Kaspar Locher: Catalogue data in Spring Semester 2020
|Name||Prof. Dr. Kaspar Locher|
|Field||Molecular Membrane Biology|
Inst. f. Molekularbiol.u.Biophysik
ETH Zürich, HPK G 11
|Telephone||+41 44 633 39 91|
|551-1323-AAL||Fundamentals of Biology II: Biochemistry and Molecular Biology|
Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement.
Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit.
|4 credits||11R||K. Locher, N. Ban, R. Glockshuber, E. Weber-Ban|
|Abstract||The course provides an introduction to Biochemistry / Molecular Biology with some emphasis on chemical and biophysical aspects.|
|Objective||Topics include the structure-function|
relationship of proteins / nucleic acids, protein folding, enzymatic catalysis, cellular pathways involved in bioenergetics and the biosynthesis and breakdown of amino acids, glycans, nucleotides, fatty acids and phospholipids, and steroids. There will also be a discussion of DNA replication and repair, transcription, and translation.
Berg/Tymoczko/Stryer, 8th edition, Palgrave Macmillan, International edition
|551-1412-00L||Molecular and Structural Biology IV: Visualizing Macromolecules by X-Ray Crystallography and EM||4 credits||2V||N. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich, further lecturers|
|Abstract||This course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models.|
|Objective||Students will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement.|
|Content||- History of Structural Molecular Biology|
- X-ray diffraction from macromolecular crystals
- Data collection and statistics, phasing methods
- Crystal symmetry and space groups
- X-ray data processing
- Principle of cryo-EM for biological macromolecules I, including hardware of TEM and detectors, image formation principle (phase contrast, spherical aberration, CTF), 3D reconstruction (central-section theorem, backprojection, missing information)
- Single particle analysis, including principle (projection matching, random conical tilt, angular reconstitution)
- Tomography I, including basics and subtomogram averaging
- Tomography - recent techniques, including cryo-FIB
- EM specimen preparation (cryo, negative stain), initial EM data processing
- EM and X-ray structure building, refinement, validation and interpretation
- Model building and refinement
|551-1556-00L||Macromolecular Structure Determination Using Modern Methods |
Number of participants limited to 11 in the 3rd semester quarter of the spring semester
Number of participants limited to 12 in the 4th semester quarter of the spring semester
The block course will only take place with a minimum of 4 participants.
The enrolment is done by the D-BIOL study administration.
|6 credits||7G||K. Locher, G. Schertler|
|Abstract||This course will expose the students to two prominent techniques for high-resolution structural characterization of biological macromolecules. The students will have the opportunity to get hands-on experience in either cryo-electron microscopy (ETH) or X-ray crystallography (PSI).|
|Objective||The goal of this course is to introduce the students to the principles of high-resolution structure determination. Students will conduct hands-on experiments and use computational techniques for data processing.|
|Content||At the ETH the students will prepare and vitrify a protein and then image it on a cryo-TEM. Next, the students will process the data and build an atomic model into the EM map. |
At the PSI the students will purify and crystallize a membrane protein, collect X-ray diffraction data using synchrotron X-ray source or with cryo-EM, analyze and build an atomic model into a density map. They will refine this model and interpret and illustrate the determined structure. The course work is trying to present insights in the use of structural information. The course also includes a demonstration of the Synchrotron capabilities at the Paul Scherrer Institute (SLS).
|Prerequisites / Notice||The students will be split into two groups for the practical part of the work: One group will work at ETH Hönggerberg, the other at the Paul Scherrer Institute (PSI) at Villigen. All students will spend one full day at the PSI for a tour of the facilities, including a visit of the synchrotron beam lines of the Swiss Light Source SLS.|
The students joining the ETH Hönggerberg group will spend the majority of the time on data processing and are therefore expected to have some basic knowledge of bash terminal commands. Basic physics, optics and linear algebra knowledge is also helpful. By the end of the course, the students will be expected to understand concepts such as the difference between Fourier and real space, image formation, contrast transfer, fast Fourier transfer and Fourier shell correlation.
|551-1620-00L||Molecular Biology, Biophysics||1 credit||1K||R. Glockshuber, F. Allain, N. Ban, K. Locher, E. Weber-Ban, K. Wüthrich|
|Abstract||The course consists of a series of research seminars on Structural Biology and Biophysics, given by both scientists of the National Center of Competence in Research (NCCR) in Structural Biology and external speakers.|
|Objective||The goal of this course is to provide doctoral and postdoctoral students with a broad overview on the most recent developments in biochemistry, structural biology and biophysics.|
|Prerequisites / Notice||Information on the individual seminars is provided on the following websites:|