Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #1
Name ___________________________________
I. Multiple Choice. Fill in the circle on the test form corresponding to the correct answer.
1. Some membrane transport proteins allow molecules to leave or enter cells moving down their concentration gradients without binding to the transport protein and without initiating a shape change in that molecule. Such a molecule is called a(n) ________ protein. a. extrinsic b. a, c and e c. transmembrane d. a and c e. carrier
2. You are studying a membrane transport molecule. You have discovered that it transports Cl
-
and glucose. You have prepared inside-out and right-side out vesicles. If the above substances are found on the opposite sides of either type of vesicle, transport is not seen to occur. If, on the other hand, glucose and Cl
-
are placed outside the right-side out vesicles, transport takes place. Which of the following statements about the transport molecule is true? a. It is an antiport, which would work if Cl
-
were placed inside and glucose were placed outside the inside-out vesicles. b. It is a symport, which would work if Cl
-
and glucose were placed outside the inside-out vesicles. c. It is a symport, which would work if Cl
-
and glucose were placed inside the inside-out vesicles. d. It is an antiport, which would work if Cl
-
were placed outside and glucose were placed inside the inside-out vesicles. e. none of the above
3. Some transport proteins convey molecules through a membrane up a concentration gradient by binding to them and then transporting them through the membrane. These transport proteins have maximal velocities of transport rather than the velocity of transport being proportional to solute concentration. What type of transport is coordinated by these proteins?
a. passive transport c. active transport e. c and d
b. facilitated diffusion d. carrier-mediated transport
4. Water is a hydrophilic molecule. Why can it pass so readily through a hydrophobic membrane?
a. It is so large. b. It is so narrow. c. It is so small. d. It is slightly hydrophobic. e. It is amphoteric.
5. _______ is a small, hydrophobic molecule that dissolves in a membrane and increases ion permeability sometimes with disastrous results for a cell. a. Streptomycin b. Gramicidin A c. An ionophore d. b and c e. Myxomycin
6. Which technique below depends on the ability of a protein like an antibody to bind to the antigen that it normally binds to and that initiated its production?
a. CM-cellulose chromatography c. ion exchange chromatography e. homogenization
b. tissue fractionation d. affinity chromatography
7. Which technique(s) is(are) routinely employed in two-dimensional (2D) gel electrophoresis?
a. ion exchange chromatography c. non-denaturing PAGE e. b and c
b. isoelectric focusing e. freeze fracture-freeze etch
8. Which of the following is attached to fluorescent molecules to localize, highlight and visualize a specific protein like actin within a cell?
a. polyacrylamide b. fluorescein c. antigens d. antibodies e. substrate
9. A(n) _________ gradient is a gradient in charge and concentration.
a. molecular b. electrochemical c. electromagnetic d. chemoelectric e. b and d

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #2
Name ___________________________________
10. Natural membranes ______________.
a. reseal spontaneously if pierced d. b and c
b. possess many properties common to artificial membranes e. a, b and c
c. have some properties that artificial membranes lack
11. Red blood cells with a surface area of 450 µ
2 are lysed and the lipids of their membranes are totally extracted. These lipids are then spread over the surface of a water tank and the surface area covered is found to be
a. 90 µ 2
______.
b. 45 µ 2 c. 150 µ 2 d
.
225 µ 2 e. 900 µ 2
12. The effect of cholesterol on eukaryotic cell membranes is to _________.
a. abolish gangliosides d. enhance transition temperature
b. abolish transition temperature
c. enhance gangliosides e. stabilize protein interactions
13. During the winter, some organisms adjust the fluidity of their membranes by __________.
a. increasing phospholipid tail length d. decreasing phospholipid tail length
b. increasing tail unsaturation e. increasing tail saturation
c. b and d
14. Which molecular component of the lipid bilayer is at least partially hydrophobic?
a. peripheral proteins b. phospholipids c. cholesterol d. b, c and e e. glycosphingolipids
15. A protein that cannot be washed off of a cellular membrane by a moderately high concentration of a salt solution is called a(n) ______ protein.
a. transmembrane b. lipid-anchored c. a and b d. peripheral e. b and d
16. A protein is embedded in the cytoplasmic leaflet of the cell membrane. It is decreased in size when either side of a red blood cell ghost membrane containing it is treated with a proteolytic enzyme like trypsin. Which word(s) below is/are correctly describes this protein?
a. extrinsic b. peripheral c. integral d. c and e e. transmembrane
17. Which of the following would be an example of the striking asymmetry found in cell membranes? a. prevalence of carbohydrates on the outer surface of the cell b. the distribution of carbohydrates on membrane cholesterol c. the distribution of nucleic acids on membrane lipids d. the distribution of branched phospholipid tails e. a and b
18. If you wish to limit the mobility of a protein in the membrane which technique would you utilize if you were a cell? a. make it very large
b. attach it to many membrane lipids
c. connect it to microtubules and/or intermediate filaments d. connect it to the nucleus e. a, b and c
19. The process of isolating a particular organelle in a bulk amount by differential centrifugation is called _______.
a. cell adaptation b. autoradiography c. liquid scintillation d. cell fractionation e. precipitation
20. Which of the following membrane components would normally be classed as amphipathic?

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #3
Name ___________________________________
a. cholesterol d. sphingolipids
b. an integral protein buried completely in the membrane e. a, c and d
c. an transmembrane protein
21. With which of the following methods are S units associated as a unit of measure?
a. gel filtration b. ultracentrifugation c. SDS-PAGE d. non-denaturing PAGE e. autoradiography
22. Two different proteins have different amino acid sequences and tertiary structures that lead to different physical properties. Which of such properties listed below is not used in the purification of proteins by the techniques that have been discussed in class?
a. molecular weight b. color c. ionic charge d. shape (conformation) e. solubility
23. SDS-PAGE has the disadvantage that it ___________.
a. c and e
b. does not allow the detection of proteins in a gel by their biological activity
c. separates on the basis of more than one property thus to some degree confusing the results
d. separates solely on the basis of molecular weight
e. separates on the basis of molecular weight and charge
24. In which technique, does a protein applied to a gel move steadily down the gel and stop before reaching the end while the current is still on?
a. isoelectric focusing c. isometric focusing
b. SDS-PAGE d. ion-exchange chromatography e. a and b
25. Which technique effectively separates proteins on the basis of their molecular charge and size?
a. ion exchange chromatography c. non-denaturing PAGE e. SDS-PAGE
b. sucrose density gradient centrifugation d. a and c
26. Which technique could be used for molecular weight determinations in proteins under at least some circumstances?
a. gel filtration c. diethylaminoethyl (DEAE) cellulose chromatography e. SDS-PAGE
b. isoelectric focusing d. a and e
27. With which of the following is clathrin associated? a. coated vesicles b. coated pits c. fuzzy coat d. a and b e. a, b and c
28. Coated pits are a site at which _______ can occur.
a. receptor-mediated endocytosis c. bulk-phase endocytosis e. adsorptive exocytosis
b. adsorptive endocytosis d. a, b and c
29. After ________ are totally internalized, the molecules the molecules surrounding them and that helped them form are recycled. a. peripheral proteins b. coated vesicles c. insulin receptors d. LDL receptors e. phospholipids
30. 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. troponins d. cadherins e. calcmodulins

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #4
Name ___________________________________
31. Ouabain is a very specific inhibitor of the active transport of potassium ions out of the cell and is therefore a valuable tool in studies of membrane transport mechanisms. Which of the following processes in your own body would you expect to be sensitive to inhibition by ouabain? a. passive transport of glucose into a muscle cell b. active transport of sodium ions out of macrophages in adipose tissue c. transport of phosphorus ions into liver cells d. active uptake of lactose by the bacteria living in your intestine e. none of the above
32. The Na + -K + pump makes the cell exterior more ___ than the interior because it pumps __ K + ions into the cell for every __ Na +
ions pumped out of the cell. a. neutral; 3; 3 b. negative; 2; 3 c. positive; 2; 3 d. negative; 3; 2 e. positive; 3; 2
33. What might the cellular basis of a disease called familial hypercholesterolemia (an inherited disease in which blood cholesterol levels are very high) be?
a. The blood produces too much cholesterol. d. b and c
b. Receptors for LDL are mutated and do not bind it. e. Receptors for HDL are not made.
c. Receptors for LDL do not bind to coated pits.
34. Which of the following molecules would not pass directly through a lipid bilayer very easily? a. water b. a peptide hormone c. O
2
d. sodium ions e. b and d
35. What property of a protein can be determined directly with gel filtration chromatography if the protein is globular in shape?
a. molecular charge b. molecular weight c. molecular shape d. Stokes' radius e. b and d
36. If a solution containing the following tripeptides were passed through a column packed with
DEAE-cellulose at pH 7, which of them would bind most effectively to the DEAE-cellulose column? (see drawing at end of Multiple Choice section for R groups)
a. N - arginine - lysine - proline - C d. N - leucine - alanine - glycine - C
b. N - aspartate - glutamate - aspartate - C e. N - aspartate - phenylalanine - leucine - C
c. N - phenylalanine - aspartate - glycine - C
37. Which technique would be most likely to result in a high degree of purification?
a. differential centrifugation c. precipitation e. affinity chromatography
b. ion exchange chromatography d. homogenization
38. Which technique could be used to detect the differences in conformation (shape) seen in enzymes that are bound or unbound to their substrates?
a. X-ray diffraction d. isoelectric focussing
b. SDS-polyacrylamide gel electrophoresis e. DEAE-cellulose chromatography
c. spectrophotometry
39. Which one of the following molecules will elute first from a gel filtration column? (Assume that all amino acids have the same molecular weight.)
a. a globular protein composed of 225 amino acids d. a globular protein with 187 amino acids
b. a very low molecular weight dye e. a protein consisting of 135 amino acids
c. a cigar-shaped protein of 226 amino acids

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #5
Name ___________________________________
40. A protein you wish to study is located in the lysosomes of rat liver cells and is readily extractable from partially purified lysosomes. It has a highly positive charge at pH 7. You propose to use a series of techniques to purify the protein. In what order would you use the techniques after you had homogenized the tissue?
a. sucrose density gradient centrifugation (SDGF)- extraction - isoelectric focussing (IEF) -
precipitation by ammonium sulfate
b. differential centrifugation - SDGF - extraction - ammonium sulfate precipitation - CM
(carboxymethyl) cellulose chromatography - affinity chromatography
c. ammonium sulfate precipitation - SDGF - extraction - CM cellulose chromatography - IEF -
SDGF
d. IEF - affinity chromatography - differential centrifugation - extraction
e. differential centrifugation- SDGF - extraction - ammonium sulfate precipitation - DEAE
(diethylaminoethyl) cellulose chromatography - affinity chromatography
41. Which technique below is the best for locating and visualizing radioactive isotope in a specimen?
a. c and d c. liquid scintillation counting e. ultracentrifugation
b. atomic force microscopy d. autoradiography
42. What is the name of the protein that helps to control the size of coated vesicles by becoming part of a cage constructed around the vesicles as they form?
a. classrin b. elastin c. tubulin d. clathrin e. vesiculin
43. Non-denaturing PAGE has the disadvantage that it ________________.
a. c and e
b. prevents the detection of proteins in a gel by their biological activity
c. separates on the basis of more than one property thus to some degree confusing the results
d. separates solely on the basis of molecular weight
e. separates on the basis of molecular weight and charge
44. Which of the techniques below might be used to effect a rapid purification and would be based on the solubility of the molecule to be purified?
a. sucrose density centrifugation
b. trichloroacetic acid (TCA) precipitation
c. sodium hydroxide precipitation d. selective precipitation e. b and d
45. You are studying the transport of two molecules through the cell membrane. Their transport appears to be linked and one enters the cell while the other leaves. If the transport of one is halted, so is the transport of the other. If an inhibitor of ATP synthesis is added to the cells containing the transport molecule, transport of the two molecules does not continue. What words best describe the transport molecule? a. active antiport b. active symport c. passive symport d. passive antiport e. active uniport

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #6
Name ___________________________________
H
CH
2 arginine
CH
2
CH
2
O
N C
NH
NH
2
CH
2 leucine
CH
CH
3
CH
3
CH
2 phenylalanine
O
H glycine
CH
2 aspartate
C HO
OH valine tyrosine
CH
CH
3
CH
3
CH
2
CH
2
CH
2
CH glutamate
2
C
OH
CH serine
2
OH
CH
2 asparagine
O
CH SH cysteine
CH
2
H
CH
2
CH
2 lysine
NH
2
C
NH
2 alanine
CH
3
CH
2 methionine
CH
2
S CH
3
H
C
CH
3
CH CH
3 isoleucine
CH
2
CH
2
CH
2 histidine
C
HN
CH
NH
+
CH
2
CH
2 glutamine
C
O
NH
2
C CH
3
OH threonine
CH
2
N
H
HC proline
CH
2 tryptophan
C
HC
C
H
N
H
II. Short Answer.
Please be as brief as possible.
1. Name one treatment that causes the denaturation of proteins when preparing them for SDS-PAGE.
(1 point)
2. You are attempting to isolate mitochondria from liver tissue and the first step is to homogenize the liver tissue. In the homogenization buffer, what condition prevents the denaturation of the enzyme you are trying to isolate? What kind of buffer is used to prevent the lysis of the mitochondria you are trying to isolate? (2 points)
4. Identify the techniques described below? (4 points)
a. separation of proteins on the basis of the pH at which they become neutral
b. separation of proteins on the basis of their Stokes' radius
c. accurate determination of the amount of radioactive molecules taken up by cultured cells
d. causes proteins to aggregate together
5. What are the two purposes of SDS in SDS-PAGE? (2 points)
6. What is the name for a membrane transport molecule that allows solutes or ions to move across the plasma membrane down their concentration gradient without an interaction between the transport molecule and the solute or ion? The transport begins only after an appropriate stimulus is detected by the transport molecule. (1 point)
BONUS QUESTIONS - LECTURE-SHORT ANSWER

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #7
Name ___________________________________
1. Briefly name and define the levels of structure in proteins. What types of bonds are instrumental in holding each level of structure together? (8 points)
Level of Structure Definition Bond(s) Involved
2. What is the name of a salt that is frequently used in selective precipitation? (1 point)
3. What American President was born exactly the same day as Charles Darwin? (1 point)
4. What eventually led to the rejection of the Unit Membrane Model of membrane structure? (1 point)
5. What is another name for the process known as transverse diffusion in the plasma membrane?
(1 point)

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #8
Name ___________________________________
6. Who was the voice Woody in Toy Story and Toy Story II ? (1 point) For an extra point, in what TV series did this actor get his start? He played a man dressed as a woman living in a hotel for women.
7. You fuse a human and a mouse cell together and then label the resultant cell with fluorescently labeled antibodies against human and mouse membrane proteins. The anti-mouse antibodies are labeled with fluorescein (green) and the anti-human antibodies are labeled with rhodamine (red). Based on the fact that the cell contains nuclei from two different cells, what is the cell called immediately after fusion? (1 point)
What does the cell look like immediately after fusion? (1 point)
What does the cell look like 40 minutes to an hour after fusion? (1 point)
8. You are designing a drug that must stay in the extracellular space outside the cell. What two properties must that molecule have in order for it to remain outside the cell? (2 points)
9. a. The name of the presently accepted model of membrane structure is the ___________.
b. What has been a constant feature of all of the models of membrane structure?
c. What type of membrane protein interacts with the polar heads of lipids and the extracellular portions of membrane proteins?
d. What type of membrane protein is in contact with the nonpolar portion of the membrane?
e. What is a lipid-anchored protein?
(5 points)
10. Draw and/or describe the presently-accepted model of membrane structure. In a drawing, label important structures like the different proteins associated with the membrane. (3 points)

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #9
Name ___________________________________
11. Look at the following experimental results obtained by a deep-space probe investigating life on other planets.
Membrane proteins were extracted with SDS and subjected to SDS-polyacrylamide gel electrophoresis on tube gels. The resultant gels were stained with Coomassie Blue, which stains proteins (a) and Periodic Acid-Schiff (PAS) stain, which specifically stains carbohydrates (b).
When whole cells or inside-out vesicles were exposed to lactoperoxidase and 125 I, the profile in Graph (c) was obtained when the gels were cut into 1 mm thick slices and the radioactivity was monitored in the scintillation counter. In Graph (d), we see the results of exposure to galactose oxidase and residues to which galactose oxidase and 3
3 H - borohydride, a process, which radioactively labels sugar
H - borohydride are exposed. In Graphs (c ) and (d), the solid line indicates labeling of whole cells and the dotted line indicates labeling of inside-out vesicles. What kind of membrane proteins are A,
B, C and D? (i. e., On which surface are they exposed? Do they have polysaccharides and on which side of the membrane are the polysaccharides exposed, if present?) Ignore any preconceived notions about membrane proteins! Just interpret the data!!! (Please see the following page for the graphs.)
Protein
A
B
Is it exposed on the intracellular or extracellular surface?
Is it a glycoprotein?
Which leaflet has the sugar groups
(if any)?
C
D
Which protein, if any, may be involved in membrane transport? (4 points)
Which protein has the highest molecular weight? (1 point)
12. What is the name of the three-legged subunit that self-assembles into the coat found on coated pits and coated vesicles that form at the membrane surface? (1 point)

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #10
Name ___________________________________
13.
4000
3500
3000
DEAE-Cellulose Chromatography of Glucocorticoid Receptors
0.45
cpm
0.4
[KCl}
0.35
0.3
2500
0.25
2000
0.2
1500
0.15
1000
0.1
A
B
500
0.05
0 0
Fraction Number a. Which peak in the graph above represents the most positive molecule? (1 point) b. Look at the graph above. At what KCl concentration does peak A wash off the column? (1 point)

Biology 362 Cell Biology
Joel Piperberg October 26, 2010
Second Exam Page #11
Name ___________________________________