Biospectroscopy

obligatory courses

Classroom

The goal of the course is to introduce students to the contemporary applications of molecular spectroscopy (with the particular emphasis being placed on optical methods) in the fields of biochemistry, biophysics, and molecular biology.

Specifically, the course is intended to:

a) revisit the physical principles of the spectroscopic methods employed in biochemistry and biophysics,

b) introduce the topic of structure and dynamics of biopolymers as the common motive in biophysical applications of molecular spectroscopy,

c) present a concrete range of research and clinical themes (both in vitro and in vivo) in the fields of molecular biophysics and biology that may be addressed by means of biospectroscopic methods,

The course will begin with an intro to the physical basis of the phenomena of absorption and emission of electromagnetic radiation by molecules. The main thematic blocks will be devoted to electronic absorption spectroscopy, fluorescence, vibrational spectroscopy: FT-IR and Raman, as well as circular dichroism. Each method will be illustrated with examples of typical applications in studies on biomolecules, proteins, nucleic acids, cells and tissues.

The following problems will be discussed in detail:

1) the hypochromic effect in electronic spectra of the double-helix DNA, and the capacity of UV-absorption spectroscopy to monitor denaturation of DNA;

2) labeling of biopolymers with fluorophores, and intracellular-movement-tracking based on FRET phenomenon;

3) fluorescence spectroscopy in clinical diagnostics, physical principles of photodynamic therapy;

4) biomedical applications of FT-IR and Raman spectroscopy;

5) conformational studies of proteins and nucleic acids employing circular dichroism.

In addition, possible applications of a variety of spectroscopic methods in solving biochemical problems (such as identification of organic compounds, structure-determination, clinical analysis) will be reviewed within the framework of the course.

Lecture = 30 hours

Individual preparation for each lecture (1 h weekly) = 15 hours

Preparation for the exam = 30 hours

Together = approximately 75 hours

In Polish:

a) P. W. Atkins, Chemia Fizyczna, PWN, Warszawa, 2003.

b) Z. Kęcki, Podstawy spektroskopii molekularnej, PWN, Warszawa, 1992.

c) L. Stryer "Biochemia" PWN, Warszawa, 2003.

d) Biospektroskopia tomy 1-5 / pod red. Jacka Twardowskiego, Warszawa, PWN, 1989.

In English:

a) Kensal E. van Holde, W. Curtis Johnson, P. Shing Ho Principles of physical biochemistry, Upper Saddle River, NJ, Pearson Education International, 2006. (Biblioteka Wydzialu Chemii UW)

b) Charles R Cantor, Paul R Schimmel Biophysical Chemistry Part I: The Conformation of Biological Macromolecules; Part II: Techniques for the Study of Biological Structure and Function; Part III: The Behavior of Biological Macromolecules, New York : W. H. Freeman and Company, 1980, 2001, 2002 (Biblioteka Wydzialu Chemii UW)

c) Donald T. Haynie Biological Thermodynamics Cambridge University Press, 2001.

Through the completion of the course, students should acquire following skills:

a) capacity to make an informed and intelligent choice of a spectroscopic method appropriate for a typical problem encountered in structural studies on proteins and nucleic acids.

b) ability to make a correct conformation-wise interpretation of circular dichroism, FT-IR, and Raman spectra of a biopolymer.

c) knowledge of the applicability range of UV-VIS, FT-IR, Raman spectroscopy, circular dichroism and fluorescence for a particular biomolecular system, given its size, homogenicity, and dynamics.

e) understanding the physical factors limiting applicability of different spectroscopic methods in biomolecular research.

Mandatory attendance. At most excused absence at 3 classes will be accepted.

Oral exam at the end of course: solving of 3 randomly selected problems. 30 minutes

None