World Index of BioMolecular Visualization Resources

K-12 Molecular Structure Visualization Tutorials

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Atkins, Thomas   (www.indiana.edu )  
Genetic Jewels: Building DNA Model Earrings (physical models of DNA, building;   models of DNA, physical, building;   beads for a model of DNA;   DNA, building a model with jewelry beads;   genetic code, lesson illustrating with secret messages;   central dogma, lesson decoding secret messages)
Students build short segments (about 10 base pairs) of DNA using jewelry beads, becoming intimately involved in DNA structure. The kinesthetic experience and durable product combine to make a lasting impression, and something useful deeply learned about a seemingly complex topic. Middle school students, high school students, and teachers in our workshops have all successfully constructed the molecule. They reinvent the process and make wonderful embellishments. Includes detailed lesson plans, a source for beads, and step-by-step photos for construction.

From the Evolution and the Nature of Science Institutes. Site includes many other lessons including Say it with DNA: Making and Translating DNA Messages (by Larry Flammer):

    This activity uses the metaphor of decoding a secret message for the Protein Synthesis process. Students teach themselves the sequence of DNA-Translation (DNA-mRNA-tRNA-protein), and practice with DNA codes which translate into amino acid sequences spelling out meaningful sentences in English!
Co-authors: Roderick, Joyce;   Flammer, Larry.   Submitted by: Martz, Eric.  (Entry 3).
      
Eckhardt, Rolf   (balloonmolecules.com )  
Balloon Molecules (English, German)
Instructions are given for "knotting" balloons in order to sculpt inexpensive and fun molecular models. Detailed steps for particular molecules are not given, however. Finished models are pictured for tetrahedron, octahedron, Buckminster-Fullerene, diamond, graphite, faujasite, cuban cluster, and a DNA double helix. If you work out details for a specific molecule, please contact emartz@microbio.umass.edu so they can be included here!

Co-authors: Karim, Asif;   Rehbein, Marcus.   Submitted by: Martz, Eric.  (Entry 5).
 
edinformatics, dotcom   (www.edinformatics.com )  
EXPLAIN IT WITH MOLECULES (jmol;   water;   ice;   carbon monoxide;   soap;   diamond;   graphite;   nicotine;   drugs;   fullerine;   salt;   benzene;   DNA;   methane;   lesson plans)
Many questions that arise in K-12 education can be better understood by seeing and interacting with molecules in 3-D. Explain it with Molecules -- Interactive Molecules-- is about "real interactivity"! All you need is to be java enabled. The Jmol Applet used with these molecular structures will allow you to view molecular structures in 3-D. Images can be viewed as wire-frame, ball and stick or CPK. As with the Chime plug-in, it is also possible to measure distances and angles.

Examples: Why does ice float? Why is water such a good solvent? Why is carbon monoxide so dangerous? How does soap work? Why can plain carbon be hard (diamond) or soft (graphite)? Why does nicotine cause cancer? How do drugs work?
Submitted by: Martz, Eric.  (Entry 7).
 
TASTE MOLECULES (jmol;   sugars;   sweeteners, artificial;   artificial sweeteners;   bitter-tasting chemicals;   sour-tasting chemicals;   capsaicin;   menthol;   lesson plans)
Many questions that arise in K-12 education can be better understood by seeing and interacting with molecules in 3-D. TASTE MOLECULES is about "real interactivity"! All you need is to be java enabled. The Jmol Applet used with these molecular structures will allow you to view molecular structures in 3-D. Images can be viewed as wire-frame, ball and stick or CPK. As with the Chime plug-in, it is also possible to measure distances and angles.

This site provides a brief introduction to the physiology of taste, and enables 3D interactive visualization of sugars, artificial sweeteners, bitter chemicals, sour chemicals, capsaicin, and menthol.
Submitted by: Martz, Eric.  (Entry 8).
        
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McClean, Phillip   (vcell.ndsu.nodak.edu )  
Virtual Cell Animation Collection (movies, short;   proton gradients;   ATP synthesis;   respiration;   electron transport chain;   protein transport;   transcription;   mRNA processing;   mRNA splicing;   translation;   lac operon function)
These very educational short movies will help help to convey major biochemical processes, and aid students to appreciate the connections between molecular structure, functional macromolecular assemblies, and the cell.

Eight separate short movies introduce proton gradients and ATP synthesis, cellular respiration (electron transport chain), protein transport (mitochondrial), transcription, mRNA processing, mRNA splicing, translation, and lac operon function.

The movies are narrated with clear and nicely paced explanations, and component "players" are labeled. Molecules, complexes, and organelles are presented in schematic simplification, enabling the key points to be appreciated without being lost in unnecessary visual complexity. Each movie tells a story that integrates biochemical, genetic, and cellular processes. There are presently eight movies, each about three minutes in length. The movies are appropriate for grades 7-12, college, or post-graduate levels, having sufficient simplicity yet sufficient detail to intrigue viewers at all levels.
Co-authors: Johnson, Christina.   Submitted by: Martz, Eric.  (Entry 4).
       
Reichsman, Frieda   (www.umass.edu )  
BioMolecular Explorer 3D (high school;   secondary school;   DNA;   proteins;   carbohydrates;   lipids;   Jmol)
BioMolecular Explorer 3D is a collection of 3D-interactive, biologically significant molecules relevant to a high school biology curriculum. The site (and a CD version) are designed to give high school biology teachers and their students easy access to exploration in 3D (no software installation required!). The molecules are listed with brief descriptions and links to background information, and there is one-click acess to the 3D displays of each. The molecules include:
  • DNA
  • Antibody
  • Carbohydrates
  • Collagen
  • Hemoglobin
  • HIV Protease
  • Lactase
  • Lipids
  • Lipid Bilayers
  • Myosin
  • The Nucleosome
  • Vitamins A and B2
  • Water
  • The site and CD use the Jmol java applet to display the structures on web pages.
    Co-authors: Martz, Eric.   Submitted by: the author.  (Entry 6).
     
    Rich, Marvin   (www.nyu.edu )  
    Mathematics and Molecules (water;   ice;   chime;   density)
    The MathMol Library of Molecular Structures contains GIF, PDB and 3-D (VRML) files of molecules that are found in most introductory biology and chemistry textbooks (e.g., water and ice, carbon, hydrocarbons, amino acids, nucleotides, lipids, sugars, photosynthetic pigments and drugs). A water module for middle and high school students that allows students to calculate the density of water and ice on-line is available here. View the structure of the Photosynthetic Reaction Center and more.

    There is a new revised Review of density, mass and volume that contain javascripts that test students knowledge as they work through the activity. Also new is an online tutorial using Chime for Middle and High School students and a revised (version2) MathMol Hypermedia Textbook which includes activities using java applets including Java Mage.

    Submitted by: the author.  (Entry 1).
                   

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    6 total first authors.

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