BIO360: The Molecular Biology of Cancer
Fall 2013
Take-Home Exam 3
The goal of this take-home exam is to assess how well you are able to read and evaluate scientific
literature because this is a central skill that you will need in whatever you do after NCC. For this to
work, it is simply essential that you are the only one answering these questions. Please read the
following statements. If you agree to these provisions, please sign and date below and turn this in with
your completed take-home exam. As always, please ask if something is unclear.
 You may not receive help from another person. This is true for any student enrolled in this
course or from any other person at North Central or elsewhere. The only exception is that you
are encouraged to ask Dr. Johnston for any clarification that is needed.
 You may not provide assistance to any other member of the class. If anyone approaches you
for help with this exam, you are obligated to report that immediately to Dr. Johnston.
 You may use any published material or on-line resource to help you answer the questions, so
long as you do not plagiarize that source. At the end of your answers to the exam questions,
please provide a brief, informal list of all sources that you used.
 Seeking or providing help to another student on the take-home exam will result in your failing
BIO360 and being reported to the Dean’s Office for further disciplinary action, including the
possibility of permanent dismissal from the College.
By signing below, I certify that I have neither received nor provided any help from another person in
completing this assignment. I have read, understood and agree to abide by all of the above terms and
conditions.
Printed Name: ___________________________________________
Signed: _________________________________________________
Date:__________________
Read the following paper and answer the questions below.
Kwong, J., M. Chen, D. Lv, N. Luo, W. Su, R. Xiang and P. Sun. 2013. Induction of p38 
expression plays an essential role in oncogenic ras-induced senescence. Mol. Cell. Biol.
33:3780-3794.
Try not to analyze what the authors of the paper say in the text – rather analyze what the data say.
Please type your answers. You are welcome to augment your written answers with hand-drawings if
that helps explain your ideas. Don’t quote this paper or any other. Be sure to refer to specific data
contained in this paper frequently to support your answers. Please put your name only on the signature
page only and not on the paper itself. All answers are due at noon on Wednesday November 6. Email
submissions are fine, but still must meet the same deadline.
1. Take a look at Figure 3E. In this experiment, what was the question that Kwong et al. were asking?
For this experiment, what were the independent variable(s) that was being manipulated by the scientists?
What were the dependent variable(s) that were being measured? (5 points)
2. Figure 7 shows a ChIP assay for two different regions of the genome. Why did Kwong et al choose
to analyze the region from -3086 to -2759? Why did Kwong et al choose to analyze the region from
-7007 to -6723? What do you conclude from these experiments? (5 points)
3. The authors assert that Raf-1 is part of the pathway that leads to transcriptional activation of the p38
gene. Where are the data that support this conclusion? Do the data show that Raf-1 is necessary for
activation of p38? Or do the data show that Raf-1 is sufficient for activation of p38? Or both? Or
neither? Please briefly explain your answer. (5 points)
4. Kwong et al. conclude that c-Jun is acting downstream of Ras to affect senescence. Which one part
of a figure directly supports this claim? If c-Jun had been acting upstream of Ras to affect senescence,
what would the outcome of the experiment looked like? If c-Jun and Ras made fully independent
contributions to senescence, what would the outcome of the experiment looked like? (5 points)
5. Activated Ras leads to more p38 kinase activity. Is this because there are a larger number of p38 
protein molecules in the cell? Or is it because each molecule of p38 is more active? Or both?
Naturally, use data from the paper to support your answer. (10 points)
6. This paper describes an interesting relationship between p38  and p53. Does p38 affect the ability
of p53 to activate transcription? Does p38 phosphorylate p53 (if so, on what amino acid? and does this
stabilize p53?)? Does p38 affect the accumulation of p53 targets, such as p21 or p16Ink4a? (5 points)
7. As we have seen, many papers end with a figure that summarizes the findings graphically, often as a
pathway. This paper didn’t do that (and it’s really long enough without it). Draw a small figure that
shows the relationships of key proteins analyzed here. Obviously, you need to include Ras and p38 but
you should also think about other proteins that are between them or up/downstream. You can use
powerpoint to make a simple drawing of boxes for proteins and regular arrows or flat-head arrows to
show relationships. Save it as a JPEG and insert it into your Word file. (5 points)
8. What else do you want to know? Good papers always tell us something new about the world which
has the effect of raising new questions. Begin by putting forth a specific hypothesis or question. In your
answer, list your hypothesis or question in one sentence and underline that sentence. Design an
additional experiment or two that will significantly extend the results of Kwong et al. Be original and
don’t just re-state your answer to an earlier question on this exam.
Be sure to explain the rationale behind your hypothesis, briefly outline an experiment or two and show
why the new results will be important. Be very clear about your dependent and independent variables.
In other words, what will you alter and how you will alter it? What will you measure and how will you
measure it? In your answer, cite at least one primary research paper other than the papers that we have
read as a class. (10 points)