Ornithine transcarbamylase catalyzes the reaction between the substrates ornithine and carbamoyl phosphate to form citrulline and phosphate. This process occurs primarily in the hepatic mitochondria, and to a lesser extent in the mitochondria of the renal cells.

Lesch-Nyhan syndrome is an x-linked deficiency of the enzyme hypoxanthine-guanine phosphoribosyltransferase (HGPRT). HGPRT plays a central role in the generation of purine nucleotides through the purine salvage pathway. Cell breakdown products cannot be reused, and are therefore degraded. This gives rise to increased uric acid, a purine breakdown product. This build-up of uric acid is associated with severe gout and kidney problems, poor muscle control and mental retardation, usually in the first year of life. In the second year of life a common sign is self-mutilating behaviors.

Because collagen is a protein, it must be broken down by a protease. Proteases exert their effects by hydrolyzing peptide bonds. The specific enzyme that breaks down collagen, predictably, is called collagenase.

The other classes of enzymes listed have actions unrelated to protein breakdown. An isomerase rearranges bonds to form an isomer, a polyermase adds nucleotides to DNA, a lipase breaks down fats, and a ligase creates a chemical bond.

Aminotransferases do not release amino groups, but rather transfer them to other amino acids. The reactions catalyzed by aminotransferases are reversible. Their blood concentrations can be used as clinical indicators for damage to liver or muscle.

Glutaminase synthetase is present predominately in the brain, liver and kidneys.The importance of the reaction catalyzed by glutamine synthetase is that excess nitrogen (in the form of toxic ammonia) from protein degradation can be removed from tissues, especially the brain. The reaction catalyzed by glutamine synthetase is irreversible. It converts glutamate to glutamine.

Mitochondrial carbamoyl phosphate synthetase is important in excretion of ammonium ions as urea. Without it there is an increase in blood ammonium levels (which are toxic to the brain), as well as decreased blood urea levels and increased levels of glutamine (the transporter of ammonium in the blood).

Ornithine transcarbamoylase is part of the urea cycle; it converts carbamoyl phosphate to citrulline in the presence of ornithine. It participates in the pathway that transforms toxic ammonium ions released in amino acid degradation to non-toxic urea that can be eliminated in urine. Ornithine transcarbamoylase is a mitochondrial membrane and its deficiency not only affects urea production, but also leads to accumulation of nucleotide bases such as uracil in the blood and urine. The levels of urea in the blood decrease (not increase) in ornithine transcarbamoylase deficiency.

Arginase catalyzes the conversion of arginine to ornithine and urea. Therefore, if there is a deficiency in arginase, there will be a buildup of arginine, and a deficiency in ornithine and urea. Without the ability to form urea, the ammonium waste from protein and amino acids degradation will not be able to be converted to urea safely. The buildup of ammonium will cause hyperammonemia, which results in some unfavorable physiological scenarios.

The correct answer is "glutamate dehydrogenase." Glutamate is the only amino acid that has an enzyme that removes its amino group as ammonia, rather than just transferring the amino group to a α-keto acid and forming a new amino acid. The transfer of amino groups, which may form glutamate, is performed by aminotransferases that require pyridoxal-5’-phosphate as a cofactor. Cathepsins are a type of proteases contained in lysosomes, and they break down proteins into amino acids rather than metabolize the amino acids themselves. Carbamoyl phosphate synthase is not involved in deamination, but rather condenses ammonia with bicarbonate to enter the urea cycle.

The first step in phenylalanine metabolism is conversion of phenylalanine to tyrosine. Tyrsoine is simply a hydroxylated version of phenylalanine.