Biochemistry, Vol. 2 - A. Lehninger 1985

Bioenergetics and Metabolism
Biosynthesis of Amino Acids and Nucleotides
Chapter Summary

10 or 20 of the Amino Acids that make up Proteins are synthesized in the bodies of humans and white rats. The remaining amino acids, which must be obtained from the diet and are therefore called essential, are synthesized by plants and Bacteria. Amino acids grouped under the term "nonessential" are formed via various pathways. Glutamate is produced through the reductive amination of a-ketoglutarate, and serves as a precursor for glutamine and Proline. Alanine and aspartate are formed by Transamination from Pyruvate and oxaloacetate, respectively. Tyrosine is produced by the hydroxylation of phenylalanine, an essential amino acid. Cysteine is synthesized from Methionine and Serine through a complex sequence of reactions in which S-adenosylmethionine and cystathionine serve as intermediates. The carbon Skeleton of serine originates from 3-phosphoglycerate. Serine is a precursor of Glycine; the ß-carbon atom of serine is transferred to tetrahydrofolate. The biosynthetic pathways of Essential Amino Acids in plants and bacteria are longer and more complex, as they are formed from certain nonessential Amino acids as well as other metabolites. Allosteric Regulation of the biosynthetic pathways leading to amino acids occurs via feedback inhibition; the regulatory enzyme, inhibited by the end product of the reaction sequence, is typically the one catalyzing the first reaction. Amino acids are precursors to many other vital Biomolecules. For instance, the porphyrin ring of Hemoproteins is derived from glycine and succinyl-CoA.

The ring system of Purines, which are components of purine NUCLEOTIDES, is built step-by-step on the 1-carbon atom of 5-phosphoribosylamine. All nitrogen atoms contained in purines are derived from amino acids. Following two ring-closure steps, the purine core is formed. Pyrimidines are synthesized from aspartic acid, CO₂, and ammonia. The addition of ribose-5-phosphate to them leads to The formation of pyrimidine ribonucleotides. Free purines released during nucleotide breakdown are conserved and reused for nucleotide synthesis via a specialized salvage pathway. A genetically determined defect in one of the Enzymes of this pathway causes a disease accompanied by highly unusual symptoms known as Lesch-Nyhan syndrome. Another genetic disorder, Gout, leads to the deposition of uric acid crystals in the joints.

Certain soil bacteria and bacteria inhabiting the ROOT nodules of legumes have The ability to fix atmospheric nitrogen using a complex Nitrogenase system. The Nitrogen Cycle in nature is the result of four processes: the formation of ammonia via MOLECULAR Nitrogen Fixation in legume root nodules; the nitrification of ammonia by soil organisms, i.e., its conversion into nitrates; the assimilation of nitrates by higher plants, leading to the formation of ammonia; and finally, the synthesis of amino acids from ammonia in PLANT AND ANIMAL organisms.

References

Biosynthetic PATHWAYS OF AMINO Acids

Bender D. A. Amino acid METABOLISM, Wiley, New York, 1975.

Blakley R. L. The Biochemistry of Folic acid and Related Pteridines, North-Holland, Amsterdam, 1969.

Cunningham E. B. Biochemistry: Mechanisms of Metabolism, McGraw-Hill, New York, 1978. An excellent description of enzymatic steps.

Meister A. Biochemistry of Amino Acids, 2d ed. Academic, New York, 1965. (Russian Introduction/27.html">Translation of the 1st ed.: Meister A. Biokhimiya aminokislot. - M.: IL, 1961.) This two-volume work is an outstanding reference guide.

Umbarger H. E., Amino acid Biosynthesis and Its Regulation, Annu. Rev. Biochem., 47, 533-606 (1978). A definitive review; the author was one of the pioneer researchers in The regulation of these biosynthetic pathways.

Genetic Disorders OF Amino Acid and Nucleotide Metabolism

Nyhan W. L., (ed.). Heritable Disorders of Amino Acid Metabolism, Wiley, New York, 1974.

Stansbury J. B., Wyngaarden J. B., Fredrickson D. S. The Metabolic Basis of Inherited Disease, 4th ed., McGraw-Hill, New York, 1978. Particularly fine articles on gout and Lesch-Nyhan syndrome.

Nitrogen Fixation

Brill W. J. Biological Nitrogen Fixation, Sci. Am., 236, 68-81, March (1977).

Delwiche C. C. The Nitrogen Cycle, Sci. Am., 223, 136-147, September (1970).

Jones T. Nitrogen Fixation and Bioenergetics: The Role of ATP in Nitrogenase Catalysis. FEBS Lett., 98, 1-8 (1979).

Mortenson L. E., Thorneley R. N. F. Structure and function of Nitrogenase, Annu. Rev. Biochem., 48, 387-418 (1979).

Heme Group Metabolism

Granick S., Beale S. I. Hemes, Chlorophyll, and Related Compounds: Biosynthesis and Metabolic Regulation, Adv. Enzymol., 40, 33-203 (1978).

Nucleotide Metabolism

Henderson J. F., Paterson A. R. P. Nucleotide Metabolism: An Introduction. Academic, New York, 1973.

Jones M. E. Pyrimidine Nucleotide Biosynthesis in Animals, Annu. Rev. Biochem., 49, 253-279 (1980).

Questions and Problems

1. Dietary features in the presence of defective phenylalanine hydroxylase (phenylalanine-4-monooxygenase). For healthy individuals, tyrosine is a nonessential amino acid, but infants with a genetic defect affecting phenylalanine hydroxylase must obtain tyrosine from their diet for normal growth. Explain why this is the case.

2. Equation Describing Aspartate Synthesis from Glucose. Write the overall equation for the Synthesis of the nonessential amino acid aspartate from glucose, carbon dioxide, and ammonia.

3. Inhibition of Nucleotide Synthesis by Azaserine. The diazo compound O-(2-diaзоанетил)-L-serine, also known as azaserine, is a potent inhibitor of enzymes that transfer amino groups from glutamine to an acceptor during biosynthesis (i.e., amidotransferases). What intermediate will accumulate in the pathway leading from α-D-ribose-5-phosphate to inosinate if Cells actively synthesizing purines are treated with azaserine? Explain your reasoning.

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4. Nucleotide Biosynthesis in Auxotrophic Bacteria Lacking the Ability to Synthesize Certain amino acids. Wild-type E. coli cells synthesize all amino acids, but certain auxotrophic mutants unable to synthesize specific amino acids require them in their growth medium for optimal growth. Amino acids are needed not only for Protein Synthesis; some are required for The biosynthesis of other nitrogenous cellular components. Suppose we have three auxotrophic mutants, each lacking the ability to synthesize one of Three amino acids: glycine, glutamine, or aspartate. The synthesis of which nitrogenous products (other than proteins) will be impaired in each of these mutants?

5. Antineoplastic Agents. Blocking Deoxythymidylate Synthesis. a) Deoxyuridine monophosphate (dUMP) is converted to deoxythymidylate (dTMP), which is essential for DNA Synthesis, via the methylation of N⁵,N¹⁰-methylenetetrahydrofolate in a reaction catalyzed by thymidylate synthase (Section 22.17)

The uridine derivative fluorouracil is converted within The Cell to fluorodeoxyuridylate (F-dUMP), a potent irreversible inhibitor of thymidylate synthase. How do you explain the fact that fluorouracil inhibits the growth of rapidly dividing Cancer cells in experimental animals?

b) The dihydrofolate generated in the thymidylate synthase reaction is converted back to tetrahydrofolate by the action of Dihydrofolate Reductase. How is tetrahydrofolate converted into N⁵,N¹⁰-methylenetetrahydrofolate? Dihydrofolate reductase is potently inhibited (K_i = 10^-9 M) by the chemotherapeutic drug methotrexate, which is used in tumor Chemotherapy

How does this drug inhibit the growth of cancer cells? Would you expect it to inhibit the growth of normal cells as well?

6. Nucleotides as poor Energy Sources. In most organisms, nucleotides are not used as metabolic fuel, i.e., as an energy source. What observations support this Conclusion? Why are nucleotides relatively poor energy sources in mammals?

7. MECHANISM OF ACTION of sulfonamides. Certain bacteria require p-aminobenzoic acid for normal growth, which is provided in their culture medium. The growth of such bacteria is drastically inhibited upon the addition of streptocide, one of the earliest antibacterial sulfonamides. Furthermore, in the presence of streptocide, the medium accumulates 5'-phosphoribosyl-4-carboxamide-5-aminoimidazole.

Both of these effects are reversible and can be overcome by adding an excess of p-aminobenzoic acid to the medium.

a) What is the role of p-aminobenzoic acid? (Hint: see Fig. 22-7 and Section 10.10.)

b) Why does 5'-phosphoribosyl-4-carboxamide-5-aminoimidazole accumulate in the presence of streptocide? (See Fig. 22-16.)

c) Why does the addition of excess p-aminobenzoic acid reverse both the inhibition of bacterial growth and the accumulation of 5'-phosphoribosyl-4-carboxamide-5-aminoimidazole?

8. Treatment of gout. Allopurinol (Fig. 22-25), a xanthine oxidase inhibitor, is used in the treatment of chronic gout. What is the biological rationale for this therapy? Patients treated with allopurinol occasionally develop xanthine calculi (stones). However, the Urinary Tract is affected by such calculi much less frequently than by untreated gout. Explain this observation based on the following solubility data for these compounds in urine: uric acid, 0.15 g/L; xanthine, 0.05 g/L; and hypoxanthine, 1.4 g/L.

9. ATP consumption by legume root nodules. Bacteroids residing in the root nodules of pea plants consume over 20% of the total ATP produced by the host plant. Propose a reason that could explain why these bacteria consume such a large amount of ATP.

10. Carbon atom pathway in pyrimidine biosynthesis. At which position will ¹⁴C be incorporated into orotate if cells are grown in the presence of a trace amount of uniformly labeled ¹⁴C-succinate? Provide a reasoned answer.

Two freshwater photosynthetic Algae. The long filaments are Spirogyra—chains of photosynthetic cells containing ribbon-like, helically coiled Chloroplasts. The large spherical structures are Volvox; each such sphere is a colony consisting of hundreds of cells. The large sphere on the right has just ruptured, releasing daughter colonies. A very small copepod is visible in the center of the photograph. Figure 23-2 shows several Other types of photosynthetic cells. THE CONTRIBUTION OF marine and freshwater microorganisms to global Photosynthesis exceeds that of terrestrial plants.