Molecular Models for Biochemistry at CMU

Molecular Models for Biochemistry at CMU

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.

SMALLMOLECULEGALLERY

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.

AMINOACIDSTRUCTURES

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:

PROTEINSTRUCTURES

Protein Architecture using Chime-generated images of Protein G.

Protein Structures shown in Campbell using Chime-generated images.

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.

NUCLEOTIDE &NUCLEICACIDSTRUCTURES

Overview of DNA & RNA Structure.

A Tour of tRNA Structure: A Chime-based tutorial on Yeast tRNA^Phe structure; and
An "animated" RasMol tour of the crystal structure.

Structures of Base Pair Stacking in DNA & RNA.

Nucleotide Identification Quizzes
The names and abbreviations are tested in two formats:

Chime images.
Ball & Stick GIF images.

STRUCTURESFORMOLECULARBIOLOGY

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:

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.

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, tRNA^Phe, and GTP
Zif268 Zinc Finger
EcoRI Restriction Endonuclease
HhaI Restriction Methylase
Nucleosome

METABOLICPATHWAYS

Glycolysis. Chime-generated intermediates on the glycolytic pathway.

TCA cycle. Chime-generated intermediates in the tricarboxylic acid cycle.

ADDITIONALTOPICS from CMU biochemistry courses.

Advanced Biochemistry (03-740) Fall Term, 1998.

Physical Biochemistry (03-438) Spring Term, 2000.

Biochemistry I: (03-231) Fall Term, 2000 and (03-232) Spring Term, 2001.
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.

LINKSto 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 3.01 or Navigator 4.05. See Netscape's home page for current information. (Microsoft Internet Explorer 4 (still) does not handle the Chime plug-in displays adequately, but may work on some of the GIF-based quizzes.); 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):; You should also look at the CMU Chime Features page, for a short demonstration on how this plug-in is used with the molecular models shown here.; Unless otherwise noted, the small molecule atomic coordinates are from Klotho: Biochemical Compounds Declarative Database.; Adjust your Netscape window to a width of about 9-10 inches (640-700).; 7.9.01