Proteins are the polymers of amino acids, with each amino acid residue joined to its neighbor by a peptide bond. There are twenty different amino acids commonly found in proteins. Asparagine was the first discovered amino acid in the year 1806 and found in asparagus.
Structural features of amino acids
The amino acids are grouped into five main classes by properties of their R groups.
Common 20 Amino acids are:-
Nonpolar, aliphatic R group – (7)
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine.
Aromatic R group – (3)
Phenylalanine, Tyrosine, Tryptophan.
Polar uncharged R group – (5)
Serine, Threonine, Cysteine, Asparagine, Glutamine.
Positively charged R group – (3)
Lysine, Histidine, Arginine.
Negatively charged R group – (2)
Aspartate (Asp, D ), Glutamate (Glu, E ).
Some uncommon amino acid and their functions:-
The protein may contain other residues formed by the modification of basic residues apart from 20 amino acids.
4-hydroxyproline – a derivative of proline.
5-hydroxylysine – derived from lysine.
4-hydroxyproline is found in plant cell wall proteins, and both are found in collagen.
Methyllysine – it is a constituent of myosin.
γ-carboxygulatamate – it is present in the prothrombin and in certain other proteins that bind Ca2+ as part of their biological function.
Amino acids can act as acid and bases, and when amino acids dissolved in water, it exists as the dipolar ion, or zwitterion. A zwitterion can serve as both an acid (protein donor) or a base (protein acceptor).
Peptide and Proteins
Peptides are the chains of amino acids. The two amino acid molecules covalently joined through a substituted amide linkage, termed as the peptide bond. The condensation reaction forms the peptide bond.
Oligopeptide – when few amino acids are joined through peptide bonds.
Polypeptide – when many amino acids are joined through peptide bonds.
In a peptide, the two ends are called as amino-terminal (or N-terminal) and carboxy-terminal (or C-terminal).
Amino-terminal – It is the end with a free α-amino group.
Carboxy-Terminal – It is the end with a free carboxy-terminal group.
Level of protein structure
The primary structure of a protein is a linked series of amino acids with a unique sequence.
In most of the protein, a repeatedly coiled or folded segment is present so that it contributes to the protein’s overall shape. Example – α helix and the β pleated sheet. The hydrogen bonds maintain the shape of α helix and the β pleated sheet.
Tertiary structure is the result of interactions between the side chains of the various amino acids and it is the overall shape of a polypeptide.
When a protein has two or more polypeptide subunits, then their arrangement in three-dimensional space is known as Quaternary structures
Other chemical groups are present in some Amino acids
Conjugated proteins – Proteins that contains permanently associated chemical components in addition to amino acids are called conjugated proteins. The non-amino part of the amino conjugated proteins is known as the Prosthetic group.
On the basis of the chemical nature of the prosthetic group, conjugated protein are divided into:-
- Lipoproteins – contains lipids as prosthetic group.
Example – β1-Lipoprotein of blood.
- Glycoproteins – contains carbohydrates as prosthetic group.
Example – Immunoglobulin G.
- Phosphoproteins – contains phosphate groups as prosthetic group.
Example – Casein of milk.
- Hemoproteins – contains heme (iron porphyrin) as prosthetic group.
Example – Hemoglobin.
- Flavoproteins – contains flavin nucleotides as prosthetic group.
Example – Succinate dehydrogenase.
- Metalloproteins – contains metals as prosthetic group.
Example – Ferritin(contains Iron), Alcohol dehydrogenase(contains Zinc), Clmodulin (contans Calcium), Dinitrogenase (contains Molybdenum), Plaastocyanin(contains Copper).