PHYS 461/561 - Fall 2008
Cell and Molecular Biophysics

Call number: 05634 (PHYS 461) or 05648 (PHYS 561)
Credit hours: 4
Classroom: 132A Clippinger Labs
Day and time: MTWF 12:10-1:00 p.m.
Prerequisite: (Undergrad: PHYS 253, CHEM 152, BIOS 170) (Graduate: Permission of instructor)

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Course Description:

Introduction to the physical principles that underlie phenomena in cell biology and the properties of biomolecules. Topics covered will include an introduction to cell and molecular biology, biorheology, Brownian motion, molecular interactions in macromolecules, protein and nucleic acid structure, physics of biopolymers, chemical kinetics, mechanical and adhesive properties of biomolecules, molecular manipulation techniques, cell membrane structure, membrane channels and pumps, molecular motors.

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Instructor: David F. J. Tees, Associate Professor, Ohio University

Office: 357A Clippinger Labs
Phone: 593-1694
E-mail: tees@ohio.edu

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Announcements

Graduate students should come and see me to register. When you come to see me, we will talk briefly about the biology knowledge required and then I will pink slip you into the class.

The lecture notes and assignment solutions will be made available on the LON-CAPA system. Click on this link to go to loncapa.phy.ohiou.edu to go to the logon page. You will need to log in with your oak ID and then click on the Cell and Molecular Biophysics role. There are links to the material on the introductory page.

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Purpose

As the scientific world becomes more multidisciplinary, it will become increasingly necessary for physical scientists and engineers to be aware of the challenges and opportunities in cellular and molecular biology. Biological scientists can also benefit from a grounding in the mathematical background commonly given to physicists. Biophysics uses theoretical and experimental techniques from physics to model biological phenomena and to understand how organisms can consistently assemble complex molecules and cellular interactions from simple organic chemicals. Techniques such as X-ray crystallography, nuclear magnetic resonance, electron microscopy and electrophoresis have contributed enormously to the toolkit of molecular biologists. Scanned probe microscopies, optical trapping, and new spectroscopic techniques promise a further revolution in molecular precision. Concepts from polymer and colloid science and statistical and thermal physics are an important basis for understanding cell and molecular biology. This course will provide a grounding in the physical principles underlying molecular and cellular biology.

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Textbooks and other resources

Notes from the instructor will form the primary course material. Readings from the literature will be assigned. Graduate students who have not taken BIOS 170 are required to get a copy of the following introductory textbook (a used, older edition copy will be fine)

Alberts et al., Molecular Biology of the Cell ($99 new, 5th edition, but I recommend getting a used 4th or 3rd edition. The biophysics parts are essentially unchanged in the 4th edition and a used copy can be got for as low as $7 - $15). The introduction to molecular biology will be based on this book. This book is regularly referenced for general things in the biophysics literature and having a copy for reference will be very useful for your future.

The following text is recommended for graduate students (but not required). Copies will be placed on reserve at Alden Library:

Philip Nelson’s Biological Physics: Energy, Information and Life, W.H. Freeman and Co., New York, 2004 ($83 on Amazon.com as of Sept 2, 2008. Used copies are also available on Amazon,com for a bitless).

Other useful resources:

Copies of all of the following books (plus the texts above) will be placed on reserve at Alden Library.

Howard C. Berg, Random Walks in Biology ($25). This is an excellent introduction to diffusion and Brownian motion.

D. Boal, Mechanics of the Cell ($55). This is an excellent reference for cell mechanical properties.

C. R. Calladine & H. R. Drew, Understanding DNA ($60). This is a wonderful reference for the structure of DNA.

Paul C. Hiemenz and Raj Rajagopalan, Principles of Colloid and Surface Chemistry ($70). This is an excellent reference for colloidal phenomena, diffusion and Brownian motion. A copy can be accessed online through the library website (see me for advice if you have trouble finding it or installing the DJvu reader).

Jacob Israelachvili, Intermolecular and Surface Forces ($78). This is still the standard reference for intermolecular forces.

D. L. Lauffenburger and J. L. Linderman Receptors: models for binding, trafficking, and signaling ($85). This is a good reference for receptor-ligand binding, signaling, cell adhesion and migration.

C. R. Cantor & P. R. Schimmel, Biophysical Chemistry pts I, II & III (1980). This is the classic text for molecular biophysics. These volumes are still in print and quite relevant, but they are expensive (a full set costs $250 new). Part III is the least expensive ($70) but the most useful. It could serve as a reference for the middle part of the course as it covers the behavior of biological macromolecules (with good sections on polymer dynamics and receptor-ligand binding).

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Web resources

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Tentative Course Outline (subject to change)

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Assignments

There will be at about 7 short assignments (a bit fewer than 1 per week) consisting of problems and activities that will reinforce and give practical experience concerning topics covered in class. There will be separate assignments for graduate and undergraduate student. Completed assignments will be due as listed on the tentative schedule. Assignments may be given to me in class, placed in my mailbox in 251A Clippinger Labs or slid under the door of my office (357A Clippinger). They must be in by 5:00 p.m. on the due date.

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Presentation (Graduate Students Only)

Graduate students will be required to present a recent paper from Biophysical Journal or the biophysics section of Proceedings of the National Academy of Sciences U.S.A. on a topic of their own choosing or suggested by the instructor. The presentations will take place in the later half of the course and may be done as part of the Biophysics Journal club.

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Quizzes

Eight to Ten short quizzes on biological nomenclature will be given at the ends of some classes to ensure that students learn the biological language they will need to communicate productively with colleagues.

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Exams

There will be midterm exam and a final exam (see the schedule above)

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Grading Scheme

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