biology of
Cancer Chapman & Hall/CRC Mathematical & Computational Biology , 2012 Original artist: Philippe Hupé
• File:Chaperonin_1AON.png Source: https://upload.wikimedia.org/wikipedia/commons/6/6c/Chaperonin_1AON.png License: CC BY-
SA 3.0 Contributors: Own work Original artist: Thomas Splettstoesser
• File:Chlorophyll_ab_spectra-en.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/23/Chlorophyll_ab_spectra-en.svg
License: CC BY-SA 3.0 Contributors: This file was derived from: Chlorophyll ab spectra2.PNG: <a href='//commons.wikimedia.org/wiki/
File:Chlorophyll_ab_spectra2.PNG' class='image'><img alt='Chlorophyll ab spectra2.PNG' src='https://upload.wikimedia.org/wikipedia/
commons/thumb/6/68/Chlorophyll_ab_spectra2.PNG/50px-Chlorophyll_ab_spectra2.PNG' width='50' height='47' srcset='https:
//upload.wikimedia.org/wikipedia/commons/thumb/6/68/Chlorophyll_ab_spectra2.PNG/75px-Chlorophyll_ab_spectra2.PNG 1.5x,
https://upload.wikimedia.org/wikipedia/commons/thumb/6/68/Chlorophyll_ab_spectra2.PNG/100px-Chlorophyll_ab_spectra2.PNG 2x'
data-file-width='664' data-file-height='629' /></a>
Original artist: Chlorophyll_ab_spectra2.PNG: Aushulz
398 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Chloroplast.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/26/Chloroplast.svg License: CC BY-SA 3.0 Contribu-

tors: own work based on Chloroplaste-schema.gif Original artist: SuperManu
• File:Chondroitin_Sulfate_Structure_NTP.png Source: https://upload.wikimedia.org/wikipedia/commons/e/eb/Chondroitin_Sulfate_
Structure_NTP.png License: Public domain Contributors: Transferred from en.wikipedia to Commons.
Original artist: The original uploader was Prithason at English Wikipedia

• File:Chromosomal_Recombination.svg Source: https://upload.wikimedia.org/wikipedia/commons/b/b2/Chromosomal_

Recombination.svg License: CC BY 2.5 Contributors: Own work, Created using Inkscape, v0.44 Original artist: David Eccles
(Gringer)
• File:Ciliate_telomerase_RNA.JPG Source: https://upload.wikimedia.org/wikipedia/commons/b/b0/Ciliate_telomerase_RNA.JPG Li-
cense: Public domain Contributors: Transferred from en.wikipedia; transferred to Commons by User:Moez using CommonsHelper. Original
artist: Original uploader was Narayanese at en.wikipedia
• File:Cis-Aconitate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/e/eb/Cis-Aconitate_wpmp.png License: Pub-
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• File:Citrate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/2/22/Citrate_wpmp.png License: Public domain Con-
tributors: en:Citrate_wpmp.png Original artist: Richard Wheeler (Zephyris)
• File:Citric_acid_cycle_with_aconitate_2.svg Source: https://upload.wikimedia.org/wikipedia/commons/0/0b/Citric_acid_cycle_with_
aconitate_2.svg License: CC BY-SA 3.0 Contributors: http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=TCA. Image
adapted from :Image:Citric acid cycle noi.svg|
(uploaded to Commons by wadester16) Original artist: Narayanese, WikiUserPedia, YassineMrabet, TotoBaggins
• File:Common_lipids_lmaps.png Source: https://upload.wikimedia.org/wikipedia/commons/2/20/Common_lipids_lmaps.png License:
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• File:Commons-logo.svg Source: https://upload.wikimedia.org/wikipedia/en/4/4a/Commons-logo.svg License: ? Contributors: ? Original
artist: ?
• File:Complex_I.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/42/Complex_I.svg License: Public domain Contributors:
Vector version of w:Image:Complex-1.png by TimVickers, slightly adapted for consistency with Image:Mitochondrial electron transport
chain—Etc4.svg. Content unchanged. Original artist: Fvasconcellos 23:51, 9 September 2007 (UTC)
• File:Complex_II.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/11/Complex_II.svg License: Public domain Contribu-
tors: Vector version of w:Image:Complex II v2.png by TimVickers, slightly adapted for consistency with Image:Mitochondrial electron
transport chain—Etc4.svg. Content unchanged. Original artist: Fvasconcellos 22:14, 29 September 2007 (UTC)
• File:Complex_III_reaction.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/10/Complex_III_reaction.svg License:
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(UTC)
• File:Complex_IV.svg Source: https://upload.wikimedia.org/wikipedia/commons/0/06/Complex_IV.svg License: Public domain Contrib-
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• File:Control_of_Acetyl_CoA_Carboxylase_corrected.png Source: https://upload.wikimedia.org/wikipedia/en/b/bb/Control_of_
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Own work
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Jimhsu77479 originally posted by Alnokta
• File:Cuisson_des_pates.jpg Source: https://upload.wikimedia.org/wikipedia/commons/f/f3/Cuisson_des_pates.jpg License: CC-BY-
SA-3.0 Contributors: ? Original artist: ?
• File:Cytosin.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/dd/Cytosin.svg License: Public domain Contributors: Own
work Original artist: NEUROtiker
• File:D+L-Alanine.gif Source: https://upload.wikimedia.org/wikipedia/commons/6/65/D%2BL-Alanine.gif License: Public domain Con-
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• File:D-glucose_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/6/60/D-glucose_wpmp.png License: Public do-
main Contributors: en:Image:D-glucose_wpmp.png Original artist: Richard Wheeler (Zephyris)
• File:D-glucose_wpmp.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/3e/D-glucose_wpmp.svg License: Public
domain Contributors: Own work Original artist: Me, Stanislaw Gackowski (Soeb)

• File:D-glyceraldehyde-3-phosphate.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/3a/

D-glyceraldehyde-3-phosphate.svg License: Public domain Contributors: Own work Original artist: Harbinary
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• File:DAMP_chemical_structure.png Source: https://upload.wikimedia.org/wikipedia/commons/c/cb/DAMP_chemical_structure.png
License: Public domain Contributors: ? Original artist: ?
22.2. IMAGES 399

• File:DAPIMitoTrackerRedAlexaFluor488BPAE.jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/63/

DAPIMitoTrackerRedAlexaFluor488BPAE.jpg License: CC BY-SA 3.0 Contributors: Own work Original artist: IP69.226.103.13
• File:DIN_4844-2_D-P005.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/89/DIN_4844-2_D-P005.svg License: Pub-
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• File:DNA-ligand-by-Abalone.png Source: https://upload.wikimedia.org/wikipedia/commons/8/8b/DNA-ligand-by-Abalone.png Li-
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• File:DNA_Repair.jpg Source: https://upload.wikimedia.org/wikipedia/commons/4/46/DNA_Repair.jpg License: Public domain Con-
tributors: Biomedical Beat National Institute of General Medical Science (NIGMS) Cool Image Gallery Original artist: Courtesy of Tom
Ellenberger, Washington University School of Medicine in St. Louis.
• File:DNA_Structure+Key+Labelled.pn_NoBB.png Source: https://upload.wikimedia.org/wikipedia/commons/4/4c/DNA_
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• File:DNA_chemical_structure.svg Source: https://upload.wikimedia.org/wikipedia/commons/e/e4/DNA_chemical_structure.svg
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file-width='91' data-file-height='31' /></a>iThe source code of this SVG is <a data-x-rel='nofollow' class='external text'
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Original artist: Madprime (talk · contribs)
• File:DNA_damage,_repair,_epigenetic_alteration_of_repair_in_cancer.jpg Source: https://upload.wikimedia.org/wikipedia/
commons/a/a8/DNA_damage%2C_repair%2C_epigenetic_alteration_of_repair_in_cancer.jpg License: CC BY-SA 3.0 Contributors:
Own work Original artist: Bernstein0275
• File:DNA_nanostructures.png Source: https://upload.wikimedia.org/wikipedia/commons/5/55/DNA_nanostructures.png License: CC
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• File:DNA_orbit_animated_static_thumb.png Source: https://upload.wikimedia.org/wikipedia/commons/d/db/DNA_orbit_animated_
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84user adapting file originally uploaded by Richard Wheeler (Zephyris) at en.wikipedia
• File:DNA_polymerase.svg Source: https://upload.wikimedia.org/wikipedia/commons/6/6f/DNA_polymerase.svg License: CC-BY-SA-
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• File:DNA_repair.ogg Source: https://upload.wikimedia.org/wikipedia/commons/4/4b/DNA_repair.ogg License: CC-BY-SA-3.0 Con-
tributors:
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Authors of the article
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• File:DNA_replication_split.svg Source: https://upload.wikimedia.org/wikipedia/commons/7/70/DNA_replication_split.svg License:
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• File:Diabetes_mellitus_world_map_-_DALY_-_WHO2004.svg Source: https://upload.wikimedia.org/wikipedia/commons/9/9a/
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• File:Diabetes_world_map_-_2000.svg Source: https://upload.wikimedia.org/wikipedia/commons/f/f5/Diabetes_world_map_-_2000.
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• File:Diatoms_through_the_microscope.jpg Source: https://upload.wikimedia.org/wikipedia/commons/3/31/Diatoms_through_the_
microscope.jpg License: Public domain Contributors: corp2365, NOAA Corps Collection Original artist: Prof. Gordon T. Taylor, Stony
Brook University
• File:Difference_DNA_RNA-EN.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/37/Difference_DNA_RNA-EN.svg
License: CC BY-SA 3.0 Contributors: chemical structures of nucleobases by Roland1952 Original artist: Difference_DNA_RNA-DE.svg:
Sponk (talk)
• File:Dna.ogg Source: https://upload.wikimedia.org/wikipedia/commons/b/bc/Dna.ogg License: CC-BY-SA-3.0 Contributors:
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• File:Dnadamage.png Source: https://upload.wikimedia.org/wikipedia/commons/7/78/Dnadamage.png License: Attribution Contributors:
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• File:Dnarepair1.png Source: https://upload.wikimedia.org/wikipedia/commons/0/09/Dnarepair1.png License: Attribution Contributors:
Original file is/was at [1] Original artist: Harold Brenner
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Contributors: Source: [1] Original artist: Photo taken by de:Benutzer:Alex Anlicker using a Nikon Coolpix 950.
400 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Earth_Day_Flag.png Source: https://upload.wikimedia.org/wikipedia/commons/6/6a/Earth_Day_Flag.png License: Public domain

Contributors: File:Earth flag PD.jpg, File:The Earth seen from Apollo 17 with transparent background.png Original artist: NASA (Earth
photograph)
SiBr4 (flag image)
• File:EcDHFR_raytraced.png Source: https://upload.wikimedia.org/wikipedia/commons/6/6d/EcDHFR_raytraced.png License: Public
domain Contributors: w:Image:EcDHFR raytraced.png Original artist: TimVickers
• File:EcoRV_1RVA.png Source: https://upload.wikimedia.org/wikipedia/commons/d/dc/EcoRV_1RVA.png License: CC-BY-SA-3.0
Contributors: Transferred from en.wikipedia to Commons. Original artist: The original uploader was Zephyris at English Wikipedia
• File:Endomembrane_system_diagram_no_text_nucleus.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a3/
Endomembrane_system_diagram_no_text_nucleus.png License: Public domain Contributors:
• Modified from File:Diagram human cell nucleus.svg (Mariana Ruiz - User:LadyofHats) by Peter Znamenskiy: labels removed for an intro-
ductory article. Original artist: Peter Znamenskiy at en.wikipedia
• File:Enoyl-ACP_reductase.png Source: https://upload.wikimedia.org/wikipedia/commons/0/0d/Enoyl-ACP_reductase.png License:
CC0 Contributors: Own work Original artist: Bochyboch
• File:Enzyme_catalysis_uniform+differential_binding.png Source: https://upload.wikimedia.org/wikipedia/commons/b/b8/Enzyme_
catalysis_uniform%2Bdifferential_binding.png License: CC-BY-SA-3.0 Contributors: Transferred from en.wikipedia to Commons by
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• File:Enzyme_mechanism_2.svg Source: https://upload.wikimedia.org/wikipedia/commons/6/69/Enzyme_mechanism_2.svg License:
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• File:Enzyme_progress_curve.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/86/Enzyme_progress_curve.svg License:
Copyrighted free use Contributors: from en.wiki [1] Original artist: en:User:Poccil, Based on public domain JPG by TimVickers.
• File:Ethanol-3D-balls.png Source: https://upload.wikimedia.org/wikipedia/commons/b/b0/Ethanol-3D-balls.png License: Public do-
main Contributors: ? Original artist: ?
• File:EukPreRC.jpg Source: https://upload.wikimedia.org/wikipedia/commons/4/45/EukPreRC.jpg License: CC BY-SA 3.0 Contribu-
tors: Own work Original artist: Lsanman
• File:Eukaryote_DNA-en.svg Source: https://upload.wikimedia.org/wikipedia/commons/e/e2/Eukaryote_DNA-en.svg License: CC BY-
SA 3.0 Contributors: This file was derived from: Eukaryote DNA.svg: <a href='//commons.wikimedia.org/wiki/File:Eukaryote_
DNA.svg' class='image'><img alt='Eukaryote DNA.svg' src='https://upload.wikimedia.org/wikipedia/commons/thumb/8/82/Eukaryote_
DNA.svg/50px-Eukaryote_DNA.svg.png' width='50' height='31' srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/8/82/
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DNA.svg/100px-Eukaryote_DNA.svg.png 2x' data-file-width='1189' data-file-height='734' /></a>
Original artist: Eukaryote_DNA.svg: *Difference_DNA_RNA-EN.svg: *Difference_DNA_RNA-DE.svg: Sponk (talk)
• File:Fat_triglyceride_shorthand_formula.PNG Source: https://upload.wikimedia.org/wikipedia/commons/b/be/Fat_triglyceride_
shorthand_formula.PNG License: Public domain Contributors: author Original artist: Wolfgang Schaefer
• File:FattyAcid-Activation.png Source: https://upload.wikimedia.org/wikipedia/commons/c/cf/FattyAcid-Activation.png License: Pub-
lic domain Contributors: Own work Original artist: Jag123 at English Wikipedia
• File:Field_Trip-_water_sampling.jpg Source: https://upload.wikimedia.org/wikipedia/commons/d/da/Field_Trip-_water_sampling.
jpg License: CC BY-SA 3.0 Contributors: Transferred from en.wikipedia to Commons by Sreejithk2000 using CommonsHelper. Orig-
inal artist: Department of Agronomy, Iowa State University (www.agron.iastate.edu)
• File:Figure_Role_of_initiators_for_initiation_of_DNA_replication.png Source: https://upload.wikimedia.org/wikipedia/commons/
d/d5/Figure_Role_of_initiators_for_initiation_of_DNA_replication.png License: CC BY-SA 3.0 Contributors: Own work Original artist:
Emply shell China dry
• File:Fluid_Mosaic.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/10/Fluid_Mosaic.svg License: CC BY 2.5 Contribu-
tors: Own work Original artist: Jerome Walker
• File:Folder_Hexagonal_Icon.svg Source: https://upload.wikimedia.org/wikipedia/en/4/48/Folder_Hexagonal_Icon.svg License: Cc-by-
sa-3.0 Contributors: ? Original artist: ?
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Original artist: Thompsma
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tors: Original Original artist: Seahen
• File:Friedrich_Miescher.jpg Source: https://upload.wikimedia.org/wikipedia/commons/b/bc/Friedrich_Miescher.jpg License: Public
domain Contributors: copied from http://www.pbs.org/wgbh/nova/photo51/images/befo-miescher.jpg Original artist: ?
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• File:Fumarate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/7/70/Fumarate_wpmp.png License: Public do-
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• File:Gene_expression_control.png Source: https://upload.wikimedia.org/wikipedia/commons/1/11/Gene_expression_control.png Li-
cense: CC BY-SA 3.0 Contributors: Own work Original artist: ArneLH
• File:GeneticCode22.svg Source: https://upload.wikimedia.org/wikipedia/commons/5/53/GeneticCode22.svg License: Public domain
Contributors: ? Original artist: ?
• File:Genetic_code.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/37/Genetic_code.svg License: CC-BY-SA-3.0 Con-
tributors: Own work Original artist: Madprime
• File:Genomics_GTL_Program_Payoffs.jpg Source: https://upload.wikimedia.org/wikipedia/commons/1/1c/Genomics_GTL_
Program_Payoffs.jpg License: Public domain Contributors: ? Original artist: ?
22.2. IMAGES 401

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Theresa Radnitz Cori (1896-1957) and Carl Ferdinand Cori (1896-1984) Original artist: Smithsonian Institution from United States
• File:Gluconeogenesis_pathway.png Source: https://upload.wikimedia.org/wikipedia/commons/0/08/Gluconeogenesis_pathway.png Li-
cense: CC BY-SA 3.0 Contributors: Own work (Original caption: “self-made”) Original artist: Unused0026 at English Wikipedia
• File:Glucose-insulin-release.svg Source: https://upload.wikimedia.org/wikipedia/commons/0/05/Glucose-insulin-release.svg
License: GFDL Contributors: <a href='//commons.wikimedia.org/wiki/File:Glucose-insulin-release.png' class='image'><img
alt='Glucose-insulin-release.png' src='https://upload.wikimedia.org/wikipedia/commons/thumb/2/21/Glucose-insulin-release.png/
100px-Glucose-insulin-release.png' width='100' height='65' srcset='https://upload.wikimedia.org/wikipedia/commons/thumb/2/21/
Glucose-insulin-release.png/150px-Glucose-insulin-release.png 1.5x, https://upload.wikimedia.org/wikipedia/commons/thumb/2/21/
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Fred the Oyster

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utors: Own work Original artist: ArthurCammers
• File:Glycogen_phosphorylase_stereo.png Source: https://upload.wikimedia.org/wikipedia/commons/f/f5/Glycogen_phosphorylase_
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• File:Glycogen_spacefilling_model.jpg Source: https://upload.wikimedia.org/wikipedia/en/b/b9/Glycogen_spacefilling_model.jpg Li-
cense: PD Contributors: ? Original artist: ?
• File:Glycogen_structure.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/47/Glycogen_structure.svg License: Public
domain Contributors:
• Structure reference: Similar image on scientificpsychic.com --> Carbohydrates - Chemical Structure. By Antonio Zamora on May 27, 2009
Original artist: Mikael Häggström.
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• File:Glycolysis_metabolic_pathway_3.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/26/Glycolysis_metabolic_
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• File:Grand_Anse_Beach_Grenada.jpg Source: https://upload.wikimedia.org/wikipedia/commons/8/8c/Grand_Anse_Beach_Grenada.
jpg License: CC BY 3.0 Contributors: Transferred from en.wikipedia to Commons by Kafuffle using CommonsHelper. Original artist:
Varun Kapoor / Vkap
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gnoni
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• File:Heart_of_Steel_(Hemoglobin).jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/68/Heart_of_Steel_
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Original artist: Photographer: Julian Voss-Andreae
• File:Helmet_logo_for_Underwater_Diving_portal.png Source: https://upload.wikimedia.org/wikipedia/commons/5/5e/
Helmet_logo_for_Underwater_Diving_portal.png License: ? Contributors: This file was derived from: Kask-nurka.jpg:
<a href='//commons.wikimedia.org/wiki/File:Kask-nurka.jpg' class='image'><img alt='Kask-nurka.jpg' src='https://upload.
wikimedia.org/wikipedia/commons/thumb/0/0a/Kask-nurka.jpg/50px-Kask-nurka.jpg' width='50' height='70' srcset='https:
//upload.wikimedia.org/wikipedia/commons/thumb/0/0a/Kask-nurka.jpg/75px-Kask-nurka.jpg 1.5x, https://upload.wikimedia.
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Original artist: Kask-nurka.jpg: User:Julo
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work Original artist: Yikrazuul
• File:Hemimethylation.svg Source: https://upload.wikimedia.org/wikipedia/commons/b/ba/Hemimethylation.svg License: CC BY-SA
3.0 Contributors: Own work Original artist: Histidine
• File:HemoglobinABDAlignment.png Source: https://upload.wikimedia.org/wikipedia/commons/d/db/HemoglobinABDAlignment.png
License: CC BY 1.0 Contributors: http://www.uniprot.org/ Original artist: http://www.uniprot.org/
402 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Hemoglobin_Test_American_Red_Cross.jpg Source: https://upload.wikimedia.org/wikipedia/en/f/f2/Hemoglobin_Test_

American_Red_Cross.jpg License: CC-BY-SA-3.0 Contributors:
Taken with my Galaxy S4 smartphone camera
Previously published: Never before published
Original artist:
Whoisjohngalt
• File:Hemoglobin_saturation_curve.svg Source: https://upload.wikimedia.org/wikipedia/commons/6/66/Hemoglobin_saturation_
curve.svg License: Public domain Contributors: This file was derived from: Hb saturation curve.png
Original artist: Hazmat2
• File:Hemoglobin_t-r_state_ani.gif Source: https://upload.wikimedia.org/wikipedia/commons/b/ba/Hemoglobin_t-r_state_ani.gif Li-
cense: CC-BY-SA-3.0 Contributors: Uploaded by Habj Original artist: en:User:BerserkerBen
• File:Hexokinase_B_1IG8_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/b/bb/Hexokinase_B_1IG8_wpmp.
png License: CC-BY-SA-3.0 Contributors: Transferred from en.wikipedia to Commons by Sreejithk2000 using CommonsHelper. Original
artist: Zephyris at English Wikipedia
• File:Hexokinase_ball_and_stick_model,_with_substrates_to_scale_copy.png Source: https://upload.wikimedia.org/wikipedia/
commons/e/e7/Hexokinase_ball_and_stick_model%2C_with_substrates_to_scale_copy.png License: Public domain Contributors:
Transferred from en.wikipedia; transferred to Commons by User:Leptictidium using CommonsHelper. Original artist: Original uploader
was TimVickers at en.wikipedia
• File:Hexokinase_induced_fit.png Source: https://upload.wikimedia.org/wikipedia/commons/d/d1/Hexokinase_induced_fit.png Li-
cense: CC BY-SA 4.0 Contributors: Own work Original artist: Thomas Shafee
• File:Holliday_Junction.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/83/Holliday_Junction.svg License: Public do-
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• derivative work: Mouagip (talk)
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utors: Own work Original artist: Opabinia regalis
• File:Humanitarian_aid_OCPA-2005-10-28-090517a.jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/69/
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tors: Own work Original artist: Edgar181
• File:Iceberg_with_hole_near_Sandersons_Hope_2007-07-28_2.jpg Source: https://upload.wikimedia.org/wikipedia/commons/4/41/
Iceberg_with_hole_near_Sandersons_Hope_2007-07-28_2.jpg License: CC BY-SA 3.0 Contributors: Own work (Own photo) Original
artist: Kim Hansen
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Uploaded by Fred the Oyster
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intramolecular_reaction_rates.png License: CC-BY-SA-3.0 Contributors: By Richard Wheeler (Zephyris) 2006. Original artist: Zephyris
at English Wikipedia
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tributors: Own work based on this source Original artist: Krishnavedala
• File:Issoria_lathonia.jpg Source: https://upload.wikimedia.org/wikipedia/commons/2/2d/Issoria_lathonia.jpg License: CC-BY-SA-3.0
Contributors: ? Original artist: ?
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Laboratory of Molecular Biology, requests for higher resolution images should be sent to archive@mrc-lmb.cam.ac.uk (original uploader
to the English Wikipedia was Dumarest)
22.2. IMAGES 403

• File:KinEnzymo(en).svg Source: https://upload.wikimedia.org/wikipedia/commons/0/09/KinEnzymo%28en%29.svg License: Public

domain Contributors: Own work Original artist: This vector image was created with Inkscape.
• File:L-amino_acid_any.png Source: https://upload.wikimedia.org/wikipedia/commons/0/0e/L-amino_acid_any.png License: CC0 Con-
tributors: Own work, based on PD File:L-valine-3D-balls.png Original artist: Incnis Mrsi
• File:L-arginine_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a7/L-arginine_wpmp.png License: CC-BY-
SA-3.0 Contributors: Transferred from en.wikipedia to Commons by Sfan00_IMG using CommonsHelper. Original artist: Zephyris at
English Wikipedia
• File:L-argino-succinate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a9/L-argino-succinate_wpmp.png Li-
cense: CC-BY-SA-3.0 Contributors: Transferred from en.wikipedia; transferred to Commons by User:Sfan00_IMG using CommonsHelper.
Original artist: Original uploader was Zephyris at en.wikipedia
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English Wikipedia
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English Wikipedia
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Original uploader was Zephyris at en.wikipedia
• File:LCHAD_deficiency.jpg Source: https://upload.wikimedia.org/wikipedia/en/7/7e/LCHAD_deficiency.jpg License: Cc-by-sa-3.0
Contributors: ? Original artist: ?
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• File:Lac_Operon.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/22/Lac_Operon.svg License: CC BY-SA 3.0 Contrib-
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• File:Lactose.svg Source: https://upload.wikimedia.org/wikipedia/commons/0/04/Lactose.svg License: ? Contributors: ? Original artist: ?
• File:Lambda_repressor_1LMB.png Source: https://upload.wikimedia.org/wikipedia/commons/8/8f/Lambda_repressor_1LMB.png Li-
cense: CC-BY-SA-3.0 Contributors: Transferred from en.wikipedia to Commons. Original artist: Zephyris at English Wikipedia
• File:Leaf_1_web.jpg Source: https://upload.wikimedia.org/wikipedia/commons/f/f4/Leaf_1_web.jpg License: Public domain Contribu-
tors: PdPhoto Original artist: Jon Sullivan
• File:Lineweaver-Burke_plot.svg Source: https://upload.wikimedia.org/wikipedia/commons/7/70/Lineweaver-Burke_plot.svg License:
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• File:Liquid-water-and-ice.png Source: https://upload.wikimedia.org/wikipedia/commons/0/03/Liquid-water-and-ice.png License: CC
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• File:Localisations02eng.jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/6e/Localisations02eng.jpg License: CC BY-
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• File:Longwood_Gardens-Italian_Garden.jpg Source: https://upload.wikimedia.org/wikipedia/commons/1/19/Longwood_
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User:Kelly using CommonsHelper. Original artist: Original uploader was MikeParker at en.wikipedia
• File:Lysine_fisher_structure_and_3d_ball.svg Source: https://upload.wikimedia.org/wikipedia/commons/5/5f/Lysine_fisher_
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• File:Lysozyme_transition_state.png Source: https://upload.wikimedia.org/wikipedia/commons/6/63/Lysozyme_transition_state.png
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CommonsHelper. Original artist: Original uploader was Zephyris at en.wikipedia
• File:MH-60S_Helicopter_dumps_water_onto_Fire.jpg Source: https://upload.wikimedia.org/wikipedia/commons/a/a2/MH-60S_
Helicopter_dumps_water_onto_Fire.jpg License: Public domain Contributors: http://www.defenselink.mil; exact source Original artist:
Mass Communication Specialist 2nd Class Chris Fahey, U.S. Navy
• File:MP_structures_2011.jpg Source: https://upload.wikimedia.org/wikipedia/commons/a/a1/MP_structures_2011.jpg License: Attri-
bution Contributors: http://blanco.biomol.uci.edu/mpstruc/ Original artist: Stephen White lab at UC Irvine
• File:MRNA.svg Source: https://upload.wikimedia.org/wikipedia/commons/9/9b/MRNA.svg License: CC BY 3.0 Contributors: Own work
Original artist: Kelvinsong
• File:Maclyn_McCarty_with_Francis_Crick_and_James_D_Watson_-_10.1371_journal.pbio.0030341.g001-O.jpg Source:
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journal.pbio.0030341.g001-O.jpg License: CC BY 3.0 Contributors: Lederberg J, Gotschlich EC (2005) A Path to Discovery: The Career
of Maclyn McCarty. PLoS Biol 3(10): e341 doi:10.1371/journal.pbio.0030341 Original artist: Marjorie McCarty
• File:Macromolecular-juggling-by-ubiquitylation-enzymes-1741-7007-11-65-S1.ogv Source: https://upload.wikimedia.org/
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tributors: Lorenz S, Cantor A, Rape M, Kuriyan J (2013). "Macromolecular juggling by ubiquitylation enzymes". BMC Biology.
DOI:10.1186/1741-7007-11-65. PMID 23800009. PMC: 3748819. Original artist: Lorenz S, Cantor A, Rape M, Kuriyan J
• File:Main_symptoms_of_diabetes.svg Source: https://upload.wikimedia.org/wikipedia/commons/0/01/Main_symptoms_of_diabetes.
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404 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Max_Perutz.jpg Source: https://upload.wikimedia.org/wikipedia/commons/3/34/Max_Perutz.jpg License: Public domain Contrib-

utors: http://www.nature.com/nature/journal/v449/n7159/full/449145a.html Original artist: Unknown, SVENSKT PRESSFOTO
• File:MbO2MO.png Source: https://upload.wikimedia.org/wikipedia/commons/3/34/MbO2MO.png License: CC BY-SA 3.0 Contribu-
tors: Own work Original artist: Smokefoot
• File:Melvin_Calvin.jpg Source: https://upload.wikimedia.org/wikipedia/commons/0/04/Melvin_Calvin.jpg License: Public domain
Contributors: LBL Collection Original artist: “Photolab”
• File:Membrane_lipids.png Source: https://upload.wikimedia.org/wikipedia/commons/8/83/Membrane_lipids.png License: Public do-
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• File:Merge-arrows.svg Source: https://upload.wikimedia.org/wikipedia/commons/5/52/Merge-arrows.svg License: Public domain Con-
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• File:Metabolism_790px.png Source: https://upload.wikimedia.org/wikipedia/commons/0/0d/Metabolism_790px.png License: CC-BY-
SA-3.0 Contributors: Own work Original artist: Zephyris
• File:Metabolism_of_common_monosaccharides,_and_related_reactions.png Source: https://upload.wikimedia.org/wikipedia/
commons/6/63/Metabolism_of_common_monosaccharides%2C_and_related_reactions.png License: CC BY-SA 3.0 Contributors: Own
work Original artist: LHcheM
• File:Metabolism_pathways_(partly_labeled).svg Source: https://upload.wikimedia.org/wikipedia/commons/5/5d/Metabolism_
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• File:Michaelis_Menten_curve_2.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/83/Michaelis_Menten_curve_2.svg
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• File:Mitochondrial_electron_transport_chain—Etc4.svg Source: https://upload.wikimedia.org/wikipedia/commons/8/89/
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• File:Molecular_structures_of_the_21_proteinogenic_amino_acids.svg Source: https://upload.wikimedia.org/wikipedia/commons/5/
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• File:Monotopic_membrane_protein.svg Source: https://upload.wikimedia.org/wikipedia/commons/c/c3/Monotopic_membrane_
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• File:Mouse_cholera_antibody.png Source: https://upload.wikimedia.org/wikipedia/commons/a/a2/Mouse_cholera_antibody.png Li-
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• File:Myoglobin.png Source: https://upload.wikimedia.org/wikipedia/commons/6/60/Myoglobin.png License: Public domain Contribu-
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• File:Nichtox_Pentosephosphatweg.png Source: https://upload.wikimedia.org/wikipedia/commons/d/de/Nichtox_
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• File:NitrogenReduction.png Source: https://upload.wikimedia.org/wikipedia/commons/d/d4/NitrogenReduction.png License: CC-BY-
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• File:Nitrogen_Cycle.svg Source: https://upload.wikimedia.org/wikipedia/commons/f/fe/Nitrogen_Cycle.svg License: CC BY-SA 3.0
Contributors:
• Cicle_del_nitrogen_de.svg Original artist: Cicle_del_nitrogen_de.svg: *Cicle_del_nitrogen_ca.svg: Johann Dréo (User:Nojhan), traduction
de Joanjoc d'après Image:Cycle azote fr.svg.
• File:Nitrous-oxide-3D-balls.png Source: https://upload.wikimedia.org/wikipedia/commons/9/93/Nitrous-oxide-3D-balls.png License:
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• File:Nonproteinogenic_AAs.svg Source: https://upload.wikimedia.org/wikipedia/commons/d/d8/Nonproteinogenic_AAs.svg License:
CC BY-SA 4.0 Contributors: Own work Original artist: Matteo Ferla (aka. Squidonius in Wikipedia)
• File:Nucleosome1.png Source: https://upload.wikimedia.org/wikipedia/commons/b/be/Nucleosome1.png License: CC BY-SA 3.0 Con-
tributors: Own work Original artist: Thomas Splettstoesser
• File:Nucleotide_synthesis.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/4f/Nucleotide_synthesis.svg License: CC0
Contributors: Own work Original artist: Kelvinsong
• File:Nucleotides_1.svg Source: https://upload.wikimedia.org/wikipedia/commons/e/e2/Nucleotides_1.svg License: Public domain Con-
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• File:Nucleotides_syn1.svg Source: https://upload.wikimedia.org/wikipedia/commons/2/25/Nucleotides_syn1.svg License: CC0 Contrib-
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Wikipedia
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22.2. IMAGES 405

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• File:Oncogenes_illustration.jpg Source: https://upload.wikimedia.org/wikipedia/commons/d/de/Oncogenes_illustration.jpg License:
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National_Cancer_Institute_Visuals_Online_with_known_IDs,<span>,&,</span>,filefrom=2351#mw-category-media'>(next)</a>. Origi-
nal artist: Unknown Illustrator
• File:One_dimensional_quantum_random_walk.png Source: https://upload.wikimedia.org/wikipedia/commons/4/4b/One_
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• File:Open_Access_logo_PLoS_transparent.svg Source: https://upload.wikimedia.org/wikipedia/commons/7/77/Open_Access_logo_
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Nina, Beao, and JakobVoss
• File:Oxaloacetate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/c/c8/Oxaloacetate_wpmp.png License: Public
domain Contributors: en:Image:Oxaloacetate_wpmp.png Original artist: Richard Wheeler (Zephyris)
• File:Oxalosuccinate_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/1/19/Oxalosuccinate_wpmp.png License:
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• File:PDB_1m6c_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/8/81/PDB_1m6c_EBI.jpg License: Public domain
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• File:PDB_1mwd_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/6d/PDB_1mwd_EBI.jpg License: Public do-
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• File:PDB_1myg_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/0/0a/PDB_1myg_EBI.jpg License: Public domain
Contributors: http://www.ebi.ac.uk/pdbe-srv/view/images/entry/1myg600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/entry/
1myg/summary Original artist: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute
• File:PDB_1myh_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/d/d0/PDB_1myh_EBI.jpg License: Public domain
Contributors: http://www.ebi.ac.uk/pdbe-srv/view/images/entry/1myh600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/entry/
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Contributors: http://www.ebi.ac.uk/pdbe-srv/view/images/entry/1myi600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/entry/
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• File:PDB_1myj_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/f/fd/PDB_1myj_EBI.jpg License: Public domain
Contributors: http://www.ebi.ac.uk/pdbe-srv/view/images/entry/1myj600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/entry/
1myj/summary Original artist: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute
• File:PDB_1pmb_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/2/25/PDB_1pmb_EBI.jpg License: Public domain
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• File:PDB_1yca_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/6/6a/PDB_1yca_EBI.jpg License: Public domain
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1yca/summary Original artist: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute
406 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:PDB_1ycb_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/b/b5/PDB_1ycb_EBI.jpg License: Public domain

Contributors: http://www.ebi.ac.uk/pdbe-srv/view/images/entry/1ycb600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/entry/
1ycb/summary Original artist: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute
• File:PDB_2mm1_EBI.jpg Source: https://upload.wikimedia.org/wikipedia/commons/b/b9/PDB_2mm1_EBI.jpg License: Public do-
main Contributors: http://www.ebi.ac.uk/pdbe-srv/view/images/entry/2mm1600.png, displayed on http://www.ebi.ac.uk/pdbe-srv/view/
entry/2mm1/summary Original artist: Jawahar Swaminathan and MSD staff at the European Bioinformatics Institute
• File:Parallel_telomere_quadruple.png Source: https://upload.wikimedia.org/wikipedia/commons/9/9e/Parallel_telomere_quadruple.
png License: CC-BY-SA-3.0 Contributors: self-made using the open source vizualization program PyMol Original artist: Thomas
Splettstoesser (www.scistyle.com)
• File:Parasite130059-fig7_Spermiogenesis_in_Pleurogenidae_(Digenea).tif Source: https://upload.wikimedia.org/wikipedia/
commons/9/97/Parasite130059-fig7_Spermiogenesis_in_Pleurogenidae_%28Digenea%29.tif License: CC BY 2.0 Contributors: Miquel,
J., Vilavella, D., Swiderski, Z., Shimalov, V. V. & Torres, J. 2013: Spermatological characteristics of Pleurogenidae (Digenea)
inferred from the ultrastructural study of Pleurogenes claviger, Pleurogenoides medians and Prosotocus confusus. Parasite, 20, 28.
doi:10.1051/parasite/2013028 Original artist: Jordi Miquel, Daniel Vilavella, Zdzisław Świderski, Vladimir V. Shimalov and Jordi Torres
• File:Pencil_sketch_of_the_DNA_double_helix_by_Francis_Crick_Wellcome_L0051225.jpg Source: https://upload.wikimedia.org/
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Contributors:
http://wellcomeimages.org/indexplus/obf_images/a2/0c/23cf65b022b84aa38d0dad401daf.jpg
Original artist: ?
• File:Pentose_Phosphate_Pathway.png Source: https://upload.wikimedia.org/wikipedia/commons/6/61/Pentose_Phosphate_Pathway.
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• File:People_icon.svg Source: https://upload.wikimedia.org/wikipedia/commons/3/37/People_icon.svg License: CC0 Contributors: Open-
Clipart Original artist: OpenClipart
• File:Peptide-Figure-Revised.png Source: https://upload.wikimedia.org/wikipedia/commons/c/c9/Peptide-Figure-Revised.png License:
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• File:Proteaosome_1fnt_side.png Source: https://upload.wikimedia.org/wikipedia/commons/5/54/Proteaosome_1fnt_side.png License:
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• File:Pyruvate_Kinase_1A3W_wpmp.png Source: https://upload.wikimedia.org/wikipedia/commons/d/d9/Pyruvate_Kinase_1A3W_
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gram, Galapagos Rift Expedition 2011
408 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

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tributors: ? Original artist: ?
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tributors: ? Original artist: ?
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Original artist: Doweexist42
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• File:Strecker_amino_acid_synthesis_scheme.svg Source: https://upload.wikimedia.org/wikipedia/commons/a/a9/Strecker_amino_
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22.2. IMAGES 409

• File:Stromatolites.jpg Source: https://upload.wikimedia.org/wikipedia/commons/c/c0/Stromatolites.jpg License: Public domain Con-

tributors: National Park Service - http://www.nature.nps.gov/geology/cfprojects/photodb/Photo_Detail.cfm?PhotoID=204 Original artist:
P. Carrara, NPS
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• File:Subsurface_drip_emission_on_loamy_soil.ogv Source: https://upload.wikimedia.org/wikipedia/commons/b/b1/Subsurface_
drip_emission_on_loamy_soil.ogv License: CC BY 3.0 Contributors: Gil, M.; Rodríguez-Sinobas, L.; Sánchez, R.; Juana, L. (2010). “Evo-
lution of the spherical cavity radius generated around a subsurface drip emitter”. Biogeosciences 7 (6): 1983. doi:10.5194/bg-7-1983-2010
Original artist: Gil, M.; Rodríguez-Sinobas, L.; Sánchez, R.; Juana, L. (2010). “Evolution of the spherical cavity radius generated around a
subsurface drip emitter”. Biogeosciences 7 (6): 1983. doi:10.5194/bg-7-1983-2010
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• File:Suckale08_fig3_glucose_insulin_day.png Source: https://upload.wikimedia.org/wikipedia/en/4/4d/Suckale08_fig3_glucose_
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Solimena Lab and Review Suckale Solimena 2008 Frontiers in Bioscience PMID 18508724, preprint PDF from Nature Precedings, original
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Jakob Suckale, Michele Solimena
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tributors: ? Original artist: ?
• File:Synthesis_of_Pseudouridine.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/4a/Synthesis_of_Pseudouridine.svg
License: Public domain Contributors: Own work Original artist: Yikrazuul
• File:T7_RNA_polymerase.jpg Source: https://upload.wikimedia.org/wikipedia/commons/e/e3/T7_RNA_polymerase.jpg License: CC
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• File:THC_2003.902.022_D._C._Bardwell_Study_of_Nitrogen_Fixation.tif Source: https://upload.wikimedia.org/wikipedia/
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• File:TapWater-china.JPG Source: https://upload.wikimedia.org/wikipedia/commons/e/ef/TapWater-china.JPG License: CC-BY-SA-
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• File:Thylakoid_membrane_3.svg Source: https://upload.wikimedia.org/wikipedia/commons/4/49/Thylakoid_membrane_3.svg License:
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• File:Thymin.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/15/Thymin.svg License: Public domain Contributors: Own
work Original artist: NEUROtiker
• File:Transcription_label_en.jpg Source: https://upload.wikimedia.org/wikipedia/commons/4/43/Transcription_label_en.jpg License:
CC-BY-SA-3.0 Contributors: ? Original artist: ?
• File:Tree_of_life_by_Haeckel.jpg Source: https://upload.wikimedia.org/wikipedia/commons/d/de/Tree_of_life_by_Haeckel.jpg Li-
cense: Public domain Contributors: First version from en.wikipedia; description page was here. Later versions derived from this scan,
from the American Philosophical Society Museum. Original artist: Ernst Haeckel
410 CHAPTER 22. TEXT AND IMAGE SOURCES, CONTRIBUTORS, AND LICENSES

• File:Tree_of_life_int.svg Source: https://upload.wikimedia.org/wikipedia/commons/9/9c/Tree_of_life_int.svg License: CC BY-SA 3.0

Contributors: Vectorization based on [1], all names in latin for possible usage in different languages. Original artist: myself, based on
TimVickers's work.
• File:Trimyristin-3D-vdW.png Source: https://upload.wikimedia.org/wikipedia/commons/6/64/Trimyristin-3D-vdW.png License: Pub-
lic domain Contributors: ? Original artist: ?
• File:Tuberculostearic_acid_synthesis.png Source: https://upload.wikimedia.org/wikipedia/commons/8/85/Tuberculostearic_acid_
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• File:Turquoise_Water.jpg Source: https://upload.wikimedia.org/wikipedia/commons/e/e8/Turquoise_Water.jpg License: CC BY-SA
4.0 Contributors: Own work Original artist: NickGibson3900
• File:Ubiquinone–ubiquinol_conversion.svg Source: https://upload.wikimedia.org/wikipedia/commons/1/1a/Ubiquinone%E2%80%
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TimVickers. Original artist: Fvasconcellos 03:07, 12 September 2007 (UTC)
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• File:Ubiquitylation.png Source: https://upload.wikimedia.org/wikipedia/commons/7/7f/Ubiquitylation.png License: CC-BY-SA-3.0
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• File:Unsaturated_fatty_acid-_Beta_oxidation.png Source: https://upload.wikimedia.org/wikipedia/commons/e/e2/Unsaturated_
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