Computer-based Visualizations for Biology
Examples for DNA Replication and Muscle Contraction

by Peter Berget, November 10, 2000
CIL/OTE/Eberly Center Seminars on Technology for Education
"Computer-Based Visualization: Can it Help Learning?"

1. Static Representation of DNA Replication

   This is an example of the way my depiction of DNA replication used to look on the chalkboard, followed by the way it is depicted in textbooks and on static Web pages. This page is excerpted from my current Web support pages for Modern Biology (03-121). There are links to both Chime and GIF images of DNA polymerases as well as to the animation listed immediately below.

2. Animation of Replication Process

   (Adapted from media provided with Purves, Orians, Heller & Sadava, 1997. Life - The Science of Biology. ISBN 0-7167-3325-0. Sinauer & Associates, Sunderland, MA.)

   This modified animation depicts the dynamic nature of the DNA replication process. It also points out one of the difficult concepts to get across to students, the continuous and discontinuous replication processes on opposite strands of the DNA template.

3. Animation of the Sliding Clamp (Beta-subunit of E. coli DNA polymerase III)

   (Adapted from media provided with Lodish, Berk, Zipursky, Matsudaira, Baltimore & Darnell, 2000. Molecular Cell Biology. ISBN 0-7167-3136-3. W. H. Freeman and Company, NY, NY)
   This extremely simple animation shows in much greater accuracy, the coupling of the discontinuous and continuous replication processes on both of the template strands. (Something that is missed in item #2 above.)

4. Beta-subunit of E. coli DNA polymerase III

   Requires Chime Plug-in
   (Adapted from media provided with Lodish, Berk, Zipursky, Matsudaira, Baltimore & Darnell, 2000. Molecular Cell Biology. ISBN 0-7167-3136-3. W. H. Freeman and Company, NY, NY)

   This is a Chime-based tutorial on the structural features of the sliding clamp depicted in item #3 above. It uses the 3D X-ray crystallographic coordinates of the atoms in the protein molecule to frame a depiction of the structure-function relationships in this molecule.

5. Deep Investigation, the T7 Polymerase Example

   Requires Chime Plug-in
   (Adapted from media provided with Lodish, Berk, Zipursky, Matsudaira, Baltimore & Darnell, 2000. Molecular Cell Biology. ISBN 0-7167-3136-3. W. H. Freeman and Company, NY, NY)

   This is another detailed tutorial using the molecular structure of both DNA and a simple DNA polymerase to delve into the mechanism of DNA polymerization and the fidelity of this process.

6. 2D Myosin-Actin Cycle

   (Adapted from media provided with Lodish, Berk, Zipursky, Matsudaira, Baltimore & Darnell, 2000. Molecular Cell Biology. ISBN 0-7167-3136-3. W. H. Freeman and Company, NY, NY)

   This is a simple animation of the Actin-myosin, ATP-driven muscle movement cycle.

7. 3D Myosin-Actin Cycle with Regulation

   (Jeff Sale and Prof. Roger Sabbadini from San Diego State University's College of Sciences developed this animation.)

   This is a slightly more complicated animation of the Actin-myosin, ATP-driven muscle movement cycle which has been done in a 3D rendering environment. This seems to give the process more realistic depth. Many more of the regulatory molecules are shown in this animation.