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Department of Physics, University of Guelph |
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Department of Physics, University of Guelph |
Course Outline - Fall 10
This course introduces students to a wide variety of physical techniques used in modern biophysics research.
The molecular biophysics of cellular membranes will be discussed in detail, including the structure and function of major membrane components, lipids,
proteins and carbohydrates. The course also aims to improve the oral and written communication skills of the students. The course work assumes knowledge
of quantum mechanics and statistical mechanics at an introductory level. It is also very useful if the students have had an exposure to molecular biology
and biochemistry.
Steffen Graether (MCB): NMR
Cezar Khursigara (MCB): Electron Tomography
Leonid Brown (Physics): FTIR
Rob Wickham (Physics): Computer Simulations
An introduction to physical techniques to determine the structure of macromolecules and macromolecular structures
of biological interest. The techniques include: differential calorimetry, X-ray and neutron scattering, electron microscopy,
Raman and infrared spectroscopy, nuclear magnetic resonance, single molecule techniques such as atomic force microscopy, and surface adsorption techniques. Applications of these
techniques in the study of proteins and biological membranes will be emphasized. Students taking this course should already have
taken PHYS*4240 (Statistical Physics II) or the equivalent course, or be taking such a course concurrently.
PHYS*3220 (Waves and Optics)
PHYS*4040 (Quantum Mechanics II)
PHYS*4240 (Statistical Physics II), if not taken as a prerequisite
The students will be provided with an electronic collection of important reviews on the techniques of interest
(licensed to University of Guelph). This collection of reviews is also available for download in the "cd" directory at the following website:
http://www.physics.uoguelph.ca/~dutcher/download/phys_4560_7510/
The students are also encouraged to read major biophysical and biochemical
journals (links are provided on the course website).
Some general references are:
B. Alberts et al., Molecular Biology of the Cell, Fourth Edition (Garland, 2002)
Biological Membranes
Proteins
Techniques
Tentative Outline (can be slightly modified due to an unknown number
of student presentations):
- introduction to biological membranes
- formation of lipid structures
- forces between lipid bilayers
- membrane protein structure
- samples in biophysics: cells, membranes, films, crystals, liposomes
- vibrational spectroscopy of biomolecules
- single molecule techniques
- protein adsorption techniques
- guest lectures throughout semester
- student presentations on research papers and biophysical techniques not covered by the lectures
-Introduce the students to a wide variety of physical techniques
used in modern biophysics research, and the biological concepts that can be probed using these techniques.
Techniques will include (to various degrees of sophistication) differential scanning calorimetry, X-ray and neutron scattering and diffraction, NMR and ESR
spectroscopy, infrared and Raman spectroscopy, electron microscopy, atomic force microscopy, absorption
spectroscopy, light scattering, circular and linear dichroism, fluorescence, as well as other methods.
-The course is also an introduction to the molecular biophysics
of cellular membranes. The structure and function of the major membrane components, lipids, protein and
carbohydrates will be discussed. The determination of the molecular structure and function using physical
techniques will be emphasized.
-Another objective of the course is to bring the students
to a level of understanding of the field of biomembranes where they are comfortable reading the most recent
research literature such as that reported in the Biophysical Journal. The students will be encouraged to
explore the literature associated with biophysical systems and techniques.
-The course also aims to improve the oral and written communication
skills of the students. Each student will have the opportunity of reviewing an important research paper in
the field. In addition, each student will give an oral presentation on
some physical technique used in modern biophysical research and will lead a class discussion on this topic. A final essay will also
be submitted on the same physical technique. The topic should not be directly related to the student's own research work and not
extensively covered in the lectures. Graduate students taking the course will have to write an additional
research proposal on applying biophysical techniques to a given problem.
Evaluation:
Lecturer:
John
Dutcher MacN 451 ext 53950 dutcher at uoguelph.ca
In John's research group, a wide range of state-of-the-art, surface-sensitive techniques are used
to probe the interaction of polymers, biopolymers and bacterial cells with a variety of different surfaces, ranging from atomically-flat surfaces
to tethered lipid bilayer films to industrial-grade and food surfaces. By tuning both the properties of the surfaces and the polymer and biopolymer
molecules, and developing simple models to interpret the data, an understanding of the underlying physical, chemical and biological principles and therefore predictive power in the
design of novel technologies can be obtained. For more information,
visit the Polymer Surface and Interface Group web page.
Guest Lecturers:
Lectures and Seminars: Tues.,
Thurs. 11:30 - 12:50, Guelph-Waterloo Link Rooms: MacN 101 (Guelph campus), EIT2053 (Waterloo campus)
Calendar Description:
Prerequisites:
Co-requisites:
References:
R. Phillips et al., Physical Biology of the Cell (Garland, 2009)
R.B. Gennis, Biomembranes: Molecular Structure and Function (Springer-Verlag, 1989)
P. Yeagle et al., The Structure of Biological Membranes (CRC Press, 1992)
P.L. Yeagle, The Membranes of Cells (Academic Press, 1993)
A. Kotyk, K. Janacek and J. Koryta, Biophysical Chemistry of Membrane Functions (John Wiley
and Sons, 1988)
R. Lipowsky and E. Sackmann, Eds., Structure and Dynamics of Membranes (Elsevier, 1995)
K.M. Merz and B. Roux, Eds., Biological Membranes (Birkhauser, 1996)
S.H. White, Membrane Protein Structure: Experimental Approaches (Oxford University Press, 1994)
H. Flyvbjerg et al., Physics of Biological Systems: From Molecules to Species (Springer-Verlag, 1997)
C. Branden and J. Tooze, Introduction to Protein Structure, Second Edition (Garland, 1999)
E. Grell, Membrane Spectroscopy (Springer-Verlag, 1981)
G. Ehrenstein and H. Lecar, Eds., Methods of Experimental Physics, Vol. 20 Biophysics (Academic Press, 1982)
I.D. Campbell and R.A. Dwek, Biological Spectroscopy, (Benjamin/Cummings, 1984)
Course Objectives:
| Problem assignment (early October) | 20% |
| Research paper report (early October) | 30% |
| Essay on one of the methods with oral presentation (second half of November) | 40% |
| Participation in the discussions of research papers and essays | 10% |
| 100% | |
| Research proposal (for graduate students only, November) | 20% | (the graduate grade will be renormalized from 120% to 100%, of course) |
A PHYS*4560/7510 Web Page has been established to allow you easy access to course-related information:
or click on Student Info on the Physics
Department home page.
HELP!:
Short questions can often be handled in the lecture room just before or after lectures. John will make every effort
to answer emails in a timely manner.
Collaboration versus Copying:
Scientists often consult fellow scientists to discuss their research problems. Collaboration between scientists is often essential to perform world-class research. However, no ethical scientist would ever publish or claim the work of others as their own. Instead, joint publication or acknowledgements of the contributions of their collaborators is given.
The work that you submit for marking must be your own and not a copy
of someone else's work. As a young scientist, you are encouraged to discuss
with your fellow students as you learn the material and work on your
assignments and presentations. However, plagiarism is a form of academic misconduct,
and will not be tolerated. In your work that you submit for marking, you
are encouraged to cite references and acknowledge discussions with others
who have helped you to achieve an understanding of the material.
This is good scientific practice.
Student Assessment for Guelph Students:
The Department of Physics requires student assessment of all courses taught by the Department. These assessments provide essential feedback to faculty on their teaching by identifying both strengths and possible areas of improvement. In addition, annual student assessment of teaching provides part of the information used by the Department Tenure and Promotion Committee in evaluating the faculty member's contribution in the area of teaching.
The Department's teaching evaluation questionnaire invites student response both through numerically quantifiable data, and written student comments. In conformity with University of Guelph Faculty Policy, the Department Tenure and Promotions Committee only considers comments signed by students (choosing "I agree" in question 14). Your instructor will see all signed and unsigned comments after final grades are submitted. Written student comments may also be used in support of a nomination for internal and external teaching awards.
NOTE: No information will be passed on to the instructor until after the final grades have been submitted.
Note:
John may be away several times during the semester to attend workshops and conferences, and to give research lectures. John will try to arrange that lectures be given at the regular times by enthusiastic and talented replacement and guest lecturers. Otherwise, makeup lectures will be arranged at times that are agreeable to the students.