Biophysical Methods (Cellular Biophysics) (PHYS*4560)

Course Information

Instruction

Guest instructors

• Vladimir Ladizhansky (Physics)
• John Dutcher (Physics)
• Steffen Graether (MCB)

The students are also encouraged to attend biophysics-related colloquia (TBA if any).

Lectures and Seminars

Please note that there will be no lecture on Oct 14th, the new “reading day”

Course Objectives

1. Introduce the students to a wide variety of physical techniques used in modern biophysics research. These include patch-clamping, 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.
2. 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.
3. 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 biological membranes.
4. 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 and leading a discussion of this work. In addition, each student will give an oral presentation on some physical technique used in modern biophysical research and a final essay will be submitted on a technique of the student’s choice. 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 the studied biophysical techniques to a given problem.

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. The course will emphasize the underlying physics involved in the techniques used to study biomembranes. The determination of the molecular structure and function of the components of membranes are given as examples of the use of the physical techniques.

References

The students will be provided with an electronic collection of important reviews on the techniques of interest (licensed to the University of Guelph). The students are also encouraged to read major biophysical and biochemical journals (the links are provided on the course website).

Course Website: http://www.physics.uoguelph.ca/~leonid/phys4560/

Evaluation

(*the graduate grade will be renormalized from 120% to 100%, of course)

Tentative outline

Can be slightly modified due to an unknown number of student presentations.

1. Brief introduction to biological membranes and protein structure (with Guest lectures)
2. Samples in biophysics: cells, membranes, films, crystals, liposomes
3. Biospectroscopy
4. Guest lectures (AFM and NMR)
5. Advances in protein X-ray crystallography
6. Student presentations of research papers
7. Student presentations on the biophysical techniques not covered by the lectures

Examples of biophysical techniques for the final essay/presentation:

1. Neutron diffraction
2. XAFS
3. Mossbauer spectroscopy
4. STM
5. Surface plasmon resonance
6. QENS
7. Mass spectrometry
8. Calorimetry
9. Low angle X-ray
10. XPS
11. ESR
12. Patch-clamping and other electrophysiological techniques
13. AFM
14. Fluorescence
15. Light scattering
16. Electron microscopy and crystallography

Course Policies

E-mail Communication

As per university regulations, all students are required to check their <uoguelph.ca> e-mail account regularly: e-mail is the official route of communication between the University and its students. This becomes even more important in this course, in view of the need to schedule two rounds of presentations.

When You Cannot Meet a Course Requirement

When you find yourself unable to meet an in-course requirement because of illness or compassionate reasons, please advise the course instructor in writing, with your name, id#, and e-mail contact. It is important to have enough time in advance to be able to reschedule you presentation, as there may be no additional time slots.

Academic Misconduct

The University of Guelph is committed to upholding the highest standards of academic integrity and it is the responsibility of all members of the University community – faculty, staff, and students – to be aware of what constitutes academic misconduct and to do as much as possible to prevent academic offences from occurring. University of Guelph students have the responsibility of abiding by the University's policy on academic misconduct regardless of their location of study; faculty, staff and students have the responsibility of supporting an environment that discourages misconduct. Students need to remain aware that instructors have access to and the right to use electronic and other means of detection.

Please note: Whether or not a student intended to commit academic misconduct is not relevant for a finding of guilt. Hurried or careless submission of assignments does not excuse students from responsibility for verifying the academic integrity of their work before submitting it. Students who are in any doubt as to whether an action on their part could be construed as an academic offence should consult with a faculty member or faculty advisor.

The Academic Misconduct Policy is detailed in the Undergraduate Calendar.

Please give appropriate credits to all sources of information (including figures) used in preparing your assignments, presentations, essays, and research proposals.

Course Evaluations

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 or by choosing "I agree" in question 14 (online process). 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.