enzyme mech and catalysis II

Question 1

enzymes accelerate reaction rates by …

Answer 1

lowering the activation energy barrier, but do not affect reaction equilibria

Question 2

what is the relationship between k and delta G?

Answer 2

k is larger when delta G is smaller

Question 3

nucleophile (Nu:)

Answer 3

electron-rich functional group (nucleus loving) that donates (shares) an electron pair with an electrophile to form a bond

Question 4

electrophile (E)

Answer 4

electron deficient functional group (electron loving) that accepts (shares) an electron pair from a nucleophile to form a bond

Question 5

transition-state stabilization

Answer 5

lowers energy of transition state making it easier to form

Question 6

orientation

Answer 6

arranges atoms for optimal activity

Question 7

desolvation

Answer 7

binding removes interactions with solvent (water)

Question 8

induced fit

Answer 8

substrate binding changes conformation of enzyme

Question 9

acid-base catalysis

Answer 9

push or pull a proton

Question 10

covalent catalysis

Answer 10

adducts or intermediates

Question 11

metal ion catalysis

Answer 11

lewis acids and redox agents

Question 12

why and how can substrates be aligned?

Answer 12

by binding to an enzyme so that nucleophiles are positions for reaction

Question 13

what does substrate binding to an enzyme active site generally exclude or reduce?

Answer 13

the concentration of water in the active site

Question 14

what does a lower dielectric environment do? (desolvation)

Answer 14

increase the strength of electrostatic interactions

Question 15

An AA residue can function …

Answer 15

both as a general acid and general base, depending on whether residue is a protonated-conjugate-acid or a deprotonated-conjugate-base

Question 16

specific acid

Answer 16

H+ really H30+

Question 17

specific base

Answer 17

-OH

Question 18

general acid

Answer 18

proton donor

Question 19

general base

Answer 19

proton acceptor

Question 20

how can a transient covalent bond form?

Answer 20

between enzyme and substrate

Question 21

what does metal ion catalysis depend on?

Answer 21

ability of metal ion to serve as a template, a lewis acid, or a redox reactant

Question 22

what do metal ions do?

Answer 22

bind and orient substrates; shield/stabilize negative charge formed in Transition state; increase acidity of bound water or alcohols; mediate redox reactions

Question 23

chymotrypsin

Answer 23

protease that catalyzes hydrolysis of a aromatic AA peptide bond at C-terminal side

Question 24

steps in each phase (I and II)

Answer 24

1. positioning
2. His57 is General Base
3. Nucleophilic Attack
4. Covalent Intermediate
5. His57 is General Acid

Question 25

what should you know about chymotrypsin?

Answer 25

THE REACTION CYCLE

Question 26

what forms the catalytic triad in chymotrypsin?

Answer 26

Asp-102, His-57, and Ser-195

Question 27

what is step 1 of phase 1 of chymotrypsin reaction?

Answer 27

the catalytic triad forms and asp102 makes his57 a better general base in the first step

Question 28

what is step 2 of phase 1 of chymotrypsin reaction?

Answer 28

his57 acts as a general base to deprotonate the hydroxyl group of ser195 and make it a better nucleophile; ser195 acts as a nucleophile and attacks the carbonyl group forming a covalent bond with the carbonyl carbon=covalent catalysis

Question 29

what is step 3 of phase 1 of chymotrypsin reaction?

Answer 29

in the short-lived intermediate: protonated his57 now acts as a general acid to protonate the amine leaving group; next, the peptide bond is broken and the C-terminal end of polypeptide chain leaves; the acyl enzyme is formed completing the 1st phase of the reaction

Question 30

what is step 4 of phase 2 of chymotrypsin reaction?

Answer 30

water enters the enzyme active site, where the C-terminal end of polypeptide used to be located

Question 31

what is step 5 of phase 2 of chymotrypsin reaction?

Answer 31

his57 acts as a general base to deprotonate water and make it more nucleophilic and water acts as a nucleophile and attacks the carbonyl carbon

Question 32

what is step 6 of phase 2 of chymotrypsin reaction?

Answer 32

protonated his57 acts as a general acid to protonate ser195 leaving group; ser195 cleaves from N-terminal end of polypeptide (to regenerate the enzyme)

Question 33

what is step 7 of phase 2 of chymotrypsin reaction?

Answer 33

final (second) product (N-terminal end of original polypeptide) leaves; enzyme is now returned to its original form

Question 34

what does hexokinase do?

Answer 34

catalyzes the phosphorylation of glucose in a reversible reaction, involving Mg ion, ADP, and ATP

Question 35

what induces a conformation shift in the enzyme structure (induced fit) at the binding site? (hexokinase catalytic reaction)

Answer 35

D-glucose binding