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2.6: Assignments with Samples - Biology


The assignments in this course are openly licensed, and are available as-is, or can be modified to suit your students’ needs.

This course provides 10 prompts and grading rubrics for written assignments, designed to align with course outcomes.

If you import this course into your learning management (Blackboard, Canvas, etc.), the assignments will automatically be loaded into the assignment tool. You can view them below or throughout the course.

Assignment FilesModule Alignment
Biological Astronaut (download the .docx, .rtf)After both Module 1: Introduction to Biology and Module 2: Chemistry of Life
Nutritionist for a Day (download the .docx, .rtf)
Example completed assignment to distribute to students
After Module 3: Important Biological Macromolecules
Cell Builder (download the .docx, .rtf)
Here is an example of what students might create
After Module 4: Cellular Structure
Membranes Alive! (download the .docx, .rtf)
Example completed assignment to distribute to students
After Module 5: Cell Membranes
Observing Energy Transactions (download the .docx, .rtf)
Here is an example of what students might create
After Module 6: Metabolic Pathways
Mitosis and Meiosis Internet Quests (download the .docx, .rtf)
See this example of what students might submit
After Module 7: Cell Division
Which Has More DNA? (download the .docx, .rtf)
See the examples contained here
After Module 8: DNA Structure and Replication
How Mutations Work (download the .docx, .rtf)
This document shows an example submission
Please note that it only includes answers to a few questions and a single snapshot to give you an idea of how to complete this assignment.
After both Module 9: DNA Transcription, Module 10: Translation, and Module 11: Gene Expression
Dragon Genetics (download the .docx, .rtf)
Here is a worked example showing a screenshot and required text explanation
Module 12: After Trait Inheritance
When Jabberjays Attack! (download the .docx, .rtf)
Hints document to distribute to students
After both Module 13: Theory of Evolution and Module 14: Modern Biology

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.

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.

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.

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.


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