Download Molecular Models for Biochemistry at CMU

Molecular Models for Biochemistry at CMU
http://info.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html
The linked pages described here have tutorials and quizzes that are based on Chime and RasMol
images of the molecules and macromolecules found in biochemistry. They are intended to complement
standard biochemistry texts where more explanation is provided, but where interactive 3-D images of
the molecules are not available.
Please see viewing suggestions below before choosing a topic.
SMALL MOLECULE GALLERY
Introduction & Index to Chime displays of some textbook examples used in the Modern
Biology (03-121) and Cell Biology (03-240) courses at CMU.
Also shown are some protein and lipid bilayer structures.
Quizzes (T-F and Chime) on functional groups are linked from the page.
Practice Quizzes: A separate listing of the Chime and GIF-based quizzes at this site.
AMINO ACID STRUCTURES
Amino Acid & Peptide Structures are viewed as Chime-generated images.
Take an Amino Acid Structure Quiz based on GIFs from the above tutorial.
Structures are shown as a collection of Amino Acid GIF images.
Amino Acid Identification Quizzes
The names, abbreviations, and one-letter codes are tested in three formats:
1.
2.
3.
Chime images.
Ball & Stick GIF images.
Spacefill GIF images.
PROTEIN STRUCTURES
Protein Architecture using Chime-generated images of Protein G.
Take a Protein Structure Quiz using GIFs from the Protein Architecture tutorial.
Selected Chime Displays of proteins & nucleic acids from CMU biochemistry courses.
Chime Displays with a RasMol Command Line of Crambin and BPTI.
MEMBRANE CHANNEL & PUMP STRUCTURES
Introduction and links to these molecular models:
KcsA K+ Channel: Closed state of the pore.
MthK K+ Channel: Open state of the pore.
KvAP: Voltage-gated K+ channel.
KirBac1.1 K+ Channel: Bacterial inward-rectifier channel.
Acetylcholine Receptor Models: AChR pore domain and the AChBP.
EcClC Chloride Channel: Wild type (closed) & mutant (open) states.
E. coli Glycerol Channel: Glycerol-specific, but water permissive.
AQP1: Aquaporin Channel: one of the 10 water-only channels in mammals.
AqpZ: Aquaporin Channel: the only water-only channel in E. coli.
MscS: Mechanosensitve small conductance channel.
MscL: Mechanosensitve large conductance channel.
SecY: Protein-conducting channel.
Ionophores: Gramicidin and Valinomycin.
ATP Synthase: Proton flows & protein conformational changes.
SERCA1 Ca2+ Pump: Two key conformations compared.
Bacteriorhodopsin: All-trans and 13-cis retinal conformations compared.
Halorhodopsin: The light-driven chloride pump.
AcrB Multidrug Resistance Pump: Four enzyme-drug complexes are compared.
BtuF & BtuCD: Vitamin B12 ("ABC") Transporter Complexes.
Lactose Permease: Symporter of galactosides and protons in E. coli.
Glycerol-3-Phosphate Transporter: Antiporter of G-3-P and Pi in E. coli.
ADP/ATP Transporter: Antiporter of nucleotides in the mitochondrion.
STRUCTURES FOR MOLECULAR BIOLOGY
Estrogen Receptor Structures & Functions: Includes an Overview of selected ER topics.
Several ligand-binding domain models and the DNA-binding domain are displayed on Chime
pages.
Ribosome Structures:
1. Overview of the 70S crystal structure and a Chime animation of steps in translation.
Separate pages show selected features of the 30S and 50S subunits.
2. 50S subunit structure
: Overview plus three pages showing details of 23S RNA
structure with close-ups of substrates and products bound to the peptidyl transferase active site.
Introduction and links to these molecular models:
B-Form DNA helix
A-Form RNA helix
cAMP Receptor Protein (CRP)
Human hnRNP A1
snRNP U1A
EF-Tu, tRNAPhe, and GTP
Zif268 Zinc Finger
EcoRI Restriction Endonuclease
HhaI Restriction Methylase
Nucleosome
METABOLIC PATHWAYS
Glycolysis. Chime-generated intermediates on the glycolytic pathway.
TCA cycle. Chime-generated intermediates in the tricarboxylic acid cycle.
ADDITIONAL TOPICS from CMU biochemistry courses.
Biochemistry I: (03-231) Fall Term, 2002 and (03-232) Spring Term, 2002.
Course links to Chime pages showing:
Small Molecules & Building Blocks and to Protein Structure Examples.
Periodic Table of Elements. Chime display that illustrates the RasMol CPK coloring scheme.
LINKS to other sites with graphics displays related to biochemistry.
Please note the following for optimal viewing:
These pages all require a frames-enabled browser, such as Netscape Navigator 4.7. See Netscape's
home page for current information. Microsoft Internet Explorer 6 displays most of the Chime plug-in
pages adequately.
In addition, JavaScript must be enabled. Navigator 4: Select Preferences... under the Netscape Edit
menu; then Advanced.
The following plug-in is required for viewing most of these pages unless "GIF" appears in the link or
description. (All of the CMU cluster Macs and PCs have Chime installed):
Chemscape Chime Plug-in v2.6.
Get the Chime plug-in from the MDL Inc. software download page. It is now available for the Mac,
Windows, and SGI IRIX computers (v0.9z, only). Internet Explorer 6, on a Windows platform, appears
to function well; see the MDL page, Release Notes v2.6 for details. After installing this plug-in, try out
the moving images at the MDL Inc. site.
The CMU Chime Tutorial, written by Dr. Gordon Rule, takes you step-by-step through most of the
features of the Chime 2.6 menu selections.
The Chime 2.6 Viewer's Guide summarizes the Chime menu choices in capsule form; it is available
as a PDF document from the CMU Chime Tutorial Introduction page.
RasMol v2.6 by Roger Sayle.
The RasMol Home Page maintained by Dr. Eric Martz, provides RasMol in versions for several
operating systems, with installation instructions, and extensive supplementary resources. Included are
Frequently Asked Questions (FAQ), tutorials on how to use RasMol, and several documents on how to
create "movie" scripts.
This site also has several different kinds of Chime-based tutorials and detailed instructions for creating
Chime images on WWW pages. See the Chime Resources page for these offerings.
The RasMol Manual (160K) has been updated to v2.6 and converted to HTML format. It can be read
(or downloaded) at the above site.
The RasMol Manual: Frames added some new features to the v2.6 HTML Manual and permits faster
navigation between topics.
The CMU RasMol Tutorial is an on-line version of the tutorial written by Dr. David Hackney for use
in our biochemistry courses.
Are you an experienced RasMol user?
The interactive RasMol Quiz will test your mastery of RasMol commands.
You should also look at the CMU Chime Features page, for a short demonstration on how this plugin is used with the molecular models shown here.
Unless otherwise noted, the small molecule atomic coordinates are from Klotho: Biochemical
Compounds Declarative Database.
Some of the topics on this page can be downloaded as StuffIt files for individual or local server use.
For information, please contact:
Dr. William McClure
[email protected].
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213
2.24.04