Physics 450: Molecule and Cell Biophysics
Course number 81660, 4 credit hours
M 1200-1250 132 SES and M T Th 0100-0150 132 SES
Lecturer: Prof. Anjum
Ansari, Department of Physics
If you have questions about the course,
don't hesitate to email
Preparation of these course
materials has been supported by the National Science Foundation
through the CAREER awards DMR-973178
(Marko) and MCB-9722295 (Ansari)
Summary: An introductory course aimed at explaining biological phenomena
inside the cell, in terms of the basic physical laws that govern biomolecular
conformations and self-organization. The course will be accessible
to undergraduates in both physical and biological sciences.
Prerequisites: Physics 245 or consent of instructor.
Please note that appropriate engineering courses are prefectly acceptable
as replacement for Physics 245; e.g. Phys 141/142 Physics + Che 201/ME
205 Thermodynamics + ME 211 Fluid Dynamics would be suitable preparation
for the course.
For chemistry students, Phys 141/142 + Chem 342/343 (physical chemistry)
would be suitable preparation; previous study of biochemistry is not required.
Be sure to let the lecturers know ahead of time if you would like approval
of alternate prerequisites.
Course Outline:
Introduction to force, time, energies at nanometer scales (1
hour, Notes 1 23)
Heat, temperature, Boltzmann distribution, chemical equilibrium, pH
(3 hours, Notes 4)
Hydrodynamic drag, Brownian motion (2 hours, Notes 5)
Gene expression, genetic code (2 hours; Notes
6)
Intermolecular interactions, electrostatic screening (2
hours, Notes 7
Notes 8 )
DNA & RNA structure, physical properties (4 hours, Notes
9)
Protein structure, physical properties (6 hours) Notes
10
General aspects of flexible polymers (4 hours) Notes
111213141516
Folding of nucleic acids and proteins (4 hours) Notes
1718
Chemical kinetics (4 hours) Notes 1920
Mechanical properties of biofilaments: dsDNA, actin filament, microtubules
(3 hours) Notes 2122
Catalysis (4 hours)
Allosteric enzymes (2 hours)
Sedimentation, size-exclusion chromatograpy and electrophoresis
(2 hours)
NMR, fluorescence, optical tweezer and other micromanipulation techniques
(3 hours)
Cell membrane structure and physical properties (6 hours)
23
Protein railways: microtubules and actin (2 hours)
Protein engines: kinesin, myosin and others (4 hours)
Energy and information flow in the cell (4 hours)
Prokaryote cell (3 hours)
Eukaryote cell (4 hours)
Suggested Reading:
Charles R. Cantor and Paul R. Schimmel ``Biophysical Chemistry (three volumes);
Part 1 - The Conformation of Biological Macromolecules; Part 2 - Techniques
for the Study of Biological Structure and Function; Part 3 - The Behavior
of Biological Macromolecules'', (W.H. Freeman 1980)
A new book suggested to us by a student is Michael Daune, ``Molecular
Biophysics - Structures in Motion'', Oxford University Press (1999) - this
book covers much of the material on structure and physical properties of
biopolymers, in rather more depth than we will study. It is a nice
book to read!
Howard C. Berg ``Random Walks in Biology'' (1993)
Pierre-Gilles de Gennes ``Scaling Concepts in Polymer Physics'' (Cornell
1988)
Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts
and James D. Watson ``Molecular Biology of the Cell'' (1994)
James Darnell, Harvey Lodish and David Baltimore ``Molecular Cell Biology''
(1992)
There are also two new books still in photocopy form, from two prominent
biological physicists, which might be very helpful to look at:
Philip Nelson ``Biological Physics: Energy, Information, Life''
- see Anjum Ansari for photocopies
David Boal ``Soft Mechanics of the Cell'' - see Anjum Ansari
for photocopies
In addition, there will be readings from the current research literature.
Grading:
Problem sets 40%
Paper outline 10%
Written paper 25%
Presentation + revised paper 25%
Problem_set_1
Solution_set_1
Problem_set_2
Problem_set_3
Problem_set_4
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