Biochemistry & Molecular Biology 3400

Biochemistry & Molecular Biology 3400 Nucleic Acid Biochemistry and Molecular Biology Prospectus; Fall Term, 2011 LECTURERS

J.M. Archibald, Department of Biochemistry & Molecular Biology (Coordinator) Room 8H, Tupper, Tel: 494-2536 Email: [email protected] P. Liu, Department of Biochemistry & Molecular Biology Room 9M1, Tupper, Tel: 494-1208 Email: [email protected] C. Slamovits, Department of Biochemistry & Molecular Biology Room 9G, Tupper, Tel: 494-8825 Email: [email protected]

TIME

MWF

10:30 - 11:30 AM

PLACE

Theatre D, Tupper Medical Building

LABORATORY

Monday Thursday

INSTRUCTOR

Paul Briggs (Room 8H, Tupper Medical Building) Tel: 494-2382

WEBSITE

http://www3.biochem.dal.ca/3400/ Watch this site for information about the course: reference lists, electronic copies of lectures, answers to frequently asked questions, changes to lab schedules / assignments, examples of questions from past midterms/finals

SUBJECT

This class focuses on the relationship of structure to function in RNA and DNA. Methods of studying the primary, secondary and tertiary structures of nucleic acids are explored in lectures and in the laboratory. Enzymatic mechanisms for biosynthesis, rearrangement, degradation and repair of nucleic acid molecules are studied, as are the processes of replication, transcription and translation. In this context, nucleic acid biochemistry is emphasized as a basis for understanding storage and transfer of biological information. Molecular biological techniques are based on underlying principles of nucleic acid biochemistry and will be described in that context.

EVALUATION

Please note the two mid-term examinations will take place during the regularly scheduled lecture periods on Friday, October 7th and Wednesday, November 9th.

2:30 - 5:30 PM 2:30 - 5:30 PM

Room 8J-1, Tupper Medical Building Room 8J-1, Tupper Medical Building

Distribution of marks toward the final grade will be as follows: 30% two mid-term examinations (15% each) 30% laboratory (4 lab reports, 4 lab assignments and 1 in-lab quiz) 40% final examination IMPORTANT—The final examination will consist of short answer, data interpretation and problem solving questions. Examination questions will be based primarily on material drawn from lectures but can include aspects of the laboratory experiments. Please note: students who fail to achieve a passing grade in both midterms must achieve a passing grade in the final exam in order to pass the course.

BIOC3400 – 2011 REFERENCE MATERIAL Recommended text: Voet and Voet: Biochemistry (4th Edn, 2011) Although this text is recommended, no single textbook covers all material in the course, and none is specified as absolutely required. Lectures will be drawn from a variety of sources, including the recent literature. Copies of most transparencies/slides shown in lectures will be provided either as handouts or on the course web site (or both). As well, specific reference material will be placed on reserve in the Kellogg Health Sciences Library (see course web site for list of reference texts). For much of the material in the course, any modern textbook of biochemistry and/or molecular biology will provide the basic background. The following general texts are also particularly clearly written and well illustrated, and encompass most of the material that will be presented in the course: -Nelson and Cox: Lehninger Principles of Biochemistry (5th Edn, 2008) -Voet and Voet: Biochemistry (3rd Edn, 2004) -Matthews, van Holde and Ahern: Biochemistry (2000) -Lodish et al.: Molecular Cell Biology (5th edn., 2003) -Nelson and Cox: Lehninger Principles of Biochemistry (3rd edn., 2000) -Watson et al.: Molecular Biology of the Gene (5th edn., 1992) -Zubay: Biochemistry (3rd edn., 1993) IMPORTANT—MISSED EXAMINATIONS AND ASSIGNMENTS In accordance with Biochemistry & Molecular Biology Department policy, a student who misses an examination (midterm test etc.) due to illness must notify the professor, instructor or department office within 48 hours and provide a valid medical certificate no more than 1 week after the scheduled examination (see Dalhousie Calendar section 16.8 and note below). Special ‘make-up’ examinations (if offered) will normally be written within 7 calendar days after the missed examination. Absence for nonmedical reasons is not ordinarily acceptable unless prearranged with the professor/instructor. A missed examination for which no satisfactory arrangement has been made will be given a mark of zero. Assignments must be submitted to the professor/instructor/department office no later than 5:00 PM (for laboratory reports - 2:30 PM) on the designated due date. Extension of the due date will be granted only in the case of illness supported by a valid medical certificate presented to the professor/instructor within one week of the due date. Other reasons, such as excessive workload, are not normally acceptable. Extension of due date will ordinarily not exceed 7 calendar days. The grade for late laboratory reports will be reduced by 10% for each day after the due date.

Biochemistry & Molecular Biology 3400 Nucleic Acid Biochemistry and Molecular Biology Schedule of Lectures; Fall Term, 2011 TIME 10:30-11:30 AM

LOCATION Theatre D, Tupper Medical Building

DATE

DAY

TOPIC

Sept. 9 12 14 16 19 21 23 26 28 30 Oct. 3 5

F M W F M W F M W F M W

1. Introduction 2. Nucleosides and nucleotides 3. Polynucleotide structure (1) 4. Polynucleotide structure (2) 5. Nucleases; DNA/RNA modifying enzymes 6. DNA replication (1): introduction 7. DNA replication (2): DNA polymerases 8. DNA replication (3): biochemical mechanism 9. DNA replication (4): biochemical mechanism 10. DNA replication (5) eukaryotes 11. DNA repair (1) 12. DNA repair (2)

F

MID-TERM EXAM #1

10 12 14 17 19 21 24 26 28 31 Nov. 2 4 7

M W F M W F M W F M W F M

NO LECTURE (Thanksgiving) 13. Denaturation, renaturation of nucleic acids 14. Restriction enzymes/restriction analysis 15. Recombinant DNA (1) 16. Recombinant DNA (2) 17. Recombinant DNA (3) 18. Nucleic acid sequencing 19. Gene structure, prokaryotic vs. eukaryotic 20. Transcription and its control (1) 21. Transcription and its control (2) 22. Transcription and its control (3) 23. Chromatin (1) 24. Chromatin (2) + review

9

W

MID-TERM EXAM #2

11 14 16 18 21 23 25 28 30 Dec. 2 5

F M W F M W F M W F M

NO LECTURE (University Study Day) 25. Transfer RNA 26. Genetic code 27. Ribosome structure, function, rRNA processing 28. Translation (1) 29. Translation (2) 30. Translation (3) 31. mRNA processing: spliceosome, snRNAs 32. RNA editing; catalytic RNAs 33. Non-coding RNAs: micro-RNA, siRNA, RNAi 34. Review

7

LECTURER P. Liu (PL) PL PL PL PL PL PL PL PL PL PL PL PL J. Archibald (JMA) JMA JMA JMA JMA JMA JMA JMA JMA JMA JMA JMA JMA C. Slamovits (CS) CS CS CS CS CS CS CS CS CS