catalysis

Question 1

what do enzymes do

Answer 1

lower activation energy

stabilize the transition state

Question 2

what do enzymes not do

Answer 2

change the deltaG of the rxn

irreversibly change shape

Question 3

a catalyst is something that

Answer 3

increases the rate (speed) of a rxn

Question 4

a catalyst does not

Answer 4

undergo any permanent chemical change as a result

Question 5

induced fit model

Answer 5

when a substrate binds, the enzyme changes shape so that the substrate is forced into the transition state

(both enzyme and substate are distorted on binding)

Question 6

catalysis is acheived through:

______ orientation

______ substrate bonds

______ a favorable microenvironment

______ and/or ______ interactions between enzyme and substrate

Answer 6

substrate

straining

creating

covalent and/or noncovalent

Question 7

covalent catalysis

Answer 7

enzyme covalently binds the transition state (electrons transferred)

Question 8

acid-base catalysis

Answer 8

partial proton transfer to the substrate

Question 9

approximation catalysis

Answer 9

enzyme works to bring substrates into proper spatial orientation and close contact

Question 10

approximation catalysis can also be called

Answer 10

entropy reduction

Question 11

electrostatic catalysis

Answer 11

stabilization of unfavorable charges on the transition state by polarizable side chains in the enzyme and/or metal ions

Question 12

serine proteases/chymotrysin and carbonic anhydrases are both what type of enzyme

Answer 12

hydrolases

Question 13

active site for serine proteases/chymotrypsin

Answer 13

catalytic triad - serine (nucleophile), histidine (base-proton acceptor), aspartic acid (acid-proton donor)

oxyanion hole

Question 14

specificity for chymotrypsin

Answer 14

hydrophobic specificity pocket

Question 15

what catalytic strategies are used with chymotrypsin

Answer 15

covalent catalysis

acid-base catalysis

(approximation)

Question 16

active site for carbonic anhydrases

Answer 16

3 histidines and Zn2+ OH-

Question 17

specificity for carbonic anhydrases

Answer 17

size of entryway

Question 18

what catalytic strategies are used with carbonic anhydrases

Answer 18

acid-base

electrostatic

approximation

Question 19

why do we need proteases/chymotrypsin

Answer 19

recycling - degradation

regulation - removing proteins from circulation

defense mechanism - help chew up proteins

Question 20

proteases are named for their

Answer 20

active sites

Question 21

oxyanion hole in chymotrypsin functions to

Answer 21

stabilize the tetrahedral intermediate (transition state)

serine and glycine

Question 22

what determines proper placement of cut with working with serine proteases such as chymotrypsin

Answer 22

specificity (S1) pocket

Question 23

______ use carbonic anhydrases for carbon fixation

Answer 23

plants

Question 24

carbonic anhydrases are important in humans for

Answer 24

pH regulation

Question 25

carbonic anhydrase active sites contains

Answer 25

Zn++ ion

(Zn is coordinated to 3 histidines and a water)

(similar to MMPs)

Question 26

carbonic anhydrases are an example of ______ evolution

Answer 26

convergent

Question 27

in carbonic anhydrases, what facilitates the transition state

Answer 27

water

(lower pKa of water to just below physiological pH –> deprotonates water)

(definition of approximation)

Question 28

specificity of carbonic anhydrases

Answer 28

very small and weakly polar molecules can get in active site

Question 29

whats special about active site of carbonic anhydrase?

Answer 29

lowers pKa of water when it binds to Zn

approximation as substrate enters the active site

nucleophilic addition (adding CO2 to OH

release of product and regeneration of enzyme (histidine proton shuttle)