lecture 42 - enzymes intro

Question 1

what are two key factors of enzymes that act as catalysts?

Answer 1

(1) they increase the approach to equilibrium for a chemical reaction
(2) they are not used up in the process

Question 2

list the 4 properties of catalytic enzymes

Answer 2

(1) allow for fast reactions
(2) provide reaction specificity
(3) the enzyme can be regulated
(4) the enzyme may require cofactors

Question 3

describe how catalytic enzymes allow for fast reactions (2)

Answer 3

• cause a 10^5-10^7 increase in rxn rate

- this allows the reaction to occur in mild conditions

Question 4

describe how catalytic enzymes provide reaction specificity (2)

Answer 4

• enzymes allow for identificiation of a substrate

- enzyme interacts with the substrate at a specific site on the enzyme called the active site

Question 5

describe the active site (3 properites)

Answer 5

• typically a cleft or pocket on the enzymes surface
• shape and chemical composition are complementary to that of its substrate
• has some parts that are only involved in binding and positioning the substrate, while others are directly involved in the catalysis actions

Question 6

can the active site be “preformed” to bind the substrate? if yes - what does this mean, if no - why not?

Answer 6

• yes

- happens when S is in a transition state

Question 7

can the active site undergo a conformational change upon binding to substrate? why or why not?

Answer 7

• yes

- often occurs to protect the substrate from any side rxn that may occur if exposed to a solvent or other molecules

Question 8

with respect to shape complementarity, what does the enzyme recognize in the substrate?

Answer 8

• shape complementarity includes stereospecificity

- means enzyme can recognize substrare chirality

Question 9

describe how a catalytic enzyme can be regulated (3)

Answer 9

• may be regulated by an allosteric effector
• may be regulated by natural inhibitors (compete with substrate for the active site)
• may be regulated by post-translational modifications (e.g. phosphorylation of S, T, Y) - this can effect the confomation or activity of the enzyme or its ability to bind substrate

Question 10

what sort of role does a cofactor play in enzyme catalysis? (3) provide examples of cofactors

Answer 10

• may affect enzyme structure, binding ability, or may be directly involved in catalysis
• e.g. metal ions, organic prosthetic groups

Question 11

what is an “apo-enzyme”?

Answer 11

the enzyme protein alone

Question 12

what is a “holo-enzyme”?

Answer 12

functional enzymes with cofactors

Question 13

explain (generally) how enzyme catalysis occurs.

is this a reversible or irriversible process?

Answer 13

• E + S <=> ES <=> EP <=> E + P

- each individual step is reversible

Question 14

describe the gibbs free energy graph for the enzyme-substrate reaction

Answer 14

• this is an exergonic reaction (reactants start higher than products)
• thus overall delta G is less than 0 and the reaction occurs spontaneously (favoured)
• the peak of the curve is the transition state (S–>P)
• since delta G for P–>S is greater than the delta G for S–>P, the reverse reaction is slower and equilibrium favours the conversion of substrate into product

Question 15

what are two key properties of a transition state?

Answer 15

• highest energy state

- transient - it exists for only a moment (NOT an intermediate - those have a finite lifetime)

Question 16

why is the transition state so high in energy?

Answer 16

(1) alignment of functional groups
(2) generation of transient charges
(3) bond rearangements (breaking and forming of bonds that results in the formation of the high energy transition state)