Structure and functions of biological macromolecules 1100-2BB25

The general aim is to present the basic topics on structure and dynamics of biological macromolecules regarding their functions in the living cell, and according to the paradygm of molecular biophysics and biology, structure - activity -relationship (SAR).
Program:
1. Physical basis of macromolecular structures and interactions, intra- and intermolecular,
- classical energy of a macromoleule; force-field approximation
- thermodynamical description of a macromolecular set in solution (free Gibbs energy),
- molecular conformation and stabilizing contacts: non-bonded electrostatic interactions (hydrogen bonds, salt bridges, van der Waals), hydrophobic interactions, pi-pi stacking and cation-pi stacking, solvent effects,
- recognition specificity of macromolecules in their complexes, dynamical models of the association: induceds fit, fly-casting.
2. General review of biophysical methods: spectroscopy and X-ray diffraction, microscopy, single molecule methods, molecular modelling and structure prediction.
3. Nucleic acids, DNA and RNA:
- DNA replication, transcription, degradation,
- biological role of nucleic acids,
- DNA sequencing,
- scond- and third order structure: helices, loops, tRNA, pseudoknot, A-minor motif, ribose zipper, chromatin and supercoiling.
4. Globular, fibrous, and membrane proteins:
- protein biosynthesis (mRNA translation), topogenesis, degradation,
- biochemical roles,
- sequencing,
- secon-, third-, and fourth-order strusture, Ramachandran plot, domains and their topological classification, subunits,
- protein folding: in silico, in vitro, in vivo,
- protein and RNA enzymes; physical foundations of the enzymatic catalysis,
5. Lipids: membrane structure and dynamics.
6. Polysacharides as structural and storage materials.
7. Macromolecular complexes
8. Molecular biophysics in biotechnology and medicine (selected aspects).

Student's effort:
Lecture = 30 h
Classes = 30 h
Self-studying (2 h per week), ca. 30 h
Preparation to the examination: ca. 20 h
Total, ca. 110 h

Classes Classes are devoted to:
(a) analysis of the intra- and intermolecular interactions including the solvent (classical force field), energy, dynamics and thermodynamics of biomolecules and their complexes;
(b) computer analysis of biopolymer conformations; classification of protein domains and RNA structural motifs.

Description by Ryszard Stolarski, September 2012