1. Define enzymes
2. What types of rxns are enzymes generally used for?
3. What do they allow for? (4)
1. Biological catalysts that increase the rate of rxns (w/o affecting equilibrium) but are unchanged at the end of the rxn.
3. increase in rxn rate, increase in frequency of collisions of reactive molecules, allows rxns to occur under mild conditions (not heated, etc), and regulates rxns (on/off)
1. How much faster can an enzyme make a rxn go?
2. How does an enzyme increase frequency of collision?
3. Why is it important that an enzyme allows us to use mild conditions?
1. 10^3 to 10^17 faster
2. By acting as a platform for reactive molecules to interact with correct orientation and proximity.
3. Usually, to increase rxn rate, we have to increase temp and pressure. But this way, with enzymes, can increase rxn rate at normal conditions for humans (pH = 7, 37 C, 1 atm).
1. What types of cofactors can enzymes use?
2. Name the six types of enzymes and their respective functions.
1. Transient (only present during rxn) or integrated into 3D structure (prosthetic group)
1. Oxidoreductases - redox
2. Transferases - transfer of functional group
3. Hydrolases - hydrolysis (break bond with H2O)
4. Lyases - add or remove groups to make or break C=C.
5. Isomerases - rearrange C skeleton
6. Ligases - form C-C, C-N, C-O, and C-S bonds with ATP.
1. What does and doesn't an enzyme change?
2. Why can't an enzyme change that particular thing?
3. What are standard conditions?
4. What is the relationship between Keq and dG?
5. Describe the above in words.
1. Can change k (rate constant), can't change Keq.
and can't change Keq without changing dG, which would break the law of thermodynamics.
3. 1 atm, 25 C, 1 M of reactants (for biochemists, pH = 7 too).
4. As Keq increases, dG becomes more negative
5. As the rxn is more product-favored, the rxn becomes more energetically favorable (exergonic and spontaneous)
1. What is the difference between dG and dH?
2. Can endothermic rxns be spontaneous? Why?
3. What factors contribute to activation energy? dG double dagger (3)
1. dG deals with energy (exer/endergonic) while dH deals with heat. (exo/endothermic)
2. yes, because it just comes down to dG.
3. (1) entropy - reduces possibility that they'll react with each other (2) solvation shell of H-bonded H2O that stabilizes most biomolecules (3) distortion of substrates
1. What is the source of energy for lowering activation energy barrier?
2. What are the sources of this energy? (2) Which is the most major source?
3. What does binding energy contribute to?
4. Why are enzymes usually so large? (3)
1. Binding energy dGB
2. (1) Rearrangement of covalent bonds between enzymes & substrates and (2) Formation of weak, noncovalent interactions between substrate and enzyme.
3. Specificity and catalysis
4. As surface area of contact between enzyme and substrate increases, binding energy increases too.
2. To keep interacting groups properly positioned to favor transition state
3. Keep cavity from collapsing.
1. How does substrate binding affect entropy? How?
2. What is the net result of binding activity?
3. What is the substantial driving force for enzyme catalysis?
1. Increases entropy by displacing solvent molecules from binding pocket.
2. Summation of unfavorable (positive) activation energy and favorable (negative) binding energy results in lower net activation energy.
3. Weak binding interactions that are formed between substrate and enzyme.
Name the six basic catalytic mechanisms that contribute to enzymes' catalytic activity
1. Proximity and orientation
2. Preferential transition state binding
3. Acid-base catalysis
4. Covalent catalysis
5. Electrostatic catalysis
6. Metal ion catalysis
Describe the importance of the following catalytic mechanisms:
1. Proximity and orientation
2. Preferential state binding - what model is used here?
1. Enzymes bind so that reactive groups are close and in correct orientation by constraining motions of substrates (reducing entropy) increasing possibility of rxn.
2. Enzymes preferentially stabilize transition state over substrate by inducing conformational change in enzyme "induced fit" model.
1. What happens if enzyme preferentially stabilizes substrate over TS? Draw picture
2. What is this basically saying about the amount of energy needed?
3. What would have to be overcome? (2)
1. ES will be at lower energy level than product (b/c release of energy due to formation of bonds to stabilize). Basically, would require more energy to go from ES --> P than S--> P, defeating purpose of using enzyme.
3. Would have to overcome original dGcat with dGM on top.
1. What happens when enzyme preferentially stabilizes TS? What does enzyme increase? For what purpose?
2. What is dGM?
1. Complex has enough energy to overcome activation barrier, preventing reverse rxn from occurring. (Enzyme increases number of substrates in forward rxn to prevent reverse rxn)
2. dGM is the difference between the transition-state energies of the uncatalyzed and catalyzed rxns.
1. Describe acid-base catalysis
2. Describe covalent catalysis
3. Describe electrostatic catalysis
4. Describe metal ion catalysis - where is this seen? What is it involved in?
1. Acid-base: side chains function as proton donors and acceptors.
2. Transient (eventually must be broken) covalent bond forms between enzyme and substrate
3. Certain R groups stabilize high energy intermediates
4. Seen in redox rxns, involved in substrate binding.
1. In chymotrypsin, which are the four most important amino acids and what are their roles?
2. What kind of catalysis occurs after nucleophilic attack?
3. What is the difference between electrostatic catalysis and acid-base catalysis?
4. What does stabilization by electrostatic catalysis do?
1. Asp 1 and 2 - stabilize His 57 (proximity and orientation)
2. his 57
3. Ser 195
His and Ser are responsible for actual chemistry steps in catalysis.
2. Covalent catalysis (may also have electrostatic for subsequent stabilization).
3. They often look very similar, but acid-base catalysis would be the actual transfer of a proton, while electrostatic catalysis is where the proton just surrounds the negatively charged anion.
4. Stabilizes TS preferentially
1. If we know Keq and dG, can we write rate equation? What would be needed?
2. What is the same as the instantaneous velocity of an equation?
3. Why are termolecular rxns rarely seen?
4. Three ways to describe instantaneous velocity of an equation A--> B
1. No, need to know intermediates.
2. Rate equation, i.e., rate = k[A][B]
3. B/c requires simultaneous collision of three substrates.
1. Which enzymatic rxns can only go forward?
2. Describe how a graph of saturation vs. [S] changes from beginning to end?
3. What is the beginning called? The end?
1. none - all enzymatic rxns can also go in reverse.
2. At first, increase in substrate leads to linear & proportional increase in product, but at a certain point, all enzymes are saturated (assuming constant [E]) and it plateaus. This plateau is Vmax.
3. Beginning = first order rxn. End = zero order rxn (no matter how much more substrate you add, it doesn't matter).
1. In deriving the M&M equation, what was assumed? (2)
2. Does k1 = k-1?
3. Draw graph of how concentrations of substrate and product changes over time.
4. What is the rate determining step in enzyme catalysis? Write the rate equation
1. Assumption of equilibrium - measurements are taken early in rxn, so we can assume that K-2 doesn't play a role (no equilibrium).
2. Steady state - the initial part of rxn reflects steady state in which [ES] remains constant; formation of ES must equal breakdown of ES.
4. ES --> Product; depends on [ES].
Rate = k2[ES]
1. Write equilibrium rxn for enzyme catalysis.
2. Write rate constant for formation of ES and breakdown of ES. Which is RDS?
3. Write result of steady state assumption
4. Write everything in terms of ES and define Km. Why do we use Km?
1. E + S <--> ES ---> E+P (k1, k-1, k2)
5. Because it simplifies equation.
1. What is MM equation?
2. Do math for Vo = 1/2 Vmax.
3. What does Km ultimately represent?
4. What should I know in terms of Km and a enzyme-substrate pair?
5. What does high Km represent? What does low Km represent?
3. Km represents enzyme's affinity for substrate (like Kd for proteins).
4. Km is unique for every pair.
5. High Km represents less affinity, low represents high affinity.
1. Why can't we use regular hyperbolic plot (Vmax vs. [S]) to determine Vmax and Km?
2. What should you do instead?
3. Draw and label an example of the above.
4. Write new linear equation. What is y-int? What is x-int?
5. How do we consider [S] vs. [E]??
1. Because it's very difficult to pinpoint, especially on an asymptote.
2. Linearize data into double reciprocal plot to get more accurate numbers.
5. We assume [S]>>[E]
1. How does competitive inhibitor affect Km and Vmax?
3. Explain why for each.
1. Vmax stays constant while Km increases (less affinity)
2. Vmax decreases while Km stays constant.
For competitive inhibitor (CI), assuming same binding affinity for substrate, Km increases b/c it will require more S to reach Km point (1/2 of Vmax) Vmax stays constant b/c competitive inhibition can be overcome by sufficiently high [S]
For noncompetitive inhibitor - Vmax decreases as a result of removing activated complex, but since I doesn't interfere with binding site, Km stays the same. It doesn't matter how much substrate is added, Vmax will decrease.
1. What is double reciprocal plot useful for? (2)
2. What happens to Hb binding affinity if you replace histidine with alanine. What will curve look like?
3. Why won't it look like stripped Hb?
4. How can we determine which AAs are important to protein structure or function?
1. Distinguishing between certain types of enzymatic rxns and analyzing enzyme inhibition.
2. Hb binding affinity will increase, b/c BPG is negatively charged and would not be able to bind as well to alanine. Curve will look more like myoglobin.
3. B/c of remaining salt bridges
4. By mutating certain ones and seeing hte result.
1. At what concentration of substrate is rxn rate the fastest?
2. How does increased affinity to O2 affect Hb dissociation curve? Decreased affinity?