Biochemistry

50 lessons, pages 3471–3520.

  1. Biochemistry as Molecular Chemistry — Proteins, enzymes, metabolism and energy as one chemical system
  2. Amino Acid Side-Chain Chemistry — Polarity, charge and side-chain pKa values in proteins
  3. The Peptide Bond: Planarity and Resonance — Partial double-bond character, trans geometry and rigid units
  4. Backbone Torsion Angles and Ramachandran Plots — Phi and psi angles, steric clashes and allowed regions
  5. Secondary Structure Geometry — Hydrogen-bonding patterns in alpha helices, beta sheets and turns
  6. Forces Stabilising Tertiary Structure — Hydrophobic effect, hydrogen bonds, salt bridges and disulfides
  7. Thermodynamics of Protein Folding — Enthalpy, entropy and the marginal stability of native proteins
  8. Folding Energy Landscapes and Chaperones — Levinthal's paradox, folding funnels and assisted folding
  9. Quaternary Structure and Allostery — Subunit interfaces, symmetry and conformational communication
  10. Haemoglobin and Cooperative Oxygen Binding — Sigmoidal binding curves, T and R states and the Bohr effect
  11. Determining Protein Structure — X-ray crystallography, NMR and cryo-electron microscopy
  12. Protein Misfolding and Aggregation — Amyloid fibrils, prions and the chemistry of misfolding disease
  13. How Enzymes Lower Activation Energy — Transition-state stabilisation, proximity and orientation
  14. Catalytic Strategies in Enzymes — General acid-base, covalent and metal-ion catalysis
  15. Serine Proteases: A Mechanism in Detail — Catalytic triad, oxyanion hole and acyl-enzyme intermediate
  16. Michaelis-Menten Kinetics — The enzyme-substrate complex and the steady-state assumption
  17. Interpreting Km, Vmax and kcat — What the kinetic constants reveal about an enzyme
  18. Catalytic Efficiency and the Diffusion Limit — The specificity constant kcat/Km and catalytic perfection
  19. Linearised Kinetic Plots — Lineweaver-Burk and Eadie-Hofstee analysis of enzyme data
  20. Competitive Inhibition — Active-site competition, apparent Km and inhibition constants
  21. Uncompetitive and Mixed Inhibition — Inhibitor binding to ES complexes and effects on Vmax
  22. Irreversible Inhibition and Drug Design — Covalent inactivators, suicide substrates and transition-state analogues
  23. Temperature and pH Effects on Enzymes — Activity optima, ionisation of catalytic groups and denaturation
  24. Coenzymes, Cofactors and Vitamins — Organic and metal helpers that extend enzyme chemistry
  25. Allosteric Enzymes and Feedback Control — Sigmoidal kinetics, effectors and pathway regulation
  26. Covalent Modification and Zymogens — Phosphorylation switches and proteolytic activation
  27. Free Energy in Living Systems — Gibbs energy, open systems and the direction of biochemical change
  28. Standard Biochemical Free Energy — The biochemical standard state, K' and actual Delta G in cells
  29. ATP and Phosphoryl-Group Transfer — Why ATP hydrolysis releases energy and high-energy compounds
  30. Coupled Reactions in Metabolism — Driving unfavourable steps with favourable ones through shared intermediates
  31. Biological Redox and Reduction Potentials — Standard reduction potentials and Delta G from electron transfer
  32. Electron Carriers: NAD, NADP and FAD — Hydride transfer, flavins and reducing power in cells
  33. Principles of Metabolism — Catabolism, anabolism, pathways and control points
  34. Glycolysis: The Investment Phase — Phosphorylation and cleavage of glucose into triose phosphates
  35. Glycolysis: The Payoff Phase — Substrate-level phosphorylation and net ATP and NADH yield
  36. Fates of Pyruvate and Fermentation — Lactate and ethanol fermentation and NAD regeneration
  37. The Pyruvate Dehydrogenase Complex — Oxidative decarboxylation to acetyl-CoA and its coenzymes
  38. The Citric Acid Cycle — Eight steps oxidising acetyl groups to carbon dioxide
  39. Regulating the Citric Acid Cycle — Control enzymes, energy charge and anaplerotic reactions
  40. The Electron Transport Chain — Complexes I to IV, ubiquinone, cytochromes and oxygen
  41. Chemiosmosis and the Proton-Motive Force — Proton gradients, membrane potential and Mitchell's hypothesis
  42. ATP Synthase: A Rotary Machine — Rotational catalysis and the binding-change mechanism
  43. Oxidative Phosphorylation Yield and Uncoupling — P/O ratios, total ATP per glucose and thermogenesis
  44. Gluconeogenesis — Bypassing irreversible glycolytic steps to make glucose
  45. Glycogen Synthesis and Breakdown — Glycogen phosphorylase, glycogen synthase and reciprocal control
  46. Fatty Acid Beta-Oxidation — Activation, carnitine transport and repeated two-carbon removal
  47. Fatty Acid Synthesis — Malonyl-CoA, fatty acid synthase and NADPH use
  48. Amino Acid Catabolism and the Urea Cycle — Transamination, deamination and nitrogen excretion
  49. Integration and Hormonal Control of Metabolism — Insulin, glucagon, fed and fasting states across tissues
  50. Biochemistry: Unit Review — Connecting protein structure, enzyme catalysis, metabolism and bioenergetics