COURSE SYLLABUS BCH 4024: INTRODUCTION TO ...

COURSE SYLLABUSBCH 4024: INTRODUCTION TO BIOCHEMISTRY AND MOLECULAR BIOLOGYCOURSE COORDINATOR: Dr. Philip J. LaipisCredit: four (4) hoursSpring Semester, 2012 Section 6680Course Description: BCH 4024 surveys the structure, function, and metabolism of amino acids, proteins, carbohydrates,lipids, and nucleic acids. It introduces concepts in cell structure, replication and growth, and metabolic regulation.Meeting Times and Places: Lectures: Held Mondays, Tuesdays, Wednesdays, and Fridays (6th period, 12:50-1:40 pm)in the second-floor Stetson MSB (Medical Sciences Building) Auditorium (room N2-200). Help sessions are held MTWF,during the hour BEFORE and AFTER class time, in ARB R3-131, and at other times and locations at the lecturer’sdiscretion.Prerequisites: Organic Chemistry (CHM 2210 and 2211, CHM 2215 and 2216, or their equivalents at other universities)or consent of course coordinator. In certain cases, with permission, CHM 2211 or CHM 2216 may be taken concurrently.CHM 2200 is NOT an acceptable prerequisite for BCH 4024.Text: Lehninger Principles of Biochemistry, 5th edition, by David L. Nelson and Michael M. Cox. New York: W.H.Freeman and Company, 2008. Textbooks may be obtained from the Health Center Bookstore, Room MG-15. Texts arealso available in several local commercial bookstores. A few copies are currently on reserve in the Health Center Library,in the Communicore building.Web Page: This syllabus, expanded policies, and other information about the course are available on the “Sakai E-learning” site http://lss.at.ufl.edu. All course notes, announcements, copies of old exams and quiz packages, and old testanswers and keys are available only at the Sakai site. The syllabus is also available on the BCH 4024 sitehttp://www.biochem.med.ufl.edu/coursetemp.php?cid=44.Lecture Notes: ALL faculty lecture notes for this course are available ONLY at the "Sakai E-Learning" site. All othercourse-related files can also be found there. There is NO approved course package.Tests and Grading: Examinations will start at 3, 5, and 7 pm, on Feb. 9, Mar. 1, Mar. 29, and Apr. 30, in Room CG-28(Computer Testing Center, Communicore Building, Health Science Center). Any changes in these times will beannounced. The final examination is scheduled at 5 and 7 pm on April 30, 2012, also in the Test Center.There will be four ninety minute examinations, each worth one-hundred (100) points, with a course total of four-hundred(400) points. Students' final letter-grades will be determined solely on the basis of their rank in the class, based on theseexams. Exams will cover the material discussed in the lectures, in the discussion periods, and in the textbook. A completedescription of exams, make-up options, and grading criteria is available at the Sakai E-Learning site.Information on UF grading policy is available at: http://www.registrar.ufl.edu/catalog/policies/regulationgrades.html .Any student requesting special-needs classroom accommodation must first register with the office of the Dean ofStudents, which will provide documentation to the student, who then must provide this documentation to the instructor inthe first two weeks of the course.A make-up examination is provided for students who miss ONE of the first three exams, WITH permission of the coursecoordinator, for an acceptable reason. Written documentation will be required by the coordinator. These makeups arescheduled for April 19, 2012. Be warned that course history suggests that missing an exam strongly correlates with alower overall grade in BCH 4024, as the makeup will be weeks later than the lectures for that area and you will also haveless time to study for the final. Do not skip an exam unless the reason is important. The makeup exams are specific to themissed exam, i.e., not cumulative. The final examination is also NOT cumulative, and no makeup is available. Students

failing to take the final exam will receive zero points for that test. All students must take the final exam, as scheduled.Exceptions will be made only with explicit prior approval of the course coordinator.Contact Information: Questions about course organization and operation, including exams and grades, should bedirected to Dr. Laipis via email at plaipis@ufl.edu. His office hours will be by appointment only.Faculty:Dr. Philip J. Laipis (abbreviated “PJL” in the syllabus), Course Coordinator.plaipis@ufl.edu (E-MAIL IS PREFERRED CONTACT METHOD)(Do not use the Sakai email without copying to my ufl.edu address!)Office: R3-216 ARBDr. Thomas Mareci (“THM”)Office: LG-183 McKnight Brain Institute; phone: 392-3375thmareci@ufl.eduDr. Joanna R. Long (“JRL”)Office: LG-126 McKnight Brain Institute; phone: 846-1506jrlong@ufl.eduDr. Charles M. Allen Jr. (“CMA”)Office: R3-252 ARB; phone: 392-3366callen@ufl.eduDr. Daniel L. Purich (“DLP”)Office: R3-126 ARB; phone: 392-1546danpurich@yahoo.comDr. Brian D. Cain (“BDC”)Office: R3-254 ARB; phone: 392-6473bcain@ufl.eduWe want to emphasize that attendance in class and at the lecturers’ office hours and help sessions is imperative for successin this course. We have discovered that those students who regularly attend class and who seek assistance or clarificationare much more successful in BCH 4024 than those who do not. Office hours for the faculty will be announced in class andare posted outside their office doors. Additional suggestions on study habits and practices are available both at the Sakaiand BCH 4024 web-sites.

COURSE OUTLINEBCH 4024: INTRODUCTION TO BIOCHEMISTRY AND MOLECULAR BIOLOGYLecture Day and Date Faculty Specific Topic & Recommended ReadingL-1 Mon, 1/9/12 PJL/THM Introduction and Organization: Water, molec. interactions,& acid-base chemistry (Ch. 1, pp.1-36, Ch. 2, pp. 43-70)L-2 Tues, 1/10/12 THM Nucleic acid structure (Ch. 8, pp. 271-302)L-3 Wed, 1/11/12 THM Amino Acids (Ch. 3, pp. 71-81)L-4 Fri, 1/13/12 THM Peptides & Peptide Bonds (Ch. 3, pp. 82-107)--- Mon, 1/16/12 No Class Rev. Dr. Martin Luther King Jr. Birthday (Holiday)L-5 Tues, 1/17/12 THM Three-Dimensional Structure of Proteins (Ch. 4, pp. 113-138)L-6 Wed, 1/18/12 THM Protein Dynamics and Protein Folding (Ch. 4, pp. 138-155).L-7 Fri, 1/20/12 THM Protein Dynamics and Protein Folding, Cont.L-8 Mon, 1/23/12 THM Protein Function (Ch. 5, pp. 155-179)L-9 Tues, 1/24/12 THM Enzyme mechanism and catalysis I(Ch. 6, pp. 183-194, Ch. 13, pp. 495-501)L-10 Wed, 1/25/12 THM Enzyme mechanism and catalysis II(Ch. 6, pp. 205-220; Ch. 13, pp. 516-520)L-11 Fri, 1/27/12 THM Enzyme kinetics and kinetics of inhibition,enzyme regulation (Ch. 6, pp. 194-205)L-12 Mon, 1/30/12 THM Enzyme kinetics and kinetics of inhibition, enzyme regulation(CH 6, PP. 194-205)L-13 Tues, 1/31/12 THM Bioenergetics (Ch. 13, pp. 489-495, 501-511)L-14 Wed, 2/1/12 JRL Carbohydrates and Glycobiology (Ch. 7, pp. 235-265);Lipid structure and properties (Ch. 10, pp. 343-357)L-15 Fri, 2/3/12 JRL Lipids (Ch. 10, pp. 343-367; Ch. 11, 372-375)L-16 Mon, 2/6/12 JRL Membrane Proteins (Properties)(Ch. 11, 375-386)L-17 Tues, 2/7/12 JRL Membrane Proteins (Functions) (Ch. 11, 387-395)L-18 Wed, 2/8/12 JRL Membrane protein transporters (Ch. 11, 395-413)E-1 Thurs, 2/9/12 EXAM 1 [ LECTURES L-1 THRU L-15]

L-19 Fri, 2/10/12 JRL Membrane protein signaling I (Ch. 12, 419-449)L-20 Mon, 2/13/12 JRL Membrane protein signaling II (Ch. 12, 449-469)L-21 Tues, 2/14/12 CMA Overview of Intermediary Metabolism and Introduction toGlycolysis (Ch. 13, 485-488; Ch. 14, 527-551; Ch. 15, 569-577)L-22 Wed, 2/15/12 CMA Glycolysis: Enzymes, Substrates, Products (Ch. 14, 527-551)L-23 Fri, 2/17/12 CMA Glycolysis: Energy Relationships; Introduction to Gluconeogenesis(Ch. 15, 551-558, 584, 588-89)L-24 Mon, 2/20/12 CMA Gluconeogenesis Cont. (Ch. 15. 582-594)L-25 Tues, 2/21/12 CMA Glycogen Metabolism (p. 246; Ch. 15. 594-609)L-26 Wed, 2/22/12 CMA Respiration: Pyruvate Dehydrogenase, TCA (Ch. 16, 615-638)L-27 Fri, 2/24/12 CMA TCA Cont.; Pentose Phosphate Shunt (Ch. 14, 558-564)L-28 Mon, 2/27/12 CMA Electron Transport I (Ch. 13, 512-521; Ch. 19, 707-722)L-29 Tues, 2/28/12 CMA Oxidative Phosphorylation (Ch 19, 723-737)L-30 Wed, 2/29/12 CMA Lipid Metabolism & Fatty Acid Oxidation (Ch. 17, 647-665)E-2 Thurs, 3/1/12 EXAM 2 [LECTURES L-16 THRU L-29]L-31 Fri, 3/2/12 CMA Fatty Acid Oxidation and Ketogenesis (Ch. 17, 666-668)----- Mon, 3/5/12 No Class Spring Bread starts (Classes Resume 5/12/12)L-32 Mon, 3/12/12 CMA Fatty Acid Biosynthesis (Ch. 21, 805-817)L-33 Tues, 3/13/12 CMA Phospholipid and Triglyceride biosynthesis (Ch. 21, 820-831)L-34 Wed, 3/14/12 CMA Sterol and Lipoprotein Metabolism (Ch 21, 831-845)L-35 Fri, 3/16/12 DLP Nitrogen Metabolism: Amino Acids I (reading)L-36 Mon, 3/19/12 DLP Amino Acid Biosynthesis I (reading)L-37 Tues, 3/20/12 DLP Amino Acid Biosynthesis II (reading)L-38 Wed, 3/21/12 DLP Nitrogen Metabolism: Specialized Amino Acids (reading)L-39 Fri, 3/23/12 DLP Urea Cycle (reading)L-40 Mon, 3/26/12 DLP Nucleotide Biosynthesis & Degradation (reading)L-41 Tues, 3/27/12 DLP Deoxynucleotide Biosynthesis (reading)L-42 Wed, 3/28/12 BDC DNA/chromatin structure, genome organization (reading)

E-3 Thurs, 3/29/12 EXAM 3 [LECTURES L-30 THRU L-41]L-43 Fri, 3/30/12 BDC DNA replication (reading)L-44 Mon, 4/2/12 BDC DNA replication (continued)L-45 Tues, 4/3/12 BDC Prokaryotic transcription and gene control (reading)L-46 Wed, 4/4/12 BDC Eukaryotic transcription & gene control I (reading)L-47 Fri, 4/6/12 BDC Eukaryotic transcription & gene control IIL-48 Mon, 4/9/12 BDC Post-transcriptional RNA processing (reading)L-49 Tues, 4/10/12 BDC Protein Synthesis I (reading)L-50 Wed, 4/11/12 BDC Protein Synthesis II & Post-Translational ProcessingL-51 Fri, 4/13/12 BDC Post-translational modifs & protein targeting(reading)L-52 Mon, 4/16/12 BDC DNA damage and repair (reading)L-53 Tues, 4/17/12 BDC Recombination & Transposition (reading)L-54 Wed, 4/18/12 BDC Recombination & Immune System (reading)M1-3 Thur 4/19/12 Makeup Exam Specific to Exam missedL-55 Fri, 4/20/12 BDC Signal transduction (reading)L-56 Mon, 4/23/12 BDC Cell-cycle control (reading)L-57 Tues, 4/24/12 BDC Cancer: Error of Replication, Repair, and Cell Cycle ControlMechanisms (reading)L-58 Wed, 4/25/12 BDC Cancer (continued)E-4 Monday 4/30/12 Exam 4 [LECTURES L-42 THRU L-58](Not cumulative)