Molecular Biophysics (PHYS*7520)

Course Information

Course Objectives

This course’s main objective is to introduce students to molecular biophysics, with emphasis on protein structure and structure/function of biologicalmembranes. We plan to cover the following topics in lectures, assignments, and presentations: Structure of biomolecules; Factors determining protein structures; Overview of methods for protein structure determination; Intermolecular interactions; Biological membranes; Protein folding and membrane insertion; Membrane proteins and their functions; Receptors and signal transduction; Membrane transport - channels and transporters; Bioenergetics.

Students will be given two assignments. The first one (individual) will introduce them to protein structures and their analysis using the most common software in the field. The second assignment (group, students will do it in pairs) will improve skills related to search, analysis, and synthesis of available literature data. Each pair of students will be given an important class of biological molecules (for example, channels, transporters, pumps, bioenergetically important enzymes, receptors) to study, and the results will have to be presented in class.

This course also aims to improve oral and written communication skills of students. Besides oral presentation of the second assignment, each student will have an opportunity to present an important research paper in the field and lead a discussion of this work in the second half of the course. In addition, a final essay will be submitted (in lieu of the final exam) on a topic of student’s choice, in consultation with the lecturer. The
topic should not be directly related to 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.

Instruction

Lectures and Presentations

Materials

Course Webpage

Additional information can be found on the course’s webpage.

References

There is no required text, but any of the following good books on Structural Biochemistry and Molecular Biophysics can be useful. Note that some of these resources are available in electronic format in PubMed.

• Lodish et al, “Molecular Cell Biology”
• Charles R. Cantor and Paul R. Schimmel, “Biophysical chemistry”
• Thomas E. Creighton, “Proteins: Structure and Molecular Properties”
• Karp, “Cell and Molecular Biology”
• Voet and Voet, “Biochemistry”
• Stryer, “Biochemistry”
•  Alberts, "Molecular Biology of the Cell"

Additionally, students will be provided with lecture notes in pdf format and given references to the appropriate research and review papers (licensed to the University of Guelph). Students are also encouraged to read major biophysical and biochemical journals (links are provided on the course website).

Evaluation

*Graduate grades will be renormalized from 125% to 100% of course)

Tentative Schedule

The following outline can change depending on the exact number of students:

1. Weeks 1-6. Lectures on general principles of protein structure, biological membranes organization and function, protein folding and insertion, overview of structural methods.
2. Weeks 7-8. Student presentations of the second assignment with discussions on biophysically important classes of proteins.
3. Weeks 9-12. Student presentations of research papers with discussions.
4. Exam period. Essay in lieu of the final exam.

Course Policies

Help in the Course, Office Hours

No regular office hours, but send me an E-mail and help will be provided either on-line or in person (we will schedule a meeting).

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.

Drop Date

The last date to drop one-semester courses, without academic penalty, is March 10th. For regulations and procedures for Dropping Courses, see the Undergraduate Calendar.

Copies of out-of-class assignments

Keep paper and/or other reliable back-up copies of all out-of-class assignments: you may be asked to resubmit work at any time.

Accessibility

The University of Guelph is committed to creating a barrier-free environment. Providing services for students is a shared responsibility among students, faculty and administrators. This relationship is based on respect of individual rights, the dignity of the individual and the University community's shared commitment to an open and supportiv learning environment. Students requiring service or accommodation, whether due to an identified, ongoing disability or a short-term disability should contact the Centre for Students with Disabilities as soon as possible.

For more information, contact CSD at 519-824-4120 ext. 56208 or email sas@uoguelph.ca or see the accessibility website.

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 fromoccurring. 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 academicmisconduct 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.

Recording of Materials

Presentations which are made in relation to course work—including lectures—cannot be recorded or copied without the permission of the presenter, whether the instructor, a classmate or guest lecturer. Material recorded with permission is restricted to use for that course unless further permission is granted.

Resources

The Academic Calendars are the source of information about the University of Guelph’s procedures, policies and regulations which apply to undergraduate, graduate and diploma programs.