Download Biophysics - Fayetteville State University

Fayetteville State University
Course Syllabus
Fall 2005
I.
Course: INTRODUCTION TO BIOPHYSICS, PHYS 302.
Meeting times: MF, 11-11:50am, Room 207; W, 11-12:50pm, Room 220.
II.
Catalog Course Description: This course introduces the use of physical methods
in the study of biological systems, including macromolecules, membranes, nerves,
muscle, photosynthetic systems and visual systems. The biological systems to which the
methods are applied will be surveyed and current interpretations of their structure and
function will be discussed. The treatment of biological phenomena will be based on
physical principles with appropriate mathematics when necessary. The emphasis will be
on the applications of physics in biology and ecology.
III.
Objectives of the course: Objectives of the course are to study selected
biological phenomena using physical principles. The biological and environmental
sciences are presently witnessing an unprecedented rate of discovery and innovation. A
number of technical advances have made a very strong impact on these subject areas,
opening up possibilities which were inconceivable only a few years ago. The enormous
impact of the biological sciences is evident from the media attention devoted to Human
Genome Project, cloning, E. coli outbreaks, biological weapons defense, and the neverending search for cancer cures. Biophysics has a prominent role to play in tackling these
and other biological problems. Biophysics makes use of physical concepts and
techniques to address problems in biology and ecology. Physics has been very successful
at illuminating fundamental aspects of biological problems at the molecular level. For
example, biophysicists use thermodynamics to understand enzyme reactions and X-ray
diffraction or nuclear magnetic resonance to determine the structures of biological
molecules such as proteins and DNA.
IV.
Instructor: Dr. A. Umantsev
Office: Lyons Sciences Bldg, Room 318;
Office Hours: M: 12:00-2pm; T W: 1-2pm.
Day Time phone: (910) 672-1449
E-mail address: [email protected]
V.
Instructional Material: In this course we will be using standard physics and
biology textbooks, which you can find in a bookstore or on the Internet. Some good
examples are listed below. Specific biophysical issues will be presented in lectures and
supported by handouts.
List of Physics textbooks:
Jones and Childers, “Contemporary College Physics” (algebra and trig based),
Cutnell & Johnson's “Physics”, (algebra and trig based) (Wiley: NY).
Giancoli “Physics”, (algebra and trig based) (Prentice Hall, NJ).
Holiday, Resnick, and Walker “Fundamentals of physics” (calculus based) (Wiley)
Sanny and Moebs, “University Physics”, (WCB/McGraw-Hill)
List of Biology textbooks:
Starr and Taggart, “Biology: The unity and diversity of life” (Wadsworth, CA)
Campbell, Reese, and Mitchell, “Biology: Concepts and Connections” (Addison Wesley)
Raven, Peter, and Johnson, “Biology”, (McGraw-Hill Companies)
VI.
Audience: Upper level undergraduates of Biology, Biotechnology, Chemistry,
Mathematics, and Computer Sciences and graduate students enrolled in these programs
will benefit from the course.
VII. Prerequisites: The course assumes knowledge of physics in the volume of
College Physics I and II courses and math in the volume of Calculus I. The course does
not assume a detailed knowledge of chemistry or biology. However, a general familiarity
with biological topics will be greatly beneficial for the students. Some biology and
chemistry will be introduced in the lectures.
VIII. Grading system: There will be 3 regular tests and a final test (not
comprehensive), 50 POINTS EACH. Students will be allowed to use their lecture notes
on the test, but NOT THE TEXTBOOKS or HANDOUTS. There will be NO MAKE-UP
TESTS FOR ANY REASON. However, the lowest score of ONE TEST will be dropped.
There will be approximately a dozen quizzes, 10 POINTS EACH. Students will have an
option of making an open-ended research-type oral presentation on one of the subjects
related to the course at the end of this class. This will bring them UP TO 50 POINTS of
extra-credit. However, the topic of the presentation must be discussed with the instructor
prior to the work on it.
A student who earns the largest number of points gets A. Also:
92 - 100% of the largest number of points
80 - 91.9% of the largest number of points
64 - 79.9% of the largest number of points
48 - 63.9% of the largest number of points
Below 48% of the largest number of points
=
=
=
=
=
A
B
C
D
F
IX.
Outline of topics:
1. Life and Its Physical Basis:
a. What is life?
Discussion question: Try to define life (living organisms).
b. Life and energy. What is energy and why do organisms need it? Where do they get it?
Discussion question: How much energy do you expend in climbing up a mountain? How
much energy is needed to pull RNA into a viral capsid?
2. Forces and energies at nanometer scales.
a. Intermolecular interactions and electrostatic screening.
b. Chemical bonding and stability of molecules.
3. Thermodynamic basis of life.
a. Heat, temperature, chemical equilibrium, Boltzmann distribution.
b. Energy type and the second law of thermodynamics.
Discussion question: Does Mother Nature play dice?
c. Brownian motion.
d. Chemical kinetics and catalysis.
e. Metabolism in animals and photosynthesis in plants.
4. Chemical composition of living systems.
a. What is so special about carbon?
Discussion question: Could life be based on another element?
b. What so special about water?
Discussion question: How do organisms survive in frozen water?
c. Structure and physical properties DNA & RNA, protein, cell membrane.
5. Proteins: Structure and Function.
a. From linear polymer to functioning molecular machine: the role of weak interactions.
The structural organization within proteins: primary, secondary, tertiary, and quaternary
levels of organization; varieties of proteins: globular and fibrous.
Discussion question: “Secondary” structures defined by Pauling, Corey, & Branson.
b. The stability of proteins as measured by free energy and denaturation. Motions within
proteins.
c. Speeding things up: how enzymes work.
d. Proteins as binding machines: measurement of binding and thermodynamic analysis.
Discussion question: myoglobin and hemoglobin at work.
5. Nucleic Acid and Genetic Information: Deciphering the genetic code.
a. Why a double helix?
b. How structure stores information.
c. The replication process.
d. From DNA to RNA to protein.
e. How DNA is packed in the cell nucleus.
Discussion question: Supercoiling.
6. The Cell: A Survey.
a. The cell as a basic unit of life's organization. The components: membranes,
cytoskeleton, organelles. The central role of macromolecules: proteins, nucleic acid,
carbohydrates.
b. Surface tension and mechanical properties of cell membranes.
c. The cell interior as a tough neighborhood: Brownian motion and viscosity and their
influence on particle motion in the cell.
d. Basic structure of prokaryotic and eukaryotic cells, mitochondria and the generation of
ATP. Energy and information flow in the cell.
7. The Cell Membrane.
a. The lipid bilayer: self assembly at work.
b. Controlling traffic: membrane proteins and transport in and out of the cell, passive
versus active transport, fusion and exocytotic release.
Discussion question: Why did Mother Nature put so many lipids in a membrane?
c. Bioenergetics: bacteriorhodopsin, photosynthesis, the role of ATP and the structure of
the ATP synthase.
d. The chemiosmotic model.
8. Molecular machines: Motility.
a. The role of the cytoskeleton in cell motion.
b. Distributing the goods: the role of motors within the cell.
c. Muscle: many actin-myosin motors at work.
Discussion question: how biological motors work: general principles of motility.
d. The role of the cytoskeleton in cell motion.
e. Distributing the goods: the role of motors within the cell.
f. Muscle: many actin-myosin motors at work.
Discussion question: how biological motors work: general principles.
g. Virus structure—an introduction to macromolecular parasites.
10. The Neuron: We all have to talk to each other.
a. Generation and propagation of the action potential: experimental observations and the
Hodgkin-Huxley analysis.
b. The role of channels and pumps.
c. The biophysics of the synapse.
d. Two cases: muscle and retina.
11. Social aspects of biological organisms.
a. Game theory for biological analysis of conflict and cooperation.
b. Natural selection acts instead of the decision maker.
c. Bacterial colony growth and pattern formation in biology.
d. Population genetics.
12. The origin of life: Can we figure out how all that happened?
a. Basic requirements of the theory
b. What do we know?
c. What needs to be done?
X.
Laboratory Exercises:
Computer Lab: Simple mathematical tools in biophysics.
Lab: Viscosity.
Lab: Polystyrene beads on a microscope grid: The nature of random motions.
Computer Lab: Simulations of Protein Structure & Dynamics
Lab: Liposomes as self-assembling sacks to trap and deliver drugs.
Lab: Diffusion through a semi-permeable membrane, osmotic force.
Computer lab: neural networks in vivo and in the computer.
XI.
Appendix: Books related to the course available at Charles Chestnut Library
1. Biophysics : an introduction / Rodney M.J. Cotterill; QH505 .C64 2002
2. Biophysics / Roland Glaser; QH505 .G5413 2001
3. Physical approaches to biological evolution / M.V. Volkenstein ; with a foreword
by Manfred Eigen QH366.2 .V625 1994
4. The rainbow and the worm : the physics of organisms / Mae-Wan Ho; QH331 .H58
5.
6.
7.
8.
9.
1993
Newton rules biology : a physical approach to biological problems / C.J.
Pennycuick; QH513 .P46 1992
Basic biophysics for biology / Edward K. Yeargers; QH505 .Y43 1992
How life learned to live : adaptation in nature / by Helmut Tributsch ; translated by
Miriam Varon; QH505 .T6813 1982
Physics for applied biologists / N. C. Hilyard and H. C. Biggin; QC21.2 .H54
Energy flow in biology; biological organization as a problem in thermal physics
[by] Harold J. Morowitz; QH505 .M6
10. Introduction to environmental biophysics / Gaylon S. Campbell, John M. Norman;
QH505 .C34 1998