Protein Folding (Stepping Stones-Full Activity)

Interactive, scaffolded model

Overview and Learning Objectives

In this activity students discover how the properties of amino acids (charge and polarity) affect the shape of a peptide chain. They explore the complex interactions of amino acids with each other and with the surrounding water molecules or lipids. Sickle Cell Anemia is used as an example of a disease caused by a single amino acid substitution.

Students will be able to:

• explain how charged amino acids can affect a protein's shape;
• reason how interactions with water molecules or lipids affect the shape of a protein;
• explain how a disease can be caused by a single amino acid substitution.

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Assessment

Using the knowledge you have gained in this activity, how would you explain the effect on a protein's activity of a point mutation in an enzyme? (Point mutation: substitution of one nucleotide in DNA that results in the substitution of one amino acid for another in the resulting protein molecule. This could possibly affect the charge on and the folded shape of the protein molecule.)

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Classroom Practice

Students need assistance in understanding that hydrophobicity is a lack of attraction to the polar water molecules and not a repulsion. The term hydrophobic itself is misleading, because hydrophobic amino acids don't actually repel water. Emphasize the idea that, as water molecules make hydrogen bonds with charged amino acids and with each other, non-polar molecules are pushed or herded away from water.

To help students understand the concept of hydrophobicity, have students look at the model Hydrophobia: Activity #203 in this database.

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Central Concepts

Key Concept:

A peptide chain folds into a specific shape as a result of interactions of amino acids with each other and with the surrounding medium. One concept organization is available at: http://www.concord.org/~btinker/workbench_web/pdfs/Protein_Structure.pdf

Additional Related Concepts

Concept Map Available

Molecular Biology

• Protein Folding
• Protein Function
• Protein structure

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Textbook References

• Biology (Miller and Levine) Prentice Hall 5th Edition - Unit 2: Chapter 7 - Nucleic Acids and Protein Synthesis
• Biology: Concepts and Connections (Pearson) 5th Ed. - Chapter 3: The Molecules of Cells
• Biology: Concepts and Connections (Pearson) 5th Edition - Chapter 11: The Control of Gene Expression
• Biology: Exploring Life - Chapter 11: DNA and the Language of Life
• BSCS Blue (8th Edition) - Chapter 9: Expressing Genetic Information
• Cell Biology (Pollard and Earnshaw) Saunders 2002 - Chapter 18: Protein Synthesis and Folding in the Cytoplasm
• Web of Life - Chapter 8: Protein Synthesis

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Benchmarks and Standards

AAAS

• THE LIVING ENVIRONMENT: CELLS - The genetic information encoded in DNA molecules provides instructions for assembling protein molecules (Full Text of Standard)
  
  

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Extensions and Connections

Protein folding is a logical precursor to such activities in the database as:

Particular Proteins

Insulin (Activity): http://molo.concord.org/database/activities/236.html

Melittin (Demo) Protein: http://molo.concord.org/database/activities/87.html

Hemoglobin Tour: http://molo.concord.org/database/activities/281.html

Particular Functions

Docking: Binding of Complementary Surfaces: http://molo.concord.org/database/activities/154.html

Self-Assembly: http://molo.concord.org/database/activities/155.html

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Activity Credits

Created by CC Project: Molecular Logic and CC Project: Molecular Workbench using Molecular Workbench

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Requirements

• Java 1.5+ - Java 1.5+ is available for Windows, Linux, and Mac OS X 10.4 and greater. If you are using Mac OS X 10.3, you can download MW Version 1.3 and explore within it instead.

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