Molecular Biophysics

Data

Official data in SubjectManager for the following academic year: 2022-2023

Topic

The aim of the Biophysics curse is to introduce the students to the methods and applications, which are routinely used in both the medical and pharmaceutical biotechnology. The principles of the state-of the art approaches and instrumentations are covered by the topics. The course presents diverse spectroscopic techniques (absorption, fluorescence, infrared, Raman, EPR, NMR, …) imaging approaches (light and fluorescence microscopy, EM, super-resolution fluorescence microscopy, MRI, …), radioactive applications and calorimetric and fast kinetics techniques. The lectures discuss in details the physical basis and principles of each approach and the field of applications. The practicals are dedicated to extend the students’ knowledge and routine in the use of the different techniques. The practicals lay special emphasis on presenting not only the routine applications, but advanced uses of each technique. The limitations, as well as the artefacts that can be caused by improper experimental planning are highlighted.

Lectures

• 1. Introduction - Dr. Bugyi Beáta
• 2. Databases, resources. - Dr. Bugyi Beáta
• 3. Electromagnetic radiations. - Dr. Grama László
• 4. Quantummechanical model of atoms, quantum numbers. - Dr. Grama László
• 5. Energy levels of atoms and molecules. - Dr. Lukács András Szilárd
• 6. Laser. - Dr. Lukács András Szilárd
• 7. UV-VIS spectroscopy. Circular dichroism (CD) spectroscopy. - Dr. Huber Tamás
• 8. Infrared and Raman spectroscopy. - Dr. Bugyi Beáta
• 9. Fluorescence spectroscopy, fluorescence parameters. Förster resonance energy transfer (FRET). - Dr. Huberné Dr. Barkó Szilvia
• 10. Flow cytometry. Fluorescence activated cell sorting. - Dr. Huberné Dr. Barkó Szilvia
• 11. Electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR) spectroscopy. - Dr. Grama László
• 12. Magnetic resonance imaging (MRI). - Dr. Grama László
• 13. Basics of light microscopy and fluorescence microscopy. - Dr. Bugyi Beáta
• 14. Advanced fluorescence microscopy: confocal microscopy, fluorescence recovery after photobleaching (FRAP), multi-photon microscopy, FRET, FLIM, TIRFM, STED, SIM, single molecule localization microscopy. - Dr. Bugyi Beáta
• 15. Scanning probe microscopy, electron microscopy. - Dr. Bugyi Beáta
• 16. Image analysis. - Dr. Bugyi Beáta
• 17. X-ray diffraction. - Dr. Talián Csaba Gábor
• 18. Rapid kinetic methods: stopped-flow, surface plasmon resonance (SPR). - Dr. Kengyel András Miklós
• 19. Sound. Ultrasound. - Dr. Kengyel András Miklós
• 20. Radioactivity, interaction of radioactive radiations with matter. - Dr. Szabó-Meleg Edina
• 21. Dosimetry, detection of radioctive radiations. - Dr. Szabó-Meleg Edina
• 22. Biological effects of radioactive radiations. - Dr. Kengyel András Miklós
• 23. Gamma-camera, computed tomography (CT), single-photon emission computed tomography (SPECT), positron emission tomography (PET). - Dr. Kengyel András Miklós
• 24. Thermodynamics: laws, thermodynamic potentials. - Dr. Lukács András Szilárd
• 25. Calorimetric methods: differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC). - Dr. Lukács András Szilárd
• 26. Analytical separation techniqes: sedimentation, electrophoresis, chromatography. - Dr. Talián Csaba Gábor
• 27. Mass spectrometry. - Dr. Talián Csaba Gábor
• 28. Revision - Dr. Bugyi Beáta

Practices

• 1. Introduction
• 2. Data bases, resources (P, S)
• 2. Laser (P)
• 3. Raman and infrared spectroscopy (P)
• 4. UV-VIS spectroscopy (P)
• 5. Fluorescence spectroscopy 1: steady state spectroscopy (P)
• 6. Fluorescence spectroscopy 2: time dependent spectroscopy (P)
• 7. Light microscopy (P)
• 8. Image analysis (P)
• 9. Rapid kinetic measurements: stopped-flow (P)
• 10. Ultrasound (P)
• 11. Revision (TBL)
• 12. Preparation for the test/consultation (TBL)
• 14. Test

Seminars

Reading material

Obligatory literature

Sándor Damjanovich, Judit Fidy, János Szöllősi (eds.): Medical Biophysics, 3rd revised version, Medicina Budapest 2009

Literature developed by the Department

http://www.biofizika.aok.pte.hu/tantargy/Molecular_Biophysics_Lectures_-_Biotechnology
http://www.biofizika.aok.pte.hu/tantargy/Molecular_Biophysics_Practicals_-_Biotechnology

Notes

http://www.biofizika.aok.pte.hu/tantargy/Molecular_Biophysics_Lectures_-_Biotechnology
http://www.biofizika.aok.pte.hu/tantargy/Molecular_Biophysics_Practicals_-_Biotechnology

Recommended literature

Recommended textbooks and resources
educational materials at the Home Page of the Department of Biophysics
http://biofizika.aok.pte.hu/en
your own notes
OpenStax College Physics: http://cnx.org/contents/031da8d3-b525-429c-80cf-6c8ed997733a@9.1:1/Preface
HyperPhysics website: http://hyperphysics.phy-astr.gsu.edu/hbase/hframe.html
HyperPhysics website

Conditions for acceptance of the semester

Maximum of 15 % absence allowed

Mid-term exams

Theoretical exam
There will be one oral exam at the end of the semester.
Exam topics are based on the lecture topics. Students pick two questions from the list of exam topics (see below), following preparation they have to present the topics explaining all the keywords that appear in the title of the question.
Grading policy: Students get two grades, one for each topic. The final exam grade is given based on the average of the two grades. If any of the two grades are failed (1), the final exam grade is failed.

Practical exam
There will be one written exam at the end of the semester (14th week).
Grading policy: Students get one final practical grade based on the following activities:

activity percentage
Result of the written exam 70 %
In-class experiments, lab notes 15 %
Written homework 15 %

Making up for missed classes

Can be discussed with the course leader.

Exam topics/questions

http://www.biofizika.aok.pte.hu/tantargy/Molecular_Biophysics_Lectures_-_Biotechnology
http://www.biofizika.aok.pte.hu/tantargy/Molecular_Biophysics_Practicals_-_Biotechnology

Examiners

• Dr. Bugyi Beáta
• Dr. Grama László
• Dr. Kengyel András Miklós
• Dr. Lukács András Szilárd
• Dr. Szabó-Meleg Edina

Instructor / tutor of practices and seminars

• Dr. Bugyi Beáta
• Dr. Bukovics Péter
• Dr. Huber Tamás
• Dr. Kengyel András Miklós
• Dr. Szabó-Meleg Edina
• Karádi Kristóf Kálmán
• Tempfliné Pirisi Katalin Erzsébet