BIBC100 Structural Biochemistry – Winter 2011 1 BIBC 100 STRUCTURAL BIOCHEMISTRY WINTER 2011 LECTURE: Tuesday and Thursday 12:30 pm – 1:50 pm Warren Lecture Hall (WLH) 2001 INSTRUCTORS: M. Montal (x40931) Office Hours: Thursday 2:00 pm – 2:50 pm 3502 Pacific Hall Project Assistant: Kathleen McPherson Pacific Hall 3100e (x43568) LECTURE DATE TOPIC Branden & Tooze REFERENCE Chapter Lehninger 5th Edition Reference Chapter* STRUCTURAL PRINCIPLES 1 JAN. 4 Tue Basics 1 1 & 2 2 6 Thu Motifs 2 3 3 11 Tue α domains 3 3 & 4 4 13 Thu α/ β and β structures 4, 5 3 & 4 5 18 Tue DNA structure 7 1 & 8 6 20 Thu Folding 6 4 7 25 Tue Folding and Flexibility 6 4 8 27 Thu RECOGNITION: Protein‐DNA 8, 10 28 9 FEB 1 Tue RECOGNITION: Immune System 15 5 3 Thu MID‐TERM IN CLASS 11 8 Tue CATALYSIS: Proteasess 11 6 12 10 Thu TRANSDUCTION: Membranes 12 10 & 11 13 15 Tue Membrane Proteins ‐ I 12 10 & 11 14 17 Thu Membrane Proteins ‐ II 12 10 & 11 15 22 Tue Channels 12 10 & 11 16 24 Thu Receptors 13 12 17 MAR 1 Tue Receptors 13 12 18 3 Thu Protein Design 17 4 19 8 Tue X‐Ray and NMR 18 4 20 10 Thu REVIEW FINAL EXAM TUESDAY, MARCH 15 11:30 am‐2:29 pmBIBC100 Structural Biochemistry – Winter 2011 2 Textbook (required): Introduction to Protein Structure. C. Branden and J.Tooze, 2nd Edition. Garland Publishing Co., NY 1999. Strongly Recommended - Kinemage Supplement to Branden and Tooze J.S. Richardson and D.C. Richardson Garland Publishing Co., NY *Optional Textbook: Lehninger Principles of Biochemistry 5th Edition D. Nelson & M. Cox W.H. Freeman & Co. 2008 If you already have Lehninger’s 5th Edition you will find the material covered in class on the corresponding Chapters indicated on page 1. Class Websites: http://www.biology.ucsd.edu/classes/bibc100.WI11/ Required Websites: http://www.rcsb.org Course Requirements: GRADE Midterm: Thursday, February 3, during class 40% Final: March 15, 11:30 am-2:29 pm 60% Note: Check your midterm and final exam schedules NOW. There are no alternate exams offered for this class regardless of whether you have other exam(s) on one day. Please plan ahead. You are only responsible for the material covered in class, not for all the material in each chapter. Figures from other sources will be included in the lectures. Many of these figures will appear in the class powerpoints which will be available on the class website. This class will not be podcast.BIBC100 Structural Biochemistry – Winter 2011 3 Graduate and Undergraduate Student Teaching Assistants Graduate: FRIEDMAN, AARON bms [email protected] 513-315-1724 Tabikh, Sara ms [email protected] 760-805-9767 Sato, Yuichiro ms [email protected] 408-460-6779 Undergraduate: TO BE UPDATED WITH NEW TASBIBC100 Structural Biochemistry – Winter 2011 4 BIBC 100: STRUCTURAL BIOCHEMISTRY GRADING INFORMATION: Plus and minus grading will not be used MIDTERM: Grade Revisions: Submit request to TA no later than February 10, 2011 No grade changes after February 17, 2011 NO EXCEPTIONS FINAL: Grade Revisions: Submit request to Professor or TA no later than March 21, 2011 No grade changes after March 28, 2011 NO EXCEPTIONS POLICY ON REGRADES: Regrades: If a student considers that his/her exam was not properly graded, they may turn in the unaltered, complete exam for a regrade to the TAs no later than 1 week after the exams become available for pick-up. Students must write up on a separate sheet attached to the exam which questions they consider require regrading and sign the bottom of this sheet. Students are responsible for understanding that, by requesting a regrade, the entire exam in addition to the indicated questions will be re-evaluated, and points may be added or taken away as a result.BIBC100 Structural Biochemistry – Winter 2011 5 BIBC 100: Structural Biochemistry Guidelines for Class Etiquette During Examination 1. All writing instruments must contain non-erasable ink. If students choose not to write in pen, they forfeit the opportunity for a future regrade. 2. All books and handbags should be placed at the front or back section of the auditorium for the duration of the exam. 3. Students should sit in alternating seats whenever possible. 4. When time is called, anyone who is still writing will automatically receive a zero for that page. THIS WILL BE STRICTLY ENFORCED. Remain in your seat and hand your exam down the aisle. UCSD Policy on Integrity of Scholarship (UCSD catalog 10-11, pages 13-17) and Rules of academic dishonesty will be strictly enforced.BIBC100 Structural Biochemistry – Winter 2011 6 Protein Data bank The Research Collaboratory for Structural Bioinformatics Protein Data Bank (PDB) <http://www.rcsb.org/> is the single international source for 3D structure files. A four character PDB ID is the identifier for the structure of a given Protein. Using the identifier and the molecular viewer Jmol you can see and study the 3D structure of these proteins (and many, many more). Enjoy and imagine! Protein PDB ID Hemoglobin 1A3N GroEL/GroES complex 1AON Chymotrypsin 6GCH Myoglobin 1MBO Myoglobin 2MBW α-hemolysin 7AHL Immunoglobulin G 2A intact 1IGT Immunoglobulin G 2A fab fragment 1GGC Immunoglobulin G 2A fab fragment (50.1) complex with 16-residue peptide 1GGI Lysozyme 1LZE Bacteriorhodopsin 2AT9 Aquaporin 2B6O Maltoporin 1AF6 Maltoporin 1MAL Lactose permease (lactose transporter 1PV7 Aquaporin 1, AQP-1 1J4N K+ channel protein 1BL8BIBC100 Structural Biochemistry – Winter 2011 7 Voltage-gated K+ channel 1J95 Voltage-gated K+ channel 2A79 Ras protein 5P21 Protein kinase A; R2C2 complex 1U7E Green fluorescent protein (GFP) 1GFL Calmodulin 1CLL SHC (SH2 domain) 1SHC Bacteriorhodopsin (rhodopsin and G protein transducin 1BAC Protein kinase (active site) 1S9I Cytochrome c oxidase 1OCC Bovine mitochondrial F1- ATP Synthase 1BMF ATP synthase chain (FoF1) 1QO1 Photosynthetic reaction center 1PRC Light harvesting complex II 2BHW Bacteriorhodopsin 1C8R
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