Chemistry 345/ 545
Advanced Biochemistry—Nucleic Acids and Genomics
Fall 2004—Professor Susan White (Room 202 PSB swhite@brynmawr.edu)
MWF 9:10-10:00
Room 278 PSB
Scope and Purpose:
The goal of this seminar style course is to examine recent advances made possible by the study of genomes. Starting with a structural examination of DNA and its protein partners we will continue to discuss methods for extracting meaningful information out the long monotonous stretches of nucleotide primary sequences. Rather than study one gene, protein, or metabolic pathway at a time, genome scientists are currently interested in how entire sets of genes, transcripts, and enzymes behave and interact. Because the amount of data generated and studied by genome studies is vast, understanding computer databases is crucial. Applications to medicine and diseases will be discussed in a “case study” format.
Course Organization:
Generally the Monday and Wednesday sessions will feature presentations by the instructor and Fridays will be devoted to student presentations, worksheets, and discussions. Student presentations of web material described in the textbook will be essential and these allow students to gain hands-on experience in using bioinformatics databases and programs. Breakfasts and snacks are welcome, but please be a tidy eater!
Texts:
Biochemistry 5th edition by Berg, Tymoczko, and Stryer (or any similar text)
Discovering Genomics, Proteomics, and Bioinformatics by Campbell and Heyer
Websites:
http://www.brynmawr.edu/Acads/Chem/chem345sw2004/biochem2004345index.html
Who can take this course?
Any advanced chemistry or biology student who has taken biochemistry.
Grading:
Your grade will be comprised of three equal parts.
***Term paper on the genome of
your choice.
In recent years there has been an explosion of genome research on animals, plants, pathogenic organisms, eubacteria, and archaea. Motivations range from curing diseases such as cholera, malaria, syphilis, and stomach ulcers to understanding evolutionary relationships among organisms and increasing food crop yields. Your 10 page paper should focus on one organism that has at least 200 genes. You may want to start with textbook or review articles but should discuss about 10 articles from the primary literature. There is absolutely no prohibition to using an article you used as a short paper. Your paper should focus on the goals, scientific methods, and major findings of the project. Each student will give a short presentation about her genome and may elect to include an “electronic supplement” to her paper as a PowerPoint or Web page. An electronic sign-up sheet will be posted.
***Oral
Presentations—approximately every third week.
Electronic sign-up sheets will be posted for the web-based blocks of “Discovery Questions” found in Campbell & Heyer. As a presenter it will be your job to thoroughly explore the questions posed and explain your finding to the class. At the end of the semester, small groups of students will present the final three chapters that deal with medical issues and case studies.
***Short written papers on the
recent primary literature.
These 2 page critical summaries are due every Monday before Nov. 15. Find a primary journal article written after 2001 relevant to the topic under discussion that week and give the complete citation for the paper. Your paper should explain the goal of the research, the major results, and describe the major experimental technique. The last paragraph is your critical analysis of this paper. Each paper will be graded satisfactory or unsatisfactory and satisfactory papers are on time and include all of the elements listed above.
The number of satisfactory papers will determine your grade as follows:
|
5 or more |
4.0 |
|
4 |
3.7 |
|
3 |
3.3 |
|
2 |
3.0 |
|
1 |
2.7 |
|
0 |
0 |