When proteins and amino acids are broken down in the body, ammonium is created as a byproduct. Ammonium is dangerous when it remains free in the human body, so something must be done to get rid of it. The major route of removal of ammonium by the body is via urea synthesis in the liver. Urea can then be excreted in urine.

Both catabolic and anabolic reactions are metabolic reactions. The difference is that catabolism is when complex molecules break down into simpler molecules, and anabolism is when simpler molecules are combined to form complex molecules. ATP (adenosine triphosphate) is used to store and transport energy in cells. There is a major difference in how ATP is used in catabolic and anabolic reactions. Anabolic reactions require energy input, and result in a net consumption of ATP. Catabolic reactions produce energy and results in a net synthesis of ATP. Therefore, catabolic pathways do not have a net consumption of ATP.

The urea cycle is vital to the excretion of ammonia, a harmful byproduct of amino acid breakdown. Via a series of enzymatic changes, ammonia is converted to urea, which can be excreted into the urine. 

The urea cycle occurs primarily in the liver, and to a lesser extent in renal cells. There is no urea conversion performed by the small intestine. 

Arginine is the amino acid in the cycle that is converted to urea and ornithine via the enzyme arginase, and is one of the products of the lysis of argininosuccinate. Glutamic acid plays a different role in the cycle; it loses its amino group to the synthesis of carbamoyl phosphate, a precursor of citrulline. Asparagine is not present in the urea cycle, but aspartic acid is. It condenses with citrulline, through the action of the enzyme argininosuccinate synthase and ATP, to produce argininosuccinate.

Triose phosphate isomerase catalyzes the isomerization between dihydroxyacetone phosphate and glyceraldehyde-3-phosphate. Glucose-6-phosphate dehydrogenase is a regulatory enzyme for the pentose phosphate pathway. Citrate synthase is a regulatory enzyme for the Krebs cycle, catalyzing the synthesis of citrate from acetyl-CoA and oxaloacetate. PFK catalyzes the rate-limiting step in glycolysis.

Ketogenic amino acids are degraded to Acetyl Coenzyme A (CoA) and ketones; glucogenic amino acids can be converted to glucose. Amino acids that are both ketogenic and glucogenic can be metabolized to both glucose and ketone bodies. Purely ketogenic aminoacids are leucine and lysine. Amino acids that are glucogenic and ketogenic are: phenylalanine, tyrosine, tryptophan, isoleucine and threonine. All the other amino acids are glucogenic.

In the urea cycle, carbomyl phosphate first combines with the molecule ornithine. This forms citrulline. Citrulline then reacts with aspartate to form arginosuccinate. Fumarate dissociates from arginosuccinate forming arginine, and then the addition of water forms urea and ornithine once again to complete the cycle. Citrate is not involved in this cycle, it is however in the Krebs cycle.

Free  and bicarbonate  can come together to form carbomyl phosphate which can then enter into the urea cycle.

NAD is required  for the oxidation of beta-hydroxyacyl-CoA to beta-Ketoacyl-CoA by hydroxyacyl-CoA dehydrogenase.