Biochemistry II Writing Assignments

Spring 2016, Dr. Stone, CHEM 4420

Assignment Due Dates and Points

in class due date Turnitin due date (no late papers accepted) Assignment Points
Feb 1 Feb 5 Describe a figure from the "hydroquinone paper" 10
Feb 8 Feb 12 Research Topic 20
Feb 15 Feb 19 List of References 10
Feb 22 Feb 26 Summary of one reference 10
Feb 29 March 4 Describe a figure from one of your references 10
March 7 March 11 Annotated Bibliography 50
March 14 March 18 Organizational Map/Outline 20
March 21 March 25 First Draft 50
April 18 April 22 Second Draft—do not miss this deadline, you will not be able to do the peer review exercise! 100
none May 6 Peer Reviews 50
none May 20 Final electronic (pdf) version 20

There are 350 total points for these writing assignments. Since this is a writing proficiency course, you must earn 245 of these points to earn a C or higher and receive WP credit toward graduation.
Get started doing this online scientific writing class (free) at Duke University.

Describe a Figure

Using the Hydroquinone paper paper, choose a figure and describe it. If you have trouble try downloading this file for the hydroquinone paper.
Be sure to include the following:
1. What experiment was done to produce the data shown in the figure?
2. How does the experiment work? (Describe the underlying theory of the
experiment.)
3. What were the controls for this experiment?
4. What is the significance of the data from this experiment?
Here is some help: Decoding the Hydroquinone Paper. Also, Mama Ji's kitchen is a great source of biochemical experiment information.

Topic Paper

State the problem that you want to study, why you want to study this problem and what impact this problem has on the general population? Be very specific. Don't state that you want to study diabetes because it is the leading cause of blindness. Do some research and learn how diabetes causes blindness, what reactions are involved? What metabolic relationships are involved? Then state your problem including this information. All papers for this class will be graded on depth of research, organization, writing style, punctuation and grammar. No quotes are allowed and paraphrasing should be avoided. Use your own words to describe what you have learned from reading about your topic.

List of references

Submit a list of your references. Include all authors, title of the journal article, title of the journal, volume, pages and year published.
e.g: Wong J, Quinn C, Gelissen I, and A.J. Brown Endogenous 24(S),25-Epoxycholesterol Fine-tunes Acute Control of Cellular Cholesterol Homeostasis*, Journal of Biological Chemistry, (2008), 283: 2, 700–707.

Summary of One Reference

(This is also the format for a later assignment: Annotated Bibliography)
Read one of your reference papers and then write a brief 2-3 paragraph summary of each paper. Include the following: What knowledge does this paper contribute to the understanding of the topic? What experiments were done? Briefly describe the experiments. Use the following template for each literature paper:

Wong J, Quinn C, Gelissen I, and A.J. Brown Endogenous 24(S),25-Epoxycholesterol Fine-tunes Acute Control of Cellular Cholesterol Homeostasis*, Journal of Biological Chemistry, (2008), 283: 2, 700–707.

This paper focuses on the timely topic of the regulation of cholesterol biosynthesis. It is known that some individuals are able to maintain low cholesterol levels while others require drug therapy. There are natural regulator molecules that control the transcription of the enzymes involved in this regulation pathway. These researchers selectively inhibit the transcription of a regulator molecule (24,25-epoxycholesterol) without inhibiting the enzymes that synthesize cholesterol. This is different from using drugs that inhibit cholesterol biosynthesis, as the drugs inhibit the biosynthesis of both the cholesterol and the regulator molecule. Several experiments were done: quantitative real time PCR, Western blotting, quantitation of cholesterol synthesis with radiolabelled acetic acid and TLC.

Real time PCR was used to measure the level of RNA present, this quantitates the amount of gene expression. (You would add: what is real time PCR? How does it work?)

Western blotting using antibodies to 2,3 oxidosqualene cyclase was used to quantitate the amount that was present. (You would add: what is western blotting, describe the mechanism of how it works.)

The authors conclude that 24,25-epoxycholesterol regulates cholesterol biosynthesis at several points. It is involved in gene regulation and in regulating release of cholesterol from the cell. It is an essential part of the negative feedback mechanism that controls the synthesis of new cholesterol from acetyl CoA.

Describe a Figure from one of your references.

Using one of the papers you are reading for your literature reveiw, choose a figure and describe it.
Be sure to include the following:
1. What experiment was done to produce the data shown in the figure?
2. How does the experiment work? (Describe the underlying theory of the experiment.)
3. What were the controls for this experiment?
4. What is the significance of the data from this experiment?

Annotated Bibliography

You need to have five currrent (2009-2016) primary sources from the biochemical literature. Each source must have biochemical experimental details and results. Experiments may involve spectroscopy, HPLC, enzyme kinetics, electrophoresis, PCR, Western blotting, FRET, DNA arrays, DNA/RNA sequencing, microarrays, protein purification and protein characterization. Include the following: What knowledge does this paper contribute to the understanding of the topic? What experiments were done? Briefly describe the experiments. Use the template that you used for "Summary of One Reference" assignment.

Organizational Map/Outline/Flowchart

Show how you are going to organize your paper. You can make a flow chart, an outline, a map, a story board. Spend some time thinking about the best way to organize the information you have gathered and then make a plan. There is no set format. The key is to present an organized plan for your writing. Remember to use the "stress" position for the important information.

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