BISC219/F13:Series 3 Questions

Assignment Series 3 Theory Questions

NOTE: There are two options for completing this assignment, due at the beginning of lab 10. You may complete the entire assignment as it is written for a total of 30 points distributed as described in the rubric at the end of this page OR you may complete only Questions 1, 2, and 3 of PART 2 (with an original figure for each of the three questions), worth 10 points each for a total of 30 points. We are offering the shortened option because we realize that it is a time-consuming assignment at a busy time in the semester; however, completing the whole assignment and getting feedback on your answers to all the questions should make your final assignment, the results analysis of our reverse genetics study of hsf-1, easier to write.

You can download a .docx version of the questions at the following link: Media:Theory_Questions_Series3_1.docx

Part I Short Answer Questions: (5pt)
1. Draw a basic picture of the flow of genetic information in the central dogma. Use the following terms in your drawing: polypeptide, protein, gene, mRNA, transcription, translation. Then indicate where dsRNA can cause an RNA interference (RNAi) effect on the flow of genetic information.

2. What is the general function of molecular chaperones? In 2 sentences or less, describe the role of molecular chaperones following cellular stress.

3. Draw and describe the way green fluorescent protein (GFP) is used in our study as a reporter for hsf.1 expression. What characteristics make GFP a good “reporter” molecule?

4. Use one sentence to summarize the potential power of RNAi for research (described in the NOVA video found at http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html).

5. In our study, in which organism is the dsRNA made? Which organism will show the effect of the RNAi? Briefly, how will dsRNA be introduced into the organism that will show the effect of downregulation of gene expression?

Part II. Your answers to the following questions will be in discussion format. Please use full sentences and provide reference citations where appropriate. You should have a separate Literature Cited section for each question. Include both a narrative AND at least one effective figure/table with a caption for each question. Since you will not use experimental data in these figures/tables, they will serve the purpose of helping your reader visualize complex or conceptually difficult information. You figures must be original: you may NOT use illustrations created and published by others even with citation, although you may adapt previously published work. (5 pt each)

1) What is the heat shock response and how does it work in C. elegans?

2) What is RNAi and how does it work in C. elegans?

3) What is a transcription factor and how does it regulate gene expression? What is HSF-1? What role does HSF-1 play during a cell’s stress response?
HSF-1 is described as part of the basic helix loop helix class of TFs with leucine zipper motifs. Describe what this molecular structure means and explain how this structure is critical to HSF-1’s function.

4) How will we silence or knockdown of expression of hsf-1? (Describe your experimental design rather than describing protocols: avoid a Materials & Methods type description.) How will we know that we achieved knockdown or silencing? What are other tools/methods that would be useful to assess knockdown?

5) Why is the C. elegans rrf-3 mutant enhanced for RNAi downregulation of gene expression compared to nematodes of the N2 wild type strain?

Grading Rubric

Rubric Part II Discussion Questions For Series 3 F13 (5 pt each)

	At or Above Standard	Below Standard
Structure	Structure of the narrative presents information in a logical sequence. Refers to figures/tables by number in the narrative & inserts figures/tables into narrative appropriately.	Did not impart information in a logical sequence.Did not reference figures/tables or insert them appropriately into the narrative
Figures/Tables	Figures/Tables are designed effectively to allow a general audience to visualize important information and make the information easy to grasp. Figure/Table titles and captions are appropriate and formatted correctly in the style of textbook figure captions (descriptive).	Figures/Tables are poorly designed or don't include appropriate information processed to be visualiy effective: it is difficult for a general audience to grasp the main message. Figure/Table titles are missing or inappropriate.
Discussion	All requested elements of answers are included. Answers are correct and directly answer the question. Explanations are clear to a general audience. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise	Not all requested elements are included. Answers incorrectly and/or not related to question. Explanations are not thorough or unclear to a general audience. Writing style is unclear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary.
Outside Sources	Includes complete, properly formatted citation for each work cited in body of report. Cites all material used that is not common knowledge. Uses an adequate number of reliable, appropriate sources including primary studies or review articles published in peer-reviewed journals. Includes a Literature Cited section with complete, properly formatted references.	Does not include complete, properly formatted citations for all references, lists works not cited in report, or fails to give reference citation for information not common knowledge. Does not use reliable or appropriate sources, or fails to use an adequate number of primary studies or review articles from peer-reviewed journals. Does not include a Literature Cited section with complete, properly formatted references.
Total	Question 1	Question 2
	Question 3	Question 4
	Question 5	Short Answers 1-5