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Protein Folding: Page 4
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<p class="pagetitle"><strong>Protein Folding:</strong> Polar and Non-Polar Amino Acids</p>
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<td><img src="chargeMainIdea.png" width="98" height="58"></td>
<td><p class="mainidea">Main idea.</p></td>
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<img width="33" height="23" src="chargeBullet.png">
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<p class="subhead">
Electron-hogging atoms make side chains polar
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<p class="firstp">
To display charge on molecules with several atoms, such as amino
acids, we can use 3D representations of the surface of the molecules. <b>The
charges that result from differing electronegativities of the bonded
atoms are "mapped" onto the surface as red and blue areas. Places where
electrons are equally shared appear much paler in color.</b>
</p>
<p>
In the activity below, first you will identify the polar bonds in the
amino acid side chains, using the electronegativites of the atoms. Then
you'll evaluate which surface representation shows the true polarity of
the amino acid side chain.
</p>
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<b>Each amino acid below has a <font color="#006800">simplified
backbone</font><br>and a side chain that is colored by element:</b><br><font color="#666666"><b>Carbon</b></font><b>
<font color="white">Hydrogen</font> <font color="yellow">Sulfur</font>
<font color="blue">Nitrogen</font> <font color="red">Oxygen</font><br><br>Use
the computer model popup (on the right) to help you to find the
polar bonds in the amino acids. </b>
<p>
<b>1. In the first amino acid in each row, look for any polar
bonds.<br>2. Take a snapshot of each of the first amino acids. Circle any polar bonds using the <img src="circleAnnotation.gif">
tool</b> (<a href="script:page:0:message p3example.html">see
example</a>).<br><b>3. In the description area, indicate whether
the amino acid is polar or non-polar. </b><br><b>4. Answer the
questions below. </b>
</p>
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<div align="center">
<p>
<img width="150" height="78" src="backboneGreen.gif">
</p>
<p class="firstp">
</p>
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<img width="264" height="129" src="gizmo.gif">
<br>
</p>
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<p class="firstp">
Each row above has the same amino acid shown three times. The second and
third in each row have a surface covering the amino acid side chain. Rotate the amino acid to look inside the "shell" of the surface.
Each surface is colored by charge, but only one of each pair is correct.
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For the amino acid Asparagine, which surface shows the correct charges?
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surface 1
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Which surface shows the correct charges for Leucine?
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surface 3
surface 4
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Which surface shows the correct charges for Threonine?
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surface 5
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Which of the three amino acids are polar?
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<p class="question">
Describe how the colors used to show charge on the surfaces of the side
chains relate to the polarity of the amino acid.
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