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. 

Carbamoyl phosphate synthetase is the rate-limiting step of the urea cycle. It is the first step of the urea cycle and occurs exclusive in the mitochondria of hepatic and renal cells.

2 molecules of ammonia and 1 molecule of carbon dioxide are converted into 1 molecule of urea in every turn of the urea cycle. In addition, each cycle regenerates 1 molecule of ornithine for use in the next turn.

Removal of the amino group is a primary step in amino acid catabolism. Humans (and some other animals) utilize the urea cycle to convert the unnecessary amino groups from amino acids into urea. The carbon skeletons will be fed into the citric acid cycle, and none of the other answers directly relate to human nitrogen metabolism. The Krebs cycle (also known as the citric acid cycle) is an intermediate between glycolysis and oxidative phosphorylation, and involves energy production. Gluconeogenesis is the process by which glucose is synthesized from non-carbohydrate organic substrates. The purine nucleotide cycle involves conversion of nucleotides into Krebs cycle intermediates, and makes ammonia as a byproduct, which is then shunted into the urea cycle to be converted into urea and excreted in the urine.

Aminotransferases (transaminases) catalyze the conversion of an amino acid to an -keto acid. To do so, they utilize a pyridoxyl phosphate coenzyme, which mediates the transfer of the amino group, leaving a ketone functional group next to the carboxyl group. This -keto acid is the product. Since the amino group in an amino acid is attached to the alpha carbon, it will not be a -keto acid. Some of the other answer choices give intermediates of the reaction mechanism, not the product.

Due to its amino group's location within the pyrrole ring derivative, proline is unable to be deaminated via the aminotransferase step of protein catabolism. Proline oxidase is the enzyme that catalyzes the first reaction in the catabolism of proline. None of the other amino acid answer choices have this limitation.