Esther M. Zimmer Lederberg
Agricultural Biochemistry 208: Sept. 1956-Jan. 1957
Biosynthesis Purine Ribotides, Potter
Archive DI.H

Course Contents

• Origins and Mechanisms of Live Processes
• Historical Survey
• Chemistry and Catabolism of Purines
• Chemistry and Catabolism of Pyrimidines
• Chemistry and Catabolism of Sugars and Nucleosides
• Chemistry and Catabolism of Nucleic Acids
• Chemistry and Catabolism of Nucleotides
• Biosynthesis of Purine Nucleotides
• Biosynthesis of Pyrimidine Nucleotides
• Biosynthesis of Sugar Moieties
• Biosynthesis of RNA
• Biosynthesis of DNA
• Feedback Mechanisms in Nucleotide Metabolism
• DNA as the Basis of Heredity
• RNA as the Basis of Enzyme Synthesis
• Cancer
• Biological Effects of Radiation
• Antimetabolites

Historical Development

• Discovery of Nucleic Acids 1869-1889
• History of the Isolation and Identification of Nucleic Acid Components
  • Occurrence of free purines 1776-1850
  • Purines as components of nucleic acids 1874-1904, 1955
  • Early chemistry of the pyrimidines 1818-1903
  • Pyrimidines as components of nucleic acids 1893-1903
• Types of Nucleic Acids
• Carbohydrate Component of Yeast Nucleic Acid (RNA)
  • Purine nucleosides yielded ribose
  • Pyrimidine nucleosides yielded ribose
  • Ring structure = furanosides
• Carbohydrate component of thymus Nucleic Acid (DNA)
• Elucidation of the structure of the Basic Units of the Nucleic Acids
  • Purine nucleosides yielded 2 deoxyribose 1929
  • Pyrimidine nucleosides enzymatically yielded 2 deoxyribosephosphate 1954
  • Configuration of the glycosidic linkage = β
  • Nucleotide Structure
• Early Proposed Structures of Polynucleotides 1925
• Recognition of Intracellular Distribution of the Nucleic Acids 1924
• Modern Era 1949

Nucleic Acids

• Catabolism (Exergonic Reactions) vs Anabolism (Endergonic Reactions)

• 

• Life
• DNA—Proteins
• RNA—Proteins

Origin of Life

• Pasteur's Experiment Wald, Sci. Amer. Aug. 1954, p. 44
• Primitive Organism (complete heterotroph and mechanism of evolution)
  • Horowitz, PNAS 31:153, 1945
  • Choice: Simple medium and complex organism vs Complex medium and simple organism
  • Wald, Scient. Amer., Aug., 1954
  • Calvin, Amer. Sci., July, 1956, p. 248
  • Miller, J. Am. Chem. Soc. 16c, Sept. 1956
  • Oro Proc. Am. Chem. Soc. Sept., 1956
  • Abelson, Carnegie Inst. Wash. Yr. Book 53:97-101 (1953-44)
  • viruses and Rickettsiae

Purine Degredation (Uricase)

• Cavalieri, Tinker, Brown, JACS 71:3973 1949
• Canellakis, Cohen, JBC 213:379, 385 1955
• Canellakis, Tuttle, Cohen, JBC 213:397 1955
• Mahler, Baum, Hübscher, Science 124:705 1956 (Metalloprotein chelation)
• Brandenberger Degradation of Uric Acid
• chemistry of Purines
  • Brandenberger Equations for Purine degredation
    • Brandenberger
      • Proc. Am. Chem. Soc., Sept. 15, 1955, p. 4c
      • B&B Acta 15, 108, 1954
      • Helv. Chim. Acta 37, 641, 2207 1954
• Nucleic Acid Metabolism

Pyrimidine Degradation

• In Vivo
  • Rutman, cantarow, Paschkiss, JBC 210: 321 1954
  • Fink, JBC 218:9 1956
• In Vitro
  • Fink, McGaughey, Cline, Fink, JBC 218:1 1956
  • Fink, Cline, Henderson, Fink, JBC 221:425 1956
  • Canellakis, JBC 221:315 1956
• β alanine Metabolism
  • Roberts, Bregoff, JBC 201:393 1953
  • Martignoni, Winnick, JBC 208:251 1954
• Oxidative Pathway
  • Wang, T. P.; Lampen, J. O., JBC 194:775, 785 1952
  • Hayaishi, O.; Kornberg, A., JBC 197:717 1952
• Chemical Degradation of Uracil vol. II, p. 299
  • Lagerkirst, Acta Chem. Scand. 7:114 1953
• Alternative Pathways of Nucleic Acid Synthesis (Pyrimidine Nucleotides)
  • U, C, T, 5-Methyl-Cytosine
• Notes
  • W. Miller, JACS 77:2351 1954
  • Potter; Heidelberger, Physiol. Rev. 30:487 1950
  • Discovery of Nucleic Acids
    • Hoppe - Seyler 1895
    • Miescher 1844-1895
    • Kossel 1853-1927
    • Historical References collected by Mary Ellen Jones (Lipman Lab), Yale J. Biol. & Med. 26:8, 1953
  • Components
    • Pre-Nucleic Acids
      • Schule Uric Acid 1776
      • Schule Xanthine 1817
      • Magnus Guanine 1845
      • Scheres Hypoxanth. 1845
      • Picardi Guanine, Xanthine 1874
      • Kossel 1885
      • Emile Fischer Uric Acid → Alanine, Guanine, Hypox, Xanthine 1897
      • Trabne 1904
      • Dunn, Smith N-MethylAdanine (E. coli mutant) Nature, 175:336 1955
    • Pyrimadines
      • Alloxan 1818
      • Alloxan and Urea, oxalic acid 1818, 1838, 1884
      • Pitter pyrimidine = pyridine + amidine
      • Gabriel barbituric acid → pyrimidine 1900
      • Orotic acid isolated from whey 1905
      • Sinsheimer Science 120:551 1954
      • A. Levine (identification of nucleic acid components), 1869-1890
      • Rockafeller (1907-1940)
      • Todd (organic synthesis of nucleic acid components),
        β galactosides, DNA: A, G, T, C,    RNA: A, G, U, C
    • Carbohydrate structure
      • Kossel 1891
      • Hammergarten 1894
      • Levine, Jacobs (RNA) 1909, 1911
      • Eckenstein, Blanksma 1913
      • Levine, La Farge 1912
      • Levine, Tipson furanoside ring 1932
      • Brachet, casperisori (intracellular distribution of nucleic acids) 1930s
      • W. Schneider simplified analytical methods 1945
      • RNA, DNA alkali seperation 1948
      • Claude cell fractionation 1942
      • Hogeboom, Palade, Schneider sucrose technique 1947
      • Post WWII: isotopic labeling, paper chromotography, column chromotography
    • RNA-ase and alkaline hydrolysis: Brown, Todd
    • Biochemistry: abbreviations of common molecules
      ADP, AIC, AICA, AICAR, AIR, AMP, ATP, DPN DPNH
      FGAR, FGADR, GAR, GMP, Hx, IMP,
      Intermediate A, Intermediate B, Intermediate C,
      IRP, IP, PP, PRA, PRPP, R5P, XMP
    • Notes from Rollin Hotchkiss (Symposium on Genetic Recombination, April, 1954)
    • Notes
      • Reference for sugars: Overend and Stacey
      • Chargaff
      • Inosine, Xanthosine, Hypoxanthine deoxyriboside
      • deoxycytidiene, deoxyuridine
      • W. C. Schneider JBC 216:287 1955
      • Spongothymidine (arabinose) J. Chem. Soc., Brown; Todd, 1956

Biosynthesis of Purine Ribotides References

• Abrams, Bentley, Arch. Biochem. Biophys. 58:109 1955
• Abrams, Bentley, JACS 77:479 1956
• Aronson, Nathan, B&B Acta 15:306 1954
• Buchanan, et al JACS 77:501 1955
• Buchanan, Levenberg, Lukens, A. Chem Soc. 128th:126 1955
• Carter, C. E. Cohen, L. H., Fed. Proc. 14:189 1955
• Carter, C. E. Cohen, L. H.,
"The preparation and properties of adenylosuccinase and adenylosuccinic acid", JBC 22:17 1956
• Goldthwaite, Greenberg, Peabody, B&B Acta 18:148 1955
• Goldthwaite. Peabody, Greenberg, JACS 76:5258 1954
• Goldthwaite, D. A.; Peabody, R. A.; Greenberg, G. R., "On the occurrence of glycinamide ribotide and its formyl derivative", JBC 221:555 1956
• Goldthwaite, D. A.; Peabody, R. A.; Greenberg, G. R., "On the mechanism of synthesis of glycinamide ribotide and its formyl derivative", JBC 221:569 1956
• Goldthwaite, D. A., "5-Phosphoribosylamine, a precursor of glycinamide ribotide", JBC 222:1051 1956 (Oct.)
• Greenberg, G. Robert, Spilman, E. L., "Isolation of 5-amino-4 imidazolecarboximide riboside"
• Greenberg, G. Robert, "Preparation of 5'-phosphoribosyl-5-amino-4imidazole carboxamide", JBC 219:423 1956
• Hartman, S. C.; Levenberg, B.; Buchanan, J. M., "Biosynthesis of the purines. XI. Structure, enzymatic synthesis, and metabolism of glycinamide ribotide and (α-N-formyl)-glycinamide ribotide"
• Kornberg, Lieberman, Simms, JBC 215, 417 1955
• Levenberg, Hartman, Buchanan, Fed. Proc. 14:243 1955
• Levenberg, B.; Hartman, S. C.; Buchanan, J. M., "Biosynthesis of the purines. x. Further studies in vitro on the metabolic origin of nitrogen atoms 1 and 3 of the purine ring", JBC 220:379 1956
• Lieberman, I. "Involvement of GTP in the synthesis of adenylosuccinate from IMP", JACS 78:251 1956
• Lukens, L. N.; Buchanan, J. M., "A new intermediate in purine biosynthesis", Fed. Proc. 15:305 1956 (March)
• Peabody, R. A.; Goldthwaite, D. A.; Greenberg, G. R., "The structure of glycinamide ribotide", JBC 221:1071 1956
• Sonne, J. C.; Lin, I.; Buchanan, J. M., "Biosynthesis of the purines. IX. Precursors of the nitrogen atoms of the purine ring", JBC 220:369 1956
• Speck, J. B. C. 179:1405 1949
• Weinfeld, Herbert; Roll, Paul M.; Carrol, Elizabeth; Brown, George Bosworth; Rhoades, C. P., "The utilization of nucleotides by a mammal. IV triply labeled purine nucleotides", Journal Biological Chemistry 220:439 1956

Biosynthesis of Pyrimidine Ribotides References

• Cooper, C.; Ray, W.; Wilsion, D. W., "Some Precursors of Pyrimidines", J. Biol. chem. 216:37 1955
• Cooper, C.; Wilson, Fed. Proc. 13:194 1954
• Fairley; Herman, "Methionine as a source of single-carbon units for Nucleaic Acid synthesis", Fed. Proc. 14:209 1955
• Jones, Spector, Lipmann, JACS 77:819 1955
• Lieberman, I., JACS 77:2661 1955
• Lieberman, I.; Kornberg, A., "Syn. and Breakdown of Orotidylic III", JBC 212:909 1955 (Feb.)
• Lieberman, I.; Kornberg, A.; Sinnas, E. S., "Enzymatic Synthesis of Pyrimidine Nucleotides", JBC 215:403 1955
• Lipman, "Studies of orotic as intermediate chemical synthesis carbamyl-P reaction... 1954
• Lowenstein; Cohen, JBC 213:689 1955
• Lowenstein, J. M.; Cohen, P. P., "Studies on the biosynthesis of Carbamylaspartic Acid", JBC 220:57 1956
• Reichard, Acta Chem. Sc. 8:1102 1954
• Reichard; Lagerkvist, Acta Chem. Sc. 7:1207 1953
• Reichard; Smith, Acta Chem. Sc. 9:194 1955
• Reichard; Smith, Acta Chem. Sc. 8:795 1955
• Rundles, R. W.; Brewer, S. S., "Hematologic Responses in P. A. to Orotic Acid", Proc. 6th Int. Congress Hematol.
• Lieberman; Kornberg, B & B Acta 12:223 1953
• Lieberman; Kornberg, JBC 207:11 1954
• Wu; Wilson, Fed. Proc. 14:309 1955

Biosynthesis of Pentose Moieties of the nucleic Acids: References

• Hexose
  • Glock, vol. II
  • Glock; McLean, "Levels of Enzymes of the Direct Oxidative Pathway of Carbohydrate in Mammalian Tissues and Tumors", Biochem. J., 56:171-175 1954
  • Racker, E., "Alternative Pathways of Glucose and Fructose Metabolism", Adv. Enzymology 15:141-182 1954
  • Kit, S., "The Role of HMP Shunt in Tumors and Lymphatic Tissues", Cancer Research 16:70-77 1956
  • Bernstein, I. A., "Biosynthesis of Ribose in E. Coli Grown on C14-labeled Glucose", J. Biol. Chem. 221:873-878 1956
• Pentose
  • Bernstein, I. A., "Synthesis of Ribose by the Rat", B&B Acta 19:179 1956
  • Heath; Hurwitz; Horecker, "Acetyl Phosphate Formation in the Phosphorolytic Cleavage of Pentose Phosphate", JACS 78:5449 1956 (Oct.)
  • Horecker, B. L.; Hurwitz, J.; Weissbach, A., JBC 218:785 1956
  • Hurwitz, J.; Weissbach, A.; Horecker, B. L.; Smyrnioti, P. Z., "Spinach phosphoribulokinase", JBC:218 769 1956
  • Newburgh, R. W.; Cheldelin, V. H., "The Intracellular Distribution of Pentose Cycle Activity in Rabbit Kidney and Liver", J. Biol. Chem. 218:89-96 1955
  • Racker, E.; de la Haba, G.; Leder, J. G., "Transketolase-Catalyzed Utilization of Fructose-6-Phosphate and its Significance in a Glucose-6-phosphate Oxidation cycle", Arch. Biochem. Biophys. 48:238 1954
  • Smyrniotis, P. Z.; Horecker, B. L., "The Pteparation of Sedoheptulosediphosphate", JBC 218:745 1956
  • Sprinson, D. B.; Weliky, F., "Conversion of Ethanolamine and Pentose to Acetate in the Rat", Fed. Proc. 13:302 1954
  • Stumpf, P. K.; Horecker, B. L., "The role of xylulose 5-phosphate in xylose metabolism of Lactobacillus pentosus", JBC 218:753 1956
  • Weissbach, A.; Horecker, B. L., Hurwitz, J., "The enzymatic formation of phosphoglyceric acid from ribulose diphosphate and carbon dioxide", JBC 218:795 1956
• Ribose-5-PO₄
  • Kornberg, A.; Lieberman, I.; Simms, E. S., "Enzymatic Synthesis and Properties of 5-Phosphoribosylpyrophosphate", J. Biol. Chem. 215:389 1955
  • Remy, C. N.; Remy, W. T.; Buchanan, John M., "Biosynthesis of the Purines VIII Enzymatic Synthesis and Utilization of α-5 Phosphorribosylpyrophosphate", J. Biol. Chem. 217:885 1955
• Deoxyribose
  • Lanning, M. C.; Cohen, S. S., "On the Origin of Deoxyribose in E. coli and T_γ⁺ Bacteriophage", J. Biol. Chem. 216:413-423 1955
  • MacGee, J.; Dondoroff, M., "A New Phosphorylated Intermediate in Glucose Oxidation (note 2-keto-3-deoxy-6-phospho-gluconic acid, tentative, from Pseudomonas saccharophila)", J. Biol. Chem. 210:617-626 1954
• General Reference
  • Horecker, B. L.; Mehler, A. H., "Carbohydrate Metabolism (esp pp. 229-239)", Ann. Rev. Biochem. 24:207 1955 (now obsolete)

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