Sunday, February 8, 2009

Levels of Complexities of Structure of Proteins

Proteins and peptides are biopolymers composed of amino acid residues interlinked by amide bonds. Their structures can be discussed in terms of four levels of complexity and are as follows:
1) Primary structure
2) Secondary structure
3) Tertiary structure
4) Quaternary structure

The linear unbranched chain of amino acids linked together by covalent bonds known as peptide bonds is called the primary structure of a protein. In addition to peptide bonds, other types of covalent linkages such as disulphide bonds, if present, are also included in the primary structures. The types and the sequence of amino acids present in the polypeptide chain determine the nature of the secondary structures at different regions of the chain. The secondary structure of a segment of a polypeptide chain is the local spatial arrangement of its main-chain atoms without regard to the conformation of its side chains or to its relationship with other segments.

The major types of secondary structures observed in protein molecules are alpha (a ) helices and beta (b ) pleated sheets in addition to random coils and beta turns. All these secondary structures may be present independently or may be together in the secondary or tertiary structures of a single polypeptide chain. The secondary structure undergoes further folding and reorganization within the molecule resulting in higher order compact structures or the tertiary structure.

There are structural components comprising a few alpha-helices or beta-strands, which are frequently repeated within structures, called supersecondary structures (being intermediate to secondary and tertiary structures). These compact structurally distinct elements are known as motifs. When these structurally distinct regions of protein molecules are associated with a specific function, those structurally and functionally distinct units are called a domain. Structurally-related domains are found in different proteins, which perform similar functions.

The molecular forces, which are responsible for the secondary and tertiary structures, are the non-covalent interactions between the various amino acid side chains within the molecule and with the water molecule surrounding it. The main molecular force responsible for the various secondary structures are the hydrogen bonds and the molecular forces behind the tertiary structures are the ionic bonds, hydrogen bonds, hydrophobic and hydrophilic interactions, and van der Waals force. Secondary and tertiary structures represent the most thermodynamically stable conformations or shapes for the molecule in a solution. The quaternary structure is the assembly of two or more independent polypeptides or proteins at their tertiary stage to form a multimeric protein. The individual component pep tides of the multimeric proteins are known as subunits and are held together via non-covalent forces. The subunits of a multimeric protein may be similar or dissimilar. For example, hemoglobin contains four polypeptide chains (20. chains and 213 chains) held together non-covalently in a specific conformation as required for its function.

The major molecular forces that cause the linear polypeptide chain to undergo a specific type of coiling and folding in space to a characteristic three-dimensional shape are the non-covalent forces. These forces, to a greater extent, lie in the chemical and structural properties of the constituent amino acid residues of the polypeptide chain. There are 20 types of amino acids by which the entire protein of the living system is composed. These amino acids can be broadly classified into three categories-hydrophobic (tryptophan, phenylalanine, leucine, etc.), polar (glutamine, serine, etc.), and charged (aspartic acid, lysine, etc.) amino acids. Therefore, these amino acids are capable of interacting with each other within the protein molecules via various non-covalent interactions leading to a very characteristic shape and biological property for the protein molecule.

Tags: Bio Technology, Bio Genetics, Proteins

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