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Activity Title: Page 5
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<strong>Proteins III:</strong> Recognizing Protein "Landscapes".
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<p class="mainidea">
How to molecular partners "recognize" each other?
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<img src="Mount_Rushmore.jpg">
</p>
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<p class="firstp">
Mount Rushmore is one of the most recognized landscapes in the United
States. It's easy for us to pick out the faces of four well-known and
admired US Presidents carved in a mountainside!
</p>
<p>
Every protein has surface peaks and valleys that other molecules can
recognize, but molecules are "blind" - they have no way to recognize
each other by sight. Much like a blind person can recognize a human face
by feel, <b>molecules "feel" each other's shape and charges to recognize
a partner molecule</b>.
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<p class="firstp">
In the model at right, a <b>receptor protein</b> is embedded in a
membrane. Nearby are three small molecules, only one of which is the
real partner for the receptor. The protein and partners are colored by
charge:
</p>
<p>
<img src="surfaceCharge.gif">
  <input name="Submit" value="Reset" script="script:mw2d:1:reset" type="submit"><br><b>Your
job</b> is to figure out which small molecule will be recognized as a
partner by the protein. <b>What to do:</b>
</p>
<ol>
<li>
Drag one partner molecule to the receptor and place it in the binding
site so it fits as well as possible.
</li>
<li>
Take a snapshot.
</li>
<li>
Repeat with all three small molecules.
</li>
</ol>
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<p class="question">
Use your knowledge of shape, intermolecular attractions, and charge to
predict which small molecule the protein in the model above will
recognize. <a href="script:page:0:message <t><font face=verdana>You may wish to look closely at your snapshots before making your choice below.</font></t>">Hint</a>
</p>
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small molecule 1
small molecule 2
small molecule 3
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<p>
<b>Check your answer to the question at left to load a new model and
control panel above, and instructions here. </b>
</p>
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After using the new model above, return to your snapshots and place the
one with the real partner molecule in the binding site here.
</p>
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<p class="question">
1. Open the snapshot you chose on the left and use the circle tool <img src="annotation-circle.gif">
to circle the partner molecule.<br>2. In the box below this question,
explain how the partner recognizes the protein while the other two small
molecules do not.
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Small molecule #1 recognizes the protein's binding site by its close fit (shape) and opposing charges. The good fit brings the atoms close together, so many intermolecular attractions can form. In addition, the areas of charge line up opposite to each other - wherever there is a positive area on the protein, the corresponding part of the partner is negative and vice versa. (The observant student may also note that a neutral area is also matched on the partner.) Small molecule #3 has the wrong charges to fit in the site, whereas small molecule #2 has the wrong shape.
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