Amino acids from ingested food (or produced from catabolism of muscle protein) that are used for the synthesis of proteins and other biological substances can be oxidized by the body as an alternative source of energy, yielding urea and carbon dioxide. The oxidation pathway starts with the removal of the amino group by a transaminase; the amino group is then fed into the urea cycle. The first step in the conversion of amino acids into metabolic waste in the liver is removal of the alpha-amino nitrogen, which produces ammonia. Because ammonia is toxic, it is excreted immediately by fish, converted into uric acid by birds, and converted into urea by mammals.
Ammonia () is a common byproduct of the metabolism of nitrogenous compounds. Ammonia is smaller, more volatile, and more mobile than urea. If allowed to accumulate, ammonia would raise the pH in cells to toxic levels. Therefore, many organisms convert ammonia to urea, even though this synthesis has a net energy cost. Being practically neutral and highly soluble in water, urea is a safe vehicle for the body to transport and excrete excess nitrogen.
Urea is synthesized in the body of many organisms as part of the urea cycle, either from the oxidation of amino acids or from ammonia. In this cycle, amino groups donated by ammonia and -aspartate are converted to urea, while -ornithine, citrulline, -argininosuccinate, and -arginine act as intermediates. Urea production occurs in the liver and is regulated by N-acetylglutamate. Urea is then dissolved into the blood (in the reference range of 2.5 to 6.7 mmol/L) and further transported and excreted by the kidney as a component of urine. In addition, a small amount of urea is excreted (along with sodium chloride and water) in sweat.
In water, the amine groups undergo slow displacement by water molecules, producing ammonia, ammonium ions, and bicarbonate ions. For this reason, old, stale urine has a stronger odor than fresh urine.