Use in urea cycle

The aspartate used in urea synthesis is generated from oxaloacetate, a citric acid cycle intermediate. 

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. 

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... 

Gene therapy for rectification of defects in the enzymes of the urea cycle is an area of active investigation. Encouraging preliminary results have been obtained, for example, in animal models using an adenoviral vector to treat citrullinemia. 

Apart from the hydrolysis step, the SCR-urea process is equivalent to that of stationary sources, and in fact the key idea behind the development of SCR-urea for diesel powered cars was the necessity to have a catalyst (1) active in the presence of 02, (2) active at very high space velocities ( 500.000 per hour based on the washcoat of a monolith) and low reaction temperatures (the temperature of the emissions in the typical diesel cycles used in testing are in the range of 120-200°C for over half of the time of the testing cycle), and (3) resistant to sulphur and phosphorus deactivation. V-Ti02-based catalysts for SCR-NH3 have these characteristics and for this reason their applications have also been developed for mobile sources. 

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. 

Introduction of photoelectric cells led to the replacement of the Duboscq colorimeter and so to quantitative spectrophotometric methods of analysis which met biochemical requirements. This introduction of spectrophotometry as a routine procedure was one of the earliest technological advances underpinning the elucidation of biochemical pathways between 1930-1960. Micromanometric methods also became available about the same time, and offered a means to measure cell respiration. Manometry was developed in Warburg s laboratory in Berlin and was one of the main techniques used by H.A. Krebs in his studies on the citric acid and urea cycles (Chapters 5 and 6). 

Pyrimidines are synthesized de novo in the cytoplasm from aspartate, COj, and glutamine as shown in Figure 1-18-2. Synthesis involves a cytoplasmic carbamoyl phosphate synthetase that differs from the mitochondrial enzyme with the same name used in the urea cycle. 

Figure 10.10 The use of benzoate and phenylacetate to lower the concentration of ammonia in patients with a deficiency of a urea cycle enzyme.

Only a few important representatives of the non-proteinogenic amino acids are mentioned here. The basic amino acid ornithine is an analogue of lysine with a shortened side chain. Transfer of a carbamoyl residue to ornithine yields citrulline. Both of these amino acids are intermediates in the urea cycle (see p.l82). Dopa (an acronym of 3,4-dihydroxy-phenylalanine) is synthesized by hydroxyla-tion of tyrosine. It is an intermediate in the biosynthesis of catecholamines (see p.352) and of melanin. It is in clinical use in the treatment of Parkinson s disease. Selenocys-teine, a cysteine analogue, occurs as a component of a few proteins—e.g., in the enzyme glutathione peroxidase (see p.284). 

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. 

Allantoin is the excretory product in most mammals other than primates. Most fish hydrolyze allantoin to allantoic acid, and some excrete that compound as an end product. However, most continue the hydrolysis to form urea and glyoxylate using peroxisomal enzymes.336 In some invertebrates the urea may be hydrolyzed further to ammonia. In organisms that hydrolyze uric acid to urea or ammonia, this pathway is used only for degradation of purines from nucleotides. Excess nitrogen from catabolism of amino acids either is excreted directly as ammonia or is converted to urea by the urea cycle (Fig. 24-10). 

The urea cycle is a mechanism for removing unwanted nitrogen. Sources of nitrogens involved in urea formation are shown in red. Five enzymes are used in the urea cycle. Three of these function in the cytosol, and two, as shown, function in the mitochondrial matrix. 

For NH3 adsorption, experimental evidence has shown that the main interaction mechanism is H bonding of Si-OH to the N atom in NH3 [124], Ammonia gas is a widely used chemical in industry, and it has to be removed to less than one ppm, for instance, from the gaseous effluents of ammonia fertilizer plants, urea plants, and other sources [127], It is evident that silica is an excellent adsorbent of NH3 [124-126], Also, adsorption of ammonia on silica gel has received considerable attention recently, owing to its potential use in solar energy cooling cycles [128],... 

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