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Activity Title: Page 4
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org.concord.modeler.text.LineIcon750.03010105<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body>
<p class="pagetitle">
<strong>Activity Title:</strong> Some subtitle. (Don't forget to set the
MW page title too.)
</p>
</body>
</html>
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org.concord.modeler.PageTextBox
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<head>
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<body background="topNavBarLeftMargin.jpg" marginwidth="0" marginheight="0">
<table cellspacing="0" width="100%" id="Table_01" cellpadding="0" border="0">
<tr>
<td>
<img width="14" src="topNavBarLeftMargin.jpg" height="26">
<font><a href="page3.cml"><img width="60" src="prev.jpg" height="26" border="0">
</a><a href="page5.cml"><img width="59" src="next.jpg" height="26" border="0">
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<td align="right">
<img width="54" src="page.jpg" height="26">
<a href="index.cml"><font><img width="46" src="index.jpg" height="26" border="0">
</font></a><font><a href="page1.cml"><img width="28" src="page1.jpg" height="26" border="0">
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org.concord.modeler.text.LineIcon750.085101015<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="mainidea">
<table cellspacing="0" cellpadding="0" border="0">
<tr>
<td>
<img height="58" src="chargeMainIdea.png" width="98">
</td>
<td>
<p class="mainidea">
How does charge affect the surface of proteins?
</p>
</td>
</tr>
</table>
</body>
</html>
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<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body>
<p class="firstp">
The complex peaks and valleys of a macromolecule are made even more
distinct by the pattern of charges present at the surface. Every
different protein has its own shape and charge pattern, giving it a
unique molecular ID. In this way, molecules can recognize each other by
both shape and charge.
</p>
</body>
</html>
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org.concord.modeler.PageJContainer
JmolApplet.jar
netscape.jar
org.jmol.applet.MwPlugin
page4$plugin$0.aps{name="load" value="1E01.pdb"}
{name="nostatepersistence" value="true"}
{name="script" value="script 1E01init.spt"}
450400
Nonehttp://mw2.concord.org/public/plugin/1E01init.spt, surfNOT33.jvxl, surfNOT25.jvxl, surfALL.jvxl, surfNOT38.jvxl, area1.spt, area2.spt
org.concord.modeler.PageTextBox
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<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body marginwidth="5" marginheight="5">
<table cellspacing="0" cellpadding="0" border="">
<tr>
<td colspan="2">
<p class="firstp">
<b>Your job: </b>Compare charges at the surface of the protein
with the atoms underneath to understand what causes the charge.<br><br><img src="surfaceCharge.gif"><br><b>What
to do: </b>To see underlying amino acids, click in the yellow
circles in the model, or use the buttons below. Use the "Sidechain
surface" buttons to view the surface color more clearly (solid) or
to view the atoms underneath (translucent).
</p>
</td>
</tr>
<tr>
<td>
<b>View:</b>
</td>
<td>
<b>Sidechain surface: </b>
</td>
</tr>
<tr>
<td>
<input script="script:textbox:3:selectcomponent 2 false; script:nativescript:plugin:1:script area1.spt;" name="button4" value="Area #1" type="submit" id="button4">
</td>
<td>
<input script="script:nativescript:plugin:1:color isosurface opaque" name="button2" value="Solid" type="submit" id="button2">
</td>
</tr>
<tr>
<td>
<input script="script:textbox:3:selectcomponent 2 false; script:nativescript:plugin:1:script area2.spt;" name="button3" value="Area #2" type="submit" id="button3">
</td>
<td>
<input script="script:nativescript:plugin:1:color isosurface translucent" name="button5" value="Translucent" type="submit" id="button5">
</td>
</tr>
<tr>
<td>
<input script="script:textbox:3:selectcomponent 0 false; script:textbox:3:selectcomponent 1 false; script:textbox:3:selectcomponent 2 false; script:nativescript:plugin:1:set echo area1Echo hidden; set echo area2Echo hidden; set echo zoomEcho hidden; moveto 1.0 { 770 282 573 98.07} 85 0.0 0.0 {1.3679996 -1.7515001 -5.9615006} 20.098276 {0.0 0.0 0.0} 8.439582 11.647305 50.0; delay 0.2; set echo circle1 displayed; set echo circle2 displayed; color isosurface opaque" name="button1" value="Reset all" type="submit" id="button1">
</td>
<td>
 
</td>
</tr>
</table>
</body>
</html>
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org.concord.modeler.PageMultipleChoice
true
4
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<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="question">
<p class="question">
Which word best describes the character of the amino acid under the
protein surface <a href="nativescript:plugin:1:script area3.spt">here</a>?
(Click to see it in the model.) Choose the BEST answer:
</p>
</body>
</html>
true
polar
nonpolar
positive
negative
2
-373738
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org.concord.modeler.PageMultipleChoice
true
4
371
195
<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="question">
<p class="question">
Which word best describes the character of the amino acid under the
protein surface <a href="nativescript:plugin:1:script area4.spt">here</a>?
(Click to see it in the model.) Select the BEST answer:
</p>
</body>
</html>
true
polar
nonpolar
positive
negative
0
-373738
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org.concord.modeler.PageTextArea
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<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="question">
<p class="question">
Areas of neutral charge are hydrophobic. Why do you think we don't we
see much in the way of neutral areas on the surface of this protein?
</p>
</body>
</html>
Simple answer: Charged parts of the protein are on the outside, because they are more attracted to water than neutral parts. Hydrophobic parts of the protein are on the inside. Advanced answer: Since water is more attracted to the polar and charged side chains, hydrophobic side chains move to the interior of a protein as it folds.
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org.concord.modeler.PageTextArea
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<html>
<head>
<link href="bioStyles.css" type="text/css" rel="stylesheet">
</head>
<body class="question">
<p class="question">
Imagine that the region shown <a href="nativescript:plugin:1:script area5.spt">here</a>
could bind stongly to another protein. Describe the shape and charge of
the part of the other protein that binds here.
</p>
</body>
</html>
The other molecule would have a cavity or deep pocket that would be complementary in shape to this "knob". In addition the pocket would be polar, with areas of positive and negative charge that would align with the opposing charges on the knob.
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<body background="navBarBottomBackground.jpg" marginwidth="0" marginheight="0">
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<tr>
<td colspan="2">
<img width="14" src="navBarBottomColorBar.gif" height="6">
</td>
</tr>
<tr>
<td>
<img width="8" src="navBarBottomLeftMargin.jpg" height="26">
<font><a href="page3.cml"><img width="60" src="prev.jpg" height="26" border="0">
</a><a href="page5.cml"><img width="59" src="next.jpg" height="26" border="0">
</a></font>
</td>
<td align="right">
<img width="54" src="page.jpg" height="26">
<a href="index.cml"><font><img width="46" src="index.jpg" height="26" border="0">
</font></a><font><a href="page1.cml"><img width="28" src="page1.jpg" height="26" border="0">
</a><a href="page2.cml"><img width="28" src="page2.jpg" height="26" border="0">
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</a><a href="page5.cml"><img width="28" src="page5.jpg" height="26" border="0">
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</font> </td>
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