Chemistry 432 - Physical Chemistry for the Life Sciences

Physical Chemistry for the Life Sciences Fall Semester 2009
Professor Peter Qin LJS 251 Tel: : (213) 821-2461 pzq@usc.edu


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Resources

2008 Midterm 1 key

2008 Midterm 2 key

2008 Final key

Additional Practice Questions / Keys

Odd questions, Aktins Ch.1 – Ch.8, Key

Questions from Tinoco Text

Chapter 2; key
Chapter 3; key
Chapter 4; key
Chapter 5; key
Chapter 7; key
Chapter 8; key
Extra problems on optical spectroscopy; key

THERMODYNAMICS

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

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

?2002, Chemistry Dept., University of Southern California

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