STEPTRACKERBIOCHEMISTRY + PHARMACOLOGY | MOLECULAR BIOLOGY | HIGH-YIELD REVIEW

Nucleotide Synthesis

Purines build the base on the sugar; pyrimidines build the base first — and almost every step is a drug target.

FOCUS ON
Purines (A, G; two rings) are built on PRPP; pyrimidines (C, T, U; one ring) make the ring (orotate) first, then add PRPP. Both need glycine/aspartate/glutamine nitrogens and folate carbons. Ribonucleotide reductase makes deoxy forms (hydroxyurea). Thymidylate synthase needs folate (5-FU, methotrexate, trimethoprim).
STEP · ENZYME
WHAT IT DOES
BLOCKED BY
CLUE
PRPP synthetase
Ribose-5-P (from HMP shunt) → PRPP — feeds both pathways and salvage
—
Overactive PRPP synthetase → gout (excess purines)
Glutamine-PRPP amidotransferase
rate-limiting · purines
Commits PRPP to purine synthesis → IMP → AMP, GMP
6-mercaptopurine, azathioprine (feedback mimic); mycophenolate blocks IMP → GMP (IMP dehydrogenase)
Inhibited by AMP, GMP, IMP
Carbamoyl phosphate synthetase II
rate-limiting · pyrimidines
Glutamine + CO₂ → carbamoyl phosphate in the cytosol
Leflunomide blocks the later step (dihydroorotate dehydrogenase)
CPS I = mitochondria, urea cycle (ammonia)
UMP synthase
Orotic acid + PRPP → UMP (two activities)
—
Deficiency → orotic aciduria (see 1.03)
Ribonucleotide reductase
Ribonucleotides (NDPs) → deoxyribonucleotides for DNA
Hydroxyurea; gemcitabine
Hydroxyurea also ↑ HbF in sickle cell
Thymidylate synthase
dUMP → dTMP using N⁵,N¹⁰-methylene-THF
5-FU (and capecitabine)
5-FU toxicity worse with folinic acid (stabilizes complex)
Dihydrofolate reductase
Regenerates THF from DHF (needed for thymidine and purines)
Methotrexate (human), trimethoprim (bacterial), pyrimethamine (protozoal)
Leucovorin (folinic acid) rescues MTX toxicity
Purine vs pyrimidine
Purines: Adenine, Guanine (two rings) · Pyrimidines: Cytosine, Uracil, Thymine (one ring)
—
Purines (A, G) have two rings; pyrimidines (C, U, T) have one
Base chemistry
Thymine = methylated uracil · cytosine deamination → uracil · G–C has 3 H-bonds, A–T has 2
—
High G–C content → higher melting temperature
Nucleoside vs nucleotide
Nucleoside = base + sugar · nucleotide = base + sugar + phosphate
—
Phosphodiester bond links 3′ of one sugar to 5′ phosphate of the next

Mechanism — two routes to a nucleotide

PurinesPRPP first
→
Build rings on sugarGly, Asp, Gln, CO₂, THF
→
IMP→ AMP, GMP
PyrimidinesRing first
→
Carbamoyl-P → orotateAsp, Gln, CO₂
→
+ PRPP → UMP→ CTP, dTMP

Folate (THF) donates carbons to purine rings and to thymidine — so antifolates hit DNA synthesis on both sides.

Drug → enzyme

DRUG
TARGET
USE
Methotrexate
DHF reductase
Cancer, RA, psoriasis, ectopic
Trimethoprim
Bacterial DHFR
UTI (with sulfamethoxazole)
5-FU
Thymidylate synthase
GI cancers
Hydroxyurea
Ribonucleotide reductase
Sickle cell, CML, PV
Mycophenolate
IMP dehydrogenase
Transplant
Leflunomide
Dihydroorotate dehydrogenase
RA
6-MP / azathioprine
De novo purine synthesis
ALL, IBD, transplant

How it's tested

COMMON CONFUSIONCPS II (cytosol, pyrimidines, uses glutamine) vs CPS I (mitochondria, urea cycle, uses ammonia, activated by N-acetylglutamate).
THE TRAPMegaloblastic anemia on a "folate antagonist" — methotrexate, trimethoprim, pyrimethamine and phenytoin all qualify; leucovorin rescues human DHFR blockade.
YOUR APPROACHName the base class → pathway (PRPP first or ring first) → step → drug that blocks it → toxicity (marrow, mucositis).

If you see… think…

Rate-limiting enzyme of purine synthesis → glutamine-PRPP amidotransferase
Rate-limiting enzyme of pyrimidine synthesis → CPS II
Drug raising HbF in sickle cell → hydroxyurea (ribonucleotide reductase)
Leucovorin given after a chemo drug → methotrexate
Leucovorin makes it more toxic → 5-FU
Toxoplasmosis treatment that blocks protozoal DHFR → pyrimethamine
Transplant drug blocking guanine synthesis in lymphocytes → mycophenolate
RA drug blocking dihydroorotate dehydrogenase → leflunomide
Base with two rings → purine (A, G)
Strand with high G–C content → more H-bonds, higher melting point