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 CLIFFSQuICKREVIEW™

Biochemistry I
By Frank Schmidt

IDG Books Worldwide, Inc.

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 About the Author Publisher’s Acknowledgments
Frank Schmidt, Ph.D., is Professor of Editorial
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 CONTENTS

CHAPTER 1: THE SCOPE OF BIOCHEMISTRY . . . . . . . . .1

Biochemistry is a Contemporary Science . . . . . . . . . . . . . . . . . 2
Extrapolating Biochemical Information . . . . . . . . . . . . . . . . . . 3
Common Themes in Biochemistry . . . . . . . . . . . . . . . . . . . . . . 4
Biochemical reactions involve small molecular structures . . . . 4
Polymers in Living Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Cell membranes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Types of Biochemical Reactions . . . . . . . . . . . . . . . . . . . . . . . . 9
Regulating biochemical reactions . . . . . . . . . . . . . . . . . . . . . 9
Large molecules provide cell information. . . . . . . . . . . . . . 10
Weak interactions and structural stability . . . . . . . . . . . . . . 10
Biochemical reactions occur in a downhill fashion. . . . . . . 10
All Organisms are Related . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
The Common Origin of Organisms . . . . . . . . . . . . . . . . . . . . . 12
CHAPTER 2: THE IMPORTANCE OF
WEAK INTERACTIONS . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
The United Strength of biochemical structures . . . . . . . . . . . . 15
Properties of Water and Biomolecular Structure . . . . . . . . . . . 16
The properties of water and hydrogen bonds . . . . . . . . . . . 16
Hydrogen bonds and biomolecules . . . . . . . . . . . . . . . . . . . 17
The Hydrophobic Effect. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Nonpolar molecules and water-solubility . . . . . . . . . . . . . . 18
Membrane associations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Electrostatic and van der Waals Interactions . . . . . . . . . . . . . . 21
Acid-Base Reactions in Living Systems . . . . . . . . . . . . . . . . . 23
pK values and protonation. . . . . . . . . . . . . . . . . . . . . . . . . . 24
Solution pH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Buffer capacity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Biological acid-base equilibria . . . . . . . . . . . . . . . . . . . . . . 27
CHAPTER 3: INTRODUCTION TO BIOLOGICAL
ENERGY FLOW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29
Types of metabolic reactions . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Enzyme Catalysts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Space and Time Links in Metabolic Reactions . . . . . . . . . . . . 30
Energy Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

BIOCHEMISTRY I
iii
 CONTENTS

Free Energy Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

The Cell’s Energy Currency. . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Free-Energy-Driven Transport across Membranes . . . . . . . . . 36
CHAPTER 4: OVERVIEW OF BIOLOGICAL
INFORMATION FLOW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .39
Complexity in Biochemical Genetics . . . . . . . . . . . . . . . . . . . 39
The Central Dogma of Molecular Biology: DNA Makes
RNA Makes Protein. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
DNA, RNA, and nucleotide structure . . . . . . . . . . . . . . . . . . . 41
DNA’s duplex nature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
The DNA double helix and genetic replication . . . . . . . . . . 47
RNA Carries Genetic Information . . . . . . . . . . . . . . . . . . . . . . 49
Messenger RNA specifies the order of amino acids
in proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Transfer RNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Ribosomes and translation. . . . . . . . . . . . . . . . . . . . . . . . . . 53
Base-Pairing and the Central Dogma. . . . . . . . . . . . . . . . . . . . 54
Genetic information expression. . . . . . . . . . . . . . . . . . . . . . 54
CHAPTER 5: PROTEIN STRUCTURE . . . . . . . . . . . . . . . . .55
Levels of Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Amino acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Amino acid side chains . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Hydroxyl and sulfer-containing side chains . . . . . . . . . . . . 60
The cyclic amino acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Primary struture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Secondary structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Fibrous and globular proteins . . . . . . . . . . . . . . . . . . . . . . . 70
Tertiary structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Protein-assisted folding . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Quaternary structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
CHAPTER 6: THE PHYSIOLOGICAL CHEMISTRY
OF OXYGEN BINDING BY MYOGLOBIN
AND HEMOGLOBIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75
The Chemistry of Molecular Oxygen . . . . . . . . . . . . . . . . . . . 75
Hemoglobin and myoglobin . . . . . . . . . . . . . . . . . . . . . . . . 76

CLIFFSQUICKREVIEW
iv
 CONTENTS

Myoglobin binds oxygen. . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Binding oxygen to hemoglobin . . . . . . . . . . . . . . . . . . . . . . 79
Physiological conditions and hemoglobin . . . . . . . . . . . . . 81
Acidic conditions and hemoglobin . . . . . . . . . . . . . . . . . . . 81
Temperature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
The regulatory compound, 2,3 — bisphosphoglycerate
(BPG) and hemoglobin. . . . . . . . . . . . . . . . . . . . . . . . . 82
Fetal hemoglobin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
CHAPTER 7: ENZYMES . . . . . . . . . . . . . . . . . . . . . . . . . . . . .83
Enzymes Are Catalysts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Six Types of Enzyme Catalysts . . . . . . . . . . . . . . . . . . . . . . . . 85
The Michaelis-Menten equation . . . . . . . . . . . . . . . . . . . . . 88
Inhibitors of enzyme-catalyzed reactions . . . . . . . . . . . . . . 93
Chemical Mechanisms of Enzyme Catalysis . . . . . . . . . . . . . . 97
The transition state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Vitamin conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Chymotrypsin: An Enzyme at Work . . . . . . . . . . . . . . . . . . . 102
Enzyme Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Allostery and enzyme regulation. . . . . . . . . . . . . . . . . . . . 105
Covalent Modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Phosphorylation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Zymogens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
CHAPTER 8: ORGANIZATION OF METABOLISM . . . .109
Metabolism: A Collection of Linked Oxidation
and Reduction Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Energy production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Catabolic pathways feed into the TCA cycle. . . . . . . . . . . 111
Biosynthetic reactions versus catabolic reactions . . . . . . . 111
CHAPTER 9: GLYCOLYSIS . . . . . . . . . . . . . . . . . . . . . . . . .113
Six-Carbon Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Glycolysis, ATP, and NADH . . . . . . . . . . . . . . . . . . . . . . . . . 118
Electron transfer to pyruvate . . . . . . . . . . . . . . . . . . . . . . . 121
Ethanol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

BIOCHEMISTRY I
v
 CONTENTS

Pyruvate to acetyl-Coenzyme A: The entry

point into the TCA cycle. . . . . . . . . . . . . . . . . . . . . . . 123
Glycolysis Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Regulation occurs at the three reactions far
from equilibrium. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Glycolysis produces short but high bursts of energy. . . . . 128
CHAPTER 10: THE TRICARBOXYLIC ACID CYCLE . .129
The First Phase of the TCA Cycle . . . . . . . . . . . . . . . . . . . . . 130
Oxidative decarboxylation . . . . . . . . . . . . . . . . . . . . . . . . 136
The third phase of the TCA cycle . . . . . . . . . . . . . . . . . . . 137
Substrate Availiability, Pyruvate, and the TCA Cycle . . . . . . 139
CHAPTER 11: OXIDATIVE PHOSPHORYLATION . . . . .141
Oxidative Phosphorylation. . . . . . . . . . . . . . . . . . . . . . . . . . . 142
The energy of oxidation. . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Biochemical reduction and concentration-dependency. . . 145
The oxidation of NADH . . . . . . . . . . . . . . . . . . . . . . . . . . 146
The Electron Transport Chain . . . . . . . . . . . . . . . . . . . . . . . . 147
Complex I and Complex II . . . . . . . . . . . . . . . . . . . . . . . . 147
ATP Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Mitochondrial Transport Systems . . . . . . . . . . . . . . . . . . . . . 153
Energy Yields from Oxidative Phosphorylation . . . . . . . . . . 155
CHAPTER 12: CARBOHYDRATE METABOLISM II . . .157
The Pentose Phosphate Pathway . . . . . . . . . . . . . . . . . . . . . . 157
Ribulose-5-phosphate . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Converting pentoses to sugars. . . . . . . . . . . . . . . . . . . . . . 160
Catabolism of other carbohydrates . . . . . . . . . . . . . . . . . . 162
The Gluconeogenic Pathway . . . . . . . . . . . . . . . . . . . . . . . . . 167
Bypassing the pyruvate kinase step. . . . . . . . . . . . . . . . . . 167
Bypassing the phosphofructokinase
and hexokinase steps . . . . . . . . . . . . . . . . . . . . . . . . . 169
Storage of Glucose in Polymeric Form as Glycogen. . . . . . . 170
Cyclic AMP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174

CLIFFSQUICKREVIEW
vi
 CHAPTER 1
THE SCOPE OF BIOCHEMISTRY

Biochemists discuss chemistry with biologists, and biology

with chemists, thereby confusing both groups. Among
themselves, they talk about baseball. –Anonymous

As the name indicates, biochemistry is a hybrid science: Biology is

the science of living organisms and chemistry is the science of atoms
and molecules, so biochemistry is the science of the atoms and mole-
cules in living organisms. Its domain encompasses all the living world
with the unifying interest in the chemical structures and reactions that
occur in living systems. Where can you find biochemistry? All through
science, medicine, and agriculture.

Biochemistry underlies ordinary life in unseen ways: For exam-

ple, take a middle-aged man (not very different from the author of
this book) who:

■ Takes a drug to lower his serum cholesterol. That drug was

developed by a pharmaceutical company’s biochemists to
inhibit a key enzyme involved in cholesterol biosynthesis.
■ Shaves with a cream containing compounds that soften his
beard. These active agents were developed after studies of the
physical properties of keratin, the protein in hair.
■ Eats a breakfast cereal fortified with vitamins identified
through nutritional biochemistry.
■ Wears a shirt made from pest-resistant cotton. The cotton
plants were bioengineered by biochemists through the trans-
fer of genes from a bacterium into plants.
■ Goes fishing after work. The conservation agents who man-
age the stream use biochemical information from the DNA
(deoxyribonucleic acid) sequences to track the genetics of the
fish population.

BIOCHEMISTRY I
1
 THE SCOPE OF
BIOCHEMISTRY

■ Drinks milk before bedtime. His sleep is helped by the amino

acids in the milk, which are converted by his brain into molec-
ular signals that lead to a resting state in other parts of his brain.

All these everyday events depend on an understanding of the

chemistry of living systems. The purpose of this book is to provide a
quick review of the chemical structures and events that govern so
much of daily life. You can use it as a supplement to existing texts
and as a review of biochemistry for standardized examinations.

Biochemistry is a Contemporary Science

In the early nineteenth century, as chemistry became recognized as a

scientific discipline, a distinction was made between inorganic and
organic chemistry. Organic compounds (those containing carbon and
hydrogen) were thought to be made only in living systems. However,
in 1828, Friedrich Wöhler in Germany heated an inorganic com-
pound, ammonium carbamate, and made an organic one, urea, found
naturally in animal urine. Wöhler’s experiment showed that the
chemistries of the living and nonliving worlds are continuous:

O O

+ −
C C
NH4 O NH2 H2N NH2
+ H2O

At the end of the nineteenth century, a parallel controversy arose

as organic chemists debated whether an intact, living cell was needed
to carry out biochemical reactions. Hans Büchner in Germany repro-
duced the synthesis of ethanol with a cell-free extract of brewer’s
yeast, showing that reactions of living systems can be reproduced in
vitro (literally, in glass), that is, away from a living system. Reactions
in living cells occur because they are catalyzed by enzymes — the
very word enzyme is derived from the Greek word for yeast, zymos.

CLIFFSQUICKREVIEW
2
 THE SCOPE OF
BIOCHEMISTRY

Biochemistry became a distinct science in the early twentieth

century. In the United States, it arose from the merger of physiologi-
cal chemistry and agricultural chemistry. Contemporary biochemistry
has three main branches:

■ Metabolism is the study of the conversion of biological mol-

ecules, especially small molecules, from one to another — for
example, the conversion of sugar into carbon dioxide and
water, or the conversion of fats into cholesterol. Metabolic
biochemists are particularly interested in the individual
enzyme-catalyzed steps of an overall sequence of reactions
(called a pathway) that leads from one substance to another.
■ Structural Biochemistry is the study of how molecules in
living cells work chemically. For example, structural bio-
chemists try to determine how the three-dimensional structure
of an enzyme contributes to its ability to catalyze a single
metabolic reaction.
■ Molecular Genetics is concerned with the expression of
genetic information and the way in which this information
contributes to the regulation of cellular functions.

These distinctions are somewhat artificial, as contemporary bio-

chemistry is intimately connected with other branches of biology and
chemistry, especially organic and physical chemistry, physiology,
microbiology, genetics, and cell biology.

Extrapolating Biochemical Information

If the reactions of every organism were different, biochemistry would

be a poor science. Contemporary biochemistry depends on the ability
to extrapolate information from one system to another. For example,
if humans and animals made cholesterol in fundamentally different
ways, scientists would have no way to find a compound to treat high
cholesterol and prevent heart attacks. It would be impossible

BIOCHEMISTRY I
3
 THE SCOPE OF
BIOCHEMISTRY

(and unethical) to screen the millions of known organic compounds in

humans to find an effective treatment. On the other hand, using enzyme
systems, researchers can screen many thousands of compounds for
their ability to inhibit an enzyme system in vitro. They can then screen
the small number of active compounds for their effectiveness in labo-
ratory animals, and then in humans.

Common Themes in Biochemistry

At first glance, the subject matter of biochemistry seems too compli-

cated to do anything other than blindly memorize it. Fortunately, bio-
chemistry has a number of unifying themes, which can help you keep
the varying branches in perspective. Some of the themes you’ll
encounter repeatedly in this book are explored in the following
sections.

Biochemical reactions involve small molecular structures

Four classes of small molecules combine to make up most of the impor-
tant bimolecular structures (see Figure 1-1). Most of these are optically
active, that is, they are found in only one of the possible stereoisomers.
(Stereoisomers are compounds that have the same kinds and numbers
of atoms but have different molecular arrangements.

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OH
H C H
COOH
H C O H
H2N C H C OH C C

CH3 HO C C OH
H OH
Alanine, an Glucose, a
Amino Acid Carbohydrate

HO O
C
CH 2 NH2
CH 2 C N
CH 2 N C
CH 2 C
C C
CH 2 N N
CH 2
O C H
CH 2 HOH2C
C H
CH 2 C C H
H
CH 2 HO OH
CH 2
CH 2 Adenosine,
a Nucleoside
CH 2
CH 2
CH 2
H C H
H
Palmitic Acid,
a Lipid

Figure 1-1

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■ Amino acids all have the common core structure shown in

Figure 1-1. Generally, amino acids found in nature are the
L-stereoisomers. Amino acids are the building blocks of pro-
teins, and have an important role in energy metabolism and in
cellular signaling. They are also a small but important part of
cell membranes.
■ Carbohydrates are molecules of the empirical formula
Cn(H2O)n where n usually ranges from 3–7. They are found in
sugars and starches and make up parts of nucleotides (the
energy currency of a cell, and the building blocks for genetic
information). They are also present in some components of all
cell membranes. They are the central components of energy-
producing pathways in biology.
■ Lipids are closely related to hydrocarbons (compounds con-
taining hydrogen and carbon atoms exclusively), although they
usually have other atoms beside C and H. Characterized by lim-
ited solubility in water, lipids are essential components of mem-
branes, and are important energy stores in plants and animals.
■ Nucleosides and nucleotides contain a carbohydrate compo-
nent joined to one of four carbon- and nitrogen-containing ring
compounds called bases. They make up the energy currency of
the cell, and, when joined end-to-end (polymerized) into DNA
or RNA chains, form the genetic information of a cell.

Polymers in Living Systems

In the cell, single amino acids, sugars, and nucleotides can be joined
together into polymers. Polymers are large molecules composed of
small subunits arranged in a “head to tail” fashion. Living systems
are based on polymers. There are several reasons why this is true:

■ Economy of synthesis: Chemical reactions occur much more

quickly and specifically in living cells than they do in an

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organic chemical reaction. The speed and specificity of bio-

chemical reactions are due to the enzymes that catalyze the
reactions in a cell. How does the cell get the many catalysts
needed to support life? They can be made one by one or mass-
produced. Mass production is much more efficient, as can be
seen by the following exercise.
Suppose that a living system needs 100 catalysts. These cata-
lysts could be synthesized one by one. Where would the
catalysts to make the catalysts come from? Making the set of
100 catalysts would require at least 100 more catalysts to
synthesize them, which would require 100 more catalysts, and
so on. A living cell would need a huge number of catalysts,
greater than the number of known organic molecules (or even
the number of atoms in the universe). Suppose, on the other
hand, that the catalysts were mass-produced. Joining the amino
acids to each other by a common mechanism allows a single
catalyst to join 20 different amino acids by the same chemical
reactions. If two amino acids join together, they can make
20 × 20 = 400 possible dimers (molecules composed of two
similar subunits); joining three together makes 20 × 20 × 20 =
8,000 trimers (molecules made of three similar subunits), and
so on. Because a single protein may contain 1,000 or more
amino acids joined end to end, a huge number of different cata-
lysts can be made from the relatively few monomer compounds.
■ Economy of reactions: Joining monomers to make macromol-
ecules is economical if the monomers can be joined by the same
chemistry. If the monomers contained different functional
groups, synthesis of each polymer would require a different
kind of catalyst for each monomer added to the chain. Clearly,
it is more economical to use a generic catalyst to put together
each of the many monomers required for synthesis.
■ Stability of cells: This argument is based on the properties of
water. If red blood cells are placed in distilled water, they burst.
Water moves across the membrane from the outside to the
inside. In general, water moves across a membrane from the
side with a lower solute concentration to the side with higher

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solute concentration; the side with higher solute concentration

has a higher osmotic pressure. The cell has to expend energy
to maintain its osmotic pressure. The osmotic pressure of a
system is based on the number of atoms or molecules
dissolved in water, not on their size. Thus, 100 molecules of a
carbohydrate monomer (a sugar) have the same osmotic pres-
sure as 100 polysaccharide molecules, each containing 100
monomers; however, the latter macromolecule can store 100
times more energy.

Cell membranes
Organisms have an inside and an outside, and the reactants and prod-
ucts of biochemical reactions are kept either in the cell for further
reaction or excreted. Membranes are formed by lipid bilayers as
shown in Figure 1-2, with proteins dissolved in the lipid. The outsides
of bilayers are charged and interact with water, while the insides are
hydrocarbon-rich. Besides defining the boundaries of a cell, mem-
branes are used for energy generation and for separating the compo-
nents from each other when necessary. For example, powerful
digestive enzymes in eukaryotic cells are kept inside a membrane-
bounded compartment, the lysosome. Substrates for these enzymes
are imported into the lysosome.

Figure 1-2

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Types of Biochemical Reactions

Although there are many possible biochemical reactions, they fall

into only a few types to consider:

■ Oxidation and reduction: For example, the interconversion

of an alcohol and an aldehyde.
■ Movement of functional groups within or between mole-
cules: For example, the transfer of phosphate groups from one
oxygen to another.
■ Addition and removal of water: For example, hydrolysis of
an amide linkage to an amine and a carboxyl group.
■ Bond-breaking reactions: For example, carbon-carbon bond
breakage.

The complexity of life results, not from many different types of

reactions, but rather from these simple reactions occurring in many
different situations. Thus, for example, water can be added to a
carbon-carbon double bond as a step in the breakdown of many
different compounds, including sugars, lipids, and amino acids.

Regulating biochemical reactions

Mixing gasoline and oxygen can run your car engine, or cause an
explosion. The difference in the two cases depends on restricting the
flow of gasoline. In the case of the car engine, you control the amount
of gasoline entering the combustion chamber with your foot on the
accelerator. Like that process, it’s important that biochemical reac-
tions not go too fast or too slowly, and that the right reactions occur
when they are needed to keep the cell functioning.

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Large molecules provide cell information

The ultimate basis for controlling biochemical reactions is the genetic
information stored in the cell’s DNA. This information is expressed in
a regulated fashion, so that the enzymes responsible for carrying out
the cell’s chemical reactions are released in response to the needs of
the cell for energy production, replication, and so forth. The informa-
tion is composed of long sequences of subunits, where each subunit is
one of the four nucleotides that make up the nucleic acid.

Weak interactions and structural stability

Heat often destroys a biochemical system. Cooking a slice of liver at
temperatures only slightly over 100°F. destroys the enzymatic activ-
ity. This isn’t enough heat to break a covalent bond, so why aren’t
these enzymes more robust? The answer is that enzymatic activity
and structure depend on weak interactions whose individual energy
is much less than that of a covalent bond. The stability of biological
structures depends on the sum of all these weak interactions.

Biochemical reactions occur in a downhill fashion

Life on earth ultimately depends on nonliving energy sources. The
most obvious of these is the sun, whose energy is captured here on
Earth by photosynthesis (the use of the light energy to carry out the
synthesis of biochemicals especially sugars). Another source of
energy is the makeup of the Earth itself. Microorganisms living in
deep water, the soil, and other environments without sunlight can
derive their energy from chemosynthesis, the oxidation and reduc-
tion of inorganic molecules to yield biological energy.

The goal of these energy-storing processes is the production of

carbon-containing organic compounds, whose carbon is reduced
(more electron-rich) than carbon in CO2. Energy-yielding metabolic
processes oxidize the reduced carbon, yielding energy in the process.
The organic compounds from these processes are synthesized into
complex structures, again using energy. The sum total of these

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processes is the use of the original energy source, that is, light from
the sun, for the maintenance and replication of living organisms, for
example, humans.

The energy available from these reactions is always less than the
amount of energy put into them. This is another way of saying that liv-
ing systems obey the Second Law of Thermodynamics, which states
that spontaneous reactions run “downhill,” with an increase in entropy,
or disorder, of the system. (For example, glucose, which contains six
carbons joined together, is more ordered than are six molecules of CO2,
the product of its metabolic breakdown.)

All Organisms are Related

The classification and grouping of organisms, the science called

taxonomy, regards organisms as similar based on their visible charac-
teristics. Thus, from the Greeks until recently, plants and animals were
regarded as the two main kingdoms of life. Later, cell biologists divided
organisms into prokaryotes and eukaryotes, that is, organisms
without and with a nucleus. Most recently, a new taxonomy has been
developed, largely by Carl Woese and associates, based on the infor-
mation in the ribosomal RNA sequences. Ribosomal RNA, used as an
evolution clock, is essential to life, easy to identify, and full of surprises.

Remarkably, the most information-rich classifications of life

shows three main divisions, sometimes called domains, which are
more fundamental than the distinction between plants and animals,
or prokaryotes and eukaryotes. These domains are:

■ Eukarya: The most familiar domain, eukarya includes organ-

isms with a nucleus. This division includes plants, animals, and
a large number of what are sometimes called protists, or organ-
isms that can be seen only under a microscope, such as yeasts
or paramecia.

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■ Bacteria: The second domain includes microorganisms with-

out a nucleus, including many that are familiar, like Escherichia
coli.
■ Archaea: The third group, on the molecular/biochemical
level, is as different from bacteria as they are from eukarya.
These remarkable microorganisms inhabit niches often
thought of as inhospitable to life — for example, locations
with high temperature, low oxygen, or high salt. Their bio-
chemistry is unique and largely unexplored. Fully half of the
known genes of these organisms are apparently unique, with
no counterparts in bacterial or eukaryotic genomes.

The Common Origin of Organisms

The basis of the study of molecular evolution and taxonomy is the

origin of organisms. Although the tree of life shown in Figure 1-3 was
derived from sequences of a single gene, the similarities among
organisms’ biochemical and molecular properties are greatest for the
organisms closely branched on the tree. Thus, human metabolism is
more similar to that of chimpanzees, a close relative, than to that of
yeast, a more distant relative. Human and yeast biochemistry are
more similar to each other than either is to an archael or bacterial
organism. The implications of this are important for the application
of biochemistry to human disease. It is obviously unethical to do
many biochemical experiments on human beings; however, animals
or cultured animal cells are similar enough to find principles in com-
mon. For example, medical researchers can study the properties of
genes that cause disease in mice, and evaluate potential treatments
for safety before trying them on humans. Although not foolproof, this
principle of similarity has been used continually in biomedical
research dedicated to disease treatment and prevention.

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Fungi
Pl
Cyanobacteria an
ts

Gr
am
ba -pos ls
cte itiv ma
ria e ria Ani
bacte
Proteo

es

us
t
yo

lob
ar
ia

lfo
cter

Eu

Su
a
Eub

Archaea
Methanogens
Ha
lop
hil
es

Original
Cell

Figure 1-3

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 CHAPTER 2
THE IMPORTANCE OF WEAK INTERACTIONS

Water, water everywhere. –Coleridge

The United Strength of Biochemical Structures

The forces that hold biomolecules together in three dimensions are

small, on the order of a few kJ/mole, and much weaker than a covalent
bond (formed through sharing of electrons between two atoms), which
has an energy of formation a hundred times larger. Would life be
possible if these molecules were held together only by covalent bonds?
Probably not. For example, muscle contraction involves movement of
the protein myosin relative to a filament composed of another protein,
actin. This movement does not involve the breakage or formation of
covalent bonds in the protein. A single contraction cycle requires about
60 kJ/mole; which is about 3% to -5% of the energy captured during
the complete combustion of a mole of glucose. If the energy required
for contraction were the same as that of forming a carbon-
carbon covalent bond, almost all the energy of combustion of a
molecule of glucose would be required for a single contraction. This
would place a much higher demand for energy on the cell, which would
require a similarly high demand for food on an organism.

If the forces holding them together are so small, how can biomol-
ecules have any sort of stable structure? Because these small forces are
summed over the entire molecule. For example, consider a double-
stranded DNA a thousand base pairs long. The energy of an average
base pair, about 0.5 kJ/mole, is not great, but the energy of 1,000 base
pairs equals 500 kJ/mole, equivalent to the energy of several covalent
bonds. This also has important consequences for the dynamics of indi-
vidual base pairs: They can be opened easily while the molecule as a
whole is held together. This property of weak interactions will become
important in the consideration of DNA replication and transcription,
later in this series.

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Properties of Water and Biomolecular Structure

Water is necessary for life. Many plant and animal adaptations con-
serve water — the thick skin of desert cacti and the intricate structure
of the mammalian kidney are just two examples. Planetary scientists
look for evidence of liquid water when speculating about the possibil-
ity of life on other planets such as Mars or Jupiter’s moon, Titan.

Water has many remarkable properties, including:

■ High surface tension: Despite being denser than water, small

objects, such as aquatic insects, can stay on top of water surface.
■ High boiling point: Relative to its molecular weight, water
boils at a high temperature. For example, ammonia, with a
molecular weight of almost 17, boils at -33° C, while water,
with a molecular weight of 18, boils at 100° C.
■ Density is dependent on temperature: Solid water (ice) is less
dense than liquid water. This property means that lakes and
ponds freeze from the top down, a benefit to the fish living there,
who can overwinter without being frozen solid.

The properties of water and hydrogen bonds

Water has a dipole, that is, a separation of partial electrical charge along
the molecule. Two of oxygen’s six outer-shell electrons form covalent
bonds with the hydrogen. The other four electrons are nonbonding and
form two pairs. These pairs are a focus of the partial negative charge,
and the hydrogen atoms correspondingly become partially positively
charged. Positive and negative charges attract each other, so that the
oxygen and hydrogen atoms form hydrogen bonds. Each oxygen in a
single molecule can form H-bonds with two hydrogens (because the
oxygen atom has two pairs of nonbonding electrons). Figure 2-1 shows
such a hydrogen bond. The resulting clusters of molecules give water
its cohesiveness. In its liquid phase, the network of molecules is
irregular, with distorted H-bonds. When water freezes, the H-bonds

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form the water molecules into a regular lattice with more room
between the molecules than in liquid water; hence, ice is less dense
than liquid water.

Figure 2-1

Hydrogen bonds and biomolecules

In water, the nonbonding electrons are the H-bond acceptors and the
hydrogen atoms are the H-bond donors. Biomolecules have H-bond
acceptors and donors within them. Consider the side chain of a simple
amino acid, serine. The oxygen contains two pairs of nonbonding
electrons, as water does, and the hydrogen is correspondingly a focus
of partial positive charge. Serine thus can be both an H-bond acceptor
and donor, sometimes at the same time. As you would expect, serine is
soluble in water by virtue of its ability to form H-bonds with the
solvent around it. Serine on the inside of a protein, away from water,
can form H-bonds with other amino acids; for example, it can serve as
an H-bond donor to the nonbonding electrons on the ring nitrogen of
histidine, as shown in Figure 2-2.

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HN H
O
C C
CH2
O H H NH
N C C
O
Hydrogen bond H C
N
H

Figure 2-2

These H-bonds normally exist only when water is not present. If

serine’s side chain is found on the surface of a protein, it is very likely
to form H-bonds, given the relatively high concentration of water
available.

The Hydrophobic Effect

Nonpolar molecules and water-solubility

Because water is so good at forming hydrogen bonds with itself, it is
most hospitable to molecules or ions that least disrupt its H-bonding
network. Watching oils float on the surface of water demonstrates that
oil molecules are nonpolar — they don’t carry a charge or polarity, and
do not dissolve in water. When an oil or other nonpolar compound
encounters water, the compound disrupts the H-bonding network of
water and forces it to re-form around the nonpolar molecule, making a
cage of sorts around the nonpolar molecule. This cage is an ordered
structure, and so is unfavored by the Second Law of
Thermodynamics, which states that spontaneous reactions proceed
with an increase in entropy (disorder).

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How to resolve this dilemma? If the nonpolar molecules come

together, then fewer water molecules are required to form a cage around
them. As an analogy, consider the ordered water structure to be like
paint around a cubic block. If you have four blocks to paint, and each
block is 1 cm along each side, each block would require 6 cm2 worth
of paint if you paint them separately. However, if you put the four
blocks together in a square pattern, you don’t need to paint the inside
surfaces of the cubes. A total of only 16 cm2 rather than 24 cm2 surface
needs to be painted as Figure 2-3 shows.

Each block has 6 sides

6 x 4 = 24

Four blocks together

have 16 sides exposed.

Figure 2-3

The tendency of nonpolar molecules to self-associate in water

rather than to dissolve individually is called the hydrophobic effect.
The term is somewhat misleading because it refers to the molecules
themselves, where in reality it is due to the H-bonding nature of water,
but it is used almost universally, and biochemists often speak of the
hydrophobic side chains of a molecule as a shorthand for the complex-
ities of discussing water structure as it is affected by nonpolar con-
stituents of biomolecules.

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Many biomolecules are amphipathic, that is, they have both

hydrophobic (water-hating) and hydrophilic (water-loving) parts. For
example, palmitic acid has a carboxylic acid functional group attached
to a long hydrocarbon tail. When its sodium salt, sodium palmitate, is
dissolved in water, the hydrocarbon tails associate due to the
hydrophobic effect, leaving the carboxylate groups to associate with
water. The fatty acid salt forms a micelle — a spherical droplet
arranged with the hydrocarbon chains inside and the carboxylate
groups inside on the outside of the droplet. Sodium palmitate is a
major constituent of soap. Fats are triglyceride esters, composed of
three fatty acids esterified to a single glycerol molecules. An ester link-
age is a covalent bond between a carboxylic acid and an alcohol. Soap
micelles mobilize fats and other hydrophobic substances by dissolv-
ing them in the interior of the micelle. Because the micelles are sus-
pended in water, the fat is mobilized from the surface of the object
being cleaned. Detergents are stronger cleaning agents than are soaps,
mostly because their hydrophilic component is more highly charged
than the fatty acid component of a soap. For example, sodium dode-
cyl sulfate is a component of commercially available hair shampoos.
It is a powerful enough detergent that it is often used experimentally
to disrupt the hydrophobic interactions that hold membranes together
or that contribute to protein shape.

Membrane associations
Glycerol esters of fatty acids are a large component of biological
membranes. These molecules differ from those found in fats in that
they contain only two fatty acid side chains and a third, hydrophilic
component, making them amphipathic. Amphipathic molecules con-
tain both polar (having a dipole) and nonpolar parts. For example,
phosphatidylcholine, a common component of membranes, contains
two fatty acids (the hydrophobic portion) and a phosphate ester of
choline, itself a charged compound:

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O
(R1)
CH2 O C
O
(R2)
O HC O C
+
(CH3)3N CH2 CH2 O P O CH2
(R3) −
O

When phosphatidylcholine is suspended in water, the molecules

associate by the hydrophobic effect, with the charged portion facing
the solvent and the fatty acid side chains associating with each other.
Instead of making a micelle, however, as palmitate does, these
molecules associate into a bilayer, which eventually forms a spherical
vesicle (termed a liposome) with a defined inside and outside.
Liposomes are clearly similar to cell membranes, although they differ
in some respects.

Biological membranes are bilayers and contain several types of

lipids; some more often associated with the outside face of the cell, and
others face the inside. Biological membranes also contain a large num-
ber of protein components. Membranes are semipermeable, naturally
excluding hydrophilic compounds (carbohydrates, proteins, and ions,
for example) while allowing oxygen, proteins, and water to pass freely.

Electrostatic and van der Waals Interactions

Opposite charges attract. For example, Mg2+ ions associate with the
negatively charged phosphates of nucleotides and nucleic acids.
Within proteins, salt bridges can form between nearby charged
residues, for example, between a positively charged amino group and
a negatively charged carboxylate ion. These electrostatic interactions
make an especially large contribution to the folded structure of
nucleic acids, because the monomers each carry a full negative
charge.

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Van der Waals interactions (see Figure 2-4) represent the attrac-
tion of the nuclei and electron clouds between different atoms. The
nucleus is positively charged, while the electrons around it are nega-
tively charged. When two atoms are brought close together, the nucleus
of one atom attracts the electron cloud of the other, and vice versa. If
the atoms are far apart (a few atomic radii away) from each other, the
van der Waals force becomes insignificant, because the energy of the
interaction varies with the 12th power of distance. If the atoms come
closer together (so that their electron clouds overlap) the van der Waals
force becomes repulsive, because the like charges of the nucleus and
electron cloud repel each other. Thus, each interaction has a character-
istic optimal distance. For two identical atoms, the optimal distance is
d=2r, where r is atom radius. Within a biomolecule, these interactions
fix the final three-dimensional shape. While van der Waals interactions
individually are very weak, they become collectively important in
determining biological structure and interactions.

−
−

+
+

Negative Electron

Van der Waal's Interaction

Figure 2-4

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Acid-Base Reactions in Living Systems

Biochemists usually discuss acids and bases in terms of their ability to

donate and accept protons; that is, they use the Brønsted definition of
acids and bases. A few concepts from general chemistry are important
to help organize your thoughts about biochemical acids and bases:

1. A compound has two components — a conjugate acid and a

conjugate base. Thus, you can think of HCl as being composed
of the proton-donating acidic part (H+) and the proton-accept-
ing basic part (Cl–). Likewise, acetic acid is composed of H+
and the conjugate base (H3CCOO–).

Bilayer membrane

Inner aqueous
compartment

2. The stronger the acid, the weaker its conjugate base. Thus,
HCl is a stronger acid than acetic acid, and acetate ion is a
stronger base than chloride ion. That is, acetate is a better pro-
ton acceptor than is chloride ion.
3. The strongest acid that can exist in appreciable concentration
in a solution is the conjugate acid of the solvent. The strongest
base that can exist in a solution is the conjugate base of the
solvent. In water, the strongest base that exists is OH –. If a
stronger base, such as NaOCH3, is added to water, the methox-
ide ion rapidly removes protons from the solvent:

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CH3O–+ H2O → OH–+ CH3OH

leaving the base OH- as the strongest base in solution. (Don’t
try these reactions at home; they are highly exergonic!) The
strongest acid that can exist in water in appreciable amounts
is H3O+, the conjugate acid of H2O:
H2O + H2O H3O++ OH–
4. Weak acids and bases — those less strong than H+or OH–—
exist in equilibrium with water:
B + H2O BH + OH–
HA + H2O H3O++ A–

pK values and protonation

The strength of an acid or base is given by its Ka or Kb, respectively.
Ka × Kb = 1014, the dissociation constant of water. Just as it is conve-
nient to describe the concentration of H+ ions in solution as:

pH = -log[H+]

it is equally convenient to describe the Ka of an acid as its negative

logarithm, so that:

pKa = -logKa

For example, acetic acid, which has a Ka = 1.74 ×10-5, has a pK =

4.76. Ammonia is more basic than water, with a pKa = 9.25, corre-
sponding to its Ka= 5.6 × 10-10. If the pKa of a group is < 7.0, it will
donate a proton to water and a solution containing that compound will
have a pH < 7, that is, it will be basic. Conversely, if the pK of a com-
pound is > 7.0, that compound will accept a proton from water, and a
solution containing that compound will have a pH > 7, which puts it in
the acidic range.

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Solution pH
Many living organisms (there are many exceptions among the
microbes) can exist only in a relatively narrow range of pH values.
Thus, vegetables are often preserved by pickling them in vinegar, a
dilute solution of acetic acid in water. The low pH of the solution
prevents many bacteria and molds from growing on the food. Similarly,
it is a cliche of movie Westerns that desert springs whose water is
alkaline (basic) are decorated with the skulls of cattle who were
unfortunate enough to drink from them. Finally, individuals with chest
injuries who are unable to breathe efficiently develop a metabolic
acidosis, as their blood pH drops below normal due to the impaired
elimination of CO2 (a weak acid) from the lungs.

Microorganisms capable of living in acidic environments expend

a large amount of energy to keep protons from accumulating inside
their membranes. These examples show the importance of controlling
the pH of biological systems: Biochemical reactions, and therefore life,
can exist only in a narrow, near-neutral pH range.

All physiological pH control relies ultimately on the behavior of

weak acids and bases as buffers. A buffer is a combination of a weak
acid and its salt or a weak base and its salt. The addition of an acid or
a base to a buffered solution results in a lesser pH change than would
occur if the acid were added to water alone.

This behavior is described quantitatively by the Henderson-

Hesselbach equation, which can be derived from the definition of Ka:

Ka = [H+] [A-]/[HA]

where HA is a weak acid — acetic acid, for example.

Taking the logarithm of each side of the equation:

log Ka = log [H+] + log [A-] - log [HA]

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Remembering that:

[A-] - log [HA] = log([A-]/[HA])

and multiplying through by (-1):

- log Ka = -log[H+] - log([A-]/[HA])

Rearranging, and remembering the definitions of pK and pH:

pH = pKa + log ([A-]/[HA])

This equation allows you to predict the pH of a buffered solution

from the values of the pKa and the amount of basic and acidic forms
of the buffer. (For convenience, the subscript of the pK brackets to
indicate concentration and charges are sometimes omitted, and the
equation becomes pH = pK +log (A/HA).)

For example, calculate the pH of a solution containing 0.1 M

acetic acid and 0.01 M sodium acetate:

pH = 4.8 + log (0.01/0.1) = 4.8 + log (0.1) = 4.8 - 1 = 3.8

If the proportions of acid and salt are reversed, the pH would be

5.8. If they are equal, the ratio is:

[A]/[HA] = (0.01/0.01) = 1

and, because log 1 = 0, pH = pKa = 4.8.

Buffer capacity
What would happen if 0.005 equivalents of a strong acid, for example,
HCl, were added to each of the preceding three solutions? The strong
acid would donate protons to the acetate ion present in each solution.
This would change the ratio [A]/[HA], and consequently, the pH, in
each case:

CLIFFSQUICKREVIEW
26
 THE IMPORTANCE
OF WEAK
INTERACTIONS

Case 1: pH = 4.76 + log (0.005/0.105) =4.76 + (-1.32) = 3.4

instead of 3.8
Case 2: pH = 4.76 + log (0.095/0.015) = 4.76 + (0.80) =5.6
instead of 5.8
Case 3: pH = 4.76 + log (0.095/0.105) = 4.76 + (-0.04) = 4.7
instead of 4.8

If the HCl is added to pure water, the pH of the solution changes

from 7 to 1.3. Thus, in each case, the change in pH was less than
would have been observed in the absence of buffer. The lowest pH
change is seen in case 3. This illustrates a general rule: The amount
of change in pH of a buffer system is lowest near the pKa of the con-
jugate acid. In other words, buffers have their highest capacity when
the amounts of acidic and basic components are nearly equal. In prac-
tice, buffers are generally useful when the ratio A/HA is between 0.1
and 10; that is, at a pH within ± 1 pH unit of their pKs.

Biological acid-base equilibria

Metabolism occurs in cells at pH values near neutrality. For example,
plasma must be maintained at a pH within half a pH unit of its normal
value of 7.4. A number of mechanisms help accomplish this, including
buffering by the mono- and di-basic forms of phosphate ion:

H3PO4 + H2O H2PO4-+H3O+pK = 2.14

H2PO4-+ H2O HPO42- H3O+pK = 6.86
H2PO42- + H2O PO43- +H3O+pK = 12.4

At physiological pH, the Henderson-Hesselbach equation shows

that the second equilibrium is most important. Phosphoric acid and
phosphate exist in vanishingly small quantities near neutrality.

When carbon dioxide is dissolved in water, it exists in equilib-

rium with the hydrated form:

BIOCHEMISTRY I
27
THE IMPORTANCE
OF WEAK
INTERACTIONS

CO2 + H2O H2CO3

which is a weak acid. Carbonic acid, H2CO3, can donate two protons
to a base:

H2CO3 + H2O HCO3- + H3O + pKa1 = 6.37

HCO3- + H2O CO32- + H3O+ pKa2= 10.25

Metabolism releases CO2, which reduces the pH of the fluid

around the cell and must be buffered for metabolism to continue. In
animals, hemoglobin and other blood proteins play an important role
in this buffering.

CLIFFSQUICKREVIEW
28
 CHAPTER 3
INTRODUCTION TO BIOLOGICAL ENERGY FLOW

Cells obey the laws of chemistry. –J.D. Watson

Consider the simple reaction of nitrogen to make ammonia:

N2 +3 H2 < 2 NH3.
About half of the world’s production of ammonia is carried out
industrially and half biologically. At first glance, the two processes
look quite different. The industrial reaction takes place at 500°C. and
uses gaseous hydrogen and a metal catalyst under high pressure. The
biological reaction takes place in the soil, uses bacterial or plant reac-
tors, and occurs at moderate temperature and normal atmospheric
pressure of nitrogen. These differences are so substantial that, histor-
ically, they were interpreted by supposing that biological systems are
infused with a vital spirit that makes life possible. However, the bio-
logical reaction can be done with a purified enzyme. The biological
reduction of nitrogen is more similar to than different from its indus-
trial counterpart: The energy change from synthesis of a mole of
ammonia is identical in both cases, the substrates are the same, and
the detailed chemical reaction is similar whether the catalyst is a
metal or the active site of an enzyme.

Types of Metabolic Reactions

Metabolism refers to the dynamic changes of the molecules within a

cell, especially those small molecules used as sources of energy and
as precursors for the synthesis of proteins, lipids, and nucleic acids.
These reactions occur in the steady state rather than all at once.
Steady state refers to dynamic equilibrium, or homeostasis, where
the individual molecules change but the rate at which they are made
equals the rate at which they are destroyed. Concentrations of indi-
vidual molecules in metabolic reactions are therefore kept relatively

BIOCHEMISTRY I
29
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

constant, while any individual molecules are present only for a brief
time. Metabolism therefore is said to be an open chemical system.
Metabolic reactions can be catabolic (directed toward the breakdown
of larger molecules to produce energy), or anabolic (directed toward
the energy-consuming synthesis of cellular components from smaller
molecules).

Enzyme Catalysts

Like almost all biochemical reactions, the biological synthesis of

ammonia requires a specific biochemical catalyst—an enzyme—to
succeed. Enzymes are usually proteins and usually act as true cata-
lysts; they carry out their reactions many times.

Space and Time Links in Metabolic Reactions

Thousands of distinct chemical reactions occur in a cell at any moment.

A bacteria must simultaneously replicate its DNA, synthesize new
enzymes, break down carbohydrates for energy, synthesize small com-
ponents for protein and nucleic acid synthesis, and transport nutrients
into and waste products out of the cell. Each of these processes is
carried out by a series of enzymatic reactions called a pathway. The
reactions of a pathway occur in succession, and the substrates for the
pathways are often channeled through a specific set of enzymes
without mixing. For example, in muscle cells, the glucose used to
supply energy for contraction does not mix with the glucose used for
transporting ions across the cell membrane.

CLIFFSQUICKREVIEW
30
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

Energy Flow

Thermodynamics is the branch of chemistry and physics that

deals with the energy flow in physical systems. The First Law of
Thermodynamics states that energy in a system is neither created nor
destroyed. The Second Law of Thermodynamics deals with the
question of whether a reaction will occur: Spontaneous reactions occur
with an increase in the entropy of a system; that is, the overall
disorder of the system will increase. Entropy can be thought of as the
energy that is not available to do work. For example, the oceans
contain vast amounts of thermal energy in the form of the motions of
individual water molecules. Yet this energy cannot be extracted to
power a boat—that requires fuel or wind energy.

The amount of energy available for work is termed the free

energy of a system and is defined as the difference in heat content
between the products and reactants, less the amount of entropy
change (multiplied by the temperature of the system):

∆G = ∆H - T∆S

where ∆G is the amount of free energy released from the reaction, ∆H

is the change in heat content, or enthalpy, T is the temperature
in degrees Kelvin, and ∆S is the change in entropy. Another way of
stating the Second Law of Thermodynamics is that reactions occur in
the direction in which the free energy change is negative.

The change in free energy of a reaction in the standard state (con-

ventionally, all reactants and products at 1M) is related to the equilib-
rium constant for the reaction by the following relation:

∆G° = - RT ln(Keq),

where R is the gas constant, T is the temperature in degrees Kelvin,

and Keq is the equilibrium constant for the reaction. A reaction that is
favored has Keq > 1, and a reaction that is unfavored has Keq<1. In the

BIOCHEMISTRY I
31
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

former case, ln(Keq) is positive, so the free energy change of a favored

reaction is negative; it is exergonic. Conversely, the natural logarithm
of a number less than 1 is negative; because the product of two nega-
tive numbers is positive, the free energy change of an unfavored reac-
tion is positive; it is endergonic.

Free energy changes associated with a biochemical reaction are

determined at a standard state, with all reactants and products at 1M.
Many biomolecules are unstable in acid, so the biochemical standard
state is set at pH = 7.0 rather than at pH = 0 (1M acid), the standard
state for chemical reactions. Biochemical standard free energies of
reaction are given as ∆G°' to where the ' indicates this change in
standard conditions.

Biomolecules are also present in much lower concentrations than

the standard state of 1M. The free energy change associated with
reactions under conditions other than the standard state is given by
the relationship:

∆G = ∆G° = + RT ln (Π[Products]/Π[Reactants])

where Π [Products] represents the concentrations of the products of the

reaction, multiplied together, and Π [Reactants] represents the concen-
trations of the reactants, multiplied together. (If more than one mole-
cule of a product or reactant is involved in a reaction, the term for that
component is raised to the power of the number of molecules involved
in the reaction, just as for any chemical reaction.) R is the gas constant,
and T is the absolute temperature of the reaction. This relationship
reduces to ∆G = ∆G° = when all the products and reactants are present
at 1M concentration, the standard state. At equilibrium, ∆G = 0, and
the equation reduces to:

∆G°' = - RT ln(Keq).

Keq is simply the equilibrium constant of the reaction at pH 7.0.

CLIFFSQUICKREVIEW
32
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

Free Energy Calculations

Biochemical free energies are usually given as standard free energies

of hydrolysis. For example, the hydrolysis of glucose-6-phosphate:

glucose-6-phosphate + H2O glucose + Pi

has ∆G° = -4.0 kcal/mole (-16.5 kJ/mole) under standard conditions.
Therefore, the opposite reaction, the phosphorylation of glucose, is
unfavored. However, the phosphorylation of glucose occurs readily
in the cell, catalyzed by the enzyme hexokinase:

glucose + ATP glucose-6-phosphate + ADP + phosphate

The other half of the phosphorylation reaction is the hydrolysis
of ATP to yield ADP and inorganic phosphate (Pi):

ATP + H2O ADP + Pi

under standard conditions has ∆G° = -7.3 kcal/mole ( -31 kJ/mole).

The standard free energy change of the reaction can be deter-

mined by adding the two free energies of reaction:

glucose + PI → glucose-6-phosphate + H2O and

∆G° = + 4.0 kcal/mole

Note that the reaction as written is unfavored; its free energy

change is positive. Another way of stating this is that the reaction is
endergonic, that is, the reaction involves a gain of free energy.

For the exergonic hydrolysis of ATP (the reaction involves a loss

of free energy):

ATP + H2O ADP + Pi ∆G° = -7.3 kcal/mole

BIOCHEMISTRY I
33
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

The two reactions are summed:

glucose + ATP glucose-6-phosphate + ADP + Pi and

∆G° = -3.3 kcal/mole

This is a simple example of energetic coupling, where an unfa-

vorable reaction is driven by a favorable one, as shown in Figure 3-1.

ATP + glucose

ATP
glucose-
6-phosphate
Free
Energy ADP
glucose + glucose-
6-phosphate
ADP + Pi

Favored Unfavored Favored

Figure 3-1

Coupling doesn’t occur all by itself. In this example, if this exper-

iment were set up so that the ATP would have to be hydrolyzed in one
tube and the glucose phosphorylated in another, no coupling would
be possible. Coupling can occur only when the partial reactions are
part of a larger system. In this example, coupling occurs because both
partial reactions are carried out by the enzyme hexokinase. In other
cases, coupling can involve membrane transport, transfer of electrons
by a common intermediate, or other processes. Another way
of stating this principle is that coupled reactions must have some
component in common.

CLIFFSQUICKREVIEW
34
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

The Cell’s Energy Currency

As noted in the previous section, the hydrolysis of ATP to yield ADP

and phosphate is highly exergonic. This loss of free energy is due to
the structure of the phosphoanhydride, which involves two negatively
charged groups being brought into close proximity. Additionally, the
phosphate group is stabilized by resonance not available to the anhy-
dride (see Figure 3-2).

O O- O- O-
P P P P O
-O - - -O O- -O
O -O O
O -O O O-

Phosphate Resonance

Figure 3-2

Because the free energy of hydrolysis of ATP’s first two phos-

phates is so highly negative, biochemists often use the shorthand term
high energy phosphate to describe the role of ATP in the cell. In gen-
eral, the reactions of catabolism lead to the synthesis of ATP from ADP
and phosphate. Anabolic reactions, as well as the other reactions
involved in cellular maintenance, use the coupled hydrolysis of ATP
to drive the reactions. For example, a muscle fiber will metabolize glu-
cose to synthesize ATP. The ATP can be used to drive muscle contrac-
tion, to synthesize proteins, or to pump Ca2+ ions out of the intracellular
space. ATP serves as cellular energy currency because it is a common
component of many reactions. It serves this role so well because it is
metastable: In the cell, it does not break down extensively by itself
over time (kinetic stability), but at the same time, it releases large
amounts of free energy when it is hydrolyzed to release inorganic
phosphate (thermodynamic instability).

BIOCHEMISTRY I
35
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

All the free energy calculations shown in the previous examples

have been done in the standard state, with all the products and reactants
present at 1M concentration. However, very few compounds, except
perhaps water, are present in the standard state. Because the free energy
change of a reaction under nonstandard concentration is dependent on
the concentrations of products and reactants, the actual ∆G of the reac-
tion of glucose and ATP will be given by the equation:

∆G' = ∆G°' + RT ln ([glucose–6–phosphate] [ADP][Pi]/[glu-

cose][ATP])

The ratio of ATP to ADP is kept very high, greater than 10 to 1,

so the actual ∆G of ATP hydrolysis is probably greater than 10
kcal/mole. This means that the reaction of ATP and glucose is even
more favored than it would be under the standard state.

LeChatelier’s Principle is fundamental to understanding these rela-

tionships. A reaction is favored if the concentration of reactants is high
and the concentration of products is low. The free energy relationships
shown in this section are a quantitative way of expressing this qualita-
tive observation.

Free-Energy-Driven Transport across Membranes

Cells expend a large amount of their free energy currency keeping the
appropriate environment inside the cell. Thus, for example, Ca2+ is pre-
sent intracellularly at < 10-7 M, while extracellular Ca2+ is present in
millimolar (10-3 M) concentrations, that is, 10,000-fold higher. The free
energy difference due to the difference in [Ca2+ ], sometimes termed its
chemical potential, can be calculated. The difference of the ∆G°' val-
ues when Ca2+ is at the same concentration (1M) on each side of a mem-
brane is, of course, zero, so the free energy is given by:

∆G = 0 + RT ln ([Ca2+]in/[Ca2+]out)

CLIFFSQUICKREVIEW
36
 INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

Converting from natural to base 10 logarithms, and substituting

values for the gas constant, and a standard temperature of 25° C.
(298° K.):

∆G = 2.303 × 1.99 cal/°/mole × 298° × (- 4)

∆G = -5.5 kcal/mole

This expression means that the influx of Ca2+ into a cell is highly
exergonic. If a channel is opened into a cell to allow Ca2+ across the
membrane, it will flood into the cell. In muscle cells, this influx of Ca2+
is the signal for contraction. Cells, especially muscle cells, have a Ca2+
active transport system, which transports two Ca2+ ions out of the cell
for every ATP hydrolyzed. The ∆G°' of ATP hydrolysis is enough to
do transport only a single ion. Because, however, the ATP/ADP ratio
is kept very high during active metabolic conditions, the concentration
gradient of higher [Ca2+] outside the cell is maintained.

BIOCHEMISTRY I
37
INTRODUCTION
TO BIOLOGICAL
ENERGY FLOW

CLIFFSQUICKREVIEW
38
 CHAPTER 4
OVERVIEW OF BIOLOGICAL INFORMATION FLOW

One gene, one enzyme. –George Beadle and Edward Tatum

Complexity in Biochemical Genetics

At first glance, the subject of biochemical genetics can seem incom-

prehensibly complicated. How can a cell’s genes possibly contain all
the information about its capabilities for metabolism, macromolecu-
lar interactions, and responses to stimuli?

This question was answered, incorrectly, in the 1930s when bio-

chemists concluded that the protein components of chromosomes had
to carry genetic information. Scientists considered the DNA in chro-
mosomes to be too simple a structure to be anything other than a scaf-
fold. But in the 1940s, experiments carried out by Avery, Macleod,
and McCarty showed that this view was wrong. Their experiments
with bacteria showed that DNA carried the information for a herita-
ble trait. This result forced a redefinition of the ideas about informa-
tion in biology, and it was only when the Watson-Crick structure was
proposed for DNA that it was understood how a “simple” molecule
could carry information from one generation to the next. Although
there are only four subunits in DNA, information is carried by the lin-
ear sequence of the subunits of the long DNA chain, just as the
sequence of letters defines the information in a word of text.

The possible information contained in a biomolecule is termed

its complexity. In molecular biology and biochemistry, complexity
is defined as the number of different sequences in a population of
macromolecules. Even a relatively small polymer has an enormous
number of potential sequences. DNA, for example, is built from only
four monomers: A, C, G, and T. If each of these monomers is linked
with every other one, these 4 monomers now produce/contain 16

BIOCHEMISTRY I
39
 OVERVIEW OF
BIOLOGICAL
INFORMATION
FLOW

possible dimers (4 × 4) because each position can have an A, C, G, or

T. There are 64 possible trimers, 4 × 4 × 4. So in any DNA chain the
number of possible sequences is 4N, where N is the chain length.

Even a relatively small DNA chain can carry a large amount of

information. For example, the DNA of a small virus, 5,000
nucleotides long, can have 45,000 possible sequences. This is a huge
number—approximately 1 with 3,010 zeroes after it. (By compari-
son, the number of elementary particles in the universe is estimated
at 1080, or 1 with 80 zeroes after it.) But the virus has only one DNA
sequence, which means that only one of the huge number of possible
sequences has been selected to encode the virus’s biochemical func-
tions. In other words, there is information in the DNA sequence. The
virus carries a large amount of information in a small space.

This concept of information is similar to the memory of a com-

puter, which is made up of small semiconductor switches, each of
which has two positions—on and off. The ability of computers to do
an ever-increasing number of tasks depends on the ability of engi-
neers to design chips that have more and more switches in a small
space. Similarly, the ability of cells to do so many biochemical tasks
depends on the large number of DNA nucleotides in the small space
of the chromosomes.

The Central Dogma of Molecular Biology:

DNA Makes RNA Makes Protein

The sum total of all the DNA in an organism is called its genome.
Genomic information is like a computer program for a cell. When you
open a computer program, the program is copied from ROM (read-
only memory) on the hard disk to RAM (random-access memory).
The instructions in RAM are the ones that actually carry out the pro-
gram, but the copy of the program in RAM exists only as long as there
is power to the machine; if your PC loses power, you have to restart

CLIFFSQUICKREVIEW
40
 OVERVIEW OF
BIOLOGICAL
INFORMATION
FLOW

the program, and it is once again copied from the disk to RAM. This
arrangement (hopefully) insures against the master copy of the pro-
gram being damaged through a power surge or operator error.

If DNA is the master copy (the ROM) of a cell’s genetic program,

its integrity must be preserved. One way the DNA is protected is
because RNA acts as the working copy (the RAM). Chemically, RNA
is very similar to DNA. Biochemically, the major difference is that
RNA either acts as a component of the metabolic machinery or is a
copy of the information for protein synthesis. The relationship
between DNA and RNA is called the central dogma of molecular
biology:

DNA makes RNA makes protein

In the first of these processes, DNA sequences are transcribed

into messenger RNA (mRNA). Messenger RNA is then translated to
specify the sequence of the protein. DNA is replicated when each
strand of DNA specifies the sequence of its partner to make two
daughter molecules from one parental double-stranded molecule.

DNA, RNA, and nucleotide structure

DNA is a polymer—a very large molecule made up of smaller units
of four components. Each monomer contains a phosphate and a
sugar component. In DNA, the sugar is deoxyribose, and in RNA the
sugar is ribose.

HO CH2 O OH

H H
H
H
HO H

Deoxyribose

BIOCHEMISTRY I
41
 OVERVIEW OF
BIOLOGICAL
INFORMATION
FLOW

and one of four bases, two of which are purines:

NH2 O
N H N
N N

N N H2N N N
H H

Adenine Guanine

Purine Bases

and two of which are pyrimidines:

O NH2

HN CH3
N

O N O N
H
Thymine Cytosine

Pyrimidine Bases

A sugar and a base make up a nucleoside. A base, sugar, and

phosphate combine to form a nucleotide, as in thymidine monophos-
phate or adenosine monophosphate:

CLIFFSQUICKREVIEW
42
 OVERVIEW OF
BIOLOGICAL
INFORMATION
FLOW

H3C
N

O
− O
O P O CH2 N
O
O−

H H

HO H
Thymidine Monophosphate,
a Deoxyribonucleotide

RNA is similar to DNA, although RNA nucleotides contain

ribose rather than the deoxyribose found in DNA. Three bases found
in DNA nucleotides are also found in RNA: adenine (A), guanine (G),
and cytosine (C). Thymine in DNA is replaced by uracil in RNA:

O O

HN CH3
HN

O N O N
H H
Thymine Uracil

BIOCHEMISTRY I
43
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