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Course, academic year 2023/2024
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Biophysical chemistry II - experimental methods - MC260P45
Title: Biofyzikální chemie II - experimentální metody
Czech title: Biofyzikální chemie II - experimentální metody
Guaranteed by: Department of Physical and Macromolecular Chemistry (31-260)
Faculty: Faculty of Science
Actual: from 2014 to 2023
Semester: summer
E-Credits: 4
Examination process: summer s.:
Hours per week, examination: summer s.:2/1, Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Additional information:
Note: enabled for web enrollment
Guarantor: prof. RNDr. Tomáš Obšil, Ph.D.
Teacher(s): prof. RNDr. Tomáš Obšil, Ph.D.
Class: MALDI-TOF MS Systém
Annotation -

The objective of the course is to provide a deep understanding of physical chemistry applied to biological problems in order to understand structure and function. The course should make the student familiar with the most important methods of studying and interpreting protein structure and function (protein x-ray crystallography, SAXS, NMR, cryo-EM, ITC and DSC, SPR, analytical ultracentrifugation and selected methods of mass spectrometry).
Last update: Obšil Tomáš, prof. RNDr., Ph.D. (20.02.2019)
Literature - Czech

ZÁKLADNÍ (povinná):
Kodíček, M., Karpenko, V.: Biofysikální chemie, Academia, Praha, 2000.
Prosser V. a kol.: Experimentální metody biofyziky, Academia, Praha, 1989.

Studijní materiály (prezentace z přednášek) jsou dostupné v systému Moodle UK.

Bergethon, P. R.: The Physical Basis of Biochemistry, Springer Verl., 2010.
Cantor, C.R., Schimmel, P.R.: Biophysical Chemistry I-III, W.H. Freeman and Company, San Francisco 1980.
Allen, J.P.: Biophysical Chemistry, Wiley-Blackwell, 2008.
Cooper, A.: Biophysical Chemistry, The Royal Society of Chemistry, 2004.

Last update: Obšil Tomáš, prof. RNDr., Ph.D. (26.06.2014)
Requirements to the exam - Czech

Forma zkoušky: kombinovaná, první část zkoušky je písemný test v rozsahu přednášené látky (nutno získat > 60% bodů), druhá část zkoušky je ústní zkoušení v rozsahu přednášené látky.

Last update: Obšil Tomáš, prof. RNDr., Ph.D. (31.10.2011)
Syllabus -

1. Comparison of techniques used to study structure of biopolymers.
2. Protein crystallization, symmetry, crystal systems, Bravais lattices, unit cell, asymmetric unit.
3. Theory of diffraction. Atomic scattering factor. Structural factor.
4. Laue conditions. Reciprocal lattice. Ewald construction. Phase problem. 
5. Methods of phase problem solution. Patterson map and identification of heavy atom locations. Principles of MIR, SIR, SAD, MAD and MR.
6. Collection and processing of diffraction data. Model building. Structure refinement. Analysis of obtained structural model.
7. Principle of NMR, 2D NMR. COSY and NOESY. Protein NMR. 
8. Cryo-electron microscopy.
9. Analytical ultracentrifugation. Sedimentation velocity and sedimentation equilibrium methods.
10. Microcalorimetry. ITC and DSC.
11. Surface plasmon resonance (SPR).
12. SAXS - small angle X-ray scattering.
13. Selected techniques of mass spectrometry (chemical cross-linking, HDX-MS).

Last update: Obšil Tomáš, prof. RNDr., Ph.D. (20.02.2019)
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