Mechanisms of Enzymes Flashcards Preview

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Flashcards in Mechanisms of Enzymes Deck (22):
1

2 common types of nucleophilic substitution

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

2

Cleavage reactions

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

3

Oxidation-reduction reactions

Transfer of electrons from one species to another

4

How catalysts increase the rate of a reaction

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

5

How enzymes act as catalysts

Bring reactants closer together
Stabilize transition state

6

Composition of active sites

Polar amino acid residues

7

Acid-base catalysis

Electron transfer catalyzes reaction

8

Covalent catalysis

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

9

pH dependence of catalysis

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

10

Rate of diffusion

Upper limit of reaction rates
Approximately 10^8- 10^9 M^-1 s^-1

11

Triose phosphate isomerase

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

12

Superoxide dismutase

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

13

Proximity effect

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

14

Transition-state stabilization

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

15

Strength of substrate-enzyme binding

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

16

Induced fit

Enzymes can fit to accommodate substrates (within reason)
Activation of an enzyme by a substrate-initiated conformational change

17

Transition state analogs

Stable compounds whose structures resemble transition states
Inhibitors of enzyme

18

Zymogens

Inactive precursors of enzymes
Hydrolyzed to become activated

19

Serine proteases

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

20

Chymotrypsin

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)

21

Trypsin

Type of serine protease
Basic amino acids fit in its binding pocket

22

Elastase

Type of serine protease
Alanine fits in its binding pocket