This article provides a note on protein structure. Proteins can occur in four structures such as: (1) Primary Structure (2) Secondary Structure (3) Tertiary Structure and (4) Quaternary structure.
The primary structure of a segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain(s), without regard to spatial arrangement (apart from configuration at the alpha-carbon atom).
The “R” in the amino acid generic structure stands for the term “radical” and represents one of twenty or so different possibilities. So with 20 different “R” groups, there are twenty different amino acids in nature.
All amino acids have attached to the same carbon both an amino group (NH2) and a carboxyl group (COOH). The hydrogen from the carboxyl group actually exists in a cloud around the amino group and itself, thus creating the zwitterion. This renders the amino acid active and proteins formed from them capable of great activity. Buffers and enzymes are examples of active proteins. The peptide bond is formed when the amino group of one amino acid and the carboxyl group of another amino acid unite with the loss of one water molecule per bond.
The commonly occurring amino acids are of 20 different kinds (a protein may contain a chain of 100 to 1000 amino acids; 26 alphabets in English making several thousand words, 20 amino acids forms different proteins) which contain the same dipolar ion group H3N+.CH.COO–. They all have in common a central carbon atom to which are attached a hydrogen atom, an amino group (NH2) and a carboxyl group (COOH). The central carbon atom is called the Calpha -atom and is a chiral centre.
All amino acids found in proteins encoded by the genome have the L-configuration at this chiral centre. This configuration can be remembered as the CORN law (Fig. 8.6). Imagine looking along the H-Calpha bond with the H atom closest to you.
When read clockwise, the groups attached to the Calpha spell the word CORN. There are 20 side chains found in proteins encoded by the genetic machinery of the cell. The side chains confer important properties on a protein such as the ability to bind ligands and catalyse biochemical reactions. They also direct the folding of the nascent polypeptide and stabilise its final conformation.
Amino acids in proteins (or polypeptides) are joined together by peptide bonds. The sequence of R-groups along the chain is called the primary structure. Proteins can occur as primary, secondary, tertiary or quaternary structures.
The secondary structure of a segment of 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. There are three common secondary structures in proteins, namely alpha helices, beta sheets and turns. The alpha-helix and beta-structure conformations for polypeptide chains are generally the most thermodynamically stable of the regular secondary structures. However, particular amino acid sequences of a primary structure in a protein may support regular conformations of the polypeptide chain other than alpha-helical or beta-structure.
The tertiary structure of a protein molecule, or of a subunit of a protein molecule, is the arrangement of all its atoms in space, without regard to its relationship with neighboring molecules or subunits.
The quaternary structure of a protein molecule is the arrangement of its subunits in space and the ensemble of its inter-subunit contacts and interactions, without regard to the internal geometry of the subunits. The subunits in a quaternary structure must be in non-covalent association. Hemoglobin contains four polypeptide chains (alph a2b2) held together non-covalently in a specific conformation as required for its function.