🎯 Module Objectives
- Classify the four major biomolecules by structure and function
- Apply Michaelis-Menten kinetics to analyse enzyme activity
- Distinguish competitive, non-competitive and uncompetitive inhibition
- Trace the major metabolic pathways from glucose through to ATP
- Explain fatty acid β-oxidation and its relationship to ketogenesis
- Describe major signal transduction pathways (GPCR, RTK, nuclear receptors)
1. Biomolecules
The four major classes of biological macromolecules are the building blocks of all living systems.
| Biomolecule | Monomers | Key Functions | Examples |
|---|---|---|---|
| Carbohydrates | Monosaccharides (glucose, fructose) | Energy storage and supply; structural roles; cell recognition | Glucose, starch, glycogen, cellulose |
| Lipids | Fatty acids + glycerol | Long-term energy storage; membrane structure; hormone signalling; insulation | Triglycerides, phospholipids, sterols (cholesterol) |
| Proteins | Amino acids (20 standard) | Enzymes; structural support; transport; immunity; cell signalling; movement | Haemoglobin, collagen, insulin, antibodies |
| Nucleic Acids | Nucleotides (base + sugar + phosphate) | Genetic information storage (DNA); gene expression (RNA); energy transfer (ATP) | DNA, mRNA, tRNA, rRNA, ATP |
Protein Structure Levels
- Primary — amino acid sequence (determined by DNA)
- Secondary — local folding: α-helices and β-sheets (via hydrogen bonds)
- Tertiary — overall 3D shape of a single polypeptide (via disulfide bonds, hydrophobic interactions, ionic bonds)
- Quaternary — multiple polypeptide subunits assembled together (e.g., haemoglobin: 4 subunits)
📌 Key Insight — Protein function depends entirely on its 3D shape. Anything that disrupts shape (heat, pH change, chemicals) causes denaturation → loss of function.
2. Enzyme Kinetics
Enzyme Fundamentals
- Enzymes are biological catalysts — proteins (mostly) that speed up reactions by lowering activation energy
- Substrate binds to the enzyme's active site to form an enzyme-substrate complex
- Enzymes are not consumed in the reaction — they are regenerated
- Specificity: one enzyme, one substrate (or class of substrates) — "lock and key" vs "induced fit" model
Michaelis-Menten Kinetics
Describes the relationship between substrate concentration [S] and reaction rate (v):
v = (Vmax × [S]) / (Km + [S])
- Vmax — maximum reaction velocity; reached when all enzyme active sites are saturated
- Km — Michaelis constant; the [S] at which v = ½Vmax. Low Km = high affinity. High Km = low affinity.
- Lineweaver-Burk plot — double reciprocal plot (1/v vs 1/[S]) used to graphically determine Km and Vmax
Types of Enzyme Inhibition
| Inhibition Type | Mechanism | Effect on Km | Effect on Vmax | Reversible? |
|---|---|---|---|---|
| Competitive | Inhibitor binds active site; competes with substrate | ↑ Km | No change | Yes |
| Non-competitive | Inhibitor binds allosteric site; active site still accessible | No change | ↓ Vmax | Yes |
| Uncompetitive | Inhibitor binds only enzyme-substrate complex | ↓ Km | ↓ Vmax | Yes |
| Irreversible | Covalently modifies active site (e.g., aspirin → COX) | N/A | ↓ Vmax | No |
📌 Pharmacology Link — Most drugs work by enzyme or receptor inhibition. Aspirin irreversibly inhibits COX enzymes. Statins competitively inhibit HMG-CoA reductase. ACE inhibitors competitively inhibit angiotensin-converting enzyme.
3. Metabolic Pathways
Carbohydrate Metabolism
- Glycolysis — glucose (6C) → 2 pyruvate (3C); net 2 ATP + 2 NADH; occurs in cytoplasm; anaerobic
- Gluconeogenesis — synthesis of glucose from non-carbohydrate precursors (pyruvate, lactate, amino acids, glycerol); primarily in liver; uses ATP
- Glycogenesis — glucose → glycogen (storage); stimulated by insulin
- Glycogenolysis — glycogen → glucose; stimulated by glucagon/adrenaline
- Pentose Phosphate Pathway — generates NADPH (for reductive biosynthesis and antioxidant defence) and ribose-5-phosphate (for nucleotide synthesis)
Fatty Acid Metabolism
- β-oxidation — fatty acids are broken down 2 carbons at a time in the mitochondrial matrix, generating acetyl-CoA, NADH and FADH₂
- Ketogenesis — excess acetyl-CoA (from high fat/fasting states) → ketone bodies (acetoacetate, β-hydroxybutyrate, acetone). Used by brain/muscle when glucose is scarce.
- Fatty acid synthesis — occurs in cytoplasm; requires NADPH; key enzyme: Acetyl-CoA carboxylase (ACC)
Amino Acid Catabolism
- Transamination — amino group transferred to α-ketoglutarate → glutamate; carbon skeleton enters TCA cycle
- Urea cycle — converts toxic ammonia (from amino acid catabolism) into urea for excretion; occurs in liver
4. Signal Transduction
Cells respond to external signals (hormones, neurotransmitters, growth factors) via receptor-mediated signal transduction pathways.
G Protein-Coupled Receptors (GPCRs)
- Most common receptor type; linked to G proteins (Gs, Gi, Gq)
- Gs pathway: ligand → GPCR → Gs → adenylyl cyclase ↑ → cAMP ↑ → PKA activation → cellular effects
- Gq pathway: ligand → Gq → phospholipase C → IP₃ + DAG → Ca²⁺ release + PKC activation
- Examples: β-adrenergic receptors (adrenaline), muscarinic receptors (acetylcholine), glucagon receptors
Receptor Tyrosine Kinases (RTKs)
- Ligand binding → receptor dimerisation → autophosphorylation → downstream kinase cascades (RAS/MAPK, PI3K/AKT)
- Key in growth, proliferation, differentiation
- Examples: Insulin receptor, EGF receptor, VEGF receptor
- Many cancer drugs target mutated/overexpressed RTKs (e.g., Imatinib targets BCR-ABL)
Nuclear Receptors
- Ligands must be lipid-soluble to cross the plasma membrane (e.g., steroid hormones, thyroid hormones, vitamin D)
- Receptor-ligand complex enters nucleus and acts as a transcription factor → directly regulates gene expression
- Slow onset, long-lasting effects (hours to days)
Knowledge Check
1. How does competitive inhibition affect Km and Vmax?
Competitive inhibition increases Km (apparent decrease in substrate affinity, because inhibitor and substrate compete for the active site) but does NOT change Vmax (can overcome with excess substrate). Think: same maximum speed, but harder to reach half-maximum velocity.
2. Where does fatty acid β-oxidation occur and what does it produce?
β-oxidation occurs in the mitochondrial matrix. It sequentially removes 2-carbon units from fatty acids, producing: Acetyl-CoA (enters Krebs cycle), NADH and FADH₂ (enter electron transport chain). A 16-carbon fatty acid (palmitate) generates 7 acetyl-CoA, 7 NADH, and 7 FADH₂, yielding ~106 ATP total.
3. What is the role of cAMP as a second messenger?
Cyclic AMP (cAMP) is generated from ATP by adenylyl cyclase (activated by Gs-coupled receptors). cAMP activates Protein Kinase A (PKA), which phosphorylates multiple target proteins to produce cellular effects. It is degraded by phosphodiesterases (PDEs). cAMP amplifies the original signal — one hormone molecule can generate thousands of cAMP molecules.
Next: Pharmacy
Biochemistry unlocks Pharmacy — you now understand enzyme kinetics, receptor signalling and metabolic pathways. Apply this to drug mechanisms of action.