Amino Acids

Twenty amino acids are the building blocks of proteins. They are linked together in a linear polypeptide chain by forming peptide bonds between them, in an order ordained by the nucleotide sequence of the corresponding gene for the protein, translated from the corresponding messenger RNA.

Nineteen of the amino acids have the general structure

and differ only in the chemical structures of the side chain R. The amino group and the carboxyl group give this class of compounds its name. At physiological pH values, both groups are ionized, and the zwitterion is the common form of the amino acid. The exceptional amino acid, proline, differs in that its side chain is bonded to the nitrogen atom of the amino group, which is then a secondary amine, and proline is an imino acid: 

The central a-carbon atom is asymmetric in 19 of the amino acids and is always the L isomer:

The exception is glycine, in which the side chain is simply another hydrogen atom, so the C^a atom is no longer asymmetric.

The structures of the side chains of the 20 normal amino acids used in protein biosynthesis are described in Figure 1, and their properties are described in individual entries. The central, asymmetric carbon atom is designated as a, and the atoms of the side chains are commonly designated b, g, d,Ɛ  and z in order away from the C^a atom. Chemical groups are, however, usually designated by the carbon atom to which they are bonded; hence, the Nz atom of a lysine residue is part of the Ɛ -amino group. A 21st amino acid that is used in protein biosynthesis in only a few instances is selenocysteine. Many variations of these 21 amino acids can be found in proteins as a result of post-translational modifications after synthesis of the polypeptide chain.

Figure 1. The side chains of the 20 amino acids that occur naturally in proteins. Small unlabeled spheres are hydrogen at labeled. Double bonds are black, and partial double bonds are shaded. In the case of proline, the bonds of the polypeptide included and are black. The three- and one-letter abbreviations commonly used appear below the name of the amino acidand threonine have asymmetric centers in their side chains, and only the isomer illustrated is used biologically.