Search result: Catalogue data in Autumn Semester 2017
Biology Master  | ||||||
 Elective Major Subject Areas | ||||||
| Elective Major: Structural Biology and Biophysics | ||||||
| Compulsory Concept Courses | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|---|
| 551-0307-00L | Molecular and Structural Biology I: Protein Structure and Function D-BIOL students are obliged to take part I and part II (next semester) as a two-semester course | O | 3 credits | 2V | R. Glockshuber, K. Locher, E. Weber-Ban | |
| Abstract | Biophysics of protein folding, membrane proteins and biophysics of membranes, enzymatic catalysis, catalytic RNA and RNAi, current topics in protein biophysics and structural biology. | |||||
| Objective | Understanding of structure-function relationships in proteins and in protein folding, detailed understanding of biophysics and physical methods as well as modern methods for protein purification and microanalytics. | |||||
| Lecture notes | Scripts on the individual topics can be found under http://www.mol.biol.ethz.ch/teaching. | |||||
| Literature | Basics: - Creighton, T.E., Proteins, Freeman, (1993) - Fersht, A., Enzyme, Structure and Mechanism in Protein Science (1999), Freeman. - Berg, Tymoczko, Stryer: Biochemistry (5th edition), Freeman (2001). Current topics: References will be given during the lectures. . | |||||
| Elective Compulsory Concept Courses See D-BIOL Master Studies Guide | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 551-0319-00L | Cellular Biochemistry (Part I) | W | 3 credits | 2V | U. Kutay, R. I. Enchev, B. Kornmann, M. Peter, I. Zemp, further lecturers | |
| Abstract | Concepts and molecular mechanisms underlying the biochemistry of the cell, providing advanced insights into structure, function and regulation of individual cell components. Particular emphasis will be put on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes such as intracellular transport, cell division & growth, and cell migration. | |||||
| Objective | The full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterisation of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry. The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain the integration of different molecules and signaling pathways into complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, cell division and cell growth. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer. | |||||
| Content | Structural and functional details of individual cell components, regulation of their interactions, and various aspects of the regulation and compartmentalisation of biochemical processes. Topics include: biophysical and electrical properties of membranes; viral membranes; structural and functional insights into intracellular transport and targeting; vesicular trafficking and phagocytosis; post-transcriptional regulation of gene expression. | |||||
| Lecture notes | Scripts and additional material will be provided during the semester. Please contact Dr. Alicia Smith for assistance with the learning materials. (alicia.smith@bc.biol.ethz.ch) | |||||
| Literature | Recommended supplementary literature (review articles and selected primary literature) will be provided during the course. | |||||
| Prerequisites / Notice | To attend this course the students must have a solid basic knowledge in chemistry, biochemistry and general biology. The course will be taught in English. | |||||
| 529-0731-00L | Nucleic Acids and Carbohydrates | W | 6 credits | 3G | D. Hilvert, P. A. Kast, S. J. Sturla, H. Wennemers | |
| Abstract | Structure, function and chemistry of nucleic acids and carbohydrates. DNA/RNA structure and synthesis; recombinant DNA technology and PCR; DNA arrays and genomics; antisense approach and RNAi; polymerases and transcription factors; catalytic RNA; DNA damage and repair; carbohydrate structure and synthesis; carbohydrate arrays; cell surface engineering; carbohydrate vaccines | |||||
| Objective | Structure, function and chemistry of nucleic acids and carbohydrates. DNA/RNA structure and synthesis; recombinant DNA technology and PCR; DNA arrays and genomics; antisense approach and RNAi; polymerases and transcription factors; catalytic RNA; DNA damage and repair; carbohydrate structure and synthesis; carbohydrate arrays; cell surface engineering; carbohydrate vaccines | |||||
| Content | Structure, function and chemistry of nucleic acids and carbohydrates. DNA/RNA structure and synthesis; recombinant DNA technology and PCR; DNA arrays and genomics; antisense approach and RNAi; polymerases and transcription factors; catalytic RNA; DNA damage and repair; carbohydrate structure and synthesis; carbohydrate arrays; cell surface engineering; carbohydrate vaccines | |||||
| Lecture notes | No script; illustrations from the original literature relevant to the individual lectures will be provided weekly (typically as handouts downloadable from the Moodle server). | |||||
| Literature | Mainly based on original literature, a detailed list will be distributed during the lecture | |||||
| 551-0313-00L | Microbiology (Part I) | W | 3 credits | 2V | W.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel, M. Pilhofer | |
| Abstract | Advanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
| Objective | This concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
| Content | Advanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
| Lecture notes | Updated handouts will be provided during the class. | |||||
| Literature | Current literature references will be provided during the lectures. | |||||
| Prerequisites / Notice | English The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture. | |||||
| 551-0309-00L | Concepts in Modern Genetics | W | 6 credits | 4V | Y. Barral, D. Bopp, A. Hajnal, M. Stoffel, O. Voinnet | |
| Abstract | Concepts of modern genetics and genomics, including principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference. | |||||
| Objective | This course focuses on the concepts of classical and modern genetics and genomics. | |||||
| Content | The topics include principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference. | |||||
| Lecture notes | Scripts and additional material will be provided during the semester. | |||||
| Elective Compulsory Master Courses | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 529-0733-00L | Enzymes | W | 7 credits | 3G | D. Hilvert | |
| Abstract | Principles of enzymatic catalysis, enzyme kinetics, mechanisms of enzyme-catalyzed reactions (group transfer reactions, carbon-carbon bond formation, eliminations, isomerisations and rearrangements), cofactor chemistry, enzymes in organic synthesis and the biosynthesis of natural products, catalytic antibodies. | |||||
| Objective | Overview of enzymes, enzyme-catalyzed reactions and metabolic processes. | |||||
| Content | Principles of enzymatic catalysis, enzyme kinetics, mechanisms of enzyme catalyzed reactions (group transfer reactions, carbon-carbon bond formation, eliminations, isomerisations and rearrangements), cofactor chemistry, enzymes in organic synthesis and the biosynthesis of natural products, catalytic antibodies. | |||||
| Lecture notes | A script will not be handed out. | |||||
| Literature | General: T. Bugg, An Introduction to Enzyme and Coenzyme Chemistry, Blackwell Science Ltd., Oxford, 1997. In addition, citations from the original literature relevant to the individual lectures will be assigned weekly. | |||||
| 551-1105-00L | Glycobiology | W | 4 credits | 2V | M. Aebi, T. Hennet | |
| Abstract | Structural principles, nomenclature and different classes of glycosylation. The different pathways of N- and O-linked protein glycosylation and glycolipid biosynthesis in prokaryotes and eukaryotes are discussed. Specific glycan binding proteins and their role in deciphering the glycan code are presented. The role of glycans in infectious diseases, antigen mimicry and autoimmunity are discussed. | |||||
| Objective | Detailed knowledge in 1) the different areas of prokaryotic and eukaryotic glycobiology, in particular in the biosynthesis of glycoproteins and glycolipids, 2) the cellular machinery required for these pathways, 3) the principles of carbohydrate/protein interaction, 4) the function of lectins, 5) the role of glycans in infectious disease. | |||||
| Content | Structure and linkages; analytical approaches; N-linked protein glycosylation (ER, Golgi); glycan-assisted protein folding and quality control; O-linked protein glycosylation; glucosaminoglycans; glycolipids; prokaryotic glycosylation pathways; lectins; glycans and infectious disease | |||||
| Lecture notes | handouts | |||||
| Literature | Introduction to Glycobiology; M.E.Taylor, K.Drickamer, Oxford University Press, 2003 Essentials of Glycobiology (second edition); A.Varki et al. Cold Spring Harbor Laboratory Press, 2009 | |||||
| Prerequisites / Notice | The course will be in English. It will include the preparation of short essays (marked) about defined topics in Glycobiology. | |||||
| 551-1103-00L | Microbial Biochemistry | W | 4 credits | 2V | J. Vorholt-Zambelli, J. Piel | |
| Abstract | The lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms. Emphasis is on processes that are specific to bacteria and archaea and that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest. | |||||
| Objective | The lecture course aims at providing an advanced understanding of the physiology and metabolism of microorganisms. | |||||
| Content | Important biochemical processes specific to bacteria and archaea will be presented that contribute to the widespread occurrence of prokaryotes. Applied aspects of microbial biochemistry will be pointed out as well as research fields of current scientific interest. Emphasis is on concepts of energy generation and assimilation. List of topics: Eating sugars and letting them in Challenging: Aromatics, xenobiotics, and oil Complex: (Ligno-)Cellulose and in demand for bioenergy Living on a diet and the anaplerotic provocation Of climate relevance: The microbial C1 cycle What are AMO and Anammox? 20 amino acids: the making of Extending the genetic code The 21st and 22nd amino acid Some exotic biochemistry: nucleotides, cofactors Ancient biochemistry? Iron-sulfur clusters, polymers Secondary metabolites: playground of evolution | |||||
| Lecture notes | A script will be provided during the course. | |||||
| 551-1401-00L | Advanced Protein Engineering (University of Zurich) No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH. UZH Module Code: BCH420 Restricted to max. 10 students from ETH Mind the enrolment deadlines at UZH: https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html | W | 2 credits | 2G | A. Plückthun | |
| Abstract | Introduction into current research strategies in protein science. | |||||
| Objective | To understand current research strategies in protein science. | |||||
| Content | Proteins have become an object of intense study in modern science, raging from their use as therapeutics to elucidating their structure and function in the cell. Moreover, it is now possible to engineer and evolve tailor-made proteins, opening up many new areas of science. This course will attempt to cover the frontiers and remaining challenges, emphasizing the biochemical foundations of the various approaches. | |||||
| Lecture notes | Slides and references will be available on OLAT server. https://www.olat.uzh.ch/olat/auth/repo/go?rid=600670219 | |||||
| Literature | PDFs will be available on OLAT server. https://www.olat.uzh.ch/olat/auth/repo/go?rid=600670219 | |||||
| Prerequisites / Notice | Solid knowledge in biochemistry strongly recommended | |||||
| 551-1153-00L | Systems Biology of Metabolism Number of participants limited to 15. | W | 4 credits | 2V | U. Sauer, N. Zamboni, M. Zampieri | |
| Abstract | Starting from contemporary biological problems related to metabolism, the course focuses on systems biological approaches to address them. In a problem-oriented, this-is-how-it-is-done manner, we thereby teach modern methods and concepts. | |||||
| Objective | Develop a deeper understanding of how relevant biological problems can be solved, thereby providing advanced insights to key experimental and computational methods in systems biology. | |||||
| Content | The course will be given as a mixture of lectures, studies of original research and guided discussions that focus on current research topics. For each particular problem studied, we will work out how the various methods work and what their capabilities/limits are. The problem areas range from microbial metabolism to cancer cell metabolism and from metabolic networks to regulation networks in populations and single cells. Key methods to be covered are various modeling approaches, metabolic flux analyses, metabolomics and other omics. | |||||
| Lecture notes | Script and original publications will be supplied during the course. | |||||
| Prerequisites / Notice | The course extends many of the generally introduced concepts and methods of the Concept Course in Systems Biology. It requires a good knowledge of biochemistry and basics of mathematics and chemistry. | |||||
| 529-0004-00L | Computer Simulation in Chemistry, Biology and Physics | W | 7 credits | 4G | P. H. Hünenberger | |
| Abstract | Molecular models, Force fields, Boundary conditions, Electrostatic interactions, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation. | |||||
| Objective | Introduction to computer simulation of (bio)molecular systems, development of skills to carry out and interpret computer simulations of biomolecular systems. | |||||
| Content | Molecular models, Force fields, Spatial boundary conditions, Calculation of Coulomb forces, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation. | |||||
| Lecture notes | Available (copies of powerpoint slides distributed before each lecture) | |||||
| Literature | See: www.csms.ethz.ch/education/CSCBP | |||||
| Prerequisites / Notice | Since the exercises on the computer do convey and test essentially different skills as those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam. For more information about the lecture: www.csms.ethz.ch/education/CSCBP | |||||
| 401-0649-00L | Applied Statistical Regression | W | 5 credits | 2V + 1U | M. Dettling | |
| Abstract | This course offers a practically oriented introduction into regression modeling methods. The basic concepts and some mathematical background are included, with the emphasis lying in learning "good practice" that can be applied in every student's own projects and daily work life. A special focus will be laid in the use of the statistical software package R for regression analysis. | |||||
| Objective | The students acquire advanced practical skills in linear regression analysis and are also familiar with its extensions to generalized linear modeling. | |||||
| Content | The course starts with the basics of linear modeling, and then proceeds to parameter estimation, tests, confidence intervals, residual analysis, model choice, and prediction. More rarely touched but practically relevant topics that will be covered include variable transformations, multicollinearity problems and model interpretation, as well as general modeling strategies. The last third of the course is dedicated to an introduction to generalized linear models: this includes the generalized additive model, logistic regression for binary response variables, binomial regression for grouped data and poisson regression for count data. | |||||
| Lecture notes | A script will be available. | |||||
| Literature | Faraway (2005): Linear Models with R Faraway (2006): Extending the Linear Model with R Draper & Smith (1998): Applied Regression Analysis Fox (2008): Applied Regression Analysis and GLMs Montgomery et al. (2006): Introduction to Linear Regression Analysis | |||||
| Prerequisites / Notice | The exercises, but also the classes will be based on procedures from the freely available, open-source statistical software package R, for which an introduction will be held. In the Mathematics Bachelor and Master programmes, the two course units 401-0649-00L "Applied Statistical Regression" and 401-3622-00L "Regression" are mutually exclusive. Registration for the examination of one of these two course units is only allowed if you have not registered for the examination of the other course unit. | |||||
| 401-6215-00L | Using R for Data Analysis and Graphics (Part I) | W | 1.5 credits | 1G | A. Drewek, M. Mächler | |
| Abstract | The course provides the first part an introduction to the statistical software R for scientists. Topics covered are data generation and selection, graphical and basic statistical functions, creating simple functions, basic types of objects. | |||||
| Objective | The students will be able to use the software R for simple data analysis. | |||||
| Content | The course provides the first part of an introduction to the statistical software R for scientists. R is free software that contains a huge collection of functions with focus on statistics and graphics. If one wants to use R one has to learn the programming language R - on very rudimentary level. The course aims to facilitate this by providing a basic introduction to R. Part I of the course covers the following topics: - What is R? - R Basics: reading and writing data from/to files, creating vectors & matrices, selecting elements of dataframes, vectors and matrices, arithmetics; - Types of data: numeric, character, logical and categorical data, missing values; - Simple (statistical) functions: summary, mean, var, etc., simple statistical tests; - Writing simple functions; - Introduction to graphics: scatter-, boxplots and other high-level plotting functions, embellishing plots by title, axis labels, etc., adding elements (lines, points) to existing plots. The course focuses on practical work at the computer. We will make use of the graphical user interface RStudio: www.rstudio.org Note: Part I of UsingR is complemented and extended by Part II, which is offered during the second part of the semester and which can be taken independently from Part I. | |||||
| Lecture notes | An Introduction to R. http://stat.ethz.ch/CRAN/doc/contrib/Lam-IntroductionToR_LHL.pdf | |||||
| Prerequisites / Notice | The course resources will be provided via the Moodle web learning platform Please login (with your ETH (or other University) username+password) at https://moodle-app2.let.ethz.ch/enrol/users.php?id=1145 Choose the course "Using R for Data Analysis and Graphics" and follow the instructions for registration. | |||||
| 529-0041-00L | Modern Mass Spectrometry, Hyphenated Methods, and Chemometrics | W | 6 credits | 3G | R. Zenobi, M. Badertscher, B. Hattendorf | |
| Abstract | Modern mass spectrometry, hyphenated analytical methods, speciation, methods of surface analysis, chemometrics. | |||||
| Objective | Comprehensive knowledge about the analytical methods introduced in this course, and their applications. | |||||
| Content | Coupling of separation with identification methods such as GC-MS, LC-MS, GC-IR, LC-IR, LC-NMR etc.; importance of speciation. Modern mass spectrometry: Time of flight and ion cyclotron resonance mass spectrometry, ICP-MS. Soft ionization methods, desorption methods, spray methods. Methods of surface analysis (ESCA, Auger, SIMS, raster microscopy methods). Employment of computer science for processing data in chemical analysis (chemometrics). | |||||
| Lecture notes | lecture notes will be available in the lecture at production cost. | |||||
| Literature | information about relevant literature will be available in the lecture & in the lecture notes. | |||||
| Prerequisites / Notice | Exercises are an integral part of the lecture. Prerequisites: 529-0051-00 "Analytische Chemie I (3. Semester)" 529-0058-00 "Analytische Chemie II (4. Semester)" (or equivalent) | |||||
| 551-1411-00L | Molecular and Structural Biology III: Current Topics  The course will only take place with a minimum of 6 participants. | W | 2 credits | 1V | K. Locher, F. Allain, N. Ban, R. Glockshuber, M. Pilhofer, E. Weber-Ban | |
| Abstract | The course discusses current topics and cutting edge research in the structural, molecular, and biochemical study of cellular macromolecules. Student participation is an essential component of the course and will contribute to the exam grade | |||||
| Objective | The goal is to discuss cutting edge research in the structural, molecular, and biochemical study of cellular macromolecules. Students will also have an opportunity to present and discuss recent breakthroughs relevant to the research fields presented by the faculty teaching the course (see http://www.mol.biol.ethz.ch/research.html for details on the topics). | |||||
| Literature | Will be distributed by the instructors | |||||
| 551-1409-00L | RNA Biology Lecture Series II: Non-coding RNAs: Biology and Therapeutics | W | 4 credits | 2V | J. Hall, M. Stoffel, further lecturers | |
| Abstract | This course covers aspects of RNA biology related to the functions of non-coding RNAs as well as their use as drugs to treat diseases. | |||||
| Objective | The students should get familiar with the wide array of roles, which non-coding RNAs play in cellular functions. | |||||
| Content | Micro RNAs; computational approaches to miRNAs; micro RNA function in metabolism; viruses and viral RNAs; nucleic acid-based drugs; ncRNA-mediated genome regulation; epigenetic programming of genome remodelling in ciliates; telomerase and telomeres; tRNA biology. http://www.nccr-rna-and-disease.ch/tiki-index.php?page=LectureSeries | |||||
| Prerequisites / Notice | Basic knowledge of cell and molecular biology. | |||||
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