Nucleotide Synthesis: De Novo and Salvage Pathways

Nucleotide Synthesis Overview

• Nucleotides are synthesized as ribonucleoside monophosphates (NMPs)
• Starting substrate for purine nucleotide synthesis is 5-phosphoribosyl-1-pyrophosphate (PRPP)
• PRPP is synthesized from ribose-5 phosphate and requires ATP, Mg2+, and is activated by free Pi
• End-product inhibition is a recurring theme in nucleotide synthesis

De Novo Pathway: Purine Synthesis

• Uses 5-phosphoribosyl 1-pyrophosphate (PRPP) as the starting "scaffold"
• The purine ring is built by additions of carbons and nitrogens from various sources including aspartate, glycine, glutamine, CO2, and N10-formyltetrahydrofolate
• The end product is inosine monophosphate (IMP)

Clinical Correlates

• Antibiotics that target folic acid metabolism:
  • Sulfonamides/sulfa drugs competitively inhibit bacterial synthesis of folic acid and slow down purine synthesis
  • Trimethoprim inhibits the reduction of dihydrofolate to tetrahydrofolate, which slows down purine synthesis
• Folic acid analogs:
  • Methotrexate is an analog of dihydrofolate

Nucleotide Functions

• Nucleotides have three components: nitrogen-base derivatives, pentose, and phosphates
• Functions:
  • Monomeric units of DNA and RNA
  • Provide free energy for chemical reactions (ATP and GTP)
  • Components of coenzymes (Flavin adenine dinucleotide, Nicotinamide adenine dinucleotide, coenzyme A)

De Novo Pyrimidine Synthesis

• Purpose: Synthesis of a pyrimidine ring from scratch through the additions of carbons and nitrogens from aspartate, glutamine, and CO2
• Then it is added to ribose-5-phosphate (from PRPP)
• The end product is UMP, an important intermediate is orotic acid
• UMP is modified to generate UTP and CTP for RNA synthesis and dCTP and dTTP for DNA synthesis
• Key steps:
  • The rate-limiting step is the formation of carbamoyl phosphate by carbamoyl phosphate synthetase II (CPSII)
  • Another important step is the generation of (d)TMP from dUMP by thymidylate synthase, which is the rate-limiting step for DNA synthesis and requires tetrahydrofolate
• Hormonal control: N/A
• Allosteric/local control: CPSII is activated by PRPP and inhibited by UTP
• Deficiencies/diseases: Orotic aciduria with high orotic acid in urine, failure to thrive, and anemia