Biology 362
Joel Piperberg
Page # 1
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
I. Multiple Choice. Fill in the circle on the test form corresponding to the correct answer.
1. Which of the following is an example of the methods by which enzymes catalyze their reactions?
a. local alterations of potassium concentration
d. b and e
b. stressing a bond
e. transitory formation of covalent bonds
c. strengthening of bonds by electrophilic attack
2. The initially accepted model of the enzyme and its active site proposed by Emil Fischer in the late
1800s states that the enzyme __________.
a. has a flexible active site that fits the substrate more tightly after substrate has bound
b. interacts with substrate magnetically
c. works by locally unfolding and refolding around the substrate
d. possesses a rigid active site that can distinguish minor differences between potential substrates
e. is made of plastic
3. A compound binds covalently to lysine in the regulatory site of an enzyme. It is extremely difficult to
remove and it alters enzyme activity. What phrase below could describe its effect on the enzyme?
a. irreversible competitive inhibition
d. b, c and e
b. irreversible noncompetitive inhibition
e. irreversible activation
c. irreversible allosteric inhibition
4. Which of the following bind to the active site of an enzyme?
a. activators
b. substrate c. competitive inhibitors
d. noncompetitive inhibitors e. a and d
5. Which of the following could be true if an active enzyme is inhibited at its active site with a molecule
called P2?
a. P2 would resemble the normal substrate for the enzyme.
b. The quantity of raw substrate would have to be very high.
c. P2 is an alternate substrate for the enzyme.
d. a and c
e. Less water would have to be made available.
6. An enzyme is inhibited at its allosteric site by an inhibitor (P3). Which of the following would have
to be true about P3?
a. P3 would have to be similar to the enzyme.
b. P3 is likely to differ from the substrate in structure.
c. P3 would be similar in structure to the substrate.
d. P3 attracts the substrate to the allosteric site
e. P3 is found at concentrations much lower than the substrate.
7. A scientist crystallizes an enzyme isolated from an alien organism and analyzes its structure with Xray diffraction crystallography. He repeats the experiment after binding a substrate to the enzyme and
the results of crystallography suggest that the shape of the enzyme has not changed significantly.
What model of the enzyme active site would be supported by these findings?
a. The Fluid-Mosaic Model
c. The Induced Fit Model
e. The Mendel Model
b. The Lock-and-Key Model
d. The Chemiosmotic Model
8. The abbreviation that represents a change in the total thermal energy of the system is ______.
a. TS
b. S
c. G
d. H
e. H
Biology 362
Joel Piperberg
Page # 2
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
9. What kind of enzyme catalyzes the rearrangement of the atoms in the substrate?
a. lyase b. ligase
c. hydrolase
d. hydrolysase
e. isomerase
10. Which of the following represents kinetic energy?
a. water behind a dam
c. a boulder rolling down a hill
b. a tank filled with gasoline. d. c and e
11. A closed system ___________.
a. exchanges matter with its surroundings
b. can exchange energy with its surroundings
c. b and e
e. a thrown ball flying through the air
d. exchanges nothing with its surroundings
e. exchanges no matter with its surroundings
12. Protein hormones are big molecules that are incapable of passing through a membrane. How do
they “notify” the cell interior that they are present outside of the cell?
a. They cause receptors to activate G proteins.
b. They lead to cyclic nucleotide elongation.
c. They directly activate phospholipase C.
d. a and e
e. They trigger the production of second messengers.
13. Non-target cells for a ________ are cells that have _________ for that particular molecule.
a. hormone, no receptors
c. growth factor, receptors
e. a and c
b. hormone, acceptors
d. growth factor, no receptors
14. Peptide hormones can exert their effects by ___________.
a. causing the activation of inactive enzymes
d. a, b and c
b. indirectly activating G proteins
e. causing the deacetylation of enzymes
c. causing the activation of protein kinases
15. Glucagon keeps the level of cAMP high by __________.
a. changing its receptor’s shape
d. increasing adenylate cyclase activity
b. activating the conversion of cAMP into ATP
e. causing the deactivation of a G protein
c. a and d
16. Which word or words below is associated with a receptor tyrosine kinase?
a. insulin
b. serine
c. cAMP
d. transautophosphorylation
e. a and d
17. You are studying an enzyme reaction and notice that the rate of the reaction decreases when you add
substance Y to the reaction mixture. If you raise the substrate concentration in the mixture (without removing
any Y), the rate of the reaction increases significantly. Which word(s) below accurately describe Y?
a. allosteric inhibitor
c. competitive inhibitor
e. noncompetitive inhibitor
b. a and e
d. activator
18. Coupled reactions __________.
a. have a net +H
b. often involve ATP condensation
c. work by having common intermediates
d. have a net -G
e. c and d
Biology 362
Joel Piperberg
Page # 3
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
19. The enzyme cheneyase responds to the presence of a regulatory molecule with decreased activity
(that is it stops shooting old people in the face). The regulatory molecule is the product of a series of
reactions for which cheneyase is the first enzyme. This is an example of _________.
a. noncompetitive inhibition
c. a and b
e. positive cooperativity
b. allosteric inhibition
d. feedback competition
20. When the rate of product formation in an enzymatic reaction rises steadily, which of the following
things is (are) likely to be happening?
a. A varying period of time is required for the conversion of substrate to product.
b. Each and every enzyme molecule is working at maximum speed.
c. Enzymes are being used only once.
d. all of the other answers
e. Substrate concentration is rising from an initially low value to higher values but has not yet saturated
the enzyme.
21. Two enzymes are analyzed to determine their abilities to bind to their substrates. Enzyme A has a
KM for its substrate of 4 mM and a Vmax of 48 µmoles of product produced per minute; enzyme B's KM
is 6.5 mM and a Vmax of 54 µmoles of product produced per minute. Which statement below is true?
a. Enzyme A exhibits lower affinity than B.
d. Enzyme B exhibits a lower affinity than A.
b. Enzyme B exhibits a higher G than A.
e. Enzyme A exhibits a higher affinity than B.
c. d and e
22. An enzyme that requires a solely organic component that assists its reaction might be said to require
a ___________.
a. cofactor b. coenzyme
c. conjugated protein
d. prosthetic group
e. a and b
23. According to the Second Law of Thermodynamics, ____________.
a. energy can be neither created nor destroyed
d. a system can never lose entropy.
b. heat is required for every process
e. none of the above
c. the entropy of the universe constantly increases
24. Which of the following would be unlikely to be required as a cofactor by a metalloenzyme?
a. Zn+2 ions b. H- ions
c. Mn+2 ions
d. Ca+2 ions
e. a, c and d
25. What is the name of the process by which inactive receptor tyrosine kinase subunits bind together to
form the full and active receptor by having both subunits bind to the same ligand molecule?
a. receptor-mediated dimerization
c. ligand-mediated trimerization e. ligand-mediated activation
b. ligand-mediated dimerization
d. receptor-mediated trimerization
26. Fibronectin is likely to have binding sites for which of the following molecules?
a. cell surface proteins b. collagen c. tubulin
d. GAGs
e. a, b and d
27. The cell coat is composed of ____________.
a. carbohydrates attached by covalent bonds to membrane proteins
b. carbohydrates attached noncovalently to transmembrane proteins
c. the glycocalyx and the fuzzy layer
28. The function of the glycocalyx is __________.
d. a and b
e. a, b and c
Biology 362
Joel Piperberg
Page # 4
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
a. to generate friction between neighboring cells
d. b, c and e
b. to mediate interactions between cells
e. to act as a molecular sieve
c. to prevent large molecules from getting to the cell membrane
29. You have just found a dead deep-sea creature in your fishing nets. It appears to be a new species.
During the post-mortem attempt to classify the organism, a jelly-like, extracellular mass is found in
the abdomen. It is found to contain protein and carbohydrate and lots of water. What kind of
molecule would you expect to find in the jelly-like mass?
a. proteoglycan aggregates b. GAGs c. proteomucoids d. mucopolysaccharides e. a, b and d
30. What can trigger the secretion of neurotransmitters and/or the rearrangement of the cytoskeleton?
a. d and e
c. uptake of Ca2+ ions
e. binding of Ca2+ ions by calmodulin
b. release of K+ ions
d. release of Ca2+ ions
31. Which of the following produces inositol triphosphate directly through its activity?
a. protein kinase A b. adenylate cyclase c. phospholipase C d. protein kinase C
32. Which of the following could be an enzyme?
a. b, c and d
b. a polypeptide
c. a polynucleotide
d. RNase
e. b and c
e. glycogen
33. At what time are living organisms said to be in steady state?
a. only at conception b. at death c. only during adolescence d. never e. from conception until they die
34. According to the First Law of Thermodynamics, _____________.
a. the universe's entropy is decreasing d. energy cannot be destroyed
b. d and e
e. energy can be converted from one form to another
c. matter cannot be destroyed
35. Which of the following is a property of enzymes?
a. They can be altered irreversibly during a reaction. d. c and e
b. They alter the equilibrium of a reaction.
e. They are usually present in low amounts.
c. They raise the energy of activation of a reaction.
36. Which of the following is known to activate protein kinase C on at least some occasions?
a. Ca2+ ions b. IP3 c. diacylglycerol
d. K+ ions
e. a and c
37. A reaction that proceeds with a ____ of heat in the system is called an ______ reaction.
a. loss; exergonic
c. d and e
e. loss; exothermic
b. gain; endergonic
d. gain; endothermic
38. Enzymes effectively catalyze reactions by ___________.
a. lowering the G of a reaction and thus increasing the reaction rate
b. raising the G of a reaction and thus raising the reaction rate
c. raising the activation energy of a reaction and thus raising reaction rates
d. raising the activation energy and thus lowering the reaction rate
e. none of the above
39. What is one way by which living organisms might manage to get a reaction, A <—> B, which has a
small +G to run spontaneously?
Biology 362
Joel Piperberg
Page # 5
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
d. by adding some substrate A
e. b, c and d
a. by coupling with a smaller -H reaction
b. by coupling to a larger -G reaction
c. by removing some product B
40. In the following branched metabolic pathway, a dotted arrow with a minus sign symbolizes inhibition
of a
metabolic step by an end product
L
M
Q
P
O
N
R
-
S
Which reaction(s) would not be inhibited if both Q and S are present in the cell in high concentrations?
a. none of the other answers b. O —> P
c. L —> N
d. O —> R
e. L —> M
41. What second messenger appears to be responsible for relieving the pain of angina?
a. carbon monoxide b. nitrous oxide c. monoamine oxidase d. NO
e. b and d
42. Cells can respond to _________ by altering gene expression.
a. steroid hormones
b. CO
c. peptide hormones
d. a and c
e. glucose
43. The fact that different types of cells contain different proteins explains why ____________.
a. different cell types respond in the same way to different hormones
d. a and b
b. different cell types respond differentially to the same hormone
e. b and c
c. the same cell types respond differentially to the same hormone
44. A molecule is known to bind to calcium ions released into the cytoplasm of a cell causing it to be
activated. It then is able to trigger a number of intracellular activities. Of what protein family is this
protein likely to be a member?
a. calpains
b. calmodulins
c. calculins
d. cadherins
e. calcmodulins
45. Which of the following would not be likely to be triggered by second messengers?
a. programmed cell death c. disassembly of the extracellular matrix
e. initiation of cell division
b. new gene expression
d. changes in cell metabolic processes
BONUS QUESTIONS
46. You homogenize the liver from a rat. After centrifugation to isolate the particulate fraction in the
pellet, you expose the resultant (initial) supernatant directly to glucagon and epinephrine. Which of
the following responses would occur following the abovementioned treatment?
a. Protein kinase activity drops.
d. Glycogen phosphorylase activity does not change.
b. Adenylate cyclase activity in the pellet drops. e. b and d
c. Phosphofructokinase activity decreases.
Biology 362
Joel Piperberg
Page # 6
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
47. You treat the pellet from #46 with glucagon and epinephrine and then wash it with physiological
saline followed by centrifugation. The resultant wash supernatant is exposed to the supernatant
mentioned in #46? What happens to the activity of different enzymes in the supernatant?
a. Phosphorylase kinase activity drops.
d. b, c and e
b. Phosphoribosylkinase activity rises.
e. Glycogen synthase activity rises.
c. Protein kinase activity increases.
48. The initial supernatant from #46 is treated directly with cyclic UMP. What happens to enzyme
activities in the supernatant?
a. Phosphorylase kinase activity increases.
d. Glycogen synthase activity stays the same.
b. Glycogen phosphorylase activity does not change.
e. b and d
c. Protein kinase activity rises.
49. What happens to glycogen synthase activity in the initial supernatant from #46 after the addition of
membrane vesicles containing activated adenylate cyclase and ATP?
a. It increases. b. It decreases. c. It stays the same. d. It increases then decreases. e. It explodes.
50. Which of the following produces a second messenger?
a. phosphorylase kinase b. adenylate lipase C c. guanylate cyclase d. c and e
e. PLC
51. Which of the following directly or indirectly helps to open calcium channels in the smooth endoplasmic
reticulum?
a. an activated G protein
b. IP2 c. diacylglycerol
d. phospholipase C
e. a and d
LECTURE SHORT ANSWER QUESTIONS Please be as brief as possible.
1. What is the name for a series of reactions in which each reaction is triggered by the one before it and
in which the result each reaction in the sequence is magnified? (1 point)
2. a. Name one molecule that activates a G-protein-coupled receptor? (1 point)
b. Name 2 substrates of protein kinase A? (2 points)
c. What removes phosphate groups from proteins that have been directly or indirectly activated by
protein kinase after a hormone leaves its receptor and the hormone response needs to be ramped
down? (1 point)
d. What enzyme releases glucose from glycogen in response to epinephrine? (1 point)
3. Sometimes two amino acid R groups containing carboxyl groups project into an enzyme's active site
but can differ in that one of them will be charged while the other is not. These two amino acid R
Biology 362
Joel Piperberg
Page # 7
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
groups may even be very close together, being separated by no more than 3 Å. Explain how two
amino acid R groups so close together in the protein could differ so greatly in their charge. (1 point)
4. The reaction G + S <—> K + L is highly exothermic and results in an increase in entropy? Is the G
of this reaction positive, negative or 0? How do you know? (2 points)
5. How does protein kinase "know" which proteins it should phosphorylate? (1 point)
SHORT ANSWER BONUS QUESTIONS
1. Who is Professor Moriarty? (1 point)
2. a. Name a molecule that activates a protein kinase A? (1 point)
b. What enzyme polymerizes glucose into glycogen? (1 point)
3. What two features must coupled reactions have? (2 points)
4. What is the thermodynamic term that deals with randomness in the universe? (1 point)
5. What is another name for an organic cofactor? (1 point)
6. To what part of an enzyme does a competitive inhibitor bind? (1 point)
7. ________________ is energy of motion. (1 point)
8. What is the advantage of positive cooperativity? (1 point)
Biology 362
Joel Piperberg
Page # 8
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
9. Since _______ organisms are ______ systems, they exhibit equilibrium instead of ________.
(3 points)
10. What two second messengers are produced from phosphatidylinositol diphosphate? (2 points)
11. What is the only gemstone composed of just one chemical element? What is the element? (2 points)
12. What is an IRS? (1 point)
13. To what does an SH2 domain bind? (1 point)
14. Name an ECM glycoprotein that helps to direct the migration of cells during embryonic development.
(1 point)
15. What kind of molecule is most prominent in the vitreous humor of the eye? (1 point)
16. What type of molecule(s) is (are) best described as large, highly hydrophilic molecules that easily participate
in the formation of gels at low concentration? The molecule has a core of hyaluronic acid. (1 point)
17. What type of signaling is typified by multiple receptors influencing a single effector? (1 point)
18. Name one molecule that activates a receptor tyrosine kinase? (1 point)
19. What is the name of the membrane proteins that interact with elements of the extracellular matrix
(ECM)? Their binding of the ECM could lead to changes in the cytoskeleton and gene expression (1 point)
20. Name two differences between the carbohydrates of proteoglycans and those found on
glycoproteins? (1 point)
Biology 362
Joel Piperberg
Page # 9
Cell Biology
November 23, 2010
Third Exam
Name _______________________________
21. Integrins bind to a specific three amino acid sequence (designated RGD) in a number of proteins. A
dish is coated with a protein containing the RGD sequence. Some cultured cells with integrins
embedded in their membranes were added to the culture dish along with tripeptides with the RGD
sequence. The cells do not bind to the dish. This is an example of _________. (1 point)
22. How would you describe the arrangement of collagen fibers in the stroma of the chick embryo
cornea? What property of the cornea is derived from the regularity of the arrangement of the
collagen fibers of which it is composed? (2 points)
23. Fibronectin is unlikely to have binding sites for which of the following molecules: GAGs, collagen,
proteoglycans, RNA? (1 points)
24. What can be defined as an organized network of extracellular materials found beyond the immediate
vicinity of the membrane? (1 point)
25. What underlies the basal surface of epithelial tissues and has as one of its functions the maintenance
of cell polarity in the epithelium? (1 point)
26. Which drug below acts as an inhibitor of the formation of peptide bonds in peptidoglycans? (1 point)
27. The primary stroma of the chick cornea has no cells within it. Yet the secondary stroma which is
derived from it contains fibroblast cells flattened between layers of collagen. How does this happen?
Describe completely. (2 points)
28. What type of molecule(s) is (are) best described as large, highly hydrophilic molecules that easily
participate in the formation of gels at low concentration? (1 point)