Lecture 12, Catalysis (Ford) Flashcards
What do enzymes do?
Lower activation energy and stabilize transition state
T or F: Enzymes alter the thermodynamics of a reaction.
False. Enzymes do not change the deltaG of a reaction.
Can enzymes irreversible change shape?
No
What is a catalyst?
Increases the rate of a reaction but does not undergo any permanent chemical change as a result
What is Gibbs Free Energy equation?
deltaG = deltaH - T*deltaS
Describe what happens when there is a negative deltaH value.
Energy is released from the system
Describe what happens when there is a positive deltaH value.
Energy is added to the system
Describe what happens when there is a negative deltaS value.
Disorder decreases
Describe what happens when there is a positive deltaS value.
Disorder increases
Describe what a negative deltaG value indicates.
Free energy released, exergonic reaction, favorable reaction, spontaneous reaction
Describe what a positive deltaG value indicates.
Free energy required, endergonic reaction, unfavorable reaction, driven reaction
Describe what deltaG = 0 means.
Equilibrium
How would you calculate deltaG when the reaction is not at equilibrium?
deltaG = deltaG’ + RT*lnQ
How would you calculate deltaG when the reaction is at equilibrium?
deltaG = deltaG’ + RT*lnK
What is the unit for temperature when used in the Gibbs Free Energy reaction?
Kelvin
What are some biochemical strategies to drive an unfavorable reaction?
Maintain Q < K; Couple it to a highly favorable reaction
What does it mean to couple an unfavorable reaction to a highly favorable one?
Reactions and deltaG values can be summed; Couple with ATP hydrolysis
What is the transition state?
High energy, unstable form of the reactants that is ready to form products
What is the activation energy?
Energy barrier that must be overcome for the reaction to proceed
How can a reaction be sped up?
- Raise temperature
2. Stabilize the transition state with 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
Give the 4 ways catalysis is achieved.
- Substrate orientation
- Sustaining substrate bonds
- Creating a favorable microenvironment
- Covalent/noncovalent interactions between enzyme and substrate
Describe covalent catalysis.
Enzyme covalently binds the transition state
T or F: Covalent catalysis is a transfer of electrons.
True.
Describe acid-base catalysis.
Partial proton transfer to the substrate
Describe catalysis through approximation.
If electrons/protons must be exchanged, proper spatial orientation and close contact (proximity) of the reactant molecules must occur; “entropy reduction”
Describe electrostatic catalysis.
Stabilization of unfavorable charges on the transition state by polarizable side chains in the enzyme/metal ions
Why are proteases needed?
Recycling, regulation, defense
What are the various applications of carbonic anhydrases?
Physiological (pH regulation, enzyme pathway regulation), medical (artificial lungs), industrial (CO2 scrubbers for reduction of greenhouse gases)
Describe the active site of chymotrypsin.
Catalytic triad: serine = nucleophile, histidine = base (proton acceptor), aspartic acid = acid (proton donor)
In chymotrypsin, what stabilizes the tetrahedral intermediate (transition state)?
Oxyanion hole
Regarding chymotrypsin, what determines the placement of the cut?
Specificity pocket
What does the active site of carbonic anhydrases contain? What is it coordinated to?
Zn2+ ion; Coordinated to 3 histidines and a water
Regarding carbonic anhydrases, what is the importance of water?
Facilitates the transition state (deprotonated)
Which catalytic strategy does water use for the transition state of a carbonic anhydrase?
Approximation
Regarding carbonic anhydrases, what determines the size of the substrate?
Entry channel
What is the reaction mechanism for a carbonic anhydrase?
- Water binds to Zn2+
- Approximation strategy as substrate enters site
- Nucleophilic addition (adds functional group to CO2)
- Release of product and regeneration of enzyme (histidine proton shuttle)
During the carbonic anhydrase reaction mechanism, what is the significance of water binding to Zn2+?
Lowers pKa (at physiological pH, water loses a proton)
