Download Chapter Eight: Enzymes: Basic Concepts and Kinetics

Chapter Eight: Enzymes: Basic Concepts and Kinetics
Use the following to answer questions 1-10:
Choose the correct answer from the list below. Not all of the answers will be used.
a) apoenzymes
e) spontaneous
i) bi-bi
b) maximal velocity
f) turnover number
j) substrates
c) active site
g) M. Menten
k) free energy
d) Cleland
h) prosthetic group
l) allosteric
1. The site on the enzyme where the reaction occurs.
Answer: c
2. Enzymes bind _________.
Answer: j
3. Enzymes that do not have the required cofactor bound are called ________.
Answer: a
4. A tightly bound cofactor might be called a ____________.
Answer: h
5. A reaction that is exergonic will be_______.
Answer: e
6. An endergonic reaction requires an input of _____________ to proceed.
Answer: k
7. Kcat is often referred to as the______.
Answer: f
8. VMAX is the ___________ at saturation substrate concentrations.
Answer: b
9. Enzymes that do not obey Michaelis-Menten kinetics.
Answer: l
10. The KM value is the substrate concentration at which the half of the ______ is measured.
Answer: b
11. Enzyme catalysts can be
A) RNA.
B) lipids.
Answer: D
C) proteins.
D) a and c.
12. What is the common strategy by which catalysis occurs?
A) increasing the probability of product formation
B) shifting the reaction equilibrium
C) stabilization of transition state
D) all of the above
E) none of the above
Answer: C
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E) none of the above.
13. What is the approximate increase in reaction rate due to enzyme catalysis for the
hydration of carbon dioxide?
A) 10 -fold
D) all of the above
7
B) 10 -fold
E) none of the above
C) 1010 -fold
Answer: B
14. Examples of cofactors include
A) Zn2+, Mg2+, and Ni2+ .
B) biotin and thiamine pyrophosphate.
C) pyridoxal phosphate and coenzyme A.
Answer: E
D) b and c.
E) a, b, and c.
15. An example of how enzymes transform energy includes
A) ion gradients.
D) b and c.
B) chemical bond energy.
E) a, b, and c.
C) mechanical energy.
Answer: E
16. The formula K'eq = 10-G°'/1.36 indicates the relationship between
A) the free energy and the equilibrium constant.
B) the reaction equilibrium and the isomerization rate.
C) the equilibrium constant and standard free energy.
D) all of the above.
E) none of the above.
Answer: C
17. Which of the following is not true?
A) Enzymes force reactions to proceed in only one direction.
B) Enzymes alter the equilibrium of the reaction.
C) Enzymes alter the standard free energy of the reaction.
D) All of the above are true.
E) None of the above are true.
Answer: E
18. The Gibbs free energy of activation is
A) the difference between the substrate and the transition state.
B) the difference between the substrate and the product.
C) the difference between the product and the transition state.
D) all of the above.
E) none of the above.
Answer: A
19. The KM is
A) equal to the product concentration at initial reaction conditions.
B) equal to the substrate concentration when the reaction rate is half its maximal value.
C) proportional to the standard free energy.
D) all of the above.
E) none of the above.
Answer: B
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20. Given are five KM values for the binding of substrates to a particular enzyme. Which has the strongest
affinity when k-1 is greater than k2?
A) 150 mM
B) 0.15 mM
C) 150 µM
D) 1.5 nM
E) 15000 pM
Answer: D
21. Which of the following is true under the following conditions: The enzyme concentration is 5 nM, the
substrate concentration is 5mM, and the Km is 5 µM.
A) The enzyme is saturated with substrate.
D) All of the above.
B) Most of the enzyme does not have substrate bound.
E) None of the above.
C) There is more enzyme than substrate.
Answer: A
22. When the substrate concentration is much greater than Km, the rate of catalysis is equal to
A) Kd.
B) kcat.
C) VMAX.
D) all of the above.
E) none of the above.
Answer: B
23. When the kcat /KM ratio is at its upper limit, it is referred to as
A) the maximum velocity.
D) all of the above.
B) Michaelis rate.
E) none of the above.
C) kinetic perfection.
Answer: C
24. Multiple substrate enzyme reactions are divided into two classes:
A) sequential displacement and double displacement.
D) a and c.
B) double displacement and concerted displacement.
E) none of the above.
C) sequential displacement and ping-pong.
Answer: D
25. Which are types of enzyme inhibition?
A) irreversible
B) reversible
Answer: E
C) temporary
D) a, b, and c
E) a and b
26. What type(s) of inhibition can be reversed?
A) competitive
D) a and b
B) non-competitive
E) a, b and c
C) suicide inhibitors
Answer: D
27. In this type of inhibition the enzyme can form a complex with either the substrate (ES) or the
inhibitor (EI), but not both.
A) Competitive
D) All of the above
B) Non-competitive
E) None of the above
C) suicide inhibitors
Answer: A
28. In many enzyme assays, the natural substrate and product are not used. Why?
Answer: Many products are difficult to measure accurately. Some are simply difficult to measure, while others
are difficult to discern against the background of other molecules present in the reaction. Instead, substrates are
chosen that the enzyme can still process, but that result in products that can be easily measured. For example,
substrates are chosen that result in products that are colored and can be detected spectrophotometrically.
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29. Why would you expect thrombin to have greater substrate specificity than trypsin?
Answer: Thrombin carries out a specific reaction in blood clotting. Trypsin is responsible for the digestion of
proteins in the digestive system, and must be able to cleave thousands of different proteins. Thus, its specificity
must be broader than thrombin's specificity.
30. Describe or draw the reaction product(s) of a peptide bond cleavage.
Answer: Peptide bond cleavage requires a water molecule. The cleavage occurs between the carbonyl and the
nitrogen of the peptide bond. The two products would be the N-terminal and the C-terminal peptide pieces, with
a carboxyl group and an amine at the new exposed ends. At pH 7, each should be charged. A diagram similar to
textbook Figure 8.1 is an example.
31. There are six basic categories of enzymes. List the categories and define the type of reaction.
Answer: The categories include Oxidoreductases (oxidation-reduction reactions), Transferases (group transfers),
Hydrolases (hydrolysis reactions), Lyases (addition or removal across a double bond), Isomerases
intramolecular group transfer), and Ligases (ATP-dependent ligation of substrates). See textbook Table 8.3 for
further details.
32. The formation of an enzyme-substrate complex is considered the first step in enzymatic catalysis.
What types of data prove that there is active binding of substrate to enzyme?
Answer: The proof is mathematical (the catalysis is dependent on the amount of enzyme
present) as well as physical (the structure of an substrate-enzyme complex, and spectroscopic evidence indicates
that the substrate is indeed bound by enzyme).
33. How is the substrate bound to the active site?
Answer: The active site is a small part of the total enzyme structure. It is usually a cleft or crevice, which is
formed from amino acids that are contributed by different regions of the peptide, where portions of the peptide
chain come together. The substrate is bound by multiple weak attractions, and its specificity is dependent on the
precise arrangement of the atoms in the binding site.
34. You believe a substrate fits into a cleft like a key into a lock, but your roommate does not. Who is
right?
Answer: You are both partially correct. Like a lock and key, the substrate fits precisely into the enzyme.
However, the site is not a rigid cleft, but is flexible. Thus, it is possible for the substrate to actually modify the
shape of the site a bit, a hypothesis known as induced fit. See textbook Figures 8.9 and 8.10 for further detail.
35. In an enzymatic reaction in a test tube, the reaction will eventually reach equilibrium. Why does this
not happen in organisms?
Answer: In a cell, the product may be utilized for a subsequent reaction, thus the reaction
may not reach equilibrium.
36. What is the Michaelis-Menten equation? Define all parameters.
Answer: V0 = VMAX([S]/([S] + KM))
Initial velocity V0; Maximum velocity VMAX; Substrate concentration [S]; Michaelis constant KM
37. What does VMAX indicate?
Answer: The number of substrate molecules converted into product by enzyme saturated with substrate during a
specified unit of time.
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38. What is the upper limit of kcat /KM?
Answer: The diffusion-controlled interaction of the substrate and enzyme determine the upper limit of the rate.
39. How do the intermediate steps in multi-substrate enzyme mechanisms differ?
Answer: In a sequential displacement reaction both substrates bind, and a ternary complex of all three is formed.
In a double displacement (ping-pong) one or more products are released prior to binding of all substrates. Thus,
a substituted enzyme intermediate is formed.
40. Would you expect the order of substrate binding to be critical for enzyme catalysis?
Answer: Yes, in some cases. For example, in ping-pong reactions the proper substrate would have to bind to
form the right substituted enzyme intermediate form. In sequential displacement, both conditions are observed.
Substrates may need to bind in a particular order (lactate dehydrogenase) or the enzyme may bind substrates and
release products in random order (creatine kinase).
41. How are the types of inhibition kinetically distinguishable?
Answer: Competitive inhibition can be overcome by the presence of large amounts of substrate. However, the
apparent KM is increased. In non-competitive inhibition substrate can bind to the EI complex, however, the
VMAX is altered. In mixed inhibition both values may be altered.
42. What are transition state analogs?
Answer: These potent inhibitors mimic the structure of the substrate during the transition state of the catalytic
process. They bind very tightly to the catalytic site and are useful in determining the structure and catalytic
mechanism of the enzyme.
43. Are vitamins used in their natural forms or are they modified?
Answer: Most are modified to an active co-enzyme form. But at least one (ascorbic acid, vitamin C) is used in
its dietary form.
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