Biochemistry

Proteins: the amino acid sequence (primary structure) determines folding. Secondary structures (α-helix, β-sheet) are held by backbone hydrogen bonds. Tertiary and quaternary structure depend on side-chain interactions. Nucleic acids, carbohydrates, and lipids each have structural features that match their jobs. For example, amphipathic phospholipids form bilayers.

Know which bonds are covalent (peptide, glycosidic, phosphodiester, ester) and which interactions are noncovalent (hydrogen bonds, ionic, hydrophobic, van der Waals). Denaturation disrupts noncovalent interactions and some disulfide bonds, but it does not break peptide bonds.

Enzymes lower activation energy. They do not change ΔG or the equilibrium constant. On a Michaelis–Menten curve, Vmax is the plateau and Km is the substrate concentration at ½Vmax. A lower Km generally means higher apparent affinity.

Competitive inhibitors raise the apparent Km, and Vmax is unchanged (enough substrate outcompetes them). Pure noncompetitive inhibitors lower Vmax and leave Km unchanged. Uncompetitive inhibitors lower both. Allosteric regulation and feedback inhibition control flow through pathways.

ΔG = ΔH − TΔS. Reactions with negative ΔG are spontaneous, but that says nothing about their speed. Cells couple unfavorable reactions to ATP hydrolysis or to ion gradients.

Redox thinking is central: NADH and FADH₂ carry electrons from fuel molecules to the electron transport chain.

Glycolysis (cytosol) → pyruvate oxidation → citric acid cycle (mitochondrial matrix) → electron transport chain (inner membrane). The chain pumps protons to build a gradient, and ATP synthase uses that gradient to make ATP. O₂ is the final electron acceptor.

Uncouplers make the inner membrane leaky to protons. Electron transport and O₂ use continue or speed up, but ATP synthesis falls and the energy is released as heat. Inhibitors of the chain stop both O₂ consumption and ATP synthesis. Without O₂, fermentation regenerates NAD⁺ so glycolysis can continue.

Light reactions (thylakoid membranes) split water, release O₂, and produce ATP and NADPH. The Calvin cycle (stroma) uses ATP and NADPH to fix CO₂ through rubisco.

C₄ and CAM plants reduce photorespiration by concentrating CO₂. C₄ plants separate the steps in space (mesophyll and bundle-sheath cells). CAM plants separate them in time (night and day).