pyrimidines

Q1: What are the two starting substrates for de novo pyrimidine ring synthesis?

A1: Carbamoyl phosphate and aspartate.

Q2: In de novo pyrimidine synthesis, is the ring built first or attached to ribose first?

A2: The pyrimidine ring is assembled first, then attached to ribose-5-phosphate (via PRPP).

Q3: What is the cellular localization of the initial steps of pyrimidine synthesis (up to orotic acid)?

A3: Cytosol (except dihydroorotate dehydrogenase, which is mitochondrial).

Q4: Where do the final steps of pyrimidine synthesis (orotate → UMP) occur?

A4: Cytosol.

Q5: Write the reaction catalyzed by carbamoyl phosphate synthetase II (CPS II), including substrates and products.

A5: Glutamine + 2 ATP + HCO₃⁻ → Carbamoyl phosphate + 2 ADP + Pi + Glutamate.

Q6: What is the committed step of pyrimidine synthesis, and which enzyme catalyzes it?

A6: Formation of carbamoyl phosphate from glutamine, ATP, and HCO₃⁻. Enzyme: Carbamoyl phosphate synthetase II (CPS II).

Q7: Name the allosteric activator and inhibitor of CPS II.

A7: Activator: PRPP. Inhibitor: UTP (feedback inhibition).

Q8: What are the three key differences between CPS I and CPS II?

A8: CPS I – mitochondrial, uses NH₃, urea cycle. CPS II – cytosolic, uses glutamine, pyrimidine synthesis.

Q9: Write the reaction catalyzed by aspartate transcarbamoylase (ATCase).

A9: Carbamoyl phosphate + Aspartate → N-carbamoylaspartate + Pi.

Q10: What enzyme converts N-carbamoylaspartate to dihydroorotate?

A10: Dihydroorotase.

Q11: Write the reaction for dihydroorotate dehydrogenase, including its coenzyme.

A11: Dihydroorotate + CoQ (ubiquinone) → Orotate + CoQH₂. Coenzyme: Ubiquinone (CoQ).

Q12: Why is dihydroorotate dehydrogenase localized in the mitochondria?

A12: It uses ubiquinone (CoQ) as an electron acceptor, linking pyrimidine synthesis to the electron transport chain for regeneration of CoQ.

Q13: Write the reaction for orotate phosphoribosyltransferase (OPRT).

A13: Orotate + PRPP → OMP (orotidine-5'-monophosphate) + PPi.

Q14: Write the reaction for OMP decarboxylase.

A14: OMP → UMP + CO₂.

Q15: What is the combined name for the bifunctional enzyme that converts orotate to UMP?

A15: UMP synthase (contains both OPRT and OMP decarboxylase activities).

Q16: Write the reaction for CTP synthesis from UTP, including enzyme and substrates.

A16: UTP + Glutamine + ATP → CTP + Glutamate + ADP + Pi. Enzyme: CTP synthetase.

Q17: How is CTP synthetase allosterically regulated?

A17: Activated by GTP; inhibited by CTP (feedback inhibition).

Q18: What is the key regulatory enzyme of pyrimidine nucleotide synthesis, and how is it controlled?

A18: CPS II. Activated by PRPP; inhibited by UTP.

Q19: What is the role of PRPP in pyrimidine synthesis beyond allosteric regulation?

A19: PRPP is the ribose-5-phosphate donor for the conversion of orotate to OMP (and for salvage pathways).

Q20: Describe the salvage pathway for uracil → UMP. Include the enzyme.

A20: Uracil + PRPP → UMP + PPi. Enzyme: Uracil phosphoribosyltransferase. No cofactor required.

Q21: Describe the salvage pathway for thymine → dTMP.

A21: Thymine + deoxyribose-1-phosphate → dTMP + Pi (via thymidine phosphorylase + thymidine kinase). Alternatively: thymine + PRPP → dTMP (thymine phosphoribosyltransferase).

Q22: How does pyrimidine salvage differ from purine salvage in terms of enzymes?

A22: Purine salvage uses HGPRT and APRT; pyrimidine salvage uses uracil phosphoribosyltransferase and thymine phosphoribosyltransferase (different enzymes, but both use PRPP).

Q23: Which enzyme does 5-fluorouracil (5-FU) inhibit, and what is its mechanism?

A23: 5-FU inhibits thymidylate synthase. It acts as a suicide inhibitor, forming a covalent ternary complex with the enzyme and N⁵,N¹⁰-methylene-THF, irreversibly blocking dTMP synthesis.

Q24: Why does inhibition of thymidylate synthase by 5-FU lead to cell death?

A24: dTMP depletion → DNA synthesis impaired → "thymineless death" in rapidly dividing cells.

Q25: Which enzyme does methotrexate inhibit, and how does that affect pyrimidine synthesis?

A25: Methotrexate inhibits DHFR → THF depletion → lack of N⁵,N¹⁰-methylene-THF → thymidylate synthase cannot make dTMP → DNA synthesis stops.

Q26: From which amino acid is the one-carbon unit for thymidylate synthesis derived, and what is the byproduct?

A26: Serine donates the one-carbon unit; glycine is formed.

Q27: Write the reaction for the formation of N⁵,N¹⁰-methylene-THF from THF and serine, including enzyme and coenzyme.

A27: Serine + THF → Glycine + N⁵,N¹⁰-methylene-THF + H₂O. Enzyme: Serine hydroxymethyltransferase. Coenzyme: Pyridoxal phosphate (PLP).

Q28: What vitamin derivative is N⁵,N¹⁰-methylene-THF derived from?

A28: Folic acid (vitamin B₉).

Q29: Write the complete reaction for dTMP synthesis from dUMP (enzyme and co-substrate).

A29: dUMP + N⁵,N¹⁰-methylenetetrahydrofolate → dTMP + dihydrofolate (DHF). Enzyme: Thymidylate synthase.

Q30: Write the reaction for regeneration of THF from DHF (DHFR reaction).

A30: Dihydrofolate (DHF) + NADPH + H⁺ → Tetrahydrofolate (THF) + NADP⁺. Enzyme: Dihydrofolate reductase (DHFR).