Biochemistry of the urea cycle

First the ammonium ions must be activated through conversion to carbamoyl phosphate by the mitochondrial form of carbamoyl phosphate synthetase. 

The entry of activated ammonia into the urea cycle occurs by the ornithine transcarbamoylase reaction where the carbamoyl group is transferred to the side chain amino group of the non-protein amino acid, ornithine. Ornithine has five carbons its carbon chain therefore has the same length as that of arginine. The product of the ornithine transcarbamoylase reaction is the amino acid citrulline. 

The addition of the second ammonia to the backbone involves the joining of the carbamoyl group of citrulline to the x-amino group of aspartate, leading to a complex compound, arginosuccinate. ATP is hydrolyzed in this step. 

The next step is cleavage of arginosuccinate to arginine and fumarate by the enzyme arginosuccinate lyase. Lyases cleave bonds with the creation of a double bond in one of the products. In this case, the double bond is the carbon-carbon double bond of fumarate. 

The final step is the release of urea by the enzyme arginase, which regenerates ornithine. 

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