Feb. 12, 2009 To: The UGC From: Patricia LiWang for Natural Sciences faculty RE: Proposed Physical Biochemistry course To the UGC, We propose the addition of a new course to the Natural Sciences Curriculum, namely Physical Biochemistry, with proposed course number BIO 107. This course would serve three purposes in the advancement of our curricular goals. First, it would provide a course that requires quantitative interpretation of experiments on biological systems, which fulfills a Program Learning Outcome in Biology. Second, it is expected that the course will have interest from students across disciplines, including Chemistry and Physics, as well as in Biology. And third, the course is intended to be a major requirement for a proposed new major (not yet approved) in Biochemistry. BIO 107, Physical Biochemistry is proposed as a 4 credit course, with three contact hours in lecture, one contact hour of Discussion and no lab component. The course has been designed to be both an undergraduate and a graduate course. The lectures would be the same, but the undergraduate sections would have a Discussion. For the graduate students, significant additional components would be added: They would be required to carry out an project that involves using actual 3-dimensional NMR data to carry out chemical shift assignments of a protein and they would also be required to read and present biophysical results from the recent literature in class. A proposed syllabus for the undergraduate course, including Student Learning Outcomes is attached. Please feel free to contact me if you need any further information. Sincerely, Patricia J. LiWang Professor School of Natural Sciences (209) 228-4568 pliwang@ucmerced.edu
Instructor: Dr. Patricia J. LiWang Office: Castle facility room 95 Office hours will be in S&E room XXX pliwang@ucmerced.edu (209) 228-4568 BIO 107 Physical Biochemistry Spring 2010 Office Hours: Meetings with Dr. LiWang can be arranged by appointment. Required Text: Principles of Physical Biochemistry Van Holde, Johnson, and Ho (Prentice Hall, 2006) ISBN 0-13-046427-9 Other texts and readings will be assigned by lecturer, and may include the Biophysical Society online textbook which can be found at: http://www.biophysics.org/education/resources.htm Course Summary and Objectives: Physical Biochemistry is the study of Biochemistry through the viewpoint of properties that can be quantitatively assessed to provide specific molecular information about a biological system. Such properties include macromolecular folding, multimerization, structure, and ligand binding. This course will seek to instruct students on these properties of macromolecules as well as on the experimental techniques that can quantitatively probe these properties, such as fluorescence, NMR and analytical ultracentrifugation. Student Learning Outcomes: By taking this course, the successful student will: 1. Be able to describe folding and unfolding pathways of proteins and DNA, and propose experiments to probe aspects of macromolecular folding. 2. Be able to quantitatively describe protein:protein interactions in terms of thermodynamic constants such as dissociation constant, as well as interpret analytical ultracentrifugation data to obtain such thermodynamic information. 3. Be able to interpret a variety of fluorescence data (including emission and anisotropy) on a biochemical system to draw conclusions about conformational changes, binding events and folding events. 4. Be able to analyze NMR spectra to obtain structural and chemical shift information about macromolecules. Grading: Exams : There are two exams, each worth 100 points, and a final exam, worth 150 points. The final exam will be largely focused on the last portion of the classwork, but may have some
questions from earlier in the semester. The exams will be held during the lecture hour, and may also include a take-home portion. Exam 1 Feb. 26, 2010 Exam 2 April 2, 2010 Final Exam: May 7, 2010 10:30 am-12:30 pm Problem sets will be made available throughout the semester, and at least one question from each will be graded: 10 points each. No late problem sets will be accepted. Grading Summary: 2 exams of 100 points each, 1 final exam of 150 points, 3-4 problem sets of 10 points. Total number of points: about 400 pts. Accomodation for Disabilities The American with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact the Disability Services Center at (209) 228-6996 or Email: disabilityservices@ucmerced.edu The Disability Services Center is located on the first floor of the Kolligian Library, West Wing, Room 113. Academic Integrity Academic Integrity is the cornerstone of academic achievement. The current policies for UC Merced are described in the UC Merced Interim Academic Honesty Policy and Adjudication Procedures and are available via the UCMCROPS site. Collaboration during an Exam or Quiz is forbidden unless expressly allowed by the instructor. Tentative Schedule: Wed January 17 Protein structure, DNA structure LiWang Ch 1 Fri January 19 Protein structure, DNA structure LiWang Ch 1 Mon January 22 Separation, characterization of macromolecules; non-analyt. ultra LiWang Ch 5 Wed January 24 Separation, characterization of macromolecules; analytical ultracentrifugation Fri January 26 Thermodynamics and Equilibria/analytical ultracentrifugation LiWang Ch 5, 13 LiWang Ch 13 Mon January 29 Thermodynamics and Equilibria LiWang Ch 13 Wed January 31 Thermodynamics and Equilibria LiWang Ch 13 Fri February 2 Thermodynamics and Equilibria LiWang Ch 13 Mon February 5 Protein Stability: Thermodynamic basics Scholtz Ch 2
Wed February 7 Protein Stability: Methods of Measurement Scholtz Ch 2 Fri February 9 Forces Contributing to Protein Stability Scholtz Ch 3 Mon February 12 Models for Helix Formation in Peptides Scholtz Ch 3 Wed February 14 Energetics of Peptide Helix Formation Scholtz Ch 4 Fri February 16 Helix transitions in nucleic acids LiWang Ch 4 Mon February 19 Equilibria involving macromolecular binding LiWang Ch 14 Wed February 21 Equilibria involving macromolecular binding LiWang Ch 14 Fri February 23 Equilibria involving macromolecular binding LiWang Ch 14 Mon February 26 Exam I Wed February 28 Equilibria involving macromolecular binding LiWang Ch 14 Fri March 2 Equilibria involving macromolecular binding LiWang Ch 14 Mon March 5 Spectroscopy, NMR LiWang Supp Wed March 7 Spectroscopy, NMR LiWang Supp Fri March 9 Spectroscopy, NMR LiWang Supp Mon March 12 Spring Break!! Wed March 14 Spring Break!! Fri March 16 Spring Break!! Mon March 19 Spectroscopy, NMR LiWang Supp Wed March 21 Spectroscopy, NMR LiWang Supp Fri March 23 Spectroscopy, NMR LiWang Supp Mon March 26 Spectroscopy/Fluorescence LiWang Ch9-11 Wed March 28 Spectroscopy/Fluorescence LiWang Ch9-11 Fri March 30 Spectroscopy/ Fluorescence Anisotropy LiWang Ch9-11 Mon April 2 Exam 2 Wed April 4 Spectroscopy/ Fluorescence Anisotropy LiWang Ch9-11 Fri April 6 Reading Day, no classes Mon April 9 Spectroscopy/ FRET LiWang Ch9-11 Wed April 11 Spectroscopy/ FRET, start Mass spec LiWang Ch11,1 5 Fri April 13 Mass Spec LiWang Ch 15 Mon April 16 Single Molecule Methods LiWang Ch 16 Wed April 18 Single Molecule Methods LiWang Ch 16 Fri April 20 Single Molecule Methods LiWang Ch 16 Mon April 23 Student-led presentation/makeup lecture LiWang Wed April 25 Student-led presentation/makeup lecture LiWang Fri April 27 Student-led presentation/makeup lecture. LiWang Mon April 30 Student-led presentation/makeup lecture. LiWang
May 7 10:30 am-12:30 pm Final Exam LiWang