• A series of pages that show a very simplified system of four molecules in a set of evenly spaced energy levels.
• Hydrogen Bonding in a water dimer.  DE(binding) = 20 kJ/mol.
  Uses Chime to view 3D structure
• a-helix hydrogen bonding
• The entropy driven hydrophobic effect
• Exploring DNA and base pairing 
  Explore how base pairing in DNA works, the constituent molecular components of DNA and where the hydrogen bonding takes place. Uses Chime scripting and thus only works in Netscape.
• Pulling a single molecule of DNA and measuring the force
• Fidelity in DNA replication
  Background on chain extension adn DNA replication 
  Mechanism of DNA Polymerase (Movies)

REDOX REACTIONS

• 3D Structure of small water-soluble Cytochrome c protein - the electron carrier from the bc₁ complex to CcO 
• General information about the terminal respiratory-chain redox protein:  cyctochrome c oxidase (CcO).  Includes 2D images, diseases links and links to research groups working on this protein.
• 3D structure of CcO (T.TSUKIHARA et al.)
• Information, including 3D structures, on the bc₁ complex
• Find any protein structure that has been solved from the RCSB protein databank.

You will need the Chime plug-in to see these structures.  This is installed on campus student computing room computers or can be obtained free by following download link at top of this page.  Use of Netscape as browser is strongly recommended when using the Chime plug-in.

KINETICS

• Timescales in Chemistry and Biology
• Reaction simulator.  Explore the forward and backward reaction kinetics at the molecular scale.  This Java simulation lets you experiment with changing the rates, temperature and concentration and graphs the time dependence of the molecular concentrations.
• The approach to equilibrium.  Use this live graph to try different values in the mathematics for the relationship between the rate and equilibrium constants.
• Collision Theory and the steric factor - real reactive collision trajectories for the Br + HI reaction
• Viewing the fleeting transition state

ENZYME KINETICS

• Michaelis-Menten enzyme kinetics
• Example of Lineweaver-Burke Analysis
• Explore the catalase enzyme (You will need the Chime plug-in to see these structures)
• Comparison of different catalysts on the decomposition of hydrogen peroxide
•  Explore Catalase structure and mechanism in greater detail (uses specifically Netscape and Chime)

SINGLE MOLECULE SPECTROSCOPY

• Using single molecule fluorescence to follow the kinetics of a single enzyme
• Near-Field (NSOM)

PHOTOBIOLOGY

• Ultrafast kinetics - the photosynthetic reaction center
• Photosynthetic proteins: LH2 You will need the Chime plug-in to see this structures.
• Fluorescence Spectroscopy of a single LH2 complex (Science 285, 400 (1999))

• Photosynthetic proteins: RC You will need the Chime plug-in to see this structures.

• Photosynthetic proteins: Background

FRET

PROTEIN STRUCTURE DETERMINATION

• Tutorial on Peptide and Protein Structure
• Home page for The Protein Data Bank (PDB)
• Nature of 3D Structural Data from PDB

SCANNING PROBE MICROSCOPY

• STM image of atomically resolved graphite surface, and a long chain molecule on a graphite surface
• AFM of operation RNA polymerase.  The DNA is pulled through the RNA polymerase, which is bound to a surface.  (Movie also)

THE HUMAN GENOME

• LLNL human genome center
• Capillary Array Electrophoresis (CAE).
   DOE Human Genome Program Report

GENERAL

• Online journals at USC