Molecular Biophysics (PHYS*4540)

Course Information

This course introduces students to the concepts of molecular biophysics, including the structure of biomolecules such as lipids, nucleic acids and proteins, the interaction of these molecules with biological membranes, and methods of studying these structures and interactions. 

Calendar Description

Physical methods of determining macromolecular structure: energetics, intramolecular and intermolecular forces, with applications to lamellar structures, information storage, DNA and RNA, recognition and rejection of foreign molecules.

Prerequisites

PHYS*4540: 0.50 credits in biochemistry, (CHEM*3860 or PHYS*3230)

Instruction

Lecturer

Professor John Dutcher, MacN 451, ext 53950, dutcher@uoguelph.ca

John's research focuses on using a broad range of experimental techniques, including many biophysical techniques, to study the fundamental soft matter and biological physics of systems with real world applications. For more information, visit the Dutcher Lab webpage.

Course Meetings

Lectures

Tuesday, Thursday; 11:30 – 12:50; MACN 203

Course Materials

References

There is no required textbook, but here are some general book references: 

• B. Alberts et al., Molecular Biology of the Cell, 4th Ed. (Garland, 2002)
• J. Kuriyan et al., The Molecules of Life (Garland, 2012)
• H. Lodish et al., Molecular Cell Biology, 8th Ed. (W.H. Freeman & Co., 2016)
• R. Phillips et al., Physical Biology of the Cell, 2nd Ed. (Garland, 2012)
• K.A. Dill & S. Bromberg, Molecular Driving Forces, 2nd Ed. (Garland, 2011)
• C. Branden & J. Tooze, Introduction to Protein Structure, 2nd Ed. (Garland, 1999)
• T.E. Creighton, Proteins: Structures and Molecular Properties, 2nd Ed. (W.H. Freeman & Sons, 1992)

In addition, students will be provided with lecture notes in pdf format with references to textbooks as well as appropriate research and review papers. Students are also encouraged to read major biophysical and biochemical journals (see CourseLink page for list of journals). 

Website

CourseLink Page

There is a PHYS*4540/7520 CourseLink page to allow you easy access to course-related material.

Course Topics

• introduction to molecular biophysics
  -    biomolecules and biological membranes
• lipids and self-assembly of lipid structures
• nucleic acids
• proteins 
  -    protein structure
  -    protein folding & misfolding 
• biological membranes
• interactions of proteins with biological membranes 
  -    techniques used to study these interactions 

In addition to lectures by the instructor on the above topics, students will select a molecular biophysics research paper from a list provided on the CourseLink page and present a lecture on this topic to the class. Students will also submit a written report based on their presentation. 

Course Learning Objectives

This course will use a multidisciplinary approach to present new concepts in molecular biophysics and build on concepts covered in previous courses. The objectives of this course are:

1. Understand the principles of the molecular biophysics approach
   •    Develop an appreciation of the experimental, theoretical, and computational approaches that can be applied to biophysical systems 
2. Understand the basic building blocks of biology and how they self-assemble to form biological molecules
   •    Expand knowledge of different types of structure within biological molecules
3. Understand different interactions between biological molecules, and between biomolecules and biological membranes 
   •    Demonstrate knowledge of the structure/function relationships between biomolecules and biological membranes
   •    Appreciate the diversity and complexity of protein-biological membrane interactions
4. Expand scientific writing and presentation skills to develop effective communication
   •    Develop ability to synthesize implications of key results of published scientific studies

Evaluation

The directed reading assignments, written report, and research proposal are due via Dropbox at 11:59 on the due date. Unless there are exceptional circumstances, marks will be deducted for lateness (10% per day). Marks will also be deducted for errors in English grammar and spelling in all work submitted for grading. Students must obtain a final grade of 50% to pass the course.

Where possible, requests for academic consideration are to be accompanied by supporting documentation. See the undergraduate calendar for information on regulations and procedures for Academic Consideration.

Course Policies

Getting 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

Students are encouraged to discuss with each other during working on the problem assignments. However, the work that you submit as your assignment must not be a copy of someone else's work. Identical scripts will be given a mark of zero and plagiarism will be dealt with severely. Proper citations should be provided when books and other articles are used in your works.

Course Assessment

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 strength 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 Promotion Committee only considers comments signed by students. 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.

University Statements

COVID-19 Disclaimer

Please note that the ongoing COVID-19 pandemic may necessitate a revision of the format of course offerings and academic schedules. Any such changes will be announced via CourseLink and/or class email. All University-wide decisions will be posted on the COVID-19 website and circulated by email.  

Email Communication

As per university regulations, all students are required to check their e-mail account regularly: e-mail is the official route of communication between the University and its students.

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 (or designated person, such as a teaching assistant) in writing, with your name, id#, and e-mail contact. The grounds for Academic Consideration are detailed in the Undergraduate and Graduate Calendars.  

Drop Date

Students will have until the last day of classes to drop courses without academic penalty. The deadline to drop two-semester courses will be the last day of classes in the second semester. This applies to all students (undergraduate, graduate and diploma) except for Doctor of Veterinary Medicine and Associate Diploma in Veterinary Technology (conventional and alternative delivery) students. The regulations and procedures for course registration are available in their respective Academic Calendars. Undergraduate Calendar - Dropping Courses 

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 promotes the full participation of students who experience disabilities in their academic programs. To that end, the provision of academic accommodation is a shared responsibility between the University and the student. When accommodations are needed, the student is required to first register with Student Accessibility Services (SAS). Documentation to substantiate the existence of a disability is required; however, interim accommodations may be possible while that process is underway. Accommodations are available for both permanent and temporary disabilities. It should be noted that common illnesses such as a cold or the flu do not constitute a disability. Use of the SAS Exam Centre requires students to book their exams at least 7 days in advance and not later than the 40th Class Day.

Academic Integrity

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 encourages academic integrity. 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. Undergraduate Calendar - Academic Misconduct 

Recording of Materials

Presentations that are made in relation to course work - including lectures - cannot be recorded or copied without the permission of the presenter, whether the instructor, a student, 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 that apply to undergraduate, graduate, and diploma programs. Academic Calendars

Note

John will be away several times during the semester for research purposes, including the week of March 6. If necessary, makeup lectures will be arranged at times that are agreeable to the students.