Structural Levels of Proteins, Biology tutorial

Introduction to Structural Levels of Proteins:

Properties of the protein are mainly determined by its three dimensional structure, that in itself is function of its amino acid sequence and regular folded polypeptide backbone. Four levels of protein structure comprise: primary structure, secondary structure, tertiary structure and quaternary structures.

Primary Structure of Proteins:

Primary structure of the protein refers to sequence of amino acid residues in it. Primary structure is stated by all covalent bonds (peptide bonds and disulfide bonds) connecting amino acid residues in polypeptide chain. Peptide bond is essential to integrity of structure of any protein molecule and is basis of primary structure. Disulfide bridge is much incorporated in cross-linking between various parts of polypeptide chain.

i) Primary Structure of Insulin:

Each protein contains distinctive amino acid sequence. For instance, primary structure of insulin comprises of two polypeptide chains (A and B) linked by means of two disulfide bridges/cross linkages as shown in figure below.

1774_Primary Structure of Insulin.jpg

ii) Primary Structure-Protein Function Relationship:

Primary structure finds folding pattern of the protein that in turn finds its function. The classical example in which there is clear relationship between amino acid sequence of protein and its function is in sickle cell anaemia.

Sickle-cell Anaemia:

Sickle cell anaemia is the painful life-threatening genetic disease. Those troubled with this disease experience frequent emergency brought about by physical exertion, leading to raise pulse rate, weakness, dizziness and complexity in breathing. Erythrocytes of individuals with this disease are fewer and abnormally long, thin and crescent compared to biconcave shape of normal erythrocytes. This is due to once haemoglobin in these abnormal erythrocytes loses oxygen; it turns into insoluble and forms polymers which aggregate in tubular fibers. Blockage of capillaries by such abnormal RBC could cause severe pain (or crisis).

Secondary Structure of Proteins:

Secondary structural level of proteins refers to common regular folding patterns of polypeptide backbone. Few secondary structures happen extensively in proteins, most famous ones being α helix and β conformations. Secondary structures are dominated by hydrogen bonds. Hydrogen bonds exist principally between side chains of hydrophilic groups of amino acids. Peptide backbone itself also contributes to constancy of the secondary structure. Its carbonyl groups (C=O) and its amino groups (N-H) are able to form hydrogen bonding with each other. As groups are frequently spaced, it isn't surprising that hydrogen bonding between them could provide rise to regular structures.

i) α- Helix:

This α-helix can be produced by winding protein chain/polypeptide backbone around imaginary axis by helix, in such a way that R groups are projected outward from helical backbone, such that there are 3.6 amino acyl units per turn of helix and axial translation of 1.47 Å per unit.

1401_a-helix.jpg

A helix may be characterised by the number, n, of polypeptide units perhelical turn and by its pitch, p, the distance the helix rises along its axis per turn. This distance can also be referred to the axial distance.

ii) β-Conformation/Structure:

In β-conformation, another regular folded structure in naturally occurring proteins, polypeptide backbone is in zigzag structure. This zigzag polypeptide chain can be hydrogen bonded to adjacent chains to create β-sheet. It is also likely to contain adjacent segments of the polypeptide chain forming β-sheet using hydrogen bonding. Adjacent chains in a β-sheet can either be parallel (with polypeptide chains having same amino-to-carboxyl orientations) or antiparallel (with chains containing opposite orientation). Hydrogen bonding pattern in parallel and antiparallel sheets are different.

iii) Determination of Secondary Structure:

X-ray diffraction has been utilized in showing presence of helices. Method is based on observation that when the parallel beam of monochromatic X-rays impinges on the crystal or fibre composed of regular array of units, light waves will be scattered by electrons of atoms of crystal or fibre and characteristic diffraction patterns will be attained. X-ray diffraction patterns from naturally occurring proteins which exists in pleated sheet conformations are considerably different from those derived from naturally occurring proteins which exist predominantly in helical conformations.

Tertiary Structure of Proteins:

Tertiary structure refers to general three-dimensional arrangement of all atoms in the protein. This comprises all bends and folds in polypeptide chains of protein. In tertiary structure, different segments of the protein's polypeptide chains are held by weak forces and at times by covalent bonds like Disulfide Bridge. It is because of their tertiary structures which proteins adopt the globular shape/conformation that provides lowest surface-to-volume ratio, therefore minimizing interaction of protein with its surrounding.

Quaternary Structure of Proteins:

Quaternary structure of protein refers to arrangement of polypeptide chains in multichain protein. Or we can say, quaternary structural levels cope with number of subunits in the given protein. These subunits are noncovalently bonded to each other, though there are other connections among them. The multisubunit protein is also referred to as the multimer. Protein with two subunits is known as the dimer whereas one with few subunits is frequently known as the oligomer. Multimer can have identical subunits or repeating groups of nonidentical subunits. Repeating structural unit in such a multimeric protein, whether it is single subunit or group of subunits, is known as protomer.

Quaternary Structure of Haemoglobin:

A good example of the oligomeric protein is haemoglobin. This transport protein has four polypeptide chains and four heme prosthetic groups, in which iron atoms are in ferrous (Fe2+) state. Protein part, called as globin, includes two α chains (141 residues each) and 2 β chains (146 residues each). Subunits of hemoglobin are set in symmetric pairs, every pair containing one α and one β subunit. Hemoglobin can, therefore, be viewed as tetramer or dimer of αβ protomer.

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