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Premedical Biochemistry
Foundational molecules, metabolism, enzymes, genetics and lab interpretation – compact, high-yield, clinically anchored. 🔥
🔢 Key Areas of Study
- Macromolecules: Amino acids & proteins (structure↔function), carbohydrates (mono/di/poly), lipids (FA, TAG, phospholipids, cholesterol), nucleotides & nucleic acids.
- Enzymes & Kinetics: Active site chemistry, Michaelis–Menten, inhibition (competitive, non-competitive, uncompetitive), allostery, cofactors & vitamins.
- Bioenergetics: ATP, redox pairs, \(\Delta G\), coupling, oxidative phosphorylation & chemiosmotic theory.
- Carbohydrate Metabolism: Glycolysis, PDH, TCA cycle, gluconeogenesis, glycogen metabolism, pentose phosphate pathway.
- Lipid Metabolism: FA synthesis/β-oxidation, carnitine shuttle, ketogenesis/ketolysis, cholesterol synthesis & transport (lipoproteins).
- Amino Acid & Nitrogen Metabolism: Transamination, urea cycle, one-carbon/BH4 pathways, key inborn errors (PKU, MSUD, homocystinuria).
- Molecular Biology: DNA replication/repair, transcription/translation, operon logic, epigenetics, recombinant techniques.
- Cell Signalling & Hormones: GPCRs, RTKs, second messengers (cAMP, IP\(_3\)/DAG, Ca\(^{2+}\)), insulin/glucagon & fed–fasted transitions.
- Acid–Base & Buffers: Henderson–Hasselbalch, bicarbonate system, titration curves, isoelectric point.
- Nutrition: Essential nutrients, vitamin/cofactor map, UK-style reference ranges/units context.
🧱 Macromolecules – clinical anchors
- Proteins: Primary→quaternary structure; misfolding (e.g. prions, amyloid) alters function without changing sequence. Disulfides stabilise extracellular proteins.
- Carbohydrates: D-glucose is the central fuel; glycogen’s α(1→6) branches speed release. Cellulose’s β(1→4) bonds are indigestible → fibre.
- Lipids: Unsaturation lowers melting point; essential ω-3/ω-6 FAs modulate eicosanoids (inflammation, thrombosis).
- Nucleotides: Purines (A,G) vs pyrimidines (C,T/U); folate/B\(_{12}\) needed for thymidylate synthesis → megaloblastic anaemia if deficient.
⚙️ Enzymes – what examiners test
- Active site: Transition-state stabilisation; acid–base, covalent catalysis; induced fit.
- Cofactors: Metals (Zn\(^{2+}\), Mg\(^{2+}\)), coenzymes (NAD\(^+\), FAD, TPP, PLP, biotin). Vitamin deficits → predictable blocks (e.g. B\(_1\) for PDH/α-KG DH).
- Regulation: Allostery (PFK-1 ↑ by AMP/F-2,6-BP; ↓ by ATP/citrate), covalent modification (phosphorylation), enzyme amount (induction/repression).
🧪 Bioenergetics – coupling intuition
\(\Delta G=\Delta G^{\circ'}+RT\ln Q\). Unfavourable steps run forward by coupling to ATP hydrolysis or by substrate/product “pull” in a pathway. Proton-motive force (\(\Delta p\)) across the inner mitochondrial membrane drives ATP synthase.
🍞 Carbs – pathway map
- Glycolysis: Hexokinase/GLUT tissue-specificity; rate-limiting PFK-1. Yields 2 ATP (net) + 2 NADH per glucose.
- PDH complex: Links glycolysis to TCA; needs TPP, lipoate, FAD, NAD\(^+\), CoA. Inhibited by arsenic; deficiency → lactic acidosis.
- TCA: Mitochondrial hub; yields NADH/FADH\(_2\) and intermediates for biosynthesis.
- Gluconeogenesis: Liver (± kidney): pyruvate carboxylase, PEPCK, F-1,6-BPase, G-6-Pase bypasses.
- PPP: G6PD → NADPH (reducing power) + ribose-5-P; deficiency → haemolysis with oxidant stress.
🥑 Lipids – shuttle & regulation
- β-Oxidation: Requires carnitine shuttle (CPT-I inhibited by malonyl-CoA). MCAD deficiency → hypoketotic hypoglycaemia.
- FA synthesis: Citrate shuttle, acetyl-CoA carboxylase (biotin) is rate-limiting; needs NADPH (PPP, malic enzyme).
- Ketone bodies: Hepatic production in fasting; brain uses after adaptation; not used by liver (lacks thiophorase).
🧠 Nitrogen – transamination & urea
- Transaminases: ALT/AST (PLP/B\(_6\) coenzyme). Amino group funnels to glutamate → ammonia → urea.
- Urea cycle: CPS-I (N-acetylglutamate activation) is gatekeeper; cycle defects → hyperammonaemia (encephalopathy).
- One-carbon/BH4: Needed for aromatic AA hydroxylation (dopamine/serotonin) and NO synthesis.
🧬 Molecular biology – repair themes
- Replication: semi-conservative, 5'→3' polymerisation, leading/lagging (Okazaki).
- Repair: base-excision (small lesions), nucleotide-excision (bulky, e.g. UV dimers), mismatch repair (post-replication).
- Transcription/translation: promoter→mRNA capping/poly-A→ribosome initiation at AUG; wobble, post-translational mods.
📏 Core Equations – Learn or Locate
| Topic | Equation | Use / Memory Tip |
|---|---|---|
| Henderson–Hasselbalch | \( \mathrm{pH}=\mathrm{p}K_a+\log\frac{[\text{A}^-]}{[\text{HA}]} \) | Buffers resist pH near \(pK_a\). |
| Bicarbonate buffer | \( \mathrm{pH}\approx6.1+\log\frac{[\mathrm{HCO_3^-}]}{0.03\times \mathrm{pCO_2}} \) | ABG interpretation (mmol/L & kPa→mmHg conversion as needed). |
| Isoelectric point (diprotic aa) | \( pI\approx\frac{pK_{a1}+pK_{a2}}{2} \) | For neutral side chains. |
| Michaelis–Menten | \( v=\frac{V_{\max}[S]}{K_m+[S]} \) | \(K_m\) = [S] at \(v=\tfrac12V_{\max}\). |
| Lineweaver–Burk | \( \tfrac1v=\tfrac{K_m}{V_{\max}}\tfrac1{[S]}+\tfrac1{V_{\max}} \) | Straight-line inhibition analysis. |
| Turnover number | \( k_{cat}=\tfrac{V_{\max}}{[E]_T} \) | “Per-enzyme speed”. |
| Gibbs free energy | \( \Delta G=\Delta G^{\circ'}+RT\ln Q \) | Negative drives spontaneity. |
| At equilibrium | \( \Delta G^{\circ'}=-RT\ln K_{eq} \) | Relates chemistry to equilibrium. |
| ATP accounting (typical) | \(\sim 30\) ATP/glucose (malate–aspartate shuttle) | Rough yield; varies by tissue/shuttle. |
| Beer–Lambert | \( A=\varepsilon c l \) | Absorbance for concentration. |
| Osmolarity | \( \mathrm{Osm}=i\sum c \) | Van ’t Hoff factor \(i\). |
| Anion gap | \(\text{AG}=[\mathrm{Na}^+]-([\mathrm{Cl}^-]+[\mathrm{HCO_3^-}])\) | Differential of metabolic acidosis. |
| Creatinine clearance (est.) | \(\text{CrCl}\approx \frac{(140-\text{age})\times \text{weight}}{72\times \text{Cr}}\) (×0.85 if female) | Cockcroft–Gault; units context required. |
🧠 Inhibition patterns (how to remember)
- Competitive: ↑\(K_m\), \(V_{\max}\) unchanged → “compete at the site; flood with substrate.”
- Non-competitive: \(K_m\) same, ↓\(V_{\max}\) → “locks activity away regardless of [S].”
- Uncompetitive: ↓\(K_m\), ↓\(V_{\max}\) → “traps ES complex; lines stay parallel on L–B.”
📝 Quick self-quiz (hover to reveal)
- At \(pH=pK_a\), what is \([\text{A}^-]:[\text{HA}]\)? Answer: \(1:1\).
- If competitive inhibitor present, what happens to \(K_m\)? Answer: Apparent \(K_m\) increases.
- Why does \(\Delta G\) of ATP hydrolysis drive reactions? Answer: Large negative \(\Delta G\) & product removal (Le Châtelier) when coupled.
🧭 Metabolic Pathways & Regulation
| Pathway (compartment) | Rate-limiting / key steps | Allostery & Hormonal Control |
|---|---|---|
| Glycolysis (cytosol) | Hexokinase/Glucokinase; PFK-1; Pyruvate kinase | PFK-1 ↑ AMP, F-2,6-BP; ↓ ATP, citrate. Insulin ↑ glycolysis via F-2,6-BP (PFK-2). Glucagon does the opposite. |
| PDH (mitochondria) | E1–E3; needs TPP, lipoate, FAD, NAD\(^+\), CoA | Inhibited by acetyl-CoA, NADH; activated by ADP. Arsenic poisons lipoate. |
| TCA (mitochondria) | Citrate synthase, isocitrate DH, α-KG DH | ↑ ADP; ↓ ATP, NADH. Fluoroacetate blocks aconitase. |
| OxPhos (mitochondria) | Complex I–IV, ATP synthase | Inhibitors: rotenone (I), antimycin A (III), cyanide/CO (IV), oligomycin (ATP synthase). Uncouplers: 2,4-DNP, thermogenin. |
| Gluconeogenesis (cytosol/mito/ER) | Pyruvate carboxylase, PEPCK, F-1,6-BPase, G-6-Pase | F-1,6-BPase ↓ by F-2,6-BP/AMP. Requires ATP/GTP and substrates (lactate, glycerol, alanine). |
| Glycogen (cytosol) | Glycogen synthase; glycogen phosphorylase | Insulin → dephosphorylation → synthase on; glucagon/epinephrine → phosphorylation → phosphorylase on. |
| PPP (cytosol) | G6PD | Produces NADPH (antioxidant/FA synthesis) & ribose. Haemolysis if deficient under oxidative stress. |
| FA Synthesis (cytosol) | Acetyl-CoA carboxylase (biotin) | ↑ by citrate/insulin; ↓ by palmitoyl-CoA/glucagon. Uses NADPH. |
| β-Oxidation (mito) | CPT-I shuttle | Blocked by malonyl-CoA. Carnitine deficiency → lipid accumulation, weakness. |
| Cholesterol synthesis (cytosol/ER) | HMG-CoA reductase | ↓ by statins; ↑ by insulin, ↓ by glucagon. LDL receptor mediates uptake. |
| Urea cycle (mito+cytosol) | CPS-I, OTC, ASS, ASL, arginase | N-acetylglutamate activates CPS-I. Defects → hyperammonaemia; treat with N-scavengers, restrict protein. |
🧩 Worked example – PFK-1 logic
PFK-1 integrates cell energy status: high ATP/citrate (plenty of energy) ↓ glycolysis; AMP/F-2,6-BP (low energy/high insulin) ↑ glycolysis. This single node explains fasting (gluconeogenesis on) vs fed (glycolysis on).
🧯 Classic tox & deficiency patterns
- G6PD deficiency: Oxidative stress (fava beans, sulfa drugs) → haemolysis (Heinz bodies, bite cells).
- PDH deficiency: ↑ lactate/alanine; treat with ketogenic diet (↑ fat) and thiamine.
- Lead poisoning: Inhibits ALA dehydratase & ferrochelatase → microcytic anaemia with basophilic stippling.
- MSUD: ↓ branched-chain α-ketoacid DH → sweet urine, neurotoxicity; give thiamine, restrict leucine/isoleucine/valine.
- PKU: PAH or BH\(_4\) issue → ↑ phenylalanine, ↓ tyrosine; musty odour, fair skin; lifelong diet, sapropterin if BH\(_4\) responsive.
🔬 Laboratory & Clinical Biochemistry Essentials
- Glucose homeostasis: Fed (insulin) → glycogenesis, glycolysis, FA synthesis; Fasting (glucagon) → glycogenolysis, gluconeogenesis, lipolysis, ketogenesis.
- Lipoproteins: Chylomicrons (dietary TAG), VLDL→IDL→LDL (endogenous TAG→cholesterol), HDL (reverse transport). ApoB-48 (chylos), ApoB-100 (VLDL/LDL), ApoA-I (HDL/LCAT).
- UK lab flavour: Many analytes in mmol/L; ABG commonly reports pH, pCO\(_2\) (kPa), HCO\(_3^-\) (mmol/L). Interpret in physiological context.
🧪 ABG workflow (bicarbonate system)
- Acidaemia vs alkalaemia? pH < 7.35 or > 7.45.
- Primary process? CO\(_2\) (respiratory) vs HCO\(_3^-\) (metabolic).
- Appropriate compensation? Use expected rules; large anion gap? \(\text{AG}=[\text{Na}^+]-([\text{Cl}^-]+[\text{HCO}_3^-])\).
- Clinical link: Lactic ketoacidosis in sepsis/diabetes ↔ core metabolic blocks (PDH, β-ox, OxPhos).
🧫 Core techniques – what they’re for
- Spectrophotometry: Beer–Lambert for enzyme assays (NADH at 340 nm), haemoglobin derivatives.
- Chromatography: HPLC/GC separate metabolites; TLC for lipids/amino acids in teaching labs.
- Electrophoresis: Protein isoforms (e.g. Hb variants), serum protein patterns (albumin, γ-globulins).
- ELISA/Western: Protein abundance/antibody detection; sandwich ELISA for low-abundance targets.
- PCR/qPCR: Amplify/quantify DNA/RNA; Sanger vs NGS for sequencing.
🥗 Vitamins & coenzymes – metabolic map
| Vitamin | Coenzyme / Role | Deficiency clue |
|---|---|---|
| B\(_1\) (Thiamine) | TPP for PDH, α-KG DH, transketolase | Wernicke–Korsakoff, beriberi; ↓ RBC transketolase. |
| B\(_2\) (Riboflavin) | FAD/FMN (redox) | Cheilosis, corneal vascularisation. |
| B\(_3\) (Niacin) | NAD\(^+\)/NADP\(^+\) (redox) | Pellagra: 3 D’s (dermatitis, diarrhoea, dementia). |
| B\(_5\) | CoA (acyl transfers) | Dermatitis, enteritis. |
| B\(_6\) (Pyridoxine) | PLP (transamination, heme) | Neuropathy, sideroblastic anaemia. |
| B\(_7\) (Biotin) | Carboxylation (ACC, pyruvate carboxylase) | Avidin in raw eggs binds biotin. |
| Folate (B\(_9\)) | THF (1-C transfers) | Megaloblastic anaemia; ↑ homocysteine, normal methylmalonic acid. |
| B\(_{12}\) | Methylmalonyl-CoA→succinyl-CoA; homocysteine→methionine | Megaloblastic, neuropathy; ↑ methylmalonic acid. |
| C | Hydroxylation (collagen), antioxidant | Scurvy (bleeding gums, poor wound healing). |
| A | Retinal/retinoic acid (vision, epithelia) | Night blindness; teratogenic in excess. |
| D | Calcium/phosphate homeostasis | Rickets/osteomalacia. |
| E | Antioxidant | Haemolysis, posterior column/ataxia. |
| K | γ-carboxylation of clotting factors | Bleeding; ↑ PT/INR. |
🧴 Lipoprotein disorders – quick cues
- Familial hypercholesterolaemia (LDL-R): ↑ LDL, tendon xanthomas, premature atherosclerosis.
- Type I (LPL/ApoC-II deficiency): ↑ chylomicrons, pancreatitis risk, eruptive xanthomas.
- Type III (ApoE): ↑ remnants (IDL/chylo), palmar xanthomas.
🧠 Study & Exam Tips
- Pathway stories: Learn rate-limiting steps + regulators + compartment. If you know the “gate” enzyme, questions collapse.
- Link to symptoms: Map lab abnormalities to blocks (e.g. hyperammonaemia ↔ urea cycle; hypoketotic hypoglycaemia ↔ FA oxidation).
- Equation fluency: HH, M–M, \(\Delta G\), Beer–Lambert – practise plugging units you’ll actually see in labs.
- Fed↔fasted tables: For liver, muscle, adipose, brain; add hormones, transporters (GLUTs), on/off pathways.
- Active recall: One-page “metabolic atlas” + daily five-minute drills; teach a peer to uncover gaps.
🚀 Rapid drill (answers hidden)
- What activates CPS-I? Ans: N-acetylglutamate.
- Why does F-2,6-BP matter? Ans: Potent allosteric ↑ of PFK-1 (glycolysis) and ↓ of F-1,6-BPase (gluconeogenesis).
- Rate-limiting steps of FA synthesis and β-oxidation? Ans: ACC (synthesis), CPT-I (β-ox).
- Which vitamin for transamination? Ans: B\(_6\) (PLP).
- Two OxPhos poisons and sites? Ans: Rotenone (I), cyanide (IV), oligomycin (ATP synthase).
Final thought: Biochemistry is logic with molecules - name the gatekeeper, the fuel state, and the regulator, and most problems unravel. You’ve got this. 💪