Biophysics (09 2023)

General description

This course is designed to introduce 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.

Lectures
1. 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.

2. 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. CD spectroscopy.

3. DNA and RNA.

Complementarity. Helix.  Hairpins. tRNA. Annealing. UV absorbance to monitor dsDNS-ssDNA transition. Atypical conformations. Viral and non-coding RNA. RNAzymes. Software for protein and DNA structure visualization.

4. Membrane.

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

5. Kinetics.

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

6. Molecular machines and bioenergetics and transport in cells.

ATP-synthase. Bacterial flagella. Tubulin microtubules. Kinesin and dynein. Actin microfilaments and myosin.

Seminars
1. Calculations of binding and dissociation constants. Equilibria in solution. Methods to study protein interactions.
2. Design of peptides with desirable properties. DNA hairpins. Online properties calculators for peptides and oligonucleotides. Model membranes.
3. Kinetics of protein interactions. Inhibition mechanism on kinetic level. Simulation of complex reaction kinetics in Excel.
Presetation_topics_for_seminar_biophys_28-10-2023.pdf (download) (open in a new tab) (Size: 0.1M)
4. VMD software for protein structure visualization. Channels. Molecular machines. Motor proteins.

Сторінка завантаження програми VMD https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Cайт де можна скачати файли структур молекул з координатами атомів https://www.rcsb.org/  (в форматі PDB).

VMD short tutorial.pptx (1.56 МБ)

Рекомендована література
Підручники

Термодинаміка
David G. Nicholls, Stuart J. Ferguson Bioenergetics https://Booksite.Elsevier.Com/9780123884251/   розділ 3

Кінетика
Dagmar Klostermeier,  Markus G. Rudolph Biophysical Chemistry ISBN 9781482252248 (e-book) / розділ 2
 

Структура протеїнів
Dagmar Klostermeier,  Markus G. Rudolph Biophysical Chemistry ISBN 9781482252248 (e-book) / розділ 16

Структура ДНК та РНК
Dagmar Klostermeier,  Markus G. Rudolph Biophysical Chemistry ISBN 9781482252248 (e-book) / розділ 17

Мембрани та біоенергетика
David G. Nicholls, Stuart J. Ferguson Bioenergetics https://Booksite.Elsevier.Com/9780123884251/ розділ 2 (іонний транспорт крізь мембрани) розділи 6 та 7 (фотосинтез та синтез АТФ)

 

Level
Bachelor and master students
Lectures
6 Lectures
Practical classes
4 Lesson
Duration
3 Months
Language
Ukrainian
Certificate
as part of the course
Lecturers

Volodymyr Shvadchak

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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