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Enzyme Regulation
Uni of Notts, Structure, function, & analysis of Proteins, year 2, topics 8-9
| Term | Definition |
|---|---|
| Why fine-control enzyme regulation is needed | Expression/degradation are slow & inflexible, so rapid control uses allostery, proteolysis, or covalent modification to alter activity quickly |
| Proteolytic activation | Irreversible activation of zymogens by peptide cleavage, causing active-site formation |
| Proteolytic cascades in blood clotting | Each activated protease activates more enzymes, allowing rapid amplification of clot formation |
| Why allosteric enzymes don't follow Michaelis–Menten kinetics | Multiple subunit interactions & conformational changes from multiple active & allosteric sites produce cooperative, sigmoidal behaviour (S-shaped graph rather than hyperbola) |
| How CTP is a non-competitive inhibitor of aspartate transcarbamoylase (ATCase) | CTP differs structurally from the substrate, so it binds an allosteric rather than active site |
| How phosphorylation PTM regulates enzymes | Adds negative charges & hydrogen-bonding capacity, altering structure & interactions |
| How cyclin dependent kinases (CDKs) are regulated by phosphorylation | CDK activation require phosphorylation at activation sites but not inhibitory sites, integrating kinase/phosphatase & cyclin signals |
| How binding energy accelerates catalysis | Enzymes stabilise the transition state, lowering activation free energy & increasing reaction rate |
| Induced fit enzyme catalysis | Substrate binding distorts the substrate &/or enzyme into a transition-state-like conformation optimal for catalysis |
| Serine proteases | Hydrolyse peptide bonds via attack on a peptide carbonyl group using a deprotonated serine residue |
| Experimental of catalytic Ser195 in chymotrypsin | Organophosphates modified Ser195 & completely abolished enzyme activity |
| Serine protease catalytic triad | Serine, histidine, & aspartate. Histidine deprotonates serine, aspartate stabilises histidine & serine forms a tetrahedral oxyanion for nucleophilic attack on peptide bonds |
| Oxyanion hole | A positively stabilised pocket that stabilises the negatively charged tetrahedral intermediate during catalysis |
| Serine protease mode of action | Attacks carbonyl group in peptide bond of substrate forcing the carbonyl into a tetrahedral intermediate, breaking double bond characteristics then fully binding the acyl group to the enzyme & releasing the N-terminal side |
| Acyl-enzyme intermediate | covalent enzyme–substrate intermediate remaining after the amine product leaves the active site during proteolysis. Can be hydrolysed away |
| How serine protease substrate specificities differ *examples* | Chymotrypsin cleaves aromatic residues, trypsin cleaves basic residues, elastase cleaves small hydrophobic residues (e.g., alanine) |
| How type II restriction endonucleases cleave DNA | Using Mg²⁺-dependent catalysis to hydrolyse phosphodiester bonds without covalent intermediates |
| Why chemical catalysis alone can’t explain enzyme efficiency | Enzymes achieve much greater rate enhancement through substrate binding & transition-state stabilisation |
| How many weak interactions contribute to enzyme specificity | Multiple hydrogen bonds, ionic interactions, & hydrophobic contacts collectively create strong, specific binding |
| How binding energy compensates for unfavourable reactions | Favourable enzyme–substrate interactions offset energetic costs during catalysis |
| How entropy contributes to enzyme binding *example* | Displacement of ordered water molecules increases entropy, making binding more energetically favourable |
| Why hydrophobic interactions are energetically favourable in proteins | Burying hydrophobic surfaces releases ordered water molecules into bulk solvent, increasing entropy & forms better contact with transition state |
| Why enzymes bind the transition state more tightly than the substrate | Tight transition-state binding preferentially lowers activation energy by optimally aligning catalytic groups with the substrate & accelerates the reaction |
Created by:
Denny12
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