Section 1 - Activities

Data Dilemma©
Description:

Modeling is an important and integral part of the practice of science. This foam puzzle set is a colorful, engaging tool to encourage scientific collaboration and facilitate discussions about how scientific models evolve.

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Topics Covered:
  • The Process of Science
  • Collecting and Analysing Data
  • Mental Models
Mystery Tube©
Description:

A fun and challenging introduction to the practice of science. Your students will assume the role of research scientists as they make observations and propose a mechanism which explains the properties of the Mystery Tube©.

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Topics Covered:
  • The Process of Science
  • Collecting and Analysing Data
  • Mental Models
David Goodsell Paintings
Description:

Dr. Goodsell creates cellular landscapes that accurately illustrate the size, shape, and distribution of proteins in their natural environment of the cell. These unique water color images connect the molecular world, inferred by X-ray crystallography and NMR spectroscopy, with the cellular world, observed by light and electron microscopy.

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Water Kit©
Description:

A FUN tool to help you teach water concepts. Your students will use these magnetic water molecules to discover hydrogen bonding, make ice, dissolve salt, evaporate water, explore transpiration, create ethanol, and much more.

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The Magic Disk Trick
Description:

We are always looking for ways to connect the macroscopic world in which kids live with the invisible world of molecules. For example, how can we help them construct an understanding of how hydrophobic and hydrophilic forces play a major role in determining the folded structure of a protein? Here is an activity that does just this.

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Topics Covered:
  • Hydrophobic and Hydrophillic Properties
Documentation:
Phospholipid & Membrane Transport Kit©
Description:

Don’t tell your students about membranes and how/why they form – let them discover the spontaneous formation of membranes for themselves using this kit that features the amphipathic structure of phospholipids – with their hydrophilic heads and hydrophobic tails. Your students will explore the chemical structure of a phospholipid and then construct a phospholipid monolayer, a micelle and a bilayer, leading to an understanding of the plasma membrane structure. Additional components of this kit allow students to construct lipid bilayers and consider the role of transport proteins in moving ions and small molecules across membranes.

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Topics Covered:
  • Phsopholipid Structure
  • Cellular Membranes
  • Osmosis
  • Active and Passive Transport
  • Hydrophobic and Hydrophillic Properties
External Resources:
★ How to Access:
Documentation:
The Molecules of Life Collection©
Description:

With this 3D molecular model collection, zoom to the 4 classes of biomolecules found in living cells – carbohydrates, lipids, proteins and nucleic acids.

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Amino Acid Building Block Models©
Description:

Your students will discover the basic repeating structure of amino acid backbones by building 2 models. Then they can form a dipeptide bond, linking the 2 models together and creating a chain. This kit enables your students to build and compare 2 generic amino acids models using atoms, covalent bonds and hydrogen bonds.

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Topics Covered:
  • Amino Acid Structure
  • Peptide Bonds
Amino Acid Starter Kit©
Description:

This engaging, hands-on protein folding kit makes teaching protein structure basics easy. Your students will fold a protein while exploring how the chemical properties of amino acids determine its final structure.

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Topics Covered:
  • Amino Acid Structure
  • Protein Structure/Function
  • Primary, Secondary, Tertiary and Quaternary Structure
External Resources:
Alpha Helix - Beta Sheet Construction Kit©
Description:

The linear amino acid sequence defines the primary structure of a protein. Regions of the linear polypeptide chain fold into the stable α-helix and β-sheet structures to form the protein secondary structure. The tertiary protein structure is the overall 3-D shape of the protein. With this model collection, students can assemble an α-helix or anti-parallel β-sheet, compare the phi-psi angles of the 2 secondary structures, and explore the contribution of hydrogen bonding to the stability of the structure.

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Topics Covered:
  • Amino Acid Structure
  • Peptide Bonding
  • Secondary Structure - Alpha Helices and Beta Pleated Sheets
  • Hydrogen Bonding
Enzymes in Action Kit©
Description:

The Enzymes in Action Kit creates catalytic connections with models. The kit’s colorful foam pieces represent enzymes, and substrates. The protein model kit allows you to simulate enzymatic actions including enzymatic specificity, inhibitors used in regulating enzymatic activity, and activation energy.

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DNA Discovery Kit©
Description:

Let your students explore the structure of DNA — just as Watson and Crick did. This self-instructive magnetic DNA model kit quickly and easily combines into accurate 3D nucleotides, which then connect to form the double helix.

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Dynamic DNA Teacher Guide

This multi-page teacher guide walks you through the features and activities for our NEW Dynamic DNA kit!

Map of the Human ß-Globin Gene©
Description:

Don’t just tell your students about triplet codons, reading frames, or introns and exons. Let them discover these eukaryotic gene features as they explore the Map of the Human ß-Globin Gene.

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Genetic Codon Chart
Description:

A must-have companion to 3D Molecular Designs' popular Amino Acid Starter Kit, ß-Globin Folding Kit, and Insulin mRNA to Protein Kit. The 3DMD Genetic Codon Chart and Genetic Codon Circle show students the link between the triplet codon in mRNA and the properties of amino acids.

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Topics Covered:
  • Triplet Codons
  • Amino Acid Properties
  • Translation
Flow of Genetic Information Kit©
Description:

It’s the product that 3DMD customers have been asking for! Our new Flow of Genetic Information Kit© will allow your students to model DNA replication using color-coded, foam nucleotides and a placemat, model RNA transcription as they copy one strand of DNA into mRNA using an RNA polymerase, and model translation/protein synthesis as they decode the mRNA into protein on the ribosome placemat.

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Topics Covered:
  • The Flow of Genetic Information: DNA > RNA > Protein
  • Replication
  • Transcription
  • Translation
  • Triplet Codons
  • Okazaki Fragments
  • DNA Directionality
External Resources:
Insulin mRNA to Protein Kit©
Description:

Insulin is an ideal protein to illustrate the post-translational processing of a protein. Our kit will let your students explore how a specific sequence of nucleotides encodes a corresponding sequence of amino acids, which then determines its final 3D protein structure.

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Model Melange
Description:

In the Model Melange activity, you will visit four different stations – each featuring a variety of different physical models of peptides or proteins - to explore levels of protein structure and different model formats.

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Topics Covered:
  • Protein Structure
  • Protein Dispaly Formats
Zinc Finger Folding Activity
Description:

A C2H2 zinc finger is a 28 amino acid protein motif composed of a short alpha helix and a two-stranded beta sheet. The structure of the zinc finger is stabilized by a zinc atom that binds 2 cysteine and 2 histidine sidechains, and by hydrophobic amino acid sidechains that are buried on the inside of the folded motif. The construction of a physical model of the 3D structure of a zinc finger serves as a good example of how Toobers can be used to model protein structures.

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Topics Covered:
  • Protein Structure
Documentation:
Substrate Specificity Activity
Description:

Each cell has thousands of proteins, many of which are enzymes. Each enzyme will catalyze a reaction with only a small subset of all the molecules in the cell. How does the enzyme know with which molecules (substrates) to react? This activity explores how the interaction between the substrate and enzyme is highly specific, such that if either the substrate or the enzyme were to change shape, even slightly, the two will no longer come in close contact.

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Topics Covered:
  • Substrate Binding
  • Protein Structure
Documentation:

Section 2 - Molecular Stories

Insulin mRNA to Protein Kit©
Description:

Insulin is an ideal protein to illustrate the post-translational processing of a protein. Our kit will let your students explore how a specific sequence of nucleotides encodes a corresponding sequence of amino acids, which then determines its final 3D protein structure.

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2017 Modeling A Protein Story (MAPS) Project: Insulin

The Online Modeling Program from the MSOE Center for BioMolecular Modeling
After signing up or logging in, join a new course using the access code: 86FGP-89WZ9



Aquaporin and the Movement of Water
Description:

Water molecules rapidly flow through the membrane-spanning protein aquaporin. Its structure consists of 6 alpha helices and 2 half alpha helices that form an hourglass shape through which water molecules move one at a time. A variety of engaging stories can be explored related to this amazing structure and the scientists that discovered it.

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2015 Modeling A Protein Story (MAPS) Project: Aquaporin




Potassium Channels and Action Potentials
Description:

Help your students better visualize and understanding ionic interactions and protein channel selectivity of the potassium channel. A variety of engaging stories can be explored related to this amazing structure and the scientists that discovered it.

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Hemagglutinin and the Influenza Virus
Description:

Help your students understand how a flu virus infects a cell, as the hemagglutinin protein undergoes a dramatic change in shape during the process. A variety of engaging stories can be explored related to this amazing structure and the scientists that discovered it.

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Acetylcholinesterase and Pesticide Resistance
Description:

The acetylcholinesterase gene and the protein it encodes can be used to demonstrate a number of biological concepts, including enzyme specificity, competitive inhibition, mutation, characteristics of the genetic code, alternate splice sites, natural selection, bioinformatics, and disease transmission.

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Topics Covered:
  • Protein Structure
  • Enzyme Specificity
  • Mutations
  • Natural Selection
  • Disease Transmission
Hemoglobin and Betaglobin
Description:

Hemoglobin, and ß-globin (a subunit of hemoglobin) are involved in the transport of oxygen throughout our bodies. These proteins have ring-like heme groups, which contain iron atoms that bind oxygen. The 1962 Nobel Prize in Chemistry was awarded jointly to Max Ferdinand Perutz and John Cowdery Kendrew "for their studies of the structures of globular proteins". Max Ferdinand Perutz solved the structure of hemoglobin in 1959.

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2016 Modeling A Protein Story (MAPS) Project: Globins

The Online Modeling Program from the MSOE Center for BioMolecular Modeling
After signing up or logging in, join a new course using the access code: XQB2J-Z56MT



Top7 Protein
Description:

Top7 is an artificial 93-residue protein, classified as a de novo protein since it was designed by Brian Kuhlman and Gautam Dantas in David Baker's laboratory at the University of Washington to have a unique fold not found in nature.

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Section 4 - Jmol Training



There are two ways for teachers and students to access Jmol, the molecular visualization tool used by all CBM outreach and professional development programs:



  1. Jmol Design Environment - This online version of Jmol runs directly in a web browser, and does not need plugins or installation to run on any device (smart phone, Chromebook, tablet, etc.).



  2. Java-based Jmol - This Java-based version of Jmol requires download as well as the installation of Java to run locally on your computer or device.

Jmol Training Guide
Description:

Jmol is a free, open source molecular visualization program used by students, educators and researchers internationally. The Jmol Training Guide will provide the tools needed to create molecular renderings, physical models using 3-D printing technologies, as well as Jmol animations for online tutorials or electronic posters.

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Topics Covered:
  • Protein Structure
  • Molecular Visualization
External Resources:
★ How to Access:
  • Getting Started in Jmol
    (Webpage)
  • Finding Protein and Molecular Structures
    (Webpage)
  • Changing Colors and Display Formats
    (Webpage)
  • The Select Command and Boolean Operators
    (Webpage)
  • Saving and Reloading Your Work
    (Webpage)
  • Adding Sidechains to Your Structure
    (Webpage)
  • Bonds and Structural Supports
    (Webpage)
  • Working with Nucleic Acids
    (Webpage)
Jmol Tutorial Creator
Description:

Jmol can be embedded directly into a web page, allowing for the creation of fully interactive molecular tutorials that run on any device, from smart phones and tablets to desktop and laptop computers. The Jmol Tutorial Creator lets you develop custom tutorials through a user-friendly online application.

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Example Tutorials:
★ How to Access:
Documentation:
Topics Covered:
  • Protein Structure
  • Molecular Visualization

Jmol Quick Reference Sheet

This two-sided reference sheet is the perfect companion for any Jmol designer. Side one includes the most important Jmol commands and side two is a handy amino acid chart.

Designing a Zinc Finger

This sample Jmol design includes all of the commands needed to make a nice zinc finger model, highlighting secondary structures and key sidechains involved in the structure and function of zinc finger.



Our work is supported by grants from the NIH National Center for Research Resources SEPA program, the NSF CCLI program, the Department of Education Institute for Educational Sciences and the Howard Hughes Medical Institute.