Revision aid · 16 pathways
Pathway Sheets
16
The pathways, one card each
Examiners ask for pathways in a fixed shape: where it happens, the irreversible or rate-limiting enzyme, what regulates it, and what it yields. Each card below is one pathway in exactly that shape. Every figure has been verified against Harper's Illustrated Biochemistry in the unit it links to.
How to use this page
Cover the right-hand side of a card and try to produce the five lines from memory. If you can do that for all sixteen, you can answer any “outline briefly” question in Section II — that section is worth 20–40% of the paper.
Glycolysis
Glucose → 2 pyruvate
- Where
- Cytosol, in every tissue
- Irreversible steps
- Hexokinase/glucokinase · PFK-1 · pyruvate kinase — the three bypassed in gluconeogenesis
- Rate-limiting
- PFK-1; activated by fructose 2,6-bisphosphate and AMP, inhibited by ATP and citrate
- Yield
- 2 ATP net anaerobically; 30–32 ATP per glucose aerobically
- Must know
- Glucokinase Km 10 mM vs hexokinase 0.1 mM, and glucokinase is not inhibited by glucose 6-phosphate
The citric acid cycle
Acetyl-CoA → 2 CO₂
- Where
- Mitochondrial matrix
- Regulated enzymes
- Citrate synthase · isocitrate dehydrogenase · α-ketoglutarate dehydrogenase
- Yield per turn
- 3 NADH · 1 FADH₂ · 1 GTP = 10 ATP
- Key idea
- Catalytic, not consumed — removing an intermediate stalls it, hence anaplerosis
- Must know
- It is amphibolic, and fat burns in the flame of carbohydrate — no oxaloacetate, no cycle
The respiratory chain
NADH/FADH₂ → H₂O + ATP
- Where
- Inner mitochondrial membrane
- Complexes
- I, III and IV pump protons; II does not
- P:O ratios
- 2.5 for NADH, 1.5 for FADH₂ — this course's Lectures 10, 11 and 15 all use these
- Inhibitors
- Rotenone/amytal (I) · antimycin A (III) · cyanide, CO, azide (IV) · oligomycin (ATP synthase) · 2,4-DNP (uncoupler)
- Must know
- Oxidative phosphorylation was set in BOTH papers — define it word-perfectly
Gluconeogenesis
Lactate, alanine, glycerol → glucose
- Where
- Liver mainly; kidney in prolonged starvation
- The four bypasses
- Pyruvate carboxylase · PEP carboxykinase · fructose 1,6-bisphosphatase · glucose-6-phosphatase
- Cost
- 6 ATP equivalents per glucose
- Control
- Acetyl-CoA activates pyruvate carboxylase; falling fructose 2,6-bisphosphate releases fructose 1,6-bisphosphatase
- Must know
- Fatty acids are not glucogenic — pyruvate dehydrogenase is irreversible
Glycogen metabolism
Glucose ⇄ glycogen
- Where
- Liver (for the blood) and muscle (for itself)
- Key enzymes
- Glycogen synthase and glycogen phosphorylase, reciprocally controlled
- Signal
- cAMP → protein kinase A → phosphorylation: synthase off, phosphorylase on
- Must know
- Muscle has no glucose-6-phosphatase, so muscle glycogen can never raise blood glucose
The pentose phosphate pathway
Glucose 6-P → NADPH + ribose 5-P
- Where
- Cytosol of liver, adipose tissue, lactating mammary gland, adrenal cortex, erythrocyte
- Two phases
- Oxidative and irreversible (G6PD → 2 NADPH + CO₂), then non-oxidative and reversible (transketolase, transaldolase)
- Recognise it by
- NADP appears · CO₂ appears · no ATP appears
- Must know
- G6PD deficiency → no NADPH → no reduced glutathione → haemolysis
β-Oxidation
Fatty acid → acetyl-CoA
- Where
- Mitochondrial matrix; carrier is CoA
- Entry
- Activation costs 2 ~P; the carnitine shuttle — CPT-I, translocase, CPT-II
- Rate-limiting
- CPT-I, inhibited by malonyl-CoA
- Per cycle
- 1 acetyl-CoA · 1 FADH₂ · 1 NADH = 4 ATP from the reducing equivalents
- Palmitate
- 106 ATP net (7 cycles; 108 gross − 2 for activation)
Fatty acid synthesis
Acetyl-CoA → palmitate
- Where
- Cytosol; carrier is ACP
- Committed step
- Acetyl-CoA carboxylase → malonyl-CoA; requires biotin
- Control
- Citrate activates (dimer → active polymer); phosphorylation and long-chain acyl-CoA inhibit
- Reductant
- 14 NADPH per palmitate, chiefly from the pentose phosphate pathway
- Must know
- Carbons 15 and 16 come from the priming acetyl-CoA; all the rest from malonyl-CoA
Ketogenesis
Acetyl-CoA → ketone bodies
- Where
- Mitochondria of the LIVER only
- Regulatory enzyme
- HMG-CoA synthase (mitochondrial — not the reductase)
- Bodies
- Acetoacetate · D-3-hydroxybutyrate · acetone; 3-hydroxybutyrate predominates
- Why the liver cannot use them
- It lacks succinyl-CoA-acetoacetate CoA transferase
- Control
- Three stages: lipolysis → CPT-I → the split of acetyl-CoA between ketogenesis and the cycle
Cholesterol synthesis
Acetyl-CoA → cholesterol
- Where
- Cytosol of virtually all tissues
- Five stages
- Acetyl-CoA → mevalonate (C6) → isoprenoid (C5) → squalene (C30) → lanosterol → cholesterol (C27)
- Rate-limiting
- HMG-CoA reductase, using 2 NADPH — the statin target
- Control
- SREBP transcription · regulated degradation · phosphorylation · feedback by cholesterol
- Must know
- The steroid nucleus cannot be degraded — the only exits are bile acids and neutral steroids
The urea cycle
NH₃ + CO₂ + aspartate → urea
- Where
- Liver; reactions 1–2 in the matrix, 3–5 in the cytosol
- Cost
- 3 ATP per mole of urea, 5 enzymes
- Rate-limiting
- Carbamoyl phosphate synthase I, active only with N-acetylglutamate
- The two nitrogens
- Free NH₄⁺ at reaction 1; the amino group of aspartate at reaction 3
- Link
- Fumarate from reaction 4 joins the citric acid cycle
Purine synthesis
PRPP → IMP → AMP and GMP
- Where
- Cytosol; the ring is built ON the ribose
- Committed step
- PRPP glutamyl amidotransferase → 5-phosphoribosylamine
- Donors
- Glycine · glutamine · aspartate · CO₂ · N¹⁰-formyl-THF
- Cross-control
- AMP synthesis needs GTP; GMP synthesis needs ATP
- Catabolism
- → uric acid, because humans lack uricase; pKa 5.8
Pyrimidine synthesis
Carbamoyl phosphate → UMP → CTP, TMP
- Where
- Cytosol; the ring is built FIRST, then joined to PRPP at OMP
- First enzyme
- Carbamoyl phosphate synthase II — cytosolic, uses glutamine
- Control
- CPS-II inhibited by UTP, activated by PRPP; aspartate transcarbamoylase inhibited by CTP, activated by ATP
- Folate
- Only thymidylate synthase needs a tetrahydrofolate — the methotrexate target
- Catabolism
- CO₂, NH₃, β-alanine, β-aminoisobutyrate — all water-soluble, so no gout equivalent
Haem catabolism
Haem → bilirubin → urobilinogen
- Start
- Heme oxygenase (mitochondrial) → biliverdin → reduced in cytosol to bilirubin
- Amounts
- 1 g haemoglobin → ~35 mg bilirubin; 250–350 mg daily
- Three hepatic stages
- Uptake · conjugation with glucuronic acid · secretion in bile (secretion is rate-limiting)
- The rule
- Only UNconjugated crosses into the brain (kernicterus); only CONJUGATED appears in urine (choluria)
- Jaundice
- Visible at 2–2.5 mg/dL; hyperbilirubinemia is >1 mg/dL
Transcription
DNA → RNA
- Enzyme
- DNA-dependent RNA polymerase; bacterial core α₂ββ′, holoenzyme +σ
- Direction
- RNA made 5′→3′; template read 3′→5′
- No primer
- RNA polymerases initiate de novo — the key contrast with replication
- Bubble
- 20 bp; whole complex 30–75 bp
- Processing
- 5′ cap · poly(A) tail (~200 A, 20 nt after AAUAAA) · splicing
Translation
mRNA → protein
- Charging
- Aminoacyl-tRNA synthetase, ester linkage, error rate < 10⁻⁴
- Initiation
- Dissociation → 43S preinitiation → 43S initiation → 80S, met-tRNAi in the P site
- Elongation
- A site binding → peptidyl transferase (a ribozyme) → EF2-GTP translocation
- Termination
- Stop codon; a water molecule is added, releasing the protein
- Cost
- 4 high-energy phosphate bonds per peptide bond