MoBio Peptides Chapter 2

A peptide is a chain of amino acids linked together by peptide bonds. Polypeptides usually refer to long peptides whereas oligopeptides are short peptides (< 10 amino acids). Proteins are made up of one or more polypeptides with more than 50 amino acids.

Primary structure

The primary structure of a protein refers to its amino acid sequence. The amino acid in a peptide is also called a residue.


Figure 2-B-1. The amino acid sequence (primary structure) of ribonuclease A (RNase A), which is an enzyme acting on RNA. Each letter represents an amino acid (see one letter code of each amino acid).

Peptide bond

A peptide bond is the linkage between two amino acids, formed by the condensation reaction, as shown below:


Figure 2-B-2. Formation of the peptide bond by condensation reaction.

Phi-Psi angles

Due to the specific electronic structure of the peptide bond, the atoms on its two ends cannot rotate around the bond. Hence, the atoms of the group, O=C-N-H, are fixed on the same plane, known as the peptide plane. The whole plane may rotate around the N-Cα bond (φ angle) or C-Cα bond (ψ angle). Cα is the carbon atom connected to the R group.


Figure 2-B-3. Illustration of the peptide plane (gray area) and φ-ψ angles. The red line formed by the repeating -Cα-C-N-Cα- is the backbone of the peptide chain.

Mathematically, phi (φ) and psi (ψ) are the dihedral angle (also known as torsional angle) which is defined as the angle between the point (e.g., Cα) at the end of a 4-point sequence and the plane (e.g., peptide plane) occupied by the other three points. In a peptide, phi-psi angles are restricted to certain ranges. A plot of their distribution is called the Ramachandran plot.