Biomolecules

3
Chapter

1 BIOMOLECULE 2 ELEMENTAL ANALYSIS

m All the carbon compounds that we get from living tissues can be called m Elemental analysis gives elemental composition of living m Carbon and hydrogen with respect to
‘biomolecules’. However, living organisms have also got inorganic tissues in the form of hydrogen, oxygen, chlorine, carbon etc. other elements are more in any living
elements and compounds in them. Weigh organisms than in earth’s crust
Wet weight
Chemical Analysis m Living tissue Dry m Oxygen is the most abundant element
Living tissue + Trichloroacetic acid All water evoporates Dry weight in living organism
(Plant tissue/animal (Cl3CCOOH) Burn ‘Ash’ (contains only m Analytical technique gives an idea about
m Dried the molecular formula and the probable
tissue/microbial paste) All carbon compounds inorganic elements)
living tissue oxidise to CO2 and H2O structure of the compound.
Thick slurry
Comparison of Elements Present in Average Composition of Cells
Non-living and Living Matter
Cheese cloth Element % Weight of Earth’s crust Human body Component % of the total cellular mass
Hydrogen (H) 0.14 0.5 Water 70-90
Carbon (C) 0.03 18.5 Proteins 10-15
Oxygen (O) 46.6 65.0 Nucleic acids 5-7
Carbohydrates 3
Nitrogen (N) very little 3.3
Filtrate (Acid soluble) Retentate (Acid insoluble) 0.03 0.3
Lipids 2
Sulphur (S) Ions 1
Roughly cytoplasmic components Sodium (Na) 2.8 0.2
Calcium (Ca) 3.6 1.5
Magnesium (Mg) 2.1 0.1 Water is the most abundant chemical in
Inorganic Organic Organic Silicon (Si) 27.7 negligible living organisms
Biomicromolecules Biomacromolecules
m Water m M.wt - 18-800 Da m M.wt - > 10,000 Da
4 CARBOHYDRATES
+ + +2
m Ions (e.g. Na , K , Ca , m Monomeric form m Polymeric form

Mg , PO4 , SO4 , etc.) E.g., Simple sugars

+2 –3 –2 Polysaccharides
Nucleotides Nucleic acids Monosaccharides/sugar Polysaccharides
m Gases
Amino acids Proteins m Single unit m Many units/long chains of sugars
Lipids (Not a polymer) No. of m Units linked together by glycosidic bond formed
Carbon 5C 6C by dehydration.
3 METABOLITES (BIOMOLECULES)
m Not strictly biomacromolecule Formula C5H10O5 C6H12O6
m M.wt < 800 Da Example Ribose Glucose Homopolysaccharides Heteropolysaccharides
Primary metabolite Secondary metabolite m Cell membrane fragments form
HOCH2 O CH2OH m Same monomer units mDifferent monomer units
m Identifiable
m Not involved in primary vesicles which are not water soluble O

metabolism Structure
OH
functions Some Secondary Metabolites OH OH OH
m Seems to have no direct Features Glycogen Starch Inulin Cellulose Chitin
m Play known function in growth and Pigments Carotenoids, Anthocyanins OH OH OH
Found in Animals Plants Plants Plants Animals
roles in development of organisms Alkaloids Morphine, Codeine
m G l y c o g e n ® R i g h t e n d i s Function Storage Storage Cell wall Exoskeleton
physiological m Many of them are useful Terpenoides Monoterpenes, Diterpenes
reducing while left end is non- (Structural) of arthropods
processes e.g. to human welfare e.g., Essential oils Lemon grass oil reducing Monomer Glucose Fructose Glucose N-acetyl
rubber, drugs, spices and Toxins Abrin, Ricin m Starch hold I2 in helical portion glucosamine
sugars, amino
pigments. Some have Lectins Concanavalin A m Cellulose can not hold I2 as no
acids lipids, ecological importance helical portion Branching P
Drugs Vinblastin, curcumin
nitrogen bases, m E.g., Flavonoids, Polymeric Rubber, gums, cellulose m Cotton fibre ® Cellulose Colour Red Blue X
etc. antibiotics etc. substances m Paper is made from plant pulp with I2

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NCERT Maps Biomolecules 25

5 NUCLEIC ACIDS Wastson-Crick model of B-DNA

Polymer of nucleotides m DNA exists as double helix (secondary m Phosphate moiety links 3¢-carbon of one
m Sugar/monosaccharide
structure) sugar of one nucleotide to 5¢ carbon of
m Each nucleotide comprises Heterocyclic Nucleoside
nitrogenous base Nucleotide m Two polynucleotide strands are helically coiled sugar of succeeding nucleotide
around a common axis m Nitrogen bases are perpendicular to
Phosphate
m The two polynucleotide strands are antiparallel backbone and faces inside.
Nitrogenous base Nucleoside Nucleotide i.e., run in opposite direction and complementary m At each step of ascent, strand turns 36°
m Adenine m Adenosine O m Adenylic acid to each other m 1 turn = 10 base pairs
NH2 HOCH2 O Adenine HO–P–OCH2 O Adenine
Substituted

m A and G of one stand compulsorily base pairs with T m 1 complete turn = 34Å
Purines

N N OH and C respectively, on the other strand m Rise per base pair = 3.4Å
m Always two hydrogen bonds exist between A and T O
N NH
and three hydrogen bonds between C and G
OH OH OH OH
Guanine Guanosine O 2 hydrogen bonds
m m m Guanylic acid
m Thymine m Thymidine m Thymidylic acid CH2 O Thymine Adenine CH2
O
m Cytosine m Cytidine m Cytidylic acid
O
Pyrimidine

Uracil Uridine m Uridylic acid

Substituted

m m Base pair Phosphodiester bond –

O O (formed by dehydration) O P O
HOCH2 O Uracil Ester bond –
HN HO–P–OCH2 O Uracil O O HO O
–
OH O P O
O 3 hydrogen bonds
N O
H Sugar
OH OH phosphate O
OH OH H 2C Guanine Cytosine O CH2
backbone
m Ribose sugar and uracil exist in RNA (Ribonucleic acid) O
m 2¢-deoxyribose sugar and thymine exist in DNA (Deoxyribonucleic acid)
m DNA and RNA function as genetic material
O

6 LIPIDS
m Generally water insoluble I. Many lipids are esters of fatty acids and glycerol II. S o m e l i p i d s h a v e p h o s p h o r o u s a n d
m Could be simple fatty acids (R – COOH) where R group could be phosphorylated organic compound called
Methyl (–CH3), ethyl (–C2H5), higher no. of –CH2 (C–1 to 19) No. of Glycerol phospholipids
l Type
m Types of fatty acids fatty acids (trihydroxy propane) e.g., Lecithin - found in cell membrane
Monoglyceride 1 1 CH2 – CH – CH2 Neural tissues - lipids with more complex
Parameter Saturated Unsaturated
Diglyceride 2 1 structure O
No. of C = C X One or more OH OH OH
Triglyceride 3 1 O CH2 – O – C – R1
double bonds
R2 – C – O – CH O
Example Palmitic acid (16 carbon Arachidonic acid (20 carbon Melting point State in winters Examples
including carboxyl including carboxyl carbon) Fats Higher Solid Ghee, Butter CH2 – O – P – O – CH2 – CH2
carbon) Oils Lower Liquid Gingelly oil H N
+

CH3 – (CH2)14 – COOH O Phospholipid (Lecithin) CH3 CH3 CH3

O CH2 – O – C – R1 III. Cholesterol, have lipid like properties
R2 – C – O – CH O
CH2 – O – C – R3
Triglyceride (R1 R2 and R3 are fatty acids) Cholesterol
HO

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26 Biomolecules NCERT Maps

7 AMINO ACIDS 8 STRUCTURE OF PROTEINS

m Organic compounds containing an amino group and an acidic group m Each protein is a heteropolymer of amino acids linked by peptide bonds (formed by dehydration) and
as substituents on same carbon i.e., a-carbon, hence called a- only 20 types of amino acids participate in their formation.
amino acids. m Biologists describe structure of proteins at four levels :
m Substituted methane, four substituent groups occupying four
valency positions. Level Typical Structure
m Chemical and physical properties of amino acids are essentially of Primary Positional information of sequence of amino COOH
m NH2
amino, carboxyl and R-functional groups acids Left end Right end
Types of amino acids m N-terminal m C-terminal
m Protein thread as extended rigid rod m First amino acid m Last amino acid
I. On the basis of R-group II. On the basis of Nature of
amino acids Secondary m Thread folded in the form of a helix i.e., similar to
R-group Amino acids
Nature Amino acids revolving stair case
–H Glycine
Acidic Glutamic acid m Only right handed helices observed in proteins
–CH3 Alanine Alpha-Helix Beta-pleated sheet
(methyl) Basic Lysine Tertiary m 3-dimensional view, like hollow woolen ball Hydrogen bond
– CH2 – OH Serine Neutral Valine m This structure is absolutely necessary for many Disulphide bond
(hydroxy methyl) Aromatic Tyrosine, tryptophan, biological activities of proteins
phenylalanine Quaternary m More than one polypeptide chains are involved eg.
III. On the basis of Body’s
requirement Haemoglobin consists of 4 subunits: 2a and 2b
Zwitterionic Form m It is based on how individual polypeptide are
Non-essential Essential m A particular property of amino arranged with respect to each other
Synthesised Not synthesised acids is the ionisable nature of
by body by body – NH2 and –COOH group. 10 DYNAMIC STATE OF BODY CONSTITUENTS Carbonic anhydrase
Not required Required m In solutions of different pH the CO2 + H2O H2CO3
m Living state is a non-equilibrium steady state to be able to
in diet in diet structure of amino acids
perform work m Carbonic anhydrase is present in
changes.
m Living process is constant effort to prevent falling into equilibrium cytoplasm
R R R m Living state and metabolism are synonymous. m With enzyme - 6,00,000 molecules of
+ + – –
H3N – CH – COOH H3N – CH – COO H2N – CH – COO m Without metabolism there can not be a living state H2CO3 formed in 1 sec, Rate increases
m Metabolism is sum total of all the reactions in the body 10 million times
Zwitterionic form m There is no uncatalysed metabolic conversion in living system
(Both positive and negative charge) m Without enzyme - 200 molecules/hr
Metabolic pathways (Series of linked reactions)
m Rate refers to the amount of product formed
9 SOME PROTEINS AND THEIR FUNCTIONS per unit time, expressed as rate = dP/dt
Catabolic pathways Anabolic pathways
Protein Functions m Degradation pathways m Biosynthetic pathways m Rate double or decreases by half for every
Collagen Intercellular ground substance m Complex structure converts m Formation of complex structure 10°C change in either direction.
into simpler structure from simple structures m Flow of metabolites through metabolic
Trypsin Enzyme Energy released (stored in Energy is used
m m pathways has a definite direction, this is
Insulin Hormone ATP) m Examples called dynamic state of body constituents
Antibody Fights infectious agents m Examples l Acetic acid ® Cholesterol m Biomolecules are constantly being changed
Receptor Sensory reception (smell, taste, hormone) anaerobic l Amino acids ® Proteins into some other biomolecules and also
l Glucose Lactic acid
GLUT-4 Enables glucose transport into cells made from some other biomolecules called
(skeletal muscle)
anaerobic turnover
l Glucose Ethanol (In yeast)
m Collagen is the most abduant protein in animal world Glycolysis m Glucose concentration in blood : 4.2 - 6.1 m
m RuBisCO is the most abduant protein in the whole of the biosphere l Glucose Pyruvic acid mol/L
10 steps

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NCERT Maps Biomolecules 27

11 ENZYMES (BIOCATALYST) 13 CLASSIFICATION AND NOMENCLATURE OF ENZYMES

Properties: m Thousands of enzymes have been discovered, isolated and studied. Most of these enzymes have been classified into
m Tertiary structure m Unchanged at the end of reaction different groups based on the type of reactions they catalyse. Enzymes are divided into 6 classes each with 4-13
m Highly specific m Not used up in the reaction subclasses and named accordingly by a four-digit number.
m Proteinaceous in nature except ribozymes (nucleic acids)

m Increases rate of reaction by lowering activation energy

Class Name Function
m Have active site/pockets where substrate binds I Oxidoreductases/ Enzymes which catalyse oxidoreduction between two substrates S and S’
m Inorganic catalysts work efficiently at high temperatures and high dehydrogenases: S reduced + S’ oxidised ® S oxidised + S’ reduced.
pressures while enzymes get denatured at high temperature
II Transferases: Enzymes catalysing a transfer of a group, G (other than hydrogen) between a pair of
(> 40°C) except enzymes of thermophilic organisms (can
tolerate 80°-90°C). substrate S and S’. S – G + S’ ¾® S + S’ – G
m For metabolic conversion, substrate ‘S’ has to bind the enzyme at III Hydrolases: Enzymes catalysing hydrolysis of ester, ether, peptide, glycosidic, C – C, C – halide or
its active site and results in obligatory formation of ‘ES’ complex P-N bonds.
(Transient phenomenon), essential for catalysis.
IV Lyases: Enzymes that catalyse removal of groups from substrates by mechanisms other than
m Structure of substrate gets Transition state
transformed into structure of Activation energy hydrolysis leaving double bonds. X Y
product(s)
Potential Energy

without enzyme
Activation C– C X–Y+C=C
E+S ES EP E+P energy with V Isomerases: Includes all enzymes catalysing inter-conversion of optical, geometric or positional
Substrate enzyme
(S) isomers.
‘Altered structural states’
(unstable) VI Ligases: Enzymes catalysing the linking together of 2 compounds, e.g., enzymes which catalyse
Product (P)
Progress of reaction joining of C-O, C-S, C-N, P-O etc. bonds.
m Difference in average
energy content of ‘S’ from (1) Temperature 12 FACTORS AFFECTING ENZYME ACTIVITY
that of transition state is m Enzyme shows highest activity at optimum temperature
called ‘Activation energy’ (3) Substrate concentration
m Enzyme activity declines both below and above optimum value

Enzyme activity
m Transition state – High m Low temperature preserves enzymes in temporarily inactive state
Initially rate of reaction increases with increase in
energy unstable state substrate concentration but becomes constant when
m High temperature destroys enzymatic activity by denaturing their
m ‘P’ is at lower level than ‘S’ – all enzymes get saturated with substrate
structure
Reaction is exothermic (2) pH (4) Binding of specific chemicals
m ‘S’ is at lower level than ‘P’ – m Enzyme shows highest activity at optimum pH When binding of chemicals shuts off enzyme activity,
Temperature
Reaction is endothermic the process is called inhibition and chemical is
m Rate of reaction declines both below and above optimum pH

Enzyme activity
called inhibitor
Enzymes 14 CO-FACTORS Prosthetic group Competitive inhibitor:
m Organic, tightly bound to apoenzyme
m Haem is prosthetic group for catalase and m Inhibitor compete with substrate for active site
Simple enzymes Conjugated enzymes
m Only protein
peroxidase m Closely resembles substrate in molecular
Co-enzyme pH structure and inhibits enzyme activity
Apo-enzyme (inactive) Co-factor m Organic, loosely bound to apo-enzyme for Vmax m Consequently, substrate can not bind and as a
m Protein part m Non-protein part transient period (just during catalysis) result enzyme action declines.
reaction (V)

e.g., NAD, NADP (Contain niacin vitamin)

Velocity of

m
Catalytically active enzyme Vmax m e.g., (1) Inhibition of succinic dehydrogenase by
Metal ions 2
m Form coordination bond with active site and malonate
Catalytic activity is lost if co-factor is one or more coordination bond with substrate (2) Control of bacterial pathogens by
+2
removed m Zn for carboxypeptidase Km [S] competitive inhibitor

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