Search result: Catalogue data in Autumn Semester 2023

Biochemistry - Chemical Biology Master Information
Core Subjects and Compensatory Courses
Core Subjects
NumberTitleTypeECTSHoursLecturers
529-0733-02LChemical Biology and Synthetic BiochemistryO6 credits3GK. Lang, M. Fottner
AbstractOverview of modern chemical biology and synthetic biochemistry techniques, focussed on protein modification and labeling and on methods to endow proteins with novel functionalities.
Learning objectiveAfter taking this course, students should be capable of the following: A) Recall different possibilities for modifying proteins in vitro and in vivo and their applications in a biological context, B) Understand the chemical and biochemical consequences of modifications and assess the different reaction possibilities in the context of in vivo - in vitro, C) Critically analyze and assess current chemical biology articles D) Question the approaches learned and apply them to new biological problems.
Contentprinciples of protein labeling and protein modification (fluorescent proteins, enzyme-mediated labeling, bioorthogonal chemistries)

advanced genetic code expansion methods (amber suppression, orthogonal ribosomes, unnatural base pairs, genome engineering and genome editing)

directed evolution and protein engineering

chemical biology of ubiquitin and targeted protein degradation
Lecture notesA script will not be handed out. Handouts to the lecture will be provided through moodle.
LiteratureCitations from the original literature relevant to the individual lectures will be assigned during the lectures.
Prerequisites / NoticeKnowledge provided in the bachelor lectures 'Nucleic Acids and Carbohydrates' and 'Proteins and Lipids' is assumed for this lecture.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingfostered
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementfostered
Social CompetenciesCommunicationfostered
Cooperation and Teamworkfostered
Customer Orientationfostered
Leadership and Responsibilityfostered
Self-presentation and Social Influence fostered
Sensitivity to Diversityfostered
Negotiationfostered
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsfostered
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
529-0240-00LChemical Biology - PeptidesO6 credits3GH. Wennemers
AbstractAn advanced course on the synthesis, properties and function of peptides in chemistry and biology.
Learning objectiveKnowledge of the synthesis, properties and function of peptides in chemistry and biology.
ContentAdvanced peptide synthesis, conformational properties, combinatorial chemistry, therapeutic peptides, peptide based materials, peptides in nanotechnology, peptides in asymmetric catalysis.
Lecture notesCitations from the original literature relevant to the individual lectures will be assigned weekly.
LiteratureNorbert Sewald, Hans Dieter Jakubke "Peptides: Chemistry and Biology", 1st edition, Wiley VCH, 2002.
529-0241-10LSelectivity in Organic SynthesisO6 credits3GJ. W. Bode
AbstractFundamentals of selective organic reactions, including current and historical examples of enantioselectivity, regioselectivity, chemoselectivity. Further aspects include recent developments in catalysis, strategies and tools for selective organic synthesis.
Learning objectiveUnderstanding and explaining the origin of selectivity in organic synthesis and the application of selective organic reactions to the construction of complex organic and biological molecules.
ContentFundamental concepts and recent advances for the selective synthesis of complex organic molecules, including natural products, pharmaceuticals, and biological molecules. Key concepts include the development of enantioselective and regioselective catalysts, the identification of new reaction mechanisms and pathways, and technological advances for facilitating the synthesis of organic molecules. Analysis of key primarily literature including identification of trends, key precendents, and emerging topics will be emphasized.
Lecture noteswill be provided in class and online
LiteratureSuggesting Textbooks

Anslyn and Dougherty, Modern Physical Organic Chemistry, 1st Ed., University Science Books, 2006.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementfostered
Social CompetenciesCommunicationassessed
Cooperation and Teamworkfostered
Customer Orientationfostered
Leadership and Responsibilityfostered
Self-presentation and Social Influence fostered
Sensitivity to Diversityfostered
Negotiationfostered
Personal CompetenciesAdaptability and Flexibilityassessed
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsfostered
Compensatory Courses
Compensatory courses can be used to compensate for core subjects that have been failed twice. The assignment of the corresponding course units to the regulatory category "core subjects and compensatory courses" in the transcript of records is only made upon application by the student to the study administration office of the degree programme.
NumberTitleTypeECTSHoursLecturers
529-0615-01LBiochemical and Polymer Reaction EngineeringW6 credits3GP. Arosio
AbstractPolymerization 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 objectiveThe 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.
ContentWe 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 notesScripts 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.
LiteratureR.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
529-0243-01LTransition Metal Catalysis: From Mechanisms to Applications Information W6 credits3GB. Morandi
AbstractDetailed discussion of selected modern transition metal catalyzed reactions from a synthetic and mechanistic viewpoint
Learning objectiveUnderstanding and critical evaluation of current research in transition metal catalysis. Design of mechanistic experiments to elucidate reaction mechanisms. Synthetic relevance of transition metal catalysis. Students will also learn about writing an original research proposal during a workshop.
ContentDetailed discussion of selected modern transition metal catalyzed reactions from a synthetic and mechanistic viewpoint. Synthetic applications of these reactions. Introduction and application of tools for the elucidation of mechanisms. Selected examples of topics include: C-H activation, C-O activation, C-C activation, redox active ligands, main group redox catalysis, bimetallic catalysis.
Lecture notesLecture slides will be provided online. A Handout summarizing important concepts in organometallic and physical organic chemistry will also be provided. Useful references and handouts will also be provided during the workshop.

Slides will be uploaded 1-2 days before each lecture on http://morandi.ethz.ch/education.html
LiteraturePrimary literature and review articles will be cited during the course.

The following textbooks can provide useful support for the course:

- Anslyn and Dougherty, Modern Physical Organic Chemistry, 1st Ed., University Science Books.
- Crabtree R., The Organometallic Chemistry of the Transition Metals, John Wiley & Sons, Inc.
- Hartwig J., Organotransition Metal Chemistry: From Bonding to Catalysis, University Science Books.
- J. P. Collman, L. S. Hegedus, J. R. Norton, R. G. Finke, Principles and Applications of Organotransition Metal Chemistry.
Prerequisites / NoticeRequired level: Courses in organic and physical chemistry (kinetics in particular) of the first and second year as well as ACI and III
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Problem-solvingassessed
Personal CompetenciesAdaptability and Flexibilityassessed
Creative Thinkingassessed
Critical Thinkingassessed
Electives
NumberTitleTypeECTSHoursLecturers
535-0030-00LPharmaceutical Immunology II & Therapeutic Proteins Restricted registration - show details
Prerequisites: Either 535-0830-00L Pharmaceutical Immunology I or 551-0317-00L Immunology I must have been taken.
W3 credits3GC. Halin Winter, D. Neri
AbstractIn 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 objectiveStudents 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
ContentThe 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 notesHandouts 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 / NoticePrerequisites: Either 535-0830-00L Pharmaceutical Immunology I or 551-0317-00L Immunology I
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Problem-solvingfostered
Social CompetenciesCommunicationfostered
Personal CompetenciesCritical Thinkingfostered
535-0230-00LMedicinal Chemistry IW2 credits2VJ. Hall
AbstractThe 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 objectiveBasic understanding of therapeutic agents with respect to molecular, pharmacological and pharmaceutical properties.
ContentMolecular mechanisms of action of drugs. Structure function and biophysical basis of ligand-target interactions
Lecture notesWill 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 / NoticeRequirements: 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).
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesfostered
Method-specific CompetenciesProject Managementfostered
Social CompetenciesLeadership and Responsibilityfostered
Personal CompetenciesSelf-awareness and Self-reflection fostered
551-0313-00LMicrobiology (Part I)W3 credits2VW.‑D. Hardt, L. Eberl, B. Nguyen, J. Piel, M. Pilhofer, A. Vagstad
AbstractAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Learning objectiveThis 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.
ContentAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
Lecture notesUpdated handouts will be provided during the class.
LiteratureCurrent literature references will be provided during the lectures.
Prerequisites / NoticeEnglish
The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture.
529-0041-00LModern Mass Spectrometry, Hyphenated Methods, and ChemometricsW6 credits3GR. Zenobi, B. Hattendorf, P. Sinués Martinez-Lozano
AbstractModern mass spectrometry, hyphenated analytical methods, speciation, chemometrics.
Learning objectiveComprehensive knowledge about the analytical methods introduced in this course and their practical applications.
ContentHyphenation 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 notesLecture notes will be made available online.
LiteratureInformation about relevant literature will be available in the lecture & in the lecture notes.
Prerequisites / NoticeExercises 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)
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingfostered
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementfostered
Social CompetenciesCommunicationfostered
Cooperation and Teamworkfostered
Customer Orientationfostered
Leadership and Responsibilityfostered
Self-presentation and Social Influence fostered
Sensitivity to Diversityfostered
Negotiationfostered
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsfostered
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
551-1299-00LBioinformatics Restricted registration - show details W6 credits4GS. Sunagawa, P. Beltrao, V. Boeva, A. Kahles, C. von Mering, N. Zamboni
AbstractStudents 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 objectiveStudents 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 / NoticeCourse 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.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingassessed
Media and Digital Technologiesassessed
Problem-solvingassessed
Project Managementfostered
Social CompetenciesCommunicationfostered
Cooperation and Teamworkfostered
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsfostered
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
551-0319-00LCellular Biochemistry (Part I)W3 credits2VU. Kutay, F. Allain, T. Kleele, I. Zemp
AbstractConcepts 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 objectiveThe 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.
ContentStructural 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 notesScripts 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)
LiteratureRecommended supplementary literature (review articles and selected primary literature) will be provided during the course.
Prerequisites / NoticeTo attend this course the students must have a solid basic knowledge in chemistry, biochemistry and general biology. The course will be taught in English.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
551-0309-00LConcepts 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
W6 credits4VY. Barral, D. Bopp, A. Hajnal, O. Voinnet
AbstractConcepts 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 objectiveThis course focuses on the concepts of classical and modern genetics and genomics.
ContentThe 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 notesScripts and additional material will be provided during the semester.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Problem-solvingassessed
Social CompetenciesCommunicationfostered
Cooperation and Teamworkfostered
Self-presentation and Social Influence fostered
Personal CompetenciesCreative Thinkingassessed
Critical Thinkingfostered
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
551-0317-00LImmunology IW3 credits2VM. Kopf, A. Oxenius
AbstractIntroduction into structural and functional aspects of the immune system.
Basic knowledge of the mechanisms and the regulation of an immune response.
Learning objectiveIntroduction 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 notesElectronic 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 / NoticeFor 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.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesfostered
Decision-makingfostered
Problem-solvingfostered
Project Managementfostered
Social CompetenciesCommunicationfostered
Cooperation and Teamworkfostered
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingfostered
Critical Thinkingassessed
Self-direction and Self-management fostered
551-0127-00LFundamentals of Biology III: MulticellularityW8 credits6GM. Stoffel, M. Künzler, O. Y. Martin, U. Suter, S. Werner, A. Wutz, S. C. Zeeman
AbstractThe 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 objective1.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.
ContentThe 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.
LiteratureAlberts 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 / NoticeSome lecture are held in English.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesfostered
Method-specific CompetenciesAnalytical Competenciesassessed
Social CompetenciesCooperation and Teamworkfostered
Personal CompetenciesCreative Thinkingfostered
Critical Thinkingassessed
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
551-1005-00LBioanalytics Information W4 credits4GP. Picotti, F. Allain, V. Korkhov, M. Pilhofer, R. Schlapbach, K. Weis, K. Wüthrich, further lecturers
AbstractThe course will introduce students to a selected set of laboratory techniques that are foundational to modern biological research.
Learning objectiveFor 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.
ContentThe 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 notesThe course is supported by a Moodle page that gives access to all supporting materials necessary for the course.
CompetenciesCompetencies
Concepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingassessed
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementfostered
Personal CompetenciesCreative Thinkingassessed
Critical Thinkingassessed
Self-awareness and Self-reflection fostered
529-0004-01LClassical Simulation of (Bio)Molecular Systems Information W6 credits4GP. H. Hünenberger, J. Dolenc, S. Riniker
AbstractMolecular 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 objectiveIntroduction to classical (atomistic) computer simulation of (bio)molecular systems, development of skills to carry out and interpret these simulations.
ContentMolecular 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 notesThe powerpoint slides of the lectures will be made available weekly on the website in pdf format (on the day preceding each lecture).
LiteratureSee: www.csms.ethz.ch/education/CSBMS
Prerequisites / NoticeSince 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
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Media and Digital Technologiesassessed
Problem-solvingassessed
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingfostered
529-0043-01LAnalytical StrategyW6 credits3GR. Zenobi, K. Eyer, S. Giannoukos, D. Günther
AbstractProblem-oriented development of analytical strategies and solutions.
Learning objectiveAbility to create solutions for particular analytical problems.
ContentIndividual 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 notesCopies of problem sets and solutions will be distributed free fo charge
Prerequisites / NoticePrerequisites:
529-0051-00 "Analytical Chemistry I (3. Semester)"
529-0058-00 "Analytical Chemistry II (4. Semester)"
(or equivalent)
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesassessed
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingassessed
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementfostered
Social CompetenciesCommunicationassessed
Cooperation and Teamworkassessed
Customer Orientationfostered
Leadership and Responsibilityfostered
Self-presentation and Social Influence fostered
Sensitivity to Diversityfostered
Negotiationfostered
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsfostered
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
529-0615-01LBiochemical and Polymer Reaction EngineeringW6 credits3GP. Arosio
AbstractPolymerization 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 objectiveThe 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.
ContentWe 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 notesScripts 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.
LiteratureR.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
227-0939-00LCell BiophysicsW6 credits4GT. Zambelli
AbstractApplying 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 objectiveEngineering 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 notesNo 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 / NoticeParticipants 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.
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesfostered
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingassessed
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementassessed
Social CompetenciesCommunicationfostered
Cooperation and Teamworkfostered
Customer Orientationfostered
Leadership and Responsibilityfostered
Self-presentation and Social Influence fostered
Sensitivity to Diversityassessed
Negotiationfostered
Personal CompetenciesAdaptability and Flexibilityassessed
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsassessed
Self-awareness and Self-reflection assessed
Self-direction and Self-management assessed
529-0231-00LOrganic Chemistry III: Introduction to Asymmetric SynthesisW4 credits3GE. M. Carreira
AbstractMethods of Asymmetric Synthesis
Learning objectiveUnderstanding of the basic principles of diastereoselective synthesis
ContentConformational 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.
LiteratureE. M. Carreira and L. Kvaerno Classics in Stereoselective Synthesis, Wiley-VCH 2009

Evans' Problems in Organic Chemistry App
CompetenciesCompetencies
Subject-specific CompetenciesConcepts and Theoriesassessed
Techniques and Technologiesfostered
Method-specific CompetenciesAnalytical Competenciesassessed
Decision-makingfostered
Media and Digital Technologiesfostered
Problem-solvingassessed
Project Managementfostered
Social CompetenciesCommunicationassessed
Cooperation and Teamworkfostered
Customer Orientationfostered
Leadership and Responsibilityfostered
Self-presentation and Social Influence fostered
Sensitivity to Diversityfostered
Negotiationfostered
Personal CompetenciesAdaptability and Flexibilityfostered
Creative Thinkingassessed
Critical Thinkingassessed
Integrity and Work Ethicsfostered
Self-awareness and Self-reflection fostered
Self-direction and Self-management fostered
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