1. Introduction

   1. Orientation
      1. The Basics
      2. The Toolbar
      3. Scripting in JSmol
   2. Methane and Cyclohexane
   3. Glucose and Its Anomers
   4. The Double Helix
2. Fundamentals

   1. Water: The Realm of Biochemistry
      1. Water and Ice
      2. The Hydrophobic Effect
         1. Introduction
         2. Hydration of Methane
         3. Janus Molecules I
         4. Janus Molecules II
      3. Amphiphilic Molecules
   2. Noncovalent Interactions
      1. Van der Waals Interactions
      2. Ionic Interactions
         1. Ionic Bonds
         2. Ion-Dipole Interactions I
         3. Ion-Dipole Interactions II
      3. Molecular Recognition
         1. Hydrogen Bonds and Coulombic Interactions
         2. Pi-Based Interactions
3. Nucleic Acids

   1. Molecular Complementarity
      1. Nucleotides
      2. Watson-Crick Base Pairs
   2. DNA Architecure
      1. From A to Z
      2. Nucleic Sugars
   3. DNA and RNA Aptamers
      1. Introduction
      2. Backbone Flexibility
      3. Oligonucleotide Conformations
      4. Case Studies
   4. Homo-DNA and Nature's Choice of Pentose
   5. Transfer RNA
   6. Pseudoknots in RNA
4. Protein-Nucleic Acid Interactions

   1. Active Site of the Ribosome
   2. Trp RNA-Binding Attenuation Protein (TRAP)
   3. Transcription Factors
5. Amino Acids and Peptides

   1. Amino Acids
      1. Overview
      2. Glycine, Alanine and Proline
      3. Branched-Chain
      4. Aromatic
      5. Polar (Charged)
      6. Polar (Uncharged)
      7. Sulfur-Containing
      8. Flash Cards
   2. Peptides and the Peptide Bond
   3. The Disulfide Bond
6. Protein Architecture

   1. Secondary Structure
      1. The Alpha Helix
         1. Introduction
         2. The α-Helix
         3. Amphipathic α-Helices
         4. Proline and the α-Helix
         5. Summary
      2. Beta Sheets and Turns
         1. Beta Strands and Antiparallel Sheets
         2. Beta Turns
         3. Parallel Beta Sheets
      3. The Beta Helix
   2. Tertiary Structure
      1. All-Beta Proteins
      2. All-Alpha Proteins
         1. Lambda Repressor
         2. HIV-1 p17
      3. Alpha/Beta Proteins
7. Quaternary Structure of Proteins

   1. Introduction
   2. Hydrophobic Interfaces
      1. Association
      2. Buried Hydrogen Bonds
      3. Interchain Salt Bridges
   3. Protein Symmetry
      1. Transthyretin
   4. Domains and Modular Proteins
      1. KIX, pKID and c-Myb
   5. Supercoiled Protein Motifs
      1. The Collagen Triple Helix
      2. Coiled-Coil Proteins
         1. GCN4 Leucine Zipper
8. Functional Diversity of Proteins

   1. Oxygen Transport
      1. Myoglobin
         1. The Globin Fold
         2. The Oxygen-Binding Pocket
         3. Helix Crossing
         4. O₂ Binding
         5. Changes in Heme Iron
      2. Hemoglobin – An Allosteric Protein
         1. Quaternary Structure
         2. Ion Pairs in Deoxyhemoglobin
         3. BPG Binding
   2. The GroE Chaperonin
      1. The GroEL-GroES Chaperone
      2. Chaperonin 60: ATP Binding and Allostery
      3. Anfinsen's Cage
      4. The Bullet Complex
9. Enzymes

   1. Pepsin
   2. Pepsinogen
10. ATP Synthase

    1. Quaternary Structure
    2. Open and Closed States
    3. Functional Side Chains
11. Review Class Lectures

    1. Jeopardy Review Board