General Structure

Further information: List of standard amino acids

The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.
In the structure shown to the right, the R represents a side chain specific to each amino acid. The central carbon atom called Cα is a chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached. Amino acids are usually classified by the properties of the side chain into four groups. The side chain can make them behave like a weak acid, a weak base, a hydrophile if they are polar, and hydrophobe if they are nonpolar. The chemical structures of the 20 standard amino acids, along with their chemical properties, are catalogued in the list of standard amino acids.
The phrase "branched-chain amino acids" or BCAA is sometimes used to refer to the amino acids having aliphatic side-chains that are non-linear, these are leucine, isoleucine and valine. Proline is the only proteinogenic amino acid whose side group links to the α-amino group, and thus is also the only proteinogenic amino acid containing a secondary amine at this position. Proline has sometimes been termed an imino acid, but this is not correct in the current nomenclature.[8]

The two optical isomers of alanine.

Isomerism
Most amino acids can exist in either of two optical isomers, called D and L. The L-amino acids represent the vast majority of amino acids found in proteins. D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as cone snails.[9] They are also abundant components of the peptidoglycan cell walls of bacteria.[10]
The L and D conventions for amino acid configuration do not refer to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of glyceraldehyde having the same stereochemistry as the amino acid. S-Glyceraldehyde is levorotary, and R-glyceraldehyde is dexterorotary, and so S-amino acids are called L- even if they are not levorotary, and R-amino acids are likewise called D- even if they are not dexterorotary.
There are two exceptions to these general rules of amino acid isomerism. Firstly, glycine, where R = H, no isomerism is possible because the alpha-carbon bears two identical groups (hydrogen). Secondly, in cysteine, the L = S and D = R assignment is reversed to L = R and D = S. Cysteine is structured similarly (with respect to glyceraldehyde) to the other amino acids but the sulfur atom alters the interpretation of the Cahn-Ingold-Prelog priority rule.