Catalysis Flashcards
What two things do enzymes do?
Lower the activation energy
Stabilize the transition state
What do enzymes not do?
Change the ∆G of the reaction
Irreversibly change the shape
What does a catalyst do?
Increases the rate (speed) of a reaction, but does not undergo any permanent chemical change as a result
What is the thermal energy equation?
∆G=∆H-T∆S
When ∆G, H, S are negative what does this mean?
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
When ∆G, H, S are positive what does this mean?
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
When ∆G, H, S are in equilibrium what does this mean?
If ∆H=0, (Closed system)
If ∆S=0, No net change in disorder
If ∆G=0, Equilibrium
Biochemically, what are the two ways to drive an unfavorable reaction?
- Maintain Q < K. Remember Q is used when the reaction is not at equilibrium. Rember K is used when the reaction is in equilibrium.
- Couple it to a highly favorable reaction
What is the definition of a transition state?
A high energy, unstable form of the reactant(s) that is ready to form products
What 2 ways can we speed up a reaction?
Raise the temperature
Stabilize the transition state by using an enzyme
Describe the induced fit model
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
In the Induced Fit Model, how is catalysis achieved?
Substrate orientation
Straining substrate bonds
Creating favorable microenvironment
Covalent and/or noncovalent interactions between enzyme and substrate
What are the 4 Catalysis Strategies? Describe each
- Covalent Catalysis- The enzyme covalently binds the transition state and transfers electrons.
- Acid-Base Catalysis- Partial proton transfer to the substrate.
- Approximation- Proper spatial orientation and close contact (proximity) of the reactant molecules must occur. This is also called Entropy Reduction*
- 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.
For what 3 purposes do we need proteases?
Recycling
Regulation
Defense
What are 3 reasons why Carbonic Anhydrase is good?
Physiological Relevance- pH regulation, Enzyme pathway regulation
Medical Application- Artificial lungs
Industrial Application- CO2 scrubbers for reduction of greenhouse gases
What is the reaction Mechanism for Carbonic Anhydrase?
- Water binds to Zn++, lowering its pka*. At physiological pH, water loses a protin.
- Catalytic strategy of approximation as substrate enters the active site.
- Nucleophilic addition (adds functional group to CO2)
- Release of product and regeneration of enzyme (histidine proton shuttle)
The chymotrypsin active site is an example of a ______ _____
Catalytic Triad
What 3 structures make up the catalytic triad active site for chymotrypsin?
Serine- a nucleophile
Histidine- a base (proton acceptor)
Aspartic Acid- an acid (proton donor)
What are these proteases active sites named after:
Cysteine Protease
Aspartyl Protease
Metalloprotease
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
____ ___ stabilizes the transition state (tetrahedral formation) for Chymotrypsin. Why?
Oxyanion hole
Because Glycine bonds with Serine and Glycine only has hydrogen as its side chain, therefore it creates a “hole”
Chymotrypsin has _____ ____ that determines the placement of the cut. Describe this in more detail
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.
For Chymotrypsin, what kind of amino acids will be found to bind to the specificity pocket?
Chymotrypsin’s specificity pocket lacks any amino acid therefore, complementary amino acids should be large, aromatic, and nonpolar.
Phenylalanine is a good choice
Where does Chymotrypsin usually get cut?
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
Trypsin has a specificity pocket composed of Aspartic acid, therefore what kind of amino acid will bind to it?
The amino acid binding to it should be complementary, therefore any positively charged amino acid will work such as Arginine, Lysine, and Histidine
Elastase has 2 valine amino acids that make up the specificity pocket. What kind of amino acids will be complementary to it?
Anything small and nonpolar would fit here such as glycine.
Learning objectives- Describe the catalytic mechanisms of chymotrypsin and carbonic anhydrase.
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.
Describe Carbonic Anhydrase in terms of its active site and which catalytic strategy it uses
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
When zinc is bound to water and 3 histidines, what is the pka and what does this mean?
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.
