Nucleotide Metabolism and Biosynthesis

Nucleotide Metabolism

• Nucleotides are the building blocks of DNA and RNA.
• Two classes of nucleotides:
  • Purines
  • Pyrimidines
• Other functions of nucleotides:
  • Energy carriers (ATP, GTP)
  • Components of co-enzymes (NAD, FAD)
  • Signal transduction (cAMP, cGMP)

Nucleotide Biosynthesis

• Ample supply of nucleotides is essential for cellular processes.
• Two pathways for nucleotide biosynthesis:
  • De novo synthesis: synthesis from simple precursors.
  • Salvage pathway: recycling of pre-existing free bases or nucleosides.

Synthesis Pathways

• Both purines and pyrimidines can be synthesized via:
  • De novo pathway
  • Salvage pathway

Purine Biosynthesis

De Novo Purine Synthesis

• Sources of nitrogen and carbon atoms of the purine ring:

  • Aspartate (N1)
  • Tetrahydrofolate (THF) (C2, C8)
  • Glutamine (N3, N9)
  • Glycine (C4, C5, N7)
  • Bicarbonate (HCO3) (C6)

• Major site of purine synthesis is the liver.

• HMP shunt produces Ribose-5-Phosphate as a starting material.

• First intermediate with a complete purine ring is IMP (Inosine Monophosphate).

• IMP is the precursor for both AMP and GMP.

• Steps in Purine Synthesis:

  • Formation of PRPP (5-Phosphoribosyl-α-pyrophosphate) from Ribose-5-phosphate using PRPP synthetase and ATP:
    $ATP \rightarrow ADP$
  • Addition of N9 (from Glutamine) to PRPP, catalyzed by Glutamine PRPP amidotransferase:
    $Glutamine + H_2O \rightarrow Glutamate + PPi$
  • Addition of Glycine (C4, C5, and N7), catalyzed by GAR synthase:
    $Glycine + ATP \rightarrow ADP + Pi$
  • Addition of C8 (from THF), catalyzed by GAR transformylase:
    $N^{10}-Formyl-THF \rightarrow THF$
  • Addition of N3 (from Glutamine), catalyzed by FGAM synthase:
    $Glutamine + ATP + H_2O \rightarrow Glutamate + ADP + Pi$
  • Cyclization (ring closure), catalyzed by FGAM cyclase:
    $ATP \rightarrow ADP + Pi + H_2O$
  • Addition of C6 (from Bicarbonate), catalyzed by AIR carboxylase:
    $HCO_3 + ATP \rightarrow ADP + Pi$
  • Addition of N1 (from Aspartate), catalyzed by SAICAR synthase:
    $Aspartate + ATP \rightarrow ADP + Pi$
  • Removal of Fumarate, catalyzed by Adenylosuccinate lyase:
    $SAICAR \rightarrow AICAR + Fumarate$
  • Addition of C2 (from THF), catalyzed by AICAR transformylase:
    $N^{10}-Formyl-THF \rightarrow THF$
  • Cyclization (ring closure), catalyzed by IMP cyclohydrolase:
    $FAICAR + H_2O \rightarrow IMP$

• Conversion of IMP to AMP:

  • Uses Aspartate and GTP.
  • Catalyzed by Adenylsuccinate synthetase and Adenylsuccinase.

• Conversion of IMP to GMP:

  • Uses Glutamine and ATP.
  • Catalyzed by IMP dehydrogenase and GMP synthetase.

Regulation of Purine Synthesis

• PRPP Synthetase:
  • Inhibited by: IMP, AMP, GMP
  • Activated by: PRPP
• PRPP-Amido-transferase:
  • Inhibited by: AMP, GMP
  • Activated by: PRPP
• Adenylosuccinate synthetase: Inhibited by AMP.
• IMP dehydrogenase: Inhibited by GMP.

Salvage Pathway of Purines

• Free purine bases or nucleosides are converted to nucleotides.
• No new nucleotides are synthesized from precursors.
• Important for tissues with low de novo pathway activity (e.g., brain, RBCs, neutrophils).
• HGPRTase (Hypoxanthine-Guanine Phosphoribosyltransferase) is the