Structure and Formation of Protein

                             Structure and Formation of Protein

Topics to be covered in this lesson

Structure of Protein :-

(1)Primary Structure

(2)Secondary Structure

(3)Tertiary Structure

(4)Quanteray Structure

Formation of Protein :-

(1) Translation Process

Primary Protein  :-

Primary Protein

Primary Structure of ProteinThere are 20 different standard L-a-amino acids used by cells for protein construction.

 Amino acids, as their name indicates, contain both a basic amino group and an acidic carboxyl group. 

This difunctionality allows the individual amino acids to join together in long chains by forming peptide bonds: amide bonds between the -NH2 of one amino acid and the -COOH of another.

Sequences with fewer than 50 amino acids are generally referred to as peptides, while the terms protein or polypeptide are used for longer sequences.

A protein can be made up of one or more polypeptide molecules. 

The end of the peptide or protein sequence with a free carboxyl group is called the carboxy-terminus or C-terminus. 

The terms amino-terminus or N-terminus describe the end of the sequence with a free a-amino group.The amino acids differ in structure by the substituent on their side chains

. These side chains confer different chemical, physical and structural properties to the final peptide or protein. 

The structures of the 20 amino acids commonly found in proteins .

Secondary Structure :-

secondary protein

Stretches or strands of proteins or peptides have distinct characteristic local structural conformations or secondary structure, dependent on hydrogen bonding.

 The two main types of secondary structure are the a-helix and the ß-sheet.

The a-helix is a right-handed coiled strand.

 The side-chain substituents of the amino acid groups in an a-helix extend to the outside. 

Hydrogen bonds form between the oxygen of the C=O of each peptide bond in the strand and the hydrogen of the N-H group of the peptide bond four amino acids below it in the helix.

 The hydrogen bonds make this structure especially stable. The side-chain substituents of the amino acids fit in beside the N-H groups.

The hydrogen bonding in a ß-sheet is between strands (inter-strand) rather than within strands (intra-strand).

 The sheet conformation consists of pairs of strands lying side-by-side. 

The carbonyl oxygens in one strand hydrogen bond with the amino hydrogens of the adjacent strand. 

The two strands can be either parallel or anti-parallel depending on whether the strand directions (N-terminus to C-terminus) are the same or opposite. 

The anti-parallel ß-sheet is more stable due to the more well-aligned hydrogen bonds.

Tertiary Structure :-

Tertiary Protein

The overall three-dimensional shape of an entire protein molecule is the tertiary structure. 

The protein molecule will bend and twist in such a way as to achieve maximum stability or lowest energy state.

 Although the three-dimensional shape of a protein may seem irregular and random, it is fashioned by many stabilizing forces due to bonding interactions between the side-chain groups of the amino acids.

Under physiologic conditions, the hydrophobic side-chains of neutral, non-polar amino acids such as phenylalanine or isoleucine tend to be buried on the interior of the protein molecule thereby shielding them from the aqueous medium.

 The alkyl groups of alanine, valine, leucine and isoleucine often form hydrophobic interactions between one-another, while aromatic groups such as those of phenylalanine and tryosine often stack together.

 Acidic or basic amino acid side-chains will generally be exposed on the surface of the protein as they are hydrophilic.

The formation of disulfide bridges by oxidation of the sulfhydryl groups on cysteine is an important aspect of the stabilization of protein tertiary structure, allowing different parts of the protein chain to be held together covalently. 

Additionally, hydrogen bonds may form between different side-chain groups

Quaternary Structure :-

Quaternary Protein

Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits. 

These subunits may be the same (as in a homodimer) or different (as in a heterodimer).

 The quaternary structure refers to how these protein subunits interact with each other and arrange themselves to form a larger aggregate protein complex.

 The final shape of the protein complex is once again stabilized by various interactions, including hydrogen-bonding, disulfide-bridges and salt bridges. 

TRANSLATION :-

Translation process

Translation refers to the process of polymerisation of amino acids to form a polypeptide .

The order and sequence of amino acidsare defined by the sequence of bases in the mRNA. 

The amino acids are joined by a bond which is known as a peptide bond. Formation of a peptide bond requires energy. 

Therefore, in the first phase itself amino acids are activated in the presence of ATP and linked to their cognate tRNA–a process commonly called as charging of tRNA or aminoacylation of tRNA to be more specific.

 If two such charged tRNAs are brought close enough, the formation of peptide bond between themwould be favoured energetically. 

The presence of a catalyst would enhance the rate of peptide bond formation.

The cellular factory responsible for synthesising proteins is the ribosome. 

The ribosome consists of structuralRNAs and about 80 different proteins. In its inactive state, it exists as two subunits; a large subunit and a small subunit. 

When the small subunit encounters an mRNA, the process of translation of the mRNA to protein begins. 

There are two sites in the large subunit, for subsequent amino acids
to bind to and thus, be close enough to each other for the formation of a peptide bond.

 The ribosome also acts as a catalyst (23S rRNA in bacteriais the enzyme- ribozyme) for the formation of peptide bond.