MCB 2210 FALL 2014

PROBLEM SET 1

1. All of the following statements are true about the Cell Theory except:
a. All living creatures are made of one or more cells.
b. The cell is the structural unit of life.
c. On the earth today, cells only arise from division of pre-existing cells.
d. Earlier versions of Cell Theory thought that living cells could arise from non-living
material.
e. All are true statements

2. Which of the following is/ are NOT evidence that RNA probably evolved before DNA and
proteins to serve important functions in the prebiotic world?
a. Proteins can substitute both for DNA and RNA functions.
b. DNA and enzymes are only present in most advanced cells.
c. RNA can both code for genetic information and act as a catalyst.
d. Advanced cells lack RNA.
e. a, b and d are NOT evidence that RNA probably evolved before DNA and proteins.

3. What characteristics distinguish prokaryotic and eukaryotic cells?
a. Eukaryotes have membrane-bound organelles; prokaryotes do not.
b. Prokaryotes have relatively little DNA; eukaryotes generally have much more.
c. Eukaryotic chromosomes are linear; prokaryotic chromosomes are circular.
d. Prokaryotes possess a unique flagellum.
e. all of the above.

Match questions 4-7 with the best description (use each only once)
a. Primary
b. Secondary
c. Tertiary
d. Quaternary
e. Protein domain
4. Alpha helix formation
5. A mutation in the DNA that changes amino acid sequence always alters this
6. A region of a protein that confers a specific function such as phospholipid binding
7. The crystal structure of a protein



8. The key difference between a plant cell and an animal cell is:
a. The presence of a plasma membrane.
b. The presence of a nucleus.
c. The presence of internal membranes.
d. The organization of DNA.
e. None of the above.

9. The method in which antibodies are conjugated to a fluorophore and used to determine the
location within the cell of a specific protein is called ________.
a. immune surveillance
b. immunotherapy
c. polarization microscopy
d. immunofluorescence
e. differential interference contrast microscopy

10. Which statement about multicellularity is false?
a. Both prokaryotes and eukaryotes can form multicellular organisms.
b. Different cell types in a multicellular organism express different genes.
c. Multicellular organisms can be much more complex than single cell organisms.
d. Single-celled organisms are in general less complex cells than the individual cells that
comprise multicellular organisms.
e. Multicellular organisms can form from the gathering of individual cells rather than
fertilization of an egg by a sperm.

11. Evolutionary relationships between groups of organisms are best determined using which of
the following types of information?
a. Comparison of nucleotide sequences.
b. Comparison of structural features.
c. Comparison of biochemical pathways.
d. b and c are both correct.
e. None of the above.

12. Which of the following is an example of an epigenetic phenomenon?
a. Several proteins share amino acid sequences that mediate calcium binding.
b. Methylation of the DNA associated with a gene resulting in the transcription of that
gene being inhibited over multiple cell generations.
c. That all children of a person with Huntingtons disease will get the disease.
d. The primary sequence of the actin in the body.
e. The information that makes your TA male or female.

13. What is defined as the ability to see two neighboring points in a field as distinct entities?
a. revolution
b. magnification
c. resolution
d. tintinnabulation
e. aberration

14. Which of the following conditions would result in the worst resolution in a light
microscope?
a. Red light and 0.95 N. A.
b. Blue light and 0.95 N. A.
c. Blue light and 0.7 N. A.
d. Red light and 0.7 N. A.
e. Green light and 0.95 N. A.

15. Which of the following things can limit resolution in microscopy?
a. Color of the specimen.
b. The wavelength of illumination light.
c. The numerical aperture of the objective.
d. b and c can limit resolution.
e. The magnification power of the ocular lens.

16. You wish to measure calcium concentration changes in living cells. Which of the following
microscopic techniques do you think would be most useful?
a. Transmission electron microscopy
b. Scanning electron microscopy
c. Fluorescence microscopy using a calcium-sensitive indicator dye that is able to cross a
living cell's plasma membrane.
d. None of the above

17. Which statement about light microscopy is true?
a. A light microscope can generate contrast using interference of out of phase light.
b. The resolution of light microscopes is limited primarily by the magnification of the
lens used.
c. Resolution is the only important aspect of visualizing cellular structures.
d. Light microscopy has the same resolving power as all types of microscopy.
e. None of the above.




18. The absorbance of invisible, UV light by a compound and the subsequent release by that
compound of some of the energy as longer, visible light wavelengths is known as
_____________.
a. fluorochrome
b. luminescence
c. fluorescence
d. fluorophore
e. phosphorescence

19. In which light microscope technique does a molecule absorb energy from light and glow with
a bright color or colors against a dark background? The method is often used to localize specific
molecules within a cell.
a. dark field microscopy
b. bright field microscopy
c. phase contrast microscopy
d. fluorescence microscopy
e. polarization microscopy

20. In a fluorescence microscope, ______-wavelength incident light is absorbed by the specimen
and reemitted at a _______ wavelength.
a. long, longer
b. short, longer
c. short, shorter
d. long, shorter
e. medium, shorter

21. The resolution limit of a typical fluorescent microscope is ~200 nm. If two ribosomes that are
50 nm in diameter and 500 nm apart are labeled with a fluorescent antibody, what will you see?
a. You wont be able to detect the ribosomes at all because they are below the resolution
limit of the microscope.
b. You wont be able to detect them because you need an electron microscope to see such
small objects.
c. You will be able to detect the ribosomes, but they will appear as a single 200 nm spot.
d. You wont be able to detect them because the wavelength of light is not short enough
to resolve them.
e. None of the above.





22. Which of the following is true of fluorescence microscopy?
a. Fluorescent microscopy is useful because light is emitted uniformly throughout the
specimen being viewed.
b. Fluorescence microscopy is useful because it presents images in three dimensions.
c. Fluorescence microscopy overcomes resolution problems inherent in light microscopy.
d. Fluorescence microscopy can used to view dead specimens only.
e. To view rounded, thicker organisms, a confocal microscope will yield the best image

23. Why do electron microscopes provide much greater resolving power than light microscopes?
a. because more electrical power is involved in running an electron microscope
b. because electron beam wavelength is much lower than that of visible light
c. because electron beam wavelength is much higher than that of visible light
d. because the numerical aperture is much larger in electron microscopes
e. because the numerical aperture is much smaller in electron microscopes

24. If two parts of a specimen are not separated by sufficient distance, what happens?
a. Magnification is impossible.
b. Diffraction is impossible.
c. The images of the two parts of the specimen cannot be resolved
d. The images of the two parts of the specimen can be seen to be distinctly separated.
e. a and b

25. Which statement is true about electron microscopy?
a. Biological specimens can be alive during electron microscopy.
b. Scanning electron microscopy (SEM) can not be utilized to examine the surface of
objects.
c. To build the image, accelerated electrons are used instead of light.
d. The image formed in a scanning electron microscope is that of biological material
itself.
e. All of the above statements are true.

26. Why does using a conventional microscope to view a whole cell in epifluorescence
microscopy result in an image that is not very crisp?
a. Such specimens have multiple planes of focus.
b. Looking at specimens in a normal light microscope damages the specimen.
c. Light coming from parts of the specimen above and below the focal plane of interest
interferes with the light coming from the part in focus.
d. Such specimens have a single, large plane of focus.
e. a and c.


27. The confocal scanning light microscope produces an image of a _____ plane called
a(n)_______situated within a much _______ specimen.
a. thick, optical section, thinner
b. thick, microtomal section, thinner
c. thin, optical section, thicker
d. thin, microtomal section, thicker
e. thin, optical section, wider

28. A scientist is examining motile protozoa. He wishes to determine their direction of
movement without the use of chemical dyes or transfection of the cells. Which of the following
microscopic techniques is least likely to be useful?
a. phase-contrast microscopy
b. differential interference contrast microscopy
c. fluorescence microscopy
d. none will be useful

29. Why does both direct and indirect immunofluorescence provide remarkable clarity in their
images?
a. Antibodies are bigger than most proteins and thus easier to see in the light microscope.
b. Antibodies absorb large amounts of light and are therefore more visible in the light
microscope.
c. Only the proteins bound by the antibody are visible because of the fluorescent label.
d. All of the unlabeled materials remain invisible in the microscope because no
fluorescent material is attached to them.
e. c and d are correct

30. You are examining the subcellular localization of a putative membrane protein using
immunofluorescence microscopy. Which is a true statement about what you might expect?
a. If the antibody you are using was raised to a portion of the protein that is expected to
be exposed to the cytoplasm, you will not need to permeabilize the membrane with
detergent.
b. Although the lipid bilayer is ~ 4nm across, you would expect to observe an apparent
structure ~ 200 nm across due to the resolution limit of light microscopy.
c. If the proteins are located 50 nm apart from each other, you will observe a dotted
appearance of the membrane due to the separation of each labeled protein.
d. None are true.




31. Which of the following is a technique used to isolate a particular organelle in bulk so that its
function can be studied or so that an enzyme can be isolated from it?
a. differential interference contrast microscopy
b. differential centrifugation
c. affinity chromatography
d. selective precipitation
e. autoradiography

32. Under what set of circumstances will organelles not move to the bottom of a centrifuge tube
in a centrifugal field?
a. if the organelle is too small- say smaller than a ribosome
b. if the organelle has too much fat content
c. if the organelle is less dense than the surrounding medium
d. if the organelle is more dense than the surrounding medium
e. a, b and c.

33. Which would be the best way to visualize dynamics of an intracellular protein in a living
cell?
a. using a fluorescently labeled antibody raised against the protein.
b. expressing a fusion of the protein to GFP
c. using a gold-labeled antibody in combination with transmission electron microscopy
d. immunoprecipitating the protein from a cytosolic extract
e. none would be useful

34. What is the name of the procedure in which proteins separated on a polyacrylamide gel are
transferred with the application of a current to a nitrocellulose filter placed against the gel and
subsequently identified by their interaction with specific antibodies?
a. a Southern blot
b. a Northern blot
c. an Eastern blot
d. a Western blot
e. an East Northeastern blot

35. Antibodies can be used to
a. visualize proteins in fixed and permeabilized cells
b. identify specific proteins on an immunoblot (western blot)
c. precipitate proteins from cellular extracts
d. identify and isolate organelle fractions
e. all are correct.

36. Which technique depends on the use of antibodies made specifically against a particular
protein (antigen)? The antibodies are then conjugated to a substance that makes them visible
under the light or electron microscope.
a. immunolocalization
b. immunocompetence
c. immunization
d. immunofenestration
e. negative staining

37. Which is not true of phospholipids in a bilayer?
a. Phospholipids are uniform in tail length, making the bilayer a uniform thickness.
b. Phospholipids can rotate rapidly around their long axis.
c. Phospholipids can easily move from one leaflet to the other leaflet by diffusion.
d. a and b are not true.
e. a and c are not true.

38. Phospholipid molecules in a membrane are arranged with their ____ on the exterior and their
____ on the interior.
a. Hydrophobic heads ... hydrophilic tails
b. Hydrophilic heads ... hydrophobic tails
c. Nonpolar heads ... polar tails
d. Hydrophobic tails ... hydrophilic heads
e. Hydrophilic tails ... hydrophobic heads
39. Specialized, cholesterol-rich regions of the membrane which possess a distinctive lipid
composition may be called _______.
a. microdomains
b. life rafts
c. lipid rafts
d. cholesterolemias
e. a and c

40. You modify the DNA sequence for an integral membrane protein so that the cytoplasmic
portions of the protein are deleted. When this DNA sequence is inserted in cells, what is the most
likely potential effect on the mobility of this protein in the membrane?
a. They move much greater distances than the intact protein.
b. They move much smaller distances than the intact protein.
c. They do not move at all.
d. They are not inserted into the membrane so nothing can be learned about their mobility.
e. They flip to the opposite leaflet.



41. You determine the amino acid sequence of a novel protein. You find that it has a single alpha
helical domain. The alpha helix has primarily hydrophobic amino acids on one face of the helix,
and primarily polar (hydrophilic) amino acids on the other (not the top and bottom, the sides).
Which statement(s) is/ are false?
a. This protein cannot be a single pass transmembrane protein.
b. This protein cannot be a membrane protein.
c. This protein is almost certainly single pass transmembrane protein.
d. This protein could form a multimeric protein complex that spans the bilayer to allow
transport of hydrophilic molecules through the lipid bilayer.
e. b and c are false statements.
42. What kind of membrane protein penetrates into the hydrophobic part of the lipid bilayer?
a. Integral membrane protein.
b. Lipid-anchored protein.
c. Peripheral proteins.
d. b and c
e. a and b

43. Which of the following statements about lipid rafts is false?
a. They can be regions enriched in lipids with saturated fatty acid chains.
b. Because of the different lipid properties, lipid raft formation is an energetically
favorable situation.
c. They can have a different complement of membrane proteins than other regions of the
bilayer.
d. Lipid rafts can be cholesterol rich regions.
e. All are correct.
44. A brain cell produces proteins that allow the assembly and release of synaptic vesicles at
synapses, but does not produce liver enzymes. This phenomenon is best described as a result of:
a. Multicellular development
b. Morphogenesis
c. Differential gene expression
d. Epigenetics
e. siRNA-induced protein knockout
45. Which statement(s) about the non-uniformity of lipid bilayers is/are correct?
a. All membranes in a particular eukaryotic cell type have the same composition.
b. A given leaflet of the bilayer of a plasma membrane can vary in its composition from
location to location.
c. The two leaflets of the lipid bilayer making up the plasma membrane do not have
identical composition.
d. b and c are correct
e. None is correct.
46. The shortest ! helix segment in a protein that can span a membrane bilayer will have about
_____ amino acid residues.
a. 5
b. 20
c. 50
d. 100
e. 200
47. What kind of protein structure is a beta sheet?
a. Quarternary structure.
b. Primary structure.
c. Secondary structure.
d. Tertiary structure.
e. None of the above.

48. Which amino acids would most likely reside in the transmembrane alpha helix of a single
pass transmembrane protein?
a. Acidic amino acids.
b. Basic amino acids.
c. Hydrophobic amino acids.
d. Hydrophilic amino acids.
e. Alpha helices are not made of amino acids.
49. Which of the following is a function of membranes?
a. Compartmentalization.
b. Selectively permeable barriers.
c. Mediates intercellular interactions.
d. Helps cells respond to external stimuli.
e. All of the above.

50. Why is it a good idea to use cultured cells in research?
a. Cultured cells can be grown in large quantities.
b. A wide variety of different cell types can be grown in culture.
c. Many different cellular activities can be studied in cell culture, including endocytosis,
cell movement, cell division, membrane trafficking, macromolecular synthesis
d. Cells can be made to differentiate in culture.
e. all of the above





51. What is the name of the fluorescent protein that is obtained from a jellyfish and can be used
to follow a specific protein through the cell and reveal the dynamic activities in which the protein
participates?
a. fluorescein
b. rhodamine
c. green fluorescent protein
d. phosphoescein
e. verdine

52. You engineered a new gene which includes GFP fused to the cytoplasmic domain of a
transmembrane protein. You then added a cardiac-specific promoter and incorporate this new
gene into the genome of the mouse. When you examine cells from these mice in the fluorescent
microscope:
a. You will see the fluorescence throughout the cytoplasm of all the cells of the mouse.
b. You will see the fluorescence throughout the cytoplasm of all cardiac cells in the mouse.
c. You will see the fluorescence from the protein in the membrane of all cardiac cells in the
mouse.
d. You will see the fluorescence in the membranes of all the cells of the mouse.
e. All of the above will be seen.

53. You are studying membrane proteins in a cell, trying to deduce their topology. You treat the outside
of the cell with trypsin, and one protein (in which you are particularly interested) is partially digested and
becomes smaller. Which statement below is true?

a. The protein of interest cannot be protein 4.
b. If the protein of interest is reduced in size to the same extent when trypsin is applied in the
presence and absence of detergent, then it must be protein 2.
c. If the protein of interest is reduced in size to the same extent when trypsin is applied in the
presence and absence of detergent, then it must be protein 3.
d. all are true statements.
e. A and B are true statements




54. How is the green fluorescent protein (GFP) attached to the protein for which it serves as a
label allowing that protein's dynamic activities to be tracked?
a. The GFP is attached to the desired protein in the laboratory.
b. A recombinant RNA is produced by attaching the GFP mRNA to the mRNA of the
desired protein.
c. GFP adheres specifically to the desired protein via weak interactions.
d. The coding region of the GFP gene is joined to the coding region of the gene of the
protein being studied.
e. The GFP protein is attached to the coding region of the gene of the protein being
studied.

55. You have fused a mouse cell with a human cell. You then treated the resultant fused cell with
antibodies to specific proteins, one of which is found on the mouse cells and one which is found
on the human cells. The antibodies to the mouse protein are labeled with a green fluorescent dye,
while the antibodies to the human protein are labeled with a red dye. What will the cell look like
a long time after fusion?
a. The cell will be half red and half green if neither protein is mobile.
b. The red and green labels will be uniformly distributed across the entire membrane if
both proteins are mobile.
c. The red and green labels will be distributed in intermingled patches no matter what the
mobility of the proteins is.
d. a and b are correct.
e. b and c are correct.
56. You have a membrane protein such as CD2 fused to GFP so that the GFP is on the
extracellular side of the membrane. What would you see when you looked in the fluorescence
microscope after you added a protease to the cytoplasm that cleaved the protein between between
the end of its transmembrane domain and its intracellular domain?
a. You would still see fluorescent membranes.
b. You would see no fluorescence at all.
c. You would see fluorescence in the cytoplasm.
d. You would see fluorescence in the culture medium.
e. a and c are correct

57. In osmosis, water always moves toward the ____ solution: that is, toward the solution with
the ____ solute concentration.
a. isotonic ... greater
b. hypertonic ... greater
c. hypertonic ... lesser
d. hypotonic ... greater
e. hypotonic ... lesser

58. If the volume of a cell decreases when it is placed in an aqueous solution, that solution is said
to be __________ to the cell.
a. Hypertonic.
b. Isotonic.
c. Hypotonic.
d. Subatomic.
e. Hypotronic.

59. You are studying an integral membrane protein that you think binds to the cytoskeleton and
is therefore immobile. Which choice is the correct set of FRAP and particle trajectory data
shown below that you would expect to observe?
a. A, II
b. D, I
c. B, II
d. a and c are likely to be observed.
e. None is correct.








60. You express a recombinant membrane protein and put it into an artificial lipid bilayer. You
tag it with a fluorescent antibody and measure its mobility using FRAP. You find that it is highly
mobile. However, when you do the same experiment on a cell that naturally expresses that
protein, you find that it is not mobile. Which explanation could account for these results?
a. In the cell, the protein binds to the cytoskeleton.
b. In the cell, the protein binds to other immobile membrane proteins.
c. In the cell, the protein binds to other mobile membrane proteins.
d. a and b could.
e. a and c could.


61. Which is true concerning protein synthesis?
a. Protein folding can start only after the entire polypeptide is synthesized.
b. Proteins can be made from either C-terminus to N-terminus or vice versa.
c. Proteins are directly synthesized using the information template in the DNA.
d. Proteins are completely folded inside the ribosome and then released.
e. Chaperones and chaperonins help some proteins fold to the right final conformation.

62. You are studying the cellular basis of protein synthesis. You have two proteins- protein A
and protein B- and you know the following about them. Protein A adopts different conformations
if it is translated in a test tube with purified ribosomes, mRNA, tRNAs, and amino acids than if
it is translated in vivo. When protein B is immuno-isolated from cells and denatured by heating
in a test-tube, it spontaneously refolds into the right conformation. Which of the statements
below is correct?
a. Protein A but not protein B likely folds with the aid of chaperones and chaperonins in
cells.
b. Protein B but not protein A likely folds with the aid of chaperones and chaperonins in
cells.
c. Both proteins require chaperones and chaperonins to fold properly.
d. Neither protein appears to require chaperones and chaperonins to fold properly.
63. What is the purpose of molecular chaperones like HSP70?
a. They bind to unfolded and misfolded RNAs and help them regain their native
structure.
b. They bind to unfolded and misfolded DNAs and help them regain their native
structure.
c. They bind to unfolded and misfolded carbohydrates and help them regain their native
structure.
d. They transport secretory proteins into secretory vesicles.
e. None of the above.

64. Protein A and B are bound stably in a complex that you expect to last for 10s of minutes.
The Kd is 10
-9
M. A regulatory protein binds to the complex, changing the Kd for the interaction
between A and B to 10
-7
M. Which describes the most likely ensuing events?
a. Nothing happens.
b. The complex becomes more stable, and will likely persist for hours.
c. The complex becomes less stable and is likely to fall apart more quickly.
d. A and B will likely collide with each other more often.
e. None is correct.



65. If the K
d
for a binding interaction is 10
-9
M, and the binding partners are present at
concentrations of10
-7
M. Which statement best describes the situation?
a. Because the concentration of the binding proteins is above the K
d
, most are likely
complexed.
b. Because the concentration of the binding proteins is above the K
d
, most are likely free.
c. Because the concentration of the binding proteins is below the K
d
, most are likely free.
d. Because the concentration of the binding proteins is below the K
d
, most are likely
complexed.
e. None of the above is correct.

66. With regard to the diagram above, which statement(s) is/ are correct?
a. Interaction (i) has the smallest K
d
.
b. Interaction (i) has the highest affinity.
c. Interaction (iii) has the lowest affinity.
d. Interaction (iii) has the greatest K
d
.
e. None are correct.

67. Protein A binds to protein B with a high K
d
, and to protein C with a low K
d
. Which of the
following statements is most likely to describe correctly the interactions of protein A with
proteins B and C?
a. For a given and equal concentration of proteins B and C, protein A probably collides
with protein B more often than protein C.
b. For a given concentration of proteins B and C, protein A probably collides with protein
C more often than protein B.
c. For a given concentration of proteins B and C, protein A probably collides with both
proteins equally often, but stays bound to protein B for a relatively longer time than it
stays bound to protein C.
d. For a given concentration of proteins B and C, protein A probably collides with both
proteins equally often, but stays bound to protein C for a relatively longer time than it
stays bound to protein B.