syllabus

syllabus - Ch 24a(3‐0‐6 Winter Term 2009/10...

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Unformatted text preview: Ch 24a (3‐0‐6) Winter Term 2009/10 Introduction to Biophysical Chemistry Ch 24a discusses the interaction of light with matter (absorption, emission, scattering), methods of identification of macromolecules (absorption spectroscopy, mass spectrometry), methods of structural determination of macromolecules (x‐ray diffraction, neutron diffraction, scattering from solutions of macromolecules, multi‐dimensional NMR, EPR, linear and circular dichroism, optical rotatory dispersion, fluorescence resonance energy transfer, and single‐molecule methods), reaction rates and mechanisms, and the methods of rapid and ultrafast kinetics. The concepts and mathematical manipulations will be illustrated with biochemical and biophysical applications. This material is covered in Chapters 9‐15 and Chapter 7 of the textbook by James P. Allen, and Chapters 10–13 and 16–17 of the textbook by Eisenberg and Crothers. GENERAL INFORMATION Instructors Sunney I. Chan, [email protected], 234A Noyes, ext. 6508 Douglas C. Rees, [email protected], 363 Broad, ext. 8393 Graduate Teaching Assistants Jeen Joo Kang, [email protected], 312 Church, ext. 6032 Kay Limapichat, [email protected], 254 Crellin, ext. 6009 Christina Ting, [email protected], 018/014 Spalding, ext. 8404 Undergraduate Teaching Assistants ZeNan Chang, [email protected] Changyi Li, [email protected] ZeNan and Changyi will hold office hours every Sunday from 9:30 ‐11:30 p.m. in the Ruddock House Library. Class Hours Ch 24a meets Mondays, Wednesdays, and Fridays at 1:00 p.m. in Broad 100. There will be recitation sessions approximately every three weeks, according to the attached syllabus. The recitation sessions will focus on the elaboration of complex concepts and subtle points made during the lectures, as well as solving the types of problems that will appear on homeworks and exams. You are strongly encouraged, if not expected, to attend ALL the lectures and recitations. Page 1 of 7 Texts Required: James P. Allen, “Biophysical Chemistry”, Wiley-Blackwell, Oxford, England (2008). Suggested: David Eisenberg and Donald Crothers, “Physical Chemistry with Applications to the Life Sciences”, Benjamin Cummings Publishing Company, Inc., 1979. Other: A selection of useful texts will be placed on reserve in Millikan Library (list attached below). Grading There will be a midterm and a final examination. Your grade is based on: homework (40%), midterm (30%), and final (30%). To encourage class and recitation participation (attendance, questions, comments, etc.), a bonus of up to 10% will be added to your final grade based on your participation, prorated according to your actual attendance. A problem set will be due approximately every three weeks. If you fail to obtain a copy of a homework set when it is handed out in class, you may download it from the course website. The midterm and final exams will not be found on the course website. See Ms. Priscilla Boon in 234 Noyes if you did not pick up the midterm or final exam in class. Completed assignments and midterm exams should be handed in during class hours, unless alternative arrangements are made with Jeen Joo Kang, the Head Teaching Assistant. Graded homework and exam papers will also be returned in class. Outside of class hours, you may pick up graded assignments from Mr. Kang. Please staple all work. Ch 24a Web Site Handouts, problem sets, answer keys, lecture notes and other useful material for this course may be found at: http://chemistry.caltech.edu/courses/ch24/a.html Problem Sets Homework will be handed out during class/recitation on a Friday (see schedule) and due 10 days later on Monday by 1:00 p.m. Solutions will be released at 5:00 p.m. Friday of the same week. Late assignments will be accepted, with the following penalties for a 100‐point assignment: 30% if turned in by Tuesday 1:00 p.m. following the Monday due date; 50% if turned in by Wednesday 1:00 p.m. following the Monday due date; 70% if turned in by Thursday 1:00 p.m. following the Monday due date; 90% if turned in by Friday 1:00 p.m. following the Monday due date; 100% if turned in after Friday 1:00 p.m. following the Monday due date. All homework must be turned in. Failure to do so will result in a grade of “F” or “I”. Page 2 of 7 Excuses for Late Homework Excuses for late homework must be arranged in advance and in writing, signed by Dr. Chan or Dr. Rees. Extensions will only be granted for medical reasons or personal/family emergencies; situations (such as clashes in assignment due dates or travel for interviews) that can be foreseen days or weeks beforehand will NOT be considered. The maximum period of extension allowed is 4 days (as solutions will be released on Fridays). A maximum of 2 extensions will be allowed for the three homework assignments during the term. Staple the excuse to your homework. NO extensions will be allowed for the midterm or the final. There will be no exceptions. Ch 24 and the Honor System Students are encouraged to cooperate on the homework; however, outright copying of solutions to the homework problems from another student, textbook, material from any previous years of Ch 24a/b, etc. is NOT permissible. Each individual is expected to personally complete the homework he/she hands in, and he/she should be able to explain the homework handed in. The examinations must be taken individually and without discussion among students. Ombudsman Meeting A student representative will be chosen to serve as a liaison between the class and the CCE Executive Officer (Dr. M. Okumura) and the CCE Division Curriculum and Undergraduate Studies Committee. If you have any complaints or suggestions about the course, please direct them to your ombudsman. However, given the timing of the ombudsman meetings, it is unlikely that this feedback will be received by the instructor in a timely fashion to help the course. Therefore, please feel free to see Dr. Chan or Dr. Rees at any time to discuss any issues related to this course. The teaching assistants also provide excellent sounding boards for feedbacks, as they communicate with the instructors on a regular basis. Page 3 of 7 BOOKS PLACED ON RESERVE IN MILLIKAN LIBRARY Books Placed on Reserve in Millikan Library 1st Floor Reserve Charles Cantor, Paul Schimmel. Biophysical Chemistry Part 1 (1980). QH345 .C36 pt.1 Charles Cantor, Paul Schimmel. Biophysical Chemistry Part 2 (1980). QH345 .C36 pt.2 Charles Cantor, Paul Schimmel. Biophysical Chemistry Part 3 (1980). QH345 .C36 pt.3 Gordon Barrow. Physical Chemistry, 6th Edition (1996). QD453.2 .B37 1996 8th Floor Reserve Alan Fersht. Enzyme Structure and Mechanism (1985). QP601 .F42 1985 Norman Davidson. Statistical Mechanics (1962). QC175 .D3 Peter Atkins, Julio de Paula. Physical Chemistry for the Life Sciences (2006). Charles Cantor, Paul Schimmel. Biophysical Chemistry Part 1 (1980). QH345 .C36 pt.1 Charles Cantor, Paul Schimmel. Biophysical Chemistry Part 2 (1980). QH345 .C36 pt.2 Charles Cantor, Paul Schimmel. Biophysical Chemistry Part 3 (1980). QH345 .C36 pt.3 David Eisenberg and Donald Crothers. Physical Chemistry with Applications to Life Sciences (1979). Norman Davidson. Statistical Mechanics (1962). QC175 .D3 Ken Dill. Molecular Driving Forces (2003). QC311.5 .D55 2003 John Edsall. Biothermodynamics (1983). Dilip Kondepudi, Ilya Prigogine. Modern Thermodynamics: From Heat Engines to Dissipative Structures. (1998). QC311.K66 1998 Philip Charles Nelson: with the assistance of Marko Radosavljevic and Sarina Bromberg. Biological Physics: Energy, Information, Life. (2004). QH505 .N37 2004 Ignacio Tinoco, et al. Physical Chemistry: Principles and Applications in Biological Sciences. (2002). QH345.T56 2002 8th Floor (non‐reserve) Robert Alberty. Physical Chemistry, 7th Edition (1987). QD453.2 .D36 1987 Robert Alberty, Robert Silbey. Physical Chemistry, 2nd Edition (1997). QD453.2.D36 1997 Robert Alberty, Robert Silbey. Physical Chemistry, 1st Edition (1992). QD453.2 .D36 1992 Gordon Barrow. Physical Chemistry, 5th Edition (1988). QD453.2 .B37 1988 Gordon Barrow. Physical Chemistry, 4th Edition (1979). QD453.2 .B37 1979 Gordon Barrow. Physical Chemistry, 2nd Edition (1966). QD453.2 .B37 1966 Richard Dickerson. Molecular Thermodynamics (1969). QD501 .D47 9th Floor (non‐reserve) Alan Fersht. Enzyme Structure and Mechanism (1985). QP601 .F42 1985 Alan Fersht. Enzyme Structure and Mechanism (1977). QP601 .F42 James Espenson. Chemical Kinetics and Reaction Mechanisms, 2nd Edition (1995). QD502.E86 1995 Page 4 of 7 CLASS SCHEDULE (23 lectures, 3 recitations, 3 homeworks, 1 midterm, 1 final) HO = Homework handed out, HD = Homework due, MT = Midterm M Jan 4 Organization. Introduction to spectroscopy. Interaction of light with matter: Classical description of absorption and dispersion. Quantum mechanics. Simple applications. Interaction of light with matter: Quantum description. Chemical Bonding. Selection rules. Electronic spectro‐ scopy of biological chromophores. (HO‐1). Martin Luther King Day. (Holiday). Infrared and Raman spectroscopy. Total attenuated FTIR Recitation 1. (Add Day). W Feb 10 Electron paramagnetic resonance. Spin labeling. (MT due). Nuclear magnetic resonance. Nuclear spin relaxation. President’s Day. (Holiday). Multi‐dimensional NMR. Protein structural determination in solution. X‐ray spectroscopy. (HO‐3). Light scattering. X‐ray, electron, and neutron scattering. X‐ray diffraction. (Drop Day). Recitation 3. Mass spectrometry of macromolecules. Proteomics. (HD‐3). Rates and mechanisms of chemical reactions. Transition state theory. Temperature dependence of reaction rates. Enzyme kinetics. W Jan 6 F Jan 8 F Feb 12 M Feb 15 W Feb 17 F Feb 19 M Jan 11 W Jan 13 F Jan 15 M Feb 22 M Jan 18 W Jan 20 F Jan 22 W Feb 24 F Feb 26 M Mar 1 M Jan 25 Spontaneous emission. Fluorescence spectroscopy. (HD‐1). Fluorescence resonance energy transfer (FRET). Fluorescence depolarization. Single‐molecule methods. (HO‐2). Spectroscopy of interacting chromophores. Exciton interaction. Hypo‐ and hyper‐chroism. W Mar 3 W Jan 27 F Mar 5 F Jan 29 M Mar 8 Methods of rapid and ultrafast kinetics. Methods of rapid and ultrafast kinetics. (Final out). Study period. M Feb 1 W Mar 10 Mar 11‐14 T Mar 16 W Feb 3 Polarized light. Circular dichroism and optical rotatory dispersion. Recitation 2. (HD‐2). (MT out). F M Feb 5 Feb 8 (Final due 1 p.m.) End of term. W Mar 17 Page 5 of 7 Reading Assignments James P. Allen, “Biophysical Chemistry”, Wiley-Blackwell, Oxford, England (2008). Part 2: Quantum mechanics and spectroscopy Chapter 9. Quantum theory: introduction and principles Chapter 10. Particle in a box and tunneling Chapter 12. Atomic structure: hydrogen atom and multi‐electron atoms Chapter 13. Chemical bonds and protein interactions Chapter 14. Electronic transitions and optical spectroscopy Chapter 11. Vibrational motion and infrared spectroscopy Chapter 16. Magnetic resonance Chapter 15. X‐ray diffraction and extended x‐ray absorption fine structure Part 1: Thermodynamics and kinetics Chapter 7. Kinetics and enzymes David Eisenberg and Donald Crothers, “Physical Chemistry with Applications to the Life Sciences”, Benjamin Cummings Publishing Company, Inc., 1979. Part Three Microscopic Systems Chapter 10. Principles of Quantum Mechanics Chapter 11. Chemical Bonds Chapter 12. Principles of Spectroscopy Chapter 13. Biochemical Spectroscopy Part Five Symmetry and Molecular Structure Chapter 16. Symmetry Chapter 17. X‐ray Diffraction and the Determination of Molecular Structure ------------------------------------------------------------------------------------------------------------------------------- Page 6 of 7 EXCUSE FOR LATE ASSIGNMENTS IN CHEM 24 ab Date: Excuse: Signature of Student: Signature of Instructor: (S.I. Chan or D.C. Rees) ------------------------------------------------------------------------------------------------------------------------------EXCUSE FOR LATE ASSIGNMENTS IN CHEM 24 ab Date: Excuse: Signature of Student: Signature of Instructor: (S.I. Chan or D.C. Rees) ------------------------------------------------------------------------------------------------------------------------------EXCUSE FOR LATE ASSIGNMENTS IN CHEM 24 ab Date: Excuse: Signature of Student: Signature of Instructor: (S.I. Chan or D.C. Rees) ------------------------------------------------------------------------------------------------------------------------------- Page 7 of 7 ...
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