Lecture 11

Proteins

Physical properties of amino acids1. Solubility:Most of the amino acids are usually soluble in

water and insoluble in organic solvents2. Melting point:Generally melt at higher temperature often

above 200oC3. Taste:They may be sweet , tasteless or bitter

4. Optical properties: All the amino acids except glycine posses

optical isomers due to the presence of asymmetric carbon atom

5. Amino acids as ampholytesAmino acids contain both acidic (-COOH) and

basic (-NH2) groups. The can donate and accept a proton

Zwitterion or dipolar ion

Chemical propertiesThe general reactions of amino acids are

mostly due to the presence of two functional groups

Carboxyl groupAmino group

Reactions due to –COOH group1. Amino acids form salts with bases and

esters with alcohol2. Amino acids undergo decarboxylation

producing corresponding amines (histamine, tyramine)

3. The carboxyl group of dicarboxylic amino acids reacts with ammonia to form amide

Aspartic acid + NH3 AsparagineGlutamic acid + NH3 glutamine

Reactions due to –NH2 group1. The amino groups behave as bases and

combine with acids to form salt2. The amino acids react with ninhydrin to

form a purple, blue or pink colour complex (Ruhemann’s purple)

3. Colour reaction of amino acids: amino acids can be identified by specific colour reactions

4. Transamination5. Oxidative deamination

Non-standard amino acidsAmino acid derivatives in proteinse.g. Collagen, Histone, cystine Non-protein amino acidsThey may be either alpha or non alpha amino acidse.g. Ornithine, Citrulline, thyroxine D-amino acidsThe vast majority of aa isolated from animals and

plants are of L-category. Certain D-amino acids are found in the antibiotics.

D-alanine and D-glutamic acid are found in bacterial cell wall

D-serine and D-aspartate are found in brain tissues

Structure of ProteinsThe structure of proteins can be divided into

four levels of organization1. Primary structure2. Secondary structure3. Tertiary structure4. Quaternary structure

Primary structure of proteinsEach protein has a unique sequence of amino acids

which is determined by the genes contained in a DNA.The primary structure is largely responsible for its

functionA vast majority of genetic disorders are due to

abnormalities in the primary structure of proteinsPeptide bondCharacteristics of peptide bondsThe peptide bond is rigid and planar with partial double

bond in character. Both –C=O and –NH groups of peptide bonds are polar and are involved in hydrogen bond formation

Writing of peptide structures:Conventionally the peptide chains are

written with the free amino end (N-terminal) at the left and the free carboxyl end (C-terminal) at the right.

The amino acid sequence is read from N-terminal end to C-terminal end

The protein synthesis also starts from the N-terminal amino acid

Shorthand to read peptides:The amino acids in a peptide or proteins are

represented by the 3-letter or one letter abbreviation. This is chemical shorthand to write proteins

Naming of peptides:The suffixes –ine, -an, -ate are changed to –yl with

the exception of C-terminal amino acidH3N-glutamate-cysteine-glycine-COO-

E C G Glu Cys Gly

Glutamyl Cysteinyl Glycine

Secondary structure of ProteinThe conformation of polypeptide chain by

twisting or folding is referred to as secondary structure

The amino acids are located close to each other in their sequence

Two types of secondary structures, alpha helix an beta sheet are mainly identified

Indian scientist Ramachandran made a significant contribution in understanding the spatial arrangement of polypeptide chains

Alpha helixα-helix is the most common spiral structure or

proteins. It has a rigid arrangement of polypeptide chain

α-helical structure was proposed by Pauling and Corey (1951)

Salient features1. the alpha helix is tightly packed coiled

structure with amino acid side chains extending outwards from the central axis

The alpha helix is stabilized by extensive hydrogen bonding. It is formed between H atom attached to peptide N, and O atom attached to peptide C. the hydrogen bonds are individually weak but collectively they are strong enough to stabilize the helix

All the peptide bonds except the first and last in polypeptide chain participate in hydrogen bonding

Each turn of alpha helix contains 3.6 amino acids and travel a distance of 0.54 nm. The spacing of each amino acid is 0.15 nm

Alpha helix is a stable conformation formed spontaneously with the lowest energy

The right handed helix is more stable than the left handed helix

Certain amino acids disrupt the alpha helix (proline, basic and acidic amino acids)

Beta pleated sheetsThey are composed of two or more

segments of fully extended peptide chainsIn the beta sheets the hydrogen bonds are

formed between the neighboring segments of polypeptide chains

Tertiary structureThe three dimensional arrangement of

protein structure is referred to as tertiary structure.

It is a compact structure with hydrophobic side chains held interior while the hydrophilic group on the surface of protein molecule

Besides the hydrogen bond, disulphide bond, ionic interaction, hydrophobic interactions and Vander wall forces also contribute to the tertiary structure of proteins

Quaternary structure A great majority of proteins are composed

of single polypeptide chainsSome of the proteins however consists of

two or more polypeptides which may be identical or unrelated. Such proteins are termed as oligomers and possess quaternary structure

The individual polypeptide chains are known as monomers, protomers or subunits

A dimer consists of two polypeptide chains while tetramer has four

Bonds The monomeric subunits are held together

by non covalent bonds namely hydrogen bonds, ionic bonds

Importance These proteins play a significant role in the

regulation of metabolism and cellular functions

ExamplesHemoglobin, aspartate tanscarbomylase,

lactate dehydrogenase.