Purine and Pyrimidine Metabolism F23_student.pdf

Purine and Pyrimidine Metabolism – Ch 22 CMB 704/DENT 604 – Fundamental Biochemistry Dr. Maryam Syed [email protected] Fall 2023 Learning Objectives 2 • Name the common Purines and Pyrimidines found in DNA and RNA. • Define nucleosides, nucleotides, and unusual bases. • Compare and contrast de...

Purine and Pyrimidine Metabolism – Ch 22 CMB 704/DENT 604 – Fundamental Biochemistry Dr. Maryam Syed [email protected] Fall 2023 Learning Objectives 2 • Name the common Purines and Pyrimidines found in DNA and RNA. • Define nucleosides, nucleotides, and unusual bases. • Compare and contrast de novo purine and pyrimidine synthesis. • Identify the regulated/committed steps in synthesis of purines and pyrimidines. • Explain the relevance of the salvage pathway for purines. • Recognize the difference between de novo and salvage pathways of purine synthesis. • Compare and contrast purine and pyrimidine degradation. • Summarize purine nucleotide breakdown, knowing key intermediates, enzymes and their role in the development of gout and Lesch-Nyhan syndrome. • Describe the role of the enzyme Ribonucleotide Reductase. Nucleotides • 3 Building blocks of DNA and RNA Nucleotides • 4 Building blocks of DNA and RNA Purines and Pyrimidines • Nucleobases classified as either purines or pyrimidines • A, T, G, C, U commonly found in DNA and RNA 5 Unusual (Modified) Bases 6 • Chemically modified bases • Found in DNA (5-methylcytosine) and RNA (tRNA) • ____________________________________________ Nucleoside 7 Ribonucleoside Deoxyribonucleoside Adenosine Deoxyadenosine Guanosine Deoxyguanosine • Pentose Sugar + Base • Purine or Pyrimidine = Base • Ribose sugar + Base = • Ribonucleoside Cytidine Deoxycytidine • 2-deoxyribose sugar + Base = • Deoxyribonucleoside Uridine Deoxythymidine or Thymidine Nucleotide 8 • Base + Pentose Sugar + Phosphate group(s) • Adenosine Monophosphate (AMP) vs. Deoxyadenosine Monophosphate (dAMP) • AMP vs ADP vs ATP (major energy source) • Pi attached to 5’-OH of pentose sugar via _____________________________________ • Second and third Pi connected by “highenergy _______________________________ bonds” Two ways to synthesize Nucleotides 9 1. De Novo Synthesis • Make from scratch 2. Salvage Pathway • Recycles nucleotides that are semi-degraded De Novo Synthesis of Purine and Pyrimidine Bases 10 • Need ______________________ (from the Pentose Phosphate Pathway) • Use enzyme PRPP synthetase • Requires ATP to produce _____________________ De Novo Synthesis of Pyrimidines Pyrimidines 11 dUMP dTTP UTP CTP UMP • Mammalian cells: • Activated by PRPP • Inhibited by UTP 12 De Novo Pyrimidine Synthesis • 13 Sources of the atoms in the pyrimidine ring are glutamine, CO2, and aspartate • Enzyme carbamoyl phosphate synthetase II (CPS II) is regulated • Pyrimidine ring is constructed before being conjugated to PRPP to yield ______________ • OMP is decarboxylated to yield ___________________ • Mammalian cells: • Activated by PRPP • Inhibited by UTP De Novo Pyrimidine Synthesis 14 1. ____________________ convert UMP  UDP  UTP 2. ____________________yields CTP by amination of UTP De Novo Pyrimidine Synthesis 15 De Novo Purine Synthesis Purine 16 IMP AMP ATP GMP GTP • Begins with glutamine, aspartate, glycine, CO2, and formate • 10-step pathway later…. you get _____________________________ De Novo Purine Synthesis • PRPP + Glutamine begin the process • • • • 17 Enzyme: GPAT (Glutamine-phosphoribosylpyrophosphate amidotransferase) Activated by PRPP Inhibited by AMP + GMP This is a committed step! • Subsequent steps build the purine ring structure  IMP • The purine nucleobase is built directly on PRPP De Novo Purine Synthesis Purine IMP AMP ATP GMP GTP AMP synthesis 18 GMP synthesis • IMP + Aspartate + GTP  AMP • IMP + Glutamine + ATP  GMP • First enzyme is negatively regulated by feedback inhibition (AMP) • First enzyme is negatively regulated by feedback inhibition (GMP) • AMP + Kinase  ATP • GMP + Kinase  GTP What’s next…? 19 • We have our RNA nucleotides – AMP, GMP, CMP, UMP • How do we make DNA nucleotides? 1. Convert RNA from monophosphate form to diphosphate form to get ADP, GDP, CDP, UDP 2. Use enzyme ___________________________ to reduce the ribose to deoxyribose to yield dADP, dGDP, dCDP, dUDP Wait a minute…? • BUT… what about dTMP? • dUMP + _____________________ dTMP Pyrimidines 20 dUMP dTTP UTP CTP UMP Pyrimidine Degradation 21 Purine Degradation 22 Purine Degradation • 23 GMP  Guanine  Xanthine  Uric Acid 1. GMP loses the ribose and phosphate to yield Guanine 2. Guanine loses an amino group to yield Xanthine 3. Xanthine is oxidized to uric acid Purine Degradation • 24 AMP  IMP  Hypoxanthine  Xanthine  Uric Acid 1. AMP loses an amino group to yield IMP 2. IMP loses the ribose and phosphate to yield Hypoxanthine 3. Hypoxanthine is oxidized to Xanthine 4. Xanthine is oxidized to uric acid Purine Degradation • Build up of uric acid = BAD • Slow excretion or excess production • Excess uric acid in joints and tissue  monosodium urate (salt crystals)  _______________________ • Excess uric acid in kidney  _______________________ 25 Salvage Pathway - Purine • Not all tissues can produce nucleotides via the De Novo pathway • Salvage pathway important in ______________ • Intermediates of AMP (Hypoxanthine) and GMP (Guanine) breakdown can be ‘salvaged’ into new nucleic acids Enzyme: _________ IMP  AMP 26 Clinical Correlation… De novo purine synthesis + ↓purine salvage = ↑uric acid De novo purine synthesis + purine salvage = ↑ ↑ uric acid Lesch-Nyhan syndrome 27 • _______________________________ • Rare, X-linked, recessive • Uric acid stones in kidney + urate crystals in joints • Motor dysfunction, cognitive deficits, self-mutilation Summary I 28 • Nucleosides are composed of a nucleobase (purine or pyrimidine) attached to ribose but containing no phosphate. • Nucleotides are the result of phosphate addition to nucleosides and they can be either mono-, di-, or triphosphate modified. • Both purine and pyrimidine nucleotide biosynthesis involves the use of the activated form of ribose-5-phosphate, 5-phosphoribosyl-1-pyrophosphate (PRPP) • The first fully formed purine nucleotide is IMP that serves as a branch point for synthesis of AMP and GMP. • ATP levels regulate GMP synthesis and GTP levels regulate AMP synthesis. • The breakdown of purine nucleotides produces the insoluble product, uric acid. • Excess purine degradation can lead to gout. Summary II 29 • Purine nucleotides are efficiently salvaged by HGPRT. • Lack of HGPRT leads to Lesch-Nyhan syndrome. • The first fully formed pyrimidine nucleotide is UMP. • Following phosphorylation to UTP, some is converted to CTP via the action of CTP synthetase. • Thymidine nucleotides are synthesized from dUMP. • Synthesis of the deoxynucleotide is catalyzed by ribonucleotide reductase (RR). 1. Which pyrimidine is found in RNA only? A. Uracil B. Cytosine C. Thymine D. Adenine 30 1. Which pyrimidine is found in RNA only? A. Uracil B. Cytosine C. Thymine D. Adenine 31 2) Which of the following pairs are both pyrimidines? A. Adenine and Guanine B. Adenine and Thymine C. Cytosine and Guanine D. Cytosine and Uracil 32 2) Which of the following pairs are both pyrimidines? A. Adenine and Guanine B. Adenine and Thymine C. Cytosine and Guanine D. Cytosine and Uracil 33 3)Which of the following is a purine base? A) Adenosine B) Cytosine C) Thymine D) Uracil 34 3)Which of the following is a purine base? A) Adenosine B) Cytosine C) Thymine D) Uracil 35 4) Nucleotides are: A) Purine Bases B) Nitrogen Bases+ Pentose Sugar C) Nitrogen Bases + Pentose Sugar + Phosphate D) None Of The Above 36 4) Nucleotides are: A) Purine Bases B) Nitrogen Bases+ Pentose Sugar C) Nitrogen Bases + Pentose Sugar + Phosphate D) None Of The Above 37 5) Which of the following is not the precursor for de novo purine biosynthesis? A) Aspartate B) Glycine C) Glutamine D) Arginine 38 5) Which of the following is not the precursor for de novo purine biosynthesis? A) Aspartate B) Glycine C) Glutamine D) Arginine 39 6) What is an activator of the enzyme “Glutamine: Phosphoribosylpyrophosphate amidotransferase” (GPAT) a committed step of de novo biosynthesis of purines? A) Adenosine Monophosphate B) Guanosine Monophosphate C) Inosine Monophosphate D) Phosphoribosyl Pyrophosphate 40 6) What is an activator of the enzyme “Glutamine: Phosphoribosylpyrophosphate amidotransferase” (GPAT) a committed step of de novo biosynthesis of purines? A) Adenosine Monophosphate B) Guanosine Monophosphate C) Inosine Monophosphate D) Phosphoribosyl Pyrophosphate 41 8) All deoxyribonucleotides are synthesized from the ribonucleotides. A) True B) False 42 8) All deoxyribonucleotides are synthesized from the ribonucleotides. A) True B) False 43 9) Which of the following is not the precursor of a purine ring? A) Glutamine B) Lysine C) Glycine D) Aspartate 44 9) Which of the following is not the precursor of a purine ring? A) Glutamine B) Lysine C) Glycine D) Aspartate 45 10) What is the final product of purine degradation in mammals? A) Guanine B) Inosine C) Uric Acid D) Hypoxanthine 46 10) What is the final product of purine degradation in mammals? A) Guanine B) Inosine C) Uric Acid D) Hypoxanthine 47 11) A 42-year-old male patient undergoing radiation therapy for prostate cancer develops severe pain in the metatarsal phalangeal joint of his right big toe. Monosodium urate crystals are detected by polarized light microscopy in fluid obtained from this joint by arthrocentesis. This patient’s pain is directly caused by the overproduction of the end product of which of the following metabolic pathways? A. De novo pyrimidine biosynthesis B. Pyrimidine degradation C. De novo purine biosynthesis D. Purine salvage E. Purine degradation 48 11) A 42-year-old male patient undergoing radiation therapy for prostate cancer develops severe pain in the metatarsal phalangeal joint of his right big toe. Monosodium urate crystals are detected by polarized light microscopy in fluid obtained from this joint by arthrocentesis. This patient’s pain is directly caused by the overproduction of the end product of which of the following metabolic pathways? A. De novo pyrimidine biosynthesis B. Pyrimidine degradation C. De novo purine biosynthesis D. Purine salvage E. Purine degradation 49 12) What is the catabolic end product of pyrimidine nucleotides? A. Uric acid B. NH3 C. CO2 D. Both B and C 50 12) What is the catabolic end product of pyrimidine nucleotides? A. Uric acid B. NH3 C. CO2 D. Both B and C 51 Review Questions • What are the purines and pyrimidines found in DNA and RNA? • What is a nucleoside? • What is a nucleotide? • What is an unusual base? What are some examples? • What are the steps involved in de novo purine synthesis? • What is the salvage pathway of purine synthesis and how does it differ from de novo purine synthesis? • What happens during purine degradation? What are the steps involved? What is the end product? How is the end product excreted? How is this related to gout and Lesch-Nyhan syndrome? What are the important enzymes? What are the rate limiting steps? How is gout distinct from Lesch-Nyhan syndrome? • What are the regulated/committed steps? What is the end product? What is the starting material? • What are the steps involved in pyrimidine synthesis? What are the important enzymes? What happens during pyrimidine degradation? What are the steps involved? How is the end product excreted? • What is ribonucleotide reductase and what role does it play in nucleotide synthesis? What are the rate limiting steps? What are the regulated/committed steps? What is the starting material? 52