# Macromolecular Structure

1. Introduction to polymers:
   - Entropy and elasticity
   - Interactions and the coil-globule transition
   - Ionic interactions
2. DNA double helix:
   - Watson-Crick pairs; symmetries
   - Energy/entropy considerations, and melting
   - Elasticity; bend, twist, and topology
   - Unzipping; translocation, packing, …
3. RNA strands:
   - Varieties: mRNA, tRNA, ribosomal RNA, …
   - Hartree equation for obtaining secondary structures without pseudo-knots
   - Kinetics folding (local minimum) vs thermodynamics hypothesis (global minimum)
4. Sequence to Structure maps
5. Protein folding:
   - Role of hydrophobicity and other interactions
   - Secondary structure elements: alpha-helices & beta-sheets
   - Classification of protein structures, and their evolution
   - Simple lattice models of protein folding, solvation model
   - Random Energy Model for freezing
   - Dynamics of fast folding
   - Folding in the cell: chaperones, co-translational, agregation and fibrils
   - Hemoglobin: evolution, polymorphism, folding and fibrilation, function, regulation, …
6. Protein-Nucleic acid composites:
   - Electrostatic interactions
   - Specific and non-specific binding of factors to DNA regulatory elements
   - Borg-von Hippel, wight matrices (profiles), information content
   - Large scale packaging of DNA; histones, heterochromatin, …

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