Course Syllabus
Biophysics of disease
BIOPHYS440 / CHEM440
Instructor Magdalena Ivanova, PhD Email: mivanova@umich.edu
Graduate Student Instructor (GSI) Jessica Dawson Email: jmdawson@umich.edu
Class Schedule 8:30am-10:00am Mon/Wen Rm 1 MLB
Description
This course focuses on biophysical methods for studying the molecular mechanism of complex diseases and the most common applications of these techniques for therapy development and disease diagnosis. Although the emphasis is on protein aggregation diseases (Parkinson's, Alzheimer's, and prion), the course will also cover diseases like cancer, viral (HIV, influenza, and SARS-CoV-2), and bacterial infections. Recently emerging cutting-edge techniques, along with classical biophysical methods such as X-ray crystallography and NMR, will be the subject of the class. Invited speakers will present some lectures about their studies of disease mechanisms allowing the students to learn from leaders in the field.
Class topics and examination dates can be found in the class calendar.
For general information related to this course and various aspects of campus life, you can use MiMaizey. This resource provides details on building locations, computer lab availability, student organizations, dining hall menus, the academic calendar, and other essential information. Additionally, you can inquire about Biophys440 specifically by mentioning the course in your question. For example, you might ask, "What are the three methods for structure determination mentioned in Biophys440?"
Reading and Materials
Multiple sources (papers, textbooks, and online posts) are utilized to keep up with the most recent advancements in the area of disease mechanisms, and each lecture has information about the resources used. Additionally, students can find descriptions of some biophysical techniques in the textbooks listed below. All materials used for the class are available through UM library database.
If you have any questions, you can also ask Maizey, the AI tutor trained on the class materials.
LaTeX equation converters can be found in
ChatGPT : https://chatgpt.com/g/g-oDmioY7gS-latex-equation-converter
LaTeXtoImage: https://latex2image.joeraut.com
LaTeX Equation in Word document : insert > equation > insert new equation > select {}LaTeX (upper left corner)
- Methods in Molecular Biophysics: Structure, Dynamics, Function (Cambridge University Press, 2007), by Igor Serdyuk, Nathan Zaccai, Joseph Zaccai, ISBN-10:052181524X
- Biophysics: tools and techniques (CRC Press, 2016) Mark Leake
- Experimental Biophysics: Biological Methods for Physical Scientists, by Jay Nadeau
- Protein NMR spectroscopy: principles and practice. (Academic Press, 2006), by Cavanagh, Fairbrother, Palmer III, Rance, and Skelton, ISBN-10:012164491X
- NMR for Physical and Biological Scientists1st Edition (2006, Garland Science) by Thomas Pochapsky and Susan Pochapsky, ISBN-10: 0815341032
- Crystallography made crystal clear. A guide for users of macromolecular models (Academic Press, 2006) by Gale Rhodes ISBN-10:0125870736
- 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
Office hours
via Zoom: https://zoom.us/my/amyloid password 430440
Magdalena Ivanova Time: Wednesdays, 10:45am-11:45am Location: Zoom
Jessica Dawson Time: Mondays, 10:15am - 11:15am Location: Zoom
Lecture files (pdf format) will be posted in Files/Lectures
Lecture recordings will be posted in Canvas under Pages.
Accommodations for Students with Disabilities
Please let us know if you need accommodation for a disability at your earliest convenience. Please be aware that exams must be scheduled at least two weeks before the exam date.
Religious holidays
Please let us know if you have conflicts with the examination dates.
Use of ChatGPT and other AI Tools
It’s your responsibility to assess every source’s reliability. AI tools like ChatGPT are a source that may inform your writing, just as books, papers, lecture notes, websites, and the results of Google searches. You should be aware that the output of AI tools is constructed to sound plausible and not checked by any expert.
Some assignments will be written papers. The writing you submit must be of your creation. Your papers will naturally be informed by other written work. When it is, you must acknowledge this through appropriate citation.
AI tools can generate text, code, and images in response to a prompt. Such automatically generated text is not your work and cannot be submitted as if it is. Exceptions are assignments that specifically ask for the use of AI.
Course requirements and grading roster
We will deduct 25% of the exam grade for late assignment submissions.
Attendance (~10%) and Participation (~5%)
This credit will be earned by attending all Guest Lectures and Student Presentations and actively engaging in the lectures by asking questions and answering discussion posts.
In-class presentation talks (15%)
Students teamed in groups of 3-4 will present once during the semester. All team members will share the same grade. The length of the talks should be between 18-20 min with 5-7 min Q&A.
We will record the presentations for teaching purposes. If you do not want to be recorded, please contact the GSI or instructor.
If you cannot attend due to sickness, please let your group members AND the instructor know as soon as possible. Group members will share the same grade.
Discussion (15% total)
Three Discussions will be posted throughout the semester. This assignment will require students to watch talks by biophysicists posted online and answer the posted questions.
Discussion #1 – post 09/09
Discussion #2 – post 09/25
Discussion #3 – post 10/16
Quizzes (40% total)
Quizzes will be 30-40min, and the list of the lectures covered by the quizzes is below.
Quiz #1 - lectures 1-6 date 09/18
Quiz #2 - lectures 7-11 date 10/07
Quiz #3 - lectures 12-16 date 10/28 - updated
Quiz #4 - lectures 17-20,26 date 12/04
Term Project (15% total)
The final Project will be a write-up which instructions will be provided as marked in the calendar.
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 |
|---|---|---|