CHEMISTRY-VIII NOTES PREPARED BY Dr.

DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

UNIT-II
Proteins 5 hours Max. Marks: 12-14
α-amino acids: Introduction, structure (Glycine, Alanine, Valine, Cysteine,
Aspartic acid, Lysine, Tyrosine and proline), classification on the basis of polarity
of R-groups, essential and non-essential amino acids with examples, ionic
properties and reactions of amino acids with alcohol, nitrous acid and Ninhydrin.
Peptides & peptide bond. Levels of organizations of Protein: Primary structure,
Secondary structure (α-helix, β-pleated structure & triple helix-Collagen), tertiary
structure(forces stabilizing tertiary structure) and quaternary structure.
Denaturation and renaturation, Anfinsen’s experiment with ribonuclease.
Classification of proteins based on shape, composition and biological function
(enzymes, hormones, transport agents, structural & antibodies with examples).

Proteins: Proteins are the polymeric molecules formed by the condensation of a

large number of amino acids. The molecular mass of proteins varies from 10000 to
a few millions.
Proteins are the most important of bio-molecules. The name protein is
derived from the Greek word “proteios” which means holding the first place. So
proteins are responsible for physical structure and chemical activity of the cell.
Amino acids: Those bio-molecules which contains both amino acid and carboxylic
acid groups and which are building block of proteins are called amino acids.
Based on the attachment of amino group and carboxylic acid group to the length of
the carbon atom, amino acids are classified as α –amino acids, β-amino acids, γ-
amino acids, and so on.
α – amino acids: Those amino acids in which both amino acids and carboxylic
acids directly attached to the same carbon atom (α- carbon atom) are called alpha
(α) –amino acids. The general formula for α – amino acids can be written as
Page 1 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Examples of α – amino acids with their structures –

1) Structure of glycine:

2) Structure of alanine:

3) Structure of valine:

4) Structure of Cysteine:

Page 2 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

5) Structure of aspartic acid:

6) Structure of lysine:

7) Structure of tyrosine:

8) Structure of proline:

Page 3 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Classification of amino acids: Amino acids are classified with different ways
namely based on polarity of side chain group and urge to the growth of the
animal body
I) Classification of amino acids based on the polarity of R (side chain)
groups: Based on the polarity of R (side chain) groups amino acids are
classified into following four categories-
1) Non –polar or hydrophobic R –groups: Those amino acids in which R -
group in α- amino acids are non-polar (do not form positive and negative
charge) are called non-polar or hydrophobic R –groups α- amino acids.
Examples:
Non-polar or hydrophobic R - Name and structure
group
-CH3

(CH3)2CH-

Page 4 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

CH3CH2CH3 used for ring

2) Polar uncharged or hydrophilic R-groups: Those amino acids in which R -

group in α- amino acids are Polar with no charge are called polar or
hydrophilic R –groups α- amino acids.
Examples:
Polar uncharged or hydrophilic R Name and structure
-group

Page 5 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

-H

-CH2OH

-CH2SH

3) Negatively charged R-groups: Those amino acids in which R - group in α-

amino acids are negatively charged ions are called negatively charged R –
groups α- amino acids.
Examples:
Negatively charged R-groups Name and structure

Page 6 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

-CH2COO-

-CH2CH2COO-

4) Positively charged R-groups: Those amino acids in which R - group in α-

amino acids are positively charged ions are called positively charged R –
groups α- amino acids.
Examples:
Positively charged R-groups Name and structure
-(CH2 )4-NH3+

Page 7 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

II) Based on the need to the animal for their growth, α-amino acids are
classified into following types
1) Essential amino acids: Those amino acids which are not synthesized in
human (or animal) body, hence they must be supplied in the form of food for
proper growth of human (or animal) are called essential amino acids.
For example: Methionine, lysine, tryptophan, etc.
2) Non-essential amino acids: Those amino acids which are synthesized in
human (or animal) body, hence they not required to supply in the form of
food for proper growth of human (or animal) are called non - essential amino
acids.
For example: Glycine, alanine, serine, etc.
Properties of amino acids:
1) Ionic properties of amino acids: Since amino acids have both amino and
carboxylic acid groups, they are amphoteric in nature. In aqueous solution
near neutral pH, most of the amino acids exist as bipolar molecules with
both positive and negative charges called zwitter ion

Page 8 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Acidic property of amino acids: At high pH (basic medium), the ammonium

ion of amino acid loses its proton and becomes uncharged amino group so
that the overall charge on the amino acids is negative. This indicates amino
acids are acidic in nature.

Basic property of amino acids: At low pH (acidic medium), the carboxylate

ion of amino acid gains proton from acid and becomes uncharged
carboxylic acid group so that the overall charge on the amino acids is
positive. This indicates amino acids are basic in nature.

Isoelectric point or isoelectric pH: At particular pH of a solution the amino

acids do not exist in bipolar form (zwitter ion) and do no migrate either of
the electrode when it placed in electric filed called isoelectric point or
isoelectric pH

Page 9 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

2) Reaction of amino acids with alcohols: When alpha amino acid is heated
with alcohol in presence of dry hydrochloric acid to form ester derivatives
of alpha amino acids

3) Reaction of amino acids with nitrous acid: When alpha amino acid is
treated with nitrous acid (nitrous acid is obtained by treating sodium nitrite
with dil. Hydrochloric acid at low temperature) at room temperature to
form hydroxyl carboxylic acid with liberation of nitrogen gas.

Page 10 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

4) Reaction of amino acids with ninhydrin: Ninhydrin heated with alpha

amino acids to form yellow coloured compounds of hydrindantin which is
further react with liberated ammonia to form coloured compounds called
Ruhemann’s purple.

OR

5) Formation of peptides: Two or more amino acids undergo condensation

reaction to form the products called peptides. During the formation of
peptides, amino group of one molecule of amino acids condenses with one
Page 11 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

carboxylic acid of another molecule of amino acid, the water molecule is

eliminated.

Peptide bond(s): When two or more (n) amino acids undergo condensation
reaction to form the products containing one or (n-1), -CONH- bond(s)
called peptide bond(s).
For examples:

Page 12 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Proteins: Polymers of less than twenty five amino acids are called peptides
Polymers of more than twenty five amino acids are called polypeptides Proteins
are polypeptides with molecular mass greater than 10000 with specific function
and biological activities.
Levels (structural) of organization of proteins: Proteins are highly complex
polymers which exhibit unique structural features which enable them to perform
specific functions in cells.
The structure of proteins is explained in four levels of organization.
Primary structure of protein: Primary structure is the unique linear sequence of
amino acids in a protein, from the amino terminus to the carboxyl terminus. The
amino acids are joined together by peptide bonds. The primary structure of a
protein is specified by the sequence of nucleotide bases in the gen that codes for
it. The primary structure therefore determines the properties of proteins and also
specifies its secondary, tertiary and quaternary structures.
Even a single change in the primary structure of a protein may cause drastic
changes in its function, leading to the molecular diseases. The determination of
the amino acid sequence of a protein is difficult task. Frederic Sanger elucidated
the complete amino acid sequence of polypeptide hormone insulin. Insulin was
first protein to be sequenced.

Page 13 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Secondary structure of protein: Secondary structure of a protein is repetitive

arrangement in space of amino acids that are close (folded) to one another in the
primary sequence. It refers to the arrangement of the polypeptide backbone rather
than to the side chains.
The most common types of secondary structure are the α –helix and the β-
pleated sheet. Another example of secondary structure is the triple helix. The
structures of many fibrous proteins are made up almost entirely of secondary
structural patterns.
a) The α-helix: This is a rigid, rod-like, spiral structure (spring –like). The
helix is stabilized by hydrogen bonds between the N –H group of each
amino acid and the carboxylic group of the amino acid four units away on
the same chain. In the α-helix, the polypeptide backbone is tightly coiled to

Page 14 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

form the core, while the R group of the component amino acids extend
outward from the helix. This minimizes steric interference between them.

Though hydrogen bonds are individually weak, so many of them are formed in an
α-helix that they collectively strengthen it considerably. The helix has 3.6 amino
acids per turn, and is right handed i.e. the coils twist clockwise around the axis.
Thus, amino acids 3 to 4 residues apart are brought specially close to each other.
α- helical structures were proposed by Linus Pauling and Robert Corey
from their studies on fibrous proteins. α- keratin consists almost entirely of the α-
helix is also found in globular proteins, where its content varies from almost 0 to
more than 75% of the total chain length. Example- In hemoglobin which is a
globular and flexible proteins, there is about 80% α- helical content.
b) The β-sheet: The β-sheet: This was also proposed by Pauling and Corey.
Fibroin of silk is composed almost entirely of β-sheet structure

Page 15 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

In the β-sheet, the polypeptide backbone is almost completely extended. The

structure is stabilized by hydrogen bond between the N-H hydrogens and carboxyl
oxygens of adjacent polypeptide chains lying side by side. These hydrogen bonds
can form between different parts of the same polypeptide chain that is folded back
on itself (interaction hydrogen bonds) or between two separate polypeptide
molecules(interachain hydrogen bonds). If the polypeptide chains run in the same
direction, with reference to their N-terminal and C-terminal ends, a parallel β-sheet
is formed. If the two chains run in opposite directions, an anti-parallelβ- sheet is
formed. The hydrogen bonding between polypeptide chains gives rise to a
repetitive zig-zag pattern, so β-sheets are often reffered to a β-pleats, β-sheets, like
the α-helix, may also be seen in globular proteins, but are much more common in
fibrous proteins like silk fibroin ( spider web).
c) The triple helix: Collegen is a water –insoluble fibrous protein of great
strength(leather is almost pure collagen). [It is the most abundant protein in
humans and serve as the framework protein in all tissues and organs. A 65
kg human will contain about 11 kg of protein of which about half is collagen
of different, closely related types. In tendons, it is bundled into fibres that
provide great strength.[ In the vitreous humour of the eye, it is dispersed as a

Page 16 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

gel which stiffens the structure. In the transparent cornea of the eye, it is
arranged in a stacked manner that transmits light with minimal scattering. In
bone and skin, collagen fibres are arranged at an angle to each other so as to
resist mechanical shear].
Each of the of the three chains of collagen is about 100 amino acid residues long.
These chains are helices which are twisted around each other to form a rope
liketriple helix, which is called tropocollagen.

Tertiary structure of protein: Tertiary structure of a protein is its overall three –

dimensional arrangement or shape. It results due to the folding of the polypeptide
into a compact nearly spherical. Therefore, tertiary structure can be said to occur
only in globular proteins. In water soluble proteins, the main force driving the
folding of the polypeptide chain are the hydrophobic interactions due to which
amino acids with non-polar side chains get buried inside the folded structure, in the
hydrophobic interior of the protein. On the other hand, most of the hydrophilic
amino acids with polar side chains remain on the surface.
Forces stabilize the tertiary structure of protein:
i) Hydrophobic interaction: These occur between hydrophobic
R groups, which are repelled by water and so tend to associate
together in the interior of the globular protein, where they are
shielded from water.

Page 17 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

ii) Electrostatic or ionic interactions: these occur between the

positively charged R group of basic amino acids and the
negatively charged R groups of acid amino acids.
iii) Hydrogen bonds: These occur between the R groups of amino
acids brought close together by folding of the polypeptide
chain. Hydrogen bonds may also form with water on the surface
of the protein.
iv) Covalent bonds (disulphide bonds): Folding of the polypeptide
chain may bring together amino acid R groups which react. Forming
strong covalent bonds. Commonly, the CH2SH groups of cysteine
react to form disulphide bridges (-CH2-S-S-CH2-)

Quaternary structure of proteins: Many proteins consist of two or more different

polypeptide chains. These are called subunits. In a protein, the subunits may be
identical or different. They are usually held together by noncovalent interactions.
Quaternary structure is the arrangement of the subunit chains of oligomeric
proteins with respect to each other. If an oligomeric protein is denatured,
quaternary structure will also be affected, in addition to secondary and tertiary. In
hamoblobin, there are four subunits, each with a heme prosthetic group. Two of
these subunits are of one type, called α- chains, which are 141 amino acid residues
long. The other two subunits are of another type, called β-chains, which are 146
Page 18 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

amino acids long. Thus, the subunit structure of hemoglobin is written as α 2β2. The
arrangement of these four subunit chains with respect to each other is called
quaternary structure of hemoglobin. Its quaternary structure enables it to work
cooperatively, i.e., the binding of oxygen to one subunit increases the affinity of
the other subunits for oxygen.
Denaturation of proteins: Destruction of the three dimensional structure of
protein by heating or by adding reagents( strong acids, strong alkalies, acetones,
alcohols, urea, detergents, organic solvents) or by mechanical shaking or by
passing strong rays which leads to loss of biological activity is called denaturation
of proteins.
Agents of denaturation: Denaturation process can be brought using following
agent
1) Physical agents: Heat, violent shaking, X-ravs, UV radiation.
2) Chemical agents: Acids, alkalis, organic solvents (ether, alcohol), salts of
heavy metals (Pb, Hg), urea, salicylate.
For example: After heating of natural egg, it became insoluble, hard and opaque
Characteristics of denaturation: The following characters of denaturation
1) The native helical structure of protein is lost
2) The primary structure of a protein with peptide linkages remains intact i.e.,
peptide bonds are not hydrolyzed.
3) The protein loses its biological activity.
4) Denatured protein becomes insoluble in the solvent in which it was
originally soluble.
5) The viscosity of denatured protein (solution) increases while its surface
tension decreases.
6) Denaturation is associated with increase in ionizable and sulphydryl groups
of protein. This is due to loss of hydrogen and disulfide bonds.
Page 19 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

7) Denatured protein is more easily digested. This is due to increased exposure

of peptide bonds to enzymes. Cooking causes protein denaturation and,
therefore, cooked food (protein) is more easily digested.
8) Denaturation is usually irreversible. For instance, omelet can be prepared
from an egg (protein-albumin) but the reversible not possible.
9) Careful denaturation is sometimes reversible (known as renaturation).
Hemoglobin undergoes denaturation in the presence of salicylate. By
removal of salicylate, hemoglobin is renatured.
10) Denatured protein cannot be crystallized.
Renaturation of proteins: Reconstruction of the three dimensional structure of
protein from denatured protein by carefully cooling or isolating or purifying which
leads to gain of biological activity is called renaturation of proteins.

Aufinsen’s experiment with ribonuclease: One of the major series of

experiments on protein folding was carried out by Anfinsen using the protein
ribonuclease. This protein is a small enzyme (124 residues) containing 4 disulphide
bonds, which catalyses the breakdown of RNA. The enzyme can be treated with
urea and reducing agent like 2-mercaptoethanol which effectively denature the
enzyme. In this state it is unfolded, the S-S bonds are reduced and it has no
activity. If this preparation is then slowly dialysed to remove the urea and the 2-
mercaptoethanol reducing agent the activity slowly returns. After dialysis is
complete 100% activity has returned. This indicates that the folding of the protein
was contained in the primary amino acid sequence. Disulfide bridges or bonds
Page 20 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

form between 2 cysteine residues in an oxidizing environment. Further

investigation suggests that the formation of the disulfide bonds is not a random
event either. Ribonuclease has 4 S-S bonds, hence 8 cysteines. If the S-S bond
formation was completely random then the chances of forming the correct disulfide
bonds is very low. If the process was completely random we would expect to
achieve only a small fraction of the original activity (~1%). The fact that 100%
activity was achieved when sufficient time was allowed indicates that correct
disulfide bond formation is favoured when correct folding takes place. Disulfide
bonds are not essential for correct folding but they do stabilize the protein once it is
folded. Disulfide bonds are usually found in proteins which are exported eg
ribonuclease, insulin. This is probably because the exterior of the cell is oxidizing
hence stabilizes –S-S- formation while the interior of the cell has a reducing
environment, favouring the reduced –SH. The proteins are often much bigger than
ribonuclease and the environment has a higher protein concentration. The chances
of misfolding are greater and the possibility of misfolded proteins aggregating
together is also greater

Classification of proteins: Proteins can be classified in different ways

I) Based on the shape, proteins are classified into following categories.

Page 21 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

1) Fibrous proteins: Those proteins which are elongated, rod-like,

tough and insoluble in water are called fibrous proteins. These
proteins have structural and protective functions. Usually, they have a
repetitive structure which is assembled into threads or cables.
Examples: α-keratin (hair, nails), fibroin (silk), collagen (tendons,
skin, bones and teeth)
2) Globular proteins: Those proteins which are compact, roughly
spherical molecules and soluble in water are called globular proteins.
These proteins have tightly folded chains with largely hydrophobic
interiors and hydrophilic surfaces. They have clefts on the surface that
bind other components with a high degree of specificity.
Examples: Enzymes (amylase, pepsin, trypsin), antibodies
II) Based on the compositions, proteins are classified into following
types-
1) Simple proteins: Those proteins which are made up of only α-amino
acids or which on complete hydrolysis to form only α-amino acids are
called simple proteins.
Examples: Insulin, hormones
2) Conjugated proteins: Those proteins which are made up of using α –
amino acids and non-amino acids(non –amino acid part is called
prosthetic group) or these are obtained on complete hydrolysis are
called conjugated proteins.
Examples:
Conjugated proteins Prosthetic group Examples
Glycoprotein carbohydrate Antibodies, mucin of
saliva

Page 22 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Haemoprotein Haeme Haemoglobin, myoglobin,

cytochromes
Lipoprotein Lipid VLDL, LDL,HDL
Metalloprotein Metal ion Alcohol dehydrogenase
(contains Zn2+)
Nucleoprotein Nucleic acid Chromatin(DNA),
Ribosomes (RNA),
Viruses
Phosphoprotein Phosphate group Casein of milk
Flavoprotein FAD or FMN Succinate dehydrogenase,
(coenzymes) NADH dehydrogenase

3) Derived proteins: Those proteins which are made up of using both

simple protein and conjugated protein or these are obtained on
complete hydrolysis are called derived proteins.
Examples: Denatured proteins, secondary derived proteins are formed
by the progressive hydrolysis of peptide bond.
III) Based on the biological functions, proteins are classified into
following categories-
1) Enzymes (catalytic proteins): These proteins are highly specialized
proteins which possess catalytic activity. All the chemical reactions
occurring in the cell are catalyzed by enzymes. Since enzymes are
highly specific in the reactions they catalyze, a very large number of
enzymes are present in cells.
2) Hormones (Regulatory proteins): These proteins (hormones) help in
the regulation of cellular activity.

Page 23 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Examples: Insulin is a hormone which regulate glucose metabolism,

Tropic hormones which secrets pituitary gland (ACTH, TSH)
3) Transport agents: These proteins bind to specific molecules and
transport them from one tissue to another.
Example: Haemoglobin is the oxygen binding protein of the red blood
cells which binds oxygen as the blood passes through the lungs and
carries it to tissues, the blood plasma contains lipoproteins which bind
lipid and carry them to other organs, plasma membrane, intracellular
membranes.
4) Structural proteins: These proteins which acquires define shape and
size.
Examples: The fibrous protein collagen which has a very high tensile
strength due to presence of tendon and cartilage. Leather is almost
pure collagen. Ligaments contain elastin which is another fibrous
protein capable of stretching in two dimensions. Hair, nails and
feathers consists largely of the tough insoluble protein keratin. Silk
fibers and spider web made up of fibroin.
5) Antibodies (protective proteins): These proteins defend organisms
against invasion by foreign cells such as virus, bacteria and foreign
proteins from other species. The immune system produces proteins
called antibodies which destroy foreign cells (antigens). Antibodies
are also called immune globulins. Each antibody can bind specifically
to one kind of antigen. Hence large numbers of antibodies are
circulating in the blood. Fibrinogen and thrombin are proteins that are
involved in blood clotting and prevent loss of blood. Snake venoms,
bacterial toxins and toxic plant proteins also serve protective
functions.
Page 24 of 25
CHEMISTRY-VIII NOTES PREPARED BY Dr. DHONDIBA VISHWANATH SURYAWANSHI, GFGC KR PURAM BENGALURU-36

Page 25 of 25