Biochemistry chapters
Amino acids, nitrogen balance and the urea cycle
Amino acid classification (essential, glucogenic and ketogenic), protein quality, nitrogen balance, how amino groups are removed (transamination, deamination), how ammonia is carried and turned into urea, urea cycle and amino acid disorders (PKU, maple syrup urine disease, alkaptonuria, homocystinuria) and the special products made from amino acids.
- Essential amino acids (cannot be made by the body) are PVT TIM HaLL: phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, leucine, lysine; leucine and lysine are purely ketogenic; most others are glucogenic.
- Amino groups are removed by transamination (aminotransferases such as ALT and AST, needing pyridoxal phosphate (vitamin B6)) and oxidative deamination of glutamate (glutamate dehydrogenase); toxic ammonia travels as glutamine and alanine to the liver, where the urea cycle (partly mitochondrial, partly cytosolic; rate-limiting enzyme carbamoyl phosphate synthetase I, activated by N-acetylglutamate) makes urea.
- Classic disorders: PKU (phenylalanine hydroxylase: intellectual disability, musty odour, fair skin; low-phenylalanine diet), alkaptonuria (homogentisate oxidase: black urine on standing, ochronosis, arthritis), albinism (tyrosinase), maple syrup urine disease (branched-chain keto-acid dehydrogenase), homocystinuria (cystathionine β-synthase: lens dislocation downwards, thrombosis), ornithine transcarbamylase deficiency (X-linked; hyperammonaemia with orotic aciduria).
On this page
Amino acids
Twenty standard amino acids build proteins. Each has an amino group, a carboxyl group and a side chain (R group); all except glycine are L-isomers. At physiological pH they exist as zwitterions. At the isoelectric point (pI) an amino acid carries no net charge.
Classification
| By side chain | Examples |
|---|---|
| Non-polar (hydrophobic) | Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline |
| Polar, uncharged | Serine, threonine, tyrosine, cysteine, asparagine, glutamine |
| Acidic (negative) | Aspartate, glutamate |
| Basic (positive) | Lysine, arginine, histidine (rich in histones) |
Special: glycine (smallest; non-chiral; collagen every third residue), proline (imino acid; bends helices; collagen), cysteine (disulfide bonds), histidine (buffer at physiological pH: its imidazole group has pKa about 6), tyrosine and tryptophan (absorb UV at 280 nm).
Essential amino acids
"PVT TIM HaLL": Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Leucine, Lysine. Arginine is semi-essential (in growth). Tyrosine becomes essential in PKU.
Glucogenic vs ketogenic
- Purely ketogenic: leucine and lysine.
- Both glucogenic and ketogenic: phenylalanine, tyrosine, tryptophan, isoleucine, threonine.
- The rest are purely glucogenic.
Protein quality and nitrogen balance
- Nitrogen balance = nitrogen intake − nitrogen loss (urine, faeces, skin). Protein is about 16% nitrogen, so protein = nitrogen × 6.25.
- Positive balance: growth, pregnancy, recovery from illness, bodybuilding.
- Negative balance: starvation, burns, trauma, surgery, fever, cancer, uncontrolled diabetes, lack of one essential amino acid.
- Biological value: how much absorbed protein is retained; egg protein is the reference standard. Cereals lack lysine; pulses lack methionine; eating them together (dal-roti) complements.
Protein (g) = nitrogen (g) × 6.25 (protein is 16% nitrogen: 100 ÷ 16 = 6.25)
Intake: 75 g protein/day → N in = 75 ÷ 6.25 = 12 g
Urinary urea nitrogen = 14 g/day, add about 4 g for other losses
N out = 14 + 4 = 18 g
Balance = 12 − 18 = −6 g/day → negative (catabolic, e.g. after burns)
Protein equivalent lost = 6 × 6.25 = 37.5 g protein per day
Removing nitrogen
Transamination
- Moves an amino group from an amino acid to α-ketoglutarate, making glutamate and a new keto acid. Reversible; no free ammonia.
- Enzymes: aminotransferases, needing pyridoxal phosphate (vitamin B6).
- ALT (alanine aminotransferase): alanine + α-ketoglutarate ⇌ pyruvate + glutamate. More specific for liver.
- AST (aspartate aminotransferase): aspartate + α-ketoglutarate ⇌ oxaloacetate + glutamate. In liver, heart, muscle, red cells.
- Lysine and threonine do not undergo transamination.
Oxidative deamination
Glutamate dehydrogenase (mitochondria, liver and kidney) releases free ammonia from glutamate, using NAD⁺ or NADP⁺.
Transport of ammonia
Ammonia is toxic to the brain. It is carried safely as:
- Glutamine (most tissues; glutamine synthetase), released in the liver and kidney by glutaminase. Kidney ammonia excretion buffers acid.
- Alanine from muscle (glucose-alanine cycle).
The urea cycle
Takes place in the liver, partly in the mitochondria and partly in the cytosol. Converts ammonia (and the nitrogen of aspartate) into urea, which the kidneys excrete.
- Carbamoyl phosphate synthetase I (CPS I) (mitochondria): NH₃ + CO₂ + 2 ATP → carbamoyl phosphate. Rate-limiting step; activated by N-acetylglutamate.
- Ornithine transcarbamylase (OTC) (mitochondria): carbamoyl phosphate + ornithine → citrulline.
- Argininosuccinate synthetase (cytosol): citrulline + aspartate (the second nitrogen) → argininosuccinate (uses ATP → AMP).
- Argininosuccinate lyase: → arginine + fumarate (links to the TCA cycle).
- Arginase: arginine → urea + ornithine (returns to the mitochondria).
Cost: about 4 high-energy bonds (3 ATP) per urea molecule.
Two nitrogens of urea come from ammonia (via carbamoyl phosphate) and aspartate.
Rate-limiting enzyme = CPS I (needs N-acetylglutamate). Order of intermediates: ornithine → citrulline → argininosuccinate → arginine → urea + ornithine.
Hyperammonaemia
Causes: liver failure (cirrhosis, hepatic encephalopathy), urea cycle defects, valproate.
Features: vomiting, lethargy, tremor (asterixis), slurred speech, confusion, cerebral oedema, coma. Ammonia depletes α-ketoglutarate in the brain (via glutamate) and raises glutamine (osmotic swelling of astrocytes).
Treatment: low-protein diet, lactulose (traps NH₄⁺ in the gut), rifaximin (kills ammonia-producing bacteria), and in urea cycle defects sodium benzoate or phenylbutyrate (bind glycine or glutamine for excretion), arginine; dialysis if severe.
| Defect | Clues |
|---|---|
| Ornithine transcarbamylase deficiency | The commonest urea cycle defect; X-linked recessive; high ammonia, orotic aciduria (excess carbamoyl phosphate enters pyrimidine synthesis), low BUN |
| CPS I deficiency | Autosomal recessive; high ammonia, no orotic aciduria |
| Argininosuccinic aciduria, citrullinaemia | Argininosuccinate or citrulline accumulate |
Disorders of amino acid metabolism
| Disorder | Enzyme defect | Features | Treatment |
|---|---|---|---|
| Phenylketonuria (PKU) | Phenylalanine hydroxylase (or its cofactor tetrahydrobiopterin, BH4) | Normal at birth, then intellectual disability, seizures, musty (mousy) odour, fair skin and hair (less melanin), eczema; phenylketones in urine. Detected by newborn screening | Low-phenylalanine diet (lifelong, especially before and during pregnancy), tyrosine supplement; avoid aspartame |
| Alkaptonuria | Homogentisate oxidase | Urine turns black on standing (oxidised homogentisic acid), ochronosis (blue-black pigment in ear cartilage and sclera), arthritis of large joints; usually benign until adulthood | Supportive; nitisinone |
| Albinism | Tyrosinase (no melanin) | Pale skin, hair, eyes; photophobia, nystagmus; high risk of skin cancer | Sun protection |
| Maple syrup urine disease | Branched-chain α-keto acid dehydrogenase (needs thiamine) | Leucine, isoleucine, valine build up: sweet-smelling urine, feeding problems, vomiting, seizures, severe brain damage | Restrict branched-chain amino acids; thiamine in some forms |
| Homocystinuria | Cystathionine β-synthase (commonest; B6-responsive form), or methionine synthase / MTHFR defects | Lens dislocation (downwards and inwards), Marfan-like body, intellectual disability, osteoporosis, thrombosis | Pyridoxine, B12, folate, betaine, low-methionine diet |
| Cystinuria | Defective renal and gut transport of cystine, ornithine, lysine, arginine ("COLA") | Cystine kidney stones (hexagonal crystals) | Fluids, urine alkalinisation, penicillamine |
| Hartnup disease | Defective transport of neutral amino acids (tryptophan) | Pellagra-like rash (low niacin), ataxia | High-protein diet, nicotinamide |
| Tyrosinaemia type I | Fumarylacetoacetate hydrolase | Liver failure, renal tubular dysfunction, cabbage odour | Nitisinone, diet |
PKU: musty odour, fair skin. MSUD: sweet urine. Alkaptonuria: black urine. Homocystinuria: lens dislocated downwards (Marfan's goes upwards).
Specialised products of amino acids
| Amino acid | Product |
|---|---|
| Tyrosine (from phenylalanine) | Dopamine, noradrenaline, adrenaline, melanin, thyroid hormones |
| Tryptophan | Serotonin, melatonin, niacin (vitamin B3) (about 60 mg tryptophan gives 1 mg niacin) |
| Histidine | Histamine (histidine decarboxylase) |
| Glycine | Haem (with succinyl-CoA), creatine, purines, glutathione, bile salt conjugation, inhibitory neurotransmitter |
| Arginine | Nitric oxide (NO synthase), creatine, urea |
| Glutamate | GABA (glutamate decarboxylase, needs B6), glutathione |
| Arginine + glycine + methionine | Creatine → creatine phosphate → creatinine (excreted; marker of kidney function) |
| Methionine | S-adenosylmethionine (methyl donor), cysteine |
| Cysteine | Glutathione, taurine |
Expect: essential amino acids, purely ketogenic amino acids, nitrogen balance (positive vs negative, × 6.25), transamination and B6, ALT vs AST, glutamate dehydrogenase, ammonia transport (glutamine, alanine), urea cycle steps, location and rate-limiting enzyme, source of urea nitrogens, hyperammonaemia and its treatment, OTC deficiency with orotic aciduria, PKU, alkaptonuria, albinism, MSUD, homocystinuria, cystinuria, Hartnup disease, and products of tyrosine, tryptophan, histidine, glycine and arginine.
Quick revision
- Essential: PVT TIM HaLL. Purely ketogenic: leucine, lysine.
- Protein = N × 6.25. Positive balance: growth, pregnancy. Negative: starvation, burns.
- Transamination: ALT, AST, B6. Ammonia transport: glutamine, alanine.
- Urea cycle: liver, mitochondria + cytosol; CPS I rate-limiting (N-acetylglutamate).
- OTC deficiency: X-linked, orotic aciduria.
- PKU (phenylalanine hydroxylase), alkaptonuria (black urine), MSUD (sweet urine), homocystinuria (lens down, thrombosis), cystinuria (COLA, stones).
- Tyrosine → catecholamines, melanin, thyroid hormone. Tryptophan → serotonin, melatonin, niacin.
Written by The House Job from standard biochemistry references (Lippincott Illustrated Reviews: Biochemistry).
FAQ
Which amino acids are purely ketogenic?
Leucine and lysine.
What is the rate-limiting enzyme of the urea cycle?
Carbamoyl phosphate synthetase I, which needs N-acetylglutamate as an activator.
Which enzyme is deficient in phenylketonuria?
Phenylalanine hydroxylase (or, less often, its cofactor tetrahydrobiopterin).
Why does urine turn black in alkaptonuria?
Homogentisic acid builds up and is excreted in urine, where it oxidises to a dark pigment on standing.