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Enzyme kinetics
Uni of Notts, Structure Function & Analysis of Proteins, year 2, topic 6
| Term | Definition |
|---|---|
| Chemotrophs | Organisms that obtain energy by oxidising electron donors to drive biochemical processes |
| How cells drive endergonic reactions | By coupling them to energetically favourable reactions (e.g. ion gradients or ATP hydrolysis) |
| How Gibbs free energy is determined in biological systems | Relative reactant concentrations & intrinsic ΔG values from thermodynamic data |
| Relationship between activation energy and reaction rate | Higher activation energy leads to slower reaction rates |
| Transition state energy coordinate (+detail about activation energy) | The highest energy point along the reaction coordinate. Difference between this & reactants is value of activation energy |
| How enzymes affect transition state | Stabilise it, lowering activation energy & increasing reaction rate |
| Why transition states are hard to study | They're extremely short-lived and unstable |
| Example of a high-energy transition state *no need to memorise* | Lysozyme creates a transient pentavalent carbon intermediate during catalysis. Exceptionally high energy intermediate |
| Acid-base catalysis | Proton donation/removal stabilises partial charges to lower enthalpy & favour 1 state over others |
| Electrostatic catalysis | Stabilisation of charged intermediates using charged residues or metal ions, usually for coordination |
| Covalent catalysis | Enzyme forms temporary weak covalent bond using a reactive group with substrate to facilitate reaction to maximise proximity & bond extension to favour transition states |
| Transition state theory | Reacting molecules must pass through an intermediate state before completion. Describes relationship between activation energy & reaction rate via formation of activated complex |
| Eyring equation | Quantifies relationship between rate constant & activation energy: A + B --> C A + B <-> AB‡ --> C K = [C]/[A][B] K‡ = [AB‡]/[A][B] K‡ = Thermodynamic equilibrium constant of "‡" |
| Enzyme kinetics | Study of reaction rates & how they change with substrate concentration over time |
| How initial rate (V0) is determined | Early linear portion of product vs time curve |
| Shape of V₀ vs substrate concentration curve | Hyperbolic due to enzyme saturation at high [S] & vice versa |
| Michalis-Menten equation + association constant equations (explanation & equation) | V₀ = (Vmax × [S]) / (Km + [S]) E + S <--K1, K-1 --> ES <-- K2, K-2 --> E + P (k2 isn't common) Ka = k1/k-1 Steady state formula: [ES] = [E][S](k1/k-1k2) |
| Km | Substrate concentration at which velocity is half of Vmax |
| Vmax | Maximum processivity of enzyme at substrate saturating concentration |
| What Km indicates about enzyme affinity | Lower Km = higher affinity; reflects both binding & catalytic rates |
| Kcat | Turnover number; number of substrate molecules converted per enzyme per second (/s-1). Even though enzymes decrease free energy requirements, there's still an energy barrier |
| Specificity constant (kcat/Km) | Measure of catalytic efficiency; approaches has a maximum upper limit (~10⁸–10⁹ M⁻¹s⁻¹) which is the limit of diffusion |
| Lineweaver-Burk equation *don't need to remember equation, just what it looks like* | Linear transformation of Michaelis-Menten to determine kinetic parameters Km & Vmax V-1 = KM/VMax x [S]-1 + Vmax-1 |
| How competitive & non-competitive inhibitors affect kinetics | Competitive: Increase Km but do not change Vmax Non-competitive: Decrease Vmax without changing Km |
| Proximity & orientation catalysis | Increases entropy by binding reactants & bringing them together in correct orientation. Raises effective concentration by treating reaction as a single molecule. Enzymes take entropy loss |
Created by:
Denny12