Protein & Enzyme Sim

✓ REAL — trust these

• HL (B1.2.9) Proteins are chains of amino acids folded into shapes pinned by weak interactions between R-groups: hydrogen bonds, ionic bonds, hydrophobic cores — plus covalent disulfide bonds between cysteines. SL needs only that heat and pH change the shape.
• Heat → more kinetic energy → faster collisions and reactions, until vibration breaks the weak intramolecular bonds: denaturation. Peptide bonds and the sequence survive. Heat damage is usually permanent.
• pH changes the charges on acidic (–COO⁻) and basic (–NH₃⁺) R-groups, breaking or re-making ionic bonds. Mild shifts can be reversible; extremes are not.
• Hydrolysis consumes water; condensation releases it — watch the blue droplets.
• In the Chemical view, the linkage geometry is the real thing: α-1,4 in maltose and starch, α-1,6 at branch points, β-1,4 in cellulose with every second glucose inverted, peptide bonds between amino acids, ester bonds in lipids.
• Cellulose is not digested here — amylase’s active site cannot bind β-1,4 chains, and humans make no cellulase. Amylase also stalls at branch points (limit dextrin) — debranching enzymes exist, but not in this beaker.
• A competitive inhibitor resembles the substrate’s shape, blocks the active site, and is not changed.
• Optima are protein-specific: these enzymes like ~37 °C and pH 7; pepsin’s optimum is stomach acid, pH ≈ 1.5.
• Substrates do not denature: denaturation is a protein word — sugars have no tertiary structure held by weak bonds, so heat and pH leave them intact here. (Real hot strong acid does slowly hydrolyse starch — that is how glucose syrup was first made — but it takes hours, so it is omitted.)
• The thresholds are literature-anchored: the ionic bond fails below pH ≈ 4 (carboxyl pKa ≈ 4, –COO⁻ gains H⁺) or above pH ≈ 10.5 (lysine pKa ≈ 10.5, –NH₃⁺ loses H⁺); the hydrogen-bond network fails below ~pH 3 and above ~pH 11–12.5; typical mesophilic enzymes unfold between ~48 and 65 °C (salivary amylase and egg albumin both fail near 60 °C). Disulfides survive heat — but sustained strong alkali (pH ≳ 13) destroys even them, slowly.
• Enzymes are reused, never used up — watch the reaction counter.