Lecture 12 Flashcards
state 2 things that enzymes DO and then state 2 things that enzymes DO NOT do.
Do:
Lower the activation energy
stabilize the transition state
Dont:
change the deltaG of the reaction
irreversibly change the shape
Define catalyst
Catalyst: increases the rate (speed) of a reaction but does NOT undergo any permanent chemical changes as a result
In terms of Q and K values, define which is used for a reaction at equilibrium and NOT at equilibrium.
Q is used for a reaction NOT at equilibrium
K is used for a reaction AT equilibrium
State the 2 biochemical strategies that are used to drive an unfavorable reaction
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)
True or False:
Reactions and DeltaG values can be summed. explain
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.
Define Transition State
Transition State: a high energy, unstable forms of the reactants that is ready to form the products
Define activation energy
Activation Energy: an energy barrier that must be overcome for the reaction to proceed
State the 2 options that can be used to speed up a reaction (catalysis)
- raise the temperature (gives more energy to everything and is tough to create inside of a cell)
- stabilize the transition state with the use of an enzyme
Describe the Induced fit model of catalysis
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
What are the 4 strategies that are used to achieve catalysis?
Substrate orientation
Straining substrate bonds
Creating a favorable microenvironment
Covalent and/or noncovalent interactions between the enzyme and substrate
Describe what occurs during Covalent catalysis
the enzyme covalently binds the transition state (electrons transfer)
Describe what occurs during Acid-Base catalysis
partial proton transfer to the substrate
Describe what occurs during approximation catalysis
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
What is entropy reduction?
entropy reduction is synonymous with approximation
different names for the same method of catalysis
describe what occurs during electrostatic catalysis
stabilization of unfavorable charges on the transition state by polarizable side chains in the enzyme and/or metal ions
Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of the reaction substrates and the reaction products involved.
Serine proteases/Chymotrypsin:
Polypeptide/peptide bond substrates react to become shorter polypeptides
Carbonic Anhydrases:
CO2/HCO3- substrates react to become HCO3-/CO2
Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their uncatalyzed and catalyzed reaction times
Serine proteases/Chymotrypsin:
uncatalyzed takes years ; catalyzed takes milliseconds
Carbonic Anhydrases:
Uncatalyzed takes seconds ; catalyzed takes microseconds
Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their Active site and how they determine specificity
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
Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their catalytic strategies
Serine proteases/Chymotrypsin:
Acid-Base catalysis
Covalent catalysis
Carbonic Anhydrases:
Acid-Base catalysis
Approximation (catalysis)
Electrostatic catalysis
Compare Serine proteases/Chymotrypsin and Carbonic Anhydrases in terms of their similarities
Serine proteases/Chymotrypsin AND Carbonic Anhydrases:
speed up reactions
Are hydrolase enzymes that conduct hydrolysis
State the 3 reasons we need proteases
recycling
regulation
defense
The active site of chymotrypsin is an example of a _____ _____.
catalytic triad
State the 3 units that make up a catalytic triad and then include the specific molecules that fulfil these roles in the chymotrypsin reaction.
A nucleophile (Serine (S195))
A base (Histidine (H57))
An acid (Aspartic Acid (D102))
What role in the chymotrypsin reaction does the oxyanion hole play?
the oxyanion hole stabilizes the tetrahedral intermediate (transition state)
what 2 molecules make up the oxyanion hole in chymotrypsin?
Serine (S195)
Glycine (G193)
what portion of chymotrypsin determines the placement of the “cut” in the peptide bond of the substrate? describe this.
the Specificity (S1) pocket
Explain the reaction of Zn++ and H20 as it acts as a carbonic anhydrase in the human body (4 steps)
- 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.
- Approximation (catalytic strategy) occurs as CO2 and the OH- group (used to be water but lost a proton) are positioned near each other
- Carbonic acid (which can lose a H+ and become bicarbonate ion) is formed by the nucleophilic addition of an OH- functional group to CO2
- the product is released and the Enzyme is regenerated (histidine proton shuttle)
Describe the atoms that make up carbonic anhydrase
A Zn++ ion in the active site, which is coordinated to 3 Histidines and a H2O molecule
State what facilitates the transition state of carbonic anhydrase and ALSO what determines the the specificity of the substrate for it.
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
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.
True
not much to explain
State the 2 physiological uses for CA (carbonic anhydrase), 1 medical application, and 1 Industrial application.
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
