7.06 Cell Biology Quiz #3

Name: ______________________________
Recitation Section: ______________________
7.06 Cell Biology

QUIZ #3
This is an open book exam, and you are allowed access to books and notes, but
not computers or any other types of electronic devices.
Please write your answers to questions in pen (not pencil) in the space allotted.
Please write only on the FRONT SIDE of each sheet.
And be sure to put your name on each page in case they become separated.
There are 7 pages to the quiz, make sure you have a complete copy!
Remember that we will Xerox all of the quizzes.
Good Luck!
Question 1. 30 pts ________
1
Question 1 (30 points) Name: ______________________________
A (4 points). You are given two separate cDNAs, each of which encodes a
glycoprotein of similar size. One of the cDNAs encodes a protein (protein A)
known to reside in lysosomes, the other encodes a protein (protein B) that is
expressed at the cell surface. What tools would you use to distinguish between
the localization of the two proteins (you may genetically modify each of the two
cDNAs)?
B (4 points). If you were given the nucleotide sequence of the two cDNAs, what
type of sequence elements would you be looking for that would indicate that you
are dealing with:
i) a secretory protein
ii) a membrane protein
iii) a type I versus a type II membrane protein
iv) a glycoprotein
C (8 points). You are allowed to make mutations in the cDNAs that were given to
you. What kind of mutation would you introduce, and what is the expected
outcome you are looking for to verify your answers given in part B.
2
Name: ______________________________
D (8 points). Having identified each of these cDNAs, you want to determine the
intracellular route traveled by each of these glycoproteins, and the speed with
which they traverse their biosynthetic pathways to arrive at their final destination.
How would you use a pulse-chase experiment in combination with monitoring the
glycosylation status of your glycoproteins to determine the speed with which
these proteins traverse their biosynthetic pathway?
E (6 points). The drug brefeldin A blocks transport of proteins from the ER to the
Golgi (anterograde transport), but not Golgi-to-ER trafficking (retrograde
transport). What are possible targets of this drug?
3
A. (5 points) Briefly describe the 5 mechanisms (or processes) by which

antibody diversity is generated.
B. (4 points) Successfully rearranged immunoglobulin heavy chains in B-cells

rarely contain multiple D segments. Why not? If you’d like, you can use a
diagram to illustrate your brief explanation.
C. (2 points) A new species of iguana is discovered the B cells of which contain

immunoglobulin heavy chain sequences demonstrating D-D fusions. Its
recombination machinery is identical to that of humans. What might be different
about the organization of this animal’s immunoglobulin heavy chain locus?
4
Name: ______________________________
D. (8points) Briefly describe the structure of the B-cell receptor in the various
stages of B cell development. How would the deletion of the exons encoding the
transmembrane segment of the μ chain affect the final outcome of B cell
development?
E. (6points) The choice between the production of an mRNA that encodes

secreted or membrane-bound IgM is determined by the choice of poly-A addition
sites. If the proximal poly-A addition site (gray circle in the diagram below) is
deleted by gene targeting, what kind of antibodies, if any, would you expect to be
circulating in this mouse? Explain your answer.
Transmembrane
Constant region domains domains
V D J Cμ1 Cμ2 Cμ3 Cμ4
Poly-A sites
5
F. (4points) The phenomenon of MHC restriction accounts for the failure of T
cells from an individual with one type of MHC products to respond to stimulation
by an antigen- presenting cell from an individual with a different type of MHC
products. What are the structural features that distinguish the MHC products in
the two individuals, and how do these features account for MHC restriction?
6
Name: ______________________________
G. (6points) You are screening mice with mutations in the interleukin-4 (IL-4)
signaling pathway. You discover a mouse that has a mutation in the STAT6
transcription factor. STAT6 in these mice is transcribed, folded correctly, and
maintained in the cells at normal levels; however, T cells of these mutant mice
are unresponsive to IL-4. Propose 2 possible mutations in STAT6 that would
account for this exact phenotype, and briefly explain them.
H. (3points) Through the screen described in part G, you discover another

mutant mouse, in which IL-4-mediated signaling, once initiated, persists and is
not attenuated with time. Propose a mutation that would result in this phenotype.
7
A (2 points). What is the concentration of ligand required to obtain a fractional

occupancy of 10% for a receptor that binds this ligand with a Kd value of 10e-9
M?
B (6 points). In order to block internalization of a receptor from the cell surface,

you decide to use a mutant form of the GTPase dynamin. What kind of mutation
would lead to blockage of internalization without affecting dynamin levels? Is
there a pharmacological trick that you could use to achieve the same effect?
C (6 points). The efficiency of bacterial phagocytosis by macrophages is

enhanced by the presence of antibodies. What portion of the antibody is most
likely involved in binding to specific receptors on macrophages and how would
you verify this suggestion experimentally?
8
Name: ______________________________
E (6 points). You have discovered that the natural product lactacystin is a potent
inhibitor of proteasomal proteolysis. When you apply this compound to cells that
express the receptor for interleukin-1, you find that the action of interleukin-1 is
reduced. The cell line you use for these experiments expresses the enzyme
luciferase under the control of an NFkB sensitive promoter. You determine the
output of the interleukin-1 pathway by monitoring luciferase activity. Explain this
result.
F (6 points). Explain how phosphorylation of proteins that are not themselves

enzymes can control full and rapid (within minutes) activation of kinases that are
part of a signal transduction cascade. Provide 2 examples.
G (6 points). Many signal transduction cascades culminate in the activation of

transcription of a select set of target genes. Such events are controlled by the
delivery of transcription factors to their proper destination. The
immunosuppressant cyclosporin prevents activation of transcription of T cell
specific genes. Explain its mechanism of action.

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Name: ______________________________

Recitation Section: ______________________

7.06 Cell Biology

Please write only on the FRONT SIDE of each sheet.

Remember that we will Xerox all of the quizzes.

Question 1. 30 pts ________

Question 2. 38 pts ________

Question 3. 32 pts ________

ii) a membrane protein

iii) a type I versus a type II membrane protein

A. (5 points) Briefly describe the 5 mechanisms (or processes) by which

B. (4 points) Successfully rearranged immunoglobulin heavy chains in B-cells

C. (2 points) A new species of iguana is discovered the B cells of which contain

E. (6points) The choice between the production of an mRNA that encodes

H. (3points) Through the screen described in part G, you discover another

A (2 points). What is the concentration of ligand required to obtain a fractional

B (6 points). In order to block internalization of a receptor from the cell surface,

C (6 points). The efficiency of bacterial phagocytosis by macrophages is

F (6 points). Explain how phosphorylation of proteins that are not themselves

G (6 points). Many signal transduction cascades culminate in the activation of

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