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Activity Overview:Key concepts:
The three-dimensional shape of a protein is the result not only of the interaction between amino acids with each other, but also of their interaction with their surrounding molecules, such as water molecules or lipids.
Students work with a dynamic model called Folding Polymer: 20 Alanine Residues, 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.Learning Objectives:
Students will be able to:
Characterize amino acids according to their response to water or lipids.
Macro to Micro Connection:
Students explore the impact of the surrounding medium, water or lipids, on the 3-D structure of protein molecule.
Conceptual Prologue:
The model follows a rule based on the fact that hydrophobic amino acids in water tend to stay as close to each other and as far away as possible from water molecules. In the case that all the amino acid "beads" on the protein chain are hydrophobic, the surrounding water molecules force the hydrophobic beads to hide in the interior of the protein -- so the protein will curl into a ball. If beads representing hydrophilic amino acid are situated along the chain, they will attempt to move as close to the water as possible. The water molecules in our model are represented by the blue background, calculating for but not showing separate water molecules. When discussing the conformations of the protein chain, try to include ways in which individual water molecules might be interacting with the chain.
ACTIVITY DESIGN AND EXECUTION
Major Science Concepts Hydrophobicity, polarity, protein folding Assumed Previous Knowledge: The polar nature of water; hydrogen bonds Time: One or two 50-minute classes Technical Note: There are two (one is optional) models in this activity, which can be launched in one of two ways:
1. From your browser. Click the links below.
(Optional) Molecular Workbench: Water: http://xeon.concord.org/webstart/jnlpFiles/water.jnlpFolding Polymer: 20 Alanine Residues: http://xeon.concord.org:8080/modeler/webstart/protein/ala20.jnlp
2. By going through the Molecular Workbench application on your computer (workbench.jar). Then you should click the following links: Student Pages, Protein Folding, A Polymer with 20 Alanines.
It may take a short while to launch the Molecular Workbench the first time.
Supporting Materials: *How do Amino Acids React to Water or Lipids [PDF version]
*Worksheet: How a Protein Gets it Shape: Responding to Water or Lipids (Student) [PDF version]
*Worksheet: How a Protein Gets it Shape: Responding to Water or Lipids (Teacher)Advanced preparation Print or bookmark support materials
Prepare model for access (See above)
Visit and bookmark Student Index
Investigative Question: Every protein is surrounded by water, lipids or both. How does the surrounding medium affect the shape of the protein?
STEPS
1. Brainstorm: Have students begin to brainstorm the answer to the investigative question. They may think of charges on amino acids and, possibly, the polar nature of water.
2. The Polar Nature of Water: You may need to review the properties of water with the class. Focus on the polar nature of water and the formation of hydrogen bonds among water molecules. If you have time you might want to have students review the properties of water by completing the computer activity Water. [http://xeon.concord.org/webstart/jnlpFiles/water.jnlp]
3. Introduce the concepts of hydrophobicity and hydrophilia. 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, as it is easy to attribute repulsion to the "herding" effect of water moleclules on theneutral amino acids. As water molecules make hydrogen bonds with charged amino acids and with each other, non-polar molecules are pushed or herded away from water. In proteins, these non-polar , hydrophobic amino acids are moved INSIDE the complex globules, where there very little water, making what is called a "hydrophobic core."
4. Choreographed Science: Hydrophobicity and Hydrophilia
This approach is useful to build a foundation of mental models that can connect with more sophisticated representations later in the activity. If students are uncomfortable with such an approach, or if there is not enough room in the classroom, you might have them do it in their imagination. (In that case you may ask for some drawings as evidence of engagement.)
Warm up (Oil and Water)
*Divide them into two groups of molecules, "Polar -no total charge, but charged parts" and "Non-polar/ no charged parts" and mark them with colored stickies. For the polar molecules, you might put a plus sticky on one shoulder and a minus on another shoulder.
*Instruct the non-polar/ (uncharged) molecules that they should wander around randomly, making no connections.
*Instruct the polar (with charged parts) molecules that they should make contact with one another by holding hands, positive to negative, without touching the nonpolar molecules. As they are water here, students could extend their two arms as plus and minus.
*Every 20 seconds or so the polar, charged molecules should drop theirr hands briefly, allowing a few non-polar, uncharged to migrate into another position. (This represents the distruptive effects of temperature, the random thernal motion of molecules.)
*Everyoner should be in some continuous motion.
*"Run" the model for a few minutes, giving time for some "oil drops" (the on polar molecules) to form within polar, hydrophilic connectionsExplain that they are behaving like (uncharged) oil molecules in (charged) water, or let them discover that themselves by opening the model: listed below. The effect is subtle, You should be eventually able to see the non-polar clumping together, which might be unexpected, as there are no apparent forces among the nonpolars. Do not spend too much time waiting for the effect, as even this precursor work will ebable the students to observe the models more clearly.
[Optional] Explain to your students that if the uncharged molecules are linked together, and placed iwith charged molecules, they behave llike lipids. Look at Workbench model: Hydrophobicity. Go to the database at http://molo.concord.org, visit the database and type in "hydrophobicity". Copy this link into the location bar of the Molecular Workbench and press return key: http://xeon.concord.org:8080/modeler1.3/student/solution/hydrophobic.cml [JNLP launch?]
5 Modeling on the computerHand out How a Protein Gets it Shape: Responding to Water or Lipids (Student) The worksheets include both instructions on how to use the model, and the activities themselves. You may choose to let the students run the model for 5 minutes of free exploration before starting the activities, and then have them get into small groups to teach each other what they have found.
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