Unit 2 Biology Course Outline Winter BIOC 305 Molecular Biochemistry (3) TTh 8 a.m.- 9:20 a.m. Art 376

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1 Unit 2 Biology Course Outline 2013 Winter BIOC 305 Molecular Biochemistry (3) TTh 8 a.m.- 9:20 a.m. Art 376 Instructor: Dr. Joyce Boon Office: Science 316 Phone: ( ) Joyce.Boon@ubc.ca Office Hours: I like to have an open door policy for students. However, now that I am the unit head for Biology, I would encourage you to make an appointment to ensure that I am available at a time convenient to you. Please me at joyce.boon@ubc.ca or contact the unit assistant Barb.Lucente@ubc.ca. My is accessible through CONNECT Course Description: Biochemistry 305 (3 credits) Molecular Biochemistry II Metabolic pathways with a mechanistic perspective including regulation and control of carbohydrate, lipid, amino acid, and nucleotide catabolism and anabolism. Oxidative- and photophosphorylation. The biochemistry and molecular biology of signal transduction, replication, DNA repair, transcription, translation, and gene regulation. Prerequisites: BIOC 304 and BIOL 200 Course Objectives: To provide students with: An understanding of the essential principles of metabolic interrelationships and regulation of metabolic conversions and turnover in catabolism and anabolism of carbohydrates, lipids and proteins. An understanding of biochemical energetics including a detailed molecular view of oxidative phosphorylation and photophosphorylation. An introduction to nucleotide metabolism and functional genomics. Applications of metabolic principles to understanding selected disease processes. Course Format: This is a lecture style course. All lectures will be posted on CONNECT, however there will be activities during class, material presented and illustrations used in class that will Page 1 of 6

2 not be posted in part because of copyright restrictions. You are advised to attend all lectures. There will be quizzes given on a regular basis to help you keep up with the lecture material. Small assignments will be posted on CONNECT that will require a quick on-line response. Please check CONNECT for those assignments. Copyright disclaimer: Diagrams and figures included in PowerPoint presentations are cited and any PowerPoint presentations uploaded to CONNECT that contain diagrams and figures are used with permission of the publisher. Required Materials: Voet, Voet and Pratt: Fundamentals of Biochemistry. Wiley publishers. 4 th edition, Course Evaluation: Midterm #1 30% February 14 th, 2013 Midterm #2 30% March 19 th, 2013 Assignments/Quizzes 10% Final 30% In final exam period Total 100% Final grades will be based on the evaluations listed above and the final grade will be assigned according to the standardized grading system outlined in the UBC Okanagan Calendar. The possibility of re-weighting of exams is available to any student who significantly underperforms on one exam. Please speak to the instructor. The final exam, while not comprehensive in the traditional sense, will have questions that rely on your knowledge of material covered in all parts of the course. Note: Any requests for changes to final exams must be sent to the office of the Associate Dean of Students (Dr. Patricia Lasserre). Missed Assignments and Exams: From UBC Okanagan Academic Calendar/Policies and Regulations/Academic Concession Students who, because of unforeseen events, are absent during the term and are unable to complete tests or other graded work, should normally discuss with their instructors how they can make up for missed work. Instructors are not required to make allowance for any missed test or incomplete work that is not satisfactorily Page 2 of 6

3 accounted for. If ill health is an issue, students are encouraged to seek attention from a health professional. Campus Health and Counselling will normally provide documentation only to students who have been seen previously at these offices for treatment or counselling specific to conditions associated with their academic difficulties. Students who feel that requests for consideration have not been dealt with fairly by their instructors may take their concerns to the Unit Head or her designate. Students are responsible for attending all lectures and are responsible for completing all assignments and examinations. If you know that you will be absent for any component of the course for which you will be evaluated you MUST make arrangements with the instructor prior to your absence. If you are absent due to unforeseen circumstances you MUST contact the instructor as soon as possible to make arrangements to make up any missed assignments or tests. Students may be excused from scheduled exams only with a physician s certificate verifying illness or other supporting documents for a compassionate leave. If a student is unable to complete a midterm examination for a good and verifiable reason, the instructor may discuss a reweighting of the exams and assignments. ) Lecture Outline: 1. Introduction to metabolic pathways in a cell: the importance of regulation of blood glucose and the consequences of lack of control i.e. Diabetes 2. Glycolysis a. Central role in catabolism b. Introduction to concepts of metabolic control mechanisms c. Glycolysis in eukaryotic cells i. Phase I: the preparatory phase ii. Phase II: the payoff phase d. Selected examples of control of reactions in glycolysis 3. The fates of pyruvate a. The use of pyruvate in the absence of oxygen i. Production of alcohol ii. Production of lactate iii. Metabolism of alcohol b. The use of pyruvate in the presence of oxygen i. The pyruvate dehydrogenase multi-enzyme complex ii. Associated coenzymes 4. The Krebs cycle a. Mitochondrial structure: review b. The reactions of the Krebs cycle c. Mechanisms of membrane transport d. Compartmentation and malate dehydrogenase Page 3 of 6

4 e. Transfer of reducing equivalents from the cytosol to the mitochondrion i. The glycerol phosphate dehydrogenase reaction. ii. The malate aspartate shuttle f. Allosteric control mechanisms for the Krebs s cycle. 5. Energetics of ATP production a. Electron transport i. Thermodynamics of electron transport ii. Structural components of electron transport iii. Pathway of electron transport b. Oxidative phosphorylation i. Chemiosmotic hypothesis ii. Proton gradient generation iii. Mechanism of ATP synthesis: ATP synthase, a rotary engine c. Photophosphorylation and photosynthesis i. Structure of the chloroplast ii. Absorption of light iii. Electron transport in the photosystems iv. Proton gradient formation, and chloroplast ATP synthase activity v. Cyclic and Non-cyclic photophosphorylation 6. Gluconeogenesis a. The rationale b. Pyruvate to PEP the importance of compartmentation c. Biotin d. Lactate as the precursor e. PFK and fructose bisphosphatase f. Glucokinase and glucose-6-phosphatase g. The glyoxylate cycle h. The pentose phosphate shunt 7. Glycogen a. Synthesis b. Degradation c. Allosteric control of glycogen metabolism 8. Second messenger systems for control of metabolism a. Insulin b. Glucagon/epinephrine 9. Fatty acid metabolism: a. Enzymatic degradation of TAG s b. Activation of fatty acids c. Carnitine shuttle d. Beta oxidation of even and odd numbered chains e. Production of ketone bodies f. Lipid biosynthesis: use of a multi-enzyme complex 10. Amino Acid metabolism a. Transamination reactions b. The Urea cycle Page 4 of 6

5 11. Molecular Genetics: a. DNA replication b. RNA function c. RNA processing and splicing d. Transcription e. Translation 12. Carbon fixation (if time allows) a. The Calvin Benson Cycle b. Synthesis of Sucrose and Starch c. Transfer of ATP and reducing equivalents to the cytosol d. C4 and CAM plants Final Exam (During Exam period, TBA) Academic Integrity: The academic enterprise is founded on honesty, civility, and integrity. As members of this enterprise, all students are expected to know, understand, and follow the codes of conduct regarding academic integrity. At the most basic level, this means submitting only original work done by you and acknowledging all sources of information or ideas and attributing them to others as required. This also means you should not cheat, copy, or mislead others about what is your work. Violations of academic integrity (i.e., misconduct) lead to the break down of the academic enterprise, and therefore serious consequences arise and harsh sanctions are imposed. For example, incidences of plagiarism or cheating may result in a mark of zero on the assignment or exam and more serious consequences may apply if the matter is referred to the President s Advisory Committee on Student Discipline. Careful records are kept in order to monitor and prevent recurrences. A more detailed description of academic integrity, including the policies and procedures, may be found at: If you have any questions about how academic integrity applies to this course, please consult with your professor. Disability Assistance: If you require disability-related accommodations to meet the course objectives, please contact the Coordinator of Disability Resources located in the Student Development and Advising area in the University Centre building. For more information about Disability Resources or academic accommodations, please visit the website at: Equity, Human Rights, Discrimination and Harassment: Page 5 of 6

6 UBC Okanagan is a place where every student, staff and faculty member should be able to study and work in an environment that is free from human rights-based discrimination and harassment. Under UBC s Policy 3 on Discrimination and Harassment, UBC prohibits discrimination and harassment on the basis of the following grounds: age, ancestry, colour, family status, marital status, physical or mental disability, place of origin, political belief, race, religion, sex, sexual orientation or unrelated criminal conviction. If you require assistance related to an issue of equity, discrimination or harassment, please contact the Equity Office or your administrative head of unit. UBC Okanagan Equity Advisor: ph ; equity.ubco@ubc.ca Web: Unit Equity Representatives: Page 6 of 6