General description

This course introduces physical aspects of the interactions of biological molecules and some cellular processes. It will also provide understanding how composition determines the structure and properties of proteins, DNA, and RNA and membranes. Practical classes will be focused on design of peptides and oligonucleotides with desirable properties, skills to use specialized software and web services, investigation of mechanisms of biological processes with special attention to the issues that arise in drug development.


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Details of the curriculum

Course: 7 lectures, 4 seminars

Lectures: Volodymyr Shvadchak

Seminars: Volodymyr Shvadchak, Ivan Muzalov


1. Structure of proteins

Covalent, hydrogen, ionic bonds. Individual molecules and biopolymers. Diffusion and size of molecules. Primary, secondary, ternary structure of proteins. Disulfide bonds. Relationship between amino acid sequence and secondary structure. Structure prediction, MD.

2. DNA and RNA

Complementarity. Helix.  Hairpins. tRNA. Annealing. UV absorbance to monitor dsDNS-ssDNA transition. Atypical conformations. Viral and non-coding RNA. RNAzymes.

3. Membrane

Lipid bilayer. Model membranes. Membrane phase. Structure and composition of cell membrane. Proteins and membranes. Membrane permeability. Membrane asymmetry. Transmembrane potential. Channels.

4. Molecular machines and bioenergetics.

ATP-synthase. Bacterial flagella.

5. Transport in cells.

Tubulin microtubules. Kinesin and dynein. Actin microfilamens and myosin.

6. Thermodynamics.

Reversible and irreversible processes. Laws of Thermodynamics. Heat and reaction enthalpy. Entropy. ΔG. Nernst equation. Hess law. Equilibrium constants. Determining Kd and stoichiometry of protein interactions.

Biophys_L6.pptx (503.06 KB)
7. Kinetics.

First-order reactions. Two-stage reactions. Reversible reaction rates and equilibrium constants. Second order reaction. Kinetics in complex systems. Basics of kinetic modelling. Modeling of epidemics development. Catalysis. Kinetics of fermentative reactions. Inhibition. Kinetics in studies of reaction mechanisms.

Seminar 1 (Shvadchak)

Protein structure. Construction of peptides. DNA/RNA structure. Online calculators of oligonucleotide and peptide properties Lipids and membranes.

Useful links: 

Oligonucleotide properties calculator

Peptide property calculator

Seminar 2 (Muzalov)


Seminar 3 (Muzaliov)

Bioenergetics. Motor proteins.

Seminar 4 (Shvadchak)

Numerical modelling of reaction kinetics.

Additional materials
Visualization of 3D structure of biological molecules

Download VMD

Download protein structrue files with atom coordinates  (PDB format).

Undergraduate students
7 Lectures
Practical classes
4 Lesson
3 Months

Chief engineer Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine


Employee of the Precarpathian University (Ivano-Frankivsk) and the Institute of Organic and Bioorganic Chemistry (Prague). Doctorate degree in Life sciences (PhD) was obtained from Strasbourg University in 2009 for research work on the development of solvatochromic fluorescent labels for studies of protein interactions.
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