BIOPHYS 440 001 FA 2022
Biophysics of disease
BIOPHYS440 / CHEM440
Instructor: Magdalena Ivanova
Email: mivanova@umich.edu
Graduate Student Instructor (GSI): Adam Decker
Email: adamdeck@umich.edu
Description
The course will introduce the most commonly used biophysical methods for studying complex diseases and the application of these techniques for developing therapies. The emphasis will be on protein aggregation diseases (Parkinson’s, Alzheimer’s, and prion), but diseases like cancer, viral (HIV, influenza, and SARS-CoV-2), and bacterial infections will also be discussed. Classical biophysical methods like x-ray crystallography, NMR, and cryoEM will be covered, as well as recently emerging cutting-edge techniques. Invited speakers will present some lectures about their studies of disease mechanisms for which they apply biophysical techniques covered by the class.
Reading and Materials
Lectures are prepared using multiple sources, with each lecture containing references to the used resources. The covered techniques are described in the textbooks listed below, and these materials are recommended but not required
1. Methods in Molecular Biophysics: Structure, Dynamics, Function (Cambridge University Press, 2007), by Serdyuk, Igor N.; Zaccai, Nathan R.; Zaccai, Joseph ISBN-10:052181524X
2. Biophysics: tools and techniques (CRC Press, 2016) Mark Leake Experimental
3. Biophysics: Biological Methods for Physical Scientists, (CRC Press, 2017, by Jay L. Nadeau
4. Protein NMR spectroscopy: principles and practice. (Academic Press, 2006), by Cavanagh, J., Fairbrother, W.J., Palmer III, A.G., Rance, M., and Skelton, N.J. ISBN-10:012164491X
5. NMR for Physical and Biological Scientists1st Edition (2006, Garland Science) by Pochapsky, Thomas; Pochapsky, Susan Sondej) ISBN-10: 0815341032
6. Crystallography made crystal clear. A guide for users of macromolecular models (Academic Press, 2006) by Gale Rhodes ISBN-10:0125870736
7. Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State2nd Edition (Oxford University Press, 2006) by Joachim Frank, ISBN-10: 0195182189
Class Schedule M and W 8:30am-10:00am
Class location MLB 1220-Lec Rm 1 (NEW)
Remote Lectures Zoom link: https://zoom.us/my/amyloid password: 430440
Guest lectures will be recorded and uploaded on Pages/Lecture Videos.
Lecture files (pdf format) will be posted in Files/Lectures.
Class assignments, exams, and quizzes will be posted on Canvas and can be taken asynchronously within the specified times.
Office hours
Magdalena Ivanova Time: Monday 5:00 - 6:00 PM
Location: 4027 BSRB or via zoom https://zoom.us/my/amyloid
Adam Decker Time: Friday 8:30 - 9:45 AM
Location: zoom (for now) https://umich.zoom.us/j/99154776738
This class will be in-person. For more information about in-person attendance, check the university Covid-19 guidelines. If you have any concerns about in-person attendance, don't hesitate to get in touch with us.
Accommodations for Students with Disabilities
Please let me know if you need accommodation for a disability at your earliest convenience. You may also need to contact the Services for Students with Disabilities (SSD) office (phone 734-763-3000), which typically recommends accommodations through a Verified Individualized Services and Accommodations (VISA) form. Please be aware that exams must be scheduled at least two weeks before the exam date. Any information you provide is private and confidential and will be treated as such.
Religious holidays
Please let us know if you have conflicts with the examination dates.
Course requirements and grading roster.
We will deduct 25% of the exam grade for late submissions.
Make-up exams are to be approved only by the Instructor.
| Graded assignment/exam | Grades |
| Assignment #1 Talk | 10 pts |
| Assignment #2 Talk | 10 pts |
| Discussion #1 | 6 pts |
| Discussion #2 | 6 pts |
| Discussion #3 | 6 pts |
| Discussion #4 | 6 pts |
| Participation | 6 pts |
| Guest lectures attendance | 5 pts |
| Quiz #1 | 5 pts |
| Quiz #2 | 5 pts |
| Quiz #3 | 5 pts |
| Mid-term Exam | 12 pts |
| Synopsis of Final Project | 3 pts |
| Final Project Write-up | 15 pts |
| Total | 100 pts |
Participation (6 pts)
Participation credit will be earned as follows
Attend 5 student presentations 2 pts (5x0.4pts)
Ask at least one question at the students' presentations. 2pts
Active class participation 2 pts
Guest Lectures Attendance (5 pts total)
Attendance will be taken for all guest lectures. To earn credit, students must attend the classes in person. If you are unable to attend, please get in touch with us.
Presentation talks (10 pts each)
Students will present in person twice over the semester and teamed in groups of 3-4 for each presentation. All team members will share the same grade. For the presentations, it is helpful to have a systematic approach to discussing the material, including an appropriate background reading, using the correct references, and an in-depth understanding of the presented material. Students should be able to explain/comment on the methodology/theory necessary for the presentation.
If you are unable to attend due to sickness, please let your group members AND the instructor know as soon as possible. Group members will share the same grade.
The length of the talks should be between 15 min + 5 min Q&A
For teaching purposes, we will record the students' presentations. Please get in touch with the GSI or instructor during the first week of class if you do not want to be recorded.
Discussion (6 pts each)
Students can find the Discussion topics posted in the Canvas/Discussions. This assignment will require students to watch talks by biophysicists posted online, and answer the posted questions. Although this assignment will be remote and asynchronous, students will have the possibility to discuss it in class and provide feedback on the assignment's contents.
Quizzes (5 pts each)
Quizzes will be 20 min and can be taken asynchronously within the specified time frame. The list of the lectures covered by the quizzes is below. Typically there will be 2-4 questions per lecture.
Quiz #1 - lectures 1-5
Quiz #2 - lectures 13-17
Quiz #3 - lectures 18, and 22-25
Mid-term exam (12 pts)
The mid-term exam can be taken remotely during the dates specified in the syllabus. The mid-term exam will cover lectures 1-9 with ~2-4 questions for each lecture.
Synopsis of the Final Project (3 pts)
Students must submit a synopsis summarizing their final exam by midnight Dec 5.
Final Project Write-Up (15 pts)
The final Project will be a write-up of 3 pages with 1-3 figures. Pages should be made with a 1-inch margin using 11 pts Arial font with single line spacing.
Final grades will be calculated using a standard scale
Grade |
Range |
|
A |
100 % |
to 93.0% |
A- |
< 93.0 % |
to 90.0% |
B+ |
< 90.0 % |
to 87.0% |
B |
< 87.0 % |
to 83.0% |
B- |
< 83.0 % |
to 80.0% |
C+ |
< 80.0 % |
to 77.0% |
C |
< 77.0 % |
to 74.0% |
C- |
< 74.0 % |
to 70.0% |
D+ |
< 70.0 % |
to 67.0% |
D |
< 67.0 % |
to 64.0% |
D- |
< 64.0 % |
to 61.0% |
F |
< 61.0 % |
to 0.0% |
Course Summary:
| Date | Details | Due |
|---|---|---|