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,    ...

lec1- Structure