Jeffrey W. Bode: Catalogue data in Spring Semester 2023 |
| Name | Prof. Dr. Jeffrey W. Bode |
| Field | Synthetic Organic Chemistry |
| Address | Lab. für Organische Chemie ETH Zürich, HCI F 315 Vladimir-Prelog-Weg 1-5/10 8093 Zürich SWITZERLAND |
| Telephone | +41 44 633 21 03 |
| bode@org.chem.ethz.ch | |
| Department | Chemistry and Applied Biosciences |
| Relationship | Full Professor |
| Number | Title | ECTS | Hours | Lecturers | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| 529-0046-00L | Protein-derived Activity Probes for Ubiquitin Pathways  Enrolment limited to max 6 students. The enrolment is done by the D-BIOL study administration. | 6 credits | 7P | J. W. Bode | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | In this block course we will prepare proteins carrying electrophilic groups to interrogate intracellular pathways. These probes will be prepared by recombinant protein expression & purification followed by site-specific protein modification with electrophilic probes. Their reactivity will be tested in mammalian whole cell lysates and analyzed by proteolytic digestion and tandem mass spectrometry. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Students should learn how to design protein-based activity probes, express and isolate the proteins from E. coli, conduct site-specific protein modification, evaluate these probes in mammalian cell lysates using a proteomics workflow, and analyze and identify known or unknown proteins trapped by the activity probes. After the course participants should be able to apply gained skills in future chemical and molecular biology lab courses and projects. Individual reports describing the experiments and obtained results must be prepared by the end of the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | This course is based on a genuine research area and emerging technique. By working in pairs participants will recombinantly express and purify different ubiquitin mutants (UbV) in parallel. Based on the previous phage display screen, the chosen variants possess tunable affinity towards ubiquitin pathway proteases. Expression of the variants as intein fusions will enable site-specific C-terminal chemical modification either by direct aminolysis of the thioesters or by acylation of C-terminal hydrazides with activated carboxylic acids. The resulted constructs bearing electrophilic warheads will be utilized in mammalian whole cell lysates to covalently crosslink with cysteine UBL domain bearing proteases. The trapped proteases will be enriched by immunoprecipitation and analyzed by proteolytic digestion and tandem MS/MS with support from Functional Genomics Center Zurich (FGCZ). Results obtained from an individual UbV pull-down will be discussed and compared in the seminars. We expect to develop novel protein activity-based probes for various ubiquitin proteases (deubiquitinating enzymes). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | All the required theoretical and experimental details will be discussed in class. Relevant research papers will be recommended for reading during the seminars. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | This laboratory block course is designed for 4 weeks, 3 days of full working hours. Students should have basic practical knowledge of protein expression and organic synthesis. The maximum number of participants is currently limited to 6. Interested applicants may inquire to J. Bode for further information. Commitment for attendance of entire course is necessary. The course cannot be interrupted by individual absences once started. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Competencies |
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| 529-0074-00L | BCB IV: Analytical Biochemistry and Biophysics | 5 credits | 7P | K. Lang, J. W. Bode, M. Fottner, C. H. Giese, E. C. Meister, T. Segawa | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Practical Introduction to Experimental Methods in Analytical and Bioanalytical Chemistry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | To acquire a sound knowledge of the instrumentation and methods for the analysis of molecules, including organic compounds and biological molecules. To learnabout the most important practical techniques in analytical chemistry. To write critical reports for each experiment and analytical technique. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | The course will comprise of maximum 10 experiments from the following themes: Spectroscopic structural characterisation, analytical characterisation, Bio-physical characterisation. Experiments that will be part of this curriculum are: Circular dichroism (CD) spectroscopy, UV spectroscopy, Mass Spectromety, Nuclear Magnetic Resonance, HPLC and Size exclusion separations, Isothermal titration calorimetry as well as a number of other bio-physical and biological characterisation techniques. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Learning Materials will be made available on an online platform (web page or Moodle) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Learning Materials will be made available on an online platform (web page or Moodle) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Prerequisites / Notice This practical course is only for students enrolled in BCB. Additionally the following courses have to be successfully completed: 529-0016-00 P BCBIII Organic Chemistry (Praktikum) 529-0011-04 "Allgemeine Chemie (Praktikum)" 529-0051-00 "Analytische Chemie" I (3. Semester) 551-0128-00L Fundamentals of Biology I Furthermore, enrolment in parallel to the lab class, or completed in an earlier semester is requested for the following course: 529-0058-00 "Analytische Chemie II" (4. Semester) BCB Students should also be enrolled in "Instumentalanalyse organischer Verbindungen". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 529-0222-00L | Organic Chemistry II | 3 credits | 2V + 1U | B. Morandi, J. W. Bode | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | This course builds on the material learned in Organic Chemistry I or Organic Chemistry II for Biology/Pharmacy Students. Topics include advanced concepts and mechanisms of organic reactions and introductions to pericyclic and organometallic reactions. The basics or retro- and forward synthesis are also introduced. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Goals of this course include a deeper understanding of basic organic reactions and mechanisms as well as advanced transformations. Reactive intermediates including carbenes and nitrenes are covered, along with methods for their generation and use in complex molecule synthesis. Frontier molecular orbital theory (FMO) is introduced and used to rationalize pericyclic reactions including Diels Alder reactions, cycloadditions, and rearrangements (Cope, Claisen). The basic concepts and key reactions of catalytic organometallic chemistry, which are key methods in modern organic synthesis, are introduced, with an emphasis on their catalytic cycles and elementary steps. All of these topics are combined in an overview of strategies for complex molecule synthesis, with specific examples from natural product derived molecules used as medicines. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Content | Redox neutral reactions and rearrangements, advanced transformations of functional groups and reaction mechanisms, carbenes and nitrenes, frontier molecular orbital theory (FMO), cycloadditions and pericyclic reactions, introduction to organometallic chemistry and catalytic cross couplings, protecting groups, retrosynthetic analysis of complex organic molecules, planning and execution of multi-step reactions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | The lecture notes and additional documents including problem sets are available as PDF files online, without charge. Link: https://morandi.ethz.ch/education.html | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Clayden, Greeves, and Warren. Organic Chemistry, 2nd Edition. Oxford University Press, 2012. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 529-0290-00L | Organic Chemistry (Seminar) | 0 credits | 2S | J. W. Bode, E. M. Carreira, H. Wennemers, R. Zenobi | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Seminars on Current Topics in Organic Chemistry, Chemical Biology, and Analytical Chemistry. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Awareness of contemporary trends in science. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 529-0299-00L | Organic Chemistry | 0 credits | 1.5K | J. W. Bode, E. M. Carreira, P. Chen, K. Lang, B. Morandi, H. Wennemers, R. Zenobi | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Updates on Research and Contemporary Literature in Organic Chemistry and Chemical Biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Problem solving in organic chemistry and chemical biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||