Lecture 12: Catalysis Flashcards
What are enzymes able to do?
Lower the activation energy and stabilize the transition state
What are enzymes NOT able to do?
Change the delta G of the reaction
irreversibly change the shape
What does a catalyst do?
increases the speed of the reaction without any permanent change in the result
Describe Q and K and describe when you would use each one
Q is the reaction when it is not at equilibrium (products/reactants)
K is the reaction at equilibrium (products/reactants)
What are strategies to drive an unfavorable reaction?
- maintain Q
Define transition state
a high energy unstable form of the reactants that is ready to form products
Define activation energy
the energy that must be overcome for a reaction to happen
What are the two ways in which a reaction can be sped up?
- raise the temperature
2. stabilize the transition state
Describe the induced fit model of catalysis
When a substrate binds, it forces the enzyme to conform into a specific shape which forces it into the transition state
What are the 4 ways in which catalysis is achieved?
- substrate orientation
- straining substrate bonds
- create a favorable microenvironment
- covalent and non covalent interactions between the enzyme and substrate
Describe covalent catalysis
enzymes covalently bind the transition site and electrons are transferred
Describe acid base catalysis
partial proton transfer to the substrate
Which two catalytic strategies are used by chymotrypsin?
covalent catalysis and acid base catalysis
Which three catalytic strategies are used buy carbonic anhydrase?
acid base catalysis
approximation
electrostatic catalysis
Describe approximation and tell why it would be an example of “entropy reduction”
Approximation is having the proper position of two molecules in order for them to react
so with an enzyme, the substrate is held near the active site in just the right approximation so that they are able to react
entropy is a form of disorder, so with approximation, you are forming more enzyme substrate complexes, which is reducing the amount of disorder that is present
Describe electrostatic catalysis
the stabilization of unfavorable charges on the transition state by the side chains in the enzyme or the metal ions
Describe the active site of chymotrypsin
It is a catalytic triad
Serine 195 acts as a nucleophile
histidine 57 acts as a base (proton acceptor)
Aspartic Acid acts as an acid (proton donor)
What is the function of the oxyanion hole of chymotrypsin? And what two amino acids are found there?
S195 and G193 (think of the letters of the a.a’s)
the hole stabilizes the tetrahedral intermediate
What is the function of the specificity pocket of chymotrypsin? Describe the pocket
It determines the placement of the cut
The pocket is lined with hydrophobic residues and it is deep which encourages the binding of residues of long hydrophobic side chains; serine 195 is positioned in a way that it is able to cleave the peptide backbone between the residue in the pocket and the next residue in the sequence
Describe the differences between the pockets that are present in chymotrypsin, trypsin, and elastase residues
chymotrypsin cleaves at the peptide bone after the residues with an aromatic or long non polar side chain
trypsin has an aspartate (D189) at the bottom of the pocket instead of a serine (chymotrypsin) which attracts positive charged a.a’s and cleaves after the positive residues
elastase has valine residues at the top (Val 190 and Val 216) which only lets small chains enter, and then the residues are cleaved after these small residues enter
Describe the active site of carbonic anhydrase and tell how it works
the active site has a Zn2+ ion that is attached to 3 histidines and a water molecule
- The site starts out as the zinc bound to 3 His and a hydroxide ion (with the help of a histidine)
- Carbon dioxide binds with the help of glutamate and threonine
- A hydroxyl group is added to the CO2 which makes the molecule a carbonic anhydrase
The amino acids, specifically the histidine are able to help the molecule be formed through conformational changes and attraction of molecules
Describe the overall mechanism of carbonic anyhdrase, specifically how water is able to facilitate the transition state
water binds to zinc (lowering the pka) and is then deprotonated (because at physiological pH it will be deprotonated) [THIS IS THE TRANSITION STATE], this allows for the approximation of the molecules to occur (CO2 is able to come in and a nucleophilic addition takes place)
then the enzyme is recycled via a histidine proton shuttle
How can thermodynamics be used to predict reaction rate?
If you have a negative delta G, then the reaction will be spontaneous BUT the free energy difference (delta G) is NOT able to predict the rate
The rate is determined by the energy that is required to initiate the conversion of reactants into products
Which is more favorable, a negative or a positive delta H?
Negative, because heat is released from the system, or it is exergonic
Which is more favorable, a negative or positive delta S
A positive delta S because you have increased disorder, which means more reactions are able to occur
BTLO: Bromelain is the protease mixture obtained from pineapples. Describe what the specificity pocket would be like
papain is one of the enzymes that is found in pineapple and it is a cysteine protease
The Cys residue is activated by the histidine that is beside it in order to cause a nucleophilic attack on the peptide bond
BTLO: Explain how the delta G of a reaction is related to the rate of that reaction with and without the enzyme
the delta G does not effect the rate of the reaction, but effects the spontaneity of the reaction. So, a negative delta G means that the reaction can occur spontaneously. A positive delta G is non spontaneous and needs something to get it to occur
The RATE of a reaction is dependent on the energy that is required to take the reactants to the products, or the activation energy. The enzyme helps to lower this amount of energy, essentially speeding up the reaction.
BTLO: Describe how the four catalytic strategies relate to chymotrypsin and carbonic anhydrase
COVALENT CATALYSIS
In covalent catalysis, the enzyme binds to the transition state and there is a proton transfer
this relates to chymotrypsin only!
The active site has a reactive group that acts as a nucleophile (Ser195) that becomes attached to the substrate
BTLO: Describe how the four catalytic strategies relate to chymotrypsin and carbonic anhydrase
ACID BASE CATALYSIS
Acid base catalysis involves the partial proton transfer to the substrate; something other than H20 is able to act as the donor or the acceptor
Chymotrypsin: Uses the His57 residue to act as the base catalyst (proton acceptor) and the Asp102 as an acid (proton donor)
Carbonic anyhdrase: uses His residue to remove H+ from water in order to attach the hydroxide ion to the Zn2+
BTLO: Describe how the four catalytic strategies relate to chymotrypsin and carbonic anhydrase
APPROXIMATION
Approximation is the reaction occurring because of proper orientation and alignment: the molecules are close in proximity and are therefore able to interact
Carbonic anyhdrase: the binding site and specificity site allows for close proximity because of the adjacent sites
BTLO: Describe how the four catalytic strategies relate to chymotrypsin and carbonic anhydrase
ELECTROSTATIC OR METALLIC
Electrostatic interactions is the stabilization of unfavorable charges by the polar side chains of a molecule or a metal ion
carbonic anhydrase: uses ZN2+ to bind to water, which is essentially creating a nucleophile. Zn2+ is able to lower the pka of the water, which in turn allows for the deprotonation to occur, as the physiological pH is higher than the pka
BTLO: Explain how the four catalytic strategies support the induced fit model (a good answer would include… definition of induced fit as well as explanations of each of the 4 models)
induced fit model states that when a substrate binds, the enzyme changes shape so that the substrate is forced into the transition state
covalent catalysis- should be supportive of the induced fit model because it binds to the transition state and allows for the complex to be formed
acid base- the reactions that occur causes a conformational change, which leads to the transition state to be reached??
Approximation: brings everything that is needed for the reaction to occur together
Electrostatic: stabilizes the transition state that the reaction can continue
