Fall 2009CH 395G BIO 395G MOL 395GFall 2009Tuesday & Thursday 11:00 -12:30WEL 2.304WEL 2.304Instructors: Barrie Kitto and Jon RobertusTeaching Assistant : Jason DickmanDr Barrie KittoImmunoassaysContraceptivesAntiviral Therapies and Vaccineshttp://www.cm.utexas.edu/kitto/Kittolabpage/ImmunoassaysContraceptivesDr. Jon RobertusStructural biology, enzyme mechanisms, drug designhttp://research.cm.utexas.edu/jrobertus/395G: GRADUATE BIOCHEMISTRY Fall 2009Course InformationCourse Instructors: OfficePhone Office HoursBarrie [email protected] WEL 4.260C 471-3279 Wed 1:30-2:30 or by appointmentJon Robertus [email protected] WEL 5.266A 471-3175 Wed 2:30-3:30 or by appointmentMeeting time and place: 11:00-12:30 Tuesday and ThursdayWEL 2.304Teaching Assistant: Jason Dickman ([email protected])Office hours: Mon and Thur 1:00-2:00 p.m. in Welch, first floor cubicles (#A)& by appointment& by appointmentCourse Description:Same as Biology 395G and Mol 395G. Detailed consideration of the structure and function of proteins and the structure of nucleic acids, with discussion of enzyme mechanisms and kinetics, biological membranes, energy metabolism and the metabolism of nucleotides and other compounds. Three lecture hours a week for one semester. Prerequisite: Graduate standing; and an undergraduate course in organic chemistry, an undergraduate course in biochemistry, or consent of instructor.A two semester undergraduate biochemistry sequence equivalent to CH 339K and 339L at the University of Texas at Austin is strongly recommended.World Wide Web site:http://courses.cm.utexas.edu/bkitto/ch395g/fall2009Log-on : 395g Password: biochemistryGrading:3 exams will be given. The first two exams will be given as scheduled on the Course Schedule. The third exam will be given at our assigned final examination period ( Dec 12, 9-12 a.m.). The exams are not cumulative. Each will count 1/3 of the final grade.CH 395G Fall 2009 Course Information Part 2not cumulative. Each will count 1/3 of the final grade.. No makeup exams will be given except for serious illness certified by a physician.Required Textbook:Biochemistry (3rd Edition), by Voet & Voet (2004)Course Schedule Fall 2009Lecture Topic Date Chapters Lecturer 1 Cells, Water, Aqueous Interactions 27-Aug 1,2 Kitto2 Bioenergetics 1-Sep 3,16 Robertus3 Protein Structure I: amino acids, peptide bonds 3-Sep 4,8 Kitto4 Protein Structure Analysis I - Purification and characterization 8-Sep 6 Kitto5 Protein Structure II: primary, secondary structure 10-Sep 7 Kitto6 Protein Structure III: Tertiary & Quaternary Structure 15-Sep 8 Kitto7 Protein Structure IV: protein dynamics, folding 17-Sep 9 Kitto8 Protein Structure V: Allosteric Proteins - Hb 22-Sep 10 Kitto9 Protein Structure Analysis II - X-ray crystallography 24-Sep readings Robertus10 Protein Structure Analysis II - NMR 29-Sep readings HoffmanExam 1 (Lectures 1-9) 1-Oct11 Carbohydrates 6-Oct 11 Kitto12 Lipids and Membranes 8-Oct 12 Kitto13 Enzymes I: kinetics: rates and analysis 13-Oct 13,14Kitto14 Enzymes II: allostery 15-Oct 13,14 Kitto15 Enzymes III: mechanisms 20-Oct 15 Kitto16 Enzymes IV: ribozymes; catalytic antibodies; enzyme engineering 22-Oct 3,15 Kitto17Carbon Metabolism I: Glycolysis27-Oct17Robertus17Carbon Metabolism I: Glycolysis27-Oct17Robertus18 Carbon Metabolism II: Gluconeogenesis 29-Oct 23 RobertusExam 2 (Lectures 10-17) 3- Nov19 Membrane transport 5-Nov 20 Robertus20 Carbon Metabolism III: TCA 10-Nov 21 Robertus21 Carbon Metabolism IV: Regulation 12-Nov 18 Robertus22 Electron Transport/Oxidative Phosphorylation 17-Nov 22 Robertus23 Photosynthesis 19-Nov 24 Robertus24 Lipid metabolism I: Fatty acid degradation 24-Nov 25 RobertusThanksgiving 26 Nov25 Lipid metabolism II: Fatty acid synthesis 1-Dec 25 Robertus26 Amino Acid Metabolism 3-Dec 26 Robertus27 Nucleotide Metabolism 8-Dec 28 RobertusExam 3 (Lectures 18-27) Dec. 14, 2-5 p.m.Class meets Tu. Th, WEL 2.304Sept. 23rd – early drop day / Dec. 4 – last drop day for Grad. StudentsSuggested Problems: See the class web site. Do these problems for every chapter. Some of these questions End of Chapter Problemschapter. Some of these questions may turn up on the exams!Other problems and suggested readings will also appear on the web site.Introductory MaterialUse the class web site at:http://courses.cm.utexas.edu/bkitto/ch395g/fall2009/for all announcements, exam dates, times and place and class schedule. Class lecture notes will also be posted there in PDF (Acrobat) format.Use of University Librarieshttp://www.lib.utexas.edu/Chemistry Library WEL 2.132Life Sciences Library MAI 220Life Sciences Library MAI 220Use of Internet:From laboratoriesComputer Center WEL 2.302Limitations of internetJournals on internetSoftware for 3D Structures(Swiss PDB Viewer, J-Mol, Pi-Mol)Lecture 1 OutlineChapter 1Small to large --- from precursors to cellsThe interior of cells---crowdedIntracellular location of processesBioelementsBiopolymersBiopolymersOrdering of informatiionChapter 2Aqueous conditionsWater --polar natureSolvent propertiesHydrogen bondsAcids and BasespHHenderson Hasselbalch EquationWhere does an Angstrom unit fit in here?Phylogenetic Trees• How do we know organisms are related in they shown in the previous diagram?• What sorts of data are used?Answers• How do we know organisms are related in they shown in the previous diagram?• Comparison of phenotypic features• Comparison with fossils?•Molecular comparisons•Molecular comparisons• What sorts of data are used?• DNA sequences• Protein sequences• Fossil remainsConstituents of Cells: E. coli%Water 70Proteins 15Nucleic Acids7Nucleic Acids7Polysaccharides 3Lipids 2Monomers 2Inorganic Ions 1Question• Both fruitflies and humans have about the same number of genes. But humans have many more types of proteins?• Quick explanation?Answer• Both fruitflies and humans have about the same number of genes. But humans have many more types of proteins?• Quick explanation?Alternate splicing of genesHemoglobin3 x 108molecules per cell5 x 106cells/mlBioelementsWater: H,OOrganics: C,H,O,N,P,SOrganics: C,H,O,N,P,SIons: Na+, K+, Mg++, Ca++, Cl-Trace Elements: Fe, Mn ,Co, Cu, ZnQuestionWater: H,OOrganics: C,H,O,N,P,S Why these elements?Ions: Na+, K+, Mg++, Ions: Na+, K+, Mg++, Ca++, Cl-Trace Elements: Fe, Mn ,Co, Cu, Zn?Chapter 2WaterAcids and BasesIonizationMolarity of Water1 liter of water weighs 1000 g1 mole of water = 18 gTherefore the