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)
• Sequence to Structure maps

4. 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, ...

5. 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,    ...