Research paper for Biochemistry II
The major writing exercise for Biochemistry II is an in depth literature report that is peer reviewed and published on the www. Students are required to write a 10 to 12 page research paper using information from the current refereed literature. There are many assignments that build up to the final submission on their literature review; there are also several peer reviews.
Instructions for Topic Paper
This paper will be graded on originality and depth of thought. State the biochemical problem that you want to study, explain why you want to study this problem and describe the impact that 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 biochemical reactions are involved? What metabolic relationships are involved? Then state your problem including this information. Make sure you can find current primary research papers on your topic. You will need at least one primary source for this topic paper assignment. Sources of information must be cited using a consistent style: ACS, APA, AMA, Chicago, etc. 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
Give a complete citation information for at least five current (no more than three years old) primary sources. Primary sources have experimental sections. A primary source publishes data for the first time.
Summary of One Reference**
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 woul 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 a Primary Source:
Choose a figure from one of your references 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?
There is a link on our web page that will help you with some of the terms and
experimental techniques. Look for “Decoding the Procainamide paper”. Also, Mama
Ji’s kitchen is a great source of biochemical experiment information.
Instructions for the Annotated Bibliography
Find at least five current (2018-present) primary sources (original, peer reviewed papers) in the biochemical literature. Read each paper 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 woul 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.
First Draft
The first draft is a spell checked, typed and formatted document. There may be sections that are not fully developed and figures that are still on the drawing board. Since we are publishing your papers on the www, **you will either need to get permission from the copyright holder to reproduce their figures, or you will need to make your own figures.
Second Draft**
The second draft is a complete manuscript that students are submitting for publication.
Final Submission
Please submit a pdf file that has the title and below it "Copyright your name and Koni Stone". This version will be published on the web at: http://biochemistry-stanislaus.wikidot.com/
These submissions will be peer reviewed. Each student who submits a paper **on time will receive two papers to review. As soon as you submit your reveiw, the author will be able to see your comments.
| Assignment | Points | Due Dates for 2024, 10% per day late penalty |
|---|---|---|
| Topic Paper | 20 | Feb 2 |
| List of References | 10 | Feb 9 |
| Summary of One Reference | 10 | Feb 16 |
| Peer Review, Summary of One Reference | (5 each x 2)= 10 | Feb 23 |
| Describe a Figure | 10 | March 8 |
| Annotated Bibliography | 50 | March 15 |
| Outline/Organizational Map | 20 | March 22 |
| First Draft | 50 | April 12 |
| Peer Reviews, 1st Draft | (10 x 2) = 20 | April 19 |
| Second Draft | 60 | May 3 |
| Peer Reviews, 2nd draft | (10 x 2) = 20 | May 10 |
| Final Version | 20 | May 22 |
There is a 10% per day late penalty. If your paper is not turned in by midnight for the peer reviewed assignments, you will not get peer review feedback and you will not get papers for the peer review exercise.