Enzyme Mechanisms C483 Spring 2013 Questions 1. Replacement of the amino acid ________ at or near an active site of an enzyme is more likely to change enzyme activity than the replacement of ________ at or near the active site.
A) histidine; leucine B) leucine; histidine C) leucine; isoleucine D) histidine; aspartate 2. The following pH dependence was found for the activity of a certain enzymecatalyzed reaction. If it is known that the only two ionizable residues in the active site are both glutamates, which conclusion can be drawn? A) The glutamates have different microenvironments which cause their pKa's to
differ. B) One of the glutamates must be amidated. C) Both glutamates have a pKa equal to 5.0. D) Both glutamates are deprotonated during the reaction. 3. An update of Fischer's lock-and-key theory of enzyme specificity views the ________ as the lock and ________ as the key.
A) enzyme; substrate B) substrate; enzyme C) enzyme; transition state D) transition state; enzyme E) substrate; transition state 4. One reason the proximity effect enhances catalysis is because A) the effective molarity of reactive substrate groups increases.
B) the enzyme changes conformation to more readily accept the substrate as it approaches the active site. C) the active site becomes smaller. D) the catalytic triad in the active site becomes more flexible. Mechanisms Four major mechanismsany or all may be
used in a given enzyme Binding Mechanisms Proximity effect Transition State Stabilization Chemical Mechanisms Acid-base catalysis
Covalent Catalysis Binding Energy Binding based on intermolecular forces Lock and Key
Selectivity Rate Enhancement Effective concentration Entropy trap Productive orientation of two molecules
in the active site Effective Molarity May be higher than actual molarity
possibility Entropic help Induced Fit Lock and Key too simplistic
Enzymes are actually somewhat flexible Substrate specificity comes at catalytic price kcat = 103 per second, but worth cost
Lowering Activation Energy Transition state stabilization is half the story Weak Binding of Substrate Substrate
binding: too much of a good thing Thermodynamic pit KM ~ 10-4 M Can be 10-6 M for
cofactors Transition State Binding Transition State Analogs Actually, high energy intermediate analog
Designing a Transition State Analog Binding of Transition State Analog Binding Catalysis and Some sidechains occur
often in active site From previous slide, polar and charged amino acids make specific contacts Charge/charge, H-bond, etc
Chemical Catalysis The same sidechains that bind can ofter conduct proton transfers Acid-Base Catalysis
General Acid-Base Catalysis H+ and HO- are specific acid/base and depend on pH Amino acid sidechains are general acid-base, and can conduct reactions inside active site pocket that arent possible in solution
Covalent Catalysis Active site nucleophile Group transfer reaction pH affects Enzyme Catalysis
Propose possible explanations of pH profile Case Study: Diffusion Controlled Enzymes Triose Phosphate Isomerase
Mechanism Be able to explain catalytic function of AA in each step of a mechanism Superoxide Dismutase:
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