๐งช Biochemistry: One Night Revision & Cram Sheet
Explain the molecules of a cell and the reactions by which those molecules are broken for energy, rebuilt, and switched between fed, fasted, and starved states.
๐ Core Axioms & High-Yield Golden Rules
10 Core PrinciplesNon-negotiable foundational truths frequently tested in direct conceptual and numerical exam questions. Click checkbox to mark as mastered.
Henderson-Hasselbalch equation: pH = pKa + log([A-]/[HA]). When [A-] = [HA], pH = pKa. Histidine (pKa ~6.0) is the primary physiological buffer in protein active sites.
๐ก pH = pKa at 50% dissociationHydrophobic interactions drive globular protein folding: non-polar side chains are sequestered in the interior, releasing ordered clathrate water cages and increasing solvent entropy.
๐ก Folding is driven by water entropy gainEnzyme Kinetics: Km is the substrate concentration at 1/2 Vmax. A lower Km indicates HIGHER substrate affinity. kcat is turnover number (catalytic constant), and kcat/Km measures catalytic efficiency.
๐ก Lower Km = Higher AffinityInhibition types: Competitive increases apparent Km (Vmax unchanged); Non-competitive decreases Vmax (Km unchanged); Uncompetitive decreases BOTH Km and Vmax proportionally.
๐ก Comp = Km up | Non = Vmax down | Un = Both downIrreversible steps of glycolysis: Hexokinase/Glucokinase (step 1), Phosphofructokinase-1 (step 3, committed pacemaker), and Pyruvate Kinase (step 10).
๐ก 1, 3, 10 = One-Way ValvesGluconeogenesis bypasses: Pyruvate Carboxylase + PEPCK bypass Pyruvate Kinase; Fructose-1,6-bisphosphatase bypasses PFK-1; Glucose-6-phosphatase bypasses Hexokinase.
๐ก 4 unique enzymes bypass 3 barriersNet ATP yield from complete aerobic oxidation of glucose is ~30 to 32 ATP, NOT 36-38, because 4 H+ are consumed per ATP synthesized and imported into cytosol.
๐ก Modern yield: 30-32 ATPComplex II (Succinate Dehydrogenase) is the only TCA cycle enzyme embedded in the inner mitochondrial membrane; it transfers electrons to FAD and does NOT pump protons.
๐ก Complex II = No H+ pumpingUncouplers (e.g. 2,4-DNP, Thermogenin) destroy the proton gradient without inhibiting electron transport: oxygen consumption INCREASES while ATP synthesis CEASES.
๐ก Uncoupling = Max O2, Zero ATP, Heat generatedBeta-oxidation of fatty acids requires carnitine shuttle (CPT-I is rate-limiting); each cycle yields 1 FADH2, 1 NADH, and 1 Acetyl-CoA, shortening chain by 2 carbons.
๐ก Carnitine carries acyls into matrix๐ Chapter-by-Chapter Rapid Cram Breakdown
13 ModulesHigh-density review of every curriculum chapter. Click any chapter title to view full in-depth lecture notes.
Water, pH, and buffers →
- Master Polarity and hydrogen bonds: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master hydrophobic effect: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master pH, pKa, HendersonโHasselbalch: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master blood and cell buffers: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Side-chain classes: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master peptide bond: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master primary to quaternary structure: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master helix, sheet, turns: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master folding and chaperones: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Enzymes →
- Master Active site: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master transition state: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master MichaelisโMenten: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master LineweaverโBurk: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master reversible inhibition: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Carbohydrates →
- Master Monosaccharides, anomers, glycosidic bonds: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master disaccharides: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master storage and structural polysaccharides: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master glycoproteins: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Lipids →
- Master Fatty acids and melting: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master triacylglycerols: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master glycerophospholipids and sphingolipids: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master cholesterol: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master micelles, bilayers, fluidity: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Nucleotides and the phosphodiester: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Chargaff and WatsonโCrick pairs: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master grooves: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master A, B, and Z: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master RNA hairpins: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Bioenergetics →
- Master ฮG and equilibrium: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master ATP group transfer: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master coupled reactions: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master NAD and FAD: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master catabolism and anabolism: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master The ten steps and their yields: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master anaerobic pyruvate: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master PDH cofactors and regulation: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master cycle yield: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master anaplerosis: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Complexes and proton pumping: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master ubiquinone and cytochrome c: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master chemiosmosis: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master ATP synthase: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master P/O and shuttles: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Gluconeogenic bypasses: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master fructose 2,6-bisphosphate: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Cori cycle: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master glycogen and hormones: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master pentose phosphate pathway and the red cell: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Lipid metabolism →
- Master Lipolysis: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master carnitine shuttle: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master ฮฒ-oxidation yield: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master ketone bodies: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master fatty-acid synthesis: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Nitrogen metabolism →
- Master Transamination and PLP: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master glutamate dehydrogenase: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master urea cycle: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master links to the citric acid cycle: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master glucogenic and ketogenic amino acids: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Organ fuels: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master fed, fasted, and starvation: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master insulin, glucagon, adrenaline, cortisol: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master type 1 diabetes and ketoacidosis: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
โ๏ธ Must-Know Comparison & Distinction Tables
2 TablesSide-by-side matrices comparing commonly confused biological mechanisms, kinetic types, and pathways.
Enzyme Inhibition Mechanisms & Kinetic Parameters
| Inhibition Type | Inhibitor Binding Site | Apparent Km | Vmax | Lineweaver-Burk Intercepts |
|---|---|---|---|---|
| Competitive | Free enzyme active site (competes with S) | Increases (weaker apparent affinity) | Unchanged | Same Y-intercept (1/Vmax), X-intercept shifts right |
| Pure Non-Competitive | Allosteric site on free E and ES equally | Unchanged | Decreases | Same X-intercept (-1/Km), Y-intercept shifts up |
| Uncompetitive | ES complex only (after substrate binds) | Decreases (apparent affinity increases!) | Decreases | Parallel lines (both intercepts shift by same factor) |
Glycolysis vs. Gluconeogenesis Key Regulatory Steps
| Pathway Phase | Glycolytic Enzyme | Gluconeogenic Bypass Enzyme | Allosteric Regulators |
|---|---|---|---|
| Hexose Phosphorylation | Hexokinase (all tissues) / Glucokinase (liver) | Glucose-6-phosphatase (ER lumen) | Inhibited by G6P (Hexokinase); Glucokinase has high Km, not inhibited by G6P |
| Committed Step | Phosphofructokinase-1 (PFK-1) | Fructose-1,6-bisphosphatase (FBPase-1) | PFK-1 activated by AMP, F-2,6-BP; inhibited by ATP, Citrate |
| Pyruvate Conversion | Pyruvate Kinase | Pyruvate Carboxylase (Mito) + PEPCK (Cyto) | Pyruvate Carboxylase requires Biotin & ATP, activated by Acetyl-CoA |
โ ๏ธ Examiner Traps & Common Student Mistakes
3 PitfallsClassic trap questions designed by examiners to catch uncritical students. Don't lose easy marks here!
Thinking Uncompetitive Inhibitors Decrease Affinity
Students assume all inhibitors make enzymes bind substrate worse (higher Km).
Uncompetitive inhibitors bind ONLY to the ES complex, pulling the equilibrium forward and causing apparent Km to DECREASE (apparent affinity actually increases!).
Assuming Uncouplers Stop Oxygen Consumption
Assuming that because ATP synthesis stops, oxygen uptake must also stop.
Uncouplers dissipate the proton electrochemical gradient. With no back-pressure from proton accumulation, the electron transport chain operates at MAXIMUM speed, INCREASING oxygen consumption while dissipating energy as heat.
Liver Using Ketone Bodies for Fuel
Thinking the liver synthesizes ketone bodies and uses them during starvation.
The liver synthesizes ketone bodies (acetoacetate, beta-hydroxybutyrate) but LACKS the enzyme beta-ketoacyl-CoA transferase (thiophorase), so it CANNOT consume them.
๐ Key Formulas & Numerical Constants
5 FormulasHenderson-Hasselbalch Equation
pH = pKa + log([A-] / [HA])Calculate buffer pH, ionization ratio of drug molecules, and physiological blood bicarbonate buffering.
Michaelis-Menten Equation
v0 = (Vmax * [S]) / (Km + [S])Initial reaction velocity calculation. When [S] = Km, v0 = Vmax / 2.
Lineweaver-Burk Double Reciprocal
1 / v0 = (Km / Vmax) * (1 / [S]) + (1 / Vmax)Y-intercept = 1/Vmax; X-intercept = -1/Km; Slope = Km/Vmax.
Standard Free Energy Change
ฮGยฐ' = -R * T * ln(Keq)Equilibrium constant Keq > 1 yields negative ฮGยฐ' (exergonic / spontaneous reaction).
Gibbs Free Energy Equation
ฮG = ฮH - T * ฮSSpontaneity criterion: negative ฮG is spontaneous; enthalpy (ฮH) and entropy (ฮS) interplay.
๐๏ธ Landmark Scientists & Nobel Discoveries
6 PioneersFrequently tested in historical milestone and match-the-following exam questions.
Sir Hans Adolf Krebs
๐ Nobel Prize in Physiology or Medicine (1953) for his discovery of the citric acid cycleMajor landmark discoveries
Frederick Sanger
๐ Two Nobel Prizes in Chemistry: 1958 (Unshared, for determining the complete primary amino acid structure of insulin) and 1980 (Shared, for inventing dideoxy DNA sequencing)Major landmark discoveries
Peter Dennis Mitchell
๐ Nobel Prize in Chemistry (1978) for his contribution to the understanding of biological energy transfer through the chemiosmotic theoryMajor landmark discoveries
Paul Delos Boyer
๐ Nobel Prize in Chemistry (1997) for the elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)Major landmark discoveries
James Watson & Francis Crick
๐ Nobel Prize in Physiology or Medicine (1962) for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living materialMajor landmark discoveries
George Emil Palade
๐ Nobel Prize in Physiology or Medicine (1974) for discoveries concerning the structural and functional organization of the cellMajor landmark discoveries
๐ฏ Rapid-Fire Active Recall Checklist
8 QuestionsTest your memory before stepping into the exam hall. Try to answer mentally, then tap "Reveal Answer" to verify!