Principles of Biochemistry Horton • Moran • Scrimgeour • Perry • Rawn Principles of Biochemistry Fourth Edition Chapter 18 Nucleotide Metabolism Copyright © 2006 Pearson Prentice Hall, Inc.

Chapter 18 - Nucleotide Metabolism Nucleotides are building blocks of DNA and RNA Nucleotides are cosubstrates (ATP) and regulatory compounds (cyclic AMP) Every nucleotide contains either a purine base or a pyrimidine base This chapter presents the biosynthesis and degradation of nucleotides

18.1 Synthesis of Purine Nucleotides Fig 18.1 Uric acid and the major purines

Fig 18.2 Sources of ring atoms in purines synthesized de novo The purine ring structure is not synthesized as a free base but as a substituent of ribose 5-phosphate.

Fig 18.3 Synthesis of 5-ribosyl 1-pyrophosphate (PRPP)

Fig 18.4 Inosine 5’-monophosphate (IMP or inosinate) IMP is the initial product of the 10-step purine nucleotide pathway Hypoxanthine (6-oxopurine) is the base for IMP

Fig 18.5 Ten-step pathway for de novo synthesis of IMP

Fig 18.5 Ten-step pathway for the synthesis of IMP (10 slides)

Fig 18.6 Mechanism for CO2 addition Carboxyaminoimidazole ribonucleotide is an intermediate in the conversion of AIR to CAIR.

18.2 Other Purine Nucleotides Are Synthesized from IMP IMP can be converted to either AMP or GMP Two enzymatic reactions are required for each AMP and GMP can then be phosphorylated to their di- and triphosphates by kinases

Fig 18.7 Pathway for conversion of IMP to AMP and to GMP

Fig 18.7 Pathway for conversion of IMP to AMP and to GMP (continued next slide)

Fig 18.7 (continued)

Fig 18.8 Feedback inhibition in purine nucleotide biosynthesis

18.3 Synthesis of Pyrimidine Nucleotides Sources of the ring atoms in pyrimidines Figure 18.9 The immediate precursor of C-2 and N-3 is carbamoyl phosphate

The Major Pyrimidines

A. The Pathway for Pyrimidine Synthesis Uridine 5’-phosphate is the precursor of other pyrimydine nculeotides A six-step pathway to UMP In eukaryotes, Steps 1-3 are catalyzed by a multifunctional protein (dihydroorotate synthase) Steps 5,6 are catalyzed by a bifunctional enzyme (UMP synthase)

Six-step pathway for the de novo synthesis of UMP in prokaryotes Fig 18.10 Six-step pathway for the de novo synthesis of UMP in prokaryotes

B. Regulation of Pyrimidine Synthesis Eukaryotic cells have 2 carbamoyl phosphate synthetases (CPS I and CPS II) Mitochondrial CPS I uses NH3 as nitrogen source

CPS II Cytosolic CPS II uses glutamine as the nitrogen donor to carbamoyl phosphate

Regulation of pyrimidine synthesis CPS II is allosterically regulated: PRPP and IMP are activators Several pyrimidines are inhibitors Aspartate transcarbamoylase (ATCase) Important regulatory point in prokaryotes Catalyzes the first committed pathway step Allosteric regulators: CTP (-), CTP + UTP (-), ATP (+)

Fig 18.11 Complex structure of ATCase from E. coli

18.4 CTP is Synthesized from UMP UMP is converted to CTP in three steps UMP first converted to UDP and UTP (18-1)

Fig 18.12 Conversion of UTP to CTP by CTP synthetase

Fig 18.13 Regulation of pyrimidine nucleotide synthesis in E. coli

18.5 Reduction of Ribonucleotides to Deoxyribonucleotides 2’-Deoxyribonucleoside triphosphates (substrates for DNA polymerase) synthesized by enzymatic reduction of ribonucleotides Ribonucleotide diphosphate reductase (RDR): ADP dADP GDP dGDP CDP dCDP UDP dUDP

Fig 18.14 Reduction of ribonucleotide diphosphates

18.6 Methylation of dUMP Produces dTMP Deoxythymidylate (dTMP) (required for DNA synthesis) is formed from UMP in 4 steps UMP UDP dUDP dUMP dTMP

Two routes for conversion of dUDP to dUMP 1. dUDP + ADP dUMP + ATP 2. dUDP + ATP dUTP dUMP + PPi H2O ADP

Fig 18.15 Synthesis of dTMP from dUMP (2 slides)

Salvage of thymidine to generate dTMP (18.6)

18.7 Salvage of Purines and Pyrimidines During cellular metabolism or digestion, nucleic acids are degraded to heterocyclic bases These bases can be salvaged by direct conversion to 5’-mononucleotides PRPP is the donor of the 5-phosphoribosyl group Recycling of intact bases saves energy (reduced nitrogen sources are scarce)

Fig 18.16 Breakdown of nucleic acids

Fig 18.17 Degradation and salvage of purines

Fig 18.18 Interconversions of purine nucleotides

Fig 18.19 Interconversions of pyrimidine nucleotides

18.8 Purine Catabolism Most free purines and pyrimidines are salvaged, however some are catabolized Birds, reptiles and primates (including humans) convert purines to uric acid

Separation of base from (deoxy) ribose Purine-nucleoside phosphorylase (PNP) separates the free purine base from the ribose (or deoxyribose) PNP (Deoxy)Nucleoside + Pi Base + (Deoxy)-a-D-Ribose 1-phosphate

Fig 18.20 Breakdown of hypoxanthine and guanine to uric acid

Gout results from excess sodium urate Gout is caused from overproduction or inadequate excretion of uric acid Sodium urate is relatively insoluble and can crystallize in tissues Gout can be caused by a deficiency of hypoxanthine-guanine phosphoribosyltransferase or defective regulation of purine biosynthesis

Allopurinol is a treatment for gout Allopurinol is converted in cells to oxypurinol, an inhibitor of xanthine dehydrogenase Allopurinol prevents high levels of uric acid Hypoxanthine, xanthine are more soluble

Fig 18.21 Further catabolism of uric acid by other organisms

18.9 The Purine Nucleotide Cycle in Muscle During intense exercise, AMP deaminase converts AMP to IMP, releasing NH3 Decreasing AMP levels shifts the equilibrium of adenylate kinase to produce more ATP for muscle contraction IMP can be recycled to AMP (Fig 18.7) Purine nucleotide cycle shown on next slide

Purine Nucleotide Cycle Net reaction for one turn of the cycle is: Aspartate + GTP + H2O Fumarate + GDP + Pi + NH3

18.10 Pyrimidine Metabolism Pyrimidine nucleotides are hydrolyzed to the nucleosides and Pi Then thymine, uracil and (deoxy) ribose 1-phosphate are produced Catabolism of the thymine and uracil bases ends with intermediates of central metabolism

Fig 18.23 Catabolism of uracil and thymine