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Instructor Tianbing Xia Stephen Levene

Office FO 3.728 FN 3.114

Email sdlevene@utdalla

Telephone UTD-6328 (883-6328) UTD-2503 (883-2503)

Office Hours MF 11 - 12 MF 11 - 12

Objectives: This is a core graduate course that is designed and structured to provide biology students with introductory quantitative knowledge of the principles and applications of various aspects of classical and modern physical chemistry. The course covers aspects of biophysical chemistry that are most fundamental and most relevant to contemporary biological science research. Topics include thermodynamics, molecular interactions, biomolecular structures, quantum principles and various spectroscopies, all selected based on their fundamental importance. The course is tailored to accommodate the ever changing applications of these principles in modern biochemistry, biophysics, and structural biology research. Therefore students are provided with necessary tools to gain quantitative understanding of these areas. Outcomes: Students will therefore be able to: 1. Appreciate the fundamental physical and chemical principles behind modern physical chemistry as applied to macromolecules. 2. Obtain a working knowledge of applying these principles in their own research and an understanding relevant published literature. 3. Students will be inspired to continue learning beyond the course content as to how modern physical chemistry can be vital throughout biological research. Assessment: The key to assess whether students have gained necessary knowledge from this course is to evaluate whether they have understood the basic concepts and the applications of the concepts to systems of interest in biological science. Homework and in-class quizzes that include practical examples of biological applications are used to evaluate whether students are making progress, and exams are designed to reinforce the progress. In-class discussion is used to gauge understanding and enthusiasm for independent learning. The results of these evaluations at the end of the course are used to adjust the contents and to improve the implementation of the course materials. Required Text: Principles of Physical Biochemistry, 2 nd ed., K.E. van Holde, W.C. Johnson, P.S. Ho. Prentice Hall, Upper Saddle River, NJ, 2006. ISBN 0-13-046427-9 Assigned as needed MF 9:00 - 10:50 am (FO 3.616)

Supplementary Reading: Lectures: Grading:

Levene, in-class quizzes (50%), take-home exam (50%) Xia, problem sets (50%), take-home exam (50%) Mon. Jan 9 through Fri. Mar 3 (Dr. Levene) Mon. Mar 13 through Mon. Apr 24 (Dr. Xia) Date Mon 1/09 Fri 1/13 Mon 1/16 Fri 1/20 Mon 1/23 Fri 1/27 Instructor Levene “ N/A Levene “ “ Topic Inter- and intramolecular forces, molecular mechanics Inter- and intramolecular forces, molecular mechanics ML King Holiday Classical thermodynamics Classical thermodynamics (cont’d), Quiz Classical thermodynamics (cont’d) Assigned Reading Ch. 3, pp. 107-133 Ch. 3, pp. 133-161 N/A Ch. 2, pp. 73 -93 “ Ch. 2, pp. 93 -103

Mon 1/30 Fri 2/3 Mon 2/6 Fri 2/10 Mon 2/13 Fri 2/17 Mon 2/20 Fri 2/24 Mon 2/27 Fri 3/3 Mon 3/6 Fri 3/10 Mon 3/13

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Solution thermodynamics, Quiz Solution thermodynamics (cont’d) Statistical thermodynamics, Quiz Statistical thermodynamics (cont’d) Polymer-chain statistics, Quiz Polymer-chain statistics (cont ’d) TBA (SDL away) Transport properties Macromolecular binding and equilibria, Quiz, Take-home exam distributed Macromolecular binding and equilibria (cont’d) Spring Break (no class) Spring Break (no class) Take-home exam due Experimental Foundations of Quantum Mechanics

Ch. 13, pp. 579-589 Ch. 13, pp. 589-600; Ch. 14, pp. 605 -615 Handout Ch. 4, pp. 166-198 Ch. 4, pp. 198-209 “ TBA Ch. 5, pp. 213-270 Ch. 14, pp. 615-654 “ N/A N/A Ch 8 and supplementary materials Ch 8 Ch 8 Ch 9 Ch 11 Ch 11 Supplementary Materials Ch 12 Ch 12 Ch 12 Ch 10 Ch 6 Ch 6


Fri 3/17 Mon 3/20 Fri 3/24 Mon 3/27 Fri 3/31 Mon 4/3 Fri 4/7 Mon 4/10 Fri 4/14 Mon 4/17 Fri 4/21 Mon 4/24

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The Postulates of Quantum Mechanics Applications of Quantum Mechanics Problem Set 1 Out Molecular Spectroscopy: Absorption Molecular Spectroscopy: Emission Problem Set 1 Due in Class Fluorescence Spectroscopy FRET Problem Set 2 Out NMR Spectroscopy NMR Spectroscopy Problem Set 2 Due in Class NMR Spectroscopy Circular Dichroism Problem Set 3 Out X-ray crystallography X-ray crystallography Problem Set 3 Due in Class Final Take Home Exam Distributed

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Fri 4/28

Final Take Home Exam Due

Students with Disabilities: If you have a disability that requires accommodation, you must notify the instructor and file a request through

Disability Services (SU 1.610, x2098) on or before the first day of class . By doing so, you can be assured of full cooperation in making appropriate arrangements. Academic Dishonesty Policy: Students are required to abide by UT-Dallas policies concerning academic integrity (for details, see Failure to comply with these terms will be subject to appropriate disciplinary action.