Proteins

Proteins are high molecular mass complex biopolymers made up of smaller

units called amino acids. All proteins contains C, H, O, N and S. Some of
these also contain phosphorus, iodine and traces of metals like Fe, Cu, Zn,
Mn. All proteins on hydrolysis first give polypeptides and finally give amino
acids.

Amino Acids
The compounds containing amino group (-NH2) and carboxylic group (-
COOH) are called amino acids. The general structure is:

Structure of Amino Acids

There are actually thousands of amino acids occurring in nature. But

only about 20 amino acids form a part of the proteins in the human
 body. These twenty acids will be our focus here. Although all these
have varied structures, the basic structure of amino acid remains
uniform.

 All amino acids contain a carbon atom in the middle of the molecule,
the alpha-carbon
 This atom is surrounded by three chemical groups.
 One is an amine group -NH2
 The second one is a carboxyl group -OOOH
 The third group is denoted by R. This is the variable radical group
and is different for every amino acid. This R group makes the amino
acid unique.

Classification of Amino Acids

Amino Acid can be classified based on their structure and the structure
of their side chains i.e. the R chains. Now two basic subcategories are

1] Non-Polar Amino Acids

These are also known as Hydrophobic. The R group can be either of

Alkyl groups (with an alkyl chain) or Aromatic groups. The acids
falling in this group are stated below. Numbers one to seven are Alkyl
and the last two are aromatic

i. Glycine (H)
ii. Alanine (CH3)
iii. Valine ( CH (CH3)2 )
iv. Methionine ( CH2CH2SCH3 )
 v. Leucine ( CH2CH(CH3)2 )
vi. Isoleucine ( -CH(CH3)CH2CH3 )
vii. Proline (special structure)
viii. Phenylalanine
ix. Tryptophan

2] Polar Amino Acids

If the side chains of amino acid contain different polar groups like
amines, alcohols or acids they are polar in nature. These are also known
as Hydrophilic Acids. These are further divided into three further
categories.

a) Acidic: If the side chain contains an extra element of carboxylic acid

component these are acid-polar amino acids. They tend to donate their
hydrogen atom. These are:

i. Aspartic Acid ( CH2COOH)

ii. Glutamic Acid ( CH2CH2COOH )

b) Basic: These have an extra nitrogen group that tend to attract a

hydrogen atom. The three basic polar amino acids are

i. Histidine
ii. Lysine ( CH2(CH2)2NH2 )
iii. Arginine
 c) Neutral: These are neither acidic nor basic. They have an equal
number of amino and carboxyl groups. Also, they have at least one
hydrogen component connected to electronegative atoms. Some of these
neutral acids are

i. Serine ( CH2OH )
ii. Threonine ( CH(OH)CH3 )
iii. Asparagine ( CH2OHNH2 )
iv. Glutamine ( CH2CH2CONH2 )
v. Cysteine ( CH2SH )
vi. Tyrosine
Amino acid can also be classified on the basis of their need to the
human body and their availability in the human body

 Properties of Amino Acids

Now that we have seen the structure and types of amino acids.
Now from this information, we can arrive at the properties of amino
acids.

 Each amino acid has both an acidic and basic group as you can see
from its structure. This is the reason they behave like salts.
 Any amino acid in the dry state is in crystalline form. They exist as a
dipolar ion. The COOH group exists as an anion. And the NH2 group
exists as a cation. This dipolar ion has a special name “Zwitter ions’.
 In aqueous solution, alpha amino acids exist in equilibrium between
a cationic form, an anionic form and dipolar ion.
 The Isoelectric point is the pH point at which the concentration of
zwitter ions is the highest ad the concentration of cationic and
anionic form is equal. This point is definite for every α-amino acid.
 They are generally water soluble and also have high melting points.

 Essential Amino Acids

These are the acids that cannot be synthesized in our bodies. We
must rely on food sources to obtain these amino acids. They are

 Leucine
 Isoleucine
 Lysine
 Theorine
 Methionine
 Phenylalanine
 Valine
 Tryptophan
 Histidine (conditionally essential)
  Non-Essential Amino Acids
These acids are synthesized in our bodies itself and we need not
rely on outside sources for them. They are either produced in our bodies
or obtained from protein breakdowns.

Zwitter ion
1. Amino acid contains both basic acidic (carboxyl group) and basic
(amino group) groups in the same molecule. In aque-ous solution, the
carboxyl group loses a proton which is accepted by the NH2 group
which results in the formation of a dipolar ion known as Zwitter ion.
This is neutral but contains both positive and negative charges.

2. In zwitter ionic form, amino acids show arnphoteric behaviour as they

react both with acids and bases.

Isoelectric point

The pH at which this dipolar ion stops moving towards the respective
electrode is known as isoelectric point. At isoelectric point, the amino acids
have the least solubility in water.

Peptides
Peptides are condensation products of two or more amino acid

Two molecules of different amino acids can form two dipeptides.Three

molecules of different amino acids can give six tripeptides.

Dipeptide has only one peptide bond, tripeptide has two peptide bonds and so
on. Thus, a polypeptide made up of n-amino acids has (n – 1) peptide bonds.

Peptide Linkage

Peptide linkage is an amide linkage formed by condensation of two amino

acids involving −NH2 group of one amino acid and the −COOH group of the
other amino acid with the loss of water.

For example:
Classification of Peptides:

• On the basis of number of amino acids undergoing the condensation, the

peptides can be classified as:

 Dipeptide: It is a peptide composed of two amino-acid residues.

 Tripeptide: It is a peptide composed of three amino-acid residue.

Polypeptides

Condensation Products of many amino acids ( ‘In P xiucts of many amino

acids (≈ 10000) is known as polypeptide and those polypeptides which
have molecular mass above than 10000 are called proteins
Protein
Peptide having molecular mass higher than 10,000 u is called a protein.

Classification of Protein

• On the basis their molecular shape, proteins can be classified as:

 Fibrous proteins: The polypeptide chains run parallel and are held
together by hydrogen and disulphide bond forming a fibre like
structure

They are generally insoluble in water.

For example: Keratin (present in hair, wool, silk) and myosin (present in
muscles), etc.

 Globular proteins: The polypeptide chains coil around to give a

spherical shape. These are soluble in water

For example: Insulin and albumins

Structure of Proteins

 Primary Protein Structure

The primary structure is the unique formation and order in which

the amino acids (the building blocks) combine and link to give us a
protein molecule. Protein gets all its properties from its primary
structure.
There are in all twenty amino acids in the human body. All of these
have a carboxyl group and an amino group. But each has a different
variable group known as the “R” group. It is this R group that lends a
particular protein its unique structure.

Every protein is determined by the sequencing of the amino acids. The

formation and ordering of these amino acids in proteins are extremely
specific. If we alter even one amino acid in the chain it results in a non-
functioning protein or what we call a gene mutation.

 Secondary Protein Structure

After the sequencing of amino acids, we now move on to the

secondary structure. This is when the peptide backbone of the protein
structure will fold onto itself, to give proteins their unique shape. This
folding of the polypeptide chains happens due to the interaction
between the carboxyl groups along with the amine groups of the peptide
chains.

There are two kinds of shapes formed in the secondary structure. These
are

 α-helix: The backbone follows a helical structure. The hydrogen

bonds with the oxygen between the different layers of the helix,
giving it this helical structure.

 β-pleated sheet: here the polypeptide chains are stacked next to

each other and their outer hydrogen molecules form intramolecular
bonds to give it this sheet-like structure
  Tertiary Structures

This is the structure that gives protein the 3-D shape and
formation. After the amino acids form bonds (secondary structure) and
shapes like helices and sheets, the structure can coil or fold at random.
This is what we call the tertiary structure of proteins. If this structure is
disrupted or disturbed a protein is said to be denatured which means it is
chemically affected and its structure is distorted.

 Quaternary Structure

Finally, we come to the fourth structure. The spatial

arrangement of two or more peptide chains leads to this structure. It is
important to note it is not necessary for proteins to have quaternary
structures. Primary, secondary and tertiary structures are present in all
natural proteins, but the same is not true for quaternary structure. Hence
if a protein has only the first three structures it is considered to be a
protein.
 Classification on the Basis of Hydrolysis Products
(i) Simple These yield only a-amino acids upon hydrolysis.
e.g., albumin.

(ii) Conjugated proteins These yield α-amino acids and non-protein part,
called prosthetic group.

Protein Prosthetic group

Nucleoproteins Nucleic acid

Phospho proteins Phosphoric acid

Glycoproteins Carbohydrates

Metalioproteins Metals

Lipoproteins Lipids

(iii) Derived proteins These are obtained by partial hydrolysis of simple or

conjugated proteins.
Proteins → Proteoses → Peptones → Polypeptides

Classification on the Basis Functions

1. Structural proteins Fibrous proteins

2. Enzymes Serve as biological catalyst e.g., pepsin, trypsin etc.
3. Hormones Insulin
4. Contractile proteins Found in muscles, e.g., myosin, actin.
5. Antibodies Gamma globulins present in blood.
6. Blood protein Albumms, haemoglobin and fibrinogen.
Haemoglobin is a globular protein. Its prosthetic group is heme. It Contains
574 amino acid units distributed in four polypeptide chains.

Two chains containing 141 amino acid residues each are called α-chains and
the two chains containing 146 amino acid residues are called β-chains.

Sickle cell anaemia is caused by defective haemoglobin obtained by replacing

only one amino acid, i.e., glutamic acid by valine.

Denaturation of Proteins

The process that changes the three dimensional structure of native proteins is
called denaturation of proteins. It can be caused by Change in pH, addition of
electrolyte, heating or addition of solvent like water, alcohol or acetone.

• The most stable conformation of a protein at a given temperature and

the pH is known as its native state.

• The loss of biological activity of proteins when a protein in its native

form, is subjected to physical change like change in temperature or chemical
change like change in pH, is called denaturation of protein.

• For example: (i) Coagulation of egg white on boiling, (ii) curdling of milk
which is caused due to the formation of lactic acid by the lactobacillus
bacteria present in milk

Tests of Proteins
(i) Biuret Test
Protein solution + NaOH + dil. CuSO4 → pink or violet colour.

(ii) Millon’s Test

Protein solution + Millon’s reagent → pink colour

Millon’s reagent is solution of mercuric nitrate and nitrite in nitric acid

containing traces of nitrous acid.

(iii) Iodine reaction

Protein solution + iodine in potassium iodide solution → yellow colour.
 (iv)Xanthoprotic test

Biological Importance of Proteins

(i) Proteins are structural components of cells.

(ii) The biochemical catalysts known as enzymes are proteins.
(iii) The proteins known as immunoglobins serve in defence against
infections.
(iv) Many hormones, such as insulin and glucagon are proteins.
(v) Proteins participate in growth and repair mechanism of body tissues.
(vi) A protein called fibrinogen helps to stop bleeding.
(vii) Oxygen is transported to different tissues from blood by haemoglobin
which is a protein attached to haeme part.