The peptide bond

A condensation reaction

The carboxyl group of one amino acid reacts with the amino group of another. A molecule of water is released and the two are joined by an amide bond. What is left of each amino acid in the chain is called a residue.

Flat and rigid

Electrons are shared between the carbonyl oxygen, the carbon and the nitrogen, which gives the bond partial double-bond character. The six atoms around it lie in one plane and the bond does not rotate freely. Almost all peptide bonds adopt the trans arrangement; bonds before proline are the main exception.

Rotation happens instead around the two bonds on either side of each alpha carbon. Those two angles, called phi and psi, describe the path of the backbone and therefore the shape of the chain.

Two different ends

A chain has a free amino group at one end, the N-terminus, and a free carboxyl group at the other, the C-terminus. Sequences are always written from N to C. Synthetic peptides are often capped, with an acetyl group at the N-terminus or an amide at the C-terminus.

From dipeptide to protein

Two residues make a dipeptide, three a tripeptide. Short chains are called oligopeptides and longer ones polypeptides. The line between a peptide and a protein is a convention, not a law: around fifty residues is the figure most often quoted.

Bridges and rings

Two cysteine residues can link through their sulfur atoms to form a disulfide bridge, which closes part of the chain into a ring. Oxytocin, nine residues long, has one such bridge between its first and sixth residues.

Why peptides are short-lived

Enzymes called peptidases cut peptide bonds by adding the water back, a reaction called hydrolysis. This is why many natural peptides last only minutes in the body, and why modified residues, ring closure or attached fatty-acid chains are common in designed peptides.

General chemistry, written for orientation. It does not describe how to use any substance.