Beruflich Dokumente
Kultur Dokumente
DO NOT write everything you know about a topic, this will waste your time. If you
provide more than one answer for a question only your first answer will be graded.
If you need extra space, continue only on the back of the page that the question is
written on. Clearly label that you are using the back for your answer.
“I pledge my honor that I have not violated the Honor Code during this
examination.”
Signature:
Printed Name:
Exam code number:____________
a) RNA polymerase (along with its sigma subunit) can initiate transcription on
its own
b) RNA polymerase (along with its sigma subunit) requires the general
transcription factors to assemble at the promoter before polymerase can
begin transcription
c) The sigma subunit must associate with the appropriate type of RNA
polymerase to produce mRNAs
d) RNA polymerase must be phosphorylated at its C-terminal tail for
transcription to proceed
2
Exam code number:____________
3
Exam code number:____________
10. Which of the following does NOT describe a mechanism by which enzymes
catalyze reactions?
a) The enzyme provides additional energy, making conditions more favorable
for the reaction.
b) The enzyme rearranges the charges in the substrate, making conditions
more favorable for the reaction.
c) The enzyme orients two substrates in a position favorable for the reaction.
d) The enzyme bends the substrate into a conformation that is more
favorable for the reaction.
11. Why did the U.S. withdraw its support for the Biological and Toxin Weapons
Convention?
a) Because the penalties for violating the convention were too strict.
b) Because it is too difficult to verify that countries are not violating the
convention.
c) Because the U.S. would have to contribute too many resources to verify
that countries are not violating the convention.
d) Because the penalties for violating the convention were not strict enough.
12. Which of the following does not occur during M phase in animal cells?
a) growth of the cell
b) condensation of chromosomes
c) breakdown of nuclear envelope
d) attachment of chromosomes to microtubules
4
Exam code number:____________
13. MPF activity was discovered when cytoplasm from a Xenopus M-phase cell
was injected into Xenopus oocytes, inducing the oocytes to form a mitotic
spindle. In a control experiment, Xenopus interphase cytoplasm was injected
into oocytes and shown not to induce the formation of a mitotic spindle. Which
of the following statements is not a legitimate conclusion from the control
experiment?
a) The piercing of the oocyte membrane by a needle is insufficient to
cause mitotic spindle formation.
b) An increased volume of cytoplasm is insufficient to cause mitotic
spindle formation.
c) Injection of extra RNA molecules is insufficient to cause mitotic
spindle formation.
d) Components of an interphase nucleus are insufficient to cause
mitotic spindle formation.
5
Exam code number:____________
Both (1 pt)
Because of the bidirectional nature of replication (or one direction is
leading and the other is lagging (1 pt)
3. Most cells in the body of an adult human lack the telomerase enzyme
because its gene is turned off and is therefore not expressed. An important
step in the conversion of a normal cell into a cancer cell, which circumvents
normal growth control, is the resumption of telomerase expression. Explain
why telomerase might be necessary for the ability of cancer cells to divide
over and over again. (2 points)
In the absence of telomerase the lifespan of a cell and its progeny is limited
because with each round of replication the length of the telomeric DNA will
shrink. If telomerase is provided to cells they can divide indefinitely because
their telomeres will remain a constant length even after each division.
6
Exam code number:____________
4. In the absence of glucose, E. coli can grow by using the sugar arabinose. The
genes that encode proteins that allow E. coli to use arabinose, araA, araB,
and araD, are arranged in an operon and are controlled by the same
promoter. The araC gene is located elsewhere and encodes a transcriptional
regulator that binds adjacent to the promoter of the arabinose operon. AraC
also has a binding site for arabinose. To understand the regulatory properties
of the AraC protein, you engineer a mutant bacterium in which the araC gene
has been deleted and look at the effect of the presence or absence of the
AraC protein on the AraA enzyme.
A. If the AraC protein works as a gene repressor, would you expect araA
RNA levels to be high or low in the presence of arabinose in the araC-
mutant cells? Explain your answer (2 points)
B. What about in the araC- mutant cells in the absence of arabinose? Explain
your answer. (2 points)
C. Your findings from the experiment are summarized below. Do the results
in the table indicate that the AraC protein regulates arabinose metabolism by
acting as a gene repressor or a gene activator? Explain your answer. (3
points)
AraC is an activator (1 point). In the araC- cells the level of AraA RNA is
always low (with or without arabinose), which indicates that transcription
needs to be activated. In the araC+ cells in the presence of arabinose the
transcription of araA increases, further supporting that it is an activator.
7
Exam code number:____________
5. In class, we discussed the possibility that RNA was the original hereditary
molecule. Based ONLY on the methods used by Hershey and Chase, in
which the bacteriophage particles were labeled with P32 & S35, what results
would they have seen if RNA, not DNA, was the molecule that carried the
genetic information? (2 points)
They would have seen the same results because P32 labels both RNA and DNA
Briefly describe another classic experiment that was performed to show that
DNA, not RNA, is the molecule that carries the genetic information. (2 points)
The Avery, MacLeod and McCarty experiment (don’t need the names)
The use of DNase and RNase allowed them to distinguish between the two
nucleic acids using the S and R bacteria transformation experiment.
6. Briefly explain what is meant when we say that biological weapons are often
infectious but not contagious. Why might this be a desirable feature of a
biological weapon? (4 points)
It means that although the weaponized disease can infect people it comes
directly into contact with, it cannot spread from person to person. This
would help to prevent unintended targets from being infected.
7. What two factors limit the resolution of an image seen through a microscope?
(2 points)
8
Exam code number:____________
8. The bacterium Bacillus subtilis sporulates (forms spores) under certain growth
conditions. You have obtained a mutant that no longer sporulates, even
when exposed to these conditions. You have managed to identify the gene
that is mutated, and have replaced it with the GFP gene to create a reporter
construct. You expose the bacteria to different conditions that result in
sporulation, and measure the fluorescence produced. The data is shown
below.
b. What conclusion can you make about how the protein of interest affects
sporulation? (2 points)
You have managed to make an antibody to your protein of interest, and you
run an SDS-PAGE gel and you perform a Western blot of unmutated cell
extracts in the same 3 conditions used above. The results are shown below.
9
Exam code number:____________
c. Based on the results of the western blot, suggest a hypothesis about how
your protein of interest affects sporulation. (2 points)
Treat the cell extract with phosphatase and run a gel to see if the upper band
goes away.
9. Thymosin is a protein that can bind actin monomers. If you were to add a
drug that inhibits the ability of thymosin to bind actin monomers, what effect
would this have on actin polymerization? Explain your answer. (3 points)
Addition of a drug that keeps thymosin from binding actin monomer will
increase the rate of actin polymerization in the cell. In this case, free actin
monomers are bound by thymosin and are thereby prevented from adding to
the end of an actin filament
(Also accepted credit for decreased as long as the answer states that
thymosin helps create seeds.)
10. Mutations in p53 are associated with >50% of cancers. What kind of protein
is p53? What does p53 do in response to stress like DNA damage? (3 points)
p53 is a tumor suppressor. In response to stress, p53 can arrest the cell
cycle or induce apoptosis.
10
Exam code number:____________
Label the lanes shown below with the restriction enzyme used for the digestion.
(4 points)
You tell him that you can determine whether the gene is cloned into the
correct orientation using only one of the digests. Which one? (1 point)
PvuII
11
Exam code number:____________
12. The E. coli MalE protein is synthesized in the cytoplasm and then secreted
across the bacterial inner membrane through the Sec channel. As part of
your thesis project, you are characterizing the E. coli mutant strain prlD21.
Pictured below are the results from a pulse-chase experiment tracking
secretion of MalE in wild-type and prlD21 mutant cells. After pulsing the cells
with radioactive (hot) amino acids, you add non-radioactive (cold) amino
acids, collect protein extracts (at 10 sec, 30 sec, 1 min, etc.), and analyze the
extracts by SDS-PAGE.
There is a size difference because the signal sequence has been cleaved in
the mMalE
12
Exam code number:____________
13. You are investigating the synthesis and trafficking of phospholipids in your favorite
eukaryotic cell line. You have devised an experimental system in which you can
feed your cells radioactive phosphorus, then break open the cells, isolate the various
organelles by density centrifugation and measure the radioactivity in different
organelles and membranes. An experiment where you add radioactive phosphate at
time zero and then analyze the cells over time gives the following data (ER =
endoplasmic reticulum, MT = mitochondrion, PM = plasma membrane):
160
140
120
CPM / mg lipid
100 ER
Golgi
80
MT
60 PM
40
20
0
0 10 20 30 40 50
Time (min)
Phospholipids are synthesized in the ER, then trafficked to the Golgi, the
mitochondrion and the plasma membrane in a linear pathway. OR, some
variation of: phospholipids are synthesized in the ER then trafficked to the
different membranes independently at different rates
50
CPM / mg lipid
40
ER
Golgi
30
MT
PM
20
10
0
0 10 20 30 40 50
Time (min)
Based on this result, what is the pathway for phospholipid synthesis and
trafficking? (2 points)
13
Exam code number:____________
What color would the neuron expressing the recombined construct be? (1
point)
Red
15. The phosphorylation status of CDK is important for regulating cell cycle
progression. Why are cdc25 mutants arrested in the cell cycle, while wee1
mutants enter the cell cycle prematurely? (3 points)
14
Exam code number:____________
16. To characterize the cell cycle of a newly discovered strain of yeast, you have
generated a library of cold-sensitive mutants and have started to take
photographs of interesting mutants. You have checked to make sure that
each strain in the library carries only a single mutation.
Small budded cells are before the “execution point” when the protein is
required. (1.5 pts) Larger budded cells are already past the point and
divide again. After cells traverse the execution point they arrest in
G2/M as large budded cells. (1.5 points)
B. Mutant B also stops growing when moved to the cold temperature, but
under the microscope it appears that half of the cells arrested at one point
in the cell cycle while the other half are arrested at a different point. How
could you explain this result? (2 points)
The mutated gene is acts at two different checkpoints. Since the
population of cells is asynchronous, individual cells in the population are at
different stages of the cell cycle and will arrest at whatever checkpoint
they hit first.
15
Exam code number:____________
Below is a table for you to keep track of whom you eliminate as suspects.
1. You decide to use microarray analysis to attempt to identify the culprit, because you
remember from class that this will allow you to examine many genes at once. You
are able to isolate RNA from the hair root cells attached to the hair found on the
pizza. And you collect a check cell sample from each of the TAs.
a. If you isolate total RNA from the cells, what property of mRNA could you use
to separate mRNA from the rest of the RNA? (1 point)
b. Name and briefly describe the function of two other types of RNA (i.e.- not
mRNA) found in the cell. (2 points)
tRNA – used in translation, links the amino acids to the correct codon
rRNA – part of the ribosome
miRNA – regulate gene expression
snRNA – part of splicing complex
c. To perform the microarray experiment, you first make cDNA from the mRNA
from the cells of the culprit and the TAs. What is the name of the enzyme
you use? (1 point)
Reverse Transcriptase
16
Exam code number:____________
d. Before you even start to perform the microarray experiment you lab partner
insists that the experiment won’t work to identify the culprit. After thinking it
over you agree. Give one reason why the experiment as outlined above
would not be helpful to identify the culprit. (2 points)
Possible answers:
You are comparing expression of genes in two different cell types (hair vs.
cheek cell)
Levels of gene expression are likely to be similar in different people, so it will
hard to identify a match with the culprit
Microarrays only show relative trends or relative changes in expression
2. You decide to start over and use the DNA samples that you collected from the culprit
and the TAs. You decide to investigate a gene, Gene T, which has a single
nucleotide polymorphism (SNP) that creates a site recognized by the restriction
enzyme, PstI. Even though this SNP is relatively common, you hope it will help you
identify the culprit.
a. Below is the portion of Gene T that has the SNP. In some people, the circled
G:C basepair is changed to generate the PstI site. Based on what you learned
about the general characteristics of restriction enzyme recognition sites, what is
the basepair change that these people possess that generates a PstI site? (1
point) G to A and C to T
5’ – C T G C G G – 3’
3’ – G A C G C C – 5’
You use PCR to amplify a 500 bp region of gene T that includes this SNP at the
200bp position. You then digest the PCR products with the enzyme PstI. Below
are the results of this experiment.
b. Knowing that the culprit is heterozygous for the SNP in Gene T, whom can you
eliminate as a suspect based on these data? Why? (2 points)
Colleen, Kenric, Julia, Jean, Leslie -- -1 point if only Colleen and Julia are mentioned.
17
Exam code number:____________
3. You still have multiple suspects, so you decide to do another test. This time, you do
a PCR-based test for a STR (short terminal repeat). At chromosomal region Z, it is
common to find one or more copies of a 25 bp sequence.
The first step in doing PCR is designing primers. Below, the two lines represent the
two strands of DNA at chromosomal region Z. The thicker region represents region Z
and is the sequence you want to amplify. Using short arrows, draw on the diagram
below where you would like your primers to anneal. (3 points)
• label the 5’ and 3’ ends of both primers
• label the 5’ and 3’ ends of the template DNA
5’ 3’
3’ 5’
(25 bp)n
5’ 3’
3’ 5’
The length of region Z without an insert is 100 bp. Below are the results of your experiment.
Unfortunately, you ran the culprit’s sample on a separate gel and forgot to add a DNA
ladder to that gel. All you know for certain is that the culprit who ate the food in lab is
homozygous for the number of repeats for this STR at chromosomal region Z. Whom
can you eliminate as a suspect after performing this experiment? (2 points)
18
Exam code number:____________
Finally, another friend from class suggests that you sequence the DNA to identify the
culprit. Since you don’t have enough money to sequence the entire genomes of all the
TAs, you choose one small region of DNA to sequence. Below is a gel that represents
the results from sequencing a portion of Gene X from the culprit:
+
a. Write the double-stranded DNA sequence for this region of Gene S as shown in
the sequencing gel above. Indicate the 5’ and 3’ ends of the DNA sequence. (2
points)
5’ AGCATCTAG 3’
3’ TCGTAGATC 5’
The sequencing results from three of the TAs: Amanda, Colleen and Leslie all
perfectly matched the culprit.
Based on all the results, which TA left the pizza in the lab? (1 point)
Amanda
19