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01:694:301 Lecture Notes - Lecture 7: Enzyme Kinetics, Chemical Kinetics, EnzymeExam


Department
Molecular Biology and Biochemistry
Course Code
01:694:301
Professor
F.Deis
Study Guide
Final

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CHM 376 Biochemistry I
Spring 2020
Problem Set 7: Enzyme Kinetics
NOTE that this Problem Set contains two kinds of questions, both of which will help
you in your studying: 1) numerical or equation-based problems that will help you
practice kinetic principles; and 2) thought-based problems that will help track your
progress to develop an understanding of the principles covered in the book (Ch. 13)
and the slides/annotations. Some of them are far more challenging than others
(and probably exceeding the level of proficiency required to do well on the
upcoming exam) but with enough time and communication with classmates (and
PGLs or instructor) you should be able to answer most of these questions.
1. Define “enzyme”. How does an enzyme differ from other chemical catalysts?
2. What is a cofactor, and how does it contribute to enzyme function? (we will get to
HOW different cofactors work soon).
3. Explain the difference between an apoenzyme and a holoenzyme.
4. Explain the concepts of lock and key and induced fit and why induced fit is
important to an overall reaction. What is the major challenge faced by the enzyme, and
how does an induced fit model help resolve this challenge?
5. Do you think stereospecificity is important in enzyme activity?
6. What class of classical enzymes would catalyze the following reaction?
7. Why would you consider it biologically advantageous to have two enzymes to
catalyze forward and reverse reactions? Under what thermodynamic conditions does
one enzyme suffice? (no, we did not address this specifically in any slide this is a
thinking question for you, and I hope you can answer it based on information presented).
- One enzyme in equilibrium
8. How does raising the temperature increase the rate of a chemical reaction?
9. How does the addition of a catalyst increase the rate of a chemical reaction?

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10. Why, in general, must enzymes bind their substrates weakly? (another thinking
question!)
11. Suppose we have a chemical reaction at equilibrium A →B, and our goal is to
make as much B as possible. Would a protein that binds B tightly be a good catalyst?
What might be the problem with an enzyme that binds tightly to B? (ditto!)
12. Why can you not make pineapple JelloTM that includes chunks of fresh pineapple?
13. What is the meaning of the term rate enhancement? Can enzymes make unfavorable
reactions favorable? Do enzymes change Keq? How can a thermodynamically
unfavorable reaction be made favorable?
14. How do catalysts accelerate the rate of a reaction? Use a plot of kinetic energy (x
axis) and number of molecules (y axis) to explain your answer. Then use transition
state theory to answer the same question.
-Reactions proceed through an unstable (high energy) intermediate, the
transition state, to products.
- The rate of the reaction is determined by the ΔG between the reactants and the
transition state (activation energy).
-Enzymes accelerate the rate of the reaction by stabilizing the transition state or
changing the reaction pathway to use a more stable transition state.
15. What are some questions we can answer through the use of enzyme kinetics?
16. Define the terms chemical kinetics, rate laws, rate constants and reaction
mechanisms. What is the meaning of the term “rate of a chemical reaction”?
17. Show that the bimolecular association rate constant (kinetic) has units of M-1 s-
1, that the unimolecular dissociation rate constant (kinetic) has units of s-1. Using
the relationship between these two different rate constants, what are the units of
the dissociation constant (thermodynamic)?
18. The rate constant for binding of O2 to myoglobin (kon or ka) is 14 M-1 sec-1,
and the rate constant for dissociation of O2 from myoglobin (koff or kd) is 12 sec-1.
Write the KD (or Kd, as it means the same thing you’ll see both in slides/books)
for myoglobin in terms of these association and dissociation rate constants.
(NOTE that RATE constants are in lower-case letters and thermodynamic
constants , e.g. Keq (= Kd in this case) are in upper case letters! do not EVER
confuse them!)
19. What do we mean by the phrase, “the binding constant is determined by how fast
things come together and how fast they fall apart”?
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20. According to Brown and Henri, what are the four parameters that determine how
fast a sample of enzymes will convert substrates into products?
- How fast enzymes turn substrates to products
21. What is the Brown-Henri hypothesis? How does the Brown-Henri hypothesis relate
enzyme function to myoglobin? What is different between an enzyme and a protein like
myoglobin? Why, according to Brown and Henri, is there a point where increasing the
concentration of substrate does not increase the rate at which product is formed?
22. What is the steady state assumption? How does it differ from the equilibrium
assumption? According to either assumption does the concentration of ES change
during enzyme catalysis?
23. Write the mathematical rate model for the Brown-Henri hypothesis. There are
three rate constants (assuming catalysis is irreversible under the conditions studied).
What chemical reaction does k1 describe and what are its units? What does k-1 describe
and what are its units? What does k2 describe and what are its units? How is an
enzyme, according to Brown and Henri, like myoglobin? How is it different?
24. Write an equation in terms of rate constants that describes the fraction of
enzymes bound by substrate. Show that the units of this expression (called KM)
are concentration. Show that when [S] = KM, vo = Vmax/2.
25. Assuming KM = 2mM, at what concentration of [S] would vo = 0.36 X Vmax?
26. Is KM an intrinsic property of an enzyme or does it describe a specific enzyme-
substrate pair? Can an enzyme have more than one KM value?
- The same enzyme will have different Km depending on the enzyme
27. Define Vmax. What is the turnover number? What are the units of turnover number?
What are the two potential units for Vmax, and in what way are they similar and
different? How does Vmax depend on [S]? How does Vmax depend on [Et]? How
many more ways can I ask the exact same question?
- Turnover number K2 (kcat) s-1 (rate at any one enzyme can turn into product
assuming the soln saturated with substrate)
28. Write the full Henri-Michaelis-Menten equation of enzyme kinetics, including
the rate constants for each step.
- How is V0 different from Vmax
-
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