BIOCHEM · NUCLEOTIDES

Purines & Pyrimidines

De novo builds from scratch. Salvage recycles what you already have. When either path breaks, the disease tells you exactly which one failed.

Opening Challenge

A 3-year-old boy is brought to clinic for self-injurious behavior, including biting his own lips and fingers to the point of scarring. His mother notes he has had orange crystals in his diaper since infancy and recently developed difficulty walking with abnormal writhing movements of his arms. He has significant developmental delay. On exam he has hypertonia and dystonic posturing of the limbs, with scarred lips and bitten fingertips. Serum uric acid is 13.6 mg/dL (3.5 to 7.2), and urinalysis shows uric acid crystals.

A) Adenosine deaminase deficiency
B) OMP decarboxylase deficiency
C) HGPRT deficiency (Lesch-Nyhan syndrome)
D) PRPP synthetase overactivity
HGPRT deficiency (Lesch-Nyhan). The purine salvage pathway is broken. Hypoxanthine-guanine phosphoribosyltransferase normally recycles hypoxanthine back to IMP and guanine back to GMP. Without it, these purines are instead catabolized all the way to uric acid via xanthine oxidase. The buildup causes gout (orange urate crystals in diapers), but the neurologic features (choreoathetosis, self-mutilation) are what make this a board classic. X-linked recessive, so it hits boys. OMP decarboxylase deficiency causes orotic aciduria but no hyperuricemia and no neuro findings. ADA deficiency causes SCID. PRPP synthetase overactivity also causes gout and hyperuricemia, but without the self-mutilation or choreoathetosis.
01 · The Framework

The Two Factories

De novo builds nucleotides from scratch. Salvage recycles broken-down ones. Same end products, very different starting materials.

Why two pathways? De novo synthesis is expensive (10 steps for purines, requires folate and glutamine). Salvage is cheap and fast, recycling preformed purine/pyrimidine bases. Most cells use both. When salvage breaks, de novo can't fully compensate and purines pile up as uric acid.

Starting Point · 10 Steps

De Novo Purine Synthesis

Starts from: Ribose-5-phosphate (from pentose phosphate pathway).

Step 1: Ribose-5-P → PRPP (phosphoribosyl pyrophosphate) via PRPP synthetase. PRPP is shared with pyrimidine/salvage pathways. The rate-limiting and committed step is Step 2: PRPP → phosphoribosylamine via glutamine-PRPP amidotransferase, inhibited by AMP and GMP.

PRPP then serves as the activated sugar scaffold. Nitrogen donors (primarily glutamine) and carbons from glycine, formate, CO2, and aspartate are added over 10 steps to build IMP (inosine monophosphate), the branch point nucleotide.

From IMP: Two branches diverge. IMP → AMP (via adenylosuccinate, requires GTP). IMP → XMP → GMP (requires ATP). Note: AMP synthesis requires GTP and GMP synthesis requires ATP. This is a cross-regulation that balances the purine pool.

Folate requirement: Steps 3 and 9 require N10-formyl-THF to donate C2 and C8 of the purine ring. This is why methotrexate and trimethoprim (DHFR inhibitors) starve purine synthesis.

Ribose-5-P start Glutamine-PRPP amidotransferase = rate-limiting (Step 2) Glutamine = nitrogen donor IMP = branch point Folate needed (C2, C8) 10 steps total
Ribose-5-P → PRPP → IMP (10 steps) → AMP / GMP
Board trap: PRPP synthetase OVERACTIVITY (gain-of-function mutation) causes excess purine synthesis. The purines pile up and get catabolized to uric acid. Clinical picture: gout plus sometimes neurologic features similar to but distinct from Lesch-Nyhan. X-linked.

Cytoplasm-Only · Simpler Than Purines

De Novo Pyrimidine Synthesis

Starts from: Carbamoyl phosphate + aspartate. These combine to form the pyrimidine ring directly, then attach to PRPP later (opposite order from purines, where PRPP is activated first).

Rate-limiting enzyme: CPS-II (carbamoyl phosphate synthetase II), which is in the cytoplasm. Critical distinction: CPS-I is the mitochondrial enzyme used in the urea cycle. CPS-II uses glutamine as the nitrogen source; CPS-I uses free ammonia.

Key intermediate: Orotic acid (orotate). Built from the ring closure product of carbamoyl-aspartate. Then orotic acid + PRPP → OMP (orotidine monophosphate) via OPRT, then OMP → UMP via OMP decarboxylase (UMP synthase).

From UMP: UMP → UDP → UTP → CTP (via CTP synthetase, uses glutamine).

For DNA synthesis: UMP → dUMP → dTMP via thymidylate synthase (requires N5,N10-methylene-THF). This is where 5-FU works.

CPS-II = cytoplasm, rate-limiting Orotic acid = key intermediate OMP decarboxylase = UMP synthase UMP → UDP → UTP → CTP dTMP needs thymidylate synthase + folate
Carbamoyl-P + Aspartate → Orotic acid → OMP → UMP → UTP / CTP / dTMP
CPS-I vs CPS-II on the board: If you see orotic acid in the urine WITHOUT elevated ammonia, it is a pyrimidine synthesis defect (CPS-II intact, so urea cycle is fine). If orotic acid appears WITH elevated ammonia, it is a urea cycle defect spilling excess carbamoyl phosphate into the pyrimidine path. The ammonia level is the discriminating lab.

Recycling System · Two Key Enzymes

Purine Salvage Pathway

When nucleotides are degraded, the free purine bases can be recycled instead of being discarded as uric acid. This saves energy and prevents buildup of toxic catabolites.

HGPRT (hypoxanthine-guanine phosphoribosyltransferase): recycles hypoxanthine → IMP and guanine → GMP. Requires PRPP as the ribose donor. This is the enzyme lost in Lesch-Nyhan syndrome.

APRT (adenine phosphoribosyltransferase): recycles adenine → AMP. Also requires PRPP. Deficiency causes 2,8-dihydroxyadenine urolithiasis (kidney stones), but without the neurologic features of Lesch-Nyhan.

When HGPRT is absent: hypoxanthine and guanine cannot be salvaged. They are instead catabolized by xanthine oxidase all the way to uric acid. PRPP accumulates (it is no longer consumed by salvage), which actually stimulates de novo purine synthesis even more, compounding the purine overproduction. This dual mechanism is why hyperuricemia in Lesch-Nyhan is so severe.

HGPRT: hypoxanthine + guanine recycled APRT: adenine recycled HGPRT absent = uric acid overload PRPP accumulates when salvage fails PRPP drives excess de novo synthesis
Hypoxanthine / Guanine → HGPRT + PRPP → IMP / GMP (salvaged)
Without HGPRT → Xanthine oxidase → Uric acid (excreted)
Why Lesch-Nyhan has worse gout than plain PRPP overactivity: HGPRT loss does two things simultaneously. It removes the recycling drain (purines can't be salvaged) AND causes PRPP accumulation (now feeding excess de novo synthesis). Both hit at once. The neurologic features are separate from the gout and their mechanism is still not fully understood, but likely involve neuromodulator depletion in dopaminergic pathways.
02 · When the Pathway Breaks

The Disease Shelf

Four diseases, four mechanisms. Tap each card to expand the full clinical picture.

HGPRT deficiency · X-linked
Lesch-Nyhan Syndrome
⌄
Enzyme: HGPRT (hypoxanthine-guanine phosphoribosyltransferase)
Inheritance: X-linked recessive (boys only)
Pathway broken: Purine salvage

Labs: Markedly elevated serum uric acid. Uric acid crystals in urine (orange sand in diapers). Gout in older children and adults.

Clinical: The board triad is self-mutilation (biting fingers and lips to the bone), choreoathetosis, and intellectual disability. Spasticity is also common. The neuro features appear in the first years of life. Gout-related joint destruction follows.

Treatment: Allopurinol controls the hyperuricemia and gout but does NOT improve the neurological features. There is no cure. Behavioral management for self-injury.
Lesch-Nyhan = Lip-biting boy with gout. X-linked, so only boys.
Self-mutilation Choreoathetosis Hyperuricemia X-linked recessive Orange urate crystals Allopurinol (gout only)
ADA deficiency · AR
ADA Deficiency (SCID)
⌄
Enzyme: Adenosine deaminase (ADA)
Inheritance: Autosomal recessive
Pathway broken: Purine catabolism

ADA normally converts adenosine to inosine and deoxyadenosine to deoxyinosine. Without it, adenosine and especially deoxyadenosine accumulate. Deoxyadenosine is selectively toxic to lymphocytes: it is phosphorylated to dATP by deoxycytidine kinase, and the excess dATP inhibits ribonucleotide reductase, blocking DNA synthesis and triggering apoptosis in both T and B lymphocytes.

Clinical: Severe combined immunodeficiency (SCID). "Bubble boy" disease. Recurrent, life-threatening infections from opportunistic organisms. No T cells, no B cells, no NK cells effectively. Usually fatal within the first 2 years without treatment.

Treatment: ADA-PEG (pegylated ADA enzyme replacement) was the first approved gene therapy target in humans. Hematopoietic stem cell transplant is also curative.
ADA gone = dATP toxic to lymphocytes = SCID. "Adenosine destroys all lymphocytes."
SCID No T or B cells dATP toxic to lymphocytes First gene therapy approved Autosomal recessive
UMP synthase deficiency · AR
Orotic Aciduria
⌄
Enzyme: OMP decarboxylase (UMP synthase, a bifunctional enzyme that includes OPRT activity)
Inheritance: Autosomal recessive
Pathway broken: Pyrimidine de novo synthesis (cannot convert OMP to UMP)

Orotic acid cannot proceed to UMP, so it accumulates and is excreted in massive amounts in urine. The pyrimidine pool is depleted, impairing DNA synthesis in rapidly dividing cells, including blood precursors.

Clinical: Megaloblastic anemia (large, immature red cells due to impaired DNA replication in erythroid precursors). Does NOT respond to B12 or folate supplementation. Normal ammonia (key distinguisher from urea cycle defects). Growth retardation.

Key distinguisher: Orotic aciduria WITHOUT hyperammonemia = pyrimidine synthesis defect. Orotic aciduria WITH hyperammonemia = urea cycle defect (excess carbamoyl phosphate from the urea cycle spills into the pyrimidine path).

Treatment: Uridine supplementation bypasses the defect (provides preformed UMP).
Orotic aciduria: big cells (megaloblastic), no ammonia, fix with uridine.
Megaloblastic anemia Orotic acid in urine Normal ammonia Uridine treatment B12/folate don't help
Xanthine oxidase endpoint
Gout (Primary Hyperuricemia)
⌄
Pathway: End-stage purine catabolism
Enzyme involved: Xanthine oxidase (too much activity, or too many purines for it to handle)

Purines (adenine, guanine) are degraded to hypoxanthine and xanthine, then xanthine oxidase converts hypoxanthine → xanthine → uric acid. Humans lack uricase, so uric acid is the final product. When production exceeds renal excretion, monosodium urate crystals precipitate in cooler tissues (joints, especially the first MTP joint).

Acute attack: Hot, red, swollen, exquisitely tender joint. Negatively birefringent needle-shaped crystals under polarized light. Treat with NSAIDs or colchicine (colchicine blocks microtubule polymerization, preventing neutrophil migration into the joint).

Treatment of chronic gout:
- Allopurinol: inhibits xanthine oxidase (substrate analog, purine base analog). Reduces uric acid production.
- Febuxostat: newer xanthine oxidase inhibitor, non-purine scaffold. Used when allopurinol is not tolerated.
- Probenecid: blocks urate reabsorption in kidney, increases excretion. Uricosuric agent.
Allopurinol blocks xanthine oxidase. Colchicine blocks neutrophils in acute. Probenecid pushes urate out through kidney.
Needle-shaped crystals Negative birefringence First MTP joint classic Allopurinol = XO inhibitor Colchicine = acute attack Febuxostat = newer XO inhibitor
The unifying logic: Lesch-Nyhan and PRPP overactivity both cause hyperuricemia because excess purines funnel to xanthine oxidase. ADA deficiency causes immune failure because dATP kills lymphocytes. Orotic aciduria causes anemia because pyrimidine depletion blocks DNA replication in erythroid cells. Each disease points to exactly one step in the pathway.
03 · Pharmacology

Drug Targets

Four drug classes that hit nucleotide synthesis at different points. Know the enzyme, know the clinical use.

5-FU and methotrexate both work by starving DNA synthesis but at different enzymes. Methotrexate blocks DHFR (no folate regeneration = no thymidylate synthase activity and no de novo purine synthesis). 5-FU directly poisons thymidylate synthase. Same endpoint: can't make dTMP, can't replicate DNA.
Drug Target Enzyme What It Blocks Clinical Use Key Fact
5-Fluorouracil (5-FU) Thymidylate synthase dUMP → dTMP conversion; depletes dTTP for DNA synthesis Colorectal, breast, GI cancers 5-FU is a pyrimidine analog. It irreversibly inhibits thymidylate synthase (suicide inhibitor when combined with N5,N10-methylene-THF).
Methotrexate Dihydrofolate reductase (DHFR) Folate regeneration; starves both thymidylate synthase and de novo purine synthesis Cancer, RA, psoriasis, ectopic pregnancy Rescued by leucovorin (folinic acid), which bypasses DHFR. Trimethoprim and pyrimethamine also inhibit DHFR (trimethoprim: bacteria; pyrimethamine: parasites).
Hydroxyurea Ribonucleotide reductase Conversion of ribonucleotides to deoxyribonucleotides; blocks dNTP pool Sickle cell disease, CML, some cancers In sickle cell: increases HbF (fetal hemoglobin) production by a mechanism independent of its enzyme inhibition effect on replication. Long-term use reduces painful crises.
Allopurinol / Febuxostat Xanthine oxidase Hypoxanthine → xanthine → uric acid conversion; reduces uric acid production Gout, hyperuricemia Allopurinol is itself metabolized by XO to oxypurinol, which is the active inhibitor. Febuxostat is non-purine, avoids this issue. Both increase levels of hypoxanthine and xanthine (which are more soluble than uric acid).
Trimethoprim vs methotrexate vs pyrimethamine: All three inhibit DHFR. Trimethoprim has selectivity for bacterial DHFR (used for UTIs, PCP prophylaxis with sulfamethoxazole). Pyrimethamine targets protozoal DHFR (malaria, toxoplasmosis). Methotrexate hits mammalian DHFR and requires leucovorin rescue. The principle is identical. The specificity comes from enzyme structure differences across species.
Leucovorin rescue: In high-dose methotrexate protocols, leucovorin (folinic acid = 5-formyl-THF) is given after to rescue normal cells. Cancer cells take up methotrexate faster and can't efflux it as quickly, so they die before rescue. Normal cells survive because leucovorin gives them active folate that bypasses DHFR.
04 · Process of Elimination

Elimination Game

Use the clues to knock out the wrong answers. One survives.

A 5-year-old boy with developmental delay is brought in for recurrent joint swelling and orange sand in his diaper. He frequently bites his fingers and lips until they bleed and has multiple scars on his hands. His mother reports this behavior began around age 2. On exam he has writhing involuntary movements and spasticity. Serum uric acid is 14.2 mg/dL (3.5 to 7.2). Urinalysis shows uric acid crystals.
Which enzyme is deficient in this condition?
HGPRT
ADA
OMP decarboxylase
PRPP synthetase (overactive)
Clue 1: Self-mutilation (compulsive biting of lips and fingers) + choreoathetosis in a young boy is the hallmark of Lesch-Nyhan syndrome. This immediately identifies the syndrome.

ADA deficiency causes SCID (recurrent infections, no immune cells) with no neurological self-injury. OMP decarboxylase deficiency causes orotic aciduria with megaloblastic anemia and normal uric acid. Neither fits.
Clue 2: Markedly elevated uric acid with purine salvage failure is the biochemical signature. HGPRT deficiency means hypoxanthine and guanine cannot be recycled, so they all become uric acid via xanthine oxidase.

PRPP synthetase overactivity also causes hyperuricemia but does NOT cause self-mutilation or choreoathetosis. It is a distinct entity with a much milder neurological profile. The behavioral finding (self-mutilation) is pathognomonic for HGPRT deficiency specifically.
HGPRT (Hypoxanthine-Guanine Phosphoribosyltransferase) Deficiency Lesch-Nyhan syndrome. X-linked recessive. Self-mutilation + choreoathetosis + hyperuricemia is the triad. Allopurinol treats the gout but not the neurological features. HGPRT is the only enzyme where loss causes this complete picture.
05 · Side by Side

Quick Reference

Every major nucleotide disease in one scrollable table. Scroll horizontally on mobile.

Disease Gene / Enzyme Pathway Key Lab Key Clinical Treatment
Lesch-Nyhan HGPRT · X-linked Purine salvage Hyperuricemia, uric acid crystals Self-mutilation, choreoathetosis, intellectual disability, gout Allopurinol (gout only; neuro not helped)
ADA Deficiency ADA · Autosomal recessive Purine catabolism No T, B, or NK cells; dATP toxic to lymphocytes SCID; recurrent opportunistic infections from birth; "bubble boy" ADA-PEG (gene therapy); HSCT
Orotic Aciduria OMP decarboxylase (UMP synthase) · AR Pyrimidine de novo Orotic acid in urine; normal NH3; megaloblastic anemia Megaloblastic anemia not responding to B12/folate; growth retardation Uridine supplementation
Gout (primary) Xanthine oxidase (excess substrate) Purine catabolism Hyperuricemia; negatively birefringent urate crystals Podagra (1st MTP), tophi, uric acid nephropathy Allopurinol / febuxostat (chronic); colchicine / NSAIDs (acute)
PRPP synthetase overactivity PRPP synthetase · X-linked Purine de novo (excess) Hyperuricemia; gout Gout, possible sensorineural hearing loss; milder neuro than Lesch-Nyhan Allopurinol
De novo starts from scratch. Salvage recycles. When salvage breaks, purines pile up as uric acid. When de novo pyrimidine synthesis breaks, pyrimidines run low and DNA replication in fast-dividing cells fails first (anemia). When purine catabolism stalls (ADA), the toxic intermediate kills immune cells specifically. The tissue hit tells you where in the pathway to look.
Ammonia as the discriminator for orotic aciduria: If orotic acid is in the urine, first check ammonia. High ammonia = urea cycle defect (excess carbamoyl phosphate overflows into pyrimidine path). Normal ammonia = OMP decarboxylase deficiency. The ammonia result is the single most important discriminating lab.
06 · Where Drugs Cut the Line

The Nucleotide Assembly Line

Two production tracks build the nucleotides DNA needs. Tap a drug to watch where it halts the line. Downstream of the cut, the supply runs dry.

Purine track (top) · Pyrimidine track (bottom)
DE NOVO PURINE PRPP amidotransferase IMP IMPDH → GMP AMP / GMP RNR (NDP → dNDP) NDP ribonucleotide reductase dNDP DE NOVO PYRIMIDINE Carbamoyl-P orotic acid UMP thymidylate synthase dTMP / CTP
Tap a drug. Each one cuts the assembly line at a different enzyme. Watch the block appear and read what stops downstream.
The pattern that wins points: name the enzyme, then name what stops. A drug that hits an early committed step starves everything downstream. A drug that hits a single late step (thymidylate synthase) starves only that one product. The block location is the whole answer.
07 · Reason It Out

Trace the Logic

Tap each answer to reveal it, one beat at a time. Reason forward before you peek.

Orotic acid in the urine: which defect?
From the Attending

When a kid spills orotic acid, your first move is not to argue orotic aciduria versus a urea cycle defect. Your first move is to check the ammonia. Normal ammonia and the problem lives in the pyrimidine factory: UMP synthase. High ammonia and the problem is the urea cycle backing carbamoyl phosphate into the pyrimidine path. The orotic acid is the same. The ammonia tells you which fire is burning.

Gout patient on allopurinol gets azathioprine: what happens?
From the Attending

Allopurinol plus a thiopurine is a marrow killer. Xanthine oxidase normally dumps most of the 6-mercaptopurine as inactive 6-thiouric acid. Block xanthine oxidase and every bit of that drug is forced toward 6-thioguanine nucleotides instead. The marrow takes the full dose. Cut the azathioprine to about a quarter, or do not combine them.

Board-Style Walkthrough

Board-Style Walkthrough

Original board-style vignettes. Shuffled, never-repeat, full Chicago explanations.