BIO360: The Molecular Biology of Cancer

Fall 2014

Take-Home Exam 2

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. Ihave 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.

Ritterhoff, S., C.M. Farah, J. Grabitzki, G. Lochnit, A.V. Skurat and M.L. Schmitz. 2010. The WD40-repeat protein Han11 functions as a scaffold protein to control HIPK2 and MEKK1 kinase functions. EMBO J. 29:3750-3761.

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. For example, don’t say “the data are in Figure 12” but rather say “the data are in the first four lanes of Figure 12C, comparing the western blot on the top versus the western blot on the bottom”. Please put your name only on the signature page only and not on the paper itself. All answers are due at noon on Wednesday October 22. Email submissions are fine, but still must meet the same deadline.

1. This paper presents a lot of coIP experiments, showing proteins that human Han11 does and does not interact with. Go through the paper and identify each human protein that was tested for Han11 binding. Indicate if the protein binds or doesn’t bind to Han11 and refer to one figure that shows this result. You may organize your answer using the table below. (5 points)

Tested Protein / Binds/Does not bind / Figure

2. Figure 1A is a very clear coIP experiment that demonstrates that Han11 and HIPK2 bind to one another. Why did the authors also do the experiment shown in Figure 1C? Similarly, it has been shown in the literature that Han11 binds to DYRK1a, so why did these scientists perform the experiment shown in Figure 1E? (5 points)

3. From the literature, the Schmitz lab knows that HIPK2 contributes to phosphorylation of p53 and to the phosphorylation of STAT3 (a transcription factor). Does active HIPK2 increase or decrease the phosphorylation of each of these proteins? Does Han11 increase, decrease or have no effect upon the phosphorylation of each p53 and STAT3?

It’s also known that MEKK1 influences the phosphorylation of p38 and Jun. Similarly, does active MEKK1 increase or decrease the phosphorylation of each of these proteins? Does Han11 increase, decrease or have no effect upon the phosphorylation of each p38 and Jun? Of course, be sure to support all of your answers with references to data. (10 points)

4. Figure 7E uses luciferase as a reporter gene by having it under the control of a NF-B inducible promoter. (This is similar to the GSY2pr-lacZ reporter that we are using in lab this term). The first two bars on the graph obviously show that this reporter is induced by the cytokine TNF. According to these data, what effect does Han11 and MEKK1 have upon this reporter? (5 points)

5. The authors argue that human Han11 is homologous to Swan-1 and Swan-2 from C. elegans. But are the WD40 repeat motifs conserved? (5 points)

6. Is there any evidence that Han11 may be involved with human cancers? If not, why is this paper included in a class called The Molecular Biology of Cancer? If so, please describe the nature of those data. Are the data more consistent with Han11 acting as a tumor suppressor or acting as an oncogene? (5 points)

7. The authors demonstrate that Han11 and HIPK2 bind one another in vivo. Does Han11 move to the same subcellular location as HIPK2 or does HIPK2 move to Han11? (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 Ritterhoffet 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 those that we’ve looked at as a class. (10 points)