One-Carbon Metabolism & Amino Acid Derivatives
Biochemistry · Proteins & Amino acids · lean revision notes
One-Carbon Metabolism & Amino Acid Derivatives
One-carbon metabolism is the central currency of methylation, nucleotide synthesis, and amino-acid interconversion. NEET PG loves it because it ties folate, vitamin B12, homocysteine, SAM, and the synthesis of neurotransmitters and pigments into one clinically integrated web. Master the carriers, the cycles, and the deficiency states and you cover a disproportionate share of biochemistry marks.
What is "one-carbon metabolism"?
A one-carbon (1-C) unit is a single carbon fragment transferred between molecules to build or modify other compounds. These units exist at different oxidation states: methyl (–CH₃, most reduced), methylene (–CH₂–), methenyl (–CH=), formyl (–CHO) and formimino (–CH=NH). They are essential for synthesising purines, thymidylate (dTMP), methionine and a host of methylated products.
There are three principal one-carbon carriers, and distinguishing them is high-yield:
| Carrier | Carbon states carried | Major role |
|---|---|---|
| Tetrahydrofolate (THF) | methyl, methylene, methenyl, formyl, formimino | Purine ring, dTMP, methionine regeneration |
| S-adenosylmethionine (SAM) | methyl only | Universal methyl donor for methyltransferases |
| Biotin | carbon dioxide (CO₂, most oxidised) | Carboxylation reactions |
High-yield: Biotin carries the most oxidised one-carbon unit (CO₂); SAM carries the methyl group and is the universal methyl donor; THF is the most versatile, carrying units at multiple oxidation states except CO₂.
Sources and fates of one-carbon units
Major donors of 1-C units to THF:
- Serine → glycine (serine hydroxymethyltransferase, SHMT; PLP-dependent) — the single most important source, generating N⁵,N¹⁰-methylene-THF.
- Glycine cleavage (glycine synthase system) — also yields N⁵,N¹⁰-methylene-THF + CO₂ + NH₄⁺.
- Histidine catabolism — formiminoglutamate (FIGLU) donates a formimino group; B12/folate deficiency causes FIGLU to accumulate (FIGLU excretion test, classically after histidine load).
- Formate, choline/betaine, tryptophan.
Major acceptors / uses:
- N⁵,N¹⁰-methylene-THF → thymidylate synthase converts dUMP to dTMP (THF is oxidised to dihydrofolate, DHF, regenerated by dihydrofolate reductase, DHFR).
- N¹⁰-formyl-THF → carbons C2 and C8 of the purine ring.
- N⁵-methyl-THF → donates methyl to homocysteine to regenerate methionine (methionine synthase, B12-dependent).
The methionine cycle and SAM
The methionine cycle links folate to methylation:
Methionine → (+ ATP, by methionine adenosyltransferase) → SAM → (donates –CH₃) → SAH (S-adenosylhomocysteine) → (hydrolysis) → Homocysteine → (+ N⁵-methyl-THF, methionine synthase, B12) → Methionine (cycle closes).
SAM is the methyl donor for: creatine (guanidinoacetate → creatine), phosphatidylcholine, epinephrine (norepinephrine → epinephrine via PNMT), melatonin, DNA/histone methylation, methylation of noradrenaline, and detoxification reactions.
High-yield: SAM is the universal methyl donor. After donating its methyl group it becomes SAH, then homocysteine. Re-methylation of homocysteine to methionine requires N⁵-methyl-THF and methylcobalamin (B12).
The methyl-folate trap (folate trap)
This is the single most tested concept linking B12 and folate.
The reaction N⁵,N¹⁰-methylene-THF → N⁵-methyl-THF (by methylene-THF reductase, MTHFR) is essentially irreversible. The only way to release THF from N⁵-methyl-THF is by donating its methyl to homocysteine via methionine synthase, which needs B12.
In B12 deficiency, methionine synthase fails → folate gets "trapped" as N⁵-methyl-THF → functional folate deficiency → impaired dTMP and purine synthesis → megaloblastic anaemia.
High-yield: In B12 deficiency, giving folic acid can correct the anaemia but NOT the neurological damage (subacute combined degeneration), and may even precipitate/worsen it. Always check/replace B12 before high-dose folate.
Flow of the trap: B12 deficiency → ↓methionine synthase → folate locked as N⁵-methyl-THF → ↓free THF → ↓N⁵,N¹⁰-methylene-THF → ↓dTMP → defective DNA synthesis → megaloblastosis; simultaneously ↑homocysteine and ↑methylmalonic acid (MMA).
The two B12-dependent reactions
Vitamin B12 (cobalamin) has only two enzyme reactions in humans — memorise both:
| Enzyme | Cofactor form | Reaction | Marker if deficient |
|---|---|---|---|
| Methionine synthase (homocysteine methyltransferase) | Methylcobalamin | Homocysteine + N⁵-methyl-THF → Methionine + THF | ↑ Homocysteine |
| Methylmalonyl-CoA mutase | Adenosylcobalamin (5'-deoxyadenosyl) | L-methylmalonyl-CoA → Succinyl-CoA | ↑ Methylmalonic acid (MMA) |
High-yield: In folate deficiency, homocysteine rises but MMA is normal. In B12 deficiency, both homocysteine and MMA rise. Elevated MMA is specific for B12 deficiency and is the key discriminator.
Defective methylmalonyl-CoA mutase (B12 def) → accumulation of methylmalonyl-CoA and abnormal odd-chain/branched fatty acid incorporation into myelin → demyelination → subacute combined degeneration of the dorsal columns and lateral corticospinal tracts.
Folate: structure, absorption, antagonists
Folic acid = pteridine + PABA + glutamate. Dietary folate is absorbed in the jejunum (proximal small bowel) after deconjugation to the monoglutamate; reduced by DHFR to DHF then THF. Body stores are small (3–4 months), so deficiency develops faster than B12 (stores 3–5 years).
Drugs interfering with one-carbon/folate metabolism (very high-yield pharmacology overlap):
| Drug | Target | Effect |
|---|---|---|
| Methotrexate | Dihydrofolate reductase (DHFR) | ↓THF → blocks dTMP & purines |
| Trimethoprim / Pyrimethamine | Bacterial/protozoal DHFR | Selective antimicrobial |
| 5-Fluorouracil (5-FU) | Thymidylate synthase (via FdUMP) | Blocks dTMP synthesis |
| Sulfonamides | Dihydropteroate synthase (bacterial) | Block folate synthesis (PABA analogue) |
| Phenytoin, methotrexate, alcohol, OCPs | Impair folate absorption/use | Folate deficiency |
High-yield: Leucovorin (folinic acid, N⁵-formyl-THF) rescues normal cells after methotrexate because it bypasses the DHFR block. It does not rescue from 5-FU. Sulfa drugs are selective because humans lack dihydropteroate synthase and cannot synthesise folate (we must ingest it).
Homocysteine and cardiovascular risk
Homocysteine sits at a metabolic crossroads:
- Re-methylation to methionine — via methionine synthase (B12 + N⁵-methyl-THF), or via betaine-homocysteine methyltransferase (uses betaine from choline; liver/kidney; B12-independent).
- Transsulfuration to cysteine — homocysteine + serine → cystathionine (cystathionine β-synthase, CBS, PLP/B6-dependent) → cysteine + α-ketobutyrate.
Hyperhomocysteinaemia causes endothelial injury, oxidative stress, and is an independent risk factor for atherosclerosis, coronary artery disease, stroke, and venous thrombosis.
Causes of raised homocysteine: deficiency of B12, folate, or B6; MTHFR polymorphism (C677T thermolabile variant); and homocystinuria (CBS deficiency — the classic inborn error).
Classical homocystinuria (CBS deficiency)
- Autosomal recessive; deficiency of cystathionine β-synthase.
- Features: ectopia lentis (downward & inward lens dislocation), marfanoid habitus, intellectual disability, osteoporosis, and thromboembolism (leading cause of death).
- Marfan vs homocystinuria: lens dislocates up & out in Marfan, down & in in homocystinuria; intellect normal in Marfan, impaired in homocystinuria.
- Treatment: high-dose pyridoxine (B6) in responders; methionine restriction + cysteine supplementation; betaine to remethylate homocysteine; folate/B12.
High-yield: Downward & inward lens dislocation + mental retardation + thrombosis = homocystinuria. Pyridoxine (B6)-responsive form is the most common.
Amino acid–derived products (the "products" half of the topic)
Many signalling molecules and pigments are built from amino acids, often using SAM, PLP (B6), tetrahydrobiopterin (BH₄), or vitamin C as cofactors.
Tyrosine derivatives
- Tyrosine → DOPA → Dopamine → Noradrenaline → Adrenaline.
- Tyrosine hydroxylase (uses BH₄) is rate-limiting; this is the committed step.
- DOPA decarboxylase (PLP).
- Dopamine β-hydroxylase (uses vitamin C / ascorbate, copper).
- PNMT (uses SAM) converts noradrenaline → adrenaline.
- Tyrosine → Melanin via tyrosinase (copper-containing) in melanocytes; defect → albinism.
- Tyrosine → Thyroid hormones (T3, T4) and fumarate + acetoacetate (catabolism). Defects: alkaptonuria (homogentisate oxidase), tyrosinaemia.
High-yield: Tyrosine hydroxylase is the rate-limiting step of catecholamine synthesis and requires BH₄ (tetrahydrobiopterin). Dopamine β-hydroxylase needs vitamin C.
Tryptophan derivatives
- Tryptophan → 5-hydroxytryptophan → Serotonin (5-HT) → Melatonin.
- Tryptophan hydroxylase (BH₄) is rate-limiting; serotonin → melatonin uses SAM in the pineal gland.
- Tryptophan → Niacin (NAD⁺/NADP⁺) — needs B6; deficiency contributes to pellagra (also seen in Hartnup disease and carcinoid syndrome where tryptophan is diverted to serotonin).
Glycine, arginine, methionine → Creatine
- Creatine synthesis: glycine + arginine → guanidinoacetate (in kidney) → creatine (methylation by SAM in liver). Creatine + ATP → phosphocreatine (energy store in muscle). Non-enzymatic breakdown → creatinine (excreted; renal function marker).
High-yield: Creatine synthesis is the largest single consumer of SAM-derived methyl groups in the body.
Glycine + succinyl-CoA → Heme
- Heme synthesis begins with glycine + succinyl-CoA → δ-aminolaevulinic acid (ALA) via ALA synthase (rate-limiting, PLP/B6-dependent) in mitochondria.
- Lead inhibits ALA dehydratase and ferrochelatase → raised ALA and protoporphyrin (basophilic stippling, lead poisoning).
- Defects in the pathway → porphyrias.
High-yield: ALA synthase is the rate-limiting enzyme of heme synthesis and is PLP (B6)-dependent; isoniazid (B6 antagonist) and lead poisoning both perturb heme/porphyrin metabolism.
Other key derivatives
- Glutamate → GABA (glutamate decarboxylase, PLP).
- Histidine → Histamine (histidine decarboxylase, PLP).
- Arginine → Nitric oxide (NO) (NO synthase) + citrulline.
- Glycine → glutathione (with glutamate + cysteine), bile salts, porphyrins, purines, creatine.
- Cysteine → taurine, coenzyme A, glutathione.
High-yield: Notice how PLP (vitamin B6) is the workhorse cofactor for almost every amino-acid decarboxylation/transamination (DOPA, serotonin, GABA, histamine, ALA synthase, CBS, SHMT). B6 deficiency therefore hits neurotransmitters, heme, and homocysteine metabolism together.
Megaloblastic anaemia — clinical integration
Megaloblastic anaemia is the clinical face of impaired one-carbon metabolism. Defective DNA synthesis (dTMP) with intact RNA/protein synthesis causes nuclear-cytoplasmic asynchrony.
| Feature | B12 deficiency | Folate deficiency |
|---|---|---|
| Serum homocysteine | ↑ | ↑ |
| Methylmalonic acid (MMA) | ↑ | Normal |
| Neurological signs (SCD) | Present | Absent |
| Common cause | Pernicious anaemia, ileal disease, vegan diet | Poor diet, alcohol, pregnancy, methotrexate/phenytoin |
| Stores | 3–5 years | 3–4 months |
Peripheral smear: macro-ovalocytes, hypersegmented neutrophils (≥5 lobes). Bone marrow: megaloblasts. Pernicious anaemia = autoimmune anti-intrinsic factor/anti-parietal cell antibodies; B12 absorbed in terminal ileum bound to IF; Schilling test (historical) localised the defect.
High-yield: Hypersegmented neutrophils are an early, sensitive marker of megaloblastosis. Subacute combined degeneration (dorsal columns + lateral corticospinal + spinothalamic tracts) is the hallmark neurological lesion of B12 deficiency.
Diagnosis & investigations of choice
- Megaloblastic anaemia work-up: CBC + peripheral smear (macrocytosis, MCV >100 fL, hypersegmented neutrophils) → serum B12 and folate → if equivocal, serum MMA and homocysteine (MMA is the more specific B12 marker).
- Pernicious anaemia: intrinsic factor and parietal cell antibodies; gastrin elevated.
- Homocystinuria: elevated plasma/urine homocysteine and methionine; cyanide-nitroprusside urine screen; confirm with CBS enzyme assay/genetics.
- Folate status historically: FIGLU excretion after histidine load.
Management / drug of choice
- B12 deficiency: parenteral (IM) hydroxocobalamin / cyanocobalamin; lifelong in pernicious anaemia. Replace B12 before folate.
- Folate deficiency: oral folic acid; periconceptional folate prevents neural tube defects (start before conception).
- Methotrexate toxicity: leucovorin (folinic acid) rescue.
- Hyperhomocysteinaemia: folate + B6 + B12 (lowers levels, though cardiovascular benefit is debated); homocystinuria → pyridoxine, betaine, methionine restriction.
Complications
- Megaloblastic anaemia; pancytopenia in severe cases.
- Irreversible neuropathy / subacute combined degeneration (B12).
- Neural tube defects (maternal folate deficiency).
- Premature atherosclerosis and venous thromboembolism (hyperhomocysteinaemia).
- Lens dislocation, osteoporosis, intellectual disability (homocystinuria).
Key differentials
- B12 vs folate deficiency — discriminated by MMA and neurological signs.
- Marfan vs homocystinuria — lens dislocation direction and intellect.
- Megaloblastic vs non-megaloblastic macrocytosis (alcohol, liver disease, hypothyroidism, reticulocytosis) — smear and MMA/homocysteine help.
- Albinism subtypes (tyrosinase-positive vs negative).
Mnemonics
- B12's two reactions — "Methyl to Methionine, Adenosyl to Mutase" (methylcobalamin → methionine synthase; adenosylcobalamin → methylmalonyl-CoA mutase).
- Methyl trap — "B12 frees folate from the trap."
- PNMT needs SAM — adrenaline = "Adrenaline Added methyl."
- Catecholamine cofactors — Tyrosine hydroxylase = BH₄; Dopamine β-hydroxylase = vitamin C.
Recently asked / exam angle
- "Universal methyl donor" → SAM (frequently asked single-best).
- Enzyme requiring adenosylcobalamin → methylmalonyl-CoA mutase (and the marker MMA).
- Which marker is elevated in B12 but normal in folate deficiency → methylmalonic acid.
- Rate-limiting enzyme of heme synthesis → ALA synthase (PLP-dependent).
- Lens dislocation down and in + thrombosis → homocystinuria (CBS deficiency, B6-responsive).
- Drug acting on thymidylate synthase → 5-FU; on DHFR → methotrexate/trimethoprim.
- Leucovorin rescues from methotrexate, not 5-FU.
- Largest consumer of SAM methyl groups → creatine synthesis.
- Why folic acid alone is dangerous in B12 deficiency → masks anaemia, worsens neuropathy.
- Cofactor for tyrosine hydroxylase and tryptophan hydroxylase → tetrahydrobiopterin (BH₄).
Rapid revision
- SAM = universal methyl donor → becomes SAH → homocysteine.
- Biotin carries the most oxidised 1-C unit (CO₂); THF the most versatile; SAM only methyl.
- B12's two reactions: methionine synthase (methylcobalamin) and methylmalonyl-CoA mutase (adenosylcobalamin).
- B12 deficiency → ↑homocysteine and ↑MMA; folate deficiency → ↑homocysteine, normal MMA.
- Methyl-folate trap: B12 deficiency locks folate as N⁵-methyl-THF → functional folate deficiency → megaloblastic anaemia.
- Replace B12 before folate; folate alone can worsen subacute combined degeneration.
- Thymidylate synthase converts dUMP → dTMP using N⁵,N¹⁰-methylene-THF; blocked by 5-FU.
- DHFR regenerates THF; blocked by methotrexate, trimethoprim, pyrimethamine; rescued by leucovorin.
- Tyrosine hydroxylase (BH₄) is rate-limiting for catecholamines; dopamine β-hydroxylase needs vitamin C.
- ALA synthase (PLP) is rate-limiting for heme; lead inhibits ALA dehydratase + ferrochelatase.
- Homocystinuria (CBS deficiency): downward-inward lens dislocation, thrombosis, B6-responsive.
- Creatine synthesis (glycine + arginine + SAM) is the biggest methyl-group consumer; breakdown → creatinine.