Root nodules of leguminous plants play a pivotal role in nitrogen fixation.
FIGURE 23.1 The flow of nitrogen in the biosphere.
FIGURE 23.5 (a) The production of glutamate from -ketoglutarate. (b) The production of glutamine from glutamate.
FIGURE 23.6 Families of amino acids based on biosynthetic pathways. Each family has a common precursor.
FIGURE 23.7 The relationship between amino acid metabolism and the citric acid cycle.
FIGURE 23.8 The role of pyridoxal phosphate in transamination reactions. (a) The mode of binding of pyridoxal phosphate (PyrP) to the enzyme (E) and to the substrate amino acid.
FIGURE 23.8 The role of pyridoxal phosphate in transamination reactions. (b) The reaction itself. The original substrate, an amino acid, is deaminated, while an -keto acid is aminated to form an amino acid. The net reaction is one of transamination. Note that the coenzyme is regenerated and that the original substrate and final product are both amino acids.
FIGURE 23.9 Transamination reactions switch an amino group from one amino acid to an -keto acid. Glutamate and -ketoglutarate ( -KG) are one donor/acceptor pair. Above, a general case. Below, a specific case, in which the other donor/acceptor pair is aspartate and oxaloacetate.
FIGURE 23.10 The biosynthesis of serine.
FIGURE 23.11 (a) The structure of folic acid, shown in nonionized form. (b) The reactions that introduce one-carbon units into tetrahydrofolate (THF) link seven different folate intermediates that carry one-carbon units in three different oxidation states (-2, 0, and +2). ( Adapted from T. Brody et al., in L. J. Machlin. Handbook of Vitamins. New York: Marcel Dekker, 1984. )
Figure 23.12 The conversion of serine to glycine, showing the role of tetrahydrofolate.
FIGURE 23.13 The biosynthesis of cysteine in plants and bacteria.
FIGURE 23.14 Electron transfer reactions of sulfur in plants and bacteria.
FIGURE 23.15 The structure of S -adenosylmethionine (SAM), with the structure of methionine shown for comparison.
FIGURE 23.16 The biosynthesis of cysteine in animals. (A stands for acceptor.)
FIGURE 23.17 Nitrogen-containing products of amino acid catabolism.
FIGURE 23.18 The urea cycle series of reactions: Transfer of the carbamoyl group of carbamoyl-P to ornithine by ornithine transcarbamoylase (OTCase, reaction 1) yields citrulline. The citrulline ureido group is then activated by reaction with ATP to give a citrullylOAMP intermediate (reaction 2a); AMP is then displaced by aspartate, which is linked to the carbon framework of citrulline via its -amino group (reaction 2b). The course of reaction 2 was verified using 18O-labeled citrulline. The 18O label (indicated by the asterisk, *) was recovered in AMP. Citrulline and AMP are joined via the ureido *O atom. The product of this reaction is argininosuccinate; the enzyme catalyzing the two steps of reaction 2 is argininosuccinate synthetase. The next step (reaction 3) is carried out by argininosuccinase, which catalyzes the nonhydrolytic removal of fumarate from argininosuccinate to give arginine. Hydrolysis of arginine by arginase (reaction 4) yields urea and ornithine, completing the urea cycle.
FIGURE 23.19 The urea cycle and some of its links to the citric acid cycle. Part of the cycle takes place in the mitochondrion and part in the cytosol. Fumarate and aspartate are the direct links to the citric acid cycle. Fumarate is a citric acid cycle intermediate. Aspartate comes from transamination of oxaloacetate, which is also a citric acid cycle intermediate.
A kangaroo rat converts some of its waste nitrogen to uric acid.
1. AMINO ACIDS CATABOLISM
2. Amino acids act principally as the building blocks and to the synthesis of variety of other biologically molecules. When a.acids deaminated (removed the α- amino group), their C-keletons can be fed to TCA cycle. They may be used as precursors of other biomolecules.Fig. 23-1, p.630
3. How are amino acidssynthesized? Reductive amination Amidation The α-amino group of glutamate and the side-chain amino group of glutamine are shifted to other compounds: transamination reactions The biosynthesis of amino acids involves a common set of reactions
4. Glutamate is formed from NH4+ and α- ketoglutarate in a reductive amination that requires NADPH. This reaction is catalyzed by g luta m a te d e hy d ro g e na s e (GDH) The conversion of Glutamate to Glutamine is catalyzed by glutamine synthetase (GS) that requires ATP Combination of GDH and GS is responsible for most assimilation of ammonia into organic compound. However, the KM of GS is lower than GDH
5. Fig. 23-6, p.635
6. Transamination reactions: Role of Glutamate and Pyridoxal phosphate Amino acids biosynthesis
7. Enzyme that catalyzed transamination require pyridoxal phosphate as coenzyme
8. Fig. 23-8b, p.637
9. Fig. 23-9, p.638
10. One-C transfer and theserine-family In amino acid biosynthesis, the one-C transfer occurs frequently E.g serine family (also include glycine and cysteine) Ultimate precursor of serine is 3- phosphoglycerate (obtainable from glycolitic pathway) The conversion of serine to glycine involves one-C unit from serine to an acceptor This is catalyzed by serine hydroxymethylase, with pyridoxal phosphate as coenzyme The acceptor is tetrahydropholate (derivative of folic acid) – its structure has 3 parts: a
12. The conversion of serine to cysteine involves some interesting reactionsIn plants and bacteria: serine is acetylated to form O-acetylserine (by serineacyltransferase, and acetyl-CoA as acyl donor) Fig. 23-13, p.641
13. Fig. 23-14, p.641
14. In animals: the reaction involves theamino acid methionineMethionine (produced by reactions ofthe aspartate family) in bacteria andplants can be obtained from dietarysources – essential amino acids
15. Fig. 23-16, p.642
16. What are essential amino acids?• The biosynthesis of proteins requires the presence of all 20amino acids• If one is missing or in short supply, the protein biosynthesisis inhibited• Protein deficiency will lead to the disease kwashiorkor;severe in growing children, not simply starvation but thebreakdown of the body’s own protein Table 23-1, p.643
17. Catabolism of amino acids In catabolism, the amino nitrogen of original amino acid is transferred to α-ketoglutarate → glutamate, leave behind the C skeletons Disposition of C skeletons There are two pathways of the breakdown of C skeletons depends on type of end product: i. Glucogenic amino acid: yields pyruvate and OAA on degradation (can be converted to glucose with OAA as intermediate) Ii. Ketogenic amino acid: one that breaks down to acetyl-CoA or acetoacetyl-CoA to form ketone bodies
18. Table 23-2, p.644
19. Excretion of excess nitrogen Excess nitrogen is excreted in one of three forms: ammonia, urea and uric acid Animal in aquatic env.: release as ammonia Terrestrial animal: urea (soluble in water) Birds: uric acid (insoluble in water) Fig. 23-17, p.644
20. Urea cycle Central pathway in nitrogen metabolism The nitrogen that enter urea cycle come from several sources A condensation reaction bet. ammonium ion and CO2 produce carbamoyl phosphate in a reaction that requires of two molecules of ATP/carbamoyl phosphate
21. In human, urea synthesis is used to excrete excess nitrogen, after consuming a high- protein meal The pathway is confined to the liver The synthesis of fumarate is a link bet. the urea cycle and TCA cycle
23. When amino acid catabolism is high,large amounts of glutamate will bepresent from degradation of glutamine,from synthesis via glutamatedehydrogenase and from transaminationreaction.Increase glutamate level leads toincrease levels of N-acetylglutamatefollowed by increasing the urea cycle p.648