Catalysis

Question 1

What two things do enzymes do?

Answer 1

Lower the activation energy

Stabilize the transition state

Question 2

What do enzymes not do?

Answer 2

Change the ∆G of the reaction

Irreversibly change the shape

Question 3

What does a catalyst do?

Answer 3

Increases the rate (speed) of a reaction, but does not undergo any permanent chemical change as a result

Question 4

What is the thermal energy equation?

Answer 4

∆G=∆H-T∆S

Question 5

When ∆G, H, S are negative what does this mean?

Answer 5

If ∆H<0, Energy is released from the system

If ∆S<0, Entropy Decreases, or in other words becoming more ordered. Ex. 2 molecules becoming one

If ∆G<0, Free energy is released, exergonic reaction. favorable, spontaneous

Question 6

When ∆G, H, S are positive what does this mean?

Answer 6

If ∆H>0, Energy is added from the system

If ∆S>0, Entropy Increases, or in other words becoming less ordered. Ex. 1 molecule breaking into 2

If ∆G>0, Free energy is required, endergonic reaction. unfavorable, nonspontaneous

Question 7

When ∆G, H, S are in equilibrium what does this mean?

Answer 7

If ∆H=0, (Closed system)

If ∆S=0, No net change in disorder

If ∆G=0, Equilibrium

Question 8

Biochemically, what are the two ways to drive an unfavorable reaction?

Answer 8

1. Maintain Q < K. Remember Q is used when the reaction is not at equilibrium. Rember K is used when the reaction is in equilibrium.
2. Couple it to a highly favorable reaction

Question 9

What is the definition of a transition state?

Answer 9

A high energy, unstable form of the reactant(s) that is ready to form products

Question 10

What 2 ways can we speed up a reaction?

Answer 10

Raise the temperature

Stabilize the transition state by using an enzyme

Question 11

Describe the induced fit model

Answer 11

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

AKA Lock and Key method

*Note that this reaction is reversible and the substrate and enzyme can go back to their starting points

Question 12

In the Induced Fit Model, how is catalysis achieved?

Answer 12

Substrate orientation
Straining substrate bonds
Creating favorable microenvironment
Covalent and/or noncovalent interactions between enzyme and substrate

Question 13

What are the 4 Catalysis Strategies? Describe each

Answer 13

1. Covalent Catalysis- The enzyme covalently binds the transition state and transfers electrons.
2. Acid-Base Catalysis- Partial proton transfer to the substrate.
3. Approximation- Proper spatial orientation and close contact (proximity) of the reactant molecules must occur. This is also called Entropy Reduction*
4. Electrostatic Catalysis- Stabilization of unfavorable charges on the transition state by the polar side chains in the enzyme and/or metal ions. It is some type of noncovalent, electrostatic interaction.

Question 14

For what 3 purposes do we need proteases?

Answer 14

Recycling
Regulation
Defense

Question 15

What are 3 reasons why Carbonic Anhydrase is good?

Answer 15

Physiological Relevance- pH regulation, Enzyme pathway regulation

Medical Application- Artificial lungs

Industrial Application- CO2 scrubbers for reduction of greenhouse gases

Question 16

What is the reaction Mechanism for Carbonic Anhydrase?

Answer 16

1. Water binds to Zn++, lowering its pka*. At physiological pH, water loses a protin.
2. Catalytic strategy of approximation as substrate enters the active site.
3. Nucleophilic addition (adds functional group to CO2)
4. Release of product and regeneration of enzyme (histidine proton shuttle)

Question 17

The chymotrypsin active site is an example of a ______ _____

Answer 17

Catalytic Triad

Question 18

What 3 structures make up the catalytic triad active site for chymotrypsin?

Answer 18

Serine- a nucleophile
Histidine- a base (proton acceptor)
Aspartic Acid- an acid (proton donor)

Question 19

What are these proteases active sites named after:

Cysteine Protease
Aspartyl Protease
Metalloprotease

Answer 19

Cysteine Protease- Cysteine is occupying the active site
Aspartyl Protease- Aspartic acid is occupying the active site
Metalloprotease- A metal is occupying the active site

Question 20

____ ___ stabilizes the transition state (tetrahedral formation) for Chymotrypsin. Why?

Answer 20

Oxyanion hole

Because Glycine bonds with Serine and Glycine only has hydrogen as its side chain, therefore it creates a “hole”

Question 21

Chymotrypsin has _____ ____ that determines the placement of the cut. Describe this in more detail

Answer 21

Specificity (S1) Pocket- an area that recognizes the amino acid prior to where it will be cut and binds to it based on complementary size and charge.

Question 22

For Chymotrypsin, what kind of amino acids will be found to bind to the specificity pocket?

Answer 22

Chymotrypsin’s specificity pocket lacks any amino acid therefore, complementary amino acids should be large, aromatic, and nonpolar.

Phenylalanine is a good choice

Question 23

Where does Chymotrypsin usually get cut?

Answer 23

Polypeptides have directionality because we start with an amino terminus and end at the carboxy terminus.

The side chain closer to the amino terminus goes into the specificity pocket and the peptide bond following that amino acid will be clipped

Question 24

Trypsin has a specificity pocket composed of Aspartic acid, therefore what kind of amino acid will bind to it?

Answer 24

The amino acid binding to it should be complementary, therefore any positively charged amino acid will work such as Arginine, Lysine, and Histidine

Question 25

Elastase has 2 valine amino acids that make up the specificity pocket. What kind of amino acids will be complementary to it?

Answer 25

Anything small and nonpolar would fit here such as glycine.

Question 26

Learning objectives- Describe the catalytic mechanisms of chymotrypsin and carbonic anhydrase.

Answer 26

This will be on the exam like the vitamins were. Slides 18-31 talk about these two catalysts. Especially know slide 18, which I printed out.

Question 27

Describe Carbonic Anhydrase in terms of its active site and which catalytic strategy it uses

Answer 27

Active site contains a Zn++ ion coordinated to 3 Histidines and a water molecule

H2O facilitates the transition state- Deprotonated and uses the Catalytic strategy of Approximation

Entry channel determines the size of the substrate- CO2 is small and weakly polar

Question 28

When zinc is bound to water and 3 histidines, what is the pka and what does this mean?

Answer 28

Pka=7
pH is also 7 because of water

If pH=pka, then the protonated state is just as likely to be found as the deprotonated state. Therefore, we will find water protonated in the H2O form or deprotonated in the OH- form.