Lecture 3: Enzyme Kinetics: Catalytic Properties of Enzymes

1. Lecture 3: Enzyme Kinetics: Catalytic Properties of Enzymes

2. What is a catalyst? • A catalyst accelerates a chemical reaction • It participates in the reaction but is not consumed, meaning that is must return to its original state after the chemical reaction has been catalyzed. • A catalyst can be a simple inorganic compound or a biological macromolecule called an “enzyme” (most often protein, but also can by RNA).

3. Catalysts, in particular, enzymes are capable of astonishing rate enhancements What sort of rate acceleration can catalysts provide? Consider the reaction: Relative rate Uncatalyzed: 1 Pt Black (inorganic catalyst): 10,000 catalase (enzyme): 300,000,000,000

4. Activation Energy Catalysts work by stabilizing the transition state of a chemical reaction, which lowers the activation energy of the reaction How do catalysts work?

5. Eact Relative Rate No Catalyst 18 kcal/mol 1 Pt black 12 kcal/mol 1X104 Catalase 2 kcal/mol 3X1011 A small reduction in activation energy results in a huge increase in the reaction rate. The rate of a chemical reaction is an exponential function of activation energy

6. ATP hydrolysis as an example

7. Does an enzyme only catalyze the forward reaction? NO! Why not? Because the free energy difference between reactants and products of a reaction and the starting concentration of each determines the direction (more on this later).

8. Catalysts DO NOT alter the final equilibrium distribution of reactants and products in a chemical reaction, they merely reduce the amount of time required to attain the equilibrium distribution.

9. How do enzymes do the amazing things they do? • Biological enzymes have evolved to form complex three-dimensional structures that present an “active site” surface to which reactants in a chemical reaction bind. • These sites also position amino acid R-groups and/or reaction cofactors (such as metals) or prosthetic groups at the appropriate positions to aid in catalysis. • Two major models for how this might work on the structural level are shown on the next slide.

10. Two models for ES complex

11. Lets take a look at a real active site! ATP Mg(2+)

12. Summary of major properties of enzymes

13. [P] [S] time time Accumulation of product over time (D[P]/Dt) Loss of substrate over time (D[P]/Dt) How does one measure enzyme activity?

14. 2 x [enzyme] D[P]/Dt = 2 0.5 x [enzyme] D[P]/Dt = 0.5 How does [enzyme] influence observed reaction velocity? 1 x [enzyme] D[P]/Dt = 1 [P] Assumes that [E] is limiting and that the uncatalyzed reaction rate is ~0 time

15. Specificity of enzymes How specific are enzymes for a given substrate? • The answer depends upon the enzyme you’re talking about. Most enzymes are highly specific, acting on only a small number of substrates that are highly similar in structure. Others, such as alkaline phosphatase mentioned in your notes, are less specific. • Specificity arises from structural and chemical complementarity between the substrate and its enzyme.

16. Specificity of enzymes (an example) Hydrogen Bonds Gln with Adenine Mg (2+) Ionic Bonds Asp with Mg(2+), Lys with Phosphates

17. Metals, coenzymes, and prosthetics groups Many enzymes bind non-protein cellular components that are used as key factors in the enzyme activity. These fall into three basic categories: (1) Metals: Metals (e.g. Mg, Ca, Zn, Fe etc.) are thought to be bound to ~1/3 of all proteins and can play key roles in activity. An example is the Mg(2+) in the ATPase on the previous slide. These ions can confer a wider array of chemical properties to proteins over those of the 20 natural amino acids.

18. Metals, cofactors, and prosthetics groups (2 & 3) Coenzymes and prosthetic groups: Low-molecular organic compounds that bind either weakly (coenzymes) or tightly (prosthetic groups) to the protein. Examples that you will see in this course include, for example, iron-sulfur clusters, heme, and coenzyme A.