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Chapter: Biochemistry: The Metabolism of Nitrogen

Amino Acid Catabolism

Amino Acid Catabolism
What is the fate of the carbon skeleton in amino acid breakdown? What is the role of the urea cycle in amino acid breakdown?

Amino Acid Catabolism

When we specifically focus on the catabolism of amino acids, the first step we consider is the removal of nitrogen by transamination. Transamination reactions are also important in the anabolism of amino acids, so it is important to remind ourselves that anabolic and catabolic pathways are not the exact reverse of each other, nor do they involve exactly the same group of enzymes. In catabolism, the amino nitrogen of the original amino acid is transferred to α-ketoglutarate to produce glutamate, leaving behind the carbon skeletons. The fates of the carbon skeleton and of the nitrogen can be considered separately.

What is the fate of the carbon skeleton in amino acid breakdown?

Breakdown of the carbon skeletons of amino acids follows two general pathways, the difference between the two pathways depending on the type of end product. A glucogenic amino acid yields pyruvate or oxaloacetate on degradation. Oxaloacetate is the starting point for the production of glucose by gluconeogenesis. A ketogenic amino acid breaks down to acetyl-CoA or acetoacetyl-CoA, leading to the formation of ketone bodies. The carbon skeletons of the amino acids give rise to metabolic intermediates such as pyruvate, acetyl-CoA, acetoacetyl-CoA, α-ketoglutarate, succinyl-CoA, fumarate, and oxaloacetate (see Figure 23.7). Oxaloacetate is a key intermediate in the breakdown of the carbon skeletons of amino acids because of its dual role in the citric acid cycle and in gluconeogenesis. The amino acids degraded to acetyl-CoA and acetoacetyl-CoA are used in the citric acid cycle, but mammals cannot synthesize glucose from acetyl-CoA. This fact is the source of the distinction between glucogenic and ketogenic amino acids. Glucogenic amino acids can be converted to glucose, with oxaloacetate as an intermediate, but ketogenic amino acids cannot be converted to glucose. Some amino acids have more than one pathway for catabolism, which explains why four of the amino acids are listed as both glucogenic and ketogenic.

Excretion of Excess Nitrogen

The nitrogen portion of amino acids is involved in transamination reactions in breakdown as well as in biosynthesis. Excess nitrogen is excreted in one of three forms: ammonia (as ammonium ion), urea, and uric acid (Figure 23.17).


Animals, such as fish, that live in an aquatic environment excrete nitrogen as ammonia; they are protected from the toxic effects of high concentrations of ammonia not only by the removal of ammonia from their bodies but also by rapid dilution of the excreted ammonia by the water in the environment. The principal waste product of nitrogen metabolism in terrestrial animals is urea (a water-soluble compound); its reactions provide some interesting comparisons with the citric acid cycle. Birds excrete nitrogen in the form of uric acid, which is insoluble in water. They do not have to carry the excess weight of water, which could hamper flight, to rid themselves of waste products.

What is the role of the urea cycle in amino acid breakdown?

A central pathway in nitrogen metabolism is the urea cycle (Figure 23.18). The nitrogens that enter the urea cycle come from several sources. One of the nitrogens of urea is added in the mitochondria, and its immediate precursor is glutamate, which releases ammonia via glutamate dehydrogenase. However, the ammonia nitrogens of glutamate have ultimately come from many sources as a result of transamination reactions. Mitochondrial glutaminase also provides free ammonia that can enter the cycle. 

A condensation reaction between the ammonium ion and carbon dioxide produces carbamoyl phosphate in a reaction that requires the hydrolysis of two molecules of ATP for each molecule of carbamoyl phosphate. Carbamoyl phosphate reacts with ornithine (Step to form citrulline. Citrulline is then transported to the cytosol. A second nitrogen enters the urea cycle when aspartate reacts with citrulline to form argininosuccinate in another reaction that requires ATP (AMP and PPiareproduced in this reaction; Step 2). The amino group of the aspartate is the source of the second nitrogen in the urea that will be formed in this series of reactions. Argininosuccinate is split to produce arginine and fumarate (Step 3). Finally, arginine is hydrolyzed to give urea and to regenerate ornithine, which is transported back to the mitochondrion (Step 4). The biosynthesis of arginine from ornithine is discussed on the Biochemistry Interactive website. Another way of looking at the urea cycle is to consider arginine as the immediate precursor of urea and to see it as producing ornithine in the process. According to this point of view, the rest of the cycle is the regeneration of arginine from ornithine.

The synthesis of fumarate is a link between the urea cycle and the citric acid cycle. Fumarate is, of course, an intermediate of the citric acid cycle, and it can be converted to oxaloacetate. A transamination reaction can convert oxa-loacetate to aspartate, providing another link between the two cycles (Figure 23.19). In fact, both pathways were discovered by the same person, Hans Krebs. Four high-energy phosphate bonds are required because of the production of pyrophosphate in the conversion of aspartate to argininosuccinate.

In humans, urea synthesis is used to excrete excess nitrogen, such as would be found after consuming a high-protein meal. The pathway is confined to the liver. Note that arginine, the immediate precursor to urea, is the most nitrogen-rich amino acid, but the source of the nitrogen in the arginine varies. The major control point is the mitochondrial enzyme carbamoyl-phosphate synthe-tase I (CPS-I), and the formation of carbamoyl-phosphate is the committed stepin the urea cycle. CPS-I is allosterically activated by N-acetylglutamate:

N-Acetylglutamate is formed by a reaction between glutamate and acetyl-CoA, which is catalyzed by N-acetylglutamate synthase. This enzyme is activated by increased concentrations of arginine. Thus, when amino acid catabolism is high, large amounts of glutamate are present from degradation of glutamine, from synthesis via glutamate dehydrogenase, and from transamination reac-tions. Increased glutamate levels lead to increased levels of N-acetylglutamate followed by increasing the activity of the urea cycle. 

In addition, any time arginine builds up, either because of protein catabolism or because ornithine is building up because of a low level of CPS-I activity, the arginine stimulates synthesis of N-acetylglutamate and therefore increases the CPS-I activity.


The carbon skeleton has two fates in the breakdown process. Some car-bon skeletons give rise to pyruvate or oxaloacetate, which can be used in gluconeogenesis. Others give rise to acetyl-CoA or acetoacetyl-CoA, which can form lipids.

The urea cycle, which has links to the citric acid cycle, plays a central role in nitrogen metabolism. It is involved in both the anabolism and the catabolism of amino acids.


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