Biochemistry: Metabolism of carbohydrates, lipids and proteins

🧪 Metabolism of carbohydrates, lipids and proteins. Metabolism is how the body extracts energy from food, stores it, and builds the molecules it needs. The pathways explain diabetes and ketoacidosis, lactic acidosis, hypoglycaemia, dyslipidaemia, gout, hyperammonaemia and the actions of many drugs. The UKMLA and MRCP test the clinically important steps, rate-limiting enzymes and regulation rather than every intermediate.
Your four questions for any metabolic problem: Is the patient fed, fasting or stressed? Which pathway is running (or blocked)? Which enzyme or cofactor is limiting? What accumulates, and what is deficient as a result?

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ATP and Energy Overview

• ATP is the universal energy currency; the body turns over roughly its own weight in ATP daily.
• Fuel sources: carbohydrate (4 kcal/g), protein (4 kcal/g), fat (9 kcal/g), alcohol (7 kcal/g).
• Where pathways occur: cytoplasm - glycolysis, fatty acid synthesis, pentose phosphate pathway; mitochondria - TCA cycle, β-oxidation, oxidative phosphorylation, ketogenesis; both - gluconeogenesis, urea cycle, haem synthesis.
• Hormonal control: insulin promotes storage (glycogen, fat, protein synthesis); glucagon, adrenaline and cortisol promote mobilisation (glycogenolysis, gluconeogenesis, lipolysis, ketogenesis).
• ATP yield: about 30–32 ATP per glucose fully oxidised (only 2 from glycolysis alone); about 106 per palmitate.

Glycolysis and Lactate

• Glucose → 2 pyruvate in the cytoplasm, producing 2 ATP (net) and 2 NADH; occurs in all cells; the only ATP source for red cells (no mitochondria).
• Rate-limiting enzyme: phosphofructokinase-1 (PFK-1) - stimulated by AMP and fructose-2,6-bisphosphate (insulin), inhibited by ATP and citrate.
• Hexokinase (most tissues - low Km, inhibited by its product) versus glucokinase (liver and pancreatic β cells - high Km, the β-cell "glucose sensor"; mutations cause MODY 2).
• Pyruvate kinase deficiency - the commonest glycolytic enzyme defect; chronic haemolytic anaemia (red cells cannot make ATP).
• Anaerobic conditions: pyruvate → lactate (lactate dehydrogenase) to regenerate NAD⁺ so glycolysis can continue.
• Lactic acidosis: type A (tissue hypoxia - shock, sepsis, ischaemia, severe anaemia, CO poisoning) and type B (no hypoxia - metformin with renal failure, liver failure, thiamine deficiency, malignancy, salbutamol, adrenaline infusions, inborn errors).
• 2,3-BPG (from a glycolytic side branch in red cells) shifts the oxygen dissociation curve to the right.

Pyruvate Dehydrogenase, the TCA Cycle and Oxidative Phosphorylation

• Pyruvate dehydrogenase (PDH) - pyruvate → acetyl-CoA in mitochondria; needs thiamine (B1), lipoic acid, CoA (B5), FAD (B2) and NAD⁺ (B3). Thiamine deficiency (alcohol misuse, malnutrition, refeeding) → lactic acidosis, Wernicke's encephalopathy and beriberi. Giving glucose before thiamine can precipitate Wernicke's in deficient patients.
• TCA (Krebs) cycle - acetyl-CoA + oxaloacetate → citrate → … → oxaloacetate; produces NADH, FADH₂ and GTP; also supplies intermediates for synthesis (e.g. succinyl-CoA for haem).
• Electron transport chain (inner mitochondrial membrane) - NADH and FADH₂ donate electrons; proton gradient drives ATP synthase (oxidative phosphorylation).
• Inhibitors - cyanide and carbon monoxide block complex IV (cytochrome oxidase) → cells cannot use oxygen → lactic acidosis with high venous oxygen; uncouplers (salicylate overdose, DNP, brown fat UCP-1) dissipate the gradient as heat → hyperthermia.
• Mitochondrial disorders - maternally inherited (mitochondrial DNA): MELAS, MERRF, Leber's hereditary optic neuropathy; heteroplasmy explains variable severity.

Glycogen Metabolism

• Glycogen - branched glucose polymer stored in liver (maintains blood glucose for about 24 hours of fasting) and muscle (local fuel; muscle lacks glucose-6-phosphatase so cannot release glucose into blood).
• Synthesis - glycogen synthase (stimulated by insulin); breakdown - glycogen phosphorylase (stimulated by glucagon and adrenaline).
• Glycogen storage diseases:

Type	Enzyme	Features
I - von Gierke	Glucose-6-phosphatase	Severe fasting hypoglycaemia, hepatomegaly, lactic acidosis, hyperuricaemia, hyperlipidaemia
II - Pompe	Lysosomal acid α-glucosidase	Cardiomegaly, hypotonia ("floppy baby"); enzyme replacement available; also a lysosomal storage disease
III - Cori	Debranching enzyme	Milder version of type I without lactic acidosis
V - McArdle	Muscle glycogen phosphorylase	Exercise intolerance, cramps, myoglobinuria; "second wind" phenomenon; no lactate rise on exercise

Gluconeogenesis

• New glucose from non-carbohydrate precursors - lactate (Cori cycle), glycerol (from fat), alanine and other glucogenic amino acids (from muscle). Occurs mainly in the liver (and kidney in prolonged fasting).
• Key enzymes bypass the irreversible steps of glycolysis: pyruvate carboxylase (needs biotin), PEP carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase.
• Even-chain fatty acids cannot be converted to glucose (acetyl-CoA cannot be converted back to pyruvate); only glycerol from fat contributes.
• Alcohol inhibits gluconeogenesis (high NADH/NAD⁺ ratio) → hypoglycaemia in fasting, alcohol-dependent or intoxicated people (and children).
• Metformin reduces hepatic gluconeogenesis (with effects on mitochondrial redox and AMPK).

The Pentose Phosphate Pathway

• Produces NADPH (for fatty acid and steroid synthesis, and to keep glutathione reduced - protecting cells against oxidative damage) and ribose-5-phosphate (nucleotide synthesis).
• Rate-limiting enzyme: glucose-6-phosphate dehydrogenase (G6PD).
• G6PD deficiency - X-linked; commonest enzyme deficiency worldwide (African, Mediterranean, Middle Eastern and Asian ancestry; protective against malaria). Red cells cannot cope with oxidant stress → acute haemolysis with Heinz bodies and bite cells after triggers: primaquine and tafenoquine, dapsone, nitrofurantoin, sulfonamides, quinolones, rasburicase, fava beans, infection. Test G6PD before primaquine or rasburicase.

Fructose and Galactose

• Hereditary fructose intolerance (aldolase B deficiency) - vomiting and hypoglycaemia after fructose or sucrose is introduced at weaning; liver damage; treat by avoiding fructose, sucrose and sorbitol.
• Essential fructosuria - benign.
• Classic galactosaemia (galactose-1-phosphate uridyltransferase deficiency) - in neonates once milk feeds start: vomiting, jaundice, hepatomegaly, E. coli sepsis, cataracts, failure to thrive; treat with a lactose-free diet (soya formula).
• Lactase deficiency - common in adults of non-European ancestry; bloating and diarrhoea with dairy; secondary lactose intolerance after gastroenteritis or coeliac disease.
• Sorbitol (polyol) pathway - aldose reductase converts glucose to sorbitol in lens, nerve and kidney → osmotic damage in diabetes (cataract, neuropathy).

Fatty Acid Synthesis and Oxidation

• Synthesis (fed state, liver and adipose, cytoplasm): acetyl-CoA → malonyl-CoA (acetyl-CoA carboxylase - rate-limiting, needs biotin, stimulated by insulin) → palmitate (fatty acid synthase, uses NADPH). Stored as triglycerides (glycerol + 3 fatty acids).
• Lipolysis (fasting): hormone-sensitive lipase (activated by adrenaline, glucagon; inhibited by insulin) releases fatty acids and glycerol from adipose tissue.
• β-oxidation (mitochondria): long-chain fatty acids enter via the carnitine shuttle (carnitine palmitoyltransferase I - inhibited by malonyl-CoA, preventing simultaneous synthesis and breakdown); each cycle removes 2 carbons as acetyl-CoA.
• Defects of fatty acid oxidation - MCAD deficiency (newborn screening): hypoketotic hypoglycaemia during fasting or illness, sudden infant death; avoid fasting; carnitine deficiency; CPT deficiencies (rhabdomyolysis with exercise).
• Essential fatty acids - linoleic (omega-6) and α-linolenic (omega-3) acids must come from the diet; precursors of eicosanoids (prostaglandins, thromboxanes, leukotrienes).

Ketone Bodies

• Ketogenesis - in liver mitochondria when fatty acid oxidation is high and insulin is low: acetyl-CoA → HMG-CoA → acetoacetate → β-hydroxybutyrate (the main ketone in DKA - measured by capillary ketone meters) and acetone (breath smell).
• The liver cannot use ketones (lacks succinyl-CoA:3-ketoacid CoA transferase); brain, heart and muscle use them in starvation.
• Ketosis states: starvation, prolonged exercise, low-carbohydrate diets (mild ketosis), diabetic ketoacidosis (absolute insulin deficiency; SGLT2 inhibitors can cause euglycaemic DKA), alcoholic ketoacidosis (alcohol binge then vomiting and starvation - often normal or low glucose; treat with fluids, glucose and thiamine).
• Urine dipsticks detect acetoacetate, not β-hydroxybutyrate - they underestimate ketosis in severe DKA (high NADH shifts the balance to β-hydroxybutyrate).
• Hypoketotic hypoglycaemia - fatty acid oxidation defects or hyperinsulinism.

Cholesterol and Lipoproteins

• Cholesterol synthesis - rate-limiting enzyme HMG-CoA reductase (target of statins); cholesterol forms cell membranes, steroid hormones, bile acids and vitamin D.

Lipoprotein	Carries	Origin	Notes
Chylomicrons	Dietary triglycerides	Intestine	ApoB-48; cleared by lipoprotein lipase
VLDL	Endogenous triglycerides	Liver	ApoB-100; becomes IDL then LDL
LDL	Cholesterol to tissues	From VLDL	Atherogenic; taken up via the LDL receptor (apoB-100)
HDL	Cholesterol from tissues to liver (reverse transport)	Liver and intestine	ApoA-I; low HDL increases CVD risk
Lipoprotein(a)	LDL-like particle with apo(a)	Liver	Genetically determined; independent CVD risk factor; measure once in life

• LDL receptor regulation - low intracellular cholesterol (e.g. statins) → SREBP activation → more LDL receptors → lower plasma LDL. PCSK9 degrades LDL receptors - PCSK9 inhibitors (evolocumab, alirocumab) and inclisiran (siRNA) raise receptor numbers.
• Ezetimibe blocks intestinal cholesterol absorption (NPC1L1); bempedoic acid inhibits ATP citrate lyase (upstream of HMG-CoA reductase); fibrates activate PPAR-α (lower triglycerides).
• Familial hypercholesterolaemia - autosomal dominant (LDL receptor, apoB or PCSK9 mutations); about 1 in 250; tendon xanthomata, premature CHD; cascade testing.
• Secondary dyslipidaemia - hypothyroidism, nephrotic syndrome, cholestasis, diabetes, alcohol (triglycerides), drugs (thiazides, steroids, antipsychotics, protease inhibitors, isotretinoin).
• Severe hypertriglyceridaemia (>10–20 mmol/L) → acute pancreatitis; eruptive xanthomata, lipaemia retinalis.

Amino Acid Metabolism

• Essential amino acids (must be eaten): phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histidine, leucine, lysine (mnemonic "PVT TIM HaLL").
• Transamination - amino groups transferred to α-ketoglutarate (forming glutamate) by ALT and AST (vitamin B6/pyridoxal phosphate as cofactor) - the basis of "liver enzymes".
• Important products: tyrosine → catecholamines, thyroid hormones, melanin; tryptophan → serotonin, melatonin, niacin; glycine + succinyl-CoA → haem (ALA synthase - B6); histidine → histamine; arginine → nitric oxide; glutamate → GABA.
• Phenylketonuria - phenylalanine hydroxylase deficiency (or BH4 deficiency) → high phenylalanine → intellectual disability, seizures, musty odour, fair skin; newborn blood spot screening; lifelong low-phenylalanine diet; maternal PKU must be controlled before conception (fetal microcephaly, heart defects).
• Homocystinuria - cystathionine β-synthase deficiency: Marfan-like habitus, downward lens dislocation, learning difficulty, thrombosis; treat with B6, B12, folate, betaine.
• Maple syrup urine disease - branched-chain ketoacid dehydrogenase deficiency.
• Alkaptonuria - homogentisic acid oxidase deficiency: dark urine on standing, ochronosis, arthritis.
• Albinism - tyrosinase deficiency.

The Urea Cycle and Ammonia

• Ammonia from amino acid breakdown (and gut bacteria) is toxic to the brain; the liver converts it to urea (excreted by the kidneys).
• Urea cycle - partly mitochondrial (carbamoyl phosphate synthetase I - rate-limiting; ornithine transcarbamylase) and partly cytoplasmic.
• Hyperammonaemia: urea cycle disorders (OTC deficiency - X-linked, the commonest; neonatal encephalopathy, vomiting, respiratory alkalosis), liver failure (hepatic encephalopathy - treated with lactulose and rifaximin), valproate, organic acidaemias, GI bleeding in cirrhosis (protein load).
• Blood urea is raised by dehydration, renal failure, upper GI bleeding (digested blood protein), high-protein diet, catabolism and steroids; low in liver failure, malnutrition and pregnancy. A disproportionately raised urea:creatinine ratio suggests pre-renal AKI or upper GI bleeding.

Purines, Pyrimidines and Uric Acid

• Purines (adenine, guanine) and pyrimidines (cytosine, thymine, uracil) are synthesised de novo or salvaged.
• Drugs targeting nucleotide synthesis: methotrexate (dihydrofolate reductase), 5-fluorouracil (thymidylate synthase), hydroxycarbamide (ribonucleotide reductase), mycophenolate (IMP dehydrogenase - lymphocytes depend on de novo purine synthesis), azathioprine/6-mercaptopurine (purine analogues; TPMT activity predicts toxicity), leflunomide (pyrimidine synthesis).
• Uric acid - the end product of purine breakdown in humans (we lack uricase): xanthine oxidase converts hypoxanthine → xanthine → uric acid.
• Hyperuricaemia - overproduction (tumour lysis, myeloproliferative disorders, psoriasis, Lesch–Nyhan syndrome - HGPRT deficiency with self-mutilation) or under-excretion (90% - CKD, thiazide and loop diuretics, low-dose aspirin, ciclosporin, alcohol, ketoacidosis, lactic acidosis).
• Treatment: allopurinol and febuxostat inhibit xanthine oxidase (allopurinol + azathioprine = dangerous - azathioprine is broken down by xanthine oxidase → marrow toxicity; HLA-B*58:01 increases allopurinol SJS/TEN risk); rasburicase (recombinant uricase - tumour lysis; contraindicated in G6PD deficiency); uricosurics (probenecid).

Metabolism at a Glance

Pathway	Rate-limiting enzyme	Key point
Glycolysis	PFK-1	Red cells depend on it; 2 ATP
Gluconeogenesis	Fructose-1,6-bisphosphatase (and PC)	Alcohol inhibits → hypoglycaemia
Glycogenolysis	Glycogen phosphorylase	Liver glycogen lasts ~24 h
Pentose phosphate	G6PD	NADPH; G6PD deficiency → haemolysis
PDH	-	Needs thiamine
Fatty acid synthesis	Acetyl-CoA carboxylase	Insulin-stimulated
β-oxidation	CPT-I	Inhibited by malonyl-CoA
Cholesterol synthesis	HMG-CoA reductase	Statins
Urea cycle	CPS-I	OTC deficiency commonest disorder
Uric acid	Xanthine oxidase	Allopurinol; beware azathioprine

Spot the Diagnosis

• A man develops dark urine and anaemia 3 days after starting primaquine. → G6PD deficiency haemolysis.
• Cramps and pigmenturia during exercise that ease if he continues ("second wind"). → McArdle disease.
• A 6-month-old has vomiting and hypoglycaemia after starting fruit purée. → Hereditary fructose intolerance.
• Neonate with jaundice, cataracts and E. coli sepsis after milk feeds. → Galactosaemia.
• Confusion, ataxia and ophthalmoplegia in a malnourished drinker given IV dextrose. → Wernicke's encephalopathy (thiamine deficiency).
• Tall teenager with downward lens dislocation and a DVT. → Homocystinuria.

Exam-style Scenarios

• Scenario. A patient with gout on azathioprine for Crohn's disease is started on allopurinol and develops pancytopenia. Why?
  Answer: Xanthine oxidase metabolises azathioprine (via 6-mercaptopurine); allopurinol inhibits it, raising thiopurine levels → marrow suppression. Avoid the combination or reduce the azathioprine dose to about a quarter with specialist monitoring.
• Scenario. A man with alcohol dependence presents after a binge with vomiting, pH 7.21, glucose 4.2, raised anion gap and a trace of urinary ketones. What is likely?
  Answer: Alcoholic ketoacidosis - β-hydroxybutyrate predominates, so urine dipsticks underestimate ketosis. Treat with IV glucose-containing fluids and thiamine (thiamine before or with glucose), not insulin.
• Scenario. A child has hypoglycaemia with low ketones after a prolonged fast during gastroenteritis.
  Answer: Hypoketotic hypoglycaemia - suggests a fatty acid oxidation defect such as MCAD deficiency (or hyperinsulinism). Avoid fasting; emergency glucose regimen during illness.

Key Points

• Know the rate-limiting enzymes and their regulation.
• Thiamine is a cofactor for PDH - give it before glucose in malnourished patients.
• G6PD deficiency: oxidant drugs cause haemolysis - test before primaquine or rasburicase.
• Statins inhibit HMG-CoA reductase; PCSK9 inhibitors increase LDL receptors.
• Allopurinol with azathioprine causes severe marrow toxicity.

Further Reading

• Lippincott Illustrated Reviews: Biochemistry
• Marshall WJ et al. Clinical Chemistry
• NICE NG238: Cardiovascular disease - lipid modification
• British Inherited Metabolic Disease Group (BIMDG): emergency guidelines