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Flashcards in Mechanisms of Enzymes Deck (22)
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1
Q

2 common types of nucleophilic substitution

A

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

2
Q

Cleavage reactions

A

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

3
Q

Oxidation-reduction reactions

A

Transfer of electrons from one species to another

4
Q

How catalysts increase the rate of a reaction

A

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

5
Q

How enzymes act as catalysts

A

Bring reactants closer together

Stabilize transition state

6
Q

Composition of active sites

A

Polar amino acid residues

7
Q

Acid-base catalysis

A

Electron transfer catalyzes reaction

8
Q

Covalent catalysis

A

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

9
Q

pH dependence of catalysis

A

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

10
Q

Rate of diffusion

A

Upper limit of reaction rates

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

11
Q

Triose phosphate isomerase

A

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

12
Q

Superoxide dismutase

A

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

13
Q

Proximity effect

A

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

14
Q

Transition-state stabilization

A

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
Q

Strength of substrate-enzyme binding

A

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

16
Q

Induced fit

A

Enzymes can fit to accommodate substrates (within reason)

Activation of an enzyme by a substrate-initiated conformational change

17
Q

Transition state analogs

A

Stable compounds whose structures resemble transition states

Inhibitors of enzyme

18
Q

Zymogens

A

Inactive precursors of enzymes

Hydrolyzed to become activated

19
Q

Serine proteases

A

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

20
Q

Chymotrypsin

A

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
Q

Trypsin

A

Type of serine protease

Basic amino acids fit in its binding pocket

22
Q

Elastase

A

Type of serine protease

Alanine fits in its binding pocket