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Overview and Learning Objectives
Central Concepts
Textbook References
Extensions and Connections
Activity Credits

Amino Acids and Water: 20 Alanine Model (4 connected model pages)

Interactive, scaffolded model

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Overview and Learning Objectives

How does a protein get its shape? Students work with a dynamic model of a folding polymer, which allows them to explore the role of the hydrophobic and hydrophilic amino acids in protein folding. They expand their mental model of protein folding from that of a simple interaction between charges to the more complex interactions between all amino acids (charged, polar, and non-polar) with each other and with the surrounding water molecules or lipids. Based on this model, students construct differently shaped proteins, and learn to reason about their shapes, considering the property of specific amino acids and their position in the chain.

An attached concept map provides examples of water-dissolving and oil-dissolving molecules

Students will be able to:

  • characterize amino acids according to their response to water;
  • explain how interactions with water molecules affect the shape of a protein;
  • reason about the impact of temperature change on protein shape.

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See questions 1a and 1b from the following pre/post-test:


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Central Concepts

Key Concept:

In addition to the interaction between charged amino acids, the three-dimensional shape of a protein is the result of the interaction of amino acids with their surrounding water molecules.

Additional Related Concepts

Concept Map Available

Molecular Biology

  • Amino acid
  • Lipid
  • Polar nature of water
  • Protein Folding
  • Protein structure


  • Hydrophobicity

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Textbook References

  • Biology: Exploring Life - Chapter 5: The Molecules of Life
  • BSCS Blue (8th Edition) - Chapter 1: The Chemistry of Life
  • BSCS Blue (8th Edition) - Chapter 9: Expressing Genetic Information

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Extensions and Connections

See teachers guide.

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Activity Credits

Created by CC Project: Molecular Workbench using Molecular Workbench

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Last Update: 12/07/2015 Maintainer: CC Web Team (webmaster@concord.org)
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These materials are based upon work supported
by the National Science Foundation under grant numbers
9980620, ESI-0242701 and EIA-0219345

Any opinions, findings, and conclusions or recommendations expressed in this
material are those of the author(s) and do not necessarily reflect
the views of the National Science Foundation.