Mechanisms of Enzymes

Question 1

2 common types of nucleophilic substitution

Answer 1

Those that proceed through tetrahedral intermediate transition state (ex- nucleophilic acyl substitution)
Those that proceed through pentavalent transition state (ex- SN2)

Question 2

Cleavage reactions

Answer 2

Breaking covalent bonds
Homolytic breakage: radicals result
Heterolytic breakage: ions result

Question 3

Oxidation-reduction reactions

Answer 3

Transfer of electrons from one species to another

Question 4

How catalysts increase the rate of a reaction

Answer 4

Decreasing the activation energy (EA) relative to the uncatalyzed reaction

Question 5

How enzymes act as catalysts

Answer 5

Bring reactants closer together

Stabilize transition state

Question 6

Composition of active sites

Answer 6

Polar amino acid residues

Question 7

Acid-base catalysis

Answer 7

Electron transfer catalyzes reaction

Question 8

Covalent catalysis

Answer 8

Substrates are covalently bound to an enzyme, forming a reactive intermediate

Question 9

pH dependence of catalysis

Answer 9

Ionizable amino acid residues in active site can be affected by pH
Most enzymes have an optimal pH range

Question 10

Rate of diffusion

Answer 10

Upper limit of reaction rates

Approximately 10^8- 10^9 M^-1 s^-1

Question 11

Triose phosphate isomerase

Answer 11

Catalyzes interconversion of dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P)
All 4 kinetic steps of catalyzed reaction are similar in energy

Question 12

Superoxide dismutase

Answer 12

Catalyzes degradation of superoxide (fast and efficient reaction)
Rate accelerated by cationic residues lining active site, an electrostatic effect

Question 13

Proximity effect

Answer 13

Correct positioning of substrates in bimolecular reactions raises the effective concentration (concentration in localized area) and decreases entropy, which increases reaction rate

Question 14

Transition-state stabilization

Answer 14

Process of distorting or straining a substrate towards the reaction’s transition state conformation
Enzymes have a higher affinity for transition states than substrates or products

Question 15

Strength of substrate-enzyme binding

Answer 15

Substrates don’t bind enzymes tightly (if they did, there would be a thermodynamic pit in the reaction coordinate)

Question 16

Induced fit

Answer 16

Enzymes can fit to accommodate substrates (within reason)

Activation of an enzyme by a substrate-initiated conformational change

Question 17

Transition state analogs

Answer 17

Stable compounds whose structures resemble transition states

Inhibitors of enzyme

Question 18

Zymogens

Answer 18

Inactive precursors of enzymes

Hydrolyzed to become activated

Question 19

Serine proteases

Answer 19

Enzymes that cleave peptide bonds on C-terminal sides of particular amino acids and have serine residues in their active sites

Question 20

Chymotrypsin

Answer 20

Type of serine protease
Aromatic amino acids fit in its binding pocket
3 catalytic residues: His-57, Asp-102, Ser-195 (collectively called the catalytic triad)

Question 21

Trypsin

Answer 21

Type of serine protease

Basic amino acids fit in its binding pocket

Question 22

Elastase

Answer 22

Type of serine protease

Alanine fits in its binding pocket