BMSC230 Mod. 13

• Nucleotide


  Building blocks of nucleic acids, important signalling molecules

  
• Purine and pyrimidines


  Degraded to form nucleic acids

  
• How DNA is made

  1. Nucleic Acid Degradation

  2. Nucleic Acid Digestion

  3. Nucleotides

  
• Anything made of cells will have nucleic acid
• There is no dietary requirement for nucleic acid
• P generates ribose 5P


  Which is a component of nucleotides
• Nucleic Acid Digestion


  1. Nucleoproteins in lumen of small intestine

  2. Acted on by proteases and nucleases

  3. Phosphodiester bonds connecting nucleotides hydrolyzed

  4. Products are monophosphate nucleotides

  
• Nucleotides


  1. Acted on by phosphatases to remove phosphate groups

  2. Produce nucleosides with purine or pyrimidine

  
• Nucleosides


  Molecules with purine or pyrimidine linked to ribose or deoxyribose sugar

  
• Purines and pyrimidines


  1. Nucleosidases hydrolyze link between sugar and nitrogenous base

  2. Most absorbed into enterocytes

  3. Only 5% of absorbed nucleosides go towards nucleic acid synthesis

  4. About 25% used for rapid regeneration of enterocytes

  5. Most degraded further

  
• Nucleotide


  Consists of N base, ribose/deoxyribose sugar, and 1 or more phosphate groups

  
• N bases


  • A, G, C, U, T
• Ribose


  • Has O on C2
• Deoxyribose


  • Has H on C2
• Diverse functions of nucleotides/nucleosides

  • ATP as major energy currency
  • Adenine based nucleotides make up major coenzymes (NAD, FAD, CoA)
  • Linking nucleotides to other biomolecules forms activated substrates
  • Physiological regulators (cAMP, GTP)

  
• Adenosine


  Potent effect on heart, decreases heart rate and force of contraction
• Purine nucleotide synthesis


  1. De novo pathway - synthesis from scratch using other molecules

  2. Salvage pathway - chemical joining of free purine bases

  
• De novo purine synthesis

  • Starts with ribose 5-P, builds purine ring on sugar
  • Uses glutamine, aspartate, glycine, CO2, formate as precursors

  
• De novo purine synthesis

  1. Ribose-5-P -> PRPP (activated substrate)

  2. PRPP + glutamine -> phosphoribosylamine

  3. Phosphoribosylamine -> IMP (precursor for AMP and GMP)

  4. IMP -> AMP or GMP

  
• Regulation of de novo purine synthesis

  • PRPP synthetase regulated by ADP, end products IMP, GMP, AMP
  • Glutamine-PRPP amidotransferase regulated by concerted and sequential inhibition

  
• Salvage pathway for purines


  Chemical joining of free purine bases (adenine, guanine, hypoxanthine) to PRPP

  
• Lesch-Nyhan syndrome


  Genetic defect in purine salvage pathway, leads to uric acid buildup and neurological defects
• Gout production


  1. Remove phosphate from AMP and GMP

  2. Deaminate adenosine to inosine

  3. Metabolize guanine and hypoxanthine to xanthine and uric acid

  
• Uric acid


  Sodium salt that builds up in joints causing inflammation (gout)
• Treatments for gout


  Dietary restrictions, drug Allopurinol (inhibits xanthine oxidase)
• Pyrimidine ring assembly


  1. Uracil, cytosine, thymine made by de novo pathway

  2. Glutamine, CO2, aspartate provide atoms

  3. Carbamoyl phosphate synthetase II catalyzes first committed step

  
• Pyrimidine synthesis overview


  1. Orotate formed first, attached to ribose ring by PRPP

  2. Orotate decarboxylated to form UMP

  3. UMP phosphorylated to UTP

  4. UTP converted to CTP using glutamine and ATP

  
• Committed step in pyrimidine synthesis

  • Catalyzed by aspartate transcarbamoylase, allosterically regulated by CTP

  
• Interconversions of nucleosides and nucleotides occur
• Sources of atoms


  • gar
  • glutamine
  • CO2
  • aspartate

  
• First, rate-limiting step


  1. Catalyzed by carbamoyl phosphate synthetase II (CPS II)

  2. Fuses the amino group from glutamine to CO2 (in form of 03] and a phosphate from ATP to form carbamoyl phosphate

  3. Energy from hydrolysis drives it forward

  
• Carbamoyl phosphate synthetase II (CPS II) and carbamoyl phosphate synthetase I (CPS I)


  • Both synthesize carbamoyl phosphate, but have different substrates, N donors, locations and effectors
  • CPS II is inhibited by UTP, a major end product of the de novo path for purines

  
• Overview + Detailed Reactions

  1. First pyrimidine-like molecule formed is orotate which gets attached to a ribose ring by PRP as activated ribose to produce protidylate

  2. Then undergoes decarboxylation to form Uridylate (UMP)

  3. UMP gets phosphorylated twice to UTP

  4. UTP gets converted to CTP using glutamine as A. group, ATP is required

  
• Committed Step


  Catalyzed by aspartate transcarbamoylase (ATCase) - allosterically regulated by CTP (final product)

  
• Interconversions of Nucleosides


  • Mono, di + tri substrates for RNA + DNA synthesis are nucleoside triphosphates
  • Nucleotide Monophosphates (NMP) - AMP or GMPs use enzyme NMP kinases, with AP as source of P group
  • Nucleoside Diphosphates acted on by nucleoside diphosphate kinase - no enzyme specificity for the base or sugar, uses ATP to generate other NTPS needed by cell

  
• Where does ATP come from?

  1. Derived primarily from oxidative phosphorylation in the mitochondria

  2. Also produced in glycolysis via substrate level phosphorylation

  
• NMP + ATP->


  1. NDP + ADP

  2. Enzyme: NMP kinase-base specific

  3. AMP + ATP->2 ADP, Enzyme: adenylate kinase

  4. GMP + ATP->GDP + ADP, Enzyme: guanylate kinase

  5. dGMP + ATP->dGDP + ADP
• NDP + NTP->


  1. NTP + NDP

  2. Enzyme: nucleoside diphosphate kinase

  
• ADP + Pi->


  1. ATP

  2. Oxidative/substrate level phosphorylation

  
• Ribonucleotides to Deoxyribonucleotides


  • Ribonucleotides consist of a phosphate group, ribose sugar and nucleobase
  • Deoxyribonucleotides are needed for DNA synthesis, synthesized by ribonucleotide reductase
  • Substrates are ADP, UDP, GDP + CDP
  • The 2'-O position on the ring gets reduced to a hydrogen group to a deoxyribose
  • Reducing equivalents are through cysteine residues, then is oxidized as a result the reduced form is regenerated by using NADPH + electron carriers