Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #1
Name ___________________________________
I. Multiple Choice. Fill in the circle on the test form corresponding to the correct answer.
1. 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
2. Natural membranes ______________.
a. reseal spontaneously if pierced
b. possess many properties in common with artificial membranes
c. have some properties that artificial membranes lack
d. b and c
e. a, b and c
3. Red blood cells with a surface area of 450 µ2 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 µ2
b. 45 µ2
c. 150 µ2
d. 225 µ2
e. 900 µ2
4. The effect of cholesterol on eukaryotic cell membranes is to _________.
a. abolish gangliosides
d. enhance transition temperature
b. abolish transition temperature
e. stabilize protein interactions
c. enhance gangliosides
5. 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
6. 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
7. 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
8. What bonds are involved in holding together tertiary structure in proteins?
a. glycosidic linkages
c. van der Waals interactions
e. b, c and d
b. hydrophobic interactions
d. ionic bonds
9. Which molecular component of the lipid bilayer is at least partially hydrophobic?
a. gangliosides b. phospholipids c. cholesterol d. all of the other answers e. neutral glycolipids
10. 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 correctly describe(s) this protein?
a. extrinsic
b. peripheral
c. integral
d. c and e
e. transmembrane
11. _________ abolish(es) __________ in cell membranes.
a. Phospholipids, fluidity
c. Cholesterol, transition temperature
b. Phospholipids, transition temperature d. Cholesterol, fluidity
e. b and c
12. Which of the following would be an example of the striking asymmetry found in cell membranes?
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #2
Name ___________________________________
a. prevalence of carbohydrates on the cytoplasmic leaflet of the cell membrane
b. the distribution of carbohydrates on membrane cholesterol
c. the distribution of nucleic acids on membrane lipids
d. the prevalence of carbohydrates on proteins exposed extracellularly
e. a and d
13. 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. connect it to microtubules and/or intermediate filaments
c. attach it to many membrane lipids
d. connect it to the nucleus
e. a, b and c
14. Which of the following membrane components would not normally be classed as amphipathic?
a. cholesterol
b. a peripheral protein bound to the cytoplasmic leaflet
c. an transmembrane protein
d. sphingolipids
e. a, c and d
15. 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
16. Which property below is typical of pleated sheet structure?
a. a high degree of extensibility c. flexibility
e. b and c
b. strength
d. rigidity
17. 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
d. selective precipitation
b. trichloroacetic acid (TCA) precipitation
e. b and d
c. sodium hydroxide precipitation
18. 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. 2D-gel electrophoresis
e. homogenization
b. tissue fractionation
d. affinity chromatography
19. Which technique(s) are routinely employed in two-dimensional (2D) gel electrophoresis?
a. ion exchange chromatography
d. freeze fracture-freeze etch
b. isoelectric focusing
e. b and c
c. non-denaturing PAGE
20. The -helix is stabilized by ______________.
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #3
Name ___________________________________
a. H bonds between polar amino acid R groups
b. covalent bonds
c. H bonds between amide (peptide) linkages oriented parallel to the molecule's axis
d. acidobasic combinations
e. H bonds between amide linkages, oriented perpendicular to the molecule's axis
21. The final protein conformation (the 3-D shape) is determined by ____________.
a. the interaction between the R groups within the protein's backbone
b. interaction between phospholipid R groups
c. the interaction between adjacent or nearly adjacent regions of the nucleic acid backbone
d. the primary structure
e. c and d
22. 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
23. 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
24. 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
25. 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
26. 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
e. a and b
b. SDS-PAGE
d. ion-exchange chromatography
27. 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
28. Which technique could be used for molecular weight determinations in proteins under some
circumstances?
a. gel filtration
d. a and e
b. isoelectric focusing
e. SDS-PAGE
c. diethylaminoethyl (DEAE) cellulose chromatography
29. An electrochemical gradient is a gradient in _______________.
a. molecular weight
b. charge c. concentration d. b and c
e. a and b
Biology 263
Joel Piperberg
Second Exam
Name ___________________________________
Cell Biology
October 27, 2009
Page #4
30. What is the highest level of polypeptide structure in a protein exhibiting multiple subunits in its
structure?
a. quaternary
b. secondary
c. tertiary
d. -helix
e. primary
31. What kind of polypeptide structure involves interaction within the same chains in the form
of H bonds parallel to the axis of the molecule?
a. primary
b. secondary
c. tertiary
d. -helix
e. b and d
32. You are purifying a protein. Before you have employed any procedures to purify it, its
specific activity is 240 units/mg protein. After 5 successive purification procedures, the specific
activity is 120,000,000 units/mg protein. How much have you purified the protein?
a. 50,000 times
b. 5,000 times
c. 500,000 times d. 0.00005 times
e. .0005 times
33. Which of the following is a reason that the Unit Membrane Model of membrane structure
was eventually rejected?
a. Membranes vary in thickness.
b. Lipid content on membranes by weight varies significantly.
c. Cholesterol content of membranes varies.
d. Ratios of the various lipids in a membrane vary from membrane to membrane.
e. all of the above
34. How are two cells fused together?
a. By using a special intracellular glue.
b. They are fused together by using special bacteria.
c. They are fused together using a special virus.
d. By inserting special proteins in the cell membranes of the two cells to be fused.
e. Through the auspices of specific oligosaccharides.
35. What was the major feature added to the last Davson-Danielli model of membrane structure
that had been missing from the earlier models? It fixed a major deficit of the earlier models.
a. carbohydrates on the extracellular surface
b. membrane pores
c. a specific membrane protein
d. carbohydrates on the cytoplasmic surface of the membern
e. cholesterol
36. Why are red blood cells (RBCs) used in the study of the plasma membrane of cells?
a. RBCs are easily available in large uncontaminated amounts.
b. RBCs have no contaminating internal membranes.
c. It is easy to prepare RBC pure membranes (ghosts)
d. a and b
e. a, b and c
37. Which of the following is a type of movement exhibited by membrane proteins?
a. rotational diffusion b. neighbor exchange c. lateral diffusion d. flip-flop e. a and c
38. What property of a protein can be determined directly with gel filtration chromatography if
the protein is globular in shape?
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #5
Name ___________________________________
a. molecular charge b. molecular weight c. molecular shape d. Stokes' radius
e. b and d
39. 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
40. 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
41. 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. CM-cellulose chromatography
c. IR spectrometry
42. 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
43. 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
44. 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
45. Proteins are able to adopt their natural conformations spontaneously, but sometimes they
must be shielded from the cell cytoplasm to allow this to happen more efficiently. Proteins
that shield other proteins under such circumstances are called ___________.
a. ubiquitins
b. chaperonenes c. molecular chaperones
d. b and c
e. flippases
Biology 263
Joel Piperberg
Second Exam
Name ___________________________________
H
CH
2
CH
2
CH
2
N
C
NH
CH
2
NH
arginine
Cell Biology
October 27, 2009
Page #6
CH3
CH
2
CH
leucine
CH
O
CH2
C
O
HO
CH2
OH
aspartate
tyrosine
CH
3
CH
valine CH
CH2 SH
cysteine
CH CH S CH
2
meth ionine
alan ine
O
CH
2
CH
2
glutamine
2
2
CH
NH2
2
CH
H
3
H
C
C
CH2 CH2
glutamate
CH2 OH
serine
C
OH
O
CH
3
CH3
H
glycine
2
phenylalanine
3
CH3
OH threonine
2
CH
2
NH
lysine
C
CH 2 CH3
CH3 isoleucine
CH
CH
2
2
CH
CH
2
C
2
NH2
asparagine
CH2
histidine
NH
+
C
H
2
HC
N proline
H
CH
C
HN
CH
2
tryptophan
C
HC
N
H
II. Short Answer. Please be as brief as possible.
1. Name one treatment that causes the denaturation of proteins. (1 point)
2. What is the highest level of structure exhibited by a protein having only one subunit? (1 point)
3. 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. You are using a variety of purification techniques to purify a protein and monitoring the specific
activity after each step. After the first purification step, the specific activity of your sample is
150 units of activity/mg of protein. After the second purification technique is applied, the
specific activity of your sample is 50 units of activity/mg of protein. What would your response
to these data be? (1 point)
5. Identify the techniques described below? (3 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. yields a measure of molecular size in S units
6. What are the two purposes of SDS in SDS-PAGE? (2 points)
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #7
Name ___________________________________
BONUS QUESTIONS
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. A region of a protein is globular and has a discrete function that is part of the full function of
the protein; it is attached to other similar globular sections of the protein by a flexible hingelike
region. What is this globular region of a protein called? (1 point)
3. What is the name of a salt that is frequently used in selective precipitation? (1 point)
4. What American President was born exactly the same day as Charles Darwin? (1 point)
5. What is the name of the process by which proteins fold in steps with each step providing clues
to the next step? (1 point)
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #8
Name ___________________________________
6. What is one treatment that is likely to make a protein lose its secondary, tertiary and quaternary
structures? (1 point)
7. JEOPARDY BONUS QUESTION (Your answer to tthhiiss aanndd oonnllyy tthhiiss qquueessttiioonn must be in the
form of a question). (1 point)
This creature makes the loudest sound issued by a living organism on Earth.
8. You are attempting to isolate mitochondria from liver tissue and the first step is to homogenize the
liver tissue. Why is the homogenization medium kept cold and why is it isotonic? (2 points)
9. Why is the lateral diffusion of bacterial lipids faster than that of eukaryotic lipids? (1 points)
10. 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)
11. Draw and/or describe the fluid-mosaic model of membrane structure. In a drawing, label
important structures. Explain why the name of the model is fluid mosaic. (3 points)
12. You design a drug that you want to reside in the extracellular fluids of the body instead of in
cells. What two properties should the drug have? (2 points)
13. 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
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #9
Name ___________________________________
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 125I, 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 3H borohydride, a process which radioactively labels sugar residues to which galactose oxidase and 3H borohydride are exposed. In Graphs © and (d), the dotted line indicates labeling of whole cells and
the solid 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.)
Exposure on intracellular or
extracellular surface?
Glycoprotein?
Which leaflet has the sugar
group (if any)?
A
B
C
D
Which protein, if any, may be involved in membrane transport? (4 points)
Which protein has the lowest molecular weight? (1 point)
14. You prepare sealed and leaky red blood cell ghosts and treat them with trypsin. Gel A shows
the proteins in the membranes before treatment with trypsin. On Gel B, draw where the
Biology 263
Cell Biology
Joel Piperberg
October 27, 2009
Second Exam
Page #10
Name ___________________________________
bands would be after treatment of the sealed red blood cell ghosts with trypsin. On Gel C,
draw where the bands would be after treatment of the leaky red blood cell ghosts with trypsin.
(4 points)
4
Extracellular Surface
3
1
5
Cytoplasmic Surface
2
1
5
3
2 4
A
Top of
Gel
Bottom of
Gel
B
Top of
Gel
Bottom of
Gel
C
Top of
Gel
Bottom of
Gel