Macromolecular structure and interactions

SUMMARY
This course covers the basic biophysical principles governing the thermodynamic and kinetic properties of biomacromolecules involved in chemical processes of life. The course is held in English.

CONTENT
1 The conformation of biological macromolecules and membranes
1 Forces in biomolecules
2 Protein primary and secondary structure
3 Tertiary structure of proteins
4 DNA structure
5 Conformations of unstructured polymers in solution (Gaussian chain models, freely-jointed chain, wormlike chain)

2 Spectroscopy of Biomolecules
1 Biomolecular absorption spectroscopy (UV absorption, circular dichroism)
2 Biomolecular fluorescence
3 X-ray crystallography of proteins

3 Conformational equilibria and dynamics of polypeptides and proteins1 Thermodynamics of protein folding (folding equilibria, calorimetry of protein folding transitions)
2 Kinetics of protein folding (folding pathways, intermediates)
3 Conformational transitions in proteins (native state fluctuations, allostery, structural rearrangements in enzyme
catalysis)
4 Thermodynamics and kinetics of alpha-helix -## coil transitions

4 Transport phenomena and stochastic processes in biology
1 Fluctuations in biology
2 Macromolecular diffusion
5 Thermodynamics and kinetics of ligand-receptor interactions
1 Equilibrium binding reactions
2 Binding inhibition
3 Kinetics of ligand binding

Keywords
biophysics, biophysical chemistry, protein, nucleic acid, structure, thermodynamics, kinetics, protein folding,
spectroscopy, fluorescence, absorption, helix-coil, fluctuations, receptor, ligand

LEARNING PREQUISITES
Required courses
Biochemistry I
Chemical thermodynamics
Important concepts to start the course
General chemical and biochemical concepts

LEARNING OUTCOMES
By the end of the course, the student must be able to:
Describe the molecular forces governing biomolecular structure
Explain experimental strategies to investigate structure and dynamics of biomolecules
Judge the quality, validity and significance of biophysical experiments in the research literature
Make order of magnitude estimates for biophysical processes
Apply kinetic models to understand dynamic processes in biomolecules
Establish basic knowledge on kinetic processes in proteins and in protein-ligand interactions
Implement models to rationalize ligand binding processes and interference with inhibitor compounds
Design quantitative experimental approaches to investigate biological processes