Chapter 6 Enzymes

Part 1: Classes of Enzymes & Identifying from Pictures

For short answer and matching questions, know the 6 main classes of enzymes and the visual cues to identify them from reaction diagrams:

  1. Oxidoreductases: Catalyze oxidation-reduction reactions (transfer of electrons, hydride ions, or H atoms).

    • Picture Clue: Look for coenzymes like NAD+ / NADH or FAD / FADH2​ being added or produced.

  2. Transferases: Catalyze group transfer reactions from one molecule to another.

    • Picture Clue: Look for ATP becoming ADP (a kinase transferring a phosphate) or an amino group moving from one molecule to another.

  3. Hydrolases: Catalyze hydrolysis reactions, breaking bonds by adding water.

    • Picture Clue: Look for H2​O as a reactant that cuts a single large molecule into two smaller ones (e.g., breaking a peptide bond).

  4. Lyases: Add groups to double bonds, or form double bonds by removing groups.

    • Picture Clue: Look for a double bond (C=C) appearing in the product or disappearing from the reactant, often involving the addition/removal of H2​O, CO2​, or NH3​.

  5. Isomerases: Transfer groups within a single molecule to yield isomeric forms.

    • Picture Clue: Look for a reaction with exactly one substrate and one product, where the atoms have just been rearranged.

  6. Ligases: Catalyze the bonding together of two substrate molecules.

    • Picture Clue: Look for two molecules joining together coupled with the cleavage of ATP to ADP to supply energy for the unfavorable reaction.

Part 2: Enzyme Kinetics, Rates, & Steady State

  • Rates of Reaction: The rate can be expressed as either the rate of disappearance of reactants (−Δ[A]/Δt) or the rate of appearance of products (Δ[P]/Δt).

  • Formation and Breakdown: In the Michaelis-Menten model, the enzyme (E) and substrate (S) bind to form an enzyme-substrate complex (ES). The rate of formation relies on the constant k1​, while the breakdown of the complex (either back to E+S or forward to product P) relies on k−1​ and k2​.

  • Steady State: This is the condition where the concentration of the [ES] complex remains constant over time. It is reached when the rate of [ES] formation exactly equals the rate of its breakdown.

  • Binding Affinity and KM​: The Michaelis constant (KM​) is an inverse measure of affinity. If KM​ is high, the binding affinity is low (meaning it takes a lot of substrate to get the enzyme working at half its maximum speed). If KM​ is low, affinity is high.

Part 3: Graphs, pH, and Amino Acids

  • Differing pHs in Graphs: Enzymes have optimal pH levels. On a graph of Reaction Velocity vs. pH, you will see bell-shaped curves. For example, Pepsin (a stomach enzyme) peaks at a highly acidic pH of ~1.5. Glucose 6-phosphatase peaks at a slightly basic pH of ~7.8.

  • Amino Acids and pKas: Enzyme active sites contain specific amino acid residues (like Glu, Asp, Lys, Arg, His, Cys, Ser, Tyr) that act as proton donors (acids) or proton acceptors (bases).

  • Awareness of pH Change: Changes in pH alter the protonation state (pKa) of these amino acid side chains. If the pH changes significantly from the optimum, the active site loses its proper charge/shape, and the enzyme cannot catalyze the reaction.

Part 4: Lineweaver-Burk Plots (Interpreting the Data)

Straight lines (Lineweaver-Burk double reciprocal plots) help us calculate exact values for Vmax​ and KM​ and determine the type of inhibition.

  • The Straight Line: Plots 1/V on the y-axis vs. 1/[S] on the x-axis. The y-intercept is 1/Vmax​ and the x-intercept is −1/KM​.

  • Competitive Inhibition:

    • The inhibitor competes for the active site.

    • Graph: The lines cross at the same y-point (Y-intercept). This means Vmax​ is unchanged.

    • Data Interpretation: As inhibitor concentration increases, the KM​ also changes (increases), shifting the x-intercept closer to zero. This shows apparent lower binding affinity.

  • Non-Competitive Inhibition:

    • The inhibitor binds to an allosteric site (a site other than the active site), distorting the active site. The substrate can bind, but no product is formed.

    • Graph: The lines cross at different y-points (meaning Vmax​ decreases) but intersect at the same x-point (KM​ stays relatively the same).

Part 5: Enzyme Regulation

Enzymes are regulated in five different ways to ensure reactions only happen when needed:

  1. Feedback Control: The product of a reaction pathway acts as an inhibitor to an enzyme earlier in the pathway, shutting it down when enough product is made.

  2. Allosteric Control: An activator or inhibitor binds to an allosteric site (a location other than the active site). This binding alters the shape of the active site to either turn the enzyme on or off.

  3. Inhibition: Direct interference by a molecule (competitive, non-competitive, uncompetitive, or irreversible) that slows the reaction rate.

  4. Covalent Modification: The enzyme is activated or deactivated by the making or breaking of a chemical bond. This includes removing a part of the protein sequence (like clipping a zymogen/proenzyme to make it active) or adding a phosphate group (phosphorylation).

  5. Genetic Control: Regulating the synthesis of the enzymes at the DNA level. Hormones can accelerate or decelerate how many enzyme molecules the cell actually builds.