PHYS 4301/5301--Cell and Molecular Biophysics

PHYS 4301/5301
Cell and Molecular Biophysics

Credit hours: 3
Classroom: 259 Clippinger
Day and time: TuTh 9:00-10:20 a.m.
Prerequisite: (Undergrad: PHYS 2052, CHEM 1520, BIOS 1700) (Graduate: A willingness to read.)

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.

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

Office: 357A Clippinger Labs
Phone: 740-593-1694
E-mail: tees@ohio.edu

Announcements

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

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.

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 1700 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. If you have a copy of a similar Cell and Molecular Biology textbook, that should also serve.

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 ($110 on Amazon.com as of late August. Used copies are also available on for a bit less). The course will largely follow this book, but with much supplementation.

Also useful is Rob Phillips, Jane Kondev and Julie Theriot, Physical Biology of the Cell, Garland Science, 2009 ($73 new on Amazon.com. as of late August)

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 ($40). This is an excellent introduction to diffusion and Brownian motion.

D. Boal, Mechanics of the Cell 2nd ed. ($24). This is an excellent reference for cell mechanical properties.

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.

Web resources

Harold P. Erickson, Stretching single protein molecules: Titin is a weird spring, Science, 276:1090-1092, 1997. - This article discusses entropic springs which are ubiquitous in biology.
Edward M. Purcell, Life at Low Reynolds Number, Am. J. Phys., 45:311, 1978. - This is a wonderful and chatty article on how bacteria and cells experience very different everyday physics from what people experience. An html version (with figures) can be downloaded from the web, or see me for a copy.
Movies of Bacteria moving - This is Howard Berg's site at the Rowlands Institute at Harvard U. It has movies of bacteria executing their persistent random walk.
Protein Data Bank - This database stores and dispenses information on the DNA and amino acid sequences and X-ray and NMR structures of proteins. One can download RASMOL (the viewer for protein structures) here. There's a very useful index to the PDB that breaks down the proteins by class
National Center for Biotechnology Information - This is the National Institutes of Health's clearinghouse for all of the national and international DNA and protein sequence and structure databases. One can get to GENBANK (the storehouse for DNA sequences by using clicking on the "Entrez" button and clicking on "Entrez--nucleotide".
Reading Frames in DNA - This site has a nice tutorial on various aspects of DNA sequence analysis
Biophysical Journal - The journal of the Biophysical Society and the best one to check out for papers of interest.
Proceedings of the National Academy of Sciences U.S.A. - The journal of The National Academy of Sciences of the U.S.A. This is a high prestige journal. There are usually 3-6 biophysics papers per issue (in a separate section) and these are often excellent papers.

Assignments

There will be about 6-8 short assignments (~ 1 per 2 weeks) 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. Unless otherwise announced in class, assignments will be due on Fridays by 5:00 p.m. You may leave assignments under the door of my office (357A Clippinger) or in my mailbox (251 Clippinger) or (if all electronic) by E-mail.

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 Seminar.

Quizzes

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

Exams

There will be midterm exam and a final exam

Grading Scheme

	Undergraduate	Graduate
Midterm exam	25	25
Final exam	25	25
Quizzes (8-10)	7	7
Assignments (~6)	40	25
Presentation	-	15
Participation	3	3

David F. J. Tees, Ph.D.

Associate Professor