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Class Schedule M,W 8:30Am-10:00Am In-Person Lectures

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Class Schedule M,W 8:30Am-10:00Am In-Person Lectures Instructor Magdalena Ivanova email [email protected] GSI Christian Kelley email [email protected] Class Schedule M,W 8:30am-10:00am In-person lectures Room 1400 Chemistry Building Remote lectures https://umich.bluejeans.com/20000000000000 /please pay attention for changes of the remote-class link Recorded lectures will be uploaded on Pages/Lecture Videos Lecture files (pdf format) will be posted in Files/Lectures Office hours Magdalena Ivanova Remote: https://umich.bluejeans.com/20000000000000 Time: TBD Christian Kelley Remote: TBD Time: TBD !!!Christian will be polling for office-hours times. Office hours won’t be recorded. In-person class In-person attendees can attend the class remotely any time. All of us who are attending the class in-person are expected to follow the required the safety guidelines of the State of Michigan and the UM. sanitize work areas maintain a minimum of 6 feet distance wear a face do not come to class when ill or in quarantine Remote class Remote attendees must attend the lectures only virtually If you change your mind, please contact us. We need to make sure that we do not exceed the recommended room capacity. We will do a poll on to determine who prefers in-person or online class. In-person/remote class All lectures will be recorded real time for synchronous and posted on Canvas for asynchronous viewing. All students (in-person or remote) can choose to attend the class asynchronously any time. We highly recommend the remote attendees to attend synchronously as this will allow a more active engagement. All class assignments, exams, and quizzes will be posted on Canvas and can be taken synchronously or asynchronously within the specified times. Please keep up with the lectures and the assignments from the beginning of the term and view the class materials (lectures, assignments etc) within 24 hours of posting. All of us have to be familiar with the guidelines for safe distancing: http://ehs.umich.edu/wp-content/uploads/2020/07/U-M-Face-Covering-Policy-for-COVID-19.pdf http://ehs.umich.edu/wp-content/uploads/2020/07/U-M-Face-Covering-Policy-for-COVID-19.pdf Course recording All course lectures will be audio/video recorded and made available to the students taking the class. As part of your participation in this course, you may be recorded. If you do not wish to be recorded, please contact me or Christian the first week of class to discuss alternative arrangements. Students are prohibited from recording/distributing any class activity without a written permission from the instructor, except as necessary as part of approved accommodations for students with disabilities. Any approved recordings may only be used for the student’s own private use. Students with Disabilities Please let us know as soon as possible and be aware that exams need to be scheduled couple of weeks in advance Religious holidays Please let us know if you have conflicts with the examination dates Lectures 20 / 20 / 20 format 20 min instruction 10 min Q&A* 20 min instruction 10 min Q&A 20 min instruction 10 min Q&A *Participation (5pts total) synchronous or asynchronous If you opt on participating asynchronously, you should post your answers 12 hours after the lecture ends. Neurodegenerative Cancer Viral and bacterial diseases infections Biophysical methods X-ray crystallography, NMR, Electron Microscopy and single molecule spectroscopy Molecular Drug Diagnosis mechanism development The course will emphasize on the basic, as well as the most recent development of biophysical studies that can be applied to advance our knowledge of disease and drug development. Some of the lectures will be given by invited speakers. These lectures will likely be virtual Treatment of cancer resistance Fluorescent Imaging of protein Prof. Stefanie Galban phase separation in cells Prof. Nils Walter NMR studies of protein aggregation Comparison between generic Dr. Bikash Sahoo and brand-name drugs Ramamoorthy Lab Prof. Anna Schwendeman Reading Materials The reading 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 LeakeExperimental 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 Scientists 1st 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 State 2nd Edition (Oxford University Press, 2006) by Joachim Frank, ISBN-10: 0195182189 Reading Materials: Articles Mackenzie, Acta Neuropathologica, 2007, vol. 114, pp 49 Reading Materials Databases for articles Google scholar: https://scholar.google.com/ Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/ Article assess Login in VPN Login in UM library database https://search.lib.umich.edu/databases Paste/type article identifiers title author (usually first), year, journal, volume, page Canvas discussion 1 Image: https://www.chronicle.com/article/the-holy-grail-of-class-discussion/ Testing and Grading One point will be deducted for late homework. 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 Assignment #2 Write up 10 pts Discussion #1 4 pts Discussion #2 4 pts Discussion #3 4 pts Discussion #4 4 pts Discussion #5 4 pts Participation/Attendance 5 pts Quiz #1 5 pts Quiz #2 5 pts Quiz #3 5 pts Mid-term Exam 10 pts Final Project Write-up 20 pts 100 pts Total Testing & Grading Presentation talks (10 pts each) Students will present twice over the course of the semester. Students will be teamed in groups of 3-4 for each presentation. The partners will be different for each presentation. All team members will share the same grade. Presentations #1 and #2 15 min Q&A 5 min Both presentations and Q& A will be virtual Please note that your presentations will be recorded. Testing and Grading Write-up (10pts each) Length of the text for Write-up should be 2-3 pages (1,000 to 1,500 word count) with 1-2 figures. Pages should be made with 1 inch margin using 11 pts Arial font with single line spacing. Final Project Write-Up (20 pts) Final Project will be a write-up of 3-4 pages (1,700 to 2,300 word count) with 2-4 figures. Pages should be made with 1 inch margin using 11 pts Arial font with single line spacing. You should use your own words for the write-up. Direct copying from the source materials will be penalized by taking 7pts from the grade. Write-up will be graded individually using the criteria below write in clear and concise manner the presented material give background information describe in your words the main subject provide adequate citations Five discussions (4 pts each) Topics for discussions will be posted in the Discussion section on Canvas. Discussion examples: comment on the zoominar series answer questions on posted papers and topics annotate papers The discussions will accommodate both synchronous and asynchronous participation. Attendance (0 pts) Testing and Grading Quizzes (6 pts each) Quiz #1 (15-20 min) lectures 1-5 with ~ 2-4 questions per lecture. Quiz #2 (15-20 min) lectures 15-16, 18-19 and 23 with ~ 2-4 questions per lecture. Quiz #3 (15-20 min) lectures 24-28 with ~ 2-4 questions per lecture. Mid-term exam (12 pts) Mid-term exam will cover lectures 1-8, and 12-14 with ~2-4 questions for each lecture. The questions will based on the material and/or papers posted with each lecture. Please note that the Quizzes and Mid-term exam may be changed to accommodate virtual examination. Final grades will be calculated using a standard scale A 93-98.0 A- 90-92.9 B+ 87-89.9 B 83-86.9 B- 80-82.9 C+ 77-79.9 C 73-76.9 C- 70-72.9 D+ 67-69.9 D 63-66.9 D- 60-62.9 Neurodegenerative Cancer Viral and bacterial diseases infections Biophysical methods X-ray crystallography, NMR, Electron Microscopy and single molecule spectroscopy Molecular Drug Diagnosis mechanism development The course will emphasize on the basic, as well as the most recent development of biophysical studies that can be applied to advance our knowledge of disease and drug development. Some of the lectures will be given by invited speakers. These lectures will likely be virtual Atoms Molecules Membrane/Vesicles Organelles Tissue Cells Organisms Viruses 1 Angstrom m mm mm nm pm 101 10-3 10-6 10-9 10-12 Human Eye Light Microscopy Scanning Electron Microscopy Transmission Electron Microscopy X-ray ED MRI NMR spectroscopy Methods for Structure Determination Power Limitations X-ray crystallography Gives 3D picture of Must crystallize the sample And very recently atoms (atomic electron crystallography resolution) No size limit NMR No need for crystals Size and resolution limits Can image cells Gives direct photo; CryoEM resolution ~1-3Å Electron microscopy no upper size limit Time consuming: must Homogeneous samples average images Electron tomography (tilt Very small samples Resolution is low. sample; combine views work: can image cells, High resolution is still for 3D image) organelles laborious to achieve Single Molecule Very vursatile Resolution is low Techniques Mass spec Accurate mass Only mass Other methods: FT-IR, Fast, small samples High purity sample Raman, Fluorescence, Mostly for 2 structure Circular dichroism etc determination Hepatitis B capsid example of combining X-ray derived atomic structure with cryo-EM- averaged electron density Average to get 3D image Insert X-ray atomic structure Crowther: The Leeuwenhoek lecture 2006.
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