TuTh, 9:30-10:45 a.m., Chemistry 0128

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

Office:                   Chemistry 2505 (in 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 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.biochem.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, emphasizing common logic and mechanisms. Topics are as follows:

• Chemistry and structure of DNA and RNA, from nucleotides to chromosomes, and some methods for studying, sequencing and manipulating nucleic acids. Simple bioinformatics.
• 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 general RNA catalysis.

Texts (note that the course is primarily lecture-based):

Required: Weaver, R. F. (2002). Molecular Biology. 2^nd ed., WCB/McGraw-Hill, Boston. Excellent source for historical and modern experiments. Also see http://www.mhhe.com/biosci/cellmicro/weaver2/.

Occasional required reading from the primary or review literature may be provided.

Recommended: Any of the standard Biochemistry texts you have used for BCHM 461, 462, or 463.

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

Bates, A. D. and Maxwell, A. (1993). DNA Topology. Oxford: IRL Press at Oxford University Press. Excellent short monograph on this difficult topic.

Bloomfield, V.A., Tinoco, I., Jr. and Crothers, D.M. (2000). Nucleic Acids: Structure, Properties and Functions. University Science Books, Sausalito CA. Nucleic acid structure, biophysical chemistry.

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.

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. (1999). Chromatin: Structure and Function. 3^rd ed. San Diego: Academic Press, Inc. Covers from structure to biology.

Requirements, Grading and Academic Honesty Policies:

There will be two 75-minute midterm exams (100 pts each), group class projects in lieu of a third exam (75 pts), and a two hour final (150 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. There will be a review session before each exam (typically Tuesday evening before a Thursday exam, or to be determined). Past years’ exams will be on the web site and the answers will be on reserve in the White Memorial Chemistry Library.

The class projects, to be conducted by small groups, are intended to give you and others an understanding of the sources of our knowledge of molecular machines. Each group of 4-5 students will study a type of DNA/RNA transaction (e.g. replication, transcription, repair, RNA splicing, recombination, translation). The panoply of components involved in the process will be schematized in web page form, with links to pages on the experiments in which they were first identified, their essential functions identified, and their structures if available. Last year’s class did similar projects, with generally excellent results. This year, some groups will refresh previous web pages with more current information, while other groups will do similar work on new topics. The goal is that at the end of this class we will all be proud to make the work generally accessible as a teaching resource useful to the world at large. More information will be provided on the projects.

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). Midterm letter grades will not be assigned. Final grades, with plus/minus, 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 project, or miss both hour exams, you will receive a failing grade.

The University has an active Student Honor Council, which administers an Honor Code. The Honor Council sets high standards for academic integrity, and I support its efforts. Please note in this regard the University Honor Pledge. The Student Honor Council proposed and the University Senate approved this Pledge: “I pledge on my honor that I have not given or received any unauthorized assistance on this assignment/examination.” The Pledge statement should be handwritten and signed on the front page of all examinations and the group project. Students who fail to write and sign the Pledge will be asked to confer with me. (Adapted from http://www.inform.umd.edu/CampusInfo/Departments/JPO/AI/honorpledge/.)

Furthermore, I otherwise expect and enforce adherence to the University’s Code of Academic Integrity, found at http://www.inform.umd.edu/CampusInfo/Departments/JPO/code_acinteg.html. Specifically, “plagiarism” will be interpreted in its broadest sense: ideas from others must be referenced; words from others must be in quotation marks and referenced (from Phil DeShong). Paraphrasing without referencing will be considered plagiarism. Extensive paraphrasing from a single source is unacceptable, referenced or not. You are hereby specifically directed to read my personal statement on plagiarism as a condition of taking this course, at http://www.biochem.umd.edu/biochem/kahn/plagiarism.html. Please do not test me on this. Plagiarism is surprisingly easy to detect and I will pull the trigger without hesitation.

Lecture Schedule (approximate):

Reading assignments are for reference, not required unless explicitly stated.

All assignments refer to Weaver, Molecular Biology.

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

—> EXAM I <— Covers through lecture 10       3/7/02

II.    DNA Transactions (10 lectures)

Spring Break March 25-29

—> EXAM II <— Covers through Lecture 19       4/18/02

III.  RNA Transactions (5 lectures)

FINAL EXAM: Covers Lectures 20-27     Tuesday, 5/21/02, 1:30-3:30 p.m., Chem. 0128