Cellular metabolism of amino acids and related molecules includes the pathways for the catabolism of amino acids, the biosynthesis of the nonessential amino acids (alanine, arginine, aspartate, asparagine, cysteine, glutamate, glutamine, glycine, proline, and serine) and selenocysteine, the synthesis of urea, and the metabolism of carnitine, creatine, choline, polyamides, melanin, and amine-derived hormones. The metabolism of amino acids provides a balanced supply of amino acids for protein synthesis. In the fasting state, the catabolism of amino acids derived from breakdown of skeletal muscle protein and other sources is coupled to the processes of gluconeogenesis and ketogenesis to meet the body’s energy needs in the absence of dietary energy sources. These metabolic processes also provide the nitrogen atoms for the biosynthesis of nucleotides and heme, annotated as separate metabolic processes (Felig 1975; Häussinger 1990; Owen et al. 1979).

Transport of these molecuels across lipid bilayer membranes is annotated separately as part of the module on "transmembrane transport of small molecules".