Lecture 9

Question 1

enzyme-transition state complementarity

Answer 1

means catalyze by binding most tightly to transition state (and stabilizing it in the process)

binding energy linking E and S is substantial. Max BE realized only in transition state``

allows specificity because various substrates’ transition states are very different usually

Question 2

how to draw and interpret plot of free energy vs reaction coordinate

Answer 2

You’ve got this! I believe in you!

Question 3

rate vs equilibrium

Answer 3

c

Question 4

relationship between rate constant for rxn and activation energy

Answer 4

increase reaction constant k, increase reaction rate => activation energy decreases

Question 5

how binding energy is uesed to bring about enzymatic catalysis

Answer 5

stabilizes transition state, and causes max BE between E and S to occur when S is in transition state

this BE is the currency used to reduce the activation energy

1. Entropy REDUCTION
   - holds substrates in proper orientation to react
   - rate enhancements to 10^8 M
2. Desolvation
   - replace H-bonds to H2O
3. Strain (this tactic isn’t usually taken)
   - facilitate any geometric or electrostatic distortion required
4. Induced fit
   - bring reactive groups on enzyme into proper orientation for catalysis

Question 6

evidence for enzyme-transition state complementarity

Answer 6

1. Structure-activity correlations
   - -one molecule has low reaction rate even with enzyme. But change structure just a little and suddenly RR is much faster!
2. Transition state analogs
   - -molecules that resemble transition state should bind tightly (and they do. Think inhibitors for example)
3. Catalytic antibodies (this one’s crossed out. So no, not this one?

Question 7

enzyme

Answer 7

biomolecule, either protein or RNA, that catalyzes a specific chemical reaction.

• doesn’t affect the equilibrium of the catalyzed reaction
• enhances rate of reaction by providing a reaction path with a lower activation energy

Question 8

cofactor

Answer 8

inorganic ion or a coenzyme required for enzyme activity

Question 9

coenzyme

Answer 9

organic cofactor required for the action of certain enzymes

-often has vitamin component

Question 10

prosthetic group

Answer 10

metal ion or organic compound (not AA though) covalently bound to a protein
-essential to its activity

Question 11

holoenzyme

Answer 11

catalytically active enzyme, including all necessary subunits, prosthetic groups, and cofactors

Question 12

apoenzyme

Answer 12

protein portion of an enzyme

-exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity

Question 13

apoprotein

Answer 13

protein portion of a protein

-exclusive of any organic or inorgainic cofactors or prosthetic groups that might be required for activity

Question 14

ground state

Answer 14

normal, stable form of an atom or molecule, as distinct from excited state

Question 15

standard free-energy change

delta G ) or (delta G’

Answer 15

delta G* (1M), related to Keq
delta G’* same except [H] is assigned to pH=7

negative delta G means forward reaction favored

G(products)-G(reactants)=delta G’*

Question 16

transition state

Answer 16

activated form of molecule in which molecule has undergone a partial chemical reaction
-highest point on the reaction coordinate

Question 17

activation energy (ΔG‡)

Answer 17

amount of energy (joules) required to convert all molecules in 1 mol of a reacting substance from the ground to transition state

Question 18

reaction intermediate

Answer 18

any chem species in a reaction pathway that has a finite chemical lifetime

Question 19

rate-limiting step

Answer 19

-usu has largest activation energy or highest free energy transition state

Question 20

rate constant

Answer 20

proportionality constant relating velocity of a chem reaction to the concentration(s) of the reactant(s)

Question 21

binding energy (delta Gb)

Answer 21

energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand

Question 22

specificity

Answer 22

ability of an enzyme or receptor to discriminate among competing substrates or ligands

Question 23

desolvation

Answer 23

in aqueous solution, the release of bound water surrounding a solute

Question 24

3 Important Points concerning Enzyme Catalysis

Answer 24

1. Enzymes affect rates, not equilibria
   - so catalyze equally forward and backward
2. Transition state complementarity
   - catalyze by binding most tightly to transition state (which stabilizes it)
3. All parts of a substrate contribute

Question 25

K’eq

Answer 25

K’eq = [P]/[S] = k1/k2 for the reaction

S —k1—->P

Question 26

velocity of reaction S—->P

Answer 26

V = k1[S]
approximately fraction of S converted to P per unit time

units M/Time
umol/min, for example