UNIT 17

BIOMOLECULES

OBJECTIVES “All biological processes are chemical

transformations.”
After studying this Unit, you will be able to:

l explain the role of a living cell in Biomolecules, common to living systems are
the regulation of energy cycle in carbohydrates, proteins, enzymes, lipids,
nature. vitamins, hor mones, nucleic acids and
compounds for storage and exchange of energy
l learn about the basic chemistry of such as adenosine triphosphate (ATP). Many of
important biomolecules e.g. these biomolecules are polymers like the
carbohydrates, proteins, nucleic synthetic polymers you have studied in Unit 16.
acids and lipids. For example, starch, proteins, nucleic acids are
condensation polymers of simple sugars, amino
l Classify and explain functions of acids and nucleotides respectively. Most of the
some of the biomolecules present
biochemical reactions take place in dilute
in biological systems e.g.
solutions (pH~7) at body temperature (nearly
hormones and vitamins.
37°C) and at 1 atmospheric pressure.
l describe the secondary and tertiary
Biochemical reactions proceed with striking
structures of proteins and the selectivity and at incredible speed. Most of the
double helical structure of DNA. biomolecules are very large and extremely
complex. Their reactions involve complex
l explain genetic code and basic mechanisms. Biomolecules are related to the
genetic mechanisms, DNA living organisms in the following sequence:
replication, transcription and Living organisms → Organs → Tissues →
protein synthesis. Cells → Organelles → biomolecules
(carbohydrates, proteins, lipids, nucleic acids).
Before discussing the chemistry of
biomolecules, we would like to know about the
sources of energy in plants and animals which
are responsible for their growth and
maintenance.

17.1 THE CELL AND ENERGY CYCLE

The cell is a fundamental structural and
functional unit of living organisms. Just as we
need energy to run, jump and think, the cell
needs a ready supply of cellular energy for many
functions that support these activities. Cells
need energy for active transport, to move
molecules between the environment and the cell,
across cells or within cells. Thus, we need a
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BIOMOLECULES

supply of energy-rich food molecules that can absorb energy from the sun to make glucose and
be oxidized to provide the needed cellular energy. oxygen from carbon dioxide, CO2 and water, H2O.
Cells obtain energy by oxidation of molecules Photosynthesis is a complex process which
like glucose. This oxidation takes place in a occurs in a sequence of steps leading to the net
complex and controlled way by means of reaction.
enzymes which are biocatalysts. (Part of the Sunlight
energy in cells is coupled to the formation of 6CO2+ 6H2O+ 2880kJ C6H12 O6+ 6O2
ATP (adenosine triphosphate, which serves to The oxygen produced in photosynthesis is
drive many chemical reactions inside the cell.) the source of all the oxygen in our atmosphere.
Photosynthesis takes place generally in a
series of reactions which occur only in
presence of light energy are called light reaction
and a series of dark reactions which can occur
in dark because they do not depend on light
energy. The dark reactions proceed on high
energy produced by the hydrolysis of ATP.
Chloroplasts present in the plant cell absorb
the released energy. Here, through a series of
reactions, water is oxidized to oxygen and the
energy released is stored in the bonds of energy
storage compounds such as ATP. In fact, ATP
drives the dark reactions which convert CO2
and hydrogen (from water) into glucose and
other carbohydrates.
In the presence of a suitable catalyst,
ATP releases energy by undergoing a three-step
hydrolysis of the P–O bond of its triphosphate
groups. In the first step, ATP is hydrolysed to
ADP and releases 31kJ mol–1 Gibbs energy. In
the second step, ADP is converted into AMP
(adenosine monophosphate) and produces
approximately the same amount of energy. In the
Fig. 17.1 Structure of Cell. last step of the hydrolysis of AMP to adenosine,
only 14 kJ mol–1 Gibb’s energy is released.
There are certain reactions which are
The living plants may convert the glucose
endergonic i.e., their Gibbs energy, ∆G>0 and
produced during photosynthesis into
as such appear to be thermodynamically
disaccharides, polysaccharides, starches,
forbidden. Nevertheless, such reactions can be
cellulose, proteins or oils. The end product
made to proceed in the desired direction by
coupling them with some suitable exergonic depends on the type of plants involved and
reactions with ∆G<0. Here coupling the reaction complexity of its biochemistry. Plants thus, are
means the two reactions are allowed to take primary source of energy for animals and
place simultaneously. You have already studied humans. This can be represented by oxidation
in Unit 4 (Section 4.6.4) that conversion of ATP of glucose which is reverse of photosynthesis.
to ADP (Fig. 17.2) (adenosine diphosphate) is C6H12O6 + 6O2 → 6CO2 + 6H2O;
highly exergonic (∆GJ= –31.0 kJ mol–1) and can ∆G J =–2880 kJ mol–1
drive any thermodynamically forbidden reaction Part of the energy is utilized while a part of it
in the desired direction. This normally happens
is stored leading to the next reaction:
in several metabolic processes in our body.
C6H12O6 + 36 ADP + 36 H3PO4 + 6O2 → 6CO2
17.1.1 Photosynthesis and Energy + 36 ATP + 42H2O
Energy for life processes basically comes from We now take up the chemistry of important
Sun. During photosynthesis, green plants biomolecules.
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CHEMISTRY

Table 17.1 Different types of monosaccharides

Carbon General Aldehydes Ketones

atoms terms

3 Triose Aldotriose Ketotriose

4 Tetrose Aldotetrose Ketotetrose
5 Pentose Aldopentose Ketopentose
6 Hexose Aldohexose Ketohexose
7 Heptose Aldoheptose Ketoheptose

For example, a disaccharide on hydrolysis yields

two monosaccharide molecules
H+
C12H22O11 + H2O → C6H12O6 + C6H12O6
(Sucrose) (Glucose) (Fructose)
A trisaccharide like raffinose on hydrolysis gives
glucose, fructose and galactose.
Fig. 17.2 The high energy phosphate bonds of ATP (iii) Polysaccharides: These are high molecular
are indicated by red colour. After mass carbohydrates which yield many molecules
hydrolysis a large amount of energy is of monosaccharides on hydrolysis. Examples are
released. All the constituent units (viz
starch and cellulose, both having general
phosphate, ribose and adenine) are also
indicated. formula (C6H10O5) n.
H+
17.2 CARBOHYDRATES (C6H10O5) n + n H2O → n C6H12O6
Starch or cellulose Glucose
Carbohydrates have the general formula
Cx(H2O)y. These can be described as optically In general monosaccharides and
active polyhydroxy aldehydes or ketones or the oligosaccharides are crystalline solids, soluble
compounds which yield them on hydrolysis. in water and sweet in taste. These are collectively
Carbohydrates are also known as saccharides. known as sugars. The polysaccharides, on the
They are the ultimate source of most of our food. other hand are amorphous, insoluble in water
We clothe ourselves with cellulose in the form of and tasteless and are known as non-sugars.
cotton, linen and rayon. We build furniture and The carbohydrates may also be classified as
houses from cellulose in the form of wood. Thus, either reducing or non-reducing sugars. All those
carbohydrates provide us with basic necessities carbohydrates which contain free aldehydic or
of life, food, clothing and shelter. ketonic group and reduce Fehling’s solution and
Tollen’s reagent are referred to as reducing
17.2.1 Classification sugars. All monosaccharides whether aldose or
The carbohydrates can be divided into three ketose are reducing sugars. In disaccharides if
major classes, depending upon whether they the reducing groups of monosaccharides i.e.,
undergo hydrolysis, and if so, on the number of aldehydic or ketonic groups are bonded, these
products formed. are non-reducing sugars e.g. sucrose, while
(i) Monosaccharides: These cannot be others in which these functional groups are free,
hydrolysed to simpler compounds. Depending are reducing sugars e.g. maltose and lactose.
upon the total number of carbon atoms in
17.2.2 Monosaccharides
monosaccharides and aldehyde or ketone
functional groups present, the terms used for All carbohydrates are either monosaccharides
their classification are given in Table 17.1. or get converted to monosaccharides on
(ii) Oligosaccharides: The oligosaccharides hydrolysis. Glucose and fructose are the specific
(Greek, oligo, few) are carbohydrates which yield examples of an aldohexose and of a ketohexose
a few but definite number (2-10) of respectively. These can be represented by the
monosaccharide molecules on hydrolysis. following formulae.
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BIOMOLECULES

HC=O CH2OH also Fehling’s solution to reddish brown cuprous

oxide and itself gets oxidized to gluconic acid. This
(HCOH)4 C=O confirms the presence of an aldehydic group in
glucose.
CH2OH (CHOH)3 HOCH2-(CHOH)4-CHO + Ag2O →
HOCH2-(CHOH)4- COOH + 2 Ag
CH2OH Gluconic acid
4. On oxidation with nitric acid glucose as well
Glucose Fructose as gluconic acid both yield a dicarboxylic acid,
17.2.3 Glucose (Dextrose; Grape sugar) saccharic acid This indicates the presence of a
C6H12O6 primary alcoholic group in glucose.
HNO3
Glucose occurs in nature in free as well as in the HOCH2-(CHOH)4-CHO →
combined form. It is present in sweet fruits and HOOC-(CHOH)4-COOH
honey. Ripe grapes contain ~ 20 % of glucose. Saccharic acid
5. Glucose on prolonged heating with HI forms
Preparation of Glucose n- hexane, suggesting that all the 6 carbon atoms
1. From Sucrose (Cane sugar): If sucrose is in glucose are linked linearly.
boiled with dilute HCl or H2SO4 in alcoholic HOCH2-(CHOH)4-CHO →
HI
solution, glucose and fructose are obtained in H3C-CH2-CH2-CH2-CH2-CH3
equal amounts, n-hexane
6. D-Glucose reacts with phenyl hydrazine to
H+
C12H22O11 + H2O → C6H12O6 + C6H12O6 give glucose phenylhydrazone. If excess of
(Sucrose) Glucose Fructose phenylhydrazine is used, a dihydrazone, known
2. From Starch: Commercially glucose is as osazone is obtained which is called
obtained by hydrolysis of starch by boiling it glucosazone.
with dilute H2SO4 at 393 K under pressure, CHO CH=NNHC6H5
+  C6H5NHNH2 
H
(C6H12O5) n + n H2O 
→ n C6H12O6 H––C––OH H––C––OH
Starch or cellulose 393 K; 2-3 bar Glucose
 –H2O 
17.2.4 Properties of Glucose (CHOH)3 (CHOH)3
Glucose has one aldehyde group, one primary  
(–CH2OH) and four secondary (–CHOH) hydroxyl CH2OH CH2OH
groups and gives the following reactions; D-Glucose D-Glucose phenylhydrazone
1. Acetylation of glucose with acetic anhydride
H2
gives glucose pentaacetate confirming the
N HN
presence of five hydroxyl groups in glucose. H
C6
5

(CH3CO)2O 2
OHC-(CHOH)4–CH2OH → NH3 + C6H5NH2 + CH=NNHC6H5
OHC–(CHOCOCH3)4-CH2OOCCH3 
2. Glucose reacts with hydroxylamine to give C=NNHC6H5
monoxime and adds a molecule of hydrogen 
cyanide to give a cyanohydrin. (CHOH)3
HOH2C-(CHOH)4-CHO + HONH2 → 
HOCH2-(CHOH)4-CH=NOH CH2OH
Glucose monoxime D-Glucosazone
HOCH2-(CHOH)4-CHO + HCN →
HOCH2-(CHOH)4-CH (OH)CN 7. On heating with conc. solution of sodium
Glucose cyanohydrin hydroxide glucose first turns yellow, then brown
These reactions confirm the presence of a and finally resinifies. However, with dilute
carbonyl group in glucose. sodium hydroxide glucose undergoes a reversible
3. Glucose reduces ammoniacal silver nitrate isomerization and is converted into a mixture of
solution ( Tollen’s reagent) to metallic silver and D-glucose, D-mannose and D-fructose. This
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CHEMISTRY

reaction is known as Lobry de Bruyn-van 19.2° is obtained on crystallization of glucose

Ekenstein rearrangement. Same results are from a hot saturated aqueous solution at a
obtained if mannose or fructose are treated with temperature above 98°C. The two forms known
alkali. It is probably on account of this as anomers of glucose differ from each other in
isomerization that fructose reduces Fehling’s the stereochemistry at C-1. If either of the two
and Tollen’s reagents in alkaline medium forms is dissolved in water and allowed to stand,
although it does not contain a –CHO group. the specific rotation of the solution changes
slowly and reaches a constant value at +52.5°.
D-glucose D-mannose D-fructose
This equilibrium is reached faster if a trace of
Glucose has been assigned a straight chain acid or base catalyst is present.
structure. The Fischer projections for D- and L-
glucose are shown below: The spontaneous change in specific
rotation of an optically active compound is
CHO CHO
called mutarotation.
H OH HO H
4. When glucose is treated with methanol in the
HO H H OH
presence of dry hydrogen chloride gas, it yields
H OH HO H
two isomeric monomethyl derivatives known as
H OH HO H
methyl α-D-glucoside and methyl β–D-glucoside.
CH2OH CH2OH These glucosides do not reduce Fehling’s
D-glucose L-glucose solution and also do not react with hydrogen
cyanide or hydroxylamine indicating the
The stereochemistry of all sugars has been absence of a free –CHO group. Their formation
determined by relating it to that of D- or can be shown as given below. (See Box)
L- glyceraldehydes (Unit 12). By analogy to the formation of these two
methyl glucosides, glucose exists in two forms
17.2.5 Cyclic Structure of D-glucose α-D-glucose and β-D-glucose.
The open chain structure of glucose proposed
by Baeyer explained most of its properties. α-D- (+) Equilibrium β-D (+)
However, it could not explain the following, glucose mixture glucose
1. Despite having an aldehydic group, glucose + 52.5°
does not give Schiff’s test and it does not react
with sodium hydrogensulphite and ammonia. As a result of cyclization, the anomeric carbon
2. The pentaacetate of glucose does not react (C-1) becomes asymmetric and the newly formed
with hydroxylamine indicating absence of –CHO –OH group may be either on the left or on right
group. in Fischer projection, thus resulting in the
3. Mutarotation: When glucose was crystallized formation of two isomers (anomers). The isomers
from a concentrated solution at 30°C, it gave having the hydroxyl group to the left of the C-1
α-form of glucose m.p. 146°C, [α]D= (+) 111°. On is designated β-D-glucose and one having the
the other hand the β form (m.p. 150°C) [α]D= (+) hydroxyl group on the right as α-D-glucose.

H C OCH3 H3CO C H
CHO
H C OH H C OH H C OH

HO C OH HO C H O HO C H O
CH3OH
HCl and
H C OH H C OH H C OH

H C OH H C H C
CH2OH CH2OH CH2OH
Methyl- -D-glucoside Methyl- -D-glucoside
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BIOMOLECULES

These two forms are not mirror images of each acids or enzymes they yield two molecules of either
other, hence are not enantiomers. The six the same or different monosaccharides, e.g.,
membered cyclic structure of glucose was HO
established by R.D. Haworth. The six membered
C12H22O11 
H+ → C6H12O6
2
+ C6H12O6
cyclic structure of glucose is called pyranose Sucrose Glucose Fructose
HO
structure (α or β), in analogy with pyran, a six C12H22O11 
H+ → C6H12O6 + C6H12O6
2
membered ring with one oxygen and five carbon Lactose Glucose Galactose
HO
atoms in the ring. The 5-membered ring structure C12H22O11 
H+ → C6H12O6
2
+ C6H12O6
of glucose is known as furanose in analogy with Maltose Glucose Glucose
furan, a five membered ring with one oxygen and The disaccharides may be reducing or
four carbons. However, glucose occurs in nature nonreducing depending upon the position of
only in the pyranose form. (Fig. 17.3) linkages between the two monosaccharide units.
O O If this glycosidic linkage involves the carbonyl
functions of both the monosacccharide units, the
resulting disaccharide would be non-reducing e.g.
sucrose. If one of the carbonyl functions in anyone
Pyran Furan of the monosaccharide unit is free, the resulting
disaccharide would be reducing sugar, e.g.,
maltose and lactose.
17.2.7 Sucrose / Cane sugar (C12H22O11)
It is the most common disaccharide widely
distributed in plants. It is manufactured either
from sugarcane or beet root. It is a colourless,
crystalline and sweet substance soluble in water.
Its aqueous solution is dextrorotatory, [α]D=
+66.5°. On hydrolysis with dilute acids or
enzyme invertase, canesugar gives equimolar
mixture of D- (+)- glucose and D-(-)-fructose.
HCl
C12 H22 O11 + H2O → C 6H 12O6 + C6H12O6
Sucrose D-glucose D-fructose
[α] D = + 66.5° [α]D= +52.5° [α]D= –92.4°
Sucrose is dextrorotatory but after hydrolysis
gives dextrorotatory glucose and laevorotatory
fructose. Since the laevorotation of fructose
(–92.4°) is more than dextrorotation of glucose
(+ 52.5°), the mixture is laevorotatory. Thus,
hydrolysis of sucrose brings about a change
in the sign of rotation, from dextro (+) to laevo
(-) and such a change is known as inversion
Fig. 17.3 Fishcer projections and Haworth structures and the mixture is known as invert sugar.
of α–D–(+)–Glucopyranose. Sucrose solution is fermented by yeast when
The lower thickened edge of the ring in the enzyme invertase hydrolyses sucrose to
Haworth structure is nearest to the observer. The glucose and fructose; enzyme, zymase converts
groups projected to the right in Fischer projection these monosaccharides to ethyl alcohol.
are written below the plane of the ring in Invertase
C12H22O11+H2O → C6H12O6+C6H12O6
Haworth structure and those on the left are Sucrose Glucose Fructose
Zymase
written above the plane of the ring. C6H12O6 
→ 2C2H5OH + 2CO2
Glucose or fructose Ethanol
17.2.6 Disaccharides
Haworth (1927) suggested the following
The disaccharides are composed of two molecules structure for sucrose. As mentioned earlier it is
of monosaccharides. On hydrolysis with dilute a non-reducing sugar.
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CHEMISTRY

On hydrolysis one mole of maltose yields two

moles of D-glucose. It is a reducing sugar.
The two glucose units are linked through a
α-glycosidic linkage between C-1 of one unit and
the C-4 of another. Both glucose units are in
pyranose form.
17.2.9 Lactose (C12 H22 O11)
Lactose occurs in milk and is also called milk
sugar. Hydrolysis of lactose with dilute acid
yields equimolar mixture of D-glucose and
D-galactose. It is a reducing sugar. It gets
hydrolysed by emulsin, an enzyme which
specifically hydrolyses β-glycosidic linkages.

Haworth’s representation of Sucrose

17.2.8 Maltose (Malt sugar, C12 H22 O11)
It is obtained by partial hydrolysis of starch by
diastase, an enzyme present in malt (sprouted
barley seeds).
Diastase
2 (C6 H10O5) n + n H2O → n C12H22O11
Starch Maltose

17.2.10 Polysaccharides
These are carbohydrates in which hundreds or
even thousands of monosaccharide units are
joined together by glycosidic linkages. Some
examples of polysaccharides are starch,
cellulose, glycogen and dextrins. However, starch
and cellulose are most important of the
polysaccharides.
Starch / Amylum (C6H10O5)n: Starch occurs in
all plants, particularly in their seeds. The main
sources are wheat, maize, rice, potatoes, barley
and sorghum. Starch occurs in the form of
granules, which vary in size and shape
depending on their plant source. Starch is a
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BIOMOLECULES

white amorphous powder, insoluble in cold water. Natural starch has approximately 10 - 20% of
Its solution in water gives a blue colour with amylose and 80-90% of amylopectin.
iodine solution. The blue colour disappears on Amylose is water soluble and gives blue colour
heating and reappears on cooling. On hydrolysis with iodine. It is a straight chain polysaccharide
with dilute acids or enzyme, starch breaks down having only D-glucose units joined together by
to molecules of variable complexity (n> n´), α-glycosidic linkages involving C-1 of one glucose
maltose and finally D-glucose. and C-4 of the next. It can have
100- 3000 D- glucose units i.e., its molecular
(C6H10 O5)n →(C6H10 O5)n, →C12H22O11 mass can range from 10,000 to 500,000.
Starch Maltose Amylopectin is a branched chain
Diastase →
polysaccharide insoluble in water which does not
give blue colour with iodine. It is composed of
C6H12 O6 chains of 25-30 D-glucose units joined by
D-glucose α-D-glycosidic linkages between C-1 of one
Starch does not reduce Fehling’s solution or glucose unit and C-4 of the next glucose unit
Tollen’s reagent and does not form an osazone, (similar to amylose). However, these chains are
indicating that all hemiacetal hydroxyl group of connected with each other by 1,6-linkages. Starch
glucose units (C-1) are linked with glycosidic is a major food material for us. It is hydrolyzed by
linkages. Starch is a mixture of two enzyme amylase present in saliva. The end
polysaccharides, amylose and amylopectin. product is glucose which is an essential nutrient.

6
CH2OH CH2OH CH2OH
O 5 O O
H H H H H H H H H
4 1 4 1 4 1
O OH H O OH H O OH H O
3 2

H OH H OH H OH

 -LINK  -LINK
Amylose

CH2OH CH2OH
O O
H H H H H H
4 1 4 1
OH H OH H  -LINK
O O

H OH H OH
O
BRANCH AT C6

CH2OH 6
CH2 CH2OH
O 5 O O
H H H H H H H H H
4 1 4 1 4 1
O OH H O OH H O OH H O

H OH H OH H OH

 -LINK  -LINK
Amylopectin
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CHEMISTRY

proteins contain the elements carbon,

CH2OH CH2OH CH2OH
hydrogen, oxygen, nitrogen and sulphur.
O O O
H H H H H H OH Some of these may also contain
O O phosphorus, iodine and traces of metals
HO OH H H OH H H OH H H like iron, copper, zinc and manganese.
All proteins on partial hydrolysis give
H OH H OH n–2 H OH peptides of varying molecular masses
Cellulose
which on complete hydrolysis give amino
acids.
Hydrolysis Hydrolysis
Cellulose (C6H10O5)n : It is the chief constituent Proteins → Peptides −→ Amino acids
of the cell walls of plants. Wood contains 45-
50% while cotton contains 90-95% cellulose. It 17.3.1 Amino Acids
is a colourless amorphous solid which Amino acids contain amino (-NH2) and carboxyl
decomposes on heating. It is largely linear and (-COOH) functional groups. Depending upon the
its individual strands align with each other relative position of the two functional groups in
through multiple hydrogen bonds. This lends the alkyl chain the amino acids can be classified
rigidity to its structure. It is thus used effectively as α, β, γ, δ and so on. Only α-amino acids are
as a cell wall material. obtained on hydrolysis of proteins. These may
Cellulose does not reduce Tollen’s reagent contain other functional groups also.
or Fehling’s solution. It does not form osazone R –– CH –– COOH
and is not fermented by yeast. It is not 
hydrolysed as easily as starch, but on heating NH2
with dilute sulphuric acid under pressure α-amino acid (R = side chain)
yields only D-glucose. 17.3.2 Nomenclature of Amino Acids
Cellulose is a straight chain polysaccharide
composed of only D-glucose units, which are All α-amino acids have trivial names, even those
joined by β-glycosidic linkages between C-1 for which IUPAC names are not cumbersome
of one glucose unit and C-4 of the next glucose e.g. H2NCH2COOH is better known as glycine
unit. The molecular mass of cellulose is in rather than α-amino acetic acid or 2-amino
the range of 50,000-500,000 (300-2500 ethanoic acid. These trivial names usually reflect
D-glucose units). It is used in the manufacture the property of that compound or its source e.g.
of rayon and gun cotton. glycine is so named since it has sweet taste (in
Large population of cellulolytic bacteria Greek glykos means sweet) and tyrosine was first
present in the stomach (rumen) of ruminant obtained from cheese (in Greek, tyros means
mammals (cattle, sheep etc.) breaks down cheese). Amino acids are generally represented
cellulose with the help of enzyme cellulase. It by a three letter symbol, sometimes one letter
is then digested and converted into glucose. symbol is also used. The structures of some
Human stomach is different and does not have commonly occurring amino acids along with
enzyme capable of breaking cellulose their 3-letter and 1-letter symbols are given in
molecules. (Table 17.2).
17.3.3 Classification of Amino Acids
17.3 PROTEINS
Proteins are high molecular mass complex Amino acids are classified as acidic, basic or
biopolymers of amino acids present in all living neutral depending upon the relative number of
cells. The protoplasm of plant or animal cell amino and carboxyl groups in their molecule.
contains 10-20% proteins. The name protein is Equal number of amino and carboxyl groups
derived from the Greek word proteios meaning make it neutral, more number of amino than
of prime importance. As enzymes these catalyze carboxyl groups make it basic and more carboxyl
biochemical reactions, as hormones they regulate as compared to amino make it acidic. The amino
metabolic processes and as antibodies they acids, which can be synthesized in the body, are
protect the body against toxic substances. All known as non-essential amino acids and those,
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BIOMOLECULES

COOH
Table 17.2 Natural Amino Acids, H 2N H
R
Name of the amino acids Characteristic feature of Three letter One letter
side chain, R symbol code
1. Glycine H Gly G
2. Alanine – CH3 Ala A
3. Valine* (H3C)2CH- Val V
4. Leucine* (H3C)2CH-CH2- Leu L
5. Isoleucine* H3C-CH2-CH- Ile I
|
CH3

6. Arginine* HN=C-NH-(CH2)3- Arg R

|
NH2

7. Lysine* H2N-(CH2)4- Lys K

8. Glutamic acid HOOC-CH2-CH2- Glu E
9. Aspartic acid HOOC-CH2- Asp D

O
||
10. Glutamine H2N-C-CH2-CH2- Gln Q

O
||
11. Asparagine H2N-C-CH2- Asn N
12. Threonine* H3C-CHOH- Thr T
13. Serine HO-CH2- Ser S
14. Cysteine HS-CH2- Cys C
15. Methionine* H3C-S-CH2-CH2- Met M
16. Phenylalanine* C6H5-CH2- Phe F
17. Tyrosine (p)HO-C6H4-CH2- Tyr Y

–CH2

18. Tryptophan* Trp W

N
H

H2C–
NH
19. Histidine* His H
N

a
COOH
HN H
20. Proline Pro P
CH2

* essential amino acid , a = entire structure

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CHEMISTRY

which cannot be synthesized in the body but amino acids obtained from the hydrolysis of
must be obtained through diet, are known as proteins.
essential amino acids (marked in Table 17.2). Except glycine, all other naturally occurring
α-amino acids are optically active, since the
17.3.4 Physical Properties of α -Amino Acids α-carbon atom is asymmetric. These exist both
Amino acids are usually colourless, crystalline in ‘D’ and ‘L’ forms. Their Fischer projection
solids. These are water-soluble high melting formulae are written with carboxyl group
solids and behave like salts rather than simple (-COOH) at the top. In the ‘D’ form amino group
amines or carboxylic acids. This behavior is due (-NH2) is written on the right side and in the ‘L’
to the presence of both an acidic (carboxyl group) form on the left side. This is similar to the
and a basic (amino group) group in the same placement of hydroxyl group (-OH) in
molecule. In aqueous solution the carboxyl group glyceraldehydes, the reference compound for
can lose a proton and amino group can accept a carbohydrates (Unit 12).
proton, giving rise to a dipolar ion known as ‘D’ and ‘L’ refer to the configuration of the
zwitter ion. This is neutral but contains both amino acid molecule about the asymmetric
positive and negative charges. carbon atom. Most naturally occurring amino
acids have L-configuration.
O O 17.3.5 Chemical Properties of α - Amino Acids
–
R–CH–C–O–H R–CH–C–O Amino acids form salts with acids as well as
+ with bases. Their chemical reactions are similar
:NH2 NH3
to primary amines and carboxylic acids (Units
14 and 15).
In zwitter ionic form, amino acids show
amphoteric behaviour as they react both with 17.3.6 Peptides
acids and bases. In acidic solution, the We have learnt earlier in this unit that proteins
–
carboxylate function (-COO ) accepts a proton on hydrolysis break down into smaller fragments
and gets converted to carboxyl substituent called peptides which finally give α - amino acids,
(-COOH), while in basic solution the ammonium The peptide bond: The reaction between two
+  molecules of the same or different amino acids,
substituent  N H3  changes to amino group proceed through the combination of the amino
group of one molecule with the carboxyl group
(-NH2) by losing a proton.
of the other. This results in the elimination of a
O O O water molecule and formation of a peptide bond
R–CH–C–O – OH– –
R–CH–C–O H+ R–CH–C–OH –CO–NH–. For example, when carboxyl group of
   glycine combines with the amino group of
+ +
NH2 NH3 NH3 alanine, we get, glycylalanine.

In acidic solution, an amino acid exists as a H2N–CH2–COOH + H2N–CH–COOH

positive ion and migrates towards the cathode 
– H2O

in an electric field, while in alkaline solution it CH3

exists as a negative ion and migrates towards
anode. At a certain hydrogen ion concentration
(pH), the dipolar ion exists as a neutral ion and H2N–CH2–CO–NH–CH–COOH
does not migrate to either electrode. This pH is 
known as the isoelectric point of the amino CH3
acid. The isoelectric point depends on other Glycylalanine (Gly-Ala)
functional groups in the amino acid, and neutral
amino acids have isoelectric points in the range Alternatively the amino group of glycine may
of pH 5.5 to 6.3. At isoelectric point the amino react with carboxyl group of alanine, resulting
acids have least solubility in water and this in the formation of a dif ferent dipeptide,
property is exploited in the separation of different alanylglycine (Ala - Gly).
 337
BIOMOLECULES

In both the dipeptides i.e., glycylalanine or bases and have an isoelectric point at which they
alanylglycine, there are free functional groups are frequently least soluble and have the greatest
at both ends. These groups can further react tendency to aggregate.
with the relevant groups of the other amino acids The functions of proteins are important and
forming tri, tetra, penta peptides and so on. varied in bio-systems, however, the smaller
peptides also have important functions though
17.3.7 Polypeptides
their total content in tissues is small compared
As a matter of convention the structure of to proteins. Some of these are very potent. Most
polypeptides is written in a way that the amino of the toxins (poisonous substances) in animal
acid with the free amino (-NH2) group known as venoms and in plant sources are polypeptides.
N-terminal residue is written on the left hand Minute amount of some oligopeptides with as
side of the polypeptide chain and the amino acid few as three modified amino acid residues are
with the free carboxyl group (C- terminal residue) effective as hormones. A derivative of dipeptide,
is written on the right hand side of the chain. aspartylphenylalanine methyl ester (aspartame)
Thus, a tripeptide, alanylglycylphenylalanine is 160 times as sweet as sucrose and is used as
is represented as follows, a sugar substitute.
HOOC–CH2 CH2–C6H5
N-terminal C-terminal | |
residue residue NH2–CH–CO–NH–CH–COOCH3
O O Aspartame

H2N–CH–C–NH–CH2–C–NH–CH–COOH
  Example 17.1
CH3 CH2C6H5 A tripeptide on complete hydrolysis gives
Alanine Glycine Phenylalanine glycine, alanine and phenylalanine. Using
Ala – Gly – Phe three letter symbols write down the possible
sequences of the tripeptide.
The name of any polypeptide is written
starting from the N-terminal residue. The suffix- Solution The possible combinations can be,
ine in the name of the amino acid is replaced by (i) Gly-Ala-Phe (ii) Gly-Phe-Ala
– yl (as glycine to glycyl, alanine to alanyl etc.) (iii) Ala-Gly-Phe (iv) Ala-Phe-Gly
for all amino acids except the C- terminal acid. (v) Phe-Gly-Ala (vi) Phe-Ala-Gly
This nomenclature is not used frequently.
Instead, the three letter or one letter abbreviation 17.3.8 Structure of Proteins
for the amino acid (as given in Table 17.2) is Proteins are considered to be biopolymers
used e.g. the above tripeptide is named as Ala- containing a large number of amino acids joined
Gly-Phe or A-G-F. to each other by peptide linkages having three
Relatively shorter peptides are known as dimensional (3 D) structures. Protein structure
oligopeptides whereas longer polymers are and shape can be studied at four different levels,
called polypeptides. A polypeptide with more i.e., primary, secondary, tertiary and quaternary
than hundred or so amino acid residues, having structures, each level being more complex than
molecular mass higher than 10,000 is called a the previous one.
protein. However, the distinction between a
polypeptide and a protein is not sharp. 17.3.9 Primary Structure of Protein
Polypeptides with fewer amino acids are likely Proteins may have one or more polypeptide
to be called proteins if they ordinarily have a chains. Each polypeptide in a protein has amino
well-defined conformation of a protein (Section acids linked with each other in a specific
17.3.9). sequence and it is this sequence of amino acids
Polypeptides are amphoteric because of the that is said to be the primary structure of that
presence of terminal ammonium and carboxylate protein. Any change in this primary structure
ions as well as the ionized side chains of amino i.e., the sequence of amino acids creates a
acid residues. Therefore, they titrate as acids or different protein.
 338
CHEMISTRY

A protein containing a total of 100 amino acid about this bond is possible. As shown in
residues is a very small protein, yet 20 different Fig. 17.4, the free rotation of a peptide chain can
amino acids can be combined at one time in only occur around the bonds joining the nearly
(20)100 different ways. planar amide groups to the α-carbons. The
angles shown as Φ and Ψ in the figure are known
17.3.10 Secondary Structure
as Ramachandran angles after the name of the
The secondary structure of a protein refers to Indian Biophysicist, G.N.A. Ramachandran. Note
the shape in which a long polypeptide chain can that C=O and -NH groups of the peptide bond
exist. There are two different conformations of are trans to each other.
the peptide linkage present in proteins viz. Hydrogen bonds between –N-H and –C=O
α-helix and β-conformation. The α-helix model groups of peptide bonds give stability to the
postulated by Linus Pauling in 1951 purely on structure. Thus, a structure having maximum
theoretical considerations was later verified hydrogen bonds shall be favoured. α-Helix is one
experimentally. In order to understand this, let of the most common ways in which a polypeptide
us look at the nature of the peptide bond, which chain forms all possible hydrogen bonds by
shows resonance as shown below. Hydrogen twisting into a right handed screw (helix) with
bonding between –NH- and –C=O groups on the –NH group of each amino acid residue
different peptides linkages is shown in Fig. 17.5. hydrogen bonded to the –C=O of an adjacent
turn of the helix as shown in Fig. 17.5(b). The
α-helix is also known as 3.6 13 helix, since each
turn of the helix has approximately 3.6 amino
acid residue and a 13 member ring is formed by
hydrogen bonding.
It may be noted that in proteins, the helix
always has a right handed arrangement. If you
hold your hand so that the thumb points in the
direction of travel along the axis of the helix, the
curl of your fingers describes the direction in
which the helix rotates, Fig. 17.5(a). All amino acids
Resonance Structure of Amide Linkage in a polypeptide chain have L-configuration and
Due to the partial double bond character of the therefore, it can only result in a stable helix if it is
C-N bond in peptide linkage, the amide part i.e., right handed. The ball and stick model of a α-helix
–CO-NH- is planar and rigid i.e., no free rotation present is shown in Fig. 17.5(c).

H O

C C C
N
N
C  C 
H

Peptide
links

Fig. 17.4 Model of a tripeptide showing peptide bonds in boxes and Ramchandran angles of rotation (Φ and
Ψ) around α-carbon.
 339
BIOMOLECULES

(a) (b) (c)

Fig. 17.5 α - helix structure of protein.
β- Structure was also proposed by Linus (Fig.17.6). N-termini are aligned head to head
Pauling and co-workers in 1951. In this i.e., on the same side in parallel β-conformation
conformation all peptide chains are stretched and are aligned head to tail i.e., N-terminus of
out to nearly maximum extension and then laid one chain and C-terminus of another chain are
side by side, held together by intermolecular on the same side in antiparallel conformation.
hydrogen bonds. The structure resembles the The β-sheet is parallel in keratin, the protein
pleated folds of drapery and therefore is known present in hair and antiparallel in silk fibroin.
as β-pleated sheet. The polypeptide chains may
run parallel i.e. in the same direction or may be 17.3.11 Tertiary Structure of Proteins
antiparallel i.e. run in opposite directions The tertiary structure of proteins represents
overall folding of the
N N N polypeptide chains i.e., further
RCH RCH RHC RCH HCR folding of the secondary
C C O RCH
C O O H C H
H H H O N C structure. Two major
N N N
N C O H O
HCR N molecular shapes are found
HCR HCR HCR RCH HCR
C N
viz. fibrous and globular. The
C C O H C O O C H fibrous proteins e.g. silk,
O H O H N O H H
N N N C N
RCH HCR RCH
collagen and =-keratins have
RCH RCH RCH H N
C C C C O H C large helical content and have
H O O O H O O
N H N H N C rod like rigid shape and are
N N
HCR HCR HCR HCR RCH HCR insoluble in water. The
C C C C N C structure of collagen triple
Parallel  -Conformation Antiparallel  -Conformation
helix is shown in Fig. 17.7. In
globular proteins e.g.,
Fig. 17.6 β - sheet of proteins. haemoglobin the polypeptide
 340
CHEMISTRY

17.3.12 Denaturation of Proteins

Protein found in a biological system with definite
configuration and biological activity is called a
native protein. If a native protein is subjected
to physical or chemical treatment which may
disrupt its higher structures (conformations)
without affecting its primary structure, the
protein is said to be denatured and it loses it’s
biological activity. The denaturation may be
reversible or irreversible. The coagulation of egg
white on boiling of egg protein is an example of
irreversible protein denaturation. However, in
some cases it is found that if the disruptive agent
is removed the protein recovers its original
physical and chemical properties and biological
activity. The reverse of denaturation is known
as renaturation.
7.3.13 Enzymes
Enzymes are naturally occurring simple or
Fig. 17.7 Collagen triple helix
conjugate proteins acting as specific catalysts
in cell processes. Some enzymes can be
chains consist partly of helical sections which nonproteins also. The enzyme facilitates a
are folded about the random cuts to give it a biochemical reaction by providing alternative
spherical shape. The primary, secondary and lower activation energy pathways thereby
higher (tertiary and quaternary) levels of increasing the rate of reaction (Unit 7). (Enzymes
heamoglobin structure are given in Fig. 17.8. being proteins have colloidal nature and often
get inactivated during
reactions and have to be
constantly replaced by
synthesis in the body.)
At present about
3000 enzymes have
been recognized by the
International Union of
Biochemistry. However,
only about 300 (~10%)
are commercially
available.
An enzyme molecule
may contain a non-
protein component
known as a prosthetic
group. The prosthetic
group which is covalently
(a) Primary (b) Secondary (c) Tertiary (d) Quaternary attached with the enzyme
structure structure structure structure
molecule is known as
C N R groups cofactor. Those prosthetic
H O Haeme group groups which get
attached to the enzyme at
the time of reaction are
Fig. 17.8 Primary, secondary, teritiary and quaternary structures of haemoglobin. known as coenzymes.
 341
BIOMOLECULES

17.3.14 Specificity and Mechanism of In higher cells, DNA is localized mainly in the
Enzyme Action nucleus, within the chromosome. A small amount
of DNA is present in the cytoplasm also where it
In case of enzymatic reaction the enzyme is so
is contained in mitochondria and chloroplasts.
built that it binds to the substrate in a specific
RNA is also present in nucleus as well as
manner (Unit 7). The enzymatic reaction may
cytoplasm. DNA is the major source of genetic
proceed through the following four stages, (i) the
information, which is copied into RNA molecules
formation of complex between enzyme and
(transcription). The sequence of nucleotides
substrate (ES), (ii) the conversion of this complex
contains the’ Code for specific amino acid
to an enzyme-intermediate complex (EI) and (iii)
sequences. Proteins are then synthesized in a
further conversion to a complex between enzyme process involving translation of RNA.
and product (EP) and (iv) the dissociation of the
enzyme-product complex, leaving the enzyme 17.4.1 Chemical Composition of Nucleic
unchanged. Acid (Primary Structure)

17.4 NUCLEIC ACIDS Complete hydrolysis of DNA (or RNA) yields a

pentose sugar (ribose in RNA and deoxyribose
Every living cell contains nucleoproteins, in DNA), two types of heterocyclic nitrogenous
substances made up of proteins combined with bases viz., purines and pyrimidines along with
biopolymers of another kind, the nucleic acids. phosphoric acid.
These are mainly of two types, the Deoxyribose differs from ribose in not having
deoxyribonucleic acids (DNA) and ribonucleic an –OH on C–2 (Fig. 17.9).
acids (RNA). Nucleic acids are long chain As shown in the figure the pyrimidines have
polymers (polynucleotides) of nucleotides. While a single heterocyclic ring while purines have two
proteins have a polyamide chain, nucleic acids fused rings. DNA contains the purine bases,
contain a polyphosphate ester chain. adenine (A) and guanine (G), and pyrimidine

HOCH2 O OH  -D-ribose
used in ribonucleic
H H acid
H H
PENTOSE C 5' O
a 5-carbon two kinds OH OH
sugar 4' 1' are used
3' 2'
HOCH2 O OH  -D-deoxyribose
used in deoxyribonucleic
H H acid
H H
OH H

Fig. 17.9 Structure of β -D-ribose and β -D-deoxyribose.

O NH2
C adenine (A) N C
NH2 HC
NH C N
C uracil (U) HC
HC HC C N C N CH
N N O
cytosine H H
HC N C
O (C) 4 N
H N 7 6
5 3 5 1N
8
O 6 2 4 2 O
1
H3C N 9 3
C N N N C
C NH H C NH
HC N C HC
PYRIMIDINE PURINE
thymine (T) H O N C N C NH
guanine (G) 2
H
Fig. 17.10 Purine and Pyrimidine Bases.
 342
CHEMISTRY

bases, thymine (T) and cytosine (C) while RNA The nucleotides are abbreviated by three
has uracil (U) in place of thymine (T). It can be capital letters, preceded by d- in case of deoxy
noted that there are two main structural series e.g.,
differences between DNA and RNA; (1) DNA has AMP = adenosine monophosphate
deoxyribose while RNA has ribose sugar, (2) DNA dAMP = deoxyadenosine monophosphate
contains thymine while RNA has uracil. ATP = adenosine triphosphate
Nucleosides: The N- glycosides of purine or UDP = uridine diphosphate etc.
pyrimidine bases with pentose sugars are known Nucleotides are joined together by
as nucleosides: phosphodiester linkages between 5' and 3'
Base + Sugar = Nucleoside (Fig. 17.11). carbon atoms of the pentose sugar. The
formation of a typical dinucleotide is shown in
N-glycosidic Fig. 17.13.
bond BASE
5'
N
O O BASE
4' SUGAR C
1' O P O CH2 O
H
3' 2' O SUGAR
Fig. 17.11 Base-Sugar linkage.
OH
Base Abbreviation Nucleoside
adenine A adenosine O BASE
guanine G guanosine
cytosine C cytidine O P O CH2 O
thymine T thymidine
O SUGAR
uracil U uridine

In nucleosides the sugar carbons are primed OH

e.g. 1', 2', 3', etc. in order to distinguish these
from the bases. The purine or pyrimidine bases
are attached to position 1' of pentoses through
N- glycosidic linkages. 5´ end of chain
Nucleotides: A nucleotide is a phosphate ester O BASE
of nucleoside and consists of a purine or 5´
O P O CH2 O
pyrimidine base, the 5-carbon sugar and one or
more phosphate groups. (Fig. 17.12) O SUGAR
Base + Sugar + Phosphate = Nucleotide
3´
BASE 3' O
Phosphodiester
NH2 linkage O P O
PHOSPHATE
N
O O BASE
N O
O P O CH2 5´CH2 O
O
O
H H
SUGAR
H H
example: DNA 3´
OH OH
OH
3´ end of chain
SUGAR

Fig. 17.12 A nucleotide. Fig. 17.13 Formation of a dinucleotide.

 343
BIOMOLECULES

A nucleic acid chain is commonly abbreviated James Dewey Watson

by a one letter code with the 5´end of the chain Born in Chicago, Illinois, in
written at the left e.g., a tetranucleotide having 1928, Dr. Watson received his
adenine, cytosine, guanine and thymine bases Ph.D. (1950) from Indiana
from 5´ end to 3´ end is represented as ACGT. University in Zoology. He is
The backbone is composed of alternating best known for his discovery of
sugar and phosphate bonds. It is extremely time the structure of DNA for which
consuming to write the complete structure of he shared with Francis Crick
these oligonucleotides. In order to simplify, the and Maurice Wilkins the 1962 Nobel prize in
Physiology and Medicine. They proposed that DNA
bases are represented by their respective
molecule takes the shape of a double helix, an
symbols, the phosphate bond is represented by elegantly simple structure that resembles a gently
symbol ‘P’ and sugar is drawn by simple Fischer twisted ladder. The rails of the ladder are made of
projection. Thus, the tetranucleotide ACGT can alternating units of phosphate and the sugar
be drawn as follows; deoxyribose; the rungs are each composed of a
pair of purine/ pyrimidine bases. This research
A C G T laid the foundation for the emerging field of
molecular biology. The complementary pairing
of nucleotide bases explains how identical copies
3´ 3´ 3´ 3´ of parental DNA pass on to two daughter cells.
P P P P This research launched a revolution in biology that
led to modern recombinant DNA techniques.
5´ 5´ 5´ 5´
Fig. 17.14 Tetranucleotide, ACGT.
The two strands are held together by hydrogen
17.4.2 DNA – A Double Helix
bonds, shown as black rods in the figure. Only
E. Chargaff found that the base composition in two base pairs i.e. AT and CG fit into this
DNA varied from one species to other species, structure. Two hydrogen bonds are formed
but in all cases the amount of adenine was equal between A and T (A = T) and three are formed
to that of thymine (A = T) and the amounts of between C and G (C ≡ G). Therefore, CG base
cytosine and guanine were also found to be equal pair has more stability as compared to AT base
(G = C). Therefore, the total amount of purines pair (Fig. 17.15). The two complementary base
was equal to the total amount of pyrimidines pairs of DNA, i.e., (T -A) and (C-G) with their
(A+G= C+T). However, the AT/CG ratio varies hydrogen bonds are shown in Fig. 17.16. In
considerably between species e.g., this ratio is addition to hydrogen bonds, other forces e.g.
1.52 in man while in E. Coli it is 0.93. hydrophobic interactions between stacked bases
In 1953, based on the X-ray diffraction studies are also responsible for stability and
of DNA, J. D Watson and F. H. C. Crick proposed maintenance of double helix.
a double helical structure for DNA which The diameter of double helix is 2 nm, as shown
explained not only the base equivalence (A = T; in Fig. 17.15, the double helical structure
G=C) but also other properties of DNA, specially repeats at intervals of 3.4 nm (one complete
its duplication in a living cell (replication). The turn), which corresponds to ten base pairs. Two
double helical structure of DNA is shown in the kinds of grooves, one major and one minor are
Fig. 17.15. evident in the structure. DNA helices can be
The double helix is composed of two right right handed as well as left handed. The
handed helical polynucleotide chains coiled β-conformation of DNA having the right-handed
around the same central axis. The two strands helices is the most stable. On heating the two
are antiparallel, i.e., their (5´→ → 3´) strands of DNA separate from each other (known
phosphodiester linkages run in opposite as melting) and on cooling these again hybridize
directions. The bases are stacked inside the helix (annealing). The temperature at which the two
in planes perpendicular to the helical axis. It is strands separate completely is known as its
like a stack of flat plates held together by two melting temperature (Tm) which is specific for
ropes of sugar- phosphate polymeric backbone each specific sequence. So far we have discussed
running along outside of stack. the secondary structure of DNA. In secondary
 344
CHEMISTRY

3´-end 5´-end

Minor groove
H
S A T S 3.4 nm
P P O
S T A S
P P C in sugar
S C G S phosphate backbone
P P C & N in bases
S G C S
Major groove P

3´-end 5´-end

2.0 nm

(a) Diagrammatic representation (b) Space filling model

Fig. 17.15 Double helical structure of DNA.

Example 17.2
The two samples of DNA , A and B have
melting temperatures (Tm) 340 and 350 K
respectively. Can you draw any conclusion
from this data regarding their base content?

Solution
The B sample of DNA having higher Tm must
be having more GC content as compared to
sample A, since GC base pair having 3
H
hydrogen bonds as compared to AT base pair
N having only 2 hydrogen bonds, results in
H
O stronger binding.
N N
H
H N
N
O Example 17.3
H N N In E.coli DNA the AT/GC ratio is 0.93. If
N
Cytosine H the number of moles of adenine in its DNA
H Guanine sample are 465,000, calculate the number
of moles of guanine present.
Fig. 17.16 Hydrogen bonds are formed between
complementary base pairs.
Solution
structure of RNA, helices are present but only Since, the number of moles of adenine
single stranded. At higher levels one deals with should be equal to those of thymine, (A+T)
the way these molecules are bound to proteins, = 930,000. Since, A+T/G+C = 0.93,
folded and supercoiled to make chromatin and the (G+C)=1000,000. Therefore, the
chromosomes. Such structures explain how four number of moles of guanine should be
meters of DNA can be filled inside a single cell. 1000,000/2 = 500,000.
 345
BIOMOLECULES

17.4.3 Heredity–the–Genetic Code acid. In order to understand fully the genetic

Nucleic acids control heredity at molecular level. code, let us first learn about replication and
The double helix of DNA is the store house of transcription.
the hereditary information of the organism. This 17.4.4 Replication
information is in the coded form as the sequence
of bases along the polynucleotide chain. Since We have already studied that in the DNA double
DNA has only four different bases, the genetic helix the sequence of bases in one chain is
message can be compared to a language which complementary to the sequence in the other
has only four letters A, C, G and T. chain, therefore one controls the other.
DNA must preserve this information and also At the time of cell division (mitosis) the two
use it in the following manner: strands of the DNA double helix partly unwind
1. DNA molecules can duplicate themselves i.e., and each serves as a template for the synthesis
can synthesize other DNA molecules identical of a new DNA molecule (Fig.17.17). DNA
with the original; this process is known as replication follows the base pairing rules by
replication.
2. A single strand of DNA can act as a template
on which a molecule of RNA is synthesized in
a specific manner; this process is known as
transcription.
3. The RNA molecule in tur n directs the
synthesis of specific proteins which are
characteristic of each kind of organism, this
process is called translation.
These concepts constitute the central dogma
of molecular biology and were summarized by
Francis Crick in the following diagram,
Replication Transcription
DNA DNA RNA
Reverse
Translation

Transcription

PROTEIN

In molecular biology, the word transcription

is used as a synonym for RNA synthesis and
translation as a synonym for protein synthesis.
Translation is unidirectional but transcription
can sometimes be reversed i.e., RNA is copied
into DNA. This reverse transcription occurs
during life cycle of some retroviruses.
We can thus infer that base sequence in DNA
indirectly controls the sequence of amino acids
in the protein. Since protein molecule can
contain a maximum of 20 different types of
amino acids, it is like a large sentence written
in a language of 20 letters, but the hereditary
message is written in a language of only 4 letters;
it is written in a code with each word of 3 letters
(triplet: codon) standing for a particular amino Fig. 17.17 Machanism of DNA replication.
 346
CHEMISTRY

which A pairs with T and G pairs with C. the t RNA molecules get attached on mRNA i.e.,
Therefore, each daughter molecule is an exact the sequence in which the amino acids are built
replication of the parent molecule. DNA into the polypeptide chain depends upon the
replication is semi-conservative i.e., only half of sequence of bases along the mRNA chain.
the parental DNA is conserved and only one Since it is the sequence of four different
strand is synthesized. DNA replication takes nucleotides that is used to convey information
place only in the 5´→3´ direction. for the combination of twenty different amino
acids into peptide chains, each amino acid must
17.4.5 Transcription
be represented by combination of at least three
This process resembles DNA replication. The nucleotides (triplet). This is true since there are
double helix of DNA partially uncoils and on one only sixteen different doublets of four nucleotides
of the two strands is formed a chain of RNA. (42) but there are 64 triplets (43). These 64 three
Here, a ribose sugar is incorporated against a letter code words are known as Codons. However,
deoxyribose moiety of the parent DNA strand there being only 20 amino acids, more than one
and a uracil is added opposite each adenine of codon can code for the same amino acid e.g.,
DNA. The newly for med chain of RNA is CUU and CUC both can call leucine. Proline is
complementary to a segment of the DNA chain. encoded by CCU, CCA, CCG and CCC. Therefore,
There are three types of RNA i.e. messenger RNA codons can be synonyms and genetic code is
(mRNA), transfer RNA (tRNA) and ribosomal RNA degenerate. A difference of a single base in the
(rRNA). The m-RNA carries a message to the DNA molecule or a single error in the reading of
ribosome where protein synthesis actually takes the code can cause a change in the amino acid
place. sequence which leads to mutation. A
diagramatic representation of the mechanism
17.4.6 Protein Synthesis (Translation)
of protein synthesis in given in Fig. 17.18.
At the ribosome, the messenger RNA dictates It may be noted that every t-RNA molecule
the binding of specific transfer RNA molecules has an amino acid attachment site and a site
each of which is bonded with a particular amino having three complementary nucleotides for
acid. Each tRNA has a specific base sequence recognition of the triplets in m-RNA (anticodon).
that binds only with the complementary The genetic code has four noteworthy
sequence in messenger RNA. The order in which features;

Amino acid

tRNA

1 codon=
3 nucleotides
Initiation Termination
Anticodon

AUG UAA
mRNA PPP OH
5' 3'
Direction of
Ribosome
translation

fMet Growing polypeptide

NH2

Fig. 17.18 Diagrammatic representation of protein synthesis.

 347
BIOMOLECULES

Har Gobind Khorana These have higher melting points than

neutral fats.
(B) Compound lipids (heterolipids): Lipids with
Har Gobind Khorana, was born
in 1922. He obtained his M.Sc. additional groups are called compound
degree from Punjab University lipids. These include:
in Lahore. He worked with 1. Phospholipids (phosphatides):These
Professor Vladimir Prelog, who contain additional groups e.g., a
molded Khorana’s thought phosphoric acid, nitrogen containing
and philosophy towards science, work and effort. bases and other substituents.
After a brief stay in India in 1949, Khorana went 2. Glycolipids: These are esters of fatty
back to England and worked with Professor G.W. acids with carbohydrates, and may
Kenner and Professor A.R.Todd. It was at
contain nitrogen but no phosphorus.
Cambridge, U.K. that he got interested in both
proteins and nucleic acids. Dr Khorana shared the (C) Derived lipids: These are the substances
Nobel Prize for Medicine and Physiology in 1968 derived from simple and compound lipids
with Marshall Nirenberg and Robert Holley for by hydrolysis. These include fatty acids, fatty
cracking the genetic code. alcohols, mono and diglycerides,
steroids, terpenes and carotenoids. These are
sometimes present as waste products of
1. It is universal metabolism. Glycerides and cholesterol
2. It is degenerate i.e. more than one codons code esters are also called neutral lipids since
for an amino acid. these do not carry any charge.
3. It is commaless
17.5.2 Chemical Structure
4. The third base of the codon is less specific
There is a single code for all living organisms. Simple lipids:
This is a strong indication that life started on 1. Glycerides: The triglycerides are esters of
earth about 3 billion years ago and only once glycerol with long chain fatty acids. Fatty acids
the genetic code was established has remained always have an even number of carbons and
unchanged since then. may be saturated, e.g. palmitic acid
17.5 LIPIDS (C15H31COOH) and stearic acid (C17H35COOH) or
unsaturated e.g. oleic acid (C17H33COOH) and
Lipids are naturally occurring compounds linolenic acid (C17H29COOH).
related to fatty acids and include fats, oils, waxes The three fatty acids in triglycerides may be
and other related compounds. The lipids are same or different. Fats are glycerides of saturated
important constituents of diet. In the body the fatty acids e.g., tripalmitin and tristearin. Oils
fats serve as an efficient source of energy, and contain unsaturated fatty acids e.g., triolein. α-
are stored in the adipose tissues. These are Oleo-β-palmito-α´-stearin is an example of mixed
hydrophobic in nature and dissolve in organic triglyceride.
solvents. Phospholipids (lipids containing
phosphorous) are important constituents of cell H2COH H2C–O–CO–(CH2)n–CH3
membrane.  
HCOH + 3HOOC–(CH2)n–CH3 HC–O–CO(CH2)n–CH3
17.5.1 Classification  
H2COH H2C–O–CO–(CH2)n–CH3
Based on their chemical composition, lipids are
classified as follows; Glycerol Fatty acid Triglyceride
(A) Simple lipids (homolipids): Simple lipids (Neutral fat)
are alcohol esters of fatty acids which H2C–O–CO–C17H35 H2C–O–CO–C17H33
include,  
1. Neutral fats (glycerides): Also known as HC–O–CO–C17H35 HC–O–CO–C17H33
triglycerides, these are triesters of fatty  
acids and glycerol. H2C–O–CO–C17H35 H2C–O–CO–C17H33
2. Waxes: These are esters of fatty acids
with long chain monohydroxy alcohols. Tristearin Triolein
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CHEMISTRY

H2C–O–CO–C15H31 H2C–O–CO–C17H33 symmetry, the two stearic acid molecules must

 
be linked to two terminal primary alcoholic
HC–O–CO–C15H31 HC–O–CO–C15H31
groups. Therefore, the structure of the fat must
 
H2C–O–CO–C15H31 H2C–O–CO–C17H35 be;

Tripalmitin α -Oleo–β
β –palmito– H2C-O-CO-C17H35
α ´–stearin |
HC-O-CO-C15H31
The presence of double bonds with less stable |
‘cis’ stereochemistry in unsaturated fatty acids H2C-O-CO-C17H35
e.g. at C-9 in oleic acid (C17H33COOH), at C-9
and C-12 in linoleic acid (C17H31COOH), at C-9, 2. Waxes: These are esters of long chain
C-12 and C-15 in linolenic acid (C17H29COOH) saturated and unsaturated fatty acids with long
is of vital biological significance. In solid state, chain monohydroxy alcohols. The fatty acids
the molecules of saturated fatty acids fit closely range between C14 and C36 and the alcohols
together due to their zig-zag tetrahedral range from C16 to C36. Most of the waxes are
structure. The cis unsaturated acid chains have mixtures.
a bend at the double bond and do not fit closely
resulting in the lowering of the melting point of 17.5.3 Biological Functions and other
the fat. Applications of Lipids
Fats are important food reserves of animals and
Example 17.4 plant cells. We can extract animal and vegetable
An unsaturated fatty acid on ozonolysis fats and oils from natural sources. While we
yields an aldehyde H 3 C(CH 2 ) 7 CHO synthesize fat in our own bodies, we also
and an aldehydic monocarboxylic acid consume fats synthesized by plants and other
OHC (CH 2 ) 7 COOH. Write down the animals.
structure and name of the acid. Phospholipids are indispensable structural
Solution components of cell membranes and are also used
An aldehyde function results as a result of as detergents to emulsify fat for transport within
ozonolysis of a double bond. Moreover, the the body. These are never stored in large
doubly bonded carbon atom must carry a amounts. Cholesterol is the principal sterol of
hydrogen. Since two aldehydes are formed, the higher animals, abundant in nerve tissues and
double bond must be –HC=CH-. Therefore, the gallstones. Cholesterol is not present in plant
structure of the unsaturated acid can be written fats.
as,
17.6 HORMONES
H3C(CH2)7HC=CH (CH2)7COOH. It is oleic acid.
Hor mones are molecules that transfer
infor mation from one group of cells to
Example 17.5 distant tissue or organ. These substances are
One mole of a naturally occurring fat on produced in small amounts by various
hydrolysis with NaOH gave one mole of endocrine (ductless) glands in the body.
glycerol together with sodium palmitate and Hormones are delivered directly to the blood
sodium stearate in 1:2 molar ratio. The stream in minute quantities and are carried by
molecule of the fat is symmetric. Write blood to various target organs where these exert
down the structure of the fat. physiological effect and control metabolic
activities. Therefore, frequently their site of
Solution action is away from their origin. Hormones are
The 1:2 molar ratio of sodium palmitate and required in trace amounts and are highly specific
sodium stearate obtained on hydrolysis with in their functions. The deficiency of any hormone
NaOH indicates that two stearic acid molecules leads to a particular disease, which can be cured
and one palmitic acid are esterified with one by the administration of that hormone.
mole of glycerol. Since the molecule of fat has
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17.6.1 Classification and Functions of I. Functions of steroid hormones:

Hormones 1. Sex hormones: Sex hormones are divided into
Hormones may be classified on the basis of (i) three groups (i) the male sex hormones, or
their structure or (ii) their site of activity in the androgens; (ii) the female sex hormones, or
cell. Classification based on structure is given estrogens; and (iii) pregnancy hormones, or
in Fig. 17.19. progestines. Testosterone is the major male sex

Hormones

Steroids Non-steroids

Adrenal cortical Sex hormones Peptide hormones Amino acid Miscellaneous

hormones (insulin, glucagon) derivatives (prostaglandins,
(corticoids) (thyroidal cytokinins)
hormones)

Female sex hormones Male sex hormones

(Androgens e.g. Testosterone)

Estrogens Progestrone
(estrone, estradiol)
Fig 17.19 Classification of Hormones

Steroids on which the above classification is hormone produced by testes. It is responsible

made are compounds whose structure is based for male characteristics (deep voice, facial hair,
on four -ring network, consisting of 3 general physical constitution) during puberty.
cyclohexane rings and 1 cyclopentane ring. Synthetic testosterone analogs are used in
The steroid nucleus is found in some vitamins, medicine to promote muscle and tissue growth,
drugs and bile acids also. The steroids nucleus for example, in pateints with muscular atrophy.
and a few sex hormones are given in Fig. 17.20. Unfortunately, such steroids are also abused
and consumed illegally, most commonly by body
builders and athletes, even though health risks
are numerous. Estradiol is the main female sex
hormone. It is responsible for development of
secondary female characteristics and
participates in the control of the menstrual cycle.
Progesterone is responsible for preparing the
uterus for implantation of the fertilized egg.
Many steroid hormones, for example,
progesterone itself, have played important role
as birth control agents.
2. Corticosteroids (Adrenal cortical
hormones):
(a)Mineralo corticoids, made by different cells in
the adrenal cortex are concerned with water-
salt balance in the body. These regulate NaCl
content of blood and cause excretion of
Fig. 17.20 Structure of few sex hormones potassium in urine.
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(b) Glucocorticoids, made by adrenal cortex, 17.7 VITAMINS

modify certain metabolic reactions and have an Vitamins can be defined as essential dietary
anti-inflammatory effect. factors required by an organism in minute
II.Functions of non-steroid hormones: quantities and their absence causes specific
deficiency diseases. Vitamins are essential for
1. Peptide hormones : Insulin has a profound life and a steady supply of these is required in
influence on carbohydrate metabolism. It food since the organism cannot synthesise many
facilitates entry of glucose and others sugars of these compounds. Plants can synthesise
into the cells, by increasing penetration of cell almost all vitamins whereas only a few are
membranes and augmenting phosphorylation of synthesized in animals. Vitamin D may be
glucose. This decreases glucose concentration supplied through food or may be produced in the
in blood and therefore insulin is commonly skin by irradiation of sterols with sunlight
known as hypoglycemic factor. It promotes (ultraviolet light). Human body can synthesise
anabolic processes and inhibits catabolic ones. vitamin A from carotene and some members of
Its deficiency in human beings causes diabetes vitamins B complex and vitamin K are
mellitus. Insulin isolated from islets of synthesised by microorganisms present in
Langerhans or islet tissue of pancreas was the intestinal tract.
first hormone to be recognized as protein. Sanger
got Nobel prize in 1958 for determining the Vitamins are widely distributed in nature both
structure of insulin (Fig. 17.21). in plants and animals. All cells in the body can

Gly Ile Tyr Gln Leu

Val
Glu
S S Leu Glu
Ser Asn
Gln Tyr
Cys Cys Cys
Cys Asn
Val S
S Ala Ser 21

S
Glu Arg Gly Phe Phe
S Cys Gly Tyr
Val Thr
Cys Leu
1 Phe Val Tyr Pro
Asn Gln His Leu
Gly Leu Lys
Ala
Glu Ala
Ser
Val
His Leu 30

Fig 17.21 Bovine insulin hormone structure has two polypeptide chains with 21 and 30 amino acids. They
are joined by sulfur bridges connecting cysteine amino-acid groups on the two chains.

2. Amino acid derivatives: The thyroidal store vitamins to some extent. However, most of
hormones e.g. thyroxin and triiodothyronine the vitamins have been synthesised and are
affect the general metabolism, regardless of the available commercially. These are effective when
nature of their specific activity. It is for this taken orally. Vitamins have varied chemical
reason why thyroid gland is known as pace setter structures.
of the endocrine system.
Vitamins are designated by alphabets A, B,
Based on the site of activity in the cell,
C, D, E, etc., in order of their discovery. Further
hormones may be divided into two categories.
any subgroup of individual vitamins is
Hormones in the first category affect the
designated by the number subscript e.g.A1, A2 ,
properties of the plasma membranes. These
B1, B2, B6, B12, D1, D2, etc.
include all peptide hormones e.g., insulin and
hormones of pituitary gland. In the other 17.7.1 Classification of Vitamins
category, hormones are taken into the cell and
transported to the nucleus where they influence Vitamins are generally classified into two broad
the nature and rate of gene expression. types based on their solubility, i.e., fat soluble
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BIOMOLECULES

and water-soluble. However, these two groups requirement of any vitamin for any individual
discharge different functions. is extremely small. However, the daily dose of
any vitamin for any individual is not a fixed
A. Fat soluble vitamins
quantity and varies according to the size, age
These are oily substances not readily soluble in and rate of metabolism of the individual.
water. The group includes vitamins A, D, E and Youngsters need higher quantity of vitamins
K. Liver cells are rich in fat soluble vitamins than elders and their requirement increases
e.g. Vitamin A and Vitamin D. This group of when a person performs exercise. The need
hydrophobic, lipid soluble vitamins as a class of growing children and pregnant mothers
are not absorbed in the body unless fat digestion for vitamins is more. The intestinal organisms
and absorption proceed nor mally. Their may synthesize vitamins in significant
deficiency can cause malabsorptive disease. amounts and play an important role in
Excess intake of these vitamins may cause regulating the quantity of vitamins available
hypervitaminoses. to the organism. Most of the vitamins of B-
complex group and vitamin K are some
B. Water soluble vitamins
vitamins synthesized by the intestinal
This group includes the remaining vitamins e.g., organisms. These may be absorbed in variable
vitamins of B group (B-Complex), vitamin C, etc. amounts and utilized.
The water soluble vitamins are stored in much A lack of one or more vitamins leads to
lesser amounts in the cells. Vitamin H (Biotin) characteristic deficiency symptoms in man.
is an exeption, since it is neither soluble in water Multiple deficiencies caused by lack of more than
nor in fat. one vitamin are more common in human beings.
This condition of vitamin deficiency is known
17.2.2 Physiological Functions of Vitamins
as avitaminosis. In Table 17.3 some important
Vitamins catalyze biological reactions in very vitamins have been tabulated along with their
low concentration, therefore the daily sources and deficiency diseases.

Table 17.3

S No. Name of vitamin Source Deficiency disease

1 Vitamin A (bright Fish oil particularly shark liver Xerophthalmia i.e hardening of cornea
eye vitamin) oil, liver of fresh water fish of eye
rice polishing, liver, kidney.
2 Vitamin B1 (thiamin) Yeast, milk, green vegetables etc Beri-beri (a disease of nervous system)
3 Vitamin B2 Yeast, vegetables, milk, egg white Dark red tongue (glossitis), dermatitis and
(riboflavin) liver and kidney cheilosis (fissuring at corners of mouth
and lips)
4 Vitamin B6 Cereal, grams, molasses, yeast, Severe dermatitis, convulsions
(pyridoxine) egg yolk and meat
5 Vitamin H ( Biotin) Yeast, liver, kidney and milk Dermatitis, loss of hair and paralysis
6 Vitamin B12 Liver of ox, sheep, pig, fish etc. Pernicious anaemia
7 Vitamin C Citrus fruits, green vegetables Scurvy
8 Vitamin E Wheat germ oil, cotton seed oil Sterility
and soybean oil
9 Vitamin K Cereals, leafy vegetable Hemorrhagic conditions
10 Coenzyme Q10 Chloroplasts of green plants and Low order of immunity of body against
mitochondria of animals many diseases
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SUMMARY

The biochemical reactions like chemical reactions follow the laws of chemistry and physics.
The energy obtained during oxidation of food, is coupled to the reaction leading to formation
of ATP (adenine triphosphate). Many biomolecules e.g., carbohydrates, proteins, nucleic
acids, lipids, hormones and vitamins play a significant role in nature’s energy cycle.
Amongst carbohydrates glucose is the most important naturally occurring sugar, which
plays a key role in release of energy. Proteins, the biopolymers of amino acids are essential
for life. As enzymes, these catalyze biochemical reactions, as hormones they regulate
metabolic processes and as antibodies these protect the body against toxic substances.
All proteins on partial hydrolysis give peptides of varying molecular masses and on complete
hydrolysis yield amino acids. The protein structure is studied at different levels, the
sequence of amino acids in polypeptide chains present in proteins constitutes it’s primary
structure. The study of the shape in which the polypeptide chains exist refers to its
secondary structure. The complete 3-D form (conformation) of polypeptide chains along
with other non-ordered segments is the tertiary/quaternary structure of proteins. Enzymes
are proteins which are highly specific in biocatalysis.
Nucleic acids, DNA and RNA are polymers of nucleotides. DNA has double helical
structure while RNA is single stranded. DNA stores the genetic information in the form of
the sequence of bases. The process in which duplication of DNA takes place during cell
division is known as replication. During replication the genetic message is passed on to
the daughter nuclei. One strand of DNA acts as a template on which a complementary
strand of RNA is synthesized. This process is called transcription. The newly formed RNA
dictates the synthesis of protein at the ribosome. This process is known as translation.
The sequence of three nucleotides on a polynucleotide chain is known as codon. There
are 64 codons, each specific for one amino acid.
Lipids are fatty acid derivatives e.g., fats, oils, waxes etc., which are important
constituents of diet. Fats are stored in adipose tissue of body as food reserve for spare
energy. Phospholipids and lipoproteins are important constituents of cell membrane.
Hormones are biomolecules produced by endocrine (ductless) glands of the body. These
transfer information from one group of cells to a distant organ or tissue and thus control
the metabolism. Vitamins are essential components of diet. Their deficiency causes specific
diseases.

EXERCISES

17.1 What are the two stages of photosynthesis in a green plant? Give the basic equation
of photosynthesis.
17.2 What are reducing and non-reducing sugars? What is the structural feature
characterizing reducing sugars?
17.3 Draw open chain structure of aldopentose and aldohexose. How many asymmetric
carbons are present in each?
17.4 Draw simple Fischer projections of D- and L-glucose. Are these enantiomers?
17.5 Draw Fisher projections of L- galactose and L- mannose.
17.6 Write down the structures and names of the products obtained when D-glucose
is treated with (i) acetic anhydride (ii) hydrocyanic acid (iii) bromine (iv) conc.HNO3
and (v) HI
17.7 Enumerate the reactions of glucose which can not be explained by its open chain
structure.
17.8 Explain mutarotation. Give its mechanism in case of D-glucose.
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BIOMOLECULES

17.9 Amylose and cellulose are both straight chain polysaccharides containing only
D-glucose units. What is the structural difference between the two?
17.10 What are essential and nonessential amino acids? Give two examples of each.
Give reasons for the following,
(i) Amino acids have relatively higher melting point as compared to corresponding
halo acids
(ii) Amino acids are amphoteric in behaviour
(iii) On electrolysis in acidic solution amino acids migrate towards cathode while
in alkaline solution these migrate towards anode.
(iv) the monoamino monocarboxylic acids have two pK values
17.12 If three amino acids viz., glycine, alanine and phenylalanine react together, how
many possible tripeptides can be formed? Write down the structures and names
of each one. Also write their names using three and one letter abbreviations for
each amino acid.
17.13 What type of linkages are responsible for the formation of,
(i) Primary structure of proteins
(ii) Cross linking of polypeptide chains
(iii) α- Helix formation
(iv) β- Sheet structure
17.14 Which forces are responsible for the stability of α-helix? Why is it named as 3.613
helix?
17.15 What is denaturation and renaturation of proteins?
17.16 Define enzymes. How do enzymes differ from ordinary chemical catalysts?
Comment on the specificity of enzyme action. What is the most important reason
for their specificity?
17.17 What are the products obtained on complete hydrolysis of DNA? Write down the
structure of pyrimidine and purine bases present in DNA.
17.18 Enumerate the structural differences between DNA and RNA. Write down the
structure of a nucleoside, which is present only in RNA.
17.19 What are complementary bases? Draw structure to show hydrogen bonding
between adenine and thymine and between guanine and cytosine.
17.20 What is the melting temperature (Tm) of DNA? A DNA molecule with more number
of GC base pairs than AT base pairs has higher Tm than the one with lesser
number of GC base pairs than AT base pairs. Explain why?
17.21 When RNA is hydrolyzed there is no relationship among the quantities of four bases
obtained unlike DNA. What does this fact indicate about the structure of RNA?
17.22 How does DNA replicate? Give the mechanism of replication. How is the process
responsible for preservation of heredity?
17.23 Genetic code is degenerate. Comment.
17.24 Answer the following about protein synthesis,
(i) Name the location where protein synthesis occurs.
(ii) How do 64 codons code for only 20 amino acids?
(iii) During translation which one of the two-end functional groups of the
polypeptide is formed first?
(iv) Which of the two bases of the codon are most important for coding, the first
two or last two?
17.25 How are lipids classified? Give an example of each class.
17.26 An unsaturated fatty acid having formula C17H33COOH has a double bond at
C-9. Amongst two stereoisomers of the acids i.e. cis and trans, which do you
expect to have higher m.p.? Explain why?
17.27 ‘Hormones are chemical messengers’. Explain.
17.28 Comment briefly on the chemical nature of insulin and its physiological activity.
17.29 Define and classify vitamins. Give at least two examples of each type.
17.30 Name the deficiency diseases caused due to lack of vitamin A, C, E, B1, B12 B6,
and K.