C5855 Methods in Biophysical Chemistry

Faculty of Science
Autumn 2020
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Taught online.
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
RNDr. Mgr. Iveta Třísková, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Timetable
Wed 8:00–9:50 Kontaktujte učitele
Prerequisites
exam of C5850 Introduction to Biophysical Chemistry
simultaneous attendance of C5855 Methods in Biophysical Chemistry is recommended
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain physicochemical foundations of biophysical methods used in genomics, proteomics, biotechnology and bionanotechnology.
Learning outcomes
Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able:
a) to explain the principles of biophysical methods,
b) to use the fundamentals of physical chemistry in biological practice,
c) to use the knowledge gained for the preparation of the bachelor thesis,
d) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations),
e) to interpret new trends, tactics and strategies of biophysical chemistry.
Syllabus
  • 1. Experiment of biophysical chemistry (tactics and strategy of choice, general procedure for solving structures and interactions of biomolecules)
  • 2. Transport in biological system (diffusion, osmosis, viscosity)
  • 3. Techniques of study of biomolecular transport (centrifugation, chromatography, electrophoresis)
  • 4. Electrical potential, energy, heat (electrophysiology, mass spectrometry, calorimetry)
  • 5. Scattering, refraction and interpretation of their data
  • 6. Electron and vibrational spectroscopy I (energy states, UV-Vis, infrared and Raman spectroscopy)
  • 7. Electron and vibrational spectroscopy II (fluorescence, FRET, phosphorescence, chiroptic spectra, X-ray spectroscopy)
  • 8. Magnetic resonance (nuclear magnetic resonance - NMR and electron paramagnetic resonance - EPR)
  • 9. Microscopy (electron microscopy - SEM and TEM, atomic force microscopy - AFM)
  • 10. Methods of study of own possibilities (manipulation, electrical and optical properties of biomolecules)
  • 11. Electrochemical methods and their use in biosensors (bioelectrochemistry, nanoelectrochemistry)
  • 12. Mathematical and statistical data processing (introduction to Fourier methods, multicomponent analysis, artificial neural networks).
Literature
    required literature
  • CAMPBELL, Iain D. Biophysical techniques. Oxford: Oxford University Press, 2012. ix, 353. ISBN 9780199642144. info
  • KODÍČEK, Milan and Vladimír KARPENKO. Biofysikální chemie. Vyd. 3., opr. a rozš. Praha: Academia, 2013. 423 s. ISBN 9788020022417. info
    recommended literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
Teaching methods
lectures, ppt presentations, discussions
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019.

C5855 Methods in Biophysical Chemistry

Faculty of Science
Autumn 2019
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
RNDr. Mgr. Iveta Třísková, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Timetable
Tue 8:00–9:50 C12/311
Prerequisites
exam of C5850 Introduction to Biophysical Chemistry
simultaneous attendance of C5855 Methods in Biophysical Chemistry is recommended
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain physicochemical foundations of biophysical methods used in genomics, proteomics, biotechnology and bionanotechnology.
Learning outcomes
Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able:
a) to explain the principles of biophysical methods,
b) to use the fundamentals of physical chemistry in biological practice,
c) to use the knowledge gained for the preparation of the bachelor thesis,
d) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations),
e) to interpret new trends, tactics and strategies of biophysical chemistry.
Syllabus
  • 1. Experiment of biophysical chemistry (tactics and strategy of choice, general procedure for solving structures and interactions of biomolecules)
  • 2. Transport in biological system (diffusion, osmosis, viscosity)
  • 3. Techniques of study of biomolecular transport (centrifugation, chromatography, electrophoresis)
  • 4. Electrical potential, energy, heat (electrophysiology, mass spectrometry, calorimetry)
  • 5. Scattering, refraction and interpretation of their data
  • 6. Electron and vibrational spectroscopy I (energy states, UV-Vis, infrared and Raman spectroscopy)
  • 7. Electron and vibrational spectroscopy II (fluorescence, FRET, phosphorescence, chiroptic spectra, X-ray spectroscopy)
  • 8. Magnetic resonance (nuclear magnetic resonance - NMR and electron paramagnetic resonance - EPR)
  • 9. Microscopy (electron microscopy - SEM and TEM, atomic force microscopy - AFM)
  • 10. Methods of study of own possibilities (manipulation, electrical and optical properties of biomolecules)
  • 11. Electrochemical methods and their use in biosensors (bioelectrochemistry, nanoelectrochemistry)
  • 12. Mathematical and statistical data processing (introduction to Fourier methods, multicomponent analysis, artificial neural networks).
Literature
    required literature
  • CAMPBELL, Iain D. Biophysical techniques. Oxford: Oxford University Press, 2012. ix, 353. ISBN 9780199642144. info
  • KODÍČEK, Milan and Vladimír KARPENKO. Biofysikální chemie. Vyd. 3., opr. a rozš. Praha: Academia, 2013. 423 s. ISBN 9788020022417. info
    recommended literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
Teaching methods
lectures, ppt presentations, discussions
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2020.

C5855 Methods in Biophysical Chemistry

Faculty of Science
Autumn 2018
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Mgr. Pavel Plevka, Ph.D. (lecturer)
Mgr. Tomáš Klumpler, Ph.D. (lecturer)
prof. RNDr. Zbyněk Prokop, Ph.D. (lecturer)
Mgr. Veronika Štěpánková, Ph.D. (lecturer)
Mgr. David Bednář, Ph.D. (lecturer)
RNDr. Mgr. Iveta Třísková, Ph.D. (lecturer)
doc. Mgr. Radka Chaloupková, Ph.D. (lecturer)
prof. Dr. Jiří Kozelka, PhD. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Supplier department: Department of Chemistry - Chemistry Section - Faculty of Science
Timetable
Mon 17. 9. to Fri 14. 12. Mon 14:00–15:50 C12/311
Prerequisites
exam of C5850 Introduction to Biophysical Chemistry
simultaneous attendance of C5855 Methods in Biophysical Chemistry is recommended
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain extensive physicochemical foundations in genomics, proteomics, biotechnology and bionanotechnology. Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry.
Learning outcomes
At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry. Na konci tohoto kurzu bude student schopen: a) porozumět principům biofyzikálních metod, b) vysvětlit moderní principy biofyzikálních metod, c) použít základy fyzikální chemie v biologické praxi, d) nabyté vědomosti použít v přípravě bakalářské práce, e) získané vědomosti využít v teorii (výpočty struktur) a v praxi (experiment, který teoretické výpočty ověří), f) interpretovat nové trendy, taktiky a stratégie biofyzikální chemie.
Syllabus
  • 1. The behavior of biological macromolecules (nucleic acids, proteins and polysaccharides)
  • 2. Biophysical chemistry cells and membranes (physical chemistry in biology and biophysics of cells and membranes, membrane transport)
  • 3. Techniques for studying the structure and function of biopolymers (method's distribution, advantages and disadvantages, applications, general procedure for solving the structure of biopolymers using different techniques)
  • 4. Introduction to Fourier methods and statistics (the use of Fourier transforms in intensive experimental methods, the advantage of a mathematical signal processing)
  • 5. Biological methods for the analysis of primary, secondary and tertiary structure of biomolecules (chemical sequencing method, PCR)
  • 6. Physical methods for the analysis of primary, secondary and tertiary structures of biomolecules (X-ray analysis, electron microscopy, light scattering)
  • 7. Spectral methods for analyzing the primary, secondary and tertiary structure of biomolecules (UV-Vis, CD, NMR, MS)
  • 8. Electrochemical methods for the analysis of primary, secondary and tertiary structures of biomolecules (electrophoresis, dynamic methods, biosensors)
  • 9. Bioinformatics, genomics and proteomics (databases, sequence analysis, genome and metagenome, microarray technology, protein-protein and protein-DNA interactions)
  • 10. Experimental methods in molecular Biotechnology I. and II. (isolation, amplification, sequencing, and recombinant DNA, expression and isolation of proteins, methods of structural and functional characterization of proteins)
  • 11. Molecular biotechnology in medicine, environmental protection, industry and agriculture (cell and gene therapy, tissue engineering and regenerative medicine, molecular diagnostics, vaccines, biosensors, bioremediation, biofuels, environmental protection and sustainable development, the use of biomass, fermentation technology, biocatalysis in the pharmaceutical and chemical industries, gray and white biotechnology in the food industry, genetic engineering of plants and animals, cloning, GMO foods, biopesticides)
  • 12. Computer modeling of the structures of nucleic acids and proteins (structural and functional significance of DNA, RNA, proteins, methods of prediction of biopolymer secondary structures).
Literature
    required literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
    recommended literature
  • Biophysical chemistry of biointerfaces. Edited by Hiroyuki Ohshima. Hoboken: Wiley, 2010. xvi, 547 p. ISBN 9780470169353. info
Teaching methods
lectures, tests, discussions, ppt presentations
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2019, Autumn 2020.

C5855 Methods in Biophysical Chemistry

Faculty of Science
autumn 2017
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Mgr. Pavel Plevka, Ph.D. (lecturer)
Mgr. Tomáš Klumpler, Ph.D. (lecturer)
prof. RNDr. Zbyněk Prokop, Ph.D. (lecturer)
Mgr. Veronika Štěpánková, Ph.D. (lecturer)
Mgr. David Bednář, Ph.D. (lecturer)
RNDr. Mgr. Iveta Třísková, Ph.D. (lecturer)
doc. Mgr. Radka Chaloupková, Ph.D. (lecturer)
prof. Dr. Jiří Kozelka, PhD. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Supplier department: Department of Chemistry - Chemistry Section - Faculty of Science
Prerequisites
exam of C5850 Introduction to Biophysical Chemistry
simultaneous attendance of C5855 Methods in Biophysical Chemistry is recommended
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain extensive physicochemical foundations in genomics, proteomics, biotechnology and bionanotechnology. Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry.
Learning outcomes
At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry. Na konci tohoto kurzu bude student schopen: a) porozumět principům biofyzikálních metod, b) vysvětlit moderní principy biofyzikálních metod, c) použít základy fyzikální chemie v biologické praxi, d) nabyté vědomosti použít v přípravě bakalářské práce, e) získané vědomosti využít v teorii (výpočty struktur) a v praxi (experiment, který teoretické výpočty ověří), f) interpretovat nové trendy, taktiky a stratégie biofyzikální chemie.
Syllabus
  • 1. The behavior of biological macromolecules (nucleic acids, proteins and polysaccharides)
  • 2. Biophysical chemistry cells and membranes (physical chemistry in biology and biophysics of cells and membranes, membrane transport)
  • 3. Techniques for studying the structure and function of biopolymers (method's distribution, advantages and disadvantages, applications, general procedure for solving the structure of biopolymers using different techniques)
  • 4. Introduction to Fourier methods and statistics (the use of Fourier transforms in intensive experimental methods, the advantage of a mathematical signal processing)
  • 5. Biological methods for the analysis of primary, secondary and tertiary structure of biomolecules (chemical sequencing method, PCR)
  • 6. Physical methods for the analysis of primary, secondary and tertiary structures of biomolecules (X-ray analysis, electron microscopy, light scattering)
  • 7. Spectral methods for analyzing the primary, secondary and tertiary structure of biomolecules (UV-Vis, CD, NMR, MS)
  • 8. Electrochemical methods for the analysis of primary, secondary and tertiary structures of biomolecules (electrophoresis, dynamic methods, biosensors)
  • 9. Bioinformatics, genomics and proteomics (databases, sequence analysis, genome and metagenome, microarray technology, protein-protein and protein-DNA interactions)
  • 10. Experimental methods in molecular Biotechnology I. and II. (isolation, amplification, sequencing, and recombinant DNA, expression and isolation of proteins, methods of structural and functional characterization of proteins)
  • 11. Molecular biotechnology in medicine, environmental protection, industry and agriculture (cell and gene therapy, tissue engineering and regenerative medicine, molecular diagnostics, vaccines, biosensors, bioremediation, biofuels, environmental protection and sustainable development, the use of biomass, fermentation technology, biocatalysis in the pharmaceutical and chemical industries, gray and white biotechnology in the food industry, genetic engineering of plants and animals, cloning, GMO foods, biopesticides)
  • 12. Computer modeling of the structures of nucleic acids and proteins (structural and functional significance of DNA, RNA, proteins, methods of prediction of biopolymer secondary structures).
Literature
    required literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
    recommended literature
  • Biophysical chemistry of biointerfaces. Edited by Hiroyuki Ohshima. Hoboken: Wiley, 2010. xvi, 547 p. ISBN 9780470169353. info
Teaching methods
lectures, tests, discussions, ppt presentations
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2018, Autumn 2019, Autumn 2020.

C5855 Methods in Biophysical Chemistry

Faculty of Science
Autumn 2016
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Mgr. Pavel Plevka, Ph.D. (lecturer)
Mgr. Tomáš Klumpler, Ph.D. (lecturer)
prof. RNDr. Zbyněk Prokop, Ph.D. (lecturer)
Mgr. Veronika Štěpánková, Ph.D. (lecturer)
Mgr. David Bednář, Ph.D. (lecturer)
RNDr. Mgr. Iveta Třísková, Ph.D. (lecturer)
doc. Mgr. Radka Chaloupková, Ph.D. (lecturer)
prof. Dr. Jiří Kozelka, PhD. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Supplier department: Department of Chemistry - Chemistry Section - Faculty of Science
Timetable
Mon 19. 9. to Sun 18. 12. Mon 9:00–10:50 C12/311
Prerequisites
exam of C5850 Introduction to Biophysical Chemistry
simultaneous attendance of C5855 Methods in Biophysical Chemistry is recommended
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain extensive physicochemical foundations in genomics, proteomics, biotechnology and bionanotechnology. Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry.
Syllabus
  • 1. The behavior of biological macromolecules (nucleic acids, proteins and polysaccharides)
  • 2. Biophysical chemistry cells and membranes (physical chemistry in biology and biophysics of cells and membranes, membrane transport)
  • 3. Techniques for studying the structure and function of biopolymers (method's distribution, advantages and disadvantages, applications, general procedure for solving the structure of biopolymers using different techniques)
  • 4. Introduction to Fourier methods and statistics (the use of Fourier transforms in intensive experimental methods, the advantage of a mathematical signal processing)
  • 5. Biological methods for the analysis of primary, secondary and tertiary structure of biomolecules (chemical sequencing method, PCR)
  • 6. Physical methods for the analysis of primary, secondary and tertiary structures of biomolecules (X-ray analysis, electron microscopy, light scattering)
  • 7. Spectral methods for analyzing the primary, secondary and tertiary structure of biomolecules (UV-Vis, CD, NMR, MS)
  • 8. Electrochemical methods for the analysis of primary, secondary and tertiary structures of biomolecules (electrophoresis, dynamic methods, biosensors)
  • 9. Bioinformatics, genomics and proteomics (databases, sequence analysis, genome and metagenome, microarray technology, protein-protein and protein-DNA interactions)
  • 10. Experimental Methods in Molecular Biotechnology I. and II. (isolation, amplification, sequencing, and recombinant DNA, expression and isolation of proteins, methods of structural and functional characterization of proteins)
  • 11. Molecular biotechnology in medicine, environmental protection, industry and agriculture (cell and gene therapy, tissue engineering and regenerative medicine, molecular diagnostics, vaccines, biosensors, bioremediation, biofuels, environmental protection and sustainable development, the use of biomass, fermentation technology, biocatalysis in the pharmaceutical and chemical industries, gray and white biotechnology in the food industry, genetic engineering of plants and animals, cloning, GMO foods, biopesticides)
  • 12. Computer modeling of the structures of nucleic acids and proteins (structural and functional significance of DNA, RNA, proteins, methods of prediction of biopolymer secondary structures).
Literature
    required literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
    recommended literature
  • Biophysical chemistry of biointerfaces. Edited by Hiroyuki Ohshima. Hoboken: Wiley, 2010. xvi, 547 p. ISBN 9780470169353. info
Teaching methods
lectures, tests, discussions, ppt presentations
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2014, Autumn 2015, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020.

C5855 Methods in Biophysical Chemistry

Faculty of Science
Autumn 2015
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
prof. Dr. Jiří Kozelka, PhD. (lecturer)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Mgr. Antonín Hlaváček, Ph.D. (lecturer)
Mgr. Pavel Plevka, Ph.D. (lecturer)
prof. RNDr. Zbyněk Prokop, Ph.D. (lecturer)
Mgr. Šárka Nevolová, Ph.D. (lecturer)
Mgr. Veronika Štěpánková, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Supplier department: Department of Chemistry - Chemistry Section - Faculty of Science
Timetable
Wed 14:00–15:50 C12/311
Prerequisites
exam of C5850 Introduction to Biophysical Chemistry
simultaneous attendance of C5855 Methods in Biophysical Chemistry is recommended
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain extensive physicochemical foundations in genomics, proteomics, biotechnology and bionanotechnology. Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry.
Syllabus
  • 1. The behavior of biological macromolecules (nucleic acids, proteins and polysaccharides)
  • 2. Biophysical chemistry cells and membranes (physical chemistry in biology and biophysics of cells and membranes, membrane transport)
  • 3. Techniques for studying the structure and function of biopolymers (method's distribution, advantages and disadvantages, applications, general procedure for solving the structure of biopolymers using different techniques)
  • 4. Introduction to Fourier methods and statistics (the use of Fourier transforms in intensive experimental methods, the advantage of a mathematical signal processing)
  • 5. Biological methods for the analysis of primary, secondary and tertiary structure of biomolecules (chemical sequencing method, PCR)
  • 6. Physical methods for the analysis of primary, secondary and tertiary structures of biomolecules (X-ray analysis, electron microscopy, light scattering)
  • 7. Spectral methods for analyzing the primary, secondary and tertiary structure of biomolecules (UV-Vis, CD, NMR, MS)
  • 8. Electrochemical methods for the analysis of primary, secondary and tertiary structures of biomolecules (electrophoresis, dynamic methods, biosensors)
  • 9. Bioinformatics, genomics and proteomics (databases, sequence analysis, genome and metagenome, microarray technology, protein-protein and protein-DNA interactions)
  • 10. Experimental Methods in Molecular Biotechnology I. and II. (isolation, amplification, sequencing, and recombinant DNA, expression and isolation of proteins, methods of structural and functional characterization of proteins)
  • 11. Molecular biotechnology in medicine, environmental protection, industry and agriculture (cell and gene therapy, tissue engineering and regenerative medicine, molecular diagnostics, vaccines, biosensors, bioremediation, biofuels, environmental protection and sustainable development, the use of biomass, fermentation technology, biocatalysis in the pharmaceutical and chemical industries, gray and white biotechnology in the food industry, genetic engineering of plants and animals, cloning, GMO foods, biopesticides)
  • 12. Computer modeling of the structures of nucleic acids and proteins (structural and functional significance of DNA, RNA, proteins, methods of prediction of biopolymer secondary structures).
Literature
    required literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
    recommended literature
  • Biophysical chemistry of biointerfaces. Edited by Hiroyuki Ohshima. Hoboken: Wiley, 2010. xvi, 547 p. ISBN 9780470169353. info
Teaching methods
lectures, tests, discussions, ppt presentations
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2014, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020.

C5855 Biophysical Chemistry II

Faculty of Science
Autumn 2014
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Mgr. Jozef Hritz, Ph.D. (lecturer)
prof. Dr. Jiří Kozelka, PhD. (lecturer)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Mgr. Antonín Hlaváček, Ph.D. (lecturer)
Mgr. Pavel Plevka, Ph.D. (lecturer)
prof. RNDr. Zbyněk Prokop, Ph.D. (lecturer)
Mgr. Šárka Nevolová, Ph.D. (lecturer)
Mgr. Veronika Štěpánková, Ph.D. (lecturer)
Mgr. Zdeněk Farka, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Supplier department: Department of Chemistry - Chemistry Section - Faculty of Science
Timetable
Fri 10:00–11:50 C12/311
Prerequisites
fundamentals of physical chemistry
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain extensive physicochemical foundations in genomics, proteomics, biotechnology and bionanotechnology. Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry.
Syllabus
  • 1. The behavior of biological macromolecules (nucleic acids, proteins and polysaccharides) 2. Biophysical chemistry cells and membranes (physical chemistry in biology and biophysics of cells and membranes, membrane transport) 3. Techniques for studying the structure and function of biopolymers (method's distribution, advantages and disadvantages, applications, general procedure for solving the structure of biopolymers using different techniques) 4. Introduction to Fourier methods and statistics (the use of Fourier transforms in intensive experimental methods, the advantage of a mathematical signal processing) 5. Biological methods for the analysis of primary, secondary and tertiary structure of biomolecules (chemical sequencing method, PCR) 6. Physical methods for the analysis of primary, secondary and tertiary structures of biomolecules (X-ray analysis, electron microscopy, light scattering) 7. Spectral methods for analyzing the primary, secondary and tertiary structure of biomolecules (UV-Vis, CD, NMR, MS) 8. Electrochemical methods for the analysis of primary, secondary and tertiary structures of biomolecules (electrophoresis, dynamic methods, biosensors) 9. Bioinformatics, genomics and proteomics (databases, sequence analysis, genome and metagenome, microarray technology, protein-protein and protein-DNA interactions) 10. Experimental Methods in Molecular Biotechnology I. and II. (isolation, amplification, sequencing, and recombinant DNA, expression and isolation of proteins, methods of structural and functional characterization of proteins) 11. Molecular biotechnology in medicine, environmental protection, industry and agriculture (cell and gene therapy, tissue engineering and regenerative medicine, molecular diagnostics, vaccines, biosensors, bioremediation, biofuels, environmental protection and sustainable development, the use of biomass, fermentation technology, biocatalysis in the pharmaceutical and chemical industries, gray and white biotechnology in the food industry, genetic engineering of plants and animals, cloning, GMO foods, biopesticides) 12. Computer modeling of the structures of nucleic acids and proteins (structural and functional significance of DNA, RNA, proteins, methods of prediction of biopolymer secondary structures).
Literature
    required literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
    recommended literature
  • Biophysical chemistry of biointerfaces. Edited by Hiroyuki Ohshima. Hoboken: Wiley, 2010. xvi, 547 p. ISBN 9780470169353. info
Teaching methods
lectures, tests, discussions, ppt presentations
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2013, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020.

C5855 Biophysical Chemistry II

Faculty of Science
Autumn 2013
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
Mgr. Tomáš Klumpler, Ph.D. (lecturer)
Mgr. Jan Brezovský, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Supplier department: Department of Chemistry - Chemistry Section - Faculty of Science
Timetable
Fri 11:00–12:50 C12/311
Prerequisites
exam of C5850
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
Students of this course will gain extensive physicochemical foundations in genomics, proteomics, biotechnology and bionanotechnology. Students will learn in detail with modern approaches in biophysically-chemical research, very useful in biophysics, biochemistry, medicine, pharmacy and food industry. At the end of this course the student will be able: a) to understand the principles of biophysical methods, b) to explain the principles of modern biophysical methods, c) to use the fundamentals of physical chemistry in biological practice d) to use the knowledge gained for the preparation of the thesis, e) to use the knowledge gained in theory (structure calculation) and experience (experiment to verify the theoretical calculations) f) to interpret new trends, tactics and strategies of biophysical chemistry.
Syllabus
  • 1. The behavior of biological macromolecules (nucleic acids, proteins and polysaccharides) 2. Biophysical chemistry cells and membranes (physical chemistry in biology and biophysics of cells and membranes, membrane transport) 3. Techniques for studying the structure and function of biopolymers (method's distribution, advantages and disadvantages, applications, general procedure for solving the structure of biopolymers using different techniques) 4. Introduction to Fourier methods and statistics (the use of Fourier transforms in intensive experimental methods, the advantage of a mathematical signal processing) 5. Biological methods for the analysis of primary, secondary and tertiary structure of biomolecules (chemical sequencing method, PCR) 6. Physical methods for the analysis of primary, secondary and tertiary structures of biomolecules (X-ray analysis, electron microscopy, light scattering) 7. Spectral methods for analyzing the primary, secondary and tertiary structure of biomolecules (UV-Vis, CD, NMR, MS) 8. Electrochemical methods for the analysis of primary, secondary and tertiary structures of biomolecules (electrophoresis, dynamic methods, biosensors) 9. Bioinformatics, genomics and proteomics (databases, sequence analysis, genome and metagenome, microarray technology, protein-protein and protein-DNA interactions) 10. Experimental Methods in Molecular Biotechnology I. and II. (isolation, amplification, sequencing, and recombinant DNA, expression and isolation of proteins, methods of structural and functional characterization of proteins) 11. Molecular biotechnology in medicine, environmental protection, industry and agriculture (cell and gene therapy, tissue engineering and regenerative medicine, molecular diagnostics, vaccines, biosensors, bioremediation, biofuels, environmental protection and sustainable development, the use of biomass, fermentation technology, biocatalysis in the pharmaceutical and chemical industries, gray and white biotechnology in the food industry, genetic engineering of plants and animals, cloning, GMO foods, biopesticides) 12. Computer modeling of the structures of nucleic acids and proteins (structural and functional significance of DNA, RNA, proteins, methods of prediction of biopolymer secondary structures).
Literature
    required literature
  • ALLEN, James P. Biophysical chemistry. Hoboken, NJ: Wiley-Blackwell Pub., 2008. xvi, 492. ISBN 9781405124362. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part II, Techniques for the study of biological structure and function. 12th print. New York: W.H. Freeman and Company, 2001. xxix, s. 3. ISBN 0-7167-1189-3. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part I, The conformation of biological macromolecules. 11th print. New York: W.H. Freeman and Company, 1999. xxii, 341. ISBN 0-7167-1042-0. info
  • CANTOR, Charles R. and Paul R. SCHIMMEL. Biophysical chemistry. Part III, The behavior of biological macromolecules. New York: W.H. Freeman and Company, 1980. xxix, s. 8. ISBN 0-7167-1191-5. info
    recommended literature
  • Biophysical chemistry of biointerfaces. Edited by Hiroyuki Ohshima. Hoboken: Wiley, 2010. xvi, 547 p. ISBN 9780470169353. info
Teaching methods
lectures, tests, discussions, ppt presentations
Assessment methods
written test and oral exam
Language of instruction
Czech
Further Comments
Study Materials
The course can also be completed outside the examination period.
The course is taught annually.
The course is also listed under the following terms Autumn 2008, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020.

C5855 Biophysical Chemistry II

Faculty of Science
Autumn 2008
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Libuše Trnková, CSc. (lecturer)
RNDr. Kamila Neplechová, Ph.D. (assistant)
Guaranteed by
prof. RNDr. Libuše Trnková, CSc.
Department of Chemistry - Chemistry Section - Faculty of Science
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
there are 12 fields of study the course is directly associated with, display
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020.
  • Enrolment Statistics (recent)