MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description

Physics in Biology


Nanosciences and Nanotechnologies, second-level study programme


prof. dr. Janez Štrancar


Students become acquainted with molecular structure of biological systems, their excitations and roles which molecular and ionic interactions play in their formation. Particularly, they will study biological polymers – nucleic acids and proteins. Through practical work in a laboratory they will learn basics of selected spectroscopy techniques used in the research of biological macromolecules. Furthermore they will get basic knowledge about dynamics of biological molecules as well as the techniques which enable exploration of the time evolution of biological processes on molecular scale. The students also learn about structure and function of the supramolecular structures. Finally, they get familiar with the tipical interaction pathways of the several bioactive substances from toxins to nanoparticles interacting with molecular, macromolecular and supramolecular biological structures.


1. Molecular Structure and Biological Systems
* Intramolecular Bonds
Atomic orbitals
Molecular orbitals, covalent bonds
Ionic bonds
Coordinative bonds, metallo-organic complexes
Van der Waals forces
Hydrogen bonds
* Excitation and Energy Transfer
Molecular excitation and energy transfer
Mechanisms of photo-induced molecular excitation
Mechanisms of molecular energy transfer
Experimental techniques:
• UV/Vis spectroscopy
• Fluorescence spectroscopy
• Fluorescence resonance energy transfer (FRET)
* Molecular and Ionic Interactions as the Basis for the Formation of Biological Structures
The water structure, effects of hydration, hydrophobic interactions, amphiphilic molecules
Ions in aqueous solutions, the Debye-Huckle radius
Intermolecular interactions
Structure formation of macrobiomolecules
2. Biological Polymers
* Nucleic Acids
The chemical structure of nucleic acids
The double-helical structure of DNA
DNA supercoiling and unusual DNA structures
The structure of transfer RNA
* Proteins
Amino acids and the primary structure of proteins
The peptide bond and secondary structure of proteins
Tertiary structure – protein folding
Quaternary structure
Virus structure
Experimental techniques:
• Circular dichroism (CD) and optical rotary dispersion (ORD)
• Infrared spectroscopy
• Raman spectroscopy
* Dynamics of protein
Time scales of local side-chain and global dynamics
Rotational conformational spaces
Quaternary structure dynamics
Experimental technique:
• Site-directed spin labeling EPR
3. Supramolecular structures
* Biological membranes – twodimenzional supramolecular structures
Lipids – constituent of biomembranes and simple lipid vesicles
Liquid crystal nature and phase diagrams
Heterogeneity and dynamics of biomembranes
Lipid bilayers as a constrained for membrane protein structuring
Experimental techniques:
• electron paramagnetic resonance (EPR) with non-specific spin labelling
* Amphiphilic transport systems – Threedimensional supramolecular structures
Lipoprotein particles – structure and function
Pharmaceutical transport systems based on lipid solid nanoparticles
Polysaccharide structures on membrane surfaces – comparison of structure and function of surfaces between eukaryotic and prokaryotic cells
Experimental techniques:
• small angle x-ray scattering (SAXS)
4. Interaction between biological structures and bioactive substances
* Examples of interactions between bioactive molecules and macromolecules
Protein /toxin – membrane protein receptor
Nanoparticles and reactive molecules – unsaturated parts of constituents of biological structures
* Examples of interactions between bioactive molecules and supramolecular structures
Toxin / viral coat protein – membrane domains
Experimental techniques:
• confocal fluorescence (micro)spectroscopy (CFMS)

Course literature:

1. Rodney Cotterill: Biophysics: An Introduction, John Wiley & Sons, New York (2002)
2. Roland Glaser: Biophysics, Springer, Heidelberg (1996)
3. V. Pattabhi, N. Gautham: Biophysics, Kluwer (2002)
4. Jack A. Tuszynski, Michal Kurzynski: Introduction to Molecular Biophysics (Pure and Applied Physics), CRC Press (2003)
5. Victor A. Bloomfield, Donald M. Crothers, Ignacio Tinoco Jr.: Nucleic Acids: Structures, Properties and Functions, University Science Books, Sausalito (2000)
6. J. Israelaschvili: Intermolecular interactions & surface forces. Academic press, London, 1992.
7. R. Nossar, H. Lecar: Molecular and cell biophyics. Addison wesley, NY, 1991.
8. M.V. Volkenstein: General biophysics, vol. 1 & 2, Academic press, Orlando, 1983.
9. S. Kauffman: At home in the universe: the search for laws of complexity. Penguin science, London 1995.

Significant publications and references:

1. A. Omerzu, D. Mihailovic, B. Anzelak, I. Turel: Optical spectra of wet and dry M-DNA, Phys. Rev. B 75, 121103 (2007)
2. A. Omerzu, M. Licer, T. Mertelj, V. Kabanov, D. Mihailovic: Hole interactions with molecular vibrations on DNA, Phys. Rev. Lett. 93, 218101 (2004)
3. G. Zocchi, G. Gruner, A. Omerzu: Electrons on the double helix: Optical experiments on DNA, Biophys. J. 82, 61 (2002)
4. G. Zocchi, K. Grzeskowiak, G. Gruner, A. Omerzu: Intermediate states in the melting transition of DNA oligomers, Biophys. J. 82, 603 (2002)
5. J. Štrancar, M. Šentjurc, M. V. Schara: Fast and accurate characterization of biological membranes by EPR spectra. J. Magn. Reson. 142, 254 (2000).
6. M. Rappolt, H. Amenitsch, J. Štrancar, C. V. Teixeira, M. Kreichbaum, G. Pabst, M. Majerkowicz, P. Laggner: Phospholipid mesophases at solid interfaces : in situ- X-ray diffraction and spin-label studies. Adv. Colloid Interface Sci. 111, 63 (2004).
7. J. Štrancar, T. Koklič, Z. Arsov, B. Filipič, D. Stopar, M. A. Hemminga: Spin label EPR-based characterization of biosystem complexity. J. Chem. Inf. Mod. 45, 394 (2005).
8. D. Stopar, J. Štrancar, R. B. Spruijt, M. A. Hemminga: Motional restrictions of membrane proteins : a site-directed spin labeling study. Biophys. J., 91, 3341 (2006).
9. J. Štrancar: Advanced ESR spectroscopy in membrane biophysics. V: L. J.Berliner (ed.), M. A. Hemmiknga: ESR spectroscopy in membrane biophysics, (Biological magnetic resonance, vol. 27). New York: Springer, pp 49-89.


Seminar and oral examination.

Students obligations:

Seminar and oral examination.