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Course, academic year 2023/2024
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Biophysical chemistry I - MC260P44
Title: Biofyzikální chemie I
Czech title: Biofyzikální chemie I
Guaranteed by: Department of Physical and Macromolecular Chemistry (31-260)
Faculty: Faculty of Science
Actual: from 2014 to 2023
Semester: winter
E-Credits: 6
Examination process: winter s.:
Hours per week, examination: winter s.:3/2, Ex [HT]
Capacity: unlimited
Min. number of students: unlimited
4EU+: no
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Note: enabled for web enrollment
Guarantor: prof. RNDr. Tomáš Obšil, Ph.D.
Teacher(s): Mgr. Karolína Honzejková, Ph.D.
Mgr. Klára Kohoutová
prof. RNDr. Tomáš Obšil, Ph.D.
Annotation -
BIOPHYSICAL CHEMISTRY I

Basic course focused on application of physical chemistry in the study of biological systems. Mainly the structure and properties of biopolymers as well as methods used to study biopolymers are discussed. In the winter semester of the academic year 2020/2021, online teaching takes place according to the schedule. Study materials are available in the Moodle system.
Last update: Obšil Tomáš, prof. RNDr., Ph.D. (09.10.2020)
Literature - Czech

ZÁKLADNÍ (povinná):

Kodíček, M., Karpenko, V.: Biofysikální chemie, Academia, Praha, 2000.

Studijní materiály (prezentace z přednášek, příklady ze cvičení) jsou dostupné v systému Moodle UK.

DOPORUČENÁ:
Vodrážka, Z.: Fyzikální chemie pro biologické vědy, Academia, Praha 1982.

Kalous, V., Pavlíček, Z.: Biofyzikální chemie, SNTL, Praha 1980.

Walla, P.J.: Modern Biophysical Chemistry, Wiley-VCH Verlag GmbH, Germany, 2009.

Allen, J.P.: Biophysical Chemistry, Wiley-Blackwell, 2008.

Cooper, A.: Biophysical Chemistry, The Royal Society of Chemistry, 2004.

Bergethon, P. R.: The Physical Basis of Biochemistry, Springer Verl., New York 1998.

Skriptum: Karpenko, V.: Řešené příklady z fyzikální chemie pro biology, SPN, Praha 1990.

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 včetně příkladů řešených v rámci cvičení k přednášce (nutno získat > 60% bodů), druhá část zkoušky je ústní zkoušení v rozsahu přednášené látky.

Last update: Obšil Tomáš, prof. RNDr., Ph.D. (09.10.2020)
Syllabus -

1. Introduction to chemical thermodynamics. Energy flow in nature. First law of thermodynamics. Internal energy. Enthalpy. Heat capacity. Second law of thermodynamics. Carnot cycle. Entropy. Gibbs energy and its properties. Chemical potential. Third law of thermodynamics. Energetic coupling. Macroergic bonds.

2. Chemical kinetics. The rates of reactions. Reaction order. Activation energy. Activated complex theory. Enzyme catalysis. Inhibition.

3. Structure of proteins: physico-chemical properties of amino acids, peptide bond, peptides, dihedral angles, secondary structure of proteins, non-bonded interactions. Tertiary structure. Structural motifs. Structural domains. Classification of protein fold. Quaternary structure.

4. Structure of DNA and RNA. Conformations of nucleic acids. Secondary structure of DNA. Nomenclature of helical parameters. Stability of DNA. Secondary structure motifs in RNA. Ribozymes.

5. Structure of lipid bilayer. Structure of biomembranes. Interaction between proteins and lipids. Prediction of transmembrane segments of integral membrane proteins. Membrane channels and pumps.

6. Prediction of 3D structure. Comparative and ab inicio modeling of protein structure. Prediction of protein-ligand interactions (docking). Molecular dynamics simulations of biopolymers. Ligand docking. Graphical representations of biopolymer structure.

7. Basic methods of protein preparation and characterization. Basic methods of cloning. Site-directed mutagenesis. PCR. Basic methods of protein expression and purification. Dialysis. Concentration of protein samples. Determination of protein concentration. Characterization of protein polydispersity. Estimation of protein purity. SDS-PAGE electrophoresis. Isoelectric focusing.

8. Spectroscopy. Principles of UV-VIS spectroscopy. Franck-Condon principle. Absorption spectra in biochemistry. Circular dichroism and optical rotary dispersion.

9. Fluorescence spectroscopy. Jablonski diagram. FRET. Applications in biochemsitry and molecular biology. Polarized fluorescence. Static and dynamic light scattering. Raman spectroscopy.

10. Nuclear magnetic resonance. 1D-NMR and 2D-NMR. Study of protein structure using NMR.

11. Protein crystallography. Techniques of protein crystallization. Principles of crystallography and diffraction theory. Phase problem.

Last update: Obšil Tomáš, prof. RNDr., Ph.D. (01.10.2007)
 
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