Problem Sets

Problem Set 1 (This resource may not render correctly in a screen reader.PDF) (This resource may not render correctly in a screen reader.PDF)
Problem Set 2 (This resource may not render correctly in a screen reader.PDF) (This resource may not render correctly in a screen reader.PDF)
Problem Set 3 (This resource may not render correctly in a screen reader.PDF) (This resource may not render correctly in a screen reader.PDF)

Optional Writing Assignments

For each third of the course, one research article related to the material covered in lecture will be assigned. Everyone should read these papers; they will be discussed in recitation and related questions may appear on the exams. With each paper, we will also hand out a discussion question. Students are encouraged to write a brief essay (2 double spaced pages) in response to this question. Essays will receive up to 15 pts and will be graded based on the completeness of answer, clarity of explanation and originality. While course grades will be calculated based exclusively on exam scores, points accumulated from completing the writing assignments will then be added to the exam totals. Grades will then be assigned without altering the point totals corresponding to each letter grade. Thus, the writing assignments will be treated as extra credit.

The answers to the discussion questions should be in the form of a 2 page essay with Title, double spaced, using 12 font size with one inch margins on top, bottom, left, and right. All papers should be left justified. No excuses! The essay should synopsize the important points of the paper that pertain to the question (no more than two paragraphs) and propose an answer to the questions posed. The quality of the answer will depend on the quality of the supporting arguments as well as the quality of the presentation.


Writing Assignment 1 (PDF)

Chong, J. P., M. K. Hayashi, M. N. Simon, R. M. Xu, and B. Stillman. "A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase." Proc Natl Acad Sci U.S.A. 97, no. 4 (Feb 15, 2000): 1530-5.

The paper by Chong and colleagues describes the purification and characterization of an archaebacterial protein (MtMcm) that is related to the eukaryotic Mcm proteins. The experiments in figure 1 indicate that MtMcm has a binding site for both ssDNA and dsDNA. It is possible that these DNAs bind the same site in the protein or that they bind separate sites. Propose an experiment to distinguish between these two possibilities and describe the results you would expect if dsDNA and ssDNA share the same binding site. If ssDNA and dsDNA share the same binding site, what part of the DNA is most likely involved in the interaction that stimulates the ATPase?

To address the ability of MtMcm protein to displace large DNA fragments, the authors created a DNA helicase substrate with variable length ssDNAs (25 to 500 bases) annealed to a large ssDNA circle and find that MtMcm can displace ssDNAs as long as 500 bases. Is this an assay for MtMcm processivity? Explain why or why not.

Writing Assignment 2 (PDF)

Yang, H., Q. Li, J. Fan, W. K. Holloman, and N. P. Pavletich. "The BRCA2 homologue Brh2 nucleates RAD51 filament formation at a dsDNA-ssDNA junction." Nature 433, no. 7026 (Feb 10, 2005): 653-7.


The paper by Yang and colleagues describes characterization of the BRCA2 homolog, Brh2. They provide evidence that Brh2 promotes assembly of Rad51 filament and that this role could explain how BRCA2 proteins function in DSB repair.

The recombination assays described in the paper require the single-stranded DNA binding protein RPA. Explain the multiple effects that RPA is thought to have on Rad51 filament assembly. In one experiment, the authors use E. coli SSB in place of RPA. What is the role of this experiment in the logic of the paper?

The authors also conclude that Brh2 preferentially promotes Rad51 filament formation at ssDNA-dsDNA junctions. Furthermore, they infer that these filaments grow specifically to coat the 3'ssDNA overhang. How would their results differ if this specific polarity of filament growth had not been observed? They suggest from their structural work that this polarity could be due to nucleation by BRC-bound Rad51. Do you find this model attractive, unattractive, or unnecessary? Explain your position on this issue.

Writing Assignment 3 (This resource may not render correctly in a screen reader.PDF)

Ibrahim, el C., T. D. Schaal, K. J. Hertel, R. Reed, and T. Maniatis. "Serine/arginine-rich protein-dependent suppression of exon skipping by exonic splicing enhancers." Proc Natl Acad Sci U.S.A. 102, no. 14 (Apr 5, 2005):5002-7. (Epub Mar 7, 2005)

The paper by Ibrahim et al. addresses the mechanisms employed to ensure proper pairing of 5' and 3' splice sites. The authors make two distinct conclusions: (1) that SR proteins, by binding to unspliced exons, direct the splicing machinery to the nearest 5' and 3' splice sites; (2) the SR proteins function to suppress splicing between upstream 5' splice sites and downstream 3' splice sites. Summarize the evidence that specifically supports the second of these conclusions.

In pre-mRNAs that carry several alternative exons (for example a gene with 4 exons, but 3 alternative versions of exon 2 that are used in different tissues) splice site choice has extra complexities. Based on the conclusions of this paper, propose a model for how alternative splicing in the different tissues could be achieved. You may include a figure if you wish, in addition to the 2 pages of written text.


Additional Writing Assignments

Gradia, S., D. Subramanian, T. Wilson, S. Acharya, A. Makhov, J. Griffith, and R. Fishel. "hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA." Mol Cell 3, no. 2 (Feb 1999): 255-61.

The paper by Gradia et al. addresses the mechanism by which the human MSH2-MSH6 proteins interact with DNA.  From their studies, they specifically propose that this protein complex initially binds to mismatch DNA when it is in the ADP-bound form.  Explain the evidence they provide that it is specifically this form of the protein that first binds to the mismatch DNA.

The authors go on to argue that the MSH2-MSH6 complex interacts with DNA similarly to the sliding clamp complex associated with the DNA replication machinery.  A possible prediction of this model is that a single MSH2-MSH6 complex may be able to direct the repair of multiple DNA mismatches present on a single plasmid template.  Design an experiment to test this hypothesis.  Assume you have available both purified MSH2-MSH6 and a cell extract that contains all the proteins other than MSH2-MSH6 that are needed to promote mismatch repair in vitro.  You may include a figure if you wish, in addition to the 2 pages of written text.

The following sample work is from an assignment given during the Spring 2004 version of 7.28. (PDF) (Courtesy of Nathan McNulty. Used with permission.)

Criteria for Evaluation

  1. The student introduced the paper's topic effectively through a concise and clear summary of the key conclusions that can be made based on the experiments presented in the reading assignment.
  2. The paper demonstrated a clear understanding of the experiments presented in the reading assignment.
  3. The paper presented an insightful perspective to the study question(s). Answers were well supported with logical arguments based on the data in the paper.
  4. The study question(s) were answered in the space allowed.
  5. The paper:
    • was well organized with informative topic sentences, effective transitions, and clear expression of ideas;
    • had a logical flow; and
    • demonstrated correct grammar and mechanics.
  6. The title of the essay concisely synopsized the topics covered and drew the reader's interest.