Urea cycle reactions

Organic sources of nitrogen in synthetic media are specific amino acids, purines, pyrimidines, and urea. Urea, depending upon the buffer capacity of the system, will raise the pH-value of the medium. Organic urea is also formed in the urea cycle reaction, starting with ammonia ... 

The urea cycle occurs partially in the cytosol and partially in the mitochondria. Discuss the urea cycle reactions with reference to their cellular locations. 

Ammonia is a universal participant in amino acid synthesis and degradation, but its accumulation has toxic consequences. Because terrestrial animals must conserve water, they convert ammonia to a form that can be excreted without large water losses. Birds, terrestrial reptiles, and insects convert most of their excess ammonia to uric acid, an oxidized purine. Most mammals excrete the bulk of their nitrogen as urea. See urea cycle reactions here. 

See also Urea Cycle Reactions, Urea, Uric Acid, The Nitrogen Cycle, Utilization of Ammonia, Metabolic Nitrogen Balance, Amino Acid Degradation, Ammonia Transport in the Body, Citric Acid Cycle, ATP as Free Energy Currency (from Chapter 12)... 

See also Urea Cycle Reactions, Urea, Antioxidants (from Chapter 15), Excessive Uric Acid in Purine Degradation (from Chapter 22), Purine Degradation (from Chapter 22), Pathways in Nucleotide Metabolism (from Chapter 22), HGPRT, Hypoxanthine, Xanthine Oxidase... 

See also Urea Cycle Reactions, Figure 11.35, Figure 22.10, Glutamine Synthetase... 

Aspartate is involved in the control point of pyrimidine biosynthesis (Reaction 1 below), in transamination reactions (Reaction 2 below), interconversions with asparagine (reactions 3 and 4), in the metabolic pathway leading to AMP (reaction 5 below), in the urea cycle (reactions 2 and 8 below), IMP de novo biosynthesis, and is a precursor to homoserine, threonine, isoleucine, and methionine (reaction 7 below). It is also involved in the malate aspartate shuttle. 

See also Urea Cycle Descriptions, Urea Cycle Reactions, Utilization of Ammonia, Uric Acid, Purine Degradation... 

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. 

If the effect of water stress is to alter regulation of the pathway such that the rate constant for reaction A G is increased or A CP is decreased (which would have an overall effect of conserving nitrogen), then the fractionation at G can be shown to be thereby increased. At present this is speculative, but in fact explanations for the water-stress effect using flow-models are rather constrained. For example, it is not possible to relate what might happen at the kidneys (e.g., resorption of urea) to the amino acid body pool, since the urea cycle is non-reversible. It should be possible to design experiments that test this suggestion. 

Urea biosynthesis occurs in four stages (1) transamination, (2) oxidative deamination of glutamate, (3) ammonia transport, and (4) reactions of the urea cycle (Figure 29-2). 

Condensation of CO2, ammonia, and ATP to form carbamoyl phosphate is catalyzed by mitochondrial carbamoyl phosphate synthase I (reaction 1, Figure 29-9). A cytosolic form of this enzyme, carbamoyl phosphate synthase II, uses glutamine rather than ammonia as the nitrogen donor and functions in pyrimidine biosynthesis (see Chapter 34). Carbamoyl phosphate synthase I, the rate-hmiting enzyme of the urea cycle, is active only in the presence of its allosteric activator JV-acetylglutamate, which enhances the affinity of the synthase for ATP. Formation of carbamoyl phosphate requires 2 mol of ATP, one of which serves as a phosphate donor. Conversion of the second ATP to AMP and pyrophosphate, coupled to the hydrolysis of pyrophosphate to orthophosphate, provides the driving... 

The activity of carbamoyl phosphate synthase I is determined by A -acetylglutamate, whose steady-state level is dictated by its rate of synthesis from acetyl-CoA and glutamate and its rate of hydrolysis to acetate and glutamate. These reactions are catalyzed by A -acetylglu-tamate synthase and A -acetylglutamate hydrolase, respectively. Major changes in diet can increase the concentrations of individual urea cycle enzymes 10-fold to 20-fold. Starvation, for example, elevates enzyme levels, presumably to cope with the increased production... 

METABOLIC DISORDERS ARE ASSOCIATED WITH EACH REACTION OF THE UREA CYCLE... 

All defects in urea synthesis result in ammonia intoxication. Intoxication is more severe when the metabolic block occurs at reactions 1 or 2 since some covalent linking of ammonia to carbon has already occurred if citrulline can be synthesized. Clinical symptoms common to all urea cycle disorders include vomiting, avoidance of high-protein foods, intermittent ataxia, irritability, lethargy, and mental retardation. The clinical features and treatment of all five disorders discussed below are similar. Significant improvement and minimization of brain damage accompany a low-protein diet ingested as frequent small meals to avoid sudden increases in blood ammonia levels. 

Hepatic urea synthesis takes place in part in the mitochondrial matrix and in part in the cytosol. Inborn errors of metabolism are associated with each reaction of the urea cycle. 

The first suggestion that substrates in carbohydrate oxidation might exert catalytic effects on the oxidation of other intermediates (cf.earlier demonstration of such action in the urea cycle by Krebs and Henseleit, 1932 see Chapter 6) arose from the work of Szent-Gyorgi (1936). He demonstrated that succinate and its 4C oxidation products catalytically stimulated the rate of respiration by muscle tissues. He also observed that reactions between the 4C intermediates were reversible and that if muscle was incubated with oxaloacetate, fumarate and malate made up 50-75% of the products, 2-oxoglutarate 10-25% and, significantly, 1-2% of the C was converted to citrate. These observations were... 

The ammonia liberated by GLDH does not itself enter the urea cycle it must first be combined with carbon dioxide to form carbamoyl phosphate. This is an energy (ATP) consuming reaction ... 

The reaction shown in Figure 8.6 is also important in the liver where glutamate dehydrogenase is involved in the catabolism of amino acids and the entry of nitrogen into the urea cycle, as explained in Chapter 6. 

Urea, which contains two nitrogens, is synthesized in the liver from aspartate and carbamoyl phosphate, which in turn is produced from ammonium ion and carbon dioxide by mitochondrial carbamoyl phosphate synthetase. The urea cycle and the carbamoyl phosphate synthetase reaction are shown in Figure 1-17-2. 

Urea is produced only in the liver, in a cyclic sequence of reactions (the urea cycle) that starts in the mitochondria and continues in the cytoplasm. The two nitrogen atoms are derived from NH4 " (the second has previously been incorporated into aspartate see below). The keto group comes from hydrogen carbonate (HC03 ), or CO2 that is in equilibrium with HC03. ... 

Ornithine is a metabolically quite active amino acid, and the important precursor of pyrrolidine nucleus, which is found in pyrrolizidine alkaloids. Ornithine itself is a non-protein amino acid formed mainly from L-glumate in plants, and synthesized from the urea cycle in animals as a result of the reaction catalyzed by enzymes in arginine. 

B. The reactions of the urea cycle are catalyzed by five enzymes (Figure 9-2). 

Citrulline is transported out of the mitochondria to the cytosol, where the other three reactions of the urea cycle take place. 

D. The overall reaction of the urea cycle indicates that handling of ammonia requires... 

Fig. 6.14. Biosynthesis of NO. The starting point of NO synthesis is arginine. Arginine is converted by NO synthase, together with O, and NAD PH, to NO and citruUine. Arginine can be regenerated from citrulline via reactions of the urea cycle.

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. 

FIGURE 3-8 Uncommon amino acids, (a) Some uncommon amino acids found in proteins. All are derived from common amino acids. Extra functional groups added by modification reactions are shown in red. Desmosine is formed from four Lys residues (the four carbon backbones are shaded in yellow). Note the use of either numbers or Creek letters to identify the carbon atoms in these structures, (b) Ornithine and citrulline, which are not found in proteins, are intermediates in the biosynthesis of arginine and in the urea cycle. 

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. 

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