Search result: Catalogue data in Autumn Semester 2023
Biochemistry - Chemical Biology Master ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Number | Title | Type | ECTS | Hours | Lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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535-0030-00L | Pharmaceutical Immunology II & Therapeutic Proteins ![]() Prerequisites: Either 535-0830-00L Pharmaceutical Immunology I or 551-0317-00L Immunology I must have been taken. | W | 3 credits | 3G | C. Halin Winter, D. Neri | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | In this course, various topics related to the development, GMP production and application of therapeutic proteins will be discussed. Furthermore, students will expand their training in pharmaceutical immunology and will be introduced to the basic concepts of pharmaceutical product quality management. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Students know and understand: - basic mechanisms and regulation of the immune response - the pathogenic mechanisms of the most important immune-mediated disorders - the concepts of vaccination and cancer immunotherapy - the most frequently used expression systems for the production of therapeutic proteins - the use of protein engineering tools for modifying different features of therapeutic proteins - the mechanism of action of selected therapeutic proteins and their application - basic concepts in the GMP production of therapeutic proteins | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | The course consists of two parts: In the first part, students will complete their training in Pharmaceutical Immunology. This part particularly focuses on the pathogenic mechanisms of immune-mediated diseases, vaccination and cancer immunotherapy. Deepened knowledge of immunology will be relevant for understanding the mechanism of action of many therapeutic proteins, as well as for understanding one major concern related to the use of protein-based drugs, namely, immunogenicity. The second part focuses on topics related to the development and application of therapeutic proteins, such as protein expression, protein engineering, reducing immunogenicity, and GMP production of therapeutic proteins. Furthermore, selected examples of approved therapeutic proteins will be discussed. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Handouts to the lectures will be available for downloading under http://www.pharma.ethz.ch/scripts/index | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | - Janeway's ImmunoBiology, by Kenneth Murphy (9th or 10th Edition) - Lecture Handouts - Paper References provided in the Scripts - EMEA Dossier for Humira | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Prerequisites: Either 535-0830-00L Pharmaceutical Immunology I or 551-0317-00L Immunology I | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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535-0230-00L | Medicinal Chemistry I | W | 2 credits | 2V | J. Hall | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | The lectures give an overview of selected drugs and the molecular mechanisms underlying their therapeutic effects in disease. The historical and modern-day methods by which these drugs were discovered and developed are described. Structure-function relationships and the biophysical rules underlying ligand-target interactions will be discussed and illustrated with examples. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Basic understanding of therapeutic agents with respect to molecular, pharmacological and pharmaceutical properties. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Molecular mechanisms of action of drugs. Structure function and biophysical basis of ligand-target interactions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Will be provided in parts before each individual lecture. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | - G.L. Patrick, "An Introduction to Medicinal Chemistry", 5th edition, Oxford University Press - D. Steinhilber, M. Schubert-Zsilavecz, H.J. Roth, "Medizinische Chemie", Deutscher Apotheker Verlag Stuttgart (2005) - J.H. Block, J.M. Beale, "Organic Medicinal and Pharmaceutical Chemistry", 11th edition, Lippincott, Williams, Wilkins (2002) - A. Gringauz, "How Drugs Act and Why", Wiley (1997) - R. B. Silverman and M. W. Holladay, "The Organic Chemistry of Drug Design and Drug Action", 3rd edition, Elsevier | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Requirements: Knowledge of physical and organic chemistry, biochemistry and biology. Attendance of Medicinal Chemistry II in the spring semester. For Pharmacy and non-Pharmacy students, Medicinal Chemistry I and II are examined in a SINGLE examination (Jahresprüfung). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-0313-00L | Microbiology (Part I) | W | 3 credits | 2V | W.‑D. Hardt, L. Eberl, B. Nguyen, J. Piel, M. Pilhofer, A. Vagstad | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Advanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
529-0041-00L | Modern Mass Spectrometry, Hyphenated Methods, and Chemometrics | W | 6 credits | 3G | R. Zenobi, B. Hattendorf, P. Sinués Martinez-Lozano | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Modern mass spectrometry, hyphenated analytical methods, speciation, chemometrics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Comprehensive knowledge about the analytical methods introduced in this course and their practical applications. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Hyphenation 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, orbitrap and ion cyclotron resonance mass spectrometry, ICP-MS. Soft ionization methods, desorption methods, spray methods. Mass spectrometry imaging. Use of statistical and computer-assisted methods for processing analytical data (chemometrics). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Lecture notes will be made available online. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-1299-00L | Bioinformatics ![]() | W | 6 credits | 4G | S. Sunagawa, P. Beltrao, V. Boeva, A. Kahles, C. von Mering, N. Zamboni | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Students will study bioinformatic concepts in the areas of metagenomics, genomics, transcriptomics, proteomics, biological networks and biostatistics. Through integrated lectures, practical hands-on exercises and project work, students will also be trained in analytical and programming skills to meet the emerging increase in data-driven knowledge generation in biology in the 21st century. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Students will have an advanced understanding of the underlying concepts behind modern bioinformatic analyses at genome, metagenome and proteome-wide scales. They will be familiar with the most common data types, where to access them, and how to analytically work with them to address contemporary questions in the field of biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Course participants have already acquired basic programming skills in UNIX, Python and R. Students bring their own computer with keyboard, internet access (browser) and software to connect to the ETH network via VPN. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-0319-00L | Cellular Biochemistry (Part I) | W | 3 credits | 2V | U. Kutay, F. Allain, T. Kleele, I. Zemp | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-0309-00L | Concepts in Modern Genetics Information for UZH students: Enrolment to this course unit only possible at ETH. No enrolment to module BIO348 at UZH. Please mind the ETH enrolment deadlines for UZH students: Link | W | 6 credits | 4V | Y. Barral, D. Bopp, A. Hajnal, 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning 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. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-0317-00L | Immunology I | W | 3 credits | 2V | M. Kopf, A. Oxenius | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Introduction into structural and functional aspects of the immune system. Basic knowledge of the mechanisms and the regulation of an immune response. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Introduction into structural and functional aspects of the immune system. Basic knowledge of the mechanisms and the regulation of an immune response. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | - Introduction and historical background - Innate and adaptive immunity, Cells and organs of the immune system - B cells and antibodies - Generation of diversity - Antigen presentation and Major Histoincompatibility (MHC) antigens - Thymus and T cell selection - Autoimmunity - Cytotoxic T cells and NK cells - Th1 and Th2 cells, regulatory T cells - Allergies - Hypersensitivities - Vaccines, immune-therapeutic interventions | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Electronic access to the documentation will be provided. The link can be found at "Lernmaterialien" | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | - Kuby, Immunology, 9th edition, Freemen + Co., New York, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | For D-BIOL students Immunology I (WS) and Immunology II (SS) will be examined as one learning entity in a "Sessionsprüfung". All other students write separate exams for Immunology I and Immunology II. All exams (combined exam Immunology I and II, individual exams) are offered in each exam session. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-0127-00L | Fundamentals of Biology III: Multicellularity | W | 8 credits | 6G | M. Stoffel, M. Künzler, O. Y. Martin, U. Suter, S. Werner, A. Wutz, S. C. Zeeman | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | The lecture conveys the fundamental concepts underlying multicellularity with an emphasis on the molecular basis of multicellular biological systems and their functional integration into coherent wholes. The structural and functional specialization in multicellular organisms will be discussed by highlighting common and specific functions in fungi, plants, and animals (including humans). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | 1.Students can describe advantages and challenges associated with being multicellular and outline independent solutions that organisms have developed to cope with the challenges of complex multicellularity . 2.Students can explain how the internal and external structures of fungi, plants and animals function to support survival, growth, behavior, and reproduction. 3.Students can explain the basic pathways and mechanisms of cellular communication regulating cellular behavior (cell adhesion, metabolism, proliferation, reproduction, development). 4.Students can describe how a single cell develops from one cell into many, each with different specialized functions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | The lecture introduces the structural and functional specialization in fungi, plants and animals, including humans. After providing an overview on the diversity of eukaryotic organisms, the lecture will discuss how fungi, plants, animals and humans have evolved structures and strategies to cope with the challenges of multicellularity. The molecular basis underlying communication, coordination and differentiation will be conveyed and complemented by key aspects of reproduction, metabolism development, and regeneration. Topics include form and function of fungi and plants, human anatomy and physiology, metabolism, cell signaling, adhesion, stem cells, regeneration, reproduction, and development. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | Alberts et al. 'Molecular Biology of the Cell' 6th edition Smith A.M., et al. “Plant Biology” Garland Science, New York, Oxford Campbell “Biology”, 11th Edition | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Some lecture are held in English. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-1005-00L | Bioanalytics ![]() | W | 4 credits | 4G | P. Picotti, F. Allain, V. Korkhov, M. Pilhofer, R. Schlapbach, K. Weis, K. Wüthrich, further lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | The course will introduce students to a selected set of laboratory techniques that are foundational to modern biological research. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | For each of the techniques covered in the course, the students will be able to explain: a) the physical, chemical and biological principles underlying the technique, b) the requirements for the sample, c) the type of raw data collected by the technique, d) the assumptions and auxiliarry information used in the interpretation of the data and e) how these data can be used to answer a given biological question. By the end of the course the students will be able to select the appropriate experimental technique to answer a given biological problem and will be able to discuss the advantages and limitations of individual techniques as well as how different techniques can be combined to gain a more complete understanding of a given biological questions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | The course will be based on a combination of lectures, selfstudy elements and exercises. The focus will be on the following experimental techniques: - DNA sequencing - chromatography - mass-spectrometry - UV/Vis and fluorescence spectrometry - light microscopy - electron microscopy - X-ray crystallography - NMR spectroscopy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | The course is supported by a Moodle page that gives access to all supporting materials necessary for the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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529-0004-01L | Classical Simulation of (Bio)Molecular Systems ![]() | W | 6 credits | 4G | P. H. Hünenberger, J. Dolenc, S. Riniker | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Introduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Molecular models, classical force fields, configuration sampling, molecular dynamics simulation, boundary conditions, electrostatic interactions, analysis of trajectories, free-energy calculations, structure refinement, applications in chemistry and biology. Exercises: hands-on computer exercises for learning progressively how to perform an analyze classical simulations (using the package GROMOS). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | The powerpoint slides of the lectures will be made available weekly on the website in pdf format (on the day preceding each lecture). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | See: www.csms.ethz.ch/education/CSBMS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Since the exercises on the computer do convey and test essentially different skills than 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 (learning component, possible bonus of up to 0.25 points on the exam mark). For more information about the lecture: www.csms.ethz.ch/education/CSBMS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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529-0043-01L | Analytical Strategy | W | 6 credits | 3G | R. Zenobi, K. Eyer, S. Giannoukos, D. Günther | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Problem-oriented development of analytical strategies and solutions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Ability to create solutions for particular analytical problems. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Individual development of strategies for the optimal application of chemical, biochemical, and physico-chemical methods in analytical chemistry solving predefined problems. Experts from industry and administration present particular problems in their field of activity. Principles of sampling. Design and application of microanalytical systems. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Copies of problem sets and solutions will be distributed free fo charge | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Prerequisites: 529-0051-00 "Analytical Chemistry I (3. Semester)" 529-0058-00 "Analytical Chemistry II (4. Semester)" (or equivalent) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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529-0615-01L | Biochemical and Polymer Reaction Engineering | W | 6 credits | 3G | P. Arosio | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Polymerization reactions and processes. Homogeneous and heterogeneous (emulsion) kinetics of free radical polymerization. Post treatment of polymer colloids. Bioprocesses for the production of molecules and therapeutic proteins. Kinetics and design of aggregation processes of macromolecules and proteins. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | The aim of the course is to learn how to design polymerization reactors and bioreactors to produce polymers and proteins with the specific product qualities that are required by different applications in chemical, pharmaceutical and food industry. This activity includes the post-treatment of polymer latexes, the downstream processing of proteins and the analysis of their colloidal behavior. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | We will cover the fundamental processes and the operation units involved in the production of polymeric materials and proteins. In particular, the following topics are discussed: Overview on the different polymerization processes. Kinetics of free-radical polymerization and use of population balance models. Production of polymers with controlled characteristics in terms of molecular weight distribution. Kinetics and control of emulsion polymerization. Surfactants and colloidal stability. Aggregation kinetics and aggregate structure in conditions of diffusion and reaction limited aggregation. Modeling and design of colloid aggregation processes. Physico-chemical characterization of proteins and description of enzymatic reactions. Operation units in bioprocessing: upstream, reactor design and downstream. Industrial production of therapeutic proteins. Characterization and engineering of protein aggregation. Protein aggregation in biology and in biotechnology as functional materials. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Scripts are available on the web page of the Arosio-group: http://www.arosiogroup.ethz.ch/education.html Additional handout of slides will be provided during the lectures. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | R.J. Hunter, Foundations of Colloid Science, Oxford University Press, 2nd edition, 2001 D. Ramkrishna, Population Balances, Academic Press, 2000 H.W. Blanch, D. S. Clark, Biochemical Engineering, CRC Press, 1995 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
227-0939-00L | Cell Biophysics | W | 6 credits | 4G | T. Zambelli | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Applying two fundamental principles of thermodynamics (entropy maximization and Gibbs energy minimization), an analytical model is derived for a variety of biological phenomena at the molecular as well as cellular level, and critically compared with the corresponding experimental data in the literature. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Engineering uses the laws of physics to predict the behavior of a system. Biological systems are so diverse and complex prompting the question whether we can apply unifying concepts of theoretical physics coping with the multiplicity of life’s mechanisms. Objective of this course is to show that biological phenomena despite their variety can be analytically described using only two principles from statistical mechanics: maximization of the entropy and minimization of the Gibbs free energy. Starting point of the course is the probability theory, which enables to derive step-by-step the two pillars of thermodynamics from the perspective of statistical mechanics: the maximization of entropy according to the Boltzmann’s law as well as the minimization of the Gibbs free energy. Then, an assortment of biological phenomena at the molecular and cellular level (e.g. cytoskeletal polymerization, action potential, photosynthesis, gene regulation, morphogen patterning) will be examined at the light of these two principles with the aim to derive a quantitative expression describing their behavior. Each analytical model is finally validated by comparing it with the corresponding experimental results from the literature. By the end of the course, students will also learn to critically evaluate the concepts of making an assumption and making an approximation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | • Basics of theory of probability • Boltzmann's law • Entropy maximization and Gibbs free energy minimization • Ligand-receptor: two-state systems and the MWC model • Random walks, diffusion, crowding • Electrostatics for salty solutions • Elasticity: fibers and membranes • Molecular motors • Action potential: Hodgkin-Huxley model • Photosynthesis and vision • Gene regulation • Development: Turing patterns Theory and corresponding exercises are merged together during the classes. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | No lecture notes because the two proposed textbooks are more than exhaustive! An extra hour (Mon 17.00 o'clock - 18.00) will be proposed via ZOOM to solve together the exercises of the previous week. !!!!! I am using OneNote. All lectures and exercises will be broadcast via ZOOM (the link of the recordings will be available in Moodle on Fri, 22 Dec after the last lesson) !!!!! | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | • (Statistical Mechanics) K. Dill, S. Bromberg, "Molecular Driving Forces", 2nd Edition, Garland Science, 2010. • (Biophysics) R. Phillips, J. Kondev, J. Theriot, H. Garcia, "Physical Biology of the Cell", 2nd Edition, Garland Science, 2012. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Participants need a good command of • differentiation and integration of a function with one or more variables (basics of Analysis), • Newton's and Coulomb's laws (basics of Mechanics and Electrostatics). Notions of vectors in 2D and 3D are beneficial. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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529-0231-00L | Organic Chemistry III: Introduction to Asymmetric Synthesis | W | 4 credits | 3G | E. M. Carreira | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Methods of Asymmetric Synthesis | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Understanding of the basic principles of diastereoselective synthesis | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Conformational analysis: acyclic and cyclic systems; Diastereoselective sigmatropic rearrangements; Diastereoselective Carbonyl addition reactions: Cram- and Felkin-Anh models, carbonyl Lewis acid interactions, chelate controlled reactions; chemistry of enolates, selective formation; asymmetic enolate alkylation; aldol reactions, allyl- and crotyl-metal chemistry; cyclisations, Baldwin rules; Diastereoselective olefin functionalization: hydroboration, dihydroxylation, epoxidation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | E. M. Carreira and L. Kvaerno Classics in Stereoselective Synthesis, Wiley-VCH 2009 Evans' Problems in Organic Chemistry App | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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327-0312-00L | Materials Synthesis I - Polymers | W | 4 credits | 4G | A. Anastasaki, D. Opris | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | The course teaches the basics and terminology of polymer synthesis. To synthesize various polymeric materials, different polymerization techniques are required. This course will introduce representative polymerization methodologies and will discuss how they operate in order to yield materials with enhanced polymeric characteristics. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | 1) The students will be able to recognize different polymer types and associate them with their chemical structure and properties (i.e. rubber elasticity, glass transition temperature, etc.) 2) The students will become familiar with various synthetic methods to produce polymers of different architectures and topologies 3) The students will be exposed to different characterization methods (e.g. size exclusion chromatography, mass-spectrometry, nuclear magnetic resonance) that are necessary to confirm the successful synthesis and structure of a polymer 4) The students will understand the mechanism of selected polymerization methodologies 5) The students will be introduced to state-of-the-art polymer synthesis and recent literature examples will be critically discussed | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | conventional chain growth polymerization, living chain growth polymerization, step growth polymerization, polymeric architectures, molecular weight determination methods, polymer properties, polymerization mechanisms, polymer characterization methods | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Lecture slides with references to further literature will be available on Moodle | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | L. Mandelkern „An Introduction to Macromolecules“ J. M. G. Cowie “Polymers: Chemistry and Physics of Modern Materials publications mentioned on the slides | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
636-0108-00L | Biological Engineering and Biotechnology | W | 4 credits | 3V | M. Fussenegger | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Biological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Biological Engineering and Biotechnology will cover the latest biotechnological advances as well as their industrial implementation to engineer mammalian cells for use in human therapy. This lecture will provide forefront insights into key scientific aspects and the main points in industrial decision-making to bring a therapeutic from target to market. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | 1. Insight Into The Mammalian Cell Cycle. Cycling, The Balance Between Proliferation and Cancer - Implications For Biopharmaceutical Manufacturing. 2. The Licence To Kill. Apoptosis Regulatory Networks - Engineering of Survival Pathways To Increase Robustness of Production Cell Lines. 3. Everything Under Control I. Regulated Transgene Expression in Mammalian Cells - Facts and Future. 4. Secretion Engineering. The Traffic Jam getting out of the Cell. 5. From Target To Market. An Antibody's Journey From Cell Culture to The Clinics. 6. Biology and Malign Applications. Do Life Sciences Enable the Development of Biological Weapons? 7. Functional Food. Enjoy your Meal! 8. Industrial Genomics. Getting a Systems View on Nutrition and Health - An Industrial Perspective. 9. IP Management - Food Technology. Protecting Your Knowledge For Business. 10. Biopharmaceutical Manufacturing I. Introduction to Process Development. 11. Biopharmaceutical Manufacturing II. Up- stream Development. 12. Biopharmaceutical Manufacturing III. Downstream Development. 13. Biopharmaceutical Manufacturing IV. Pharma Development. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Lecture notes | Handout during the course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
529-0233-01L | Organic Synthesis: Methods and Strategies ![]() | W | 6 credits | 3G | E. M. Carreira | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | The complex relation between structural analysis, methods leading to desired transformations, and insight into reaction mechanisms is exemplified. Relations between retrosynthetic analysis of target structures, synthetic methods and their combination in a synthetic strategy. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Extension and deepening of the knowledge in organic synthesis and the principles of structure and reactivity. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Concepts of the planning of organic synthesis (strategy and tactics), retrosynthetic analysis. Structure-reactivity relation in the context of the synthesis of complex molecules. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Literature | K. C. Nicolaou, E. J. Sorensen, Classics in Total Synthesis, Wiley-VCH 1996. K. C. Nicolaou, S. A. Snyder, Classics in Total Synthesis II, Wiley-VCH 2003. K. C. Nicolaou, J. Chen, Classics in Total Synthesis III, Wiley-VCH 2011. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | OC I-IV | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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551-1407-00L | RNA Biology Lecture Series I: Transcription & Processing & Translation Does not take place this semester. | W | 4 credits | 2V | F. Allain, N. Ban, S. Jonas, U. Kutay, further lecturers | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | This course covers aspects of RNA biology related to gene expression at the posttranscriptional level. These include RNA transcription, processing, alternative splicing, editing, export and translation. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | The students should obtain an understanding of these processes, which are at work during gene expression. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Transcription & 3'end formation ; splicing, alternative splicing, RNA editing; the ribosome & translation, translation regulation, RNP biogenesis & nuclear export, mRNA surveillance & mRNA turnover; signal transduction & RNA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Prerequisites / Notice | Basic knowledge of cell and molecular biology. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
529-0132-00L | Inorganic Chemistry III: Organometallic Chemistry and Homogeneous Catalysis | W | 4 credits | 3G | M. Bezdek, C. Copéret | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Abstract | Fundamental aspects of the organometallic chemistry of the transition elements. Mechanistic homogeneous catalysis including oxidative additions, reductive eliminations and insertion reactions. Catalytic hydrogenation, carbonylation, C-C bond-forming and related reactions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning objective | Towards an understanding of the fundamental coordination-chemical and mechanistic aspects of transition-metal chemistry relevant to homogeneous catalysis. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Content | Fundamental aspects of the organometallic chemistry ot the transition elements. Mechanistic homogeneous catalysis including oxidative additions, reductive eliminations and insertion reactions. Catalytic hydrogenation, carbonylation, C-C bond-forming and related reactions. |
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