Nucleic Acid Metabolism Robert F. Waters, PhD 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

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

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

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

PRPP 5-Phosphoribosyl 1-Pyrophosphate Addition of the ribose sugar component HMP ATP Required Mg++ Pi activates and nucleosides inhibit

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

Carbamoyl Phosphate Synthetase II

Formation of Uridine 5’-phosphate

Enzymes of Pyrimidine Biosynthesis

UTP to CTP Conversion CTP Synthetase Reaction

Conversion of Ribonucleotides to Deoxyribonucleotides Ribonucleotide reductase NADP Thioredoxin reductase Example is production of dCDP

Allosteric Inhibition of Ribonucleotide Reductase ATP activates dATP inhibits

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

Conversion of dUMP to dTMP:Overall 5-fluorouracil Methotrexate

Thymidylate Pathway:Specific

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.

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

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

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.

Purine Biosynthesis IMP (Inosine Monophosphate) Utilizes (Substrates) 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

IMP Pathway

IMP to AMP and GMP Glutamine, NAD, ATP used in GMP production Aspartate, GTP used AMP production

AMP and GMP Pathway

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

Pyrimidine Catabolic Pathway

Purine Catabolism

Regulation of Nucleotide Metabolism Pyrimidine Regulation Primary regulatory step is Carbamoyl Phosphate via Carbamoyl Phosphate Synthetase II Purine Regulation

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

Action of Allopurinol:Pathway

Biosythesis of Nucleotide Coenzymes CoA OTC is pantothenate Uses ATP, CTP, Cysteine

Coenzyme A Pathway

FMN and FAD OTC is riboflavin Consumes ATP