Instructor Office Email Telephone Office Hours

Tianbing Xia FO 3.728 tianbing.xia@utdallas.edu UTD-6328 MF 11 - 12

(883-6328)
Stephen Levene FN 3.114 sdlevene@utdalla s.edu UTD-2503 MF 11 - 12
(883-2503)

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
Supplementary
Reading: Assigned as needed

Lectures: MF 9:00 - 10:50 am (FO 3.616)

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 Instructor Topic Assigned Reading

Mon 1/09 Levene Inter- and intramolecular forces, Ch. 3, pp. 107-133
molecular mechanics
Fri 1/13 “ Inter- and intramolecular forces, Ch. 3, pp. 133-161
molecular mechanics
Mon 1/16 N/A ML King Holiday N/A
Fri 1/20 Levene Classical thermodynamics Ch. 2, pp. 73 -93
Mon 1/23 “ Classical thermodynamics (cont’d), “
Quiz
Fri 1/27 “ Classical thermodynamics (cont’d) Ch. 2, pp. 93 -103
 Mon 1/30 “ Solution thermodynamics, Quiz Ch. 13, pp. 579-589
Fri 2/3 “ Solution thermodynamics (cont’d) Ch. 13, pp. 589-600;
Ch. 14, pp. 605 -615
Mon 2/6 “ Statistical thermodynamics, Quiz Handout
Fri 2/10 “ Statistical thermodynamics (cont’d) Ch. 4, pp. 166-198
Mon 2/13 “ Polymer-chain statistics, Quiz Ch. 4, pp. 198-209
Fri 2/17 “ Polymer-chain statistics (cont ’d) “
Mon 2/20 “ TBA (SDL away) TBA
Fri 2/24 “ Transport properties Ch. 5, pp. 213-270
Mon 2/27 “ Macromolecular binding and equilibria, Ch. 14, pp. 615-654
Quiz, Take-home exam distributed
Fri 3/3 “ Macromolecular binding and equilibria “
(cont’d)
Mon 3/6 N/A Spring Break (no class) N/A

Fri 3/10 “ Spring Break (no class) N/A

Mon 3/13 Xia Take-home exam due Ch 8 and

supplementary
Experimental Foundations of Quantum
materials
Mechanics
Fri 3/17 “ The Postulates of Quantum Mechanics Ch 8
Mon 3/20 “ Applications of Quantum Mechanics Ch 8
Problem Set 1 Out
Fri 3/24 “ Molecular Spectroscopy: Absorption Ch 9
Mon 3/27 “ Molecular Spectroscopy: Emission Ch 11
Problem Set 1 Due in Class
Fri 3/31 “ Fluorescence Spectroscopy Ch 11
“
Mon 4/3 FRET Supplementary
Materials
Problem Set 2 Out
Fri 4/7 “ NMR Spectroscopy Ch 12
“
Mon 4/10 NMR Spectroscopy Ch 12
Problem Set 2 Due in Class
Fri 4/14 “ NMR Spectroscopy Ch 12
Mon 4/17 “ Circular Dichroism Ch 10
Problem Set 3 Out
Fri 4/21 “ X-ray crystallography Ch 6
Mon 4/24 “ X-ray crystallography Ch 6
Problem Set 3 Due in Class
Final Take Home Exam Distributed
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
http://www.utdallas.edu/student/slife/scholastic.html). Failure to comply with these terms will be subject to
appropriate disciplinary action.