3d Molecular Designs Flow Of Genetic Information Kit

Day 1 - Proteins, DNA and RNA

Proteins:

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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★ How to Access:

Borrow from the Lending Library
Purchase from 3D Molecular Designs

Documentation:

Starter Kit Contents and Assembly Instructions (PDF)
Starter Kit Introduction (PDF)
Starter Kit Teacher Notes (PDF)
Starter Kit Activity 1 - Amino Acids and Protein Folding
- Student Handout(PDF)
- Form to Obtain Answer Key (Webpage)
Starter Kit Activity 2 - Secondary Structures
- Student Handout(PDF)
- Form to Obtain Answer Key (Webpage)
Starter Kit Activity 3 - Folding an Enzyme Active Site
- Student Handout(PDF)
- Form to Obtain Answer Key (Webpage)
Amino Acid Sidechain Chart (PDF)
Additional Activities (PDF)
The Genetic Codon Chart (PDF)
Starter Kit Jmol Tutorials
- Amino Acid Tutorial(Webpage)
- Principles that Drive Protein Folding - Part 1 (Webpage)
- Principles that Drive Protein Folding - Part 2 (Webpage)
- Zinc Finger Tutorial (Webpage)
Amino Acid Starter Kit in Breif (PDF)
The Starter Kit and the Next Generation Science Standards (Webpage)

David Goodsell Landscape

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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A document from the RCSB Protein Databank

By Helen Berman, David Goodsell and Philip Bourne in the American Scientist

By Yigong Shi in the journal Cell

DNA:

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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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

By James Watson and Francis Crick in Nature, April, 1953

By James Watson and Francis Crick in Nature, May, 1953

By Thomas Steitz in Nature

By Francis Crick

RNA:

By Jeannie Lee and Marisa Bartolomel in Cell

By Anna Marie Pyle in RNA

Day 2 - Enzymes and Metalloproteins

Hemoglobin:

Hemoglobin Models

Description:

Hemoglobin is a protein that every science classroom needs to explore. It transports oxygen throughout our bodies and features primary through quanternary structure and the ß-globin mutation that causes sickle cell anemia.

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Topics Covered:

Protein Structure
Oxygen Transport
Structure Function Relationships
Sickle Cell Mutation

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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Topics Covered:

Protein Reading Frames
Triplet Codons
Introns and Exons
Mutations

By David Goodsell in RCSB Protein Databank

By Linus Pauling, Harvey Itano, S.J. Singer and Ibert Wells in Science

Enzymes:

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

An Activity in the Amino Acid Starter Kit from 3D Molecular Designs

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

By Mylene Weill, Georges Lutfalla, Knud Mogensen, Fabrice Chandre, Arnaud Berthomieu, Claire Berticat, Nicole Pasteur, Alexandre Philips, Philippe Fort, and Michel Raymond in Nature

Sepiapterin Reductase:

By Matthew Bainbridge in Science - Translational Medicine

By Richard Knox for NPR

Neurotransmitters Module: The Beery Twins' Story

By Gunter Auerbach, Anja Herrmann, Markus Gutlich, Markus Fischer, Uwe Jacob, Adelbert Bacher and Robert Huber in the Euorpean Molecular Biology Organization Journal

Neurotransmitters Module: The Beery Twins' Story

Day 3 - Channels

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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The Online Modeling Program from the MSOE Center for BioMolecular Modeling

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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Topics Covered:

Protein Structure
The Process of Science
Action Potential

The Nicotinic Acetylcholine Receptor

Description:

After the neurotransmitter acetylcholine is released from the pre-synaptic neuron into the synaptic cleft, it binds to the acetylcholine receptor embedded in the membrane of the post-synaptic neuron. This channel protein is also the binding site for nicotine.

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Topics Covered:

Protein Structure
Neurotransmission
Drug Binding

Protein Structure
The Process of Science
Gene Sequencing
Personalized Medicine

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.