Nucleic Acid Metabolism

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Nucleic Acid Metabolism

• Nucleotides
• Essential for all cells
• Carriers of activated intermediates in
  carbohydrate, lipids and proteins
• CoA
• FAD
• NAD
• NADP
• Energy Carriers
• ATP
• Inhibiting or activating enzymes
• DNA
• RNA

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Nucleotide Structure

• Ribose Sugar
• Ribose
• Deoxyribose
• Base
• Purines
• Pyrimidines
• Nucleoside
• Base plus sugar
• Nucleotide
• E.g., AMP, ADP, ATP

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Nomenclature

• DNA Purine Bases
• Adenine
• Guanine
• Purine Nucleosides
• Adenosine
• Guanosine
• DNA Nucleotides (Purine)
• dAMP (deoxyadenylate)
• dGMP (deoxyguanylate)
• RNA Nucleotides (Purine)
• Adenylate (AMP)
• Guanylate (GMP)

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Nomenclature Continued

• DNA Pyrimidine Bases
• Thymine
• Cytosine (Also RNA)
• DNA Pyrimidine Nucelosides
• Thymidine
• Cytidine
• DNA Pyrimidine Nucleotides
• (dTMP) deoxythymidylate
• (dCMP) deoxycytidylate
• RNA Pyrimidine Nucleotides
• (CMP) cytidylate
• (UMP) uridylate

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PRPP 5-Phosphoribosyl 1-Pyrophosphate

• Addition of the ribose sugar component
• HMP
• ATP Required
• Mg
• Pi activates and nucleosides inhibit

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Pyrimidine Synthesis

• UMP (Uridine 5-monophosphate) to UTP
• Precursor to CTP
• Occurs on mitochondria inner membrane
• Carbamoyl phosphate synthetase II
• Different from CPS I
• CPS I uses free ammonia
• CPS II uses glutamine for amino source

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Carbamoyl Phosphate Synthetase II

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Formation of Uridine 5-phosphate
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Enzymes of Pyrimidine Biosynthesis
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UTP to CTP Conversion

• CTP Synthetase Reaction

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Conversion of Ribonucleotides to
Deoxyribonucleotides

• Ribonucleotide reductase
• NADP
• Thioredoxin reductase
• Example is production of dCDP

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Allosteric Inhibition of Ribonucleotide Reductase

• ATP activates
• dATP inhibits

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Thymidylate Biosynthesis

• Substrates and Vitamins
• dUMP
• Folate (N5, N10,-Methylene-THF)
• Glycine/Serine
• NADP

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Conversion of dUMP to dTMPOverall

• 5-fluorouracil
• Methotrexate

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Thymidylate PathwaySpecific

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Thymidylate Synthesis and Cancer Chemotherapy

• Thymidylate synthase is target for fluorouracil
• Action is 5-fluorouracil (5-FU)is converted to
  5-fluoro-2-deoxyuridylate (dUMP structural
  analog)
• Then 5-fluoro-2-deoxyuridylate binds to the
  enzyme Thymidylate Synthase and undergoes a
  partial reaction where part of the way through
  5-fluoro-2-deoxyuridylate forms a covalent
  bridge between Thymidylate Synthase and N5,
  N10-Methylene THF and is an irreversible
  inhibition.
• Normally, the enzyme, Thymidylate Synthase and
  the vitamin would NOT be linked together
  permanently
• This type of inhibition is called suicide-based
  enzyme inhibition because the inhibitor
  participates in the reaction causing the enzyme
  to react with the compound producing a compound
  that inactivates the enzyme itself.

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Fluorouracil Pathway
Suicide inhibition because Flurouracil does not
directly inhibit enzyme.

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Methotrexate

• Competitive inhibitor of Dihydrofolate Reductase
• Used in,
• Acute lymphoblastic leukemia
• Osteosarcoma in children
• Solid tumor treatment
• Breast, head, neck, ovary, and bladder
• Prevents regeneration of tetrahydrofolate and
  removes activity of the active forms of folate

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Leucovorin Rescue Strategy in Methotrexate
Chemotherapy

• Patients given sufficient methotrexate that if
  were not followed by Leucovorin (N5-methenyl-THF)
  would be fatal.
• All neoplastic cells are killed
• Patients are rescued (6-36 hours) by the
  Leucovorin (Folate) otherwise would die due to
  permanent tetrahydrofolate shutdown.
• Tumor resistance to methotrexate can occur in
  patients who have gene amplification of
  dihydrofolate reductase (in tumor cells)
• More dihydrofolate reductase is produced by more
  than the normal active genes usually present in
  normal cells.

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Purine Biosynthesis

• IMP (Inosine Monophosphate)
• Precursor to
• GMP and AMP
• Utilizes (Substrates)
• Glycine
• Glutamine
• ATP
• Folate (N10-formyl-THF)
• Aspartate
• CO2
• PRPP amidotransferase is rate limiting
• Inhibited by AMP and GMP

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IMP Pathway

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IMP to AMP and GMP

• Glutamine, NAD, ATP used in GMP production
• Aspartate, GTP used AMP production

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AMP and GMP Pathway

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Nucleotide Pyrimidine Catabolism

• Degradation of pyrimidine metabolites
• UMP, CMP, TMP
• End products are acetyl-CoA and Propionyl-CoA
• Ribose sugar component may be converted to
  ribose-5-phosphate which is a substrate for PRPP
  Synthetase
• Ribose sugar component may be further catabolized
  in HMP pathway

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Pyrimidine Catabolic Pathway

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Purine Catabolism

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Regulation of Nucleotide Metabolism

• Pyrimidine Regulation
• Primary regulatory step is Carbamoyl Phosphate
  via Carbamoyl Phosphate Synthetase II
• Purine Regulation

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Action of Allopurinol

• Allopurinol is purine
• base analog
• Three mechanisms
• Allopurinol is oxidized to alloxanthine by
  xanthine dehydrogenase
• Then Allopurinol and alloxanthine are inhibitors
  of xanthine dehydrogenase
• This inhibition decreases urate formation
• Then concentrations of Allopurinol and
  alloxanthine increase but do not precipitate as
  urate does.
• Allopurinol and alloxanthine are excreted into
  the urine

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Action of AllopurinolPathway

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Biosythesis of Nucleotide Coenzymes

• CoA
• OTC is pantothenate
• Uses ATP, CTP, Cysteine

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Coenzyme A Pathway

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FMN and FAD

• OTC is riboflavin
• Consumes ATP