Laboratory of elementary biophysics 1100-3BB13

The lists of obligatory and complementary exercises changes in subsequent years, depending on the possibility of presenting a specific experimental method in a given academic year.

The first two weeks of the semester - consisting of two 6-hour sessions - are dedicated to learning how to analyze and process experimental data.

The sample set of ten obligatory exercises:
1. UV/VIS absorption spectroscopy
2. Infrared spectroscopy
3. Molecular dynamic simulations
4. Isothermal titration calorimetry (ITC)
5. Fluorescence titrations
6. UV/VIS emission spectroscopy
7. Analytical ultracentrifugation
8. Kinetic studies using the stopped-flow method
9. Crystallization of proteins
10. Spectroscopic experiments that make use of microplate reader

The sample list of complementary exercises:
1. Differential scanning calorimetry (DSC)
2. Spectroscopy of circular dichroism (CD)
3. NMR spectroscopy
4. ATR FTIR spectroscopy
5. Scintillation counter in enzymatic activity measuremets
6. Isotope methods
7. Chromatographic methods
8. Life-times of excited states
9. Mass spectrometry (MS)
10. Spectroscopic studies of tautomeric forms of nucleic acid components.
11. Ionic forms, spectrophotometric determination of pK and pK*

Course coordinators

Maria Bzowska
Maria Winiewska-Szajewska

Type of course

obligatory courses

Mode

Classroom

Prerequisites (description)

Laboratory classes in the basics of molecular biophysics are available for students who passed the following exams: Physics I, II, III, Mathematics I, II, III, Analysis of measurement uncertainties, Preliminary laboratory for biophysicists, Cassical mechanics, Introduction to quantum mechanics of molecular systems, Physics of molecules and macromolecules in aqueous media, Introduction to microbiology and molecular biology, Organic and bioorganic chemistry, Laboratory of chemistry, Methods of molecular biophysics The main goal of Laboratory of elementary biophysics is to introduce students of specialization Molecular biophysics to modern experimental methods used in molecular biophysics. Theoretical bases of these methods were described in the frame of two previous courses. e.g. “Methods of molecular biophysics”. The laboratory consists of short, 6-hours, one-day experiments that are conducted together by two students. In the case of sophisticated equipment such as analytical centrifuge or microcalorimeter experiments are done by two such groups (maximum four students) working together. The course of all experiments is well defined to use the short time devoted to each experiment in the optimal way. Most of the methods presented during these experiments will be then studied in more detail on the frame of Laboratory of biophysics for advanced, which consists of longer experiments that give students more freedom to plan their experiments, similar as in Laboratory of physics for advanced. The first two weeks of the semester - consisting of two 6-hour sessions - are dedicated to learning how to analyze and process experimental data.

Learning outcomes

Knowledge:
1. Basis of molecular spectroscopy
2. Structure and spectroscopic properties of nucleosides, nucleotides, nucleic acids, aminoacids and proteins
3. Spectroscopic methods used in biophysical studies
4. Methods to analyze protein-ligand interactions
5. Kinetics and inhibition of enzymatic reactions
6. Basis of analytical ultracentrifugation
7. Methods for crystallization of proteins

Skills:
1. To conduct simple experiments in molecular biophysics
2. To work in team
3. To use basic equipment useful in biophysical studies
4. To analyze and present the results of experiments

Attitudes:
1. Understanding what means ethics in science
2. Responsibility for results of experiments
3. Proper behaviour while working with chemical and biological samples and with the equipment use in biophysical studies

Assessment criteria

Number of permitted absences and the rules of absence management:
maximum two justified absences per semester

Credits for the Laboratory are given based on:
1. positive notes for entrance colloquia
2. performance while conducting experiments
3. positive notes for laboratory reports that were prepared individually by each student

Bibliography

1. R.A. Copeland, „Enzymes” Wiley-VCH, New York
2. A. Fersht, „Structure and mechanism in protein science” W.H. Freeman and Company, New York
3. G.U. Nenhaus „Protein-ligand interactions. Methods and applications” Human Press, Totowa, New Jersey.
4. C.A. Parker „Photoluminescence of solutions” Elsevier, Amsterdam
5. J.R. Lakowicz, „Principles of Fluorescence Spectroscopy”, Kluwer Academic/Plenum Press Publisher, New York, Boston, Dordrecht, London, Moscow
6. T.A. Waigh "Applied Biophysics", John Wiley & Sons Ltd
7. J. Drenth "Principles of Protein X-Ray Crystallography" Springer
8. P.W. Atkins "Physical chemistry"

Additional information

Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:

Applications of Physics in Biology and Medicine, first cycle programme