Further Fates of Incorporated Ammonia

The reduced nitrogen is transferred from glutamate and glutamine into a variety of compounds that participate in a variety of reactions in the cell.

Amino acids Glutamate (along with aspartate) is a key substrate and product in transamination (aminotransferase) reactions for amino acid interconversions. Aminotransferases carry out the general reaction: 

Aminotransferases operate in both directions. Their mechanism uses the cofactor pyridoxal phosphate to form Schiff bases with amino groups, as shown in Figure 1 .


            Figure 1

The pyridoxal group is bound to the enzyme by a Schiff base with the ε‐amino group of a lysine side chain. This Schiff base is displaced by the amino group of amino acid(1), for example, glutamate. The keto acid, for example, α‐ketoglutarate, is released, leaving the amino group on the cofactor, which is now in the pyridoxamine form. The rest of the reaction is now the reverse of the first step: The keto group of the second substrate forms a Schiff base with the pyridoxamine, and amino acid(2) is released, with the regeneration of the lysine Schiff base of the enzyme, ready to carry out another cycle.

Nutritionally, humans derive their pyridoxal coenzyme from vitamin B 6. Most symptoms of vitamin B 6 deficiency apparently result from the involvement of the coenzyme in the biosynthesis of neurotransmitters and the niacin group of NAD and NADPH rather than from amino acid deficiency.


The amino group on glutamine is the nitrogen source of a variety of products, including aromatic amino acids, purine and pyrimidine bases, and amino sugars. Glutamine synthetase is therefore an important step in the assimilation of ammonia. Because the enzyme uses ATP, it needs to be regulated to prevent energy wasting. In bacterial cells, two enzymes regulate glutamine synthetase. First, the enzyme is subject to feedback inhibition. Each of the many end products to which GS serves as a precursor partially inhibits the GS reaction. Feedback inhibition in the living body of a plant or animal depends on the enzymatic modification of the GS protein. A separate regulatory system senses the ratio of glutamate to α‐ketoglutarate in the cell. If the ratio of these two compounds is high, an enzyme, uridylyl transferase, transfers a UMP group from UTP to a regulatory protein, called P II. The UMP‐P II protein associates with another enzyme, adenylyl transferase, and the active adenylyl transferase transfers an AMP from ATP to each of the 12 subunits of glutamine synthetase. This shuts down the enzyme activity almost completely. Intermediate amounts of adenylation result in intermediate levels of enzyme activity. Thus, the level of nitrogen assimilation is regulated in response to the needs of the bacterial cell.

Carbamoyl phosphate

Carbamoyl phosphate is an “activated ammonia” group that is important in the biosyntheses of the amino acid arginine and of the pyrimidine nucleotides found in DNA and RNA.

           Figure 2

The bacterial carbamoyl phosphate synthetase reaction uses either glutamine or ammonia as substrate. 


In eukaryotic cells, the two enzymes are in different cellular compartments. Form I uses ammonia and is mitochondrial; its function is to provide activated ammonia for arginine biosynthesis (and urea formation during Nitrogen elimination). Form II uses glutamine and is cytoplasmic; it functions in pyrimidine biosynthesis.