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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">When all the atoms in a side chain have a similar attraction for electrons, the side chain is non-polar. On the other hand, one or a few electron-greedy atoms make side chains polar.</p></td>
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Electron-greedy atoms make side chains polar
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Amino acids are composed of atoms of five different elements: carbon,
hydrogen, oxygen, nitrogen, and sulfur. <b>The only ones that we
consider to be electron greedy, compared to the others, are oxygen and
nitrogen. So the polar amino acid side chains are the ones containing
oxygen and/or nitrogen.</b>
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<p>
To judge whether a side chain is polar or non-polar, remember that in
images of molecules, oxygen atoms are most often colored red, and
nitrogen atoms blue.
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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> </b>
<p>
<b>1. Rotate each amino acid</b> to look for any polar bonds. Use
the computer model popup (on the right) to help you to find the
polar bonds.<br><b>2. Take a snapshot</b> of each that will show
the polar bonds (if any) clearly.<br><b>3. Circle any polar bonds</b>
using the <img src="circleAnnotation.gif"> tool. (<a href="script:page:0:message p3example.html">See
example</a>).<br><b>4. In the description area, indicate whether
the amino acid is polar or non-polar.</b>
</p>
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<p>
<img height="78" src="backboneGreen.gif" width="150">
</p>
<p>
<a href="gizmoElecNeg.html"><font><img src="gizmo.gif">
</font></a><br>
</p>
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<p class="subhead">
Will the real side chain surface please step forward?
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<p class="firstp">
We display charge on molecules using 3D representations of the surface
of the molecules, or the part of the surface that we are interested in. <b>Red
and blue areas show us where electron-greedy atoms have pulled electrons
away from other atoms, leaving partially negative and positive areas.
Pale surfaces indicate that electrons are equally shared.</b>
</p>
<p>
Each row below has the same amino acid shown twice, with surfaces on the
side chains only, so you can look inside at the side chain bonds. <b>Each
side chain surface is colored by charge, but only one of each pair is
colored correctly.</b> To answer the questions, rotate the amino acid,
look inside the "shell" to see the bonds, and decide whether the atoms
will share electrons equally.
<!--You can use <a href="gizmoElecNeg.html"><font>pop-up
computer model</font></a> if you wish. -->
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For Asparagine, which surface shows the correct charges?
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surface 1
surface 2
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Which surface shows the correct charges for Leucine?
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surface 3
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Which surface shows the correct charges for Threonine?
</p>
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surface 5
surface 6
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<p class="question">
Which of the three amino acids is/are NON-polar?
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true
Asparagine
Leucine
Threonine
none of them
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Explain how the colors on the surfaces of the side chains indicate
whether it is polar or non-polar.
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