Structural levels of Protein

Proteins have been assigned four levels of structural organization, primary, secondary, territory and quaternary levels of structure.

Primary structure (I). The number of sequence of amino acids in the polypeptide chain constitutes the primary structure. A few plant proteins exist at the primary level of structure in the form of straight chains of amino acids. The nature and the sequence of the amino acids determine the three-dimensional structure and properties of proteins.

Secondary structure (II). Most long polypeptide chains are folded or coiled in a number of ways. The brings about a second level of organization called the secondary structure. The most common form of coiling is the right handed alpha helix. Although the hydrogen bond is fairly weak, the large number of bonds involved maintains a stable structure. All the amino acid side chains are accommodated into the α-helix. They disrupt the α-helical structure and cause sharp bends or changes in the direction of the chain. Another form of secondary structure is the β-conformation β-pleated sheet. This results from hydrogen bonding between two peptide chains. The chains may be parallel or antiparallel. In a parallel chain β-pleated sheet the N atoms point in the same direction, while in the antiparallel chain β-pleated sheet, alternate chains are oriented in the same direction. The antiparallel structure permits maximum hydrogen bonding.



Tertiary structure (III). The polypeptide chain may undergo coiling and folding to produce the tertiary structure. The way the structure folds has an important bearing on the properties of the protein. The folding brings together active amino acids, which are otherwise scattered along the chain, and may form a distinctive cavity or cleft in which the substrate is bound. The tertiary structure is maintained by a number of bonds which are of different types.
(1) Disulphide bonds are covalent links which give some rigidity to the protein molecule. They are relatively more stable than the other types of bonds. A disulphide bonds is formed between two cysteine residues.
(2) Hydrogen bonds are weak but since they are numerous they give considerable stability to the protein molecule. Hydrogen bonds can be formed by sharing hydrogen between amide nitrogen and carbonyl oxygen of the peptide backbone. They are also formed between groups present in the side chain.
(3) Ionic or electrostatic bonds are formed when an acid and a basic amino acid are ionized and lie close together, Ionic bonds play an important role in binding a basic protein with an acidic marco-molecule, e.g. in the formation of nucleoproteins.
(4) Hydrophobic bonds are formed because of the tendency of the nonpolar side chains of neutral amino acids to closely associate with one another. When a protein molecule is submerged in an aqueous medium there is a tendency to expose a maximum number of its polar groups to the surrounding medium.

Quaternary Structure (IV) is shown by proteins containing more than one polypeptide chain. Two or more polypeptide chains may associated to give rise the quaternary structure. If the protein consists of identical units it is said to have a homogenous quaternary structure, e.g. the isozymes H4 and M4 of lactic dehydrognease (LDH) and the enzyme phosphorylase. If the units are dissimilar the protein is said to have a heterogeneous quaternary structure, e.g., haemoglobin which consists of two α chains and two β chains.