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Chapter written by Sylvain GERBER and Yoland SAVRIAMA.

Proteins are involved in most cellular functions at all levels, from DNA duplication to chemical metabolism, cell structuring and signal transmission. Despite their very varied activities, these molecules are quite homogeneous: proteins 1 are polymers composed of 20 base units, the amino acids (or residues when polymerized). The latter are composed of a central carbon atom (Cα) linked to an amino group (NH 2), a carboxylic group (COOH), a hydrogen atom and one of 20 different chemical groups called “side chains” ( Figure 2.1). Residues and their different chemical functions allow the functional diversity of proteins. In the polypeptide chain, the α-carboxylic group of an amino acid is linked to the α-amino group of the next amino acid through an amide bond (peptide bond −CO−NH−, Figure 2.2). Most natural proteins contain between 50 and 2,000 amino acid residues. The unbranched chain of residues is oriented: it starts at the amino end (N-terminal) and ends at the carboxy end (C-terminal). The chain of atoms regularly repeating the peptide bonds is called the “peptide backbone”. The peptide bond is rigid and flat because of the partial double bond character of the −CO−NH− bond, but rotations are possible around the other bonds of the backbone.