A comprehensive introduction to the proteins, amino acids and polypeptides. This will give readers a overall view of this topic. All types of queries and suggestions are most welcome

2. -300 amino acids occur in nature
-Out of this 20 amino acids are standard amino acids which
repeatedly found in protein structure
-Amino acids are a group of organic compounds containing two
functional group- amino and carboxyl attached to α- carbon atom.
Hence, all these are called α- amino acids.
-Amino acids share many features, differing only at the R
substituent
-Amino group (-NH2) is basic while the carboxyl group (-COOH) is
acidic in nature
- Amino acids are obtained from proteins by hydrolysis, catalyzed by
acid, base or enzymes such as pepsin, trypsin and chymotrypsin
General Structure ofAmino Acid

3. Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation:
– start from -carbon and go down the R-group
Lysine : Basic Amino
Acid

4. Most -Amino Acids are Chiral
• The -carbon has always four different substituents and is
tetrahedral therefore exhibits optical isomerism
• Each amino acid has an unique fourth R-substituent
• Except In glycine, the R-substituent is also a hydrogen so it
is non-chiral

5. Proteins only contain L amino acids

6. Amino Acids: Classification
A. Amino acids classification based on their structure
Common amino acids can be placed in seven basic groups depending on their
R substituent
1. Aliphatic amino acids
- Contains aliphatic R- chain
- these are hydrophobic and non-polar in nature
- these shows presence of simple or branched chain in R-group

7. 2. Aromatic amino acids
-Contains aromatic R- chain

8. 3. Acidic amino acids
i) Dicarboxylic monoamino acids- Aspartic acid and Glutamic acid
ii) Amides form of above acids

9. 4. Basic amino acids
- These amino acids are basic in nature

10. 5. Sulphur containing amino acids
- These amino acids contain sulphur atom in the structure
6. Hydroxyl group containing amino acids
- These amino acids contain hydroxyl group in the structure

11. 7. Imino acids
- These amino acids contain imino group(=NH) in place of amino
group (-NH2) i.e. α- amino nitrogen is part of the structure

12. B. Amino acids classification based on their Nutritional requirements
1. Essential amino acids
-the amino acids which can not be synthesized in the body but are
required for normal functioning of body are called as essential amino
acids.
-These should be supplied through diet and supplements.
-They required for proper growth and maintenance of the individual
-Valine -Lysine
- Arginine - Methionine
-Histidine - Phenylalanine
- Isoleucine - Threonine
- Leucine - Tryptophan
2. Non-essential amino acids
- these are synthesized in the body hence they need not be consumed in
the diet
- Glycine -Alanine
- Serine - Cysteine
- Aspartic acid - Glutamic acid
- Glutamine - tyrosine
- Proline - Asparagine

13. Some physical properties of amino acids
1. Solubility
all amino acids are soluble in water, but their solubility varies
to a great extent. Solubility depends on the nature of the R- group
i.e. polarity of amino acids. Polar amino acids are highly soluble in
water while non-polar amino acids are highly soluble in organic
solvents like chloroform, ether, etc.
2. Optical activity
all standard amino acids except glycine have an asymmetric or
chiral carbon atom. Due to this, amino acids are optically active.
Also, they exist as stereo- isomers. All naturally occuring amino
acids found in proteins are L- amino acids. Certain D- amino acids
are found in some biological systems.
3. Acid- base behavior
amino acids contain the acidic carboxyl group (-COOOH) and
the basic group amino (-NH2). Hence, amino acids are called as
amphoteric molecules or ampholytes (i.e. amphoteric electrolyte).

14. Zwitterion/dipolar ionic form- Can act as acid (proton donor) and base (proton
acceptor)
Amphoteric (ampholytes)- non-ionic form
Functions or Role of amino acids
Amino acids are required for the body for various reasons:
1) For synthesis of various enzymes, hormones, plasma proteins and
immuno-globulins
2) For the growth and repairs of body tissues
3) Source of energy when body is having inadequate supply of
carbohydrates or fats

15. PEPTIDE/POLYPEPTIDES
-Peptides are polymers of amino acids.
- Peptides are small condensation products of amino acids
-Their structure and functions depend upon
- Nature of amino acids present in them,
-Sequence of amino acids,
-Spatial relationship of amino acids.
-Many peptides are formed from breakdown of proteins
Peptide- Peptides are relatively small polymers, 2-10 amino acid unit. If 2 amino
acids were involved then called Dipeptide viz, tripeptide for 3 amino acid unit and
Decapeptide for 10 unit.
Oligopeptide :a few amino acids
Polypeptide- big peptides are called polypeptides more than 50 amino acids
Polypeptide : many amino acids

16. Amino terminal-
N-terminal-
Carboxyl terminal-
C-terminal
Amide bond
Condensation reaction
Pentapeptide Ser-Gly-Tyr-Ala-Leu

17. Functions or Role of peptides
• Hormones and pheromones
– insulin (sugar uptake)
– oxytocin (childbirth)
– sex-peptide (fruit fly mating)
• Neuropeptides
– substance P (pain mediator)
• Antibiotics:
– polymyxin B (for Gram - bacteria)
– bacitracin (for Gram + bacteria)
• Protection, e.g. toxins
– amanitin (mushrooms)
– conotoxin (cone snails)
– chlorotoxin (scorpions)
Biologically important peptides
Glutathione
Thyrotropin releasing hormone (TRH)
Oxytocin
Vasopressin
Angiotenins
Bradykinin
Methionine enkephalin

18. Proteins
-Are the most abundant organic molecules of the life.
-From Greek Proteios: holding the first place.
-Proteins are polymers of amino acids (Heteropolymers).
-Proteins generally contains more than 50 to several hundreds of amino
acid units.
Elemental composition of Proteins:
Carbon- 50-55%
Hydrogen- 6-7.3%
Oxygen- 19-24%
Nitrogen- 13-19%
Sulphur- 0-4%
Also, contains
P, Fe, Cu, I, Mg,Mn, Zn

19. Classification of proteins on the basis of chemical nature:

20. 1. Simple proteins
-This types of proteins are made up of only from amino acid
residue and no other bound material.
-They may be further classified on the basis of their solubility
A) Globular proteins
these are spherical or oval in shape, soluble in water or other
solvents and digestable.
i) Albumins: soluble in water and dilute salt solutions and
coagulated by heat. E.g. Serum albumin, ovalbumin (egg),
lactalbumin (milk).
ii) Globulins: soluble in neutral and dilute salt solution e.g.
Serum globulins, vitelline (egg yolk).
iii) Glutelins: soluble in dilute acids and alkalies. Mostly found in
plants e.g. Glutelin (wheat), oryzenin (rice).
iv) Prolamines: soluble in 70% alcohol e.g. Gliadin (wheat), zein
(maize).

21. v) Histones: strongly basic proteins, soluble in water and dilute
acids but insoluble in dilute ammonium hydroxide e.g.
Thymus histones.
vi) Globins: these are generally considered along with histones.
However, globins are not basic proteins and are not
precipitated by ammonium hydroxide.
vii) Protamines: they are strongly basic similar to histones but
smaller in size and soluble in ammonium hydroxide.
Protamines are also found in association with nucleic acids
e.g. Sperm proteins.
viii) Lectins: are carbohydrates binding proteins and are involved
in the interaction between cells and proteins. They help to
maintain tissue and organ structures. E.g. Concanavalin A,
agglutinin.

22. B) Fibrous proteins/ Scleroproteins
these are fiber like in shape, insoluble in water and resistant to
digestion. Albuminoids or scleroproteins are predominant group of fibrous
proteins.
i) Collagens: are connective tissue proteins. Collagens, on boiling with
water or dil. Acids, yield gelatin which is soluble and digestible.
ii) Elastins: these proteins are found in elastic tissues such as tendons
and arteries.
iii) Keratins: these are present in exoskeletal structures e.g. Hair, nails,
horns.

23. 2. Conjugated proteins: formed from alpha amino acids+ non protein co
factor or group
A) Nucleoproteins: conjugated with nucleic acid (DNA or RNA) e.g.
Nucleohistones, nucleoprotamines.
B) Glycoproteins: conjugated with carbohydrates, which is less than 4% of
protein. The term mucoprotein is used if the carbohydrate content is
more than 4% e.g. Mucin (saliva), ovomucoid (egg white).
C) Lipoproteins: conjugated with lipids e.g. Serum lipoproteins.
D) Phosphoproteins: conjugated with phosphoric acid e.g. Casein (milk),
vitelline (egg yolk).
E) Chromoproteins: conjugated with coloured group e.g. Hemoglobins,
cytochromes.
F) Metalloproteins: these proteins contain metal ions such as Fe, Co, Zn,
Cu, Mg, etc., e.g. Ceruloplasmin (Cu), carbonic anhydrase (Zn).

24. 3. Derived proteins: Intermediate degradation products of protein hydrolysis
A) Primary derived proteins
The primary derived are the denatured or coagulated or first hydrolysed
products of proteins.
i) Coagulate proteins: these are the denatured proteins produced by agents
such as heat, acids, alkalies, etc., e.g. Cooked proteins, coagulated
albumin (egg white).
ii) Proteans: these are the earliest products of protein hydrolysis by
enzymes, dilute acids, alkalies etc. Which are insoluble in water., e.g.
Fibrin formed from fibrinogen.
iii) Metaproteins: these are the second stage products of protein hydrolysis
obtained by treatment with slightly stronger acids and alkalies e.g. Acid
and alkali metaproteins.
B) Secondary derived proteins:
These are the progressive hydrolytic products of protein hydrolysis. These
include proteoses, peptones, polypeptides and peptides.

25. Structural organization of proteins
-Proteins perform a variety of functions
-Functions are closely related to the structures of proteins
-Fundamentally, all proteins are made of amino acids linked to one another by
peptide bonds
-A complex three-dimensional structureis formed by:
-Coiling and folding of peptide chains
-Union of several peptide chains with one another
-The three-dimensional structure is also known as conformation of the protein
-The conformation is unique to each protein
-The biological functions of a protein depend upon its conformation
-Any change in conformation may lead to loss of function
-The conformation depends upon the sequence of amino acids

26. Structure of proteins is formed by:
A) Covalent or strong bonds
B) Non-covalent or weak bonds
A) Covalent or strong bonds
These bonds are relatively strong
i) Peptide bonds
-These are the basic linkages between two consecutive amino acids
-As they are formed between amino groups and carboxyl groups,
they are known as peptide bonds
-All amino acids present in a protein take part in the formation of
peptide bonds
H2N—CH—COOH+H2N—CH—COOH
|
R1
|
R2 R1
|
H2N—CH—C—N—CH—COOH
O
||
H R2
| |–H2O
Aminoacid Aminoacid Dipeptide
Peptide
bond
‫׀‬

27. ii) Disulphide bonds
-A disulphide bond is formed between two cysteine residues
-The sulphydryl groups of residues are linked together
|
S
|
S
|
CH2
|
— HN — CH — CO —
SH
|
CH2
|
— HN — CH — CO —
A
cysteine
residue
Disulphide
bond
between
two
cysteine
residues
— HN—CH—CO—
|
CH2
|
SH
— HN—CH—CO—
|
CH2
←
Another
cysteine
residue

28. B) Non-covalent or weak bonds
-Non-covalent bonds are much weaker than the covalent bonds
-But they contribute significantly to the stability of protein structure
The main non-covalent bonds in proteins are
(i) Hydrogen bonds
(ii) Electrostatic bonds
(iii) Hydrophobic bonds
(i) Hydrogen bonds
-Hydrogen bonds are formed between two peptide linkages
-The peptide linkages may be present in the same polypeptide or in different
polypeptide chains
-The hydrogen atom of the N–H group participating in a peptide bond is
shared between nitrogen and oxygen atoms

29. -The nitrogen atom involved in sharing belongs to one peptide bond, and
the oxygen atom belongs to another peptide bond
R
|
R
|
H R
| |
R
|
—CH —C—N—CH—
||
O
H
|
.......
—CH —C— N—CH—
||
O

30. (ii) Electrostatic bonds
-Electrostatic bonds or salt bonds are formed between two oppositely charged
groups
-Side chains of several amino acids contain ionizable groups e.g. amino
groups, carboxyl groups, sulphydryl groups, phenol groups etc
-Such groups may form electrostatic bonds with other groups bearing opposite
charges
(iii) Hydrophobic bonds
-The side chains of non-polar amino acids attract each other because of their
hydrophobic nature
-However, this is only a physical attraction and no chemical bonds are really
formed

31. Structure of protein
The structure of proteins can be considered to have four levels of
organization: Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Primary, secondary and tertiary structure are present in all
the proteins Quaternary structure is present in many but not
all

32. Levels of structure in proteins

33. A) Primary structure
-Primary structure means the sequence of amino acids in the polypeptide chain
-This is the most fundamental level of structural organization
-Only peptide bonds are responsible for the formation of primary
structure
-Each amino acid takes part in forming peptide bonds
-The amino acids present in the polypeptide chain are known as its amino acid
residues
-Each chain has an N-terminus and a C- terminus
-Some polypeptides are cyclic, and have no N- and C-terminus
-The higher levels of structural organization also depend upon the primary
structure

34. -Any change in amino acid sequence will alter the higher levels of organization
-This will change the conformation of the protein
-Many genetic diseases are caused by minor changes in amino acid sequence
of proteins
-Such proteins are abnormal in structure as well as function
Arg-Val-Cys-Ala-Tyr-Lys-Gly-Phe-Ser
Arg-Val-Cys-Ala-Lys-Tyr-Gly-Phe-Ser
Two different primary structures

35. B) Secondary structure
This is the next higher level of organization
The polypeptide chain is twisted, turned and coiled to form various types of
secondary structure
Secondary structures include -helix, - pleated sheet, -bend etc
I) -Helix
- The polypeptide chain is coiled to form a helical structure
- The -helix is produced by formation of hydrogen bonds between peptide
linkages
- These are formed between peptide linkage three amino acid residue apart
- This means that hydrogen bonds are formed between the 1st and the 4th
peptide linkages, between the 2nd and the 5th peptide linkages and so on

36. - Each peptide linkage in the polypeptide chain participates in hydrogen
bonding
- There are 3.6 amino acid residues in each turn of the helix
- The pitch of the helix (vertical distance per turn) is 0.54 nm
- Side chains of amino acid residues protrude outwards from the centre of
helix
- The helix may be right-handed or left- handed
- The right-handed helix is more stable
- Certain amino acids (proline) disrupt the -Helix. Large number of acidic
(aspartic acid, glutamic acid) or basic (lysine, arginine, histidine) amino acids
also interfare with -Helix structure.

38. II) -Pleated sheets
-Portions of same peptide chain or different peptide chains running side by side
are joined
-They are joined by hydrogen bonds formed between peptide linkages
-This produces an extended zigzag structure resembling a series of pleats
The polypeptide chains forming the - pleated sheets may be running:
-In opposite directions (N→C) forming anti-parallel -pleated
sheets or
-In the same direction forming parallel -pleated sheets

39. O
||
C
H
|
C
|
R
H
|
N
O
||
C
H
|
C
|
R
H
|
N
N
|
H
C
||
O
C
||
O
N
|
H
R
|
C
|
H
O
||
C
H
|
N
R
|
C
|
H
O
||
C H
|
C
|
R
H
|
NH
|
C
|
R
C
||
O
C
||
O
N
|
H
N
|
H
Anti-parallel -sheet
C-terminal N-terminal
N-terminal C-terminal

40. O
||
C
H
|
C
|
R
H
|
N
O
||
C
H
|
C
|
R
H
|
N
N
|
H
C
||
O
C
||
O
N
|
H
R
|
C
|
H
O
||
C
H
|
C
|
R
H
|
N
O
||
C
H
|
C
|
R
H
|
N
N
|
H
C
||
O
C
||
O
N
|
H
R
|
C
|
H
Parallel -sheet
N-terminal
N-terminal
C-terminal
C-terminal

41. C) Tertiary structure
-The polypeptide chain is folded in complex ways
-Folding produces different types of secondary structures in different regions of
the chain
-Some supersecondary motifs are also formed
The folding occurs due to formation of: Disulphide bonds, Hydrogen
bonds, Electrostatic bonds, Hydrophobic bonds
-Some amino acid residues which are distant from each other in the
polypeptide chain are brought closer
-Some residues are buried into the interior of the molecule
-Some are exposed on the surface of the molecule

42. -Helix (ribbon)
-Pleated sheets (arrows)

44. D) Quaternary structure
-Many proteins are made up of two or more polypeptide chains
-Each chain is known as a protomer or a sub-unit
-The sub-units may be similar or dissimilar
-The sub-units are joined to each other by non-covalent bonds
-Joining of sub-units produces the quaternary structure of the protein
Examples of proteins having quaternary structure are: Haemoglobin,
Lactate dehydrogenase, Creatinine kinase
Quaternary structure
Sub-unit
Sub-unit

46. Qualitative tests for proteins
1) Heat test: when a protein solution is heated in a boiling water bath, the
protein gets coagulated and loose their biological activity. This is called
thermal denaturation of proteins e.g. Boiling of eggs.
2) Biuret test: biuret reagent consist of copper suplhate in an alkaline
medium. When proteins are treated with biuret reagent, it shows a
violet colour. This test is used for the identification and estimation of
the all proteins.
3) Hydrolysis test: protein, on hydrolysis gives free amino acids. Hydrolysis
can be carried out by acids like HCl, H2SO4 or alkalies like NaOH, KOH.
Protein hydrolysis is a conventional source of amino acids. Extent of
hydrolysis is tested by carrying out ninhydrin and biuret tests with
respect to time for which the hydrolysis reaction carried out. Ninhydrin
reaction is negative for protein but after hydrolysis, it is positive as free
amino acids are formed.

47. 4) Xanthoproteic test: nitration of aromatic amino acids of proteins gives
yellow colour. Conc. Nitric acid is used for nitration. On the treatment of
nitric acid, proteins give yellow colour ppt., which turns to orange colour
on the treatment with alkali.
5) Millon’s test: phenolic group of tyrosine containing proteins react with
mercuric sulphate in the presence of sodium nitrite and sulphuric acid to
give red colour.
6) Precipitation reaction: proteins are precipitated by using different
agents like, salt, organic solvents, heavy metal ions, acids etc.
i) Salts: ammonium sulphate, sodium chloride.
ii) Organic solvents: acetone, alcohol.
iii) Heavy metal ions: sodium tungstate, ammonium molibdate,
copper or mercury salts.
iv) Acids: Trichloroacetic acid (TCA), acetic acid, HCl

48. 1. Dynamic function
a) Enzyme in Catalysis:
-A very important function of proteins is to serve as biological catalysts i.e.
enzymes
-Except for some ribozymes(RNA enzymes), all enzymes are proteins
-Biochemical reactions can occur at a significant rate only in the presence of
enzymes
–enolase (in the glycolytic pathway)
–DNA polymerase (in DNA replication)
b) Regulatory proteins (Receptors and Signal
Transducers)
-Chemically, all the receptors are proteins
-Examples are insulin and hormone receptors, LDL receptors, transferrin
receptors, T-cell receptors, etc.

49. C) Transport: carrier proteins
–hemoglobin (transports O2 in the blood)
–membrane channels and associated proteins- Chemically, these
channels are made of proteins
Examples- chloride channel, calcium channel, sodium-potassium
channels, etc lactose permease (transports lactose across the cell
membrane)
• Transferrin
• Lipoproteins
• Transcobalamins
• Thyroxine-binding globulin
• Corticosteroid-binding globulin
• Retinol-binding protein
• Albumin

50. 2. Static Function
a) Structure:
–collagen (connective tissue)
–keratin (hair, nails, feathers, horns)
b) Motion: Muscle contraction occurs because of movement of
actin and myosin filaments. Both are contractile proteins
–myosin (muscle tissue)
–actin (muscle tissue, cell motility)
C) Storage
-Ferritin and haemosiderin store iron
-Transcobalamin I stores vitaminB12
d) Defence- Responsible to protect from infection and other toxic
substances
- Antibodies

51. Biological value of proteins
Proteins is one of the important components of diet. It is required to
maintain growth and healthy functioning of the body.
Protein give amino acids on hydrolysis during digestion and these amino
acids are absorbed in the blood. Amino acids are the building blocks
required for a cell to synthesize proteins like structural proteins, enzymes,
etc.
Proteins are the structural component of protoplasm, cells and tissues.
Proteins are also classified on a nutritional value:
Complete proteins: proteins contains all the essential amino acids in
required quantities are called complete proteins e.g. Milk and egg
proteins.
Incomplete proteins: proteins not containing all essential amino acids are
called incomplete proteins e.g. Maize, gelatin.

52. Under certain conditions, dietary proteins or body proteins are diverted
for the production of energy. This may be due to inadequate supply of
carbohydrates and fats or because of protein intake itself is very high.
A low intake of proteins results in deficiency symptoms. Such conditions
are developed may be due to low dietary intake or malfunctioning of the
body such as mal absorption and non conversions.

53. Protein deficiency diseases
A) KWASHIORKAR
B) MARASMUS
C) NUTRITIONAL EDEMA
A) KWASHIORKAR
Causes:
Occurring in children due to lack of protein in diet. Common in
countries that are facing famine, political unrest, natural disasters
such as earthquakes, landslides, floods, etc.
Symptoms:
Change in skin and hair colour,Fatigue, Diarrhea, Stunted
physical and mental growth, Edema

54. Stunted physical and
mental growth
Edema
Treatment: Consume Protein Rich Food
EGGS
FISH &MEAT
DAIRY PRODUCTS
NUTS
FRUITS

55. B) MARASMUS
Causes: Malnutrition, Lack of energy and protein, Poverty, Contaminated
water, Metabolic and anatomic changes
Symptoms: Lean body, Projected ribs, Sunken eyes, Dry skin
Sunken eyes
Projected ribs
Treatment: Consume Protein Rich Food- eggs, fish, meat, dairy
products, fruits and nuts

56. B) NUTRITIONAL EDEMA
Causes: It results from long continued deprivation of proteins and usually
occurs in famine areas.
Symptoms: loss of weight, reduced fat, anaemia, susceptibility to
infection, general lethargy, delay in healing of wounds.
Treatment: Consume Protein Rich Food- soyabean, eggs, fish, meat, dairy
products, fruits and nuts