Search result: Catalogue data in Autumn Semester 2020

Biology Master Information
Elective Major Subject Areas
Elective Major: Biological Chemistry
Elective Compulsory Master Courses
NumberTitleTypeECTSHoursLecturers
529-0733-01LEnzymesW6 credits3GD. Hilvert
AbstractPrinciples 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.
ObjectiveOverview of enzymes, enzyme-catalyzed reactions and metabolic processes.
ContentPrinciples 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 notesA script will not be handed out.
LiteratureGeneral:
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.
529-0004-01LClassical Simulation of (Bio)Molecular Systems Information W6 credits4GP. H. Hünenberger, 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).
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 notesScript booklet (copies of powerpoint slides) distributed at the first or second lecture.
LiteratureSee: Link
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: Link
529-0233-01LOrganic Synthesis: Methods and Strategies Information W6 credits3GE. M. Carreira
AbstractThe 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.
ObjectiveExtension and deepening of the knowledge in organic synthesis and the principles of structure and reactivity.
ContentConcepts of the planning of organic synthesis (strategy and tactics), retrosynthetic analysis. Structure-reactivity relation in the context of the synthesis of complex molecules.
LiteratureK. 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 / NoticeOC I-IV
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
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 Link
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 ACIII

Special requirement: each participant will have to come up with an independent research proposal to be presented orally (or handed in in written form) at the end of the semester. A dedicated workshop will be organized in the middle of the semester to introduce the students to proposal writing and presentation.
529-0041-00LModern Mass Spectrometry, Hyphenated Methods, and ChemometricsW6 credits3GR. Zenobi, M. Badertscher, D. Günther, B. Hattendorf, P. Sinués Martinez-Lozano
AbstractModern mass spectrometry, hyphenated analytical methods, speciation, methods of surface analysis, chemometrics.
ObjectiveComprehensive knowledge about the analytical methods introduced in this course, and their applications.
ContentCoupling 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 noteslecture notes will be available in the lecture at production cost.
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)
529-0240-00LChemical Biology - PeptidesW6 credits3GH. Wennemers
AbstractAn advanced course on the synthesis, properties and function of peptides in chemistry and biology.
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.
636-0108-00LBiological Engineering and Biotechnology
Attention: This course was offered in previous semesters with the number: 636-0003-00L "Biological Engineering and Biotechnology". Students that already passed course 636-0003-00L cannot receive credits for course 636-0108-00L.
W4 credits3VM. Fussenegger
AbstractBiological 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.
ObjectiveBiological 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.
Content1. 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 notesHandout during the course.
551-1407-00LRNA Biology Lecture Series I: Transcription & Processing & Translation Information W4 credits2VF. Allain, N. Ban, S. Jonas, U. Kutay, further lecturers
AbstractThis 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.
ObjectiveThe students should obtain an understanding of these processes, which are at work during gene expression.
ContentTranscription & 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 / NoticeBasic knowledge of cell and molecular biology.
551-1409-00LRNA Biology Lecture Series II: Non-coding RNAs: Biology and Therapeutics
Does not take place this semester.
W4 credits2VJ. Hall, M. Stoffel, further lecturers
AbstractThis course covers aspects of RNA biology related to the functions of non-coding RNAs as well as their use as drugs to treat diseases.
ObjectiveThe students should get familiar with the wide array of roles, which non-coding RNAs play in cellular functions.
ContentMicro 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. Link
Prerequisites / NoticeBasic knowledge of cell and molecular biology.
529-0241-10LAdvanced Methods and Strategies in SynthesisW6 credits3GJ. W. Bode
AbstractAdvanced Modern Methods and Strategies in Synthesis
ObjectiveKnowledge of modern methods in asymmetric stereocontrol, enantioselective catalysis, and organic reaction mechanisms.
ContentCurrent trends in methods for and approaches to synthesis of complex natural products, pharmaceuticals, and biological molecules; fragment coupling and protecting group strategies; chemical ligation and biomolecules synthesis; enantioselective catalysis including ligand design and optimization; cross coupling reactions from preactivated precursors; C-H activation and oxidation chemistry; building block synthesis with chiral auxiliaries and reagents; new concepts in asymmetric catalysis. 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
1. Walsh and Kozlowski, Fundamentals of Asymmetric Catalysis, 1st Ed., University Science Books, 2009.
2. Anslyn and Dougherty, Modern Physical Organic Chemistry, 1st Ed., University Science Books, 2006.
227-0939-00LCell BiophysicsW6 credits4GT. Zambelli
AbstractA mathematical description is derived for a variety of biological phenomena at the molecular and cellular level applying the two fundamental principles of thermodynamics (entropy maximization and Gibbs energy minimization).
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 concepts 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 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 according to experimental data.

By the end of the course, students will also learn to critically evaluate the concepts of making an assumption and making an approximation.
Content1. Basics of theory of probability

2. Boltzmann's law

3. Entropy maximization and Gibbs free energy minimization

4. Two-state systems and the MWC model

5. Random walks and macromolecular structures

6. Electrostatics for salty solutions

7. Elasticity: fibers and membranes

8. Diffusion and crowding: cell signaling

9. Molecular motors

10. Action potential: Hodgkin-Huxley model

11. Photosynthesis

12. Gene regulation

13. Development: Turing patterns

14. Sequences and evolution
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 (calculus) as well as of Newton's and Coulomb's laws (basics of mechanics and electrostatics). Notions of vectors in 2D and 3D are beneficial.

Theory and corresponding exercises are merged together during the classes.
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