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BIOCHEMISTRY 300B General Biochemistry II Course Outline: Spring 2013 Place: Time: Textbook: Web site:
ECS123 Tuesday, Wednesday, Friday: 12:30 - 1:20 pm Biochemistry by Berg, Tymoczko, and Stryer, 7th edition UVic Moodle
Instructors:
Dr. PJ Romaniuk (Jan 4 – Feb 13). Office: Petch 223b; Office hours: M 1:30-2:30 pm, Th 10:30-11:30 am (or by appointment); email:
[email protected] Dr. D Briant (Feb 15 – Apr 3), Office: Petch 227; Office hours: T, W, F 10:00 - 11:00 am (or by appointment); email:
[email protected]
Course Description: BIOC 300B in conjunction with BIOC300A provides detailed coverage of foundation topics for students majoring in biochemistry or microbiology. In this course, the structures and functions of DNA, RNA and genes are discussed along with the regulation of gene expression in prokaryotes and eukaryotes. Also discussed are metabolic processes and their control. Students need to have a good understanding of the principles of cell biology and organic chemistry before taking this course. Marking Policy: There will be four class tests held during the regular lecture period on January 23, February 13, March 15, and April 3. The first class test will cover the material discussed in lectures 1-8 (worth 20% of the final grade), the second will cover the material discussed in lectures 9-16 (worth 20% of the final grade), the third will cover the material discussed in lectures 17-25 (worth 25% of the final grade), and the fourth will cover the material discussed in lectures 26-30 (worth 15% of the final grade). Students may bring their textbook, calculator, pens and pencils to the class tests. Students having a cell phone, tablet, or computer on their person during a class test will be assumed to have it for the purpose of cheating. Test papers written in pencil will not be reviewed or remarked. In addition to the class tests there will be 2 problem sets assigned, one in the first half of the course and one in the second half. Each will be worth 10% of the final grade. Lecture Content: Each lecture will conform approximately to the organization used in the text. Additional material and examples may be added by the lecturer and will be posted on Moodle. The lecture schedule given below is a close approximation of what will be followed. Readings from the text for each lecture have been assigned and must be read prior to the lecture. Information designed to guide students with the readings is available on Moodle. Students are responsible for the lecture material and reading assignments for the class tests.
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Biochemistry 300B. Lecture Schedule and Topics Lect # 1 2 3 4 5 6 7 8 T1 9 10
Date Jan 4 8 9 11 15 16 18 22 23 25 29
11 12 13 14 15
30 Feb 1 5 6 8
16 T2 17 18 19 20 21 22 23 24 25 T3 26 27 28
12 13 15 18-22 26 27 Mar 1 5 6 8 12 13 15 19 20 22
29 30
26 27
31 T4
29 Apr 2 3
Topic Structure of Nucleotides and Nucleic Acids Flow of Genetic Information I Flow of Genetic Information II DNA structure and replication Replication DNA Repair and Recombination Transcription in Prokaryotes Transcription in Eukaryotes Class Test I (20%) Lectures 1-8 Post-transcriptional Modification (continued) [Problem Set I Posted on Moodle] Overview of Gene Regulation Regulation of Transcription in Prokaryotes Regulation of Transcription in Eukaryotes Protein Synthesis (continued) [Problem Set I Due in Class] Post-transcriptional Regulation Class Test II (20%) Lectures 9-16 Metabolism preamble Reading Break Bioenergetics Bioenergetics (continued) Intermediary Metabolism: Glycolysis (continued) Gluconeogenesis Glycogen metabolism Citric Acid Cycle (continued) Class Test III (25%) Lectures 17-25 Chemiosmosis and ATP synthesis (continued) Fatty degradation and Synthesis [Problem Set 2 Due in Class] (continued) Lipids, cholesterol and their synthesis Good Friday Protein and Amino Acid Catabolism Class Test IV (15%) Lectures 26-30
Text Reference Ch. 4: 109-118 Ch. 4: 118-127 Ch. 4: 127-135 Ch. 28: pp. 819-837 Ch. 28: pp. 819-837 Ch. 28: pp. 837-846 Ch. 29: pp. 851-863 Ch. 29: pp. 864-869 Ch. 29: pp. 869-876 Ch. 29: pp. 876-882 Ch. 31: pp. 921-933 Ch. 31: pp. 921-933 Ch. 32: pp. 937-951 Ch. 30: pp. 887-899 Ch. 30: pp. 899-914 Ch. 31: pp. 951-954
Ch. 15 Ch. 15 Ch. 16: pp. 453-479 Ch. 16: pp. 479-493 Ch. 21: pp. 615-624 Ch. 17: pp. 497-520 Ch. 18: pp. 525-555 Ch. 12: p 347-348 Ch. 22: pp. 639-667 Ch. 12: pp 348-350 Ch. 26: pp 759-770 Ch. 23: pp. 673-690
3 FINAL EXAM There will not be a final exam in this course.
Revised UVic Grading Scheme (effective May 1, 2012) Passing Grades
Grade Point Value
A+ A A-
9 8 7
Percentage for Instructor Use Only * 90 – 100 85 – 89 80 – 84
B+ B B-
6 5 4
77 – 79 73 – 76 70 – 72
C+ C
3 2
65 – 69 60 – 64
D
1
50 – 59
F
0
0-49
N*
0
0-49
Description
Exceptional, outstanding and excellent performance. Normally achieved by a minority of students. These grades indicate a student who is self-initiating, exceeds expectation and has an insightful grasp of the subject matter. Very good, good and solid performance. Normally achieved by the largest number of students. These grades indicate a good grasp of the subject matter or excellent grasp in one area balanced with satisfactory grasp in the other area. Satisfactory, or minimally satisfactory. These grades indicate a satisfactory performance and knowledge of the subject matter. Marginal Performance. A student receiving this grade demonstrated a superficial grasp of the subject matter. Unsatisfactory performance. Wrote final examination and completed course requirements; no supplemental. Did not write examination or complete course requirements by the end of term or session; no supplemental.
* N grades Students who have completed the following elements will be considered to have completed the course and will be assigned a final grade: • •
All four class tests scheduled for Jan 23, Feb 13, Mar 15, and Apr 3 One of the two assigned problem sets
Failure to complete one or more of these elements will result in a grade of “N” regardless of the cumulative percentage on other elements of the course. An N is a failing grade, and it factors into a student’s GPA as O. The maximum percentage that can accompany an N on a student’s transcript is 49
4 DEPARTMENT INFORMATION AND POLICIES 1. The Department of Biochemistry and Microbiology upholds and enforces the University’s policies on plagiarism and cheating. These policies are described in the current University Calendar. All students are advised to read this section. 2. Cell phones, computers and other electronic devices must be turned off at all times unless being used for a purpose relevant to the class. Students having a cell phone, tablet, or computer on their person during an exam will be assumed to have it for the purpose of cheating. 3. Any recordings of lectures may only be performed with written permission of the instructor, and are for personal use only. The instructor retains copyright to such recordings and all lecture materials provided for the class (electronic and otherwise); these materials must not be shared or reposted on the Internet. 4. Students are expected to be present for the midterm and final exams. Instructors may grant deferrals for midterm examinations for illness, accident, or family affliction, and students must provide appropriate documentation 48 hours after the midterm exam. The Department of Biochemistry and Microbiology considers it a breach of academic integrity for a student taking a deferred examination to discuss the exam with classmates. Similarly, students who reveal the contents of an examination to students taking a deferred examination are considered to be in violation of the University of Victoria policy on academic integrity (see current University Calendar). Deferral of a final exam must be requested with an Academic Concession form and submitted directly to Undergraduate Records. Deferred final exams for fall term courses will be arranged by the instructor. Deferred final exams for spring term courses will be arranged through Undergraduate Records and must be written before the end of the summer term as stipulated in the University Calendar. 5. Scan sheets for multiple choice exams (bubble sheets) will not be made available for review. Therefore, in addition to filling in answers on the scan sheet, students should also circle their answers in ink on their exam. 6. Professors may refuse to review/remark exams not written in ink. In addition, requests for review/remark of a midterm exam must be made within one week of the exam being returned. Students are expected to promptly pick up midterm exams after marking has been completed, either in class or from the instructor. 7. Examination papers that have pages removed, or are mutilated will not be marked.
