Syllabus Biochemistry Metabolism and Regulation CID # Spring 1999 Room 348B Noble Research Center, 9:30-10:20 a.m.

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1 Syllabus Biochemistry Metabolism and Regulation CID # Spring 1999 Room 348B Noble Research Center, 9:30-10:20 a.m. MWF Instructor: Franklin R. Leach Room: 348F NRC Phones: (Office), (Departmental Office), or home (before 10 p.m.) FAX ; firefly@biochem.okstate.edu; Course news group: bmbforum Personal homepage: Course homepage: Prerequisites: Biochemistry 3653, 4113, or 5753, or consent of the Instructor. Goals Goals of this course are: 1. To learn the metabolic pathways of Electron transport Oxidative Phosphorylation Photosynthesis The Tricarboxylic Acid Cycle Glycolysis Pyruvate Synthesis and Utilization Glyconeogenesis and Other Carbohydrate Synthesis Lipid Degradation and Synthesis Amino Acid Degradation and Synthesis Urea Cycle Nitrogen Fixation and Heme Synthesis and Degradation Purine and Pyrimidine Degradation and Synthesis 2. To learn the interrelationships among the pathways. 3. To learn the energetic relationships. 4. To learn the chemical principles of metabolism and biochemical conversions. 5. To learn the enzymes and coenzymes involved in metabolism and how they participate in the reactions.

2 6. To learn how metabolic signals are sent, received, interpreted, and answered. 7. To learn how the structures of cells, tissues, and organs influence metabolism. 8. To learn how the whole metabolic system and subsystems are integrated and controlled. 9. To learn of the errors or defects that occur in metabolism and how they can be treated. 10. To develop effective learning and study habits and a thirst for life-long learning. 11. To develop metabolic problem-solving skills. 12. To explore mathematical analysis of control phenomena. 13. To learn the experimental methods used to study metabolism. 14. To gain a perspective of the history and contribution of investigators to our knowledge of metabolism. 15. To identify unanswered questions concerning metabolism. 16. To learn how to identify and utilize current biochemical literature on specific topics. 17. To appreciate the breadth and practical application of biochemical science. 18. To learn how to use the internet for obtaining biochemical information. 19. To develop, explore, and use different teaching/learning technologies. 20. To develop writing, analysis, and communication skills and ethical scientific perspectives.

3 Grades Components of the Grade: Two examinations (100 points each) will be given in the evenings of the dates indicated in the schedule. The exams will consist of 1/3 (1 h) closed book questions on pathways and 2/3 (2 h) open book on metabolic topics. A final examination (100 points) constituting both materials from the last quarter of the lectures and comprehensive material will also be given at the regularly scheduled final examination time (with an allowance to extend the time). Three written review papers (50 points each) on the current status of an assigned topic in 1) metabolism, 2) inborn error, and 3) regulation will be required at the indicated times. These papers (2-4 typed pages) should include current references (at least two from primary literature) on the assigned topic. They should be crafted as the Minireviews of the Journal of Biological Chemistry (see the on-line or printed instructions to authors). Files of the text and illustrations (or copies suitable for scanning) will be handed in on disks so that they may be translated to HTML and placed on the web. Electronic Conferencing [class discussions - bmbforum {primary} or okstate.class.bioch5853 {secondary}] (at least 15 responses required at weekly intervals (for 5 points each). The instructor and classmembers will pose questions; make comments; point out interesting subjects, papers, net sites, and resources; and answer questions; the instructor and classmembers will have the total dialogue available for study. (See for net etiquette). A course on inernet skills can be found at: Hints for contributing to news groups can be found at: The Netscape Handbook has a useful section on newsgroups. Grading will be based on total points accumulated. Grading will based on a percentage scale of: A B C Final grades may be adjusted on a sliding scale to ranges lower than those indicated (if appropriate). However, students consistently receiving 70 or below on exams are in serious difficulty and should seek help from the instructor. Contact with the Instructor: The instructor will generally be available for short questions immediately following the scheduled lectures. Other times by coming to his office or by appointment. Do not wait until the last minute before examinations to make an appointment. communication is encouraged (read the contributions to gain additional information). Particpation in the newsgroup and discussion group is encouraged and rewarded.

4 Texts Texts Primary Text: Biochemistry, Second Edition by Donald Voet () and Judith G. Voet () (1995), John Wiley & Sons (), New York, pp. 1361, assigned readings from other references will be made. Secondary Texts: Metabolism at a Glance by J. G Salway (1994) Blackwell Scientific Publications, Oxford, pp. 95. Biochemistry by Lubert Stryer (1995) Fourth Edition, W.H. Freeman, New York, pp You can find lecture notes based for a course taught at the University of Arizona at: Understanding the Control of Metabolism by David Fell (1997) Portland Press, London, pp Supplemental materials Supplemental materials Biochemical Pathways by William Soffer of Rugters University -Computer programs

5 Glycolysis; TCA Metabolic Pathways by Tully Turney Slice of Life, Integrated Biochemistry Learning Series, by Link to Mirror in UT Mirror in Italy Other current text books Biochemistry by R.H. Abeles, P.A. Frey, & W.P. Jencks, Jones & Bartlett, Boston, 1992, 838 pp. Textbook of Biochemistry, edited by T.M. Devlin, Wiley-Liss, New York, 1992, 1185 pp. Biochemistry by Reginald H. Garrett and Charles M. Grisham, Saunders College Publishing, Fort Worth, TX, 1995, pp see for biochemimages. Molecular Aspects of Cell Biology, by Reginald H. Garrett and Charles M. Grisham, Saunders College Publishing, Fort Worth, TX, 1995, supplement p Clinical Detective Stories, by M.L. Halperin & F.S. Rollestyon, Portland, London, 1993, 300 pp. Principles of Biochemistry by A.L. Lehninger, D.L. Nelson, & M.M. Cox, Second editon, Worth, New York, 1993, 1013 pp. Biochemistry, by C. Matthews & K.E. vanholde, Second Edition, Benjamin/Cummings, Redwood City, 1996, pp Biochemistry, by Laurence A. Moran, K. Gary Scimgeour, H. Robeet Horton, Raymod S. Ochs, and J. David Rawn, Second edition, N. Patterson, Englewood Cliffs, NJ, 1994, page numbers for each chapter. Harper s Biochemistry, by Robert K. Murray, Daryl K. Granner, Peter A. Mayes, and Victor W. Rodwell, Twenty-third edition, Appleton & Lange, Norwalk, CT, 1993, pp The Metabolic & Molecular Bases of Inherited Disease, edited by C.R. Scriver, A.L. Beaudet, W.S. Sly, & D. Valle, McGraw Hill, New York, 7 th edition, Three volumes, 1995, pp (Available in the instructor s office; the library does not have this edition) Principles of Biochemistry, by G.L. Zubay, W.W. Parson, & D.E. Vance, Wm. Brown Publishers, Dubuque, IA, 1995, 863+ pp.

6 Schedule 99 Schedule 99 Lecture # Date Topic Reading Assignment 1 Jan. 11 Introduction to Metabolism Ch Introduction to Metabolism Ch Introduction to Metabolism Handout, Martin Luther King Day no class 4 20 Introduction to Regulation Handout 5 22 Introduction to Regulation Handout 6 25 Introduction to Regulation Handout 7 27 Mitochondrial Electron Transport Ch Mitochondrial Electron Transport Ch Feb 1 Oxidative Phosphorylation - Control Ch Photosynthesis - Light Reactions Ch & Tricarboxylic Acid Cycle Ch Tricarboxylic Acid Cycle Ch Digestion & TransportCh Embden-Meyerhof Pathway Ch. 16 Paper 1 12 Metabolism Fate of Pyruvate Ch Pyruvate Dehydrogenase Complex Ch Exam I 18 7:00-10:00 p.m. Lectures Regulation of PDH & integration p Gluconeogensis / Regulation Ch Glyoxylate Cycle, Propionate Metabolism Ch Pentose / Calvin Cycle Ch. 21.4, Ch March 1 Glycogen & Other Hexoses Ch. 16.5, Ch Regulation of Glycogen Metabolism Ch Lipid Metabolism / Digestion / Transport Ch Fatty Acid Degradation Ch Fatty Acid Synthesis Ch Regulation of Fat MetabolismCh Spring Break Ch P-Lipid & Glycolipid Metabolism Ch Cholesterol Metabolism Ch. 23 Exam II 25 7:00-10:00 p.m. Lectures Paper 2 26 Inborn Errors of Metabolism No lecture Lipoprotein Metabolism Ch Amino Acid Metabolism - Breakdown Ch April 2 Urea Cycle Ch Heme Biosynthesis Ch. 24

7 33 7 Amino Acid Metabolism - Synthesis Ch Nitrogen Fixation Ch Nucleotide Synthesis - Purines Ch Nucleotide Synthesis - Pyrimidines Ch Nucleotide Breakdown Ch Nucleotide Breakdown Ch Integration of Metabolism Ch. 25 & handout Integration of Metabolism Ch. 25 & handout Integration of Metabolism Ch. 25 & handout Integration of Metabolism Ch. 25 & handout Integration of Metabolism Ch. 25 & handout Paper 3 30 Regulation of Metabolism Finals week 3-9 Final 3 8:30-12:20 available 10:30-12:20 scheduledinclusive Required Statement If any member this class feels that he/she has a disability and needs special accommodations of any nature whatsoever, the instructor will work with the student and the Office of Student Disability Services, 326 Student Union, to provide reasonable accommodations to ensure that he/she has a fair opportunity to perfom in this class. Please advise the instructor of such disability and the desired accommodations at some point before, during, or immediately after the first scheduled class period. Revised 1/4/99