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Course Syllabus UHSA Bioch205 Winter 2005 University Health Sciences Antigua On-line 10 January - 4 April Course description Metabolic biochemistry: electron transport; oxidative phosphorylation; glycolysis; gluconeogenesis; glycogen; pentose phosphate and photosynthesis; fatty acid oxidation and synthesis; amino synthesis and degradation, purine and pyrimidine synthesis, degradation, and recycling; lipids; synthesis and degradation of macromolecules proteins and nucleic acids; and regulation and signaling. Calendar Sun Mon discussion communication due, each wk Tue Wed Thu Fri Sat 16 Jan 10 17 11 18 13 20 24 31 25 Feb 1 14 21 chat 1b 28 4 chat 15 22 23 30 12 19 chat 1a 26 2 chat glycolysis 27 3 29 5 2a exam 6 13 2b 7 14 8 15 9 16 chat 3a 10 17 11 18 chat 3b 12 19 20 21 22 23 24 25 27 28 Mar 1 3 6 13 7 14 8 15 20 27 21 28 22 29 2 chat 4a 9 16 chat 5a 23 30 chat 6a 4 chat 4b 11 18 chat 5b 25 Apr 1 chat 6 26 MidExam 5 citric acid cycle exam 10 17 24 31 b 3 4 Final Exam Instructor Franklin R. Leach Home addresses 2304 Fox Glern LN Temple, TX 76502-7906 Phone: 254-770-3235 12 19 26 2 email this course: [email protected]; Other email [email protected]; [email protected]; [email protected]; Personal homepage: http://biochem2.okstate.edu/~leach/homepage.ht ml Metabolism Course homepage: http://biochem2.okstate.edu/~leach/bioch5853/homepage.html UHSABioch205 Course homepages: Embanet http://campus.embanet.com/uhsa Alternative site http://opbs.okstate.edu/~leach/bioch2 05/bioch205.home.htm Goals 1. To learn biochemical principles as a foundation for your medical education and to allow you to pass the board examinations. 2. To transform your view of biochemistry from being a required basic science hurdle to being a useful companion in your quest to improve the health and treatment of your patients. 3. To learn sufficient chemistry so that we may understand the pervasive structure/function theme. This will entail learning the major players, their structures, and some of their properties. Amino acids and proteins Purine and pyrimidines and nucleic acids Fatty acids, steroids, and lipids Carbohydrates and polysaccharides. 4. 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 5. To learn the interrelationships among the various metabolic pathways. 6. To learn the energetic relationships. 7. To learn the chemical principles of metabolism and biochemical conversions. 8. To learn the enzymes and coenzymes involved in metabolism and how they participate in the reactions. 9. To learn how metabolic signals are sent, received, interpreted, and answered. 10. To learn how the structures of cells, tissues, and organs influence metabolism. 11. To learn how the whole metabolic system and subsystems are integrated and controlled. 12. To learn of the errors or defects that occur in metabolism and how they can be treated. 13. To develop effective learning and study habits and a thirst for life-long learning. 14. To develop biochemical problem-solving skills. 15. To gain a perspective of the history and contribution of investigators to our knowledge of biochemistry. 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 learn how biochemical science relates to physiology, the other basic medical sciences, and the clinical medical sciences. 21. To integrate biochemical knowledge into the larger biological system of the human body. 22. To recognize the limitations of biochemical science, its data, and to develop an enquiring mind that see each patient as a biochemical individual. Grades Components of the Grade: A. On line 2/3 of course grade 1. Pathway examinations Two examinations on the glycolytic pathway and on the citric acid cycle will be given January 30 and February 13 via email. Each of these examinations will be worth 50 points and they will not be solely multiple choice. 2. Multiple choice course examinations Two major examinations, a mid-term and a final exam will be given Februry 26 and April 4, respectively. Each exam will be worth 100 points of the inresidence grade. These exams will be multiple choice and hosted by thetestingcenter. 2. Discussion Twelve contributions worth 5 points each required by Monday morning of each class week. These are to be contributed on the Embanet discussion site. They may consist of: the posing of a significant biochemical question, answering a question of another participant, discovering a new resource or important finding in biochemistry as related to bioch205, or a written minireview on an appropriate subject (consult the instructor). Specific tasks (I will look specifically for each one of these topics): find a new internet site for metabolism, ans wer at least one ques tion fro m anot her, pose a met abol ic ques tion (to whic h you do not kno w the ans wer - not a "tex tboo k type ques tion ", and disc uss a met abol ic dise ase. 3. On line chat. Participation in Embanet's chat site for this course on chat #1 Janurary 19, or 21; chat #2 February 2, or 4,; chat #3 February 16, or 18; chat #4 March 2, or 4; chat #5 March 16, or 18; and chat #6 March 30, or April 1 between 1:00 p.m. Central Time (Fridays only) or 9:0010:30 pm eastern, 8:009:30 pm central, 7:008:30 pm mountain, and 6:00-7:30 pm pacific times (both Wednesdays and Fridays). B. On-campus 1/3 of final grade 1. Laboratory in Antigua A grade of 70 is required to pass the course. Students consistently receiving 70 or below on exams are in serious difficulty and should seek help from the instructor. Text Primary Text: Biochemistry by Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer (2002) Fifth Edition, W.H. Freeman, New York, 974 + pp. ISBN 0-7167-3051-0. Supplemental materials Web sites Slice of Life, Integrated Biochemistry Learning Series, by James Baggott Link to http://www.mcphu.edu/ netbiochem/NetWelco.ht m Mirror in UT http://www- medlib.med.u tah.edu/NetBi ochem/NetWe lco.htm Medical Biochemistry, by M.W. King Home http://www.indsta te.edu/thcme/mwk ing/subjects.html Mirror - England http://www.dentist ry.leeds.ac.uk/bioc hem/thcme/home. html Mirror - Italy http://www.med.u nibs.it/~marchesi/s ubjects.html Other current text books Textbook of Biochemistry with Clinical Correlations, Fifth Edition, edited by T.M. Devlin, Wiley-Liss, New York, 2002, 1186 pp. ISB 0-471-15451-2 Strength and weakness is the multiauthor nature. Expert written and uneven differing type of coverage. Biochemistry by Reginald H. Garrett and Charles M. Grisham, Second Edition, Saunders College Publishing, Fort Worth, TX, 1999, 1127+pp. ISBN 0-03-022318-0 This is an excellent text. See text books section. See http://faculty.virgi nia.edu/biochema ges/ for biochemimages. Principle of Biochemistry with a Human Focus by Reginald H. Garrett and Charles M. Grisham, First edtion, Brooks/Cole, Thompson Learning, 1997, 893 pp., ISBN 003-097369-4 Their earlier text on a diet with lost muscle mass. Biochemistry by C. Matthews, K.E. van Holde, and K. Ahern, Third Edition, Benjamin/Cummings, Redwood City, 2000, 1186 pp. ISBN 0-80533066-6 This is an excellent text. See text books section online. Lehninger Principles of Biochemistry by D.L. Nelson, & M.M. Cox, Third edition, Worth, New York, 2000, 1152 pp. ISBN 157259-931-6 or 1-57259-153-6 (two numbers listed) This is an excellent text. See text books section on-line. The Metabolic & Molecular Bases of Inherited Disease edited by C.R. Scriver, A.L. Beaudet, W.S. Sly, & D. Valle, McGraw Hill, New York, 7th edition, Three volumes, 1995, 4605 pp. ISBN 0-07-909826-6. This version is on CD. and The Metabolic & Molecular Bases of Inherited Disease edited by C.R. Scriver, A.L. Beaudet, W.S. Sly, & D. Valle, McGraw Hill, New York, 8th edition, Three volumes, 2001, 5568 pp. has been released. $495 ISBN 0-07-913035-6 Biochemistry, Second Edition by Donald Voet (http://www.sas.upenn.edu/chem/faculty/voet/ voet.html) and Judith G. Voet (http://www.swarthmore.edu/NatSci/che mistry/voet/) (1995) John Wiley & Sons, New York, 1361 pp. ISBN 0-471-58651-X Biochemistry, Third Edition by Donald Voet, and Judith Voet, (2004) 1178 pp., + seven chapters ISBN: 0-47119350-X, A top textbook, recently revised. A good text for majors. http://hecda.wiley.com/WileyCDA/HigherEdTitle/p roductCd-047119350X.html Biochemistry: The Chemical Reactions of Living Cells by David E. Metzler, Two volumes Volume 1, 2001, Academic Press, San Diego, ISBN 0-12-492540-5, 937 pp. Volume 2, 2003, Academic Press, San Diego, ISBN 0-12-49254185, 1037 pp. The ultimate in biochemical information. Amazing accomplishment by a sole author with thousands of literature references documenting the points. Information that every biochemist wants handy in a two-volume series. Biochemistry, Fourth Edition by G.L. Zubay, Wm. Brown Publishers, Dubuque, IA, 1998, 990+ pp. 0-697-21900-3 [Your instructor reviewed some of the chapters for the previous edition.] Course Reading Assignments based on Biochemistry, Fifth Edition Berg, Tymoczko, & Stryer W.H. Freeman, 2002 Week Chapter Title # 1 14 15 2 16 17 18 19 20 21 3 4 5 22 Metabolism: Basic Concepts and Design Signal-Transduction Pathways Glycolysis and Gluconeogenesis The Citric Acid Cycle Oxidative Phosphorylation The Light Reactions of Photosynthesis The Calvin Cycle and The Pentose Phosphate Pathway Glycogen Metabolism Fatty Acid Metabolism 23 6 7 8 9 24 25 26 27 28 29 30 Protein Turnover and Amino Acid Catabolism Nitrogen Fixation Nucleotide Biosynthesis The Biosynthesis of Membrane Lipids And Steroids DNA Replication, Recombination and Repair RNA Synthesis and Splicing Protein Synthesis The Integration of Metabolism Additional topics web supplements are exspected to be posted Hormones Digestion and Absorption of Basic Nutritional Constituent Nutrition UHSA Biochemistry 2 2005 List of Topics bioch205 Jan 10 - Apr 4, 2005 class-lesson-module [clm] Two modules or topics per week, 12 weeks. Designated as B205clm# 1. Metabolism: Basic Design, Coenzymes 2. Pathways, Maps, and Strategies 3. Energetics, ATP 4. Electron Transport Chain 5. Oxidative Phosphorylation and Photophosphorylation 6. Glycolysis 7. Pyruvate Metabolism 8. Tricarboxylic Acid Cycle 9. Gluconeogenesis 10. Glycogen Metabolism 11. Pentose Phosphate Pathway/Photosynthesis 12. Fatty acid Degradation and Ketone Bodies 13. Fatty Acid Synthesis 14. Other Lipids, Cholesterol , Eicosanoids 15. Nitrogen Fixation, Heme Metabolism 16. Amino Acid Degradation 17. Amino Acid Synthesis 18. Urea Cycle and Nitrogen Excretion 19. Purine and Pyrimidine and dRTP Synthesis 20. Nucleotide Metabolism and Recycling 21. DNA Replication, Repair, and Recombination 22. RNA Transcription, Processing, and Function 23. Protein Synthesis, Genetic Code, and Turnover 24. Integration Possible Additional topics (reading) 1. Transport & digestion 2. Nutrition 3. Hormones FRL 1/01/05