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Activity Title: Page 3
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<p class="pagetitle">
<strong>Proteins III:</strong> Molecular Surfaces Can be Charged.
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<img height="58" src="chargeMainIdea.png" width="98">
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<p class="mainidea">
How do different groups of atoms affect the charges on a
molecule's surface?
</p>
</td>
</tr>
</table>
</body>
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<p class="firstp">
<img src="surfaceChargeHorizontal.png">
</p>
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<p class="firstp">
On the previous page you learned that shape is important for
binding of molecules. Next we'll see how charges affect binding.
Let's see where the charges come from.
</p>
<p>
A surface view of a molecule is actually a view of clouds of
electrons that surround each atom. As shown at left, electrons can
be distributed unequally between atoms, creating a separation of
charge, or evenly, creating an area of neutral charge.
</p>
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<b>What to do:</b> use the control panel and model on the right to
remove one hydrogen atom (the one with the yellow halo) from ethane,
replacing it with a group of atoms. See how each atom group has its own
characteristic shape and charge. <b>Make sure to use the Surface buttons
to see how different atoms affect charge and polarity</b> at the surface
of the molecule.
</p>
</body>
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page3$plugin$0.aps{name="load" value="ethane-series.mol2"}
{name="nostatepersistence" value="true"}
{name="script" value="#console on; #set debugscript on; script ethane-series.spt; script ethane-series-ethane.spt"}
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<b>Atom group:</b>
</p>
<table border="0">
<tr>
<td align="right">
<input type="radio" alt="" checked="checked" script="script:nativescript:plugin:1:set echo off; script ethane-series-ethane.spt" name="RadioGroup1">
</td>
<td>
-H
</td>
<td align="right">
<input type="radio" alt="" script="script:nativescript:plugin:1:set echo off; script ethane-series-ethanol.spt" name="RadioGroup1">
</td>
<td>
-OH
</td>
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<tr>
<td align="right">
<input type="radio" alt="" script="script:nativescript:plugin:1:set echo off; script ethane-series-propionic.spt" name="RadioGroup1">
</td>
<td>
-COOH
</td>
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<input type="radio" alt="" script="script:nativescript:plugin:1:set echo off; script ethane-series-amine.spt" name="RadioGroup1">
</td>
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-NH<font size="2" face="Verdana, Arial, Helvetica, sans-serif"><sub>2</sub></font>
</td>
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<input type="radio" alt="" script="script:nativescript:plugin:1:set echo off; script ethane-series-amide.spt" name="RadioGroup1">
</td>
<td>
-CNH<font size="2" face="Verdana, Arial, Helvetica, sans-serif"><sub>2</sub></font>O
</td>
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<input type="radio" alt="" script="script:nativescript:plugin:1:set echo off; script ethane-series-butane.spt" name="RadioGroup1">
</td>
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-C<font size="2" face="Verdana, Arial, Helvetica, sans-serif"><sub>2</sub></font>H<font size="2" face="Verdana, Arial, Helvetica, sans-serif"><sub>5</sub></font>
</td>
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<td align="right">
<input type="checkbox" alt="show the part of each molecule that is different" script_selected="script:nativescript:plugin:1:script:nativescript:plugin:1:select ~funcGroupsAll; halos on; highlightFuncGroup = true; select all;" checked="checked" name="checkbox2" script_deselected="nativescript:plugin:1:select ~funcGroupsAll; halos off; highlightFuncGroup = false; select all;">
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<td>
highlight
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<td colspan="2">
<b>Surface:</b>
</td>
<td align="right">
<input type="radio" alt="" checked="checked" script="script:nativescript:plugin:1:select all; isosurface off; isosurfaceFlag=false; translucentFlag = false; " name="RadioGroup2">
</td>
<td>
off
</td>
</tr>
<tr>
<td align="right">
<input type="radio" alt="" script="script:nativescript:plugin:1:select all; isosurface on; isosurfaceFlag=true; translucentFlag = true; color isosurface translucent 4" name="RadioGroup2">
</td>
<td>
translucent
</td>
<td align="right">
<input type="radio" alt="" script="script:nativescript:plugin:1:select all; isosurface on; isosurfaceFlag=true; translucentFlag = false; color isosurface opaque;" name="RadioGroup2">
</td>
<td>
solid
</td>
</tr>
</table>
</body>
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<link href="bioStyles.css" rel="stylesheet" type="text/css">
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<body class="question">
<p class="question">
How does oxygen or nitrogen affect the sharing of electrons with nearby
carbon or hydrogen?
</p>
</body>
</html>
Oxygen and nitrogen cause unequal sharing of electrons with carbon and hydrogen. They create areas of negative charge around themselves, and so the carbon and hydrogen atoms have a positive charge. (An advanced answer could include the fact that N and O attract electrons more strongly than C and H).
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<body class="question">
<p class="question">
Imagine you are a carbon atom in a molecule composed entirely of carbon
and hydrogen. One of the atoms you are bonded to is changed to an
oxygen. Describe how the electron cloud around you is affected, and the
resulting change in surface charge.
</p>
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The oxygen pulls more of the electrons away from me than either hydrogen or another carbon would. So, the electron cloud around me shifts toward the oxygen. The surface near the oxygen is negative, and near me, positive.
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