Amino acids are used for three main purposes. They can form structural and enzymatic proteins; they are precursors for a variety of signaling molecules (hormones and neurotransmitters); and they can be catabolized to generate ATP.
Unlike carbohydrates and fatty acids, amino acids are nitrogen-rich. Their catabolism occurs via the urea cycle, which transfers nitrogen from the amino acid to urea -- a small, non-polar molecule which can be excreted in urine. Without the urea cycle, nitrogens become ammonium ions (NH4+) and lower blood pH.
Disorders of amino acid metabolism typically cause clinical problems because of a build-up of toxic precursors along a degradation pathway or because of an inability to eliminate nitrogen in the form of urea. For this reason, treatment often includes avoidance of foods high in a particular amino acid.