Lecture 12

Question 1

state 2 things that enzymes DO and then state 2 things that enzymes DO NOT do.

Answer 1

Do:
Lower the activation energy
stabilize the transition state

Dont:
change the deltaG of the reaction
irreversibly change the shape

Question 2

Define catalyst

Answer 2

Catalyst: increases the rate (speed) of a reaction but does NOT undergo any permanent chemical changes as a result

Question 3

In terms of Q and K values, define which is used for a reaction at equilibrium and NOT at equilibrium.

Answer 3

Q is used for a reaction NOT at equilibrium

K is used for a reaction AT equilibrium

Question 4

State the 2 biochemical strategies that are used to drive an unfavorable reaction

Answer 4

maintain Q > K
(ex. create a pathway that uses the products of the previous reaction as the reactants for the following reaction)

Couple it to a highly favorable reaction
(ex. ATP hydrolysis)

Question 5

True or False:

Reactions and DeltaG values can be summed. explain

Answer 5

True

When considering an pathway of reactions in the body, not every DeltaG has to be a favorable reaction. You can “sum” the entire pathway, so as long as the entire pathway has a favorable DeltaG (even if not every reaction is favorable), then the pathway will be able to complete the cycle.

Question 6

Define Transition State

Answer 6

Transition State: a high energy, unstable forms of the reactants that is ready to form the products

Question 7

Define activation energy

Answer 7

Activation Energy: an energy barrier that must be overcome for the reaction to proceed

Question 8

State the 2 options that can be used to speed up a reaction (catalysis)

Answer 8

1. raise the temperature (gives more energy to everything and is tough to create inside of a cell)
2. stabilize the transition state with the use of an enzyme

Question 9

Describe the Induced fit model of catalysis

Answer 9

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

after acting upon the substrate, the enzyme resumes the shape it was prior to binding to the substrate. THE ENZYME DOES NOT IRREVERSIBLY CHANGE SHAPE

Question 10

What are the 4 strategies that are used to achieve catalysis?

Answer 10

Substrate orientation

Straining substrate bonds

Creating a favorable microenvironment

Covalent and/or noncovalent interactions between the enzyme and substrate

Question 11

Describe what occurs during Covalent catalysis

Answer 11

the enzyme covalently binds the transition state (electrons transfer)

Question 12

Describe what occurs during Acid-Base catalysis

Answer 12

partial proton transfer to the substrate

Question 13

Describe what occurs during approximation catalysis

Answer 13

the enzyme captures both reactants and holds them in the proper orientation right next to each other, which makes them more likely to react with one another.

this basically achieves the proper spatial orientation and close contact of the reacting molecules

Question 14

What is entropy reduction?

Answer 14

entropy reduction is synonymous with approximation

different names for the same method of catalysis

Question 15

describe what occurs during electrostatic catalysis

Answer 15

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

Question 16

Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of the reaction substrates and the reaction products involved.

Answer 16

Serine proteases/Chymotrypsin:
Polypeptide/peptide bond substrates react to become shorter polypeptides

Carbonic Anhydrases:
CO2/HCO3- substrates react to become HCO3-/CO2

Question 17

Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their uncatalyzed and catalyzed reaction times

Answer 17

Serine proteases/Chymotrypsin:
uncatalyzed takes years ; catalyzed takes milliseconds

Carbonic Anhydrases:
Uncatalyzed takes seconds ; catalyzed takes microseconds

Question 18

Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their Active site and how they determine specificity

Answer 18

Serine proteases/Chymotrypsin:
A catalytic triad and Oxyanion hole composes their active site
A hydrophobic specificity pocket determines their specificity

Carbonic Anhydrases:
3 His + Zn++-OH composes the active site
The size of the entryway determines their specificity

Question 19

Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their catalytic strategies

Answer 19

Serine proteases/Chymotrypsin:
Acid-Base catalysis
Covalent catalysis

Carbonic Anhydrases:
Acid-Base catalysis
Approximation (catalysis)
Electrostatic catalysis

Question 20

Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their similarities

Answer 20

Serine proteases/Chymotrypsin AND Carbonic Anhydrases:
speed up reactions
Are hydrolase enzymes that conduct hydrolysis

Question 21

State the 3 reasons we need proteases

Answer 21

recycling

regulation

defense

Question 22

The active site of chymotrypsin is an example of a _____ _____.

Answer 22

catalytic triad

Question 23

State the 3 units that make up a catalytic triad and then include the specific molecules that fulfil these roles in the chymotrypsin reaction.

Answer 23

A nucleophile (Serine (S195))

A base (Histidine (H57))

An acid (Aspartic Acid (D102))

Question 24

What role in the chymotrypsin reaction does the oxyanion hole play?

Answer 24

the oxyanion hole stabilizes the tetrahedral intermediate (transition state)

Question 25

what 2 molecules make up the oxyanion hole in chymotrypsin?

Answer 25

Serine (S195)

Glycine (G193)

Question 26

what portion of chymotrypsin determines the placement of the “cut” in the peptide bond of the substrate? describe this.

Answer 26

the Specificity (S1) pocket

Question 27

Explain the reaction of Zn++ and H20 as it acts as a carbonic anhydrase in the human body (4 steps)

Answer 27

1. the Zn++ portion of the enzyme binds to Water, which lowers it’s pka to the point that it loses a proton at physiological pH.
2. Approximation (catalytic strategy) occurs as CO2 and the OH- group (used to be water but lost a proton) are positioned near each other
3. Carbonic acid (which can lose a H+ and become bicarbonate ion) is formed by the nucleophilic addition of an OH- functional group to CO2
4. the product is released and the Enzyme is regenerated (histidine proton shuttle)

Question 28

Describe the atoms that make up carbonic anhydrase

Answer 28

A Zn++ ion in the active site, which is coordinated to 3 Histidines and a H2O molecule

Question 29

State what facilitates the transition state of carbonic anhydrase and ALSO what determines the the specificity of the substrate for it.

Answer 29

H2O facilitates the transition state by being deprotonated (once the Zn++ lower’s it’s pka to cause it’s deprotonation at physiological pH) and allows the catalytic strategy of approximation to occur

The “entry channel” that determines the size of the substrate is what conducts the specificity of carbonic anhydrase

Question 30

True or False:

Catalysis can speed up a reaction to the point that an uncatalyzed version of the reaction will take billions of years, while a catalyzed version of the reaction will take seconds. explain.

Answer 30

True

not much to explain

Question 31

State the 2 physiological uses for CA (carbonic anhydrase), 1 medical application, and 1 Industrial application.

Answer 31

2 physiological uses:
pH regulation

Enzyme pathway regulation

Medical use: in artificial lungs (to get rid of/reduce CO2)

Industrial use: CO2 scrubbers for the reduction of greenhouse gasses