This is an archived course. A more recent version may be available at ocw.mit.edu.

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Macromolecular Structure

  1. Introduction to Polymers:
    • Entropy and Elasticity
    • Interactions and the Coil-globule Transition
    • Single Molecule Experiments, Optical Tweezers
  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
    • Sequence Evolution and Neutral Networks
  4. Protein Folding:
    • Role of Hydrophobicity and Other Interactions
    • Secondary Structure Elements: Alpha-helices and 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: