Biochemistry 465 (Biochemistry III: Molecular Genetics) -- Spring, 1999

TuTh, 9:30-10:45 a.m., Chemistry 0127

Lecture Schedule

Prof. Jason D. Kahn, Dept. of Chemistry and Biochemistry, Univ. of Maryland, College Park

Office: Chemistry 2505 (Biochemistry, Wing 5 of the Chemistry complex)

Office hours: Weds. 2-3 p.m., Thurs. 1-2 p.m., Chemistry 2505; there is no TA for the course

Contacting me: jdkahn@umd.edu much preferred to 301-405-0058. Please do not drop in to my office or lab, but I will be happy to set up appointments outside of office hours if necessary.

Class web site: http://www.chem.umd.edu/biochem/kahn/bchm465; there will also be an e-mail reflector

Course Description:

This course concerns the structure and function of nucleic acids and the mechanisms of nucleic acid transactions: a biochemical approach to molecular genetics. We will generally cover both prokaryotic and eukaryotic systems and emphasize common mechanisms. Topics are as follows:

• Chemistry and structure of DNA and RNA, from nucleotides to chromosomes.
• Interactions between nucleic acids and proteins.
• Selected aspects of the biochemistry and regulation of DNA replication, transcription, recombination, and repair, and how these processes interact with each other.
• Translation, RNA splicing, and RNA catalysis.

Texts:

• Required: Lewin, Genes VI, 1997 (Oxford University Press)
  
• Occasional required reading from the primary literature may be provided
• Recommended: Mathews and van Holde, Biochemistry, 2^nd ed., 1996 (Benjamin/Cummings), "MvH"
  
• Ako and Shimeld, Study Guide to Accompany MvH (Benjamin/Cummings)
  

Other recommended sources, available on reserve in the White Memorial Chemistry Library:

• Adams, R. L. P., Knowler, J. T., and Leader, D. P. (1992). The Biochemistry of the Nucleic Acids. 11^th ed. London: Chapman & Hall. Fact compendium.
  
• Bates, A. D. and Maxwell, A. (1993). DNA Topology. Oxford: IRL Press at Oxford University Press. Excellent short monograph on this difficult topic.
  
• Kornberg, A. and Baker, T. A. (1992). DNA Replication. 2^nd ed. New York: W.H. Freeman and Co. Great source for historical background, good breadth.
  
• Ptashne, M. (1992). A Genetic Switch: Phage l and Higher Organisms. 2^nd ed. Cambridge, MA: Cell Press and Blackwell Scientific. Heuristics of gene regulation.
  
• Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer—Verlag. Very detailed.
  
• Schleif, R. (1993). Genetics and Molecular Biology. 2^nd ed. Baltimore: The Johns Hopkins University Press. Eclectic, emphasizing experiments leading to conclusions.
  
• Travers, A. (1993). DNA-Protein Interactions. London: Chapman & Hall. Focuses on DNA structure.
  
• Wolffe, A. (1998). Chromatin: Structure and Function. 3^rd ed. San Diego: Academic Press, Inc. Covers from structure to biology.

Grading Policy:

There will be two 75-minute midterm exams (100 pts each), a paper in lieu of a third exam, and a two hour final (200 pts). Exams will be about 50% short-answer questions, testing your comprehension of lecture material, and about 50% essay or computational questions, testing your ability to apply and extend this basic knowledge. The final will explicitly cover only the latter part of the course but will inevitably draw on older material. Past years’ exams from my related graduate course (Biochem 674) will be on reserve.

Your final letter grade will be based on your performance relative to the class as a whole and to my expectations (i.e. it's curved, but I draw the lines between grade levels depending on how I felt the class as a whole performed). Final grades will be given out only through the MARS system. The exams are quite difficult, but in the past I have had few complaints about final grades. I encourage questions and discussion in class, but class participation does not affect grading.

If you absolutely must miss a midterm exam, you must call me in advance or within 24 hours after the exam, and you must also present a valid University excuse, in order to be eligible for the assignment of a grade based on the remaining course work. If you miss the final, do not turn in a paper, or miss both hour exams, you will receive a failing grade. Do not cheat or plagiarize.

The paper, due 5/13/99, is intended to help you connect what we learn in this course to the role of science in society. You should find a non-technical science article which interests you in the popular press, e.g. Discover magazine, the New York Times, Science News, Wired, NPR, Nova. (Paper topics are due on 4/8, and please discuss them with me in advance of that date.) Then, follow up on the science in the article using the primary research literature. Present the background and significance of the discovery and how it connects with material we have covered in this course. The paper should be 5-8 pages of text. In addition, provide figures as needed, a sample page from a database search, and formal literature references (no more than 20% URLs!). This is an experiment for me, so suggestions are welcome.

Lecture Schedule (approximate)

I. Nucleic Acid Structure and Chemistry, Protein-Nucleic Acid Interaction (12 lectures)

EXAM I Covers through lecture 9: 3/4/99

II. DNA Transactions (10 lectures)

Spring Break March 22-28

EXAM II Covers through Lecture 18: 4/15/99

RNA Transactions (5 lectures)

FINAL EXAM: Covers Lectures 19-27: Friday, 5/21/99, 1:30-3:30 p.m., Chem. 0127