1. komponenta

Lecture type	Total
Lectures	45
Practicum	30
Seminar	15

* Load is given in academic hour (1 academic hour = 45 minutes)

LEARNING OUTCOMES:
1 to understand models for describing noncovalent interaction, such as H-bonds, van der Waaals interactions and electrostatic interactions
2 to explain hydrophobic effect
3 to explain influence of noncovalent interactions on structural and dynamical properties of biological macromolecules
4 to use thermodynamical principles for understanding biochemical processes on molecular level
5 to explain physical principles of biophysical methods: NMR, UV, IR, CD and EPR spectroscopy, crystallography, molecular modelling, atomic force microscopy, fluorescence, mass spectrometry
6 to discriminate advantages and disadvantages of each biophysical method: NMR, UV, IR, CD and EPR spectroscopy, crystallography, molecular modelling, atomic force microscopy, fluorescence, mass spectrometry
7 to compare biophysical methods: NMR, UV, IR, CD and EPR spectroscopy, crystallography, molecular modelling, atomic force microscopy, fluorescence, mass spectrometry
8 to select the most appropriate biophysical method for solution of specific biological problem

COURSE CONTENT:
LECTURES
1 (1st hour) Definition and division of biophysics. Hierarchy of biological systems that are studied by biophysics. Basic concepts of molecular biophysics.
2 (2nd-8th hour) Non-covalent interactions. Models for calculating: dipole-dipole interactions, dipole-monopol interactions, monopol-monopol interactions, induced dipole-induced dipole interactions, induced dipole-monopol interactions, induced dipol-dipol interactions, hydrogen bonds, van der Waals interactions. Hydrophobic effect. Structure of water molecule and properties of water as a solvent.
3 (9th-11th hour) Structural properties of proteins, RNA and DNA, levels of their structure, importance of certain domains, their structural and dynamical properties regarding the environment.
4 (12th-18th hour) Thermodynamics of biological systems, the first and the second law of thermodynamics, interpretation of thermodynamical properties of biochemical systems. Maxwell relations. Gibbs-Duhem equation. Thermodynamical potential.
5 (19th-23rd hour) Thermodynamics of macromolecular solutions. Usefulness and interpretation of thermodynamical parameters for understanding biological processes. Microcalorimetry, details of ITC and DSC technics.
6 (24th-267h hour) Structure and function of membranes, membrane transport, thermodynamics of membrane transport.
7 (28th-29th hour) Physical principles of crystallography, advantages and disadvantages of crystallography as biophysical methods for investigation of biochemical systems.
8 (30th-31st hour) Computational biophysics, basic concepts of molecular modelling of biochemical systems.
9 (32nd-33rd hour) Physical principles of ultraviolet (UV) spectroscopy, advantages and disadvantages of ultraviolet (UV) spectroscopy as biophysical methods for investigation of biochemical systems.
10 (34th-35th hour) Physical principles of circular dichroism (CD) spectroscopy, advantages and disadvantages of circular dichroism (CD) spectroscopy as biophysical method for investigation of biochemical systems.
11 (36th-37th hour) Physical principles of atomic force microscopy, advantages and disadvantages of atomic force microscopy (AFM) as biophysical method for investigation of biochemical systems.
12 (38th-39th hour) Physical principles of electron paramagnetic resonance (EPR) spectroscopy, advantages and disadvantages of electron paramagnetic resonance (EPR) spectroscopy as biophysical method for investigation of biochemical systems.
13 (40th-41st hour) Physical principles of fluorescence, advantages and disadvantages of fluorescence as biophysical method for investigation of biochemical systems.
14 (42sd-43rd hour) Physical principles of nuclear Magnetic Resonance (NMR) spectroscopy, advantages and disadvantages of NMR as biophysical methods for investigation of biochemical systems.
15 (44th-45th hour) Physical principles of mass spectrometry, advantages and disadvantages of mass spectrometry as biophysical methods for investigation of biochemical systems.

LABORATORY EXERCISES
Laboratory exercises are organised regarding the access to the available equipment. Laboratory exercises are performed by students and/or by the expert in the field.
1 Biomacromolecular crystallography and computational biophysics. Crystallisation of biomacromolecules, each student starts crystallisation of Lysozyme. Students are introduced with the process of data collection and basic parts of diffraction instrument. Basic principles of molecular modelling that are performed after determination of 3D structure of biomacromolecule.
2 Fluorescence. Study of interaction between bovine serum albumin and indole-3-acetic acid using fluorescence, performed by students. Interpretation of the results.
3 Electron paramagnetic resonance (EPR) spectroscopy. Determination of free radicals in different samples using EPR spectroscopy. Interpretation of the results.
4 Atomic force microscopy (AFM). Preparation of samples for AFM measurements performed by students. Study of different samples using AFM. Interpretation of the results.
5 Ultraviolet (UV) and circular dichroism (CD) spectroscopy. Study of denaturation of biomacromolecules and their interactions with small molecules using CD and UV spectroscopy. Interpretation of the results.
6 Mass spectrometry (MS). Structural characterisation of biological samples by MS.

SEMINARS
Seminars follow topics of the lectures.
1 (1st-2nd hour): Numeric exercises regarding the topic of non-covalent interactions in biochemical systems.
2 (3rd hour): Numeric exercises regarding the topic of macromolecular solutions.
3 (4th-7th hour): Numeric exercises regarding the topic of thermodynamics of biophysical systems.
4 (8th hour): Numeric exercises regarding the topic of membrane transport.
5 (9th-11th hour): Numeric exercises regarding some of the biophysical methods (UV, CD, NMR spectroscopy, fluorescence).
6 (11th-15th hour): Students seminars based on selected scientific publications. Each student presents short seminar regarding the chosen biophysical method and its application on solution of biological problem.

1. K.E. van Holde,W.C. Johnson,P.S. Ho: Principles of Physicsl Biochemistry, Pearson Prentice Hall, Upper Saddle River, USA 2006.
2. R.M.J. Cotterill: BIOPHYSICS (An Introduction), J. Wiely, West Sussex, 2006.
3. A. Miller, J. Tanner: Essentials of chemical biology, J. Wiely, Chichester, 2009.
4. M.B. Jackson: Molecular and Cellular Biophysics, Cambridge University Press, Cambridge, 2006
5. T.A. Waigh: Applied Biophysics, J. Wiely, Chichester, 2007.
6. P. W. Atkins, Physical chemistry, 8. izd., Oxford University Press, Oxford, 2006.
7. G.U. Nienhaus: Protein-Ligand Interactions: Methods and Application, Human Press Inc., Totowa, New Jeresy, 2005.
8. D. Sheehan: Physical Biochemistry: Principles and Applications, West Sussex, 2000.

Izborni predmeti - Regular study - Molecular Biology