Protein

ISC 11>Content>Unit-4>Biomolecules :PROTEINS

CLASS PRESENTATION

Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells. Proteins also occur in great variety; thousands of different kinds, ranging in size from relatively small peptides to huge polymers with molecular weights in the millions,may be found in a single cell. Moreover, proteins exhibit enormous diversity of biological function and are the most important final products of the information pathways.

SOURCES OF PROTEIN
Proteins are obtained from animal and plant sources.
The animal sources of proteins include milk, egg, meat, fish, liver etc.
Plant sources of proteins are pulses, nuts and cereals.

AMINO ACIDS (BUILDING BLOCKS OF PROTEINS )

Amino acids are the simplest units of a protein molecule and they form the building blocks of protein structure.
The general formula of an amino acid can be written as,

An amino acid is an amino carboxylic acid.
R is the side chain or residue and it represents the group other than -NH2 and -COOH.
It may be a hydrogen atom (H) or a methyl group (-CH3) or an aliphatic group or an aromatic group or a heterocyclic group.
The amino acids are classified based on the nature of R groups.
Twenty different amino acids are commonly found in proteins.
The first to be discovered was asparagine, in 1806.

D and L amino acids

Based on the position of amino group on the asymmetric carbon atom, amino acids exist in two types. They are D and L amino acids.
The amino acid having the NH2 group on the right is called D-amino acid. The amino acid having the NH2 group on the left is called L-amino acid. These isomers are the mirror images of each other.
All amino acids are a amino acids because the NH2 group is attached to the a carbon atom which is next to the COOH group.
Examination of the structure of an amino acid except glycine, reveals that the a carbon atom has four different groups attached to it, thus making it asymmetric.
Because of the presence of asymmetric carbon atom, amino acids exist in two optically active forms, dextrorotatory and levorotatory.
Dextrorotatory, they rotate plane polarised light in the clockwise direction. Levorotatory, they rotate plane polarised light in the anti clockwise direction.
The direction of optical rotation of an amino acids indicated by the symbol + and - (+ indicates dextro and - indicate levo).
It has been found that L-amino acids are more common than D forms and most of the naturally occuring amino acids are L-amino acids.
Therefore L-amino acids are called natural amino acids.

PROPERTIES OF AMINO ACIDS
a) Physical properties :
Amino acids are coloureless, crystalline, generally soluble in water,in acid and in alkali but sparingly soluble in organic solvents.
b) Chemical properties: Zwitterion
Due to the presence of an acidic and a basic group in the same molecule, the amino acid exists largely as a dipolar ion or a zwitterion, which can react as an acid as well as a base. In zwitterion, the proton from the carboxylic group is transferred to the amino group. Thus a zwitterion carries both positive and negative charges.

CLASSIFICATION OF AMINO ACIDS

Amino acids can be divided on the basis of:

Requirement (Essential, nonessential)
Functional group (Basic, acidic, neutral)
R group (Polar or non polar)

1. Essential and non essential proteins:

Out of the twenty amino acids found in proteins in living organisms, following ones are essential are for human, because these can not be synthesised inside the cells.
These are taken from the plants directly by herbivores and indirectly by carnivores.

Essential and nonessential amino acids

2. Types of amino acids (Functional group) :

Basic- 1 carboxyl and 2 amino groups.
Acidic- 2 carboxyl and 1 amino group.
Neutral– 1 carboxyl and 1 amino group.

Acidic amino acids

Basic amino acids

3. R group (Polar or non polar)

Structural formula of amino acids (20)

FORMATION OF PEPTIDE BOND

In proteins, amino acids are linked together by linkages called peptide bonds. The carboxyl group of one amino acid is joined to the a amino group of another amino acid by a peptide bond.
The peptide bond is also called as the amide bond. The two aminoacids, joined by a peptide bond, constitute a dipeptide. The dipeptide is formed by simple condensation reaction.
The product formed by a peptide bond is called a peptide.
The compound formed by the linking of three amino acids is called as tripeptide.
A peptide formed of less than 10 amino acids constitute an oligopeptide.
More than 10 amino acids join together to form a polypeptide chain.

N and C terminal ends of protein

An amino acid in a polypeptide is called a residue.
A polypeptide have two ends, namely amino and carboxyl terminal end.
The end of the polypeptide chain containing amino group is called amino terminal or N-terminal.
The end of the polypeptide chain containing carboxyl group is called carboxyl terminal or C-terminal.
The terminal amino acid with the free amino group is called N-terminal amino acid and the terminal amino acid with the free carboxyl group is called C-terminal amino acid.

Functions of amino acids

Formation of proteins
Formation of biologically active compound like thyroxin, melanin, adrenalin, IAA, Coenzymes etc.
Formation of glucose
Formation of amines
Nitrogen storage
Antibiotics
Biological buffers
Cell wall of prokaryotes

Proteins

The term coined by' Berzelius'.
Proteins are among the most important macromolecule of the cell.
They play a very important role in structure and metabolism of cell.
Protein is made up of one or more polypeptide chains.
Many proteins, such as myoglobin, consist of a single polypeptide chain. Others contain two or more chains, which may be either identical or different. For example haemoglobin is formed of 4 polypeptide chains, of which two a chains are of one kind and the other two b chains are of another kind.

Properties of proteins

Physical properties

Colour and taste :Proteins are colourless and usually tasteless. These are homogeneous and crystalline.
Solubility: Solubility of proteins is influenced by pH. Solubility is lowest at isoelectric point and increased with increasing acidity of alkalinity.
Optical activity: All protein solutions rotate the plane polarised light to the left i.e. these are levorotatory.
Colloidal nature :Because of their giant size, the proteins exhibit many colloidal properties are:

Their diffusion rate is extermely low.
They may produce considerable light-scattering in solution, thus resulting in visible turbidity (Tyndall effect)

Chemical properties

Hydrolysis

By acidic agents : Proteins upon hydrolysis with concentrated mineral acids such as, HCl yield amino acids in the form of their hydrochlorides.
By proteolytic enzymes like pepsin and trypsin.

2. Colour reaction with Biuret reagent

When a protein solution is treated with alkaline CuSO4 reagent, the peptide bonds present in the protein interact with copper ions and forms violet coloured Biuret complex . The colour deepens which depend on the number of peptide bond present in the protein. All proteins except dipeptides react with Biuret reagent because a minimum of two peptide linkages are involved in this reaction.

Biuret test

STRUCTURE OF PROTEINS
Linder strom - Lang suggest four types of structural organisation for proteins.

Primary structure
Secondary structure
Tertiary Structure and
Quaternary strucutre

1. Primary structure

Primary structure refers to the linear sequence of amino acid residues.
The proteins are linear and unfolded.
The protein is formed of one or more polypeptide chains.
The amino acid residues are linked by repeating polypeptide bonds.
The adjacent polypeptide chains are linked by disulphide bonds.
Most of the structural proteins which are in the form of fibres exhibit primary structure.
The primary structure provides information on the number and proportion of different amino acids in a protein.

Human insulin has 51 amino acids distributed in two poly peptide chains. A chain-31 amino acids, B chain-20 amino acids and the polypeptides are linked by disulphide bridges.
Cytochrome C contains 104 amino acids.

Animation: Primary structure

2. Secondary structure

Secondary structure refers to the shape taken up by the polypeptide chain(s) within a protein molecule as the result of the formation of hydrogen bond between amino acids.
Secondary structure includes two forms
a) α-helix
b) β- pleated sheet

Animation : Secondary structure

a) α-helix :

A polypeptide chain forms regular helical coils called a-helix.
These coils are stabilized by hydrogen bonds between carbonyl oxygen of first amino and amide N of fourth amino acid residues.
Hair, nail, skin contain a group of proteins called keratins rich in helical structure.

b) β- pleated sheet

It consists of a number of adjacent polypeptide chain, which can run in the same direction (parallel) or in opposite direction (anti parallel) .
The sheet is stabilized by hydrogen bonds between CO group of one polypeptide chain and the NH group of adjacent polypeptide chains.
The protein fibroin (silk) has the β- pleated sheet structure.

3. Tertiary structure

The polypeptide chain with secondary structure may be further folded, super-folded, twisted about itself forming many sizes. Such a structural confirmation is called tertiary structure.
These are common in globular proteins.
The bonds responsible for interaction between groups of amino acids are as follows:

Hydrophobic interactions :Normally occur between nonpolar side chains of amino acids such as alanine, leucine, methionine, isoleucine and phenyl alanine. They constitute the major stabilzing forces for tertiary structure forming a compact three-dimentional structure.
Hydrogen bonds :Normally formed by the polar side chains of the amino acids.
Ionic or electrostatic interactions:The interaction occurs between opposite charged polar side chains of amino acids, such as basic and acidic amino acids.
Vander -wall forces : Occurs between non polar side chains.
Disulphide bonds :These are S-S bonds formed between - SH groups of distant cysteine residues.

Animation : Tertiary structure

4. Quaternary structure

Proteins formed of more than one polypeptide chain, each having primary, secondary and tertiary chain.
Each constituent peptide chain is called as a monomer or sub unit. The monomers of protein can be identical or quite different in primary, secondary or tertiary structure.
Proteins with 2 monomers (dimer) eg. Creatine phosphokinase
Proteins with 4 monomers (tetramer) eg. Haemoglobin has a quaternary structure with two α chains and two β chains.

Animation: Quaternary structure

TYPES OF PROTEINS ( Based on shape)

On the basis of shape of the molecule, proteins can be divided into two groups
a) Fibrous proteins
b) Globular proteins

a) Fibrous proteins

b) Globular protein

TYPES OF PROTEINS (Based on composition)

Simple protein : These proteins on hydrolysis yield only a-amino acids. (eg). albumin, globulin
Conjugated protein : These are proteins composed of simple proteins combined with non-protein part called as prosthetic groups.

They are further subdivided as follows:

FUNCTIONS OF PROTEINS

Functional diversity of proteins
Proteins are the fundamental constituents of all protoplasm and are involved in the structure and functions of living cells. Proteins have many different biological functions.

Catalytic proteins : Enzymes are proteins which have catalytic power, far beyond that of man-made catalysts. They enhance the rate of biochemical reactions. (eg.) amylase, carbonic anhydrase etc.
Nucleoproteins :Histones are basic proteins found in association with nucleic acids.They serve as carriers of genetic characters and hence govern inheritance of traits.
Hormonal proteins :Some hormones are proteins which regulate numerous physiological functions. (eg) growth hormone, insulin and glucagon.
Storage proteins :They have the function of storing amino acids as nutrients and as building blocks for the growing embryo. (eg) casein of milk, ovalbumin of egg white.
Transport proteins :They are capable of binding and transporting specific types of molecules via blood. (eg) hemoglobin and albumin.
Contractile proteins :Proteins such as actin and myosin in skeletal muscle function as essential elements in contractile and motile systems.
Defensive proteins : Some proteins have protective or defensive functions. The blood proteins - thrombin and fibrinogen participate in blood clotting. Antibodies or immunoglobulins are protective proteins which prevent the onset of diseases in the body.
Structural proteins :

Wall of pollen grains is also proteinaceous.
Matrix of connective tissue contains collagen, elastin and reticulin proteins in the form of fibres.
Matrix of cartilage (chondrin) is formed of protein and the bones formed of protein ossein.
Horny layer of skin, scales, scales, feather, hair, wool, etc are formed of keratin sulphate.
Fibrous proteins from supporting filaments, cables or sheets and form structures like tendons and ligaments.
Tendons are formed of collagen proteins and ligaments elastin.
Keratin is found in hair, nails and feathers.Proteins such as collagen, keratin etc. serve as structural elements.

9. Toxic proteins: Ricin of caster bean, diphtheria toxin and botulinum toxin represents another group of proteins which cause dysfunctions and disorders in the body.
10. Visual Pigment: Pigment rhodopsin present in the rod cells and iodopsin of cone cells of retina are proteins. These enable us to see in dark as well as in light and also differentiate colors.

ANIMATION :PROTEIN FUNCTIONS

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