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Proteins III: Page 1
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<p class="pagetitle">
<strong>Proteins III:</strong> "Life-size" Molecules
</p>
</body>
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<link type="text/css" rel="stylesheet" href="bioStyles.css">
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<body class="mainidea">
<table border="0" cellspacing="0" cellpadding="0">
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<td>
<img width="98" height="58" src="chargeMainIdea.png">
</td>
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<p class="mainidea">
Life requires macromolecules. What advantages do they offer over
small molecules?
</p>
</td>
</tr>
</table>
</body>
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<p class="firstp">
Macromolecules are very large molecules. They are hard to build, and
they are fragile. For example, protein structures can be crippled by a
small rise in body temperature. This is because it causes an increase
thermal motion, which can cause the protein chain to unfold and lose its
function. Why does life require such delicate molecules, when small
molecules are much more stable?
</p>
<p>
<b>What to do:</b>
</p>
<blockquote>
<b>    1. View different small and large molecules</b>
using the controls above the structures.<br><b>    2. Compare the size,
shape, and surfaces of small molecules and macromolecules</b> using the
controls below the structures.<br><b>    3. Turn on the surface view</b>
using the controls below the model and take a snapshot of a protein that
shows its details, such as "peaks" and "valleys". <a href="script:page:0:message <t><font face=verdana> You can zoom in to see more detail by clicking on the molecule <br> and dragging downward with the SHIFT key held down. </font></t>">Hint</a>
</blockquote>
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<b>Small molecules</b>
</p>
<table border="0" width="100%" cellspacing="0" cellpadding="0">
<tr>
<td colspan="4">
 
</td>
</tr>
<tr>
<td align="right" style="width: 25%">
<input name="RadioGroup1" checked="checked" script="nativescript:plugin:1:load methane.mol2; script methane.spt; nativescript:plugin:2: script allMolFlagsOff.spt; methaneFlag = true;" value="radio" type="radio" id="RadioGroup1_0">
</td>
<td width="35%">
Methane
</td>
<td width="5%" align="right">
<input name="RadioGroup1" script="nativescript:plugin:1:load caffeine.mol2; script caffeine.spt; nativescript:plugin:2: script allMolFlagsOff.spt; caffeineFlag = true;" value="radio" type="radio" id="RadioGroup1_2">
</td>
<td width="35%">
Caffeine
</td>
</tr>
<tr>
<td align="right">
<input name="RadioGroup1" script="nativescript:plugin:1:load propane.pdb; script propane.spt; nativescript:plugin:2: script allMolFlagsOff.spt; propaneFlag = true;" value="radio" type="radio" id="RadioGroup1_1">
</td>
<td>
Propane
</td>
<td align="right">
<input name="RadioGroup1" script="nativescript:plugin:1:load benzene.pdb; script benzene.spt; script surfaceControl.spt; nativescript:plugin:2: script allMolFlagsOff.spt; benzeneFlag = true;" value="radio" type="radio" id="RadioGroup1_3">
</td>
<td>
Benzene
</td>
</tr>
</table>
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<p align="center" class="firstp">
<b>Macromolecules</b>
</p>
<table border="0" width="100%" cellspacing="0" cellpadding="0">
<tr>
<td colspan="4">
 
</td>
</tr>
<tr>
<td align="right" width="25%">
<input name="RadioGroup2" checked="checked" script="nativescript:plugin:2:load insulin.pdb; script insulin.spt; nativescript:plugin:1: script allMolFlagsOff2.spt; insulinSilkFlag = true; script smallMolZoom.spt; " value="radio" type="radio" id="RadioGroup2_0">
</td>
<td width="35%">
Insulin
</td>
<td width="5%" align="right">
<input name="RadioGroup2" script="nativescript:plugin:2:load silk.mol2; script silk.spt; nativescript:plugin:1: script allMolFlagsOff2.spt; insulinSilkFlag = true; script smallMolZoom.spt; " value="radio" type="radio" id="RadioGroup2_2">
</td>
<td width="35%">
Silk
</td>
</tr>
<tr>
<td align="right">
<input name="RadioGroup2" script="nativescript:plugin:2:load 1hho.pdb; script hemoglobin.spt; nativescript:plugin:1: script allMolFlagsOff2.spt; hbFlag = true; script smallMolZoom.spt; " value="radio" type="radio" id="RadioGroup2_1">
</td>
<td>
Hemoglobin
</td>
<td align="right">
<input name="RadioGroup2" script="nativescript:plugin:2:load igg1-all.pdb; script antibody.spt; nativescript:plugin:1: script allMolFlagsOff2.spt; abFlag = true; script smallMolZoom.spt; " value="radio" type="radio" id="RadioGroup2_3">
</td>
<td>
Antibody
</td>
</tr>
<!--
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<td> </td>
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org.concord.modeler.PageButton
Take a snapshot of the protein
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<tr>
<td>
<b>Display Style:</b>
</td>
<td align="right" width="30">
<input name="RadioGroup1" script="nativescript:plugin:1:script ballstick.spt; nativescript:plugin:2:script ballstick.spt;" value="radio" type="radio" id="RadioGroup1_1">
</td>
<td>
<div align="left">
ball and stick
</div>
</td>
<td width="30" align="right">
<input name="RadioGroup1" script="nativescript:plugin:1:script stick.spt; nativescript:plugin:2:script stick.spt;" value="radio" type="radio" id="RadioGroup1_2">
</td>
<td>
<div align="left">
stick
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</td>
<td width="30" align="right">
<input name="RadioGroup1" checked="checked" script="nativescript:plugin:1: script cpk.spt; nativescript:plugin:2:script cpk.spt" value="radio" type="radio" id="RadioGroup1_3">
</td>
<td>
<div align="left">
spacefill
</div>
</td>
</tr>
<tr>
<td>
<b>Surface:</b>
</td>
<td align="right">
<input name="RadioGroup2" script="nativescript:plugin:1: surfFlag=true; translucentFlag=true; script surfaceControl.spt; nativescript:plugin:2:surfFlag=true; translucentFlag=true; script surfaceControl.spt" value="radio" type="radio" id="RadioGroup2_1">
</td>
<td>
<div align="left">
translucent
</div>
</td>
<td align="right">
<input name="RadioGroup2" script="nativescript:plugin:1:isosurface on; color isosurface opaque; surfFlag=true; translucentFlag=false; script surfaceControl.spt; nativescript:plugin:2: surfFlag=true; translucentFlag=false; script surfaceControl.spt" value="radio" type="radio" id="RadioGroup2_2">
</td>
<td>
<div align="left">
solid
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<td align="right">
<input name="RadioGroup2" checked="checked" script="nativescript:plugin:1: surfFlag=false; translucentFlag=false; script surfaceControl.spt; nativescript:plugin:2: surfFlag=false; translucentFlag=false; script surfaceControl.spt" value="radio" type="radio" id="RadioGroup2_3">
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<div align="left">
none
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</td>
</tr>
<tr>
<td colspan="7">
<div align="center">
<font face="verdana" size="3">To <b>zoom in or out</b>, click on
the molecule and<br>hold the SHIFT key down while dragging
vertically. <input name="zoom" script="nativescript:plugin:1:script smallMolZoom.spt; nativescript:plugin:2:zoom 100" value="Reset Zoom" type="submit" id="zoom">
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<head>
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<body class="question">
<p class="question">
Which molecules seem to have the most varied shapes?
</p>
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true
both have an equal variety of shapes
macromolecules
small molecules
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<link type="text/css" rel="stylesheet" href="bioStyles.css">
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<body class="question">
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Place your protein snapshot here. Use the annotation tool <img src="textboxAnnotation.gif">
to point to peaks and valleys on the surface of the protein.
</p>
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What ideas do you have about why it is important for biological
molecules to have a great variety of sizes, shapes, and surfaces?
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<img width="14" src="navBarBottomColorBar.gif" height="6">
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<img width="8" src="navBarBottomLeftMargin.jpg" height="26">
<a href="index.cml"><font><img width="60" border="0" src="prev.jpg" height="26">
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<img width="54" src="page.jpg" height="26">
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