Module 1 : Basics of proteomics
Lecture 2 : Basics of Amino acids and Protein
 

2. Peptide Bond

The covalent bond that holds two adjacent amino acid residues together is known as a peptide bond, which is formed between the carboxyl group of one amino acid and the amino group of other amino acid and is accompanied by release of a water molecule. The peptide bond is stabilized by resonance structure. The amide bond exhibits partial double bond character and is planar. In other words, it can exist in “cis” and “trans” form. In the unfolded form of a given protein, the peptide bonds have the liberty to take up either of the two forms; however the folded conformation has the peptide bond in a single form alone. The “trans” form is usually preferred as it's conformation is stable as compared to the “cis” form (Exception: Proline, which can exist in “cis” as well as “trans” form). The psi and phi are the angles of rotation about the bond between the a-carbon atom and carboxyl and amino groups, respectively. These angles determine which protein conformations will be favourable during protein folding.

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Illustration: Peptide Bond formation

Amino acids are the building blocks or monomers that make up proteins. Amino acids are oriented in a head-to-tail fashion and linked together such that the carboxyl group of one amino acid combines with the amino group of another. Two amino acids are joined together by means of such a condensation reaction with the loss of a water molecule forms a dipeptide. Many such amino acids linked together form a polypeptide. The peptide bond is rigid due to its partial double bond character arising from resonance structures. However, the bonds between the a-carbon and amino and carboxyl groups are pure single bonds that are free to rotate.