Why the body converts ammonia to urea
Ammonia is a constant byproduct of amino acid breakdown, and it is toxic to the brain even at modest concentrations. The liver solves this by combining ammonia with carbon dioxide and, eventually, the nitrogen of aspartate to form urea, a far less toxic molecule that the kidneys can excrete in urine. A healthy adult disposes of a substantial amount of nitrogen this way each day.
The pathway is divided between two compartments. The first reactions occur inside the mitochondrial matrix, then citrulline moves to the cytosol where the remaining steps complete the cycle and regenerate the starting molecule, ornithine.
The five enzymatic steps in order
Carbamoyl phosphate synthetase I fixes ammonia and bicarbonate into carbamoyl phosphate. Ornithine transcarbamylase joins it to ornithine to make citrulline. Argininosuccinate synthetase then adds aspartate, argininosuccinate lyase splits off fumarate to yield arginine, and arginase finally cleaves arginine into urea and ornithine, closing the loop.
When the cycle fails
Inherited deficiencies in any of these enzymes, ornithine transcarbamylase deficiency being the most common, can cause ammonia to accumulate, which is a medical emergency. This page describes the biochemistry for general education and is not a guide to diagnosis or treatment; suspected metabolic disorders require evaluation by a qualified clinician.