Learn / Metabolism

Metabolic pathways

Every FMK pathway as a clickable map. Pick one pathway to hammer it — next step, enzyme, regulator, cofactor, and the facts that get tested (NADPH and who needs it, rate-limiting steps, deficiencies) — or set it to all pathways for a mixed drill. Every answer says which enzyme and which pathway.

Pathway
Heme synthesis (porphyrias) · Mitochondria (steps 1, 6–8) and cytosol (steps 2–5); ~85% in marrow erythroid precursors, the rest mostly liver (P450 turnover). Enzymes sit beside the arrows, ★ = rate-limiting, ⊕/⊖ = activators/inhibitors (toggle), −ATP +NADH = what the step spends and makes (toggle ⚡), dashed = allosteric signal, shaded bands = compartment. Drag to pan.
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Why the ring matters

Four pyrroles, joined in a line, then closed

Porphobilinogen is a single pyrrole. Four of them are strung together head-to-tail into a linear chain, and only then closed into a macrocycle. That closure is the line the whole classification hangs on: what accumulates before it is linear and cannot absorb light, and what accumulates after it is a ring that can.

① Porphobilinogen (PBG) one pyrrole ring 2 ALA → 1 PBG N A P CH₂NH₂ A = acetate · P = propionate the CH₂NH₂ arm becomes the bridge PBG deaminase 4 PBG joined head to tail AIP blocks HERE ② Hydroxymethylbilane four pyrroles in a LINE — not a ring linear · colourless · NOT photoactive N A P N A P N A P N A P C C C HOCH₂ ALA and PBG pile up behind a block here → NEUROVISCERAL: pain, neuropathy, psych. No rash. Uro'gen III synthase RING CLOSES ring D FLIPS (cosynthase) ③ Uroporphyrinogen III CLOSED macrocycle — 4 rings, 4 bridges ring D is REVERSED (A and P swapped) C C C C N A P A N A P B N A P C N P A D now oxidisable to a conjugated porphyrin → CUTANEOUS: blisters, photosensitivity oxidise ferrochelatase inserts Fe²⁺ ④ Heme protoporphyrin IX + Fe²⁺ — fully conjugated, absorbs ~400 nm C C C C N M V N M V N M P N P M Fe²⁺ FOUR rings, ONE iron — the whole molecule is one big ring BEFORE ring closure — steps 1–3 ALA and PBG are LINEAR. No conjugated ring, so they cannot absorb light — but they are neurotoxic. Abdominal pain without peritoneal signs, neuropathy, psychiatric symptoms, autonomic instability. Never a rash. (AIP) AFTER ring closure — steps 4–8 Closed porphyrinogens auto-oxidise to conjugated porphyrins, which absorb hard at ~400 nm (Soret) → photosensitivity. (PCT, CEP, EPP) Uroporphyrinogen itself is colourless — the methylene (C) bridges are not conjugated. Photoactivity arrives with oxidation, which happens readily once the ring exists. Without cosynthase the linear chain cyclises on its own into the type I isomer (ring D NOT flipped) — a dead end, and the lesion in congenital erythropoietic porphyria.
MITOCHONDRION — step 1 CYTOSOL — steps 2–5 MITOCHONDRION — steps 6–8Glycine + succinyl-CoAGlycine + succinyl-CoAδ-Aminolevulinic acid (ALA)δ-Aminolevulinic acid (ALA)Porphobilinogen (PBG)Porphobilinogen (PBG)Hydroxymethylbilane (LINEAR tetrapyrrole)Hydroxymethylbilane (LINEARtetrapyrrole)Uroporphyrinogen IIIUroporphyrinogen IIICoproporphyrinogen IIICoproporphyrinogen IIIProtoporphyrinogen IXProtoporphyrinogen IXProtoporphyrin IXProtoporphyrin IXHEME (Fe²⁺ in the ring)HEME (Fe²⁺ in the ring)① ALA SYNTHASE ★rate-limiting — PLP (B₆) ·heme ⊖② ALA DEHYDRATASE — Zn²⁺ ·⊖ LEAD #1③ PBG DEAMINASE — AIP(acute, NO rash)④ RING CLOSES HERE —uro'gen III synthase · CEP⑤ UROD — PCT, commonestporphyria⑥ COPRO'GEN OXIDASE — HCP(acute + skin)⑦ PROTO'GEN OXIDASE — VP(acute + skin)⑧ FERROCHELATASE — Fe²⁺ ·⊖ LEAD #2 · EPP

Heme synthesis (porphyrias)

Glycine + succinyl-CoA → ALA (ALA synthase, PLP; rate-limiting; ALAS1 repressed by heme, induced by P450-inducing drugs, hormones and fasting). Two ALA → PBG (ALA dehydratase, Zn — lead). Four PBG → hydroxymethylbilane (PBG deaminase — AIP) → uroporphyrinogen III (ring closure) → copro'gen III (UROD — PCT) → proto'gen IX → protoporphyrin IX → heme (ferrochelatase — lead, EPP). Blocks BEFORE ring closure accumulate linear ALA/PBG → neurovisceral attacks; blocks AFTER accumulate photoactive porphyrins → cutaneous photosensitivity.

Click any metabolite on the map for its reactions. Source: FMK-08.4 Porphyrins, heme & bile pigments.

Reactions

StepEnzymeCofactorsRegulation
Glycine + succinyl-CoA → δ-Aminolevulinic acid (ALA) ALA synthase (ALAS1 liver / ALAS2 erythroid) ★
ALAS2 (erythroid isoform) — X-linked sideroblastic anemia: microcytic anemia with ring sideroblasts and iron-loaded mitochondria; responds to pyridoxine
X-linked sideroblastic anemia →Isoniazid-induced vitamin B6 (pyridoxine) deficiency →IV hemin (hematin) for acute porphyria →Givosiran →
Pyridoxal phosphate (B₆)
+ Drugs & hormones that induce P450 (barbiturates, anticonvulsants, rifampin, alcohol, OCPs/progesterone); Fasting / low carbohydrate
− Heme (represses ALAS1 transcription and blocks its mitochondrial import); Glucose (the 'glucose effect')
δ-Aminolevulinic acid (ALA) → Porphobilinogen (PBG) ALA dehydratase (porphobilinogen synthase)
ALA dehydratase-deficiency porphyria (rare, AR) — neurovisceral only; ALA ↑ with normal PBG, like lead poisoning. LEAD POISONING itself acts here and at ferrochelatase: child with microcytic anemia, basophilic stippling, ↑ ALA and ↑ urinary coproporphyrin III but NORMAL PBG
Lead poisoning →ALA dehydratase deficiency porphyria →
Zn²⁺
− LEAD (displaces zinc) — lead-sensitive step #1
Porphobilinogen (PBG) → Hydroxymethylbilane (linear tetrapyrrole) PBG deaminase (hydroxymethylbilane synthase, HMBS)
Acute intermittent porphyria (AD, ~50% activity) — colicky abdominal pain without peritoneal signs, vomiting, neuropsychiatric symptoms, motor neuropathy, tachycardia/hypertension; urine darkens to port-wine on standing; markedly ↑ urine PBG (and ALA); no photosensitivity; attacks after P450 inducers, OCPs/luteal phase, fasting; treat with IV hemin, IV glucose, givosiran
Acute intermittent porphyria (AIP) →
—
Hydroxymethylbilane (linear tetrapyrrole) → Uroporphyrinogen III Uroporphyrinogen III synthase (cosynthase)
Congenital erythropoietic porphyria (Günther, AR) — hydroxymethylbilane cyclises non-enzymatically into the dead-end type I isomer; severe photosensitivity and mutilation from infancy, red urine, erythrodontia
Congenital erythropoietic porphyria (Gunther disease, CEP) →
—
Uroporphyrinogen III → Coproporphyrinogen III Uroporphyrinogen decarboxylase (UROD)
Porphyria cutanea tarda (the MOST common porphyria; often acquired with hepatitis C, alcohol, estrogen, iron overload) — blisters and skin fragility on sun-exposed skin, hypertrichosis, onset 4th–5th decade; tea-coloured urine with ↑ uroporphyrin that fluoresces coral-pink under Wood's lamp; no acute attacks; treat with phlebotomy, low-dose hydroxychloroquine, treat HCV
Porphyria cutanea tarda (PCT) →
—
Coproporphyrinogen III → Protoporphyrinogen IX Coproporphyrinogen oxidase
Hereditary coproporphyria (AD) — straddles the line: acute neurovisceral attacks AND cutaneous photosensitivity
Hereditary coproporphyria (HCP) →
O₂
Protoporphyrinogen IX → Protoporphyrin IX Protoporphyrinogen oxidase
Variegate porphyria (AD) — acute attacks AND photosensitivity
Variegate porphyria (VP) →
O₂
Protoporphyrin IX → Heme Ferrochelatase
Erythropoietic protoporphyria (marrow origin) — painful, burning photosensitivity WITHOUT frank blistering from childhood; protoporphyrin in RBCs and skin; hepatobiliary disease from biliary protoporphyrin in severe cases
Erythropoietic protoporphyria (EPP) →
Fe²⁺
− LEAD — lead-sensitive step #2

Conditions that live on this map

Acute intermittent porphyria (AIP)ALA dehydratase deficiency porphyriaCongenital erythropoietic porphyria (Gunther disease, CEP)Erythropoietic protoporphyria (EPP)GivosiranHereditary coproporphyria (HCP)Isoniazid-induced vitamin B6 (pyridoxine) deficiencyIV hemin (hematin) for acute porphyriaLead poisoningMethemoglobinemiaPorphyria cutanea tarda (PCT)Variegate porphyria (VP)X-linked sideroblastic anemia

Blue pills sit on one specific arrow; grey ones are whole-pathway problems. Each opens the full condition card, which links back here with the arrow lit.

Facts worth knowing

Rate-limiting step

  • Rate-limiting enzyme of heme synthesis and its cofactor — ALA synthase — pyridoxal phosphate (vitamin B₆)
  • Rate-limiting enzyme of heme synthesis (porphyrias) — ALA synthase (ALAS1 liver / ALAS2 erythroid) (Mitochondrial matrix; ties heme to the TCA cycle via succinyl-CoA. ALAS2 (X-linked, erythroid) is iron-regulated — its mutations cause X-linked sideroblastic anemia, not a porphyria. Isoniazid antagonises B₆ and can impair the step.)

Regulation

  • How an oral contraceptive can trigger an acute porphyria attack — Steroid hormones induce hepatic cytochrome P450 (a heme protein) → free heme pool falls → ALAS1 derepressed → ALA/PBG surge past a half-capacity PBG deaminase
  • Why IV glucose treats a mild acute attack — Carbohydrate loading suppresses ALAS1 induction (the 'glucose effect')

Treatment

  • Mainstay of an acute porphyria attack — IV hemin — repletes the free heme pool and re-represses ALAS1 (Plus IV glucose, stop porphyrinogenic drugs; givosiran (siRNA vs ALAS1 mRNA) for recurrent attacks)

Toxin

  • The two heme-synthesis enzymes inhibited by lead — ALA dehydratase and ferrochelatase (Signature: microcytic anemia, basophilic stippling, ↑ ALA, ↑ urinary coproporphyrin III, ↑ zinc protoporphyrin, PBG normal)

Diagnosis

  • Lab discriminator: lead poisoning vs acute intermittent porphyria — Lead: ALA ↑, PBG normal. AIP: ALA AND PBG markedly ↑
  • Bedside clue for excess porphyrins in urine or blister fluid — Coral-pink fluorescence under a Wood's (UV) lamp

Classification

  • Rule of thumb for porphyria symptoms by position of the block — Before ring closure (steps 1–3) = neurovisceral (AIP); after ring closure (4–8) = cutaneous (PCT, EPP); HCP and VP straddle both
  • Why ALA and PBG cause pain and psychosis but never blisters — They are linear, not yet a conjugated tetrapyrrole — only the closed ring absorbs light (Soret band ~400 nm)

Enzyme deficiency

  • Most common porphyria overall — Porphyria cutanea tarda (UROD) (Often acquired: hepatitis C, alcohol, estrogen, iron overload)
  • Woman on OCPs with colicky abdominal pain, confusion, tachycardia and urine that turns port-wine on the windowsill — Acute intermittent porphyria (PBG deaminase) (PBG oxidises and polymerises non-enzymatically in light and air)
  • Deficiency of ALA synthase (ALAS1 liver / ALAS2 erythroid) causes… — ALAS2 (erythroid isoform) — X-linked sideroblastic anemia: microcytic anemia with ring sideroblasts and iron-loaded mitochondria; responds to pyridoxine (Mitochondrial matrix; ties heme to the TCA cycle via succinyl-CoA. ALAS2 (X-linked, erythroid) is iron-regulated — its mutations cause X-linked sideroblastic anemia, not a porphyria. Isoniazid antagonises B₆ and can impair the step.)
  • Deficiency of ALA dehydratase (porphobilinogen synthase) causes… — ALA dehydratase-deficiency porphyria (rare, AR) — neurovisceral only; ALA ↑ with normal PBG, like lead poisoning. LEAD POISONING itself acts here and at ferrochelatase: child with microcytic anemia, basophilic stippling, ↑ ALA and ↑ urinary coproporphyrin III but NORMAL PBG (2 ALA → PBG. Cytosol.)
  • Deficiency of PBG deaminase (hydroxymethylbilane synthase, HMBS) causes… — Acute intermittent porphyria (AD, ~50% activity) — colicky abdominal pain without peritoneal signs, vomiting, neuropsychiatric symptoms, motor neuropathy, tachycardia/hypertension; urine darkens to port-wine on standing; markedly ↑ urine PBG (and ALA); no photosensitivity; attacks after P450 inducers, OCPs/luteal phase, fasting; treat with IV hemin, IV glucose, givosiran (4 PBG → linear tetrapyrrole. Still BEFORE ring closure — accumulated ALA/PBG are not photoactive.)
  • Deficiency of Uroporphyrinogen III synthase (cosynthase) causes… — Congenital erythropoietic porphyria (Günther, AR) — hydroxymethylbilane cyclises non-enzymatically into the dead-end type I isomer; severe photosensitivity and mutilation from infancy, red urine, erythrodontia (RING CLOSURE — the line that separates neurovisceral (before) from cutaneous (after) porphyrias.)
  • Deficiency of Uroporphyrinogen decarboxylase (UROD) causes… — Porphyria cutanea tarda (the MOST common porphyria; often acquired with hepatitis C, alcohol, estrogen, iron overload) — blisters and skin fragility on sun-exposed skin, hypertrichosis, onset 4th–5th decade; tea-coloured urine with ↑ uroporphyrin that fluoresces coral-pink under Wood's lamp; no acute attacks; treat with phlebotomy, low-dose hydroxychloroquine, treat HCV (4 acetate → methyl. Cytosol.)
  • Deficiency of Coproporphyrinogen oxidase causes… — Hereditary coproporphyria (AD) — straddles the line: acute neurovisceral attacks AND cutaneous photosensitivity (Re-enters the mitochondrion; 2 propionate → vinyl.)
  • Deficiency of Protoporphyrinogen oxidase causes… — Variegate porphyria (AD) — acute attacks AND photosensitivity
  • Deficiency of Ferrochelatase causes… — Erythropoietic protoporphyria (marrow origin) — painful, burning photosensitivity WITHOUT frank blistering from childhood; protoporphyrin in RBCs and skin; hepatobiliary disease from biliary protoporphyrin in severe cases (Inner mitochondrial membrane. When iron can't be inserted, zinc is — zinc protoporphyrin is the lab marker.)

Compare

  • PCT vs EPP — PCT: hepatic, UROD, adult onset, blistering, acquired triggers. EPP: erythropoietic, ferrochelatase, childhood onset, burning without blisters, liver risk

Structure

  • Which iron state binds O₂ reversibly, and what the other one is called — Fe²⁺ (ferrous). Fe³⁺ = methemoglobin — cyanosis unresponsive to O₂, chocolate-brown blood; methylene blue
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