World Index of BioMolecular Visualization Resources

K-12 Molecular Structure Visualization Tutorials

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artificial sweeteners :
TASTE MOLECULES. (edinformatics, dotcom)

ATP synthesis :
Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)  

  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!

beads for a model of DNA :
Genetic Jewels: Building DNA Model Earrings. (Atkins, Thomas;   Roderick, Joyce;   Flammer, Larry)

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benzene :
EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

  BioMolecular Explorer 3D:
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.

    bitter-tasting chemicals :
    TASTE MOLECULES. (edinformatics, dotcom)  

    capsaicin :
    TASTE MOLECULES. (edinformatics, dotcom)

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    carbohydrates :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)

    carbon monoxide :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    central dogma, lesson decoding secret messages :
    Genetic Jewels: Building DNA Model Earrings. (Atkins, Thomas;   Roderick, Joyce;   Flammer, Larry)

    chime :
    Mathematics and Molecules. (Rich, Marvin)  

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    density :
    Mathematics and Molecules. (Rich, Marvin)

    diamond :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    DNA :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)

    DNA :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    DNA, building a model with jewelry beads :
    Genetic Jewels: Building DNA Model Earrings. (Atkins, Thomas;   Roderick, Joyce;   Flammer, Larry)

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    drugs :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)  

    electron transport chain :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)

      EXPLAIN IT WITH MOLECULES:
    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?  

    fullerine :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)  

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    genetic code, lesson illustrating with secret messages :
    Genetic Jewels: Building DNA Model Earrings. (Atkins, Thomas;   Roderick, Joyce;   Flammer, Larry)

      Genetic Jewels: Building DNA Model Earrings:
    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):

    graphite :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)  

    high school :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)  

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    ice :
    Mathematics and Molecules. (Rich, Marvin)

    ice :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)  

    Jmol :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)

    Jmol :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    Jmol :
    TASTE MOLECULES. (edinformatics, dotcom)   

    lac operon function :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)

    lesson plans :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    lesson plans :
    TASTE MOLECULES. (edinformatics, dotcom)

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    lipids :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)  

      Mathematics and Molecules:
    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.

    menthol :
    TASTE MOLECULES. (edinformatics, dotcom)

    methane :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

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    models of DNA, physical, building :
    Genetic Jewels: Building DNA Model Earrings. (Atkins, Thomas;   Roderick, Joyce;   Flammer, Larry)

    movies, short :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)

    mRNA processing :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)

    mRNA splicing :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)  

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    nicotine :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)   

    physical models of DNA, building :
    Genetic Jewels: Building DNA Model Earrings. (Atkins, Thomas;   Roderick, Joyce;   Flammer, Larry)

    protein transport :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)

    proteins :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)

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    proton gradients :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)   

    respiration :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)  

    salt :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    secondary school :
    BioMolecular Explorer 3D. (Reichsman, Frieda;   Martz, Eric)

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    soap :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)

    sour-tasting chemicals :
    TASTE MOLECULES. (edinformatics, dotcom)

    sugars :
    TASTE MOLECULES. (edinformatics, dotcom)

    sweeteners, artificial :
    TASTE MOLECULES. (edinformatics, dotcom)  

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      TASTE MOLECULES:
    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.

    transcription :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)

    translation :
    Virtual Cell Animation Collection. (McClean, Phillip;   Johnson, Christina)   

      Virtual Cell Animation Collection:
    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.  
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    water :
    Mathematics and Molecules. (Rich, Marvin)

    water :
    EXPLAIN IT WITH MOLECULES. (edinformatics, dotcom)      

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    53 total subject cross-indexing terms.

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