20 standard amino acids classified by side chain (R group) properties. Nonpolar (hydrophobic): Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Methionine. Located in protein interior (buried from water). Polar uncharged: Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine. Side chains can H-bond with water. Acidic (negatively charged at pH 7): Aspartic acid (D), Glutamic acid (E). pKa of side chain ~3.7 and 4.1 respectively. Fully ionised (-COO-) at physiological pH. Basic (positively charged at pH 7): Lysine (K), Arginine (R), Histidine (H). Side chains carry positive charge at physiological pH. Essential amino acids (cannot be synthesised, must be obtained from diet): Valine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Histidine (9 essential in adults). Conditionally essential: Arginine, Cysteine, Tyrosine, Glutamine, Glycine, Proline (essential under certain conditions).

Lysine (K): side chain = -(CH2)4-NH2. pKa of epsilon-NH3+ = 10.5. At pH 7.4: protonated (+1 charge). pI = 9.74. Found in: histones (interact with DNA phosphate groups), collagen (cross-linking by lysyl oxidase), active sites of many enzymes. Deficient in cereal proteins (wheat, rice) - lysine is first limiting amino acid in vegetarian diet. Supplemented in animal feed. Arginine (R): side chain = -(CH2)3-NH-C(=NH)-NH2 (guanidinium group). pKa ~12.5. Strongest basic amino acid. At pH 7.4: +1 charge. pI = 10.76. Role: precursor of nitric oxide (NO) via nitric oxide synthase (NOS). Important in urea cycle (argininosuccinate → arginine → urea + ornithine). Histidine (H): side chain = imidazole ring. pKa ~6.0. Partially protonated at pH 7.4 (unique buffering ability near physiological pH). pI = 7.59. Critical in enzyme catalysis: acts as acid/base catalyst (proton shuttle). Found in active site of serine proteases (catalytic triad: Ser, His, Asp), haemoglobin (Bohr effect).

Primary structure: sequence of amino acids (peptide bonds). Peptide bond: CO-NH bond formed between carboxyl of one aa and amino group of next, with loss of water. Peptide bond is planar (partial double bond character), trans configuration. Secondary structure: local regular structures. Alpha helix: right-handed, H-bonds between C=O of residue n and N-H of residue n+4. 3.6 residues per turn. Pitch 5.4 Angstrom. R groups pointing outward. Beta sheet: extended strands H-bonded laterally. Parallel (strands same direction) or antiparallel. Tertiary structure: overall 3D shape. Stabilised by: H-bonds, hydrophobic interactions (most important), ionic bonds (salt bridges), disulfide bonds (covalent, between Cys residues). Quaternary structure: multiple polypeptide subunits. Haemoglobin: 2 alpha + 2 beta subunits. Collagen: triple helix of 3 polypeptides. Protein denaturation: disruption of secondary/tertiary/quaternary structure. Heat, acid/base, urea, detergents.

Enzymes: biological catalysts (mostly proteins; some RNA = ribozymes). Increase rate of reaction by lowering activation energy (Ea). Highly specific (substrate specificity). Active site: region where substrate binds and reaction occurs. Lock and key model (Fischer, 1894): rigid complementarity between enzyme and substrate. Induced fit model (Koshland, 1958): enzyme changes conformation when substrate binds - better explains enzyme flexibility and allosteric regulation. Michaelis-Menten kinetics: v = Vmax[S]/(Km + [S]). Km = substrate concentration at half-Vmax. Low Km = high affinity. Vmax = maximum rate when all enzyme saturated. Lineweaver-Burk plot (double reciprocal): 1/v vs 1/[S]. Competitive inhibition: inhibitor resembles substrate, competes for active site. Increases apparent Km, Vmax unchanged. Non-competitive: inhibitor binds elsewhere (allosteric site), reduces Vmax, Km unchanged. Mixed inhibition: changes both Km and Vmax.

Structural proteins: collagen (most abundant protein in body, triple helix, bone/tendon/skin), keratin (hair, nails, skin), elastin (elastic tissues, lungs, blood vessels), actin and myosin (muscle). Transport proteins: haemoglobin (O2 transport, 2 alpha + 2 beta subunits), myoglobin (O2 storage in muscle), albumin (blood, transports fatty acids, bilirubin, drugs), transferrin (iron transport), ceruloplasmin (copper). Regulatory proteins: hormones (insulin, glucagon, growth hormone - all proteins), transcription factors. Immunological: antibodies (immunoglobulins), complement proteins. Enzymes: catalysts (discussed above). Receptor proteins: on cell membranes or intracellular. Signal transduction. Motor proteins: myosin (muscle contraction), dynein (cilia, flagella, mitosis), kinesin (anterograde transport along microtubules). Channel/transporter proteins: ion channels, Na+/K+ ATPase, GLUT transporters.

DNA: deoxyribonucleic acid. Sugar = deoxyribose. Bases: A, T, G, C. Double-stranded helix (usually). Carries genetic information. Relatively stable. RNA: ribonucleic acid. Sugar = ribose (has 2-OH). Bases: A, U, G, C (uracil instead of thymine). Usually single-stranded. Less stable than DNA (2-OH makes RNA susceptible to hydrolysis). Types: mRNA (template for translation), tRNA (adaptor), rRNA (ribosome component), snRNA (splicing), miRNA (gene regulation), lncRNA (gene regulation). Nucleotide: base + sugar + phosphate(s). ATP (adenosine triphosphate): energy currency of cell. Hydrolysis of terminal phosphate releases ~30.5 kJ/mol. NAD+, FAD: electron carriers in metabolism. cAMP, cGMP: second messengers. Nucleotides also in coenzymes (CoA contains ADP).

Lipids: diverse group of biomolecules, insoluble in water, soluble in organic solvents. Fatty acids: long hydrocarbon chains with terminal -COOH. Saturated: no double bonds (palmitic C16:0, stearic C18:0). Unsaturated: one or more double bonds. Monounsaturated (oleic acid C18:1, omega-9). Polyunsaturated (linoleic C18:2 omega-6, linolenic C18:3 omega-3, EPA, DHA). Triglycerides: 3 fatty acids + glycerol. Storage form of energy. Energy dense: 9 kcal/g (vs 4 kcal/g for carbs/proteins). Phospholipids: 2 fatty acids + glycerol + phosphate + head group. Amphipathic. Major component of cell membranes. Steroids: cholesterol (membrane component, steroid hormone precursor), bile acids, steroid hormones (cortisol, testosterone, estrogen). Fat-soluble vitamins: A, D, E, K. Eicosanoids: prostaglandins, leukotrienes, thromboxanes (from arachidonic acid). Inflammatory mediators.

Glycolysis: cytoplasm. Glucose (C6) to 2 pyruvate (C3). Net yield: 2 ATP + 2 NADH. 10 steps. Key enzymes: hexokinase, PFK-1 (rate-limiting), pyruvate kinase. Pyruvate decarboxylation: pyruvate to acetyl-CoA + CO2 + NADH. Pyruvate dehydrogenase complex (PDC). Citric acid (Krebs) cycle: mitochondrial matrix. Acetyl-CoA (C2) + oxaloacetate (C4) to citrate (C6) to... per turn: 3 NADH + 1 FADH2 + 1 GTP + 2 CO2. Oxidative phosphorylation: electron transport chain in inner mitochondrial membrane. NADH and FADH2 oxidised. Electrons pass through complexes I-IV. Proton gradient drives ATP synthase (Complex V). Total ATP from 1 glucose: ~30-32 ATP. Pentose phosphate pathway: alternative glucose metabolism. Produces ribose-5-phosphate (nucleotide synthesis) and NADPH (reductive biosynthesis, antioxidant). Gluconeogenesis: glucose synthesis from non-carbohydrate precursors (pyruvate, lactate, glucogenic amino acids, glycerol). In liver and kidney. Regulated by insulin (inhibits) and glucagon (stimulates).