LECTURE NOTES

Session : 2014-15

ORGANIC CHEMISTRY
TOPIC : BIOMOLECULES & POLYMERS

JEE(Advanced) Biomolecules & Polymers # 1

 CARBOHYDRATE (Molecules of Support and Energy)
1. Concept

Old Concept :
The compounds in which carbon forms hydrate, is called carbohydrate.
Eg. : Cn(H2O)n ; n  3, 4, 5, 6, 7
If n  1 ; CH2=O (Formaldehyde)
n  2 ; CH3COOH (Acetic acid)
n  3 ; then Glyceraldehyde (Carbohydrate) ; CH3CH(OH)COOH (Lactic acid) is not carbohydrate.

Modern Concept :
(i) These are polyhydroxy aldehydes and ketones or any substances that hydrolysed to yield polyhydroxy
aldehydes and ketones.
(ii) These carbonyl group is not present in the free form but exists in combination with one of the hydroxyl
group of the molecule in the form of hemiacetals or hemiketals.

OH
Carbonyl
sp2 * H
carbon
Eg.1 : CH2–CH2–CH2–CH O O
OH

(Because its similarity with furan) O

OH
Carbonyl
2
sp * H
carbon
Eg.2 : CH2–CH2–CH2–CH2–CH O O
OH

(Because its similarity with Pyran) O

Note : 5/6 membered cyclic hemiacetal/hemiketal are stable.

2. Classification of Carbohydrate
Carbohydrates are classified on the basis of --------.
(A) Classification on the basis of number of hydrolysed products
(i) Monosaccharide : A carbohydrate that can not be hydrolyzed to simpler compounds is called
monosaccharide. e.g. : Glyceraldehyde, Erythrose, Threose, Ribose, 2-Deoxyribose, Glucose, Mannose,
Allose, Galectose, Fructose etc.
(ii) Oligosaccharides : Carbohydrates that yield two to ten monosaccharide units, on hydrolysis, are
called oligosaccharides. They are further classified as disaccharides, trisaccharides, tetrasaccharides,
etc., depending upon the number of monosaccharides, they provide on hydrolysis. Amongst these the
most common are disaccharides. The two monosaccharides units obtained on hydrolysis on a
disaccharide may be same or different. For example, sucrose on hydrolysis gives one molecule each of
glucose and fructose whereas maltose gives two molecules of glucose only.
(iii) Polysaccharide : A carbohydrate that can be hydrolyzed to many monosaccharide molecules is called
a polysaccharide. Example : Starch, Glycogen, Cellulose, Gums, Resins etc.

JEE(Advanced) Biomolecules & Polymers # 2

(B) Classification on the basis of Reducing and non Reducing properties :
(I) Reducing sugars (II) Non Reducing sugars
1. Reduces Tollen’s reagent, Fehling’s solution Don’t reduce Tollen’s Fehling’s &
& Benedicts’s solution. Benedict’s solution.
2. Should have atleast one hemiacetal or Should have acetal linkage.
hemiketal functional group.
Ex. All mono and oligosaccharides Ex. All polysaccharides and
except Sucrose few oligosaccharides (Ex. Sucrose)

O OH O O–R

R R
Hemiacetal Acetal

(C) Classification on the basis of Functional groups

(I) Aldoses (II) Ketoses
1. If aldehyde is present. If Ketone is present.

CH2OH
CH=O
C=O
(CHOH)n
2. (CHOH)3
CH2OH
CH2OH
n = 1 ; Aldotrioses n = 0 ; Ketotrioses
eg. Glyceraldehyde
n = 2 ; Aldotetroses n = 1 ; Ketotetroses
eg. Erythrose & Threose
n = 3 ; Aldopentoses n = 2 ; Ketopentoses
eg. Ribose & 2-Deoxyribose
n = 4 ; Aldohexoses n = 3 ; Ketohexoses
eg. Glucose, Mannose, Allose eg. fructose
& Galactose etc.
Note :
1. Number of carbons in sugars are generally 3-7.
2. Simplest aldoses is Glyceraldehyde and Ketoses is Dihydroxyacetone.

CH=O CH2OH
H OH C=O
CH2OH CH2OH
(D-Glyceraldehyde) (Dihydroxyacetone)

3. Most naturally occuring monosacharides are :

(a) Pentoses eg. D-Ribose (present in RNA) and 2-Deoxyribose (present in DNA)
(b) Hexoses eg. D-Glucose, D-Mannose, D-Allose, D-Galactose and D-Fructose

CH=O CH=O
H OH H H
H OH H OH
H OH H OH
CH2OH CH2OH
(D-Ribose) (D-2-Deoxyribose)

JEE(Advanced) Biomolecules & Polymers # 3

 CH 2 – OH
|
CHO CHO CHO CHO C=O
|
H OH HO H H OH H OH HO – C – H
HO H HO H H OH HO H |
H – C – OH
H OH H OH H OH HO H |
H OH H – C – OH
H OH H OH H OH
|
CH2OH CH2OH CH2OH CH2OH CH 2 – OH
D(+)-glucose D(+)-mannose D(+)-allose D(+)-galactose D-Fructose
C2-Epimer C3-Epimer C4-Epimer

Epimers : Such diastereomers in which there will be change of configuration at only one asymmetric
centre (chirality centre) are called epimers, and the carbon atom where they differ is generally stated. If
number of carbon is not specified it is assumed to be C2.
D-Glucose and D-mannose are epimers (Change in configuration at C2 atom only).
Erythrose and Threose (Aldotetroses) are also C2 epimers.

3. Monosacharides (eg. Glucose, Fructose)

(a) Glucose : Glucose is the most common monosaccharide. It is known as Dextrose because it occurs
in nature principally as the optically active dextrorotatory isomers. It is act as a reducing agent (reduces both
Fehling’s solution and ammonical silver nitrate solution ; Tollen’s reagent). It is known as dextrose and
found as grapes, honey, cane sugar, starch and cellulose.

(b) Fructose : Also said to be fruit sugar

(1) It occur both in combined as well as in free state.
(2) Fructose is named as fruit sugar because it is present in honey and most sweet fruit in free state.
(3) It is sweetest monosaccharide and present in cane sugar and insulin in combined state.
(4) It is also known as -Laevulose i.e. natural occurring compound is laevorotatory

(c) Preparation :
(i) By acid hydrolysis of canes sugar (a disaccharide) :
H O / H
C12H22O11 2  C6H12O6 + C6H12O6
Disaccharides -glucose -fructose
Sucrose

(ii) By enzymatic action over starch :

Diastase Maltase
Starch   Maltose    Glucose
Polysaccharides Disaccharides Monosaccharides
(C6H10O5)n (C12H22O11) (C6H12O6)

(d) Properties :
Glucose Fructose
(1) It is white crystalline solids having melting (1) It is colourless crystalline solid.
point 146ºC. It is readily soluble in water.
(2) Glucose is sweet in taste and also (2) It is soluble in water but insoluble in
optically active (dextro rotatory). ether, ketone and benzene.
(3) Glucose shows mutarotation. (3) It is pentahydroxy ketone and shows
mutarotation like glucose.

JEE(Advanced) Biomolecules & Polymers # 4

(e) Structure of monosacceharides :
Open chain structure (Fisher projection) and Cyclic structure (Haworth projection) :
Open chain structure of glucose explained most of its properties but the following reactions and facts could
not be explained by this structure.
1. Despite having the aldehyde group, glucose does not give 2,4-DNP test, Schiff’s test and it does not form
the hydrogensulphite addition product with NaHSO3.
2. The pentaacetate of glucose does not react with hydroxylamine indicating the absence of free-CHO group.
3. Glocose is found to exist in two different crystalline forms which are named as , and . The -form of
glucose (m.p. 419 K) is obtained by crystallisation from concentrated solution of glucose at 303 K while the
-form (m.p. 423 K) is obtained by crystallisation from hot and saturated aqueous solution at 371 K.
This behaviour could not be explained by the open chain structure for glucose. It was proposed that one of
the -OH groups may add to the -CO group and form a cyclic hemiacetal structure.
4. In solution, cyclic hemiacetal exists as an equilibrium mixture with open-chain form.
5. Aldohexose such as glucose can form cyclic hemiacetals containing either five membered or six membered
rings. For most common aldohexoses, the equilibrium favours six membered rings with a hemiacetal linkage
between the aldehyde carbon and the hydroxyl group on C5. In aldoses hemiacetals has a new chiral carbon
atom at C1 and in ketoses at C2. So two form of sugars are present in nature i.e.  &  which is represented
by Haworth projection however open chain is represented by Fischer projection.

H OH HO H
H || O
|

C
H OH H OH H OH
HO H H O
HO HO H O
H
+
OH
H OH H OH
H OH
H H
CH2OH

D-Glucose CH2OH CH2OH

Specific rotation (+52.7º) alfa-D-glucose
beta-D-glucose
Specific rotation (+112º)
Specific rotation (+19º)

Haworth projection

anomeric anomeric
6 CH2OH carbon carbon
6 CH2OH
H 5
O O
H H 5 OH
4 H H 1 4 H
OH OH OH H 1
HO H
2 HO
3 3 2
H OH H OH
Specific rotation (112º) Specific rotation (19º)
alfa-D-glucose beta-D-glucose
alfa-D-glucopyronose beta-D-glucopyranose

and-Glucose are anomer’s of each other (i.e change in configuration of 1st carbon atom only)

JEE(Advanced) Biomolecules & Polymers # 5

 +

D-fructose -D-fructose -D-fructose

Specific Rotation (– 92º) Specific Rotation (– 21º) Specific Rotation (– 133º)
Haworth projection : Fructofuranose

anomeric anomeric
carbon carbon
6 CH2OH
6 CH2OH
O O OH
CH2OH
5
5 H HO 2 CH2OH
H HO 2 OH H
H 4 3
4 3
OH H
OH H
Specific rotation (-21º) Specific rotation (-133º)
alfa-fructose beta-fructose
alfa-fructofuranose beta-fructofuranose

Note: Anomers : Anomer’s are those diastereoisomers having change in the configuration at the Hemiacetal/
acetal carbon atom only. eg. C1 of Aldoses and C2 of Ketoses.and-Glucose are anomer’s of each other
(i.e change in configuration of 1st carbon atom only). The hemiacetal carbon is called anomeric carbon. In
anomers, anomeric hydroxyl group and terminal –CH2OH group are trans in -and cis to each other in .
4. Properties of Anomers : Mutarotation
When one of the pure glucose anomers dissolve in water, an intersting change in the specific rotation is
observed. When the -anomer dissolves, its specific rotation gradually decreases from an initial value of
+112º to +52.7º. When the pure  anomer dissolves, its specific rotation gradually increases from +19º to the
same value of +52.7º. This change (mutation) in the specific rotation is called mutarotation. What is
happening is that each solution, initially containing only one anomeric form, undergoes equilibrium to the
same mixture of -and -forms. The open chain forms is in intermediate in the process.
For mutarotation atleast one hemiacetal group must be present in the sugar therefore all reducing sugars will
mutarotate.

anomeric anomeric
6 CH2OH carbon 6 CH2OH 6 CH2OH carbon
H 5
O H OH H O
H 5 5 OH
4 H H CHO H
OH H 1 4 H 4 H 1
OH OH OH H
HO HO HO
3 2 3 2 3 2
H OH H OH H OH
Open chain form Specific rotation (19º)
Specific rotation (112º)
of -D-glucose beta-D-glucose
alfa-D-glucose
alfa specific (+ 52.7º) beta-D-glucopyranose
alfa-D-glucopyronose

JEE(Advanced) Biomolecules & Polymers # 6

5. Chemical Reactions of Anomers (Glucose)
(1) Reaction due to OH group :
6CH2OCOCH3
Pyridine
+ OCOCH3
CH3COCl (Acylation)
OAc
(A) AcO
or
(CH3CO)2O OCOCH3
Glucose penta acetates
6CH2OCH3 1 CH=O
2
(B) (1) Na/NaH/NaNH2/Pyridine OCH3 H OCH3
3
2
H3CO H
(2) CH3–Br(SN ) OCH3 4
H3CO H OCH3
5
OCH3 H OH
6
Pentamethylderivative CH2OCH3
( glucopyranose) 6 CH2OH
6 CH2OH
O
CH3OH/H+ H 5
H H 5
O
(C) 4 H OMe
OH H 1 OMe + 4 H
HO OH H 1 H (Formation of Acetal)
3 2 HO Non reducing sugars
3 2
H OH
H OH

or methyl D-glucopyranoside
Note : (A) Acylation with acid halide or acetic anhydride gives pentaacetates which confirms the presence of five –
OH groups.
(B) After Hydrolysis product of pentamethyle derivatives, aldehyde group and hydroxy of C5 regenerated
hence hydroxy of C5 is involved in the hemiacetal formation.
(C) (i) Sugars in the form of acetals are called glycosides. (glucose  glucoside, mannose  mannoside,
ribose  riboside, fructose  fructoside etc).
(ii) In the formation of glycosides only one mole of alcohol is required so monosacchardies are already
present in the hemiacetal form with one of the hydroxyl group and carbonyl group.
(iii) Glycosides are known reducing and will not show mutarotation because in neutral are basic condition
glycosides are stable (cyclic form cannot open to the free carbonyl compound).
(iv) After acidic hydrolysis of glycosides product form will have reducing property and also show
mutarotation.
(2) Reaction due to aldehyde :
In aquous solution, -Anomer or -Anomer remains in the equilibrium with each other by small amount of
open chain forms (0.02%), in which carbonyl group is regenerated & gives various reactions.

CN
*CH–OH Glucocyanohydrin
HCN
(1) (C2 Epimer)
(CHOH)4
CHO CH2OH
CHOH
CHOH CH=N–OH
(2) H2NOH
CHOH (CHOH)4 (Gluco oxime)
–H2O
CHOH CH2OH
CH2OH
(+)–Glucose CH=N–NH–Ph
H2NNHPh
(3) (CHOH)4 (Gluco phenylhydrozone)
–H2O
CH2OH

JEE(Advanced) Biomolecules & Polymers # 7

 3
(4) (Gluco Osazone)
–H2O, –NH3
–PhNH2

NaHSO3
(5) No reaction

D.N.P.
(6) No reaction

Schiff’s reagent
(7) No reaction

(8)

NH4OH + AgNO3 or
(9) Ag O aq. or COO
–
2
(Tollen’s reagent)
Ag(NH3)+
2 OH¯
(CHOH)4 + Ag
(Silver mirror)
CH2OH

(10)
NaOH + CuSO4 COO
–
(Fehling’s solution)
+ Na/K Tartrate
(11) (CHOH)4 + Cu2O (Cuprous oxide)
NaOH + CuSO4 (Red precipitate)
(Benedict’s solution) CH2OH
+ Na/K Citrate

(12)

(13)

(14)

(15) Red P + HI
n-Hexane

JEE(Advanced) Biomolecules & Polymers # 8

Chemical Reactions of furctose :
Due to OH group at 2nd carbon :
(1) It froms fructose pentaacetate with acetyl chloride :

Pyridine OAc
+ OAc
(1)
AcO OAc

OAc
Fructopentaacetate

D-fructose
( D-fructofuranose) (2) Methyl -D-fructofuranoside

(2) Reaction due to keto group :

HCN
(1) Fructose cyanohydrin

H2NOH
(2) Fructo oxime

H2NNHPh
(3) Fructose phenylhydrazone

H2NNHPh(3 mole)
(4) Osazone

NaHSO3
(5) –ve
CH2–OH
DNP
C=O (6) –ve
HO H
(7) Schiff's reagent
H OH –ve
H OH
Br2 + H2O
CH2OH (8) –ve
D-(+)-fructose
(Ketoses) COO–
Tollen's reagnet
(9) (CHOH)4 + Ag
(Silver mirror)
CH2OH
(10)
NaOH + CuSO4 COO–
(Fehling’s solution)
+ Na/K Tartrate
(11) (CHOH)4 + Cu2O (Cuprous oxide)
NaOH + CuSO4 (Red precipitate)
(Benedict’s solution) CH2OH
+ Na/K Citrate
COOH

HNO3 C=O
(12)
(CHOH)3
COOH
HIO4
(13) 2HCH=O + 3HCOOH + CO2 + H2O

H2 + Ni
(14)
or Na–Hg + H2O +
or NaBH4 or LiAlH4

Sorbitol Mennitol

(15) Red P + HI n-Hexane

JEE(Advanced) Biomolecules & Polymers # 9

Note :
1. Since glucose & fructose (Aldoses/Ketoses) reacts with HCN, H2N–OH, H2NNHPh so carbonyl group is
present but they don’t react with DNP, NaHSO3 & Schiff’s reagent (weak reagents) so carbonyl group is not
free, but remains in the form of cyclic structures.
2. In the formation of osazone, C1 & C2 are only involved so glucose & fructose, C-2 epimers (Glucose &
Mannose, Threose and Erythrose) give same osazone.
Osazone are crystalline solid having sharp melting point so used for identifying the carbohydrates.
In the osazone formation, two molecules of H2NNHPh react by different mechanism & one molecule of
H2NNHPh react by different mechanism.

+ H2N.NH.Ph (1 mol)  
H 2 O

H NNHPh( 2 mol )
2   
– NH3
– H 2O

3. We can not identified aldoses and ketoses with Tollen’s reagent, Fehling’s solution & Benedict’s solution
because in the basic medium, ketoses remains in the form of dynamic equilibrium with Aldoses (C-2 epimers)
by the process of tautomerisation/enediol rearrangement, also called Lobry de Bruyn Van Ekenstien
trans-formation.
Action of alkali with aldoses & Ketoses

D-fructose D-Glucose D-Mannose

4. Only Br2–H2O is used for the identification of Aldoses & Ketoses. (Mild oxidising agent like bromine water
(Neutral) Oxidises only aldehydic group).
5. Oxidation product with HNO3, gives information that one primary alcohol is present in aldoses and two
primary alcohols are present in ketoses.
6. Reduction product with Na–Hg + H2O gives only one alcohol with aldoses and two alcohols with ketoses
(C-2 epimers)
7. Reduction product with Red P & HI, gives n-Hexane which indicates that all the six carbon atoms are linearly
arranged.

JEE(Advanced) Biomolecules & Polymers # 10

Some more reactions :
Chain lengthing :

Chain shortening :
COOH
|
Br2 / H2O CHOH Ca salt
   |   2
H2O 2 / Fe 
(CHOH)3
|
CH2OH

Disacharides
(condensation of two monosacharides after loss of water molecule
(Glycosidic bond), gives disacharides)

H3O
(a) Sucrose (Cane sugar)   -glucose + -fructose
Formation of sucrose (C12H22O11)
–D-glucose + -D-fructose
C1 C2
Pyranose form Furanose form

HO
2

(i) Sucrose is a white crystalline solid, soluble in water.

(ii) When heated above its melting point, it forms a brown substance known as caramel.
(iii) Sucrose is dextrorotatory, its specific rotation being + 66.5°.
(iv) On hydrolysis with dilute acids sucrose yields an equimolecular mixture of D(+)-glucose and
D(–)-fructose :
HCl
C12H22O11 + H2O  C 6H12 O 6 + C 6H12O 6
D  glucos e D  fructose
[] = + 66.6° [] = + 52.7° [] = – 92.2°

JEE(Advanced) Biomolecules & Polymers # 11

 Since D(–)-fructose has a greater specific rotation than D(+)-glucose, the resulting mixture is laevorotatory.
Because of this, hydrolysis of cane-sugar is known as the inversion of cane-sugar or Inversion of sucrose
(this is not to be confused with the Walden inversion), and the mixture of sugars are known as invert sugar
Ex. D - Glucose & D-Fructose. The inversion (i.e., hydrolysis) of cane-sugar may also be effected by the
enzyme invertase which is found in yeast.
(v) Sucrose is not a reducing sugar, e.g., it will not reduce Fehling’s solution or Tollen’s reagnet. It does not
form an oxime or an osazone, and does not undergo mutarotation. This indicates that hemiacetal group is
not present in the rings.

(b) Maltose (Malt sugar)  H3O
 -glucose + -glucose
Formation of Maltose (C12H22O11)
–D-Glucose + -D-Glucose
C1 C4
Pyranose form Pyranose form

CH2OH CH2OH
O O
H H H H
– H2O H H
 1 4
OH H O OH H
HO OH

H OH H OH
Glycosidic bond
between C1 & C4
Non Reducing Reducing
Ring Ring

Maltose (malt sugar), C12H22O11, is produced by the action of malt (which contains the enzyme diastase)
on starch :

C12H22O11   2C2H12O6 -D-Glucose
H3O

When it is hydrolysed with dilute acids or by the enzyme maltase, maltose yields two molecules of
D (+)-glucose. Maltose is a reducing sugar, e.g., it reduces Fehling’s solution or Tollen’s reagent ; it forms an
oxime and an osazone, and undergoes mutarotation. This indicates that at least one hemiacetal group (of
the two glucose molecules) is free in maltose.

(c) Lactose (Milk sugar)   -galactose + -glucose
H3O

Formation of Lactose (C12H22O11)

–D-Galactose + -D-Glucose
C1 C4
Pyranose form Pyranose form

CH2OH H OH CH2OH H OH
O OH H O
HO H HO H
H OH H O
H OH H
+  1 4
OH H H OH H H
H H HO OH H OH
O H H O
H OH CH2OH H OH CH2OH
Glycosidic bond
between C1 & C4
Non Reducing Reducing
Ring Ring

JEE(Advanced) Biomolecules & Polymers # 12

 Lactose occurs in the milk of all animals and is dextrorotatory. It is hydrolysed by dilute acids or by the
enzyme lactase, to an equimolecular mixture of D(+)-glucose and D(+)-galactose. Lactose is a reducing
sugar.

(d) Cellubiose   -glucose + -glucose
H3O

–D-Glucose + -D-Glucose
C1 C4
Pyranose form Pyranose form


(e) Isomaltose 
H3 O
 -glucose + -glucose
–D-Glucose + -D-Glucose
C1 C6
Pyranose form Pyranose form

Polysacharides  Starch (Plant Storage, Polymer of D-glucose), Glycogen (Animal Storage,

Polymer of D-glucose), Cellulose (Plant Skeleton, Polymer of D-glucose)
It contains large number of monosaccharide units joined together by glycosidic linkage (acetal bond). They
are food storage or structural material.
Starch, (C6H10O5)n
Starch is the main contributor of carbohydrates in our diet. It exists exclusively in plants, stored in the seeds,
roots, and fibres as food reserve. Example rice, potato.
+
I2 H3O
Blue colour Starch n molecules of -D-glucose
Partial
Hydrolysis

Amylose Amylopectin

(i) 10 to 20 % part of starch (i) 80 to 90 % part of starch

(ii) H2 O soluble (ii) H2O insoluble
(iii) Blue colour with Iodine (iii) No blue colour with Iodine
(iv) Similar to amylose but in it chains are
branched after every 20-25 glucose units between
C1 & C6 of glucose units by glycosidice linkage
i.e. chain is formed by C1 – C4 glycosidic linkage and
branching occurs by C1 – C6 glycosidic linkage
(Natural branched polymer)
6 6
CH2OH CH2OH
5 O O
H H 5 H
H H H
4 1 4 1
OH H OH H
3 2 3 2 O
O
H OH H OH n
 (1  4) Glucosidic
linkage
Amylose

JEE(Advanced) Biomolecules & Polymers # 13

 6
Branch CH2 OH CH2 OH
O H H 5
O H
H H H
4 1
OH H OH H  (1  6)
......O 3 2 O
O branch point
H OH H OH
6
CH2 OH CH2 OH CH2
O O H H 5
O H
Main Chain H H
H H H
1 4 1
OH H OH H OH H
......O 3 2
O O O.........
H OH H OH H OH

Amylopectin  (1  4)

Glycogen (Animal Storage)

It is also like amylopectin but branching will take place after every 5 to 6 glucose unit. (highly branched)

Cellulose, (C6H10O5)n

6
CH2 OH
 (1   4)
H 5
O O
6 H
CH 2 OH 4 1
OH H
5 O 3 2
O H
H H
4 1 H OH
OH H
3 2 H
H OH n
Cellulose

1. Cellulose is linear chain natural polymers of -D glucose units joined by 1, 4-glycosidic linkage (Natural
linear polymers).

2. Cellulose is the main structural material of tree and other plants. Wood is 50% cellulose, while cotton
wool is almost pure cellulose.

3. Artificial silk, rayon, is used collectively to cover all synthetic or manufactured fibres from cellulose.

4. The nitrates are prepared by the reaction of cellulose with a mixture of nitric and sulphuric acids, and the
degree of ‘nitration’ depends on the concentrations of the acids and the time of the reaction. Cellulose
trinitrate (12.2 – 13.2%N) is known as gun-cotton and is used in the manufacture of blasting explosives
and smokeless powders.

JEE(Advanced) Biomolecules & Polymers # 14

 PROTIENS & AMINO ACIDS
Proteins : Proteins are the most abundant-biomolecules of the living beings. The chief source of proteins
are milk, cheese, pulses peanuts, fish meat etc. These are high molecular mass complex, biopolymers of
amino acids. They occur in every part of the body and form fundamental basis of structures and determine
functions of life. The word protein is derived from Greek word proteios which means primary or of prime
importance. Proteins are present in almost all the living cells of plant and animals. The protoplasm of plant
and animal cells contains IU 20% proteins. In human beings they are the main constituent of muscles, skin,
hair, nail, tendons, arteries and connective tissue.
Amino Acids : Each living cell is made up of thousands of different proteins All proteins contain the elements
like carbon, hydrogen, oxygen, nitrogen and sulphur. Some of these also contain phosphorus, iodine and
traces of metals such as, Fe, Cu, Zn, & Mn. All proteins are polymers of -amino acids and on partial
hydrolysis give peptides of varying molecular masses which upon complete hydrolysis give -amino acids.
Hydrolysis Hydrolysis
Proteins    Peptides    -amino acids
Type of -amino acids :

JEE(Advanced) Biomolecules & Polymers # 15

These organic compounds contain amino as well as carboxylic acid group. On the basis of position of amino
group in the chain, these are named as , ,  etc. amino acid.

Amino Acid : Building Blocks of Proteins

Amino acids are the building blocks of the molecular structure of the important and very complex class of
compounds known as proteins. The proteins on hydrolysis yield mixture of the component amino acids.
Amino acids are bifunctional compounds containing both an amino and a carboxylic acid group. They are
represented by the general formula :
H O
| ||
H2N  C  C  OH or H2N  CH  COOH where, R = alkyl, aryl, or any other group.

Amine |
  
Carboxylic
|
R Acid group R
Zwitter ion (Dipolar Nature of Amino acids) : ..
In a neutral amino acid solution, the –COOH loses a proton and the – NH2 of the same molecule picks up
one.The resulting ion is dipolar, charged but overall electrically neutral. This is called Zwitterion (German,
“two ions”). Therefore amino acids are amphoteric.
H O H O
| ||   | ||
H
H2N  C  C  OH  H3 N C  C  O ¯
|  H |
R R
Zwitter ion

There are around 20 amino acids in the living system.

Classification of Amino Acids :
(A) On the basis of synthesis :
(i) Non essential amino acids : 10 amino acids are synthesis in our body and these are said to be non
essential amino acids (eg. Gly, Ala, Glu, Asp, Pro and Cys).
(ii) Essential amino acid : 10 amino acids which are necessarily be present in our diet are called essential
amino acids (eg. Val, Leu, I leu, Lys and Phe).
(B) On the basis of functional groups present :
(i) Neutral amino acids : If only one – NH2 and one – COOH groups are present. eg. Glycine, Alanine,
Valine, Leucine etc.
(ii) Acidic amino acid : If one basic and two acidic groups are present. Additional acidic functional group
must be present in the side chain. E.g. Aspartic acid and Glutamic acid.
(iii) Base amino acid : If two basic and one acidic group is present. Additional basic group must be present
in the side chain. E.g. Arginine, Lysine & Histidine.

Isoelectric point of -amino acids :

When an ionised amino acid is placed in an electric field, it will actually migrate towards the opposite
electrode. Depending upon the pH of the medium, three things can happen. The positive form (II) will migrate
to the cathode, the neutral form (I) (Zwitter ion) will not migrate, while the negative form (III) will migrate to the
anode. The pH at which the amino acid shows no tendency to migrate when placed in an electric field is
known as its isoelectric point. This is characteristic of a given amino acid. Thus glycine has its isoelectric
point at pH 6.1.

H O H O
H O
| ||
 | || H  | || HO¯
H3 N C  C  OH   H3N  C  C  O ¯   H2 N C  C  O ¯
| pK a1 | pK a2 |
R R R
Zwitterion High pH (Basic soln .)
Low pH ( Acid soln. )
Neutral form (I) Anionic form (III)
Cationic form (II)

JEE(Advanced) Biomolecules & Polymers # 16

Isoelectric Point : The pH at which the amino acid shows no tendency to migrate when placed in an
electric field is known as its isoelectric point.
Because of amphoteric nature in acidic solution it exist as the +ve ion. Hence it migrate towards cathode
while in basic solution it exist as –ve ion and migrates towards anode.
At some intermediate pH amino acids exist as a neutral dipolar ion i.e. the concentration of the cation and
anions are equal and it does not migrate towards either electrode, this pH is called iso electric point of amino
acid which is different for different amino acids.
For example :
(i) For neutral amino acid : pH of isoelectric point varies between 5.1 to 6.5. e.g. Glycine has pH value 6.0.
pK a1  pK a2
PI for neutral amino acid is calculated as
2
(ii) For acidic amino acid : Where there are two COOH groups and one NH2 group then isoelectric pH is
around 3. e.g. Aspartic acid.
Aspartic acid :

pK a1  pK a2
PI for acidic amino acid is calculated as
2
The pI of aspartic acid is the average of pKa1 (1.88) and the pKa of the side chain (3.65) or 2.77.
(iii) For basic amino acid : where there are two NH2 groups and one COOH group then isoelectric point
varies between 7.6 to 10.8.
e.g. Lysine (9.8)
Lysine :

pK a2  pK a3
PI for basic amino acid is calculated as
2
The PI of lysine is the average of pKa2 (8.95) and the pKa of the side chain (10.53) or 9.74.
Note : Amino acid has minimum aqueous solubilities at their isoelectric points.

JEE(Advanced) Biomolecules & Polymers # 17

Informations about some amino acids are given in following table :

JEE(Advanced) Biomolecules & Polymers # 18

* Essential  -amino acids

(a) General methods of preparation

1. Aminolysis of -halocarboxylic acid
HO
CH3 CHCO 2H  2NH3 2
| excess
Br
2  Bromo propanic acid

2. By strecker synthesis : Aldehyde reacts with a mixture of NH4Cl and NaCN to form -aminonitrile (as an
intermediate) which on hydrolysis gives an amino carboxylic acid.
O
||
NH4Cl 1. H2O / HCl, 
CH3 CH   CH3 CHCN     
NaCN 2. OH ¯
|
NH2
2  a min opropaneni trile
3. From aceto acetic ester :

NaOC H
2 5 RX
 

 C2H5OH

hydrolysis
RCHCO 2H  reduction
   

|
NH2

JEE(Advanced) Biomolecules & Polymers # 19

4. By Gabriel Synthesis :

O
||
+ ClCH2COC 2H5 

ethyl   chloroacetate

O
||
H2NCH2COH +

glycine

(b) Chemical reactions :

1. Formaldehyde reacts with amino acids to form N-methylene amino acids. In this reaction basic character is
lost and thus, free acid can be determined by titration - Sorenson titration method for amino acids.

O O
|| ||
CH2O  H2NCH2COH  CH2  NCH2COH  H2O
N  methylene glycine

2. DNFB (2, 4-dinitrofluorobenzene) also called Sanger’s reagent reacts with the free amino group of terminal
amino acid in a peptide or protein to form yellow coloured dinitro phenyl amino acid. This is thus, used to
determine N-terminal amino acid.

H
|
R  C  NH2 + Na CO
2 3
  
 
|
COOH

3. Cu2+ salts form blue coloured complex with amino acids which is a bidentate legand.

O O
||

2CH2COH + Cu2+ 
|
NH 2

4. Effect of Heat :
-amino acids undergo intermolecular dehydration on heating at about 200°C to give diketopiperazines.


 + 2H2O

JEE(Advanced) Biomolecules & Polymers # 20

 -amino acids undergo intramolecular deamination on heating to form -unsaturated acids.




-amino acids and -amino acid undergo intramolecular dehyderation to form cyclic amides called.

CH2– CH 2
| | O 
Lactams. CH2 C 

NH–H OH
amino acid butyrolactam




In case of -amino acid, intramolecular cyclisation would given a seven-membered ring, which is formed with
difficulty. Hence, there is intermolecular polymerisation forming nylon-6.

nH2N(CH2)5COOH 

(c) Other Reactions of -Amino Acid :

Peptides bonds and Proteins :

Peptides (Proteins) : Peptides (Proteins) may be defined as condensation polymers of -amino acids
formed by condensation of amino group of one -amino acid with the carboxyl group of another molecule of
the same or differnet -amino acid by elimination of water.
They are classified as di, tri, tetra, pentapeptides etc. according as two, three, four, five etc molecules of the
same or different amino acid combine together. It determines their specific physiological functions in the
living organism.

JEE(Advanced) Biomolecules & Polymers # 21

 Structure of Proteins (Peptides)
Amino acids are bifunctional molecules with – NH2 group at one end and – COOH at the other. Therefore,
–COOH of one molecule and – NH2 of another molecule interact by elimination of H2O to form an amide-like
linkage.

Peptide Linkage : Amino acids are bifunctional molecules with – NH2 group at one end and – COOH at
the other. Therefore, –COOH of one molecule and – NH2 of another molecule interact by elimination of H2O to
form an amide-like linkage.
The amino acid unit having free – NH2 groups is called N-terminal end whereas the amino acid unit with free
– COOH group is called C-terminal end. The structure is written with N-terminal end to the left and C-terminal
end to the right. At N-terminal or C-terminal further bond formation take place and tri, tetra, pentapeptide are
R O
| ||
formed. – NH – CH – C unit repeated in polypeptides.
Polypepties : More than 10 aminoacids join together called polypeptides which is linear chain natural
polymer.
Naming of polypeptides :
Starting from –N–terminal residue.
Suffix -ine of amino acids is replaced by -yl for all except amino acid of C-terminal residue example :
Glycine  Glycyl, Alanine  Alanyl, Lysine  Lysyl
Alanylglycylphenylalanine means Ala-Gly-Phe or A-G-F.

Determining sequence of polypetides by partial hydrolysis :

Q.1 Tripeptides

Write the structure of tripeptide?

Ans. Gly-Ala–Val.

Q.2 Tripeptides

Write the structure of tripeptide?

Ans. Gly-Val-Lys.

JEE(Advanced) Biomolecules & Polymers # 22

Protiens : A polypeptide with more than 100 amino acid residues (mol. mass > 10,000) is called a protein
but polypeptide with fewer amino acid is also called proteins example insulin have 51 amino acids.

Classification of Proteins :
(I) On the basis of molecular structure : Proteins have been classified into two parts.
(i) Fibrous proteins (ii) Globular proteins
(i) Fibrous Proteins : When polypeptide chain run parallel and are held together by hydrogen and disulphide
bonds then fiberlike structure is formed such proteins are generally insoluble in water. Some common example
are keratin (present in hair wool, silk) and myosin (present in muscles) etc. These proteins are stable to
moderate change in temperature and pH.
(ii) Globular proteins : The polypeplide chain in these proteins is folded around it self to form spheroidal
shape. The folding takes place in such a manner that lipophilic (non-polar, fat soluble) parts are pushed
inwards and hydrophilic part (solar, water soluble) are pushed outwards. As a result water molecules interact
strongly with the polar groups and hence globular proteins are soluble in water. As compare to fibrous
proteins these are very sensitive to small changes in temperature and pH. Insulin, albumin, thyoglobulin,
antiadiodies, haemoglobin fibrinogen etc are the common examples of globular protein.
Differences between Globular and Fibrous Proteins
S.No. Globular Proteins Fibrous Proteins

They are cross-linked condensation

1 They are linear condensation products.
polymers of acidic and basic amino acids.

They are soluble in water of aqueous They are insoluble in common solvent but
2
solutions of acid bases of salts. soluble in acidic or basic solution.

They are folded to give rise in three The long linear protein chains are held
3
dimensional spheroidal shape. together by intermolecular H-bonds.

Examples : albumins in egg, enzyme and Examples : fibroin in silk ; collagen in

4
some hormones, etc. tendons ; myosin in muscles, etc.

(II) On the basis of chemical composition :

(i) Simple proteins : These proteins on hydrolysis give only -aminoacids. For example albumin in the
white portion of eggs, glutenin in wheat, oxygenin in rice, keratin in hair, nails horns etc.
(ii) Conjugated Proteins : These are the proteins in which protein part is combined with non-protein part.
These proteins on hydrolysis give a non protein in addition to the -amino acids. This non protein portion is
called PROSTHETIC GROUP. The main function of prosthetic group is to control the biological function of the
protein. Prothetic groups are carbohydrate, phophate group, lipids (ester of higher fatty acids) and so on.
Casein of milk, haemoglobin of blood are congugated proteins.
(iii) Derived Proteins : These are the degradation products obtained by partial hydrolysis of simple or
conjugated proteins with acids, alkalies or enzymes. For example, proteoses peptones, and polypeptides
Protein  Proteoses  Peptones  Polypeptides
Structure of Proteins :
Proteins are biopolymers obtained by condensation of large number of amino acids through peptide bonds
having three dimensional (3D) structures. Structure and shape of proteins can be studied at four different
levels i.e. primary, secondary, tertiary and quarternary, each level being more complex than the previous one.
(i) Primary structure of Proteins :
Proteins may have one or more polypeptide chains. Each polypeptide in a protein has amino acids linked
with each other in a specific sequence and it is this sequence of amino acids that is said to be the primary
structure of that protein. Any change in this primary structure i.e sequence of amino acids creates a different
proteins.

JEE(Advanced) Biomolecules & Polymers # 23

The first primary structure of a protein i.e INSULIN was determined by Frederic Sanger (a British chemist)
and for this work he was awarded the Nobel prize in 1958. The different chemical and biological properties of
various proteins are primarily due to the difference in their primary structures.
Normal Haemoglobin –Val – His – Leu – Thr – Pro – Glu –Lys–
Sickle cell anemia Val – His – Leu – Thr – Pro – Val – Lys–
(ii) Secondary structure of Proteins :
The conformation in which the polypeptides assume as a
result of hydrogen bonding is called the secondary
structure of proteins depending upon the size of R group.
The following two different secondary structure are
possible.

(a) -Helix structure

(b) -pleated sheet structure

(a) -Helix structure :

-Helix model was postulated by Linus Pauling in 1951

purely on theoretical grounds and was verified later on
experimentally. If the size of R-groups is quite large the
intramolecular bonds are formed between the C=O of one
amino acid and the N–H group of the forth amino acid
residue in the chain. This causes the polypeptide chain
to coil up into a spiral structure called right handed -
helix structure.

(b) -pleated sheet structure or simply -structure :

This structure was also proposed by Linus Pauling in 1951. In this conformation the polypeptide chains lie
side by side in a zig zag manner with alternate R groups on the same side situated at fixed distances apart.
The two such neighboring polypeptide chains are held together by interbounded to form a sheet. These
sheets are then stacked one above the other like the pages of a book to form a three dimensional structure.
This structure resembles pleated folds of drapery and hence is also called -pleated sheet structure.
The poly peptide chains can link together in parallel and antiparallel sequence. Such sheet like structure can
easily slip on each other. Proteins of this structure are soft. Keratin the protein present in hair has parallel
-pleated sheet structure while Silk has has anti parallel -pleated sheet structure. These are represented as
follows :-

JEE(Advanced) Biomolecules & Polymers # 24

(iii)Tertiary structure of proteins :
The tertiary structure of protein represent overall folding of the polypeptide chains i.e further folding of the
secondary structure. In other words, tertiary structure refers to the manner in which the entire protein molecule
folds up in the three dimensional space to produce a specific shape forming 3D structure. It gives rise to
two major molecular shapes fibrous and globular. The main forces which stabilise the 2º and 3º structures
of proteins are hydrogen bonds, disulphide linkages, vander waals and electrostatic forces of attraction.
(iv) Quarternary structure of proteins :
Although many proteins exist as a single polypeptide chain but there are certain proteins which are composed
of two or more polypeptide chains referred to as sub-units or protomoss. These subunits may be identical or
different and are held together by non-polar covalent forces such as, H-bonds, vanderwaals interaction and
electrostatic interactions. The quarternary structure refers to the determination of the number of sub-units
and their special arrangement w.r.t . each other in an aggregate protein molecule The Haemoglobin possesses
quarternary structure and it is an aggregate of four polypeptide chains or sub-units.
A diagramatic representation of all four structure is given below, each ball represent an amino acid.

Denaturation of proteins :
A protein found in a biological sytem having a unique three dimensional structure and specific biological
activity is called a native protein. When a protein in its native form is subjected to a physical change like
change in temperature or pH, the hydrogen bonds are disturbed. As a result-globules unfold and helices get
uncoiled and protein loses its biological activity. This is called Denaturation of proteins. During denaturation
2º and 3º structure are destroyed but 1º structure remain intact. The coagulation of egg white on boiling
and curdling of milk caused by the bacteria present in milk are common examples of denaturation of protein.

Renaturation of proteins :
The denaturation may be reversible or irreversible. The coagulation of egg white on boiling and curdling of
milk are an example of irreversible protein denaturation. There is some cases where the process in actually
reversible. The reverse process is called renaturation. In such cases when the temperature and pH of a
denatured protein are brought back, the secondary and tertiary structures of protein are restored.

Chemical Test :
(i) Biurate Test : CuSO4 + alkaline solution + Protein  Violet colour.
Biurate Test is for peptide linkage (Atleast two peptide linkage must be present ; Dipeptide do not give this
test).
(ii) Nin Hydrin Test : Blue or violet colour with Nin Hydrin.

*Molish Test is for carbohydrate.

JEE(Advanced) Biomolecules & Polymers # 25

 POLYMERS
These are very high molecular mass substances where each molecule is derived from very large number of
simple molecules joined together in a regular way. This simple molecule is monomer and the process of
formation of polymers from simple molecule is polymerization.
n CH2 = CH2  –[ CH2–CH2–]n
polyethene
Polymers are two types :
(i) Homopolymers :
Polymers in which repeating structural units are derived from only one type of monomer units are called
homopolymers.

Other examples of homopolymers are polypropylene, polyvinyl chloride (PVC), polyisoprene, neoprene
(polychloroprene) polyacrylonitrile (PAN), nylon-6, polybutadiene, teflon (polytetrafluoroethylene), cellulose,
starch, glycogen etc.
(ii) Copolymers :
Polymers in which repeating structural units are derived from two or more types of monomer units are called
copolymers.

Polymers can be classified by following ways :

(a) Classification based on source :

Polymer

Natural polymer Semi synthetic Synthetic polymer (man made)

e.g. protein (peptide linkage) Polymers e.g. Nylon–6,6 Dacron, PVC etc.
carbohydrate (glycosidic linkage) i.e. Cellulose derivatives
i.e. Starch, cellulose, resins and as cellulose acetate (rayon)
rubber and cellulose nitrate.

(b) Classification based on mode of Polymerisation :

JEE(Advanced) Biomolecules & Polymers # 26

 Exmples of addition polymers :
Formed by repeated unit of molecules having multiple bonds.

(1)

(2) Polyvinyl Chloride (PVC) :

It is obtained by polymerization of vinyl chloride. PVC is used in the manufacturing of imitation leather, floor
covering and gramophone records.
Cl  Cl 
|  | 
Polymerisation 
      CH  CH 
n CH 2  CH  2 n

Vinyl chloride PVC

Vinyl chloride is obtained from acetylene by treatment with HCl in the presence of HgCl2.
2 HgCl
HC  CH + HCl  
  CH2 = CH – Cl
Acetylene Vinyl chloride

Ph  Ph 
|  | 
(3) Polymerisation 
      CH  CH 
n CH 2  CH  2 n

Styrene Polystyrene
CN  CN 
|  | 
(4) Polymerisation 
      CH  CH 
n CH 2  CH  2 n

Acrylonitrile Polyacrylonitrile

 
OCOCH3  OCOCH3 
(5) | Polymerisation |
nCH2  CH       
n
 CH2  CH

Vinylacetate Polyvinylacetate

(6) Teflon (PTFE) :

It is obtained by polymerization of tetrafluoroethylene. Teflon is familiar because of its use as non-stick
coating particularly for cooking utensils. Nirlep non-stick frying pans have teflon coating. Because of its low
chemical reactivity, excellent toughness, electrical and heat resistance, teflon is used as insulation for
electrical items and in the manufacture of gaskets and valves.

 F F
| |
n CF2  CF2 Polymerisation C  C
    
Tetrafluoroethylene | | 
F F  n
Teflon

Tetrafluoroethylene is obtained from chloroform as follows :

CHCl3 + 2HF  CHClF2 + 2HCl
Chlorodifluoromethane
900C
2CHClF2   CF2 = CF2 + 2HCl
Tetrafluoroethylene

JEE(Advanced) Biomolecules & Polymers # 27

  
COOCH3  COOCH3 
(7) | Polymerisation |
nCH2  CH       
n
CH
 2  CH 
Methylmethacrylate Polymethylmethacrylate

(8) Rubbers :
(a) Natural Rubber : Rubber is a natural polymer and possesses esastic properties. It is also termed as
elastomer and has a variety of uses. It is manufactured from rubber latex which is a colloidal dispersion of
rubber in water. This latex is obtained from the bark of rubber tree and is foun in India, Srilanka, Indonesia,
Malaysia and South America.
Natural rubber may be considered as a linear polymer of isopreen (2-methyl-1, 3-butadiene) and is also
called as cis-1, 4 -polyisoprene.

n CH2 C CH CH2
By n
(1, 4 adition) cis-polyisoprene
CH3
or
(Isoprene) cis-poly-2-methyl butadiene

* Gutta parcha, has isoprene unit in trans-form (dentist used it in the filling of teeth).

Vulcanization : Natural rubber becomes soft at high temperature (>335 K) and brittle at low temperatures
(<283 K) and shows high water absorption capacity. It is soluble in non-polar solvents and is non-resistant to
attack by oxidising agents. To improve upon this physical properties, a process of vulcanisation is carried
out. In the vulcanization process, raw rubber is mixed with small amount of sulphur and heated.
The sulphur reacts with polymer molecules forming a cross-linked net work at the reactive sites of double
bonds and thus the rubber gets stiffened.
1-3 % S is used for rubber bands & 5% S is used for tyre rubber.

CH3
CH2–C–CH–CH2
S S
CH2–C–CH–CH2
CH3

(b) Synthetic Rubber : Synthetic rubber is any valcanisable rubber like polymer, which is capable of
getting stretched to twice its length. However, it returns to its original shape and size as soon as the external
stretching force is released. Thus, synthetic rubbers are either homoplymers of 1 ,3-butadiene derivatives or
copolymers of 1, 3-butadiene or its derivatives iwth another unsaturated monomer.

(i)
n CH2 CH CH CH2
By n
butadiene (1, 4 adition) cis-polybutadiene

n CH2 C CH CH2
By
(1, 4 adition)
(ii) Cl Cl Cl Cl n
Chloroprene
Neoprene (transform)

Note : Above all examples are homopolymers.

JEE(Advanced) Biomolecules & Polymers # 28

 (iii) Buna - N :

CN
|
Copolymerisation
nCH2  CH – CH  CH2  nCH2  CH  
1, 3  Butadiene Acrylonitrile

It is used in making oil seals, tank lining, etc.

(iv) Buna-S : It is a copolymer of 1,3-butadiene and styrene. It is obtained by the polymerization

of butadiene and styrene in the ratio of 3 : 1 in the presence of sodium. It is also known as styrene
butadinene rubber (SBR).
Na
nCH2  CH – CH  CH2 + CH  CH2 

Butadiene | Heat
C6H5
Styrene
It is used in the manufacture of tyres, rubber soles, belts, etc.

(v) ABS : Obtained by polymerisation of Acrylonitrile + Butadiene + Styrene

(vi) SARAN : Obtained by polymerisation of CH2=CH–Cl + CH2=CCl2

(vinylchloride) (Vinylidinechloride)
Note : Above all examples are Copolymers.

Zeigler Natta Catalyst : (C2H5)3Al + TiCl4  Used in polymer industry.

Triethylalumnium

Plasticisers : DBP (Dibutylphthalate), DOP (Dioctylphthalate)

Examples of Condensative Polymers :

This type of polymerisation involves a repetitive condensation reaction between two bi-functional monomers
after loss of simple molecules such as water alcohols etc and gives condensation polymers.
1. Polyamides : eg. Nylon-6, Nylon 6, 6 & Nylon 6, 10

NH2OH
O

HOOC–(CH2)4–COOH
–NH–(CH2)6–NH–C–(CH2)4–C–
Adipic acid n
O O
 H2N–(CH2)6–NH2 Nylon 6, 6
Hexamethylene HOOC–(CH2)8–COOH
Diamine –NH–(CH2)6–NH–C–(CH2)8–C–
Sebacic acid n
O O
Nylon 6, 10

JEE(Advanced) Biomolecules & Polymers # 29

2. Polyesters : eg. Dacron or Terylene, Glyptal, Kodel

O O
–O–CH2–CH2–O–C C–
HOOC COOH n

(Phthalic acid)
Glyptal
HOCH2CH2OH (used in paints and lacquers)
Glycol
O O
–H2O
–O–CH2–CH2–O–C C–
n
HOOC COOH
(Terphthalic acid)
(Terylene or Dacron)

HOCH2 CH2–OH + Terphthalic Acid  –O–CH2 CH2–O–C C–

n
O O
KODEL

3.

Melamine formaldehyde polymer is formed by the condensation polymerisation of melamine and formaldehyde
called Melmac (used in the manufacture of unbreakable crockery).
Phenol - formaldehyde polymers are the oldest synthetic polymers. These are obtained by the condensation
reaction of phenol with formaldehyde the presence of either an acid or a base catalyst.
The initial product could be a linear product - Novalac used in paints.

OH OH OH OH
CH2OH CH2OH HOH2C CH2OH
H+ or
+ CH2O OH
+ +

CH2OH CH2OH

OH OH OH OH
CH2OH +
H H2C CH2 CH2 CH2
n

Novolac

Novolac on heating with formaldehyde undergoes cross linking to form an infusible solid mass called bakelite.
It is used for making combs, phonograph records, electrical switches and handles of various utensils.

JEE(Advanced) Biomolecules & Polymers # 30

 OH OH OH
H2C CH2 CH2 CH2

CH2 CH2 CH2

H2C CH2 CH2 CH2

OH OH OH
Bakelite

4. ROH
Polyurethane : (RHCO  R–NH–COOR’ (Urethane))

CH3 O CH3
O=C=N N=C=O + HO–CH –CH –OH  –C–HN NH–C–CH2–CH2–O–
2 2 
(Glycol) O
n
(Polyurethane) (Copolymer)

(c) Classification based on structure of polymers :

(d) Calssification based upon molecular force :

(i) Elastomers : Polymers in which the intermolecular forces of attraction between the polymer chains are
the weakest are called elastomers.
(ii) Fibres : Polymers in which the intermolecular forces of attraction are the strongest are called fibers.
These forces are either due to H-bonding or dipole-dipole interactions. In case of nylon (polyamides), the
intermolecular forces are due to H-bonding while in polyesters (terylene, dacron etc.) and polyacrylonitrile
(orlon, acrylin etc.) Dipole-dipole interactions between the polar carbonyl (C = O) groups and, between
carbonyl and cyano (– C  N) groups respectively.
(iii) Thermoplastics : Polymers in which the intermolecular forces of attraction are in between those of
elastomers and fibres are called thermoplastics. The process of heat softening and cooling can be repeated
as many times as desired without any change in chemical composition and mechanical properties of the
plastic.

JEE(Advanced) Biomolecules & Polymers # 31

(iv) Thermosetting polymers : These are semifluid substances with low molecular weights which when
heated in a mould, undergo change in chemical composition to give a hard, infusible and insoluble mass.
This hardening on heating is due to extensive cross-linking between different polymer chains to give a three-
dimensional network solid. Examples : Phenol-formaldehyde (bakelite), urea-formaldehyde, etc.

(e) Classification based on Mechanism :

(1) Free radical :

This mechanism involve catalyst which generate free radical. Steps involved are :

(i) Chain initiation step :

2CO 2
(RCOO)2  2RCOO    R ; R + CH2= CH2  R–CH2–CH2

(ii) Chain propagation step :

nCH CH2
R–CH2–CH2 + CH2=CH2  R–CH2–CH2–CH2–CH2  2    R–(CH2–CH2)n–CH2–CH2

(iii) Termination step :

R–(CH2–CH2)n –CH2–CH2 + R–(CH2–CH2)n–CH2–CH2 R(CH2–CH2)n–CH2–CH2–CH2–CH2(CH2–CH2)nR

or R–(CH2–CH2)n–R  (–CH2–CH2–)n

(2) Cationic addition polymerisation.

This polymerisation is initiated by acid. Steps involved are :

(i) Chain initiation step : A + CH2=CH2  A –CH2– CH

2

(ii) Chain propogation step : A–CH2– CH

2 + nCH2=CH2
 A–(CH2–CH2)n–CH2– CH
2

(iii) Termination step : A (–CH2–CH2)n–CH2–CH2  A –(CH2–CH2)n–CH=CH2

(3) Anionic addition polymerization :


(i) Chain initiation step : B + CH2=CH2  B–CH2– CH2

 
(ii) Chain propagation : B–CH2– CH2 + nCH2 = CH2  B –(CH2–CH2)n–CH2– CH2

 
H
(iii) Termination step : B–(CH2–CH2)n – CH2– CH2  B–(CH2–CH2)n–CH2–CH3

JEE(Advanced) Biomolecules & Polymers # 32

Some polymers and their uses

Some commercially Important Polymers]

Biodegradable Polymers :
A large number of polymers are quite resistant to the environmental degradation processes and are thus
responsible for the accumulation of polymeric soild waste materials. These soild wastes cause acute
environmental problems and remain undegraded for quite a long time. In view of the general awareness and
concern for the problems created by the polymeric soild wastes, certain new biodegradable synthetic polymers
have been designed and developed. These polymers contain functional groups similar to the functional
groups present in biopolymers.
Aliphatic polyesters are one of the important classes of biodegradable poylmers. Some examples are given
below :

JEE(Advanced) Biomolecules & Polymers # 33

 (A) Poly -hydroxybutyrate – co–-hydroxy valerate (PHBV) :
It is obtained by the copolymerisatin of 3-hydroxybutanoic acid. PHBV is used in speciality packaging,
orthopaedic devices and in controlled release of drugs. PHBV undergoes bacterial degradation in the
environment.
OH OH
| |
CH3  CH  CH2  COOH + CH3  CH2  CH  CH2  COOH 
(3  Hydroxybu tanoic acid) (3  Hydroxypentanoic acid)

(B) Nylon–2–nylon–6 :
It is an alternating polyamide copolymer of glycine (H2N–CH2–COOH) and amino caproic acid
[H2N (CH2)5 COOH] and it is also biodegradable polymer.

Enzymes and Hormones :

(a) Enzymes : Nitrogenous complex compounds with basic nature are called Enzymes. Enzymes are biological
catalysts. All biological reactions are catalysed by enzyme. enzyme lower the activation energy thereby
increasing the rate of the reaction. For example activation energy for acid hydrolysis of sucrose is 6.22 KJ
mol–1, while hydrolysis by SUCRASE enzyme the activation energy is 2.15 KJ mol–1.
Composition of enzymes : Chemically all enzymes are globular proteins. However some enzymes are
also associated with some non-protein component called the cofactor. For their activity. These cofactors are
of two types : -
(a) Inorganic ions, such as Zn2+, Mg2+ , Mn2+ , Fe2+ , Cu2+ , Co2+ , Mo3+ , K+, Na+ etc
(b) organic molecules :- These are also of two types.
(i) Coenzymes : These are small organic molecules which are loosely held to protein and can be easily
separated by dialysis. These are usually derived from vitamins such as thiamine, riboflavin, niacin etc.
(ii) Prosthetic group : These are also organic molecules which are tightly held to protein by covalent
bonds but can be separated by only careful hydrolysis. Most of these are derived from vitamins such as
biotin. Enzymes are vital for biological process without them the life process would be very slow. For example
with out enzyme the meal would take 50 years to digest.
Examples of few enzymes and their catalysed reaction.

JEE(Advanced) Biomolecules & Polymers # 34

 Characteristics of Enzymes :
(i) Specificity : Each enzyme catalyses only one chemical reaction.
(ii) Efficiency : Enzymes are very efficient catalyst. They increase the rate of reaction by 10 times.
(iii) Small quantity :- Only small amount of enzyme can be highly efficient because. They are regenerated
after their catalytic activity
(iv) Optimum temp. and pH :- Enzymes catalyse reactions at pH of 7.4 and temperature range is 298-310
K (25ºC to 37ºC)
Application of Enzymes :
(i) In the manufacture of BEER and WINE and vinegar by the fermentalion of carbohydrates.
(ii) In the manufacture of sweet syrup from corn starch.
(iii) In the production of cheese by coagulation of milk.
(iv) Enzymes are helpfull mainly in the digestion process. Besides enzymes are used for controlling diseases
such as (i) Albinism diseases caused by the deficiency of the enzyme triosinase (ii) streptokinase is used to
dissolve blood clots in the treatment of heart disease.
(b) Hormones : These are the chemicals which are secreted by ductless glands and transported to different
parts of the body by the blood stream where they control different physiological action of the body. The word
hormone is derived from Greek language, which means to gear up or to excite.

Name of Hormones Source (organ) Function

Steroid Hormones
(a) Adrenal cotex hormones
Controls mineral balance in the body and
(i) Cortisone Adrenal cortex
metabolism of fat, carbohydrates and protein.
(b) Sex hormones
(ii) Testosterone Testes Regulates and stimulates male sex organs.
(iii) Progesterone Corpus luteum It controls the development and maintenance of pregnancy.
(iv) Estrogens, Estrone or Estradiol Ovary It maintains the normal function of female sex organs.
(c) Amine hormones
(v) Thyroxine Thyroid It regulates metabolism of lipid, proteins and carbohydrates.
It controls blood pressure and increases pulse rate. It helps
(vi) Epinephrine or Adrenaline Adrenal medulla
to release fatty acids from get and glucose from liver glycogen.
(d) Peptide hormones
(vii) Insulin Pancreas Maintains glucose level in blood and glucose metabolism.
It helps to release milk from mammary glands. It also helps to
(viii) Oxytocin Posterior pitutary gland
contract uterus after the child birth.
(ix) Vasopressin Pitutary glands It regulates reabsorption of water in the kidney.

Vitamins :
Definition : Vitamins may be defined as a group of biomolecules which are required in small amounts for
normal metabolic process and for the life, growth and health of human beings and animal organisms .
Sources of Vitamins : Human body can synthesize vitamin eg. some members of vitamin B complex
synthesized by micro organisms present in the intestinal tract. Most of the vitamins can not be synthesize
by our body, Therefore they must be supplied in the food. Plants can synthesize almost all vitamins. Vitamin
D may either be supplied in the food or may be produced in the skin by the irradiation of ergosterol (a sterol
present in our body) with ultraviolet light.
Classification of Vitamins : There is very little common to the various vitamins, therefore there are
usually desiganated by alphabet letters A, B, C, D, E and K. Some of these are classified as sub groups eg.
B1, B2, B3, B4, B6, B12 D1, D2 etc. About 25 vitamins are known to date. Vitamins are broadly classified into
two catagories
(i) Water soluble vitamins : Vitamin B-complex and vitamin C are water soluble vitamins and must be
supplied regularly in diet.
(ii) Fat soluble vitamins : These are oily substances and soluble in fats These are A,D,E and K. They are
stored in liver and adipose (fat storing) tissues.
(iii) Biotin (Vitamin H) : It is neither soluble in water nor in fats. Lack of particular vitamin causes a specific
deficinecy disease. Some important vitamins Their characteristics, sources and deficiency diseases are
summarised in the following table.

JEE(Advanced) Biomolecules & Polymers # 35

S.No. Vitamines Characteristics Sources Deficiency disease
Soluble in oils and fats stable Milk, Butter, eggs fish, liveroil,
Xerophthalmia (hardening of
A to heat. Promote growth and rice kidney , green vegetables,
1 eye) corhea night blindness and
(Retinal) vision and increases angoes sweet potatoes carrots,
xerosis (drying of skin)
resistance to diseases tomatoes etc
Pulses, nuts, cereals (rice,
Beriberi (paralysis of legs and
B1 Soluble in water destroyed by wheat) rice polishings, yeast,
2 general weakness) loss of
Thiamine heat above 313 K. egg yolk, milk green vegetables
appetite
and fruits.
Retards groath general
B2 Daily dosage -2-3 mg milk, yeast inflammation of tongue i.e
Soluble in water sensitive to
3 (Riboflavin or green vegetables meat, liver darkened tongue dermatitis and
light but stable to heat.
lactoflavin) kidney, egg white etc cheilosis (racking at corners of
mouth and lips).
B6 Cause specific dermatitis and
Rice, bran, yeast molases,
4 (Pyridoxin or Soluble in water anaemia in man effects central
meat, fish, egg yolk etc.
adermin) nervous system.
B 12 Anemia (RBC deficient)
5 Water soluble, stable to heat. Milk, egg, liver of animals
(cyanocobalamine inflammation of tongue and mouth

H Neither soluble in water not in Dermatitis, loss of hairs and

6 Yeast, liver, kidney and milk
(Biotin) fats. paralysis
Citrus fruits amla tomatoes
Soluble in water destroyed by Cause scurvy (bleeding of gums
7 C (Ascorbic acid) green leafy vegetables. Daily
cooking. pyorrhea bleeding of teath)
dosage 75 mg.
Soluble in oil, fats stable to
Rickets (deformation of bones)
D heat and resistants to Milk, butter, eggs, liver & meat.
8 osteomalacia (soft bones and
(Ergocalciferol) oxidation to controls calcium Daily dosage 0.025 mg.
joint pain)
and Phosphorus meta- bolism.

E Vegitable oil wheat germ oil

Loss of sexual power of
(It is mixture of 4- Soluble in oils and fats, stable cotton seed oil peanut oil,
9 reproduction (sterility) increased
vitamins a, b,g d to heat and oxidation. soyabean, eggs, milk, fish. Daily
muscular weakness.
tocoferols) dosage 5 mg.
K Haemorrhage lengthons the
Soluble in oils and fats stable Vitmain K1 affalfa leafs
(phylloquinone time of blood clotting. Excessive
10 to heat sensible to light and vegetables, vit. K 2 occurs mainly
mixture of two bleeding in injury. vitamin K 1& K 2)
alkali in bacteria.
vitamin K 1 & K2) and alkali bacteria.

Nucleic acids :
Nucleic acids were first discovered by a Swiss biochemist, Friedrich Miescher (1869) who called them
nuclein due to their acidic nature.
Chemical analysis of chromosomes shows presence of two nucleic acids-DNA (Deoxyribo nucleic acid)
and RNA (Ribo nucleic acid).
Nucleic acid is a macromolecule & consists of many (polymer) monomeric units, called nucleotides. Each
nucleotide is composed of a nucleoside and a phosphate group. Thus nucleotide is a phosphoric ester of
nucleoside.
Each nucleoside consists of sugar molecule and a nitrogenous base. The relationship can be shown as
given below.
Nucleic acid =many nucleotides
Nucleotide =nucleosides + phosphate
Nucleoside =sugar + nitrogenous base
Thus nucleotide =phosphate + sugar+ nitrogenous base
Nucleic acids bear different components that are briefly discussed below.
1. Phosphoric acid : The acidic nature of nucleic acids is due to the presence of phosphoric acid. Sugar
of nucleoside combines with phosphoric acid by a phosphodiester bond formed at 5th or 3rd carbon of the sugar.
2. Sugar : It is a five carbon (pentose) sugar. There are two types of pentose sugars-ribose and
deoxyribose. Deoxyribose sugar has one oxygen atom less at second carbon. Ribose sugar is present in
RNA while deoxyribose sugar occurs in DNA.
3. Nitrogenous bases : they have two catagories
(a) Pyrimidine :- It includes cytosine, thymine and uracil. Pyrimidine bases are made of only one ring of
carbon.
JEE(Advanced) Biomolecules & Polymers # 36
(b) purine :- It includes Adenine and guanine. Purine bases are made of two ring of carbon and nitrogen
bases of DNA contains adenine, guanine, cytosine and thymine. In RNA, uracil is present in place of
thymine.

Many nucleotide monomer units join one another to give rise to polynucleotide chain.

JEE(Advanced) Biomolecules & Polymers # 37

 The two adjacent nucleotides are joined by formation of phosphodiester bond (a bond that involves two
ester bonds). A polynucleotide chain is often written as 5’p 3’OH. This indicates that it is a dinucleotide with
phosphate group (p) attached to the 5th carbon of terminal nucleotide and hydroxyl group (OH) is present at
3rd carbon of basal nucleotide.
(a) Structure of DNA (Deoxyribonucleic acid) :
J.D. Watson and F.H.C. Crick (1953) proposed double helical structure of DNA based on the results of
M.H.F.Wilkins and co-workers. All these three persons were awarded Nobel Prize in 1962 for this work.
The following are some of the characteristic features of double helical structure of DNA.
(i) Each nucleotide consists of sugar, phosphate and a nitrogenous base. Many such nucleotides are
linked by phosphodiester bonds to form a polynucleotide chain or strand.
(ii) Phospho diester bonds are formed between 5’carbon of sugar of one nucleotide and 3' carbon of sugar
of the next nucleotide.
(iii) Nitrogenous base is attached to1’ carbon of sugar. At this place purine base is attached by its 5'
position and pyrimidine by its 3' position.
(iv) Polynucleotide strand is made of backbone of sugar and phosphate forming its long axis and bases at
right angles to it.

Chargaff (1950) made observations on the base and other contents of DNA. These observations or
generalizations are called Chargaffs rule.
(1) Purine and pyrimidine base pairs are in equal amount, that is, adenine + guanine =thymine + cytosine.
(2) Molar amount of purine-adenine is always equal to the molar amount of pyrimidine thymine. Similarly,
guanine is equalled by cytosine.

JEE(Advanced) Biomolecules & Polymers # 38

 (3) Sugar deoxyribose and phosphate occur in equimolar proportions.
(4) The ratio of A + T/G + C is constant for a species.
(5) Chargaffs rule states that in natural DNAs the base ratio A/T is always close to unity and the G/C ratio
also to always close to unity. It indicate that A always pairs with T and G pairs with C. A and T, G and C,
therefore,are complementary base pairs.
(6) Thus, if one DNA strand has A, the other would have T and if it has G, the other, would have C. Therefore,
if the base sequence of one strand is CAT TAG GAC, the base sequence of other strand would be GTA ATC
CTG. Hence, the two poly nucleotide strands are called complementary to one another.
(7) Two such complementary strands are joined with each another by hydrogen bonds between their
complementary nitrogenous bases. There are three hydrogen bonds between cytosine and guanine and two
hydrogen bonds between adenine and thymine.
(8) The two polynucleotide chains are helically coiled around the same axis in such a way that these can
separate from one another only by uncoiling. Helical coiling is supposed to be right handed. Such a form of
DNA is now called B-DNA
(9) The two chains or strands are antiparallel, i.e., they run in opposite directions in relation to their sugar
molecules. Their 5’p 3' OH phosphodiester linkages are in opposite directions
(10) Double stranded DNA molecule has a diameter of 20Aº.
(11) The helix makes one complete turn every 34 Aº along its length.
(12) There are 10 nucleotides per turn of helix.Thus the distance between two neighbouring base pairs is
3.4 A.
RNA : RNA is ribonucleic acid formed in the nucleus and is found in the cytoplasm of the cell.
(b) Types of RNA and their functions :
(1) r-RNA (Ribosomal – RNA) : It is found in the ribosomes and it is usually associated with protein to
form the ribosomes. It is synthesised in the nucleus by DNA. It is single stranded, comprising about 80% of
the total RNA. It is metabolically stable.
Functions : (i) This forms the site for protein synthesis.
(ii) It is also supposed to help the binding of m-RNA to the ribosomes during protein synthesis.
(2) m-RNA (Messenger RNA) : It is carries the genetic message code from the D.N.A. to ribosomes. It
is produced by the DNA ; m-RNA is also single stranded and constitutes about 15% of total RNA.
Functions : It carries the genetic information from DNA to the ribosomes where protein is synthesised.
(3) t-R.N.A (Transfer–RNA) : It is synthesised in the nucleus by the DNA. It is also called soluble RNA.
It is single stranded. There are 20 different kindes of t-RNA and each type has a specificity for a particular
amino acid. It constitutes about 5% of total RNA. It has very short life.
Functions : It carries amino acids from different parts of cytoplasm to the ribosomes during protein synthesis.
Differences Between DNA and RNA
DNA RNA
1. It usually occurs inside nucleus and some cell 1. Very little RNA occurs inside nucleus. most organelles .
of it is found in the cytoplasm.
2. DNA is the genetic material. 2. RNA is not the genetic material except in
certain viruses, e.g. Reovirus.
3. It is double stranded with the exception of 3. RNA is single stranded except reovirus where
itsome viruses (e.g. × 174). is double stranded.
4. DNA contains over a million nucleotides. 4. Depending upon the type, RNA contains
70-1200 nucleotides.
5. DNA is of only two types; intra-nuclear and 5. There are at least three types of RNAs—
extra-nuclear. mRNA, rRNA and tRNA
6. It contains deoxyribose sugar. 6. It contains ribose sugar.
7. Nitrogen base thymine occurs in DNA 7. Thymine is replaced by uracil in RNA The
alongwith three others — adenine, cytosine other three are similar — adenine, cytosine
and guanine. and guanine.
8. It replicates to form new DNA molecules. 8. It cannot normally replicate itself.
9. DNA transcribes genetic infromation to RNA. 9. RNA translates the transcribed message
for forming polypeptides.
10. DNA controls metabolism and genetics 10. It only controls metabolism under
Including variations. instruction from DNA.
11. Purine and pyrimidine bases are in equal 11. There is no poroportionality between
number. number of purines and pyrmidine bases.

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