| 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 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/bchm674; there is also an e-mail reflector. |
Required papers from the literature will be assigned for some lectures (may be read after the lecture), as indicated on the Course Outline below. All papers will be on reserve at the White Memorial Chemistry Library. In addition, two textbooks are strongly recommended for the course, for background and for reference in your research careers. I may also provide occasional handouts with some figures, hints on what you should take away from the assigned reading, and additional entries into the literature. Some of these additional sources, especially books, are on reserve.
There will be two 75-minute exams (100 pts each), a short (7-10 pp.) paper (100 pts), and a two hour final examination (150 pts). Exams will emphasize lecture material, with some coverage of key concepts from the reading. You will be asked to design and interpret experiments as well as to recapitulate assigned material. Review sessions will be held and past exams will be on reserve. The paper will be an examination of the historical development of our understanding of a particular topic, with emphasis on critical experiments and how they caused reinterpretation of earlier work. I encourage questions and discussion in class, but class participation does not affect grading. Plus/minus final grades will be given.
If you absolutely must miss an 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 two exams and the paper. If you miss the final or both hour exams, you will receive a failing grade. The exams are quite difficult, but in the past I have had few complaints about final grades. Your course grade will be based on exam and paper performance relative to a curve and to my expectations.
I 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. Paraphrasing without referencing will be considered plagiarism. Extensive paraphrasing from a single source is unacceptable, referenced or not. Course Outline
Recommended texts, available at the University Book Center. Chapters to be read for background or amplification are specified for each lecture (W3 = Weaver, Chapter 3, etc.). You are not responsible for material covered only in the book unless this is specifically announced.Bloomfield, V.A., Crothers, D.M., and Tinoco, I., Jr. (2000). Nucleic Acids: Structure, Properties and Functions. University Science Books, Sausalito CA. Biophysical chemistry.
Weaver, R. F. (2001). Molecular Biology. 2nd ed., WCB/McGraw-Hill, Boston. Excellent source for historical and modern experiments.
| 1. | Nucleic acid building blocks; BCT2, W1, 2, 3 | 8/30/01 |
| Central dogma, nucleotide structure, primary structure, chemical stability, nomenclature | ||
| 2. | Structures of double helices; BCT4, W2 | 9/4/01 |
| A, B, and Z form helices, base pairing and hydrogen bonding | ||
| Watson and Crick, 1953; Dickerson, 1983 | ||
| 3. | DNA and RNA hybridization and thermodynamics; BCT8, W5 | 9/6/01 |
| Base-pair stability rules, melting, hybridization, hypochromism, gene chips | ||
| Holstege et al., 1999 | ||
| 4. | RNA structure and triple helices; BCT8, W19 | 9/11/01 |
| Tertiary structure and tRNA, prediction of RNA folding, antisense | ||
| Moser and Dervan, 1987 | ||
| 5. | Sequencing and synthesis of DNA and RNA; BCT3, W5, 24 | 9/13/01 |
| Maxam-Gilbert and Sanger sequencing, chemical and enzymatic synthesis, genomics and bioinformatics | ||
| Fleischmann et al., 1995 | ||
| 6. | Drug and cation binding, chemical probing methods; BCT11, 12 | 9/18/01 |
| Intercalation, groove-binding, ion atmosphere, reactivity of nucleotides, altered backbone chemistries | ||
| 7. | DNA bending, flexibility, and cyclization; BCT9 | 9/20/01 |
| Bending and twisting flexibility, sequence-directed bending, methods for detection and quantitation | ||
| Zinkel and Crothers, 1987 | ||
| 8. | Topology, supercoiling, topoisomerases; BCT10, W20 | 9/25/01 |
| Linking number, superhelix structure, topoisomerase reaction mechanisms, knots and catenanes | ||
| Bauer et al., 1980 | ||
| 9. | Enzymatic manipulation of nucleic acids; BCT3, W4, 5 | 9/27/01 |
| Restriction enzymes, nucleases, radiolabeling, basic genetic engineering, polymerases, PCR | ||
| Arnheim and Levenson, 1990 | ||
| 10. | Catch-up day | 10/2/01 |
| 11. | Biochemical methods for studying complexes; BCT13, W5 | 10/4/01 |
| Binding curves, gel mobility shift, footprinting/interference, crosslinking, filter binding, ChIP | ||
| 12. | Protein structural motifs for nucleic acid binding; BCT13, W9, 12 | 10/9/01 |
| Helix-turn-helix, zinc fingers, bZIP proteins, TBP, hnRNP, etc. | ||
| Harrison, 1991; Nikolov et al., 1995 |
| 13. | Sequence- and structure-specific recognition of nucleic acids; BCT13, W9 | 10/16/01 |
| Major groove vs. minor groove, hydrogen bonding, direct vs. indirect readout, deformability, RNA recognition | ||
| Seeman et al., 1976 | ||
| 14. | Chromosome structure; BCT14, W13 | 10/18/01 |
| Nucleosomes, chromatin, higher-order structure, telomeres | ||
| Luger et al., 1997 |
| 15. | DNA replication: fundamental mechanisms; W20, 21 | 10/23/01 |
| Polymerization reaction mechanisms, fidelity, structure | ||
| Brutlag and Kornberg, 1972 | ||
| 16. | Genome replication; W20,21 | 10/25/01 |
| Origin recognition and polymerase holoenzymes in E. coli; the cell cycle. | ||
| Naktinis et al., 1996 | ||
| 17. | Transcription: fundamental mechanisms; W6 | 10/30/01 |
| RNA polymerases, transcription cycle, transcription bubble, supercoiling | ||
| Nudler et al., 1997; Liu and Wang, 1987 | ||
| 18. | Regulation in prokaryotes; repression, activation, looping; W7, 8 | 11/1/01 |
| Paradigms: lac operon, araC, ntrC. Searching mechanisms. | ||
| 19. | Transcription in eukaryotes: chromatin and complexity; W10, 11, 12, 13 | 11/6/01 |
| Holoenzyme vs. initiation complex assembly, activators, enhancers, chromatin, recruitment | ||
| Struhl, 1999; Cosma et al., 1999 | ||
| 20. | Recombination; W22, 23 | 11/8/01 |
| Holliday junctions, recABCD, l phage integration and excision |
| 21. | DNA repair; W20 | 11/13/01 |
| BER (base excision repair), NER (nucleostide excision repair), mismatch repair, connections to cancer |
| 22. | "Interprocess Communication" | 11/20/01 |
| Review of regulatory and biochemical connections among replication, transcription, repair |
| 23. | Catalytic RNA; W14 | 11/27/01 |
| Self-splicing RNA, ribozymes, origin of life | ||
| 24. | RNA splicing and degradation; W14, 16 | 11/29/01 |
| Splicing mechanisms, control of mRNA lifetime | ||
| Nilsen, 1994 | ||
| 25. | Translation; W18, 19 | 12/4/01 |
| Chemistry of protein biosynthesis, ribosome structure, the translation cycle | ||
| Nissen et al., 2000 | ||
| Paper Due: | 12/4/01 | |
| 26. | Selection-amplification methods for nucleic acids | 12/6/01 |
| Selection of optimal DNA and RNA ligands or catalysts, in vitro evolution | ||
| Ellington and Szostak, 1990 | ||
| 27. | Review and/or catch up day. | 12/11/01 |
General texts for further reading and background:
Kornberg, A. and Baker, T. A. (1992). DNA Replication. 2nd ed. New York: W.H. Freeman and Co. Focuses on classical biochemistry experiments.
Lewin, B. (1999). Genes VII. Oxford: Oxford University Press. Deeply flawed but relatively up-to-date.
Schleif, R. (1993). Genetics and Molecular Biology. 2nd ed. Baltimore: The Johns Hopkins University Press. Eclectic, emphasizing experiments leading to conclusions.
Bates, A. D. and Maxwell, A. (1993). DNA Topology. Oxford: IRL Press at Oxford University Press. 114 pp. Excellent short monograph on this difficult topic.
Ptashne, M. (1992). A Genetic Switch: Phage l and Higher Organisms. 2nd ed. Cambridge, MA: Cell Press and Blackwell Scientific. 192 pp. Heuristics of gene regulation.
Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer–Verlag. 556 pp. Very technical and detailed.
Steitz, T. A. (1993). Structural Studies of Protein-Nucleic Acid Interaction: The sources of sequence-specific binding. Cambridge, England: Cambridge University Press. 79 pp. Good pictures.
Travers, A. (1993). DNA-Protein Interactions. London: Chapman & Hall. 180 pp. And DNA structure.
Wolffe, A. (1999). Chromatin: Structure and Function. 3rd ed. San Diego: Academic Press, Inc. 400 pp. Covers from structure to biology.
Arnheim, N. and Levenson, C. H. (1990). “Polymerase Chain Reaction.” Chem. & Eng. News (October 1), 38-47.
Bauer, W. R., Crick, F. H. C., and White, J. H. (1980). “Supercoiled DNA.” Scientific American243(1), 118-133.
Brutlag, D. and Kornberg, A. (1972). “Enzymatic Synthesis of Deoxyribonucleic Acid: XXXVI. A proofreading function for the 3' -> 5' exonuclease activity in deoxyribonucleic acid polymerases.” J. Biol. Chem.247, 241-248.
Cosma, M. P., Tanaka, T. and Nasmyth, K. (1999). “Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter.” Cell97(3), 299-311.
Dickerson, R. E. (1983). “The DNA Helix and How It Is Read.” Sci. Am. (December), 94-111.
Ellington, A. D. and Szostak, J. W. (1990). “In vitro selection of RNA molecules that bind specific ligands.” Nature346, 818-822.
Fleischmann, R. D., Adams, M. D., White, O., many others and Venter, J. C. (1995). “Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd.” Science269, 496-512.
Harrison, S. C. (1991). “A structural taxonomy of DNA-binding domains.” Nature353, 715-719.
Holstege, F. C. P., Jennings, E. G., Wyrick, J. J., Lee, T. I., Hengartner, C. J., Green, M. R., Golub, T. R., Lander, E. S. and Young, R. A. (1999). “Dissecting the Regulatory Circuitry of a Eukaryotic Genome.” Cell95, 717-728.
Liu, L. F. and Wang, J. C. (1987). “Supercoiling of the DNA Template During Transcription.” Proc. Nat. Acad. Sci. USA84, 7024-7027.
Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F. and Richmond, T. J. (1997). “Crystal structure of the nucleosome core particle at 2.8 Å resolution.” Nature389, 251-260.
Moser, H. E. and Dervan, P. B. (1987). “Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation.” Science238, 645-650.
Naktinis, V., Turner, J. and O’Donnell, M. (1996). “A Molecular Switch in a Replication Machine Defined by an Internal Competition for Protein Rings.” Cell 84, 137-145.
Nikolov, D. B., Chen, H., Halay, E. D., Usheva, A. A., Hisatake, K., Lee, D. K., Roeder, R. G. and Burley, S. K. (1995). “Crystal structure of a TFIIB-TBP-TATA element ternary complex.” Nature377, 119-128.
Nilsen, T. W. (1994). “RNA-RNA Interactions in the Spliceosome: Unraveling the Ties That Bind.” Cell78, 1-4.
Nissen, P., Hansen, J., Ban, N., Moore, P. B. and Steitz, T. A. (2000). “The Structural Basis of Ribosome Activity in Peptide Bond Synthesis.” Science289, 920-930.
Nudler, E., Mustaev, A., Lukhtanov, E., and Goldfarb, A. (1997). “The RNA-DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase.” Cell89, 33-41.
Seeman, N. C., Rosenberg, J. M., and Rich, A. (1976). “Sequence-specific recognition of double helical nucleic acids by proteins.” Proc. Natl. Acad. Sci. USA 73, 804-808.
Struhl, K. (1999). “Fundamentally Different Logic of Gene Regulation in Eukaryotes and Prokaryotes.” Cell 98, 1-4.
Watson, J. D. and Crick, F. H. C. (1953). “Molecular Structure of Nucleic Acids: A structure for deoxyribose nucleic acid.” Nature171, 737-738.
Zinkel, S. S. and Crothers, D. M. (1987). “DNA bend direction by phase sensitive detection.” Nature328, 178-181.