Urea cycle steps

One step in the urea cycle for ridding the body of ammonia is the conversion of argininosuccinate to the amino acid arginine plus fumarate. Propose a mechanism for the reaction, and show the structure of arginine. 

The nitrogen contained in the amino acids is usually disposed of through the urea cycle. One of the early, if not the first, steps in amino acid catabolism involves a transamination using oxaloacetate or a-ketoglutarate as the amino-group acceptor. This converts the amino acid into a 2-keto acid, which can then be metabolized further. 

Figure 9-2. The urea cycle. The enzymes that catalyze each step are indicated in boxes.

In the urea cycle, two molecules of ammonia combine with a molecule of carbon dioxide to produce a molecule of urea and water. The overall cycle involves a series of biochemical reactions dependent on enzymes and carrier molecules. During the urea cycle the amino acid ornithine (C5H12N202) is produced, so the urea cycle is also called the ornithine cycle. A number of urea cycle disorders exist. These are genetic disorders that result in deficiencies in enzymes needed in one of the steps in the urea cycle. When a urea cycle deficiency occurs, ammonia cannot be eliminated from the body and death ensues. 

The urea cycle begins inside liver mitochondria, but three of the subsequent steps take place in the cytosol the cycle thus spans two cellular compartments (Fig. 18-10). The first amino group to enter the urea cycle is derived from ammonia in the mitochondrial matrix—NHj arising by the pathways described above. 

The carbamoyl phosphate, which functions as an activated carbamoyl group donor, now enters the urea cycle. The cycle has four enzymatic steps. First, carbamoyl phosphate donates its carbamoyl group to ornithine to form citrulline, with the release of Pj (Fig. 18-10, step ). Ornithine plays a role resembling that of oxaloacetate in the citric acid cycle, accepting material at each turn of the cycle. The reaction is catalyzed by ornithine transcarbamoylase, and the citrulline passes from the mitochondrion to the cytosol. 

Aspartate now donates its amino group in two steps ((8) and (9)) formation of an amide bond, followed by elimination of the carbon skeleton of aspartate (as fu-marate). Recall that aspartate plays an analogous role in two steps of the urea cycle (see Fig. 18-10). The final carbon is contributed by N1 "-formyltetrahydrofolate (step ), and a second ring closure takes place to yield the second fused ring of the purine nucleus (step (Q)). 

Carbamoyl phosphate synthetases. The first of the individual steps in the urea cycle is the formation of carbamoyl phosphate.163 Carbon dioxide and ammonia equilibrate spontaneously with carbamic acid ... 

Synthesis of arginine by the salvage pathway found in vertebrates and by the de novo pathway found in plants and bacteria. The final steps from ornithine to arginine are also part of the urea cycle (see fig. 22.7). 

Next, in steps 7 and 8, N-l of the purine ring is contributed by aspartate. Aspartate forms an amide with the 4-carboxyl group, and the succinocarboxamide so formed is then cleaved with release of fumarate. Energy for carboxamide formation is provided by ATP hydrolysis to ADP and phosphate. These reactions resemble the conversion of cit-rulline to arginine in the urea cycle (chapter 22) and the conversion of IMP to AMP (see fig. 23.11). 

Then the amino group of aspartate is transferred to the carboxyl, making an amide. This condensation uses ATP and the amide is cleaved to release fumarate, leaving behind the imidazole with a 5-amino group (left from the amidation of glycine four steps earlier) and a 4-carboxamide. (Note how this reaction is similar to the formation of arginine during the urea cycle.)... 

CPSI catalyzes the formation of carbamoyl phosphate from bicarbonate, ammonium, and two adenosine triphosphate molecules (Fig. 18-1).This first step of the urea cycle occurs in the mitochondrial matrix and assimilates the first of the two nitrogen atoms that will eventually be found in urea. While two ATP molecules are hydrolyzed, there is formation of a lower energy bond in carbamoyl phosphate. CPSI is a homodimer that accounts for 15-30% of the total protein mass in liver mitochondria. jV-Acetylglutamate (NAG) is an essential allosteric activator of CPSI activity, and magnesium ions are also required for its activity. 

The second intramitochondrial step of the urea cycle is the reversible condensation of carbamoyl phosphate and ornithine, catalyzed by OTC. The high-energy phosphate bond in carbamoyl phosphate is cleaved during this... 

Citrulline is exchanged for ornithine across the inner mitochondrial membrane by ORNT-1. Ornithine is produced in the cytosol as the final step in the urea cycle and must be returned to the mitochondrial matrix for transcarbamoyla-tion by OTC. A second ornithine-citrulline antiporter (ORNT-2) is also expressed in the liver mitochondria and may attenuate the severity of disease in patients with HHH (Hyperammonemia, Hyperornithinemia, Homocitrullinuria) disease due to ORNT-1 deficiency. This disorder typically manifests later in life with intermittent hyperammonemic encephalopathy and protein aversion. Intramitochondrial ornithine deficiency causes both hyperammonemia and hyperornithinemia due to a lack of substrate for OTC. Homocitrullinuria occurs due to the use of lysine by OTC as an alternate substrate. The diagnosis is confirmed by mutation analysis. 

The final step of the urea cycle is the cleavage of arginine to release urea and regenerate ornithine. Ornithine then reenters the mitochondria via the ORNT-1 ornithine-citrulline antiporter. ARG-1 is a cytosolic homotrimeric enzyme of 35-kd monomers that is expressed in fiver and red blood cells. A second mitochondrial arginase (ARG-2) most likely plays a role in nitric oxide synthesis and is most abundant in brain, kidney, and prostate. ARG-1 deficiency is unique among the urea cycle deficiencies as patients do not present with hyperammonemia and encephalopathy but rather develop progressive spasticity of the lower limbs. Biochem-... 

The first sub-cellular organelle to be isolated (other than the nucleus), mitochondria are the powerhouse of the cell, generating ATP through aerobic oxidative phosphorylation the TCA (Krebs) cycle (the hub of metabolism ) and fatty acid oxidation take place entirely within mitochondria. Other pathways and cycles (urea cycle, haem biosynthesis, cardiohpin synthesis, quinone and steroid biosynthesis) include steps both outside and inside the mitochondria. 

Most amino acid degradation takes place in tissues other than the liver. For instance, muscle uses amino acids as a source of fuel during prolonged exercise and fasting. How is the nitrogen processed in these other tissues As in the liver, the first step is the removal of the nitrogen from the amino acid. However, muscle lacks the enzymes of the urea cycle, so the nitrogen must be released in a form that can be absorbed by the liver and converted into urea. 

What about the other enzymes in the urea cycle Ornithine transcarbamoylase is homologous to aspartate transcarbamoylase and the structures of their catalytic subunits are quite similar (Figure 23.18). Thus, two consecutive steps in the pyrimidine biosynthetic pathway were adapted for urea synthesis. The next step in the urea cycle is the addition of aspartate to citrulline to form argininosuccinate, and the subsequent step is the removal of fumarate. These two steps together accomplish the net addition of an amino group to citrulline to form arginine. Remarkably, these steps are analogous to two consecutive steps in the purine biosynthetic pathway (Section 25.2 3). 

The enzymes that catalyze these steps are homologous to argininosuccinate synthetase and argininosuccinase, respectively. Thus, four of the five enzymes in the urea cycle were adapted from enzymes taking part in nucleotide biosynthesis. The remaining enzyme, arginase, appears to be an ancient enzyme found in all domains of life. 

The nonessential amino acids are synthesized by quite simple reactions, whereas the pathways for the formation of the essential amino acids are quite complex. For example, the nonessential amino acids alanine and aspartate are synthesized in a single step from pyruvate and oxaloacetate, respectively. In contrast, the pathways for the essential amino acids require from 5 to 16 steps (Figure 24.8). The sole exception to this pattern is arginine, inasmuch as the synthesis of this nonessential amino acid de novo requires 10 steps. Typically, though, it is made in only 3 steps from ornithine as part of the urea cycle. Tyrosine, classified as a nonessential amino acid because it can be synthesized in 1 step from phenylalanine, requires 10 steps to be synthesized from scratch and is essential if phenylalanine is not abundant. We begin with the biosynthesis of nonessential amino acids. 

---