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Four Levels of Protein Structure: Tertiary Structure
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<p class="pagetitle">
<strong>Four Levels of Protein Structure:</strong> Tertiary Structure
</p>
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<p class="mainidea">
The third, or tertiary, level of protein structure is the
three-dimensional structure of the folded protein chain.
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<p class="subhead">
Stabilizing Tertiary Structure
</p>
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<p class="firstp">
In tertiary structure, the secondary structures of the protein come
together. While secondary structure is secured by backbone hydrogen
bonds, tertiary structure is stabilized largely through the side chains,
by a combination of these types of interactions:
</p>
<ul>
<li>
hydrophobic interactions (for proteins in a watery environment)
</li>
<li>
attraction between oppositely charged side chains (“salt bridges”)
</li>
<li>
covalent bonds between cysteine side chains (“disulfide bonds”)
</li>
<li>
hydrogen bonds between side chains
</li>
</ul>
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<body marginheight="10" marginwidth="10">
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<td colspan="6">
<p class="firstp">
<b>Explore the attractions that keep the protein folded: </b>
</p>
<br>
</td>
</tr>
<tr>
<td colspan="2" align="right">
<input name="RadioGroup1" id="RadioGroup1_5 " selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1: restrict none; select all; labels off; set echo off; isosurface off; cpk; color [x9ab9a4]; delay 0.2; moveto 2.0 { 358 -786 -505 36.5} 109.3 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2;" type="radio" checked="checked" value="radio">
</td>
<td colspan="4">
original view
</td>
</tr>
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<td colspan="2" align="right">
<input name="RadioGroup1" id="RadioGroup1_1" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1:restrict none; select all; labels off; set echo off; isosurface off; cpk; select polar; color [x00dddd]; select hydrophobic; color [xfeaeae]; moveto 2.0 { 254 -917 -307 108.9} 109.3 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2; set echo polarecho 0% 100%; echo polar amino acids; font echo 16 sans bold; color echo [x00dddd]; set echo nonpolarecho 0% 90%; echo nonpolar amino acids; color echo [xfeaeae]; select all; " type="radio" value="radio">
</td>
<td colspan="4">
hydrophobic core
</td>
</tr>
<tr>
<td colspan="2" align="right">
</td>
<td width="24">
<input name="checkbox3" script_selected="script:jmol:1:select hydrophobic; color atoms translucent;" script_deselected="script:jmol:1:select hydrophobic; color atoms opaque;" type="checkbox" value="checkbox">
</td>
<td colspan="3">
make hydrophobic translucent
</td>
</tr>
<tr>
<td colspan="2" align="right">
</td>
<td>
<input name="checkbox5" script_selected="script:jmol:1:select polar; color atoms translucent;" script_deselected="script:jmol:1:select polar; color atoms opaque;" type="checkbox" value="checkbox">
</td>
<td colspan="3">
make hydrophilic translucent
</td>
</tr>
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<td colspan="6">
 
</td>
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<td colspan="6">
disulfide bonds:
</td>
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<td colspan="2" align="right">
 
</td>
<td>
<input name="RadioGroup1" id="RadioGroup1_2" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1: restrict none; select all; labels off; set echo off; isosurface off; color cpk; cartoon; color cartoon structure; delay 0.3; moveto 2.0 { 358 -786 -505 36.5} 140.3 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2; delay 0.3; select 4 and (sidechain or *.ca); wireframe 0.3; cpk 0.5; delay 0.3; moveto 2.5 { 958 -112 262 62.0} 898.0 0.0 0.0 {8.344 36.030083 45.891502} 39.8; delay 0.2; select (4.ca); label a cysteine side chain; set labeloffset 15 10; color label white; delay 0.8; moveto 2.0 { -937 185 -298 32.6} 898.0 0.0 0.0 {8.344 36.030083 45.891502} 39.8; delay 0.8; select 60 and (sidechain or *.ca); wireframe 0.3; cpk 0.5; delay 0.8; select (60.ca); label another cysteine|side chain; set labeloffset 1 10; color label white; delay 0.5; moveto 2.0 { 202 315 927 19.7} 898.5 0.0 0.0 {8.344 36.030083 45.891502} 39.8; ssbonds 0.3; select 4.sg; label disulfide bond; set labeloffset 1 -10; delay 0.5; select 4 or 60; ssbonds off; delay 0.3; ssbonds 0.3; delay 0.3; ssbonds off; delay 0.3; ssbonds 0.3; delay 0.3; ssbonds off; delay 0.3; ssbonds 0.3; select all; delay 1; labels off " type="radio" value="radio">
</td>
<td width="56">
one
</td>
<td width="24">
<input name="RadioGroup1" id="RadioGroup1_5" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1: restrict none; select all; labels off; set echo off; isosurface off; color cpk; cartoon; color cartoon structure; select cys and (sidechain or *.ca); color cpk; wireframe 0.3; cpk 0.5; ssbonds on; ssbonds 0.3; moveto 2.0 { -981 194 -19 171.0} 140.0 0.0 0.0 {5.8269205 30.078653 31.643835} 26.4; select all; delay 0.3; ssbonds off; delay 0.3; ssbonds 0.3; delay 0.3; ssbonds off; delay 0.3; ssbonds 0.3; " type="radio" value="radio">
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<td width="485">
all
</td>
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<tr>
<td colspan="6">
salt bridges:
</td>
</tr>
<tr>
<td colspan="2" align="right">
 
</td>
<td>
<input name="RadioGroup1" id="RadioGroup1_3" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1: restrict none; isosurface off; select all; labels off; set echo off; color cpk; cartoon; color cartoon structure; delay 0.3; moveto 2.0 { 358 -786 -505 36.5} 130 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2; delay 0.3; select (72 or 168) and (sidechain or *.ca); wireframe 0.3; cpk 0.5; select 72.cz; label +; font label 20 sans bold; set labeloffset 0 0; color label white; select 168.cg; label -; font label 20 sans bold; set labeloffset 0 0; color label white; moveto 2.0 { 212 -972 104 176.4} 537.0 0.0 0.0 {2.3153076 30.738 23.735462} 30.8; select 72 and (*.nh2,*.nh1,*.cz,*.ne); isosurface sb72 ignore (not selected) sasurface 0.1; color isosurface translucent red; select 168 and (*.cg, *.od1,*.od2); isosurface sb169 ignore (not selected) sasurface 0.1; color isosurface translucent blue; select all;" type="radio" value="radio">
</td>
<td>
one
</td>
<td>
<input name="RadioGroup1" id="RadioGroup1_7" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1: restrict none; select all; labels off; set echo off; isosurface off; color cpk; cartoon; color cartoon structure; script saltbridges.spt;" type="radio" value="radio">
</td>
<td>
all
</td>
</tr>
<tr>
<td colspan="6">
side chain hydrogen bonds:
</td>
</tr>
<tr>
<td colspan="2" align="right">
 
</td>
<td>
<input name="RadioGroup1" id="RadioGroup1_8" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1:script:jmol:1: restrict none; isosurface off; select all; labels off; set echo off; color cpk; cartoon; color cartoon structure; delay 0.3; moveto 2.0 { -328 -928 177 124.2} 140.0 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2; select 98 and (sidechain or *.ca) or 88; wireframe 0.3; cpk 0.5; connect (atomno=737) (atomno=661) hbond; color hbond violet; hbond 0.15; delay 0.3; moveto 2.0 { -219 -704 676 113.7} 736.9 0.0 0.0 {21.314 21.824 20.9475} 41.2; delay 0.3; select all" type="radio" value="radio">
</td>
<td>
one
</td>
<td>
<input name="RadioGroup1" id="RadioGroup1_9" selfscript="selectcomponent 2 false; selectcomponent 3 false" script="script:jmol:1: moveto 2.0 { 218 -976 -9 144.2} 130 -8.7 -2.7 {7.0289993 32.1175 32.2415} 28.2; restrict none; select all; labels off; set echo off; isosurface off; color cpk; cartoon; color cartoon structure; delay 0.3; script hbonds-tertiary.spt; " type="radio" value="radio">
</td>
<td>
all
</td>
</tr>
<tr>
<td colspan="6">
<p>
<b><font size="3">To center your view on an atom: click the
checkbox below, then click a visible atom.</font></b>
</p>
</td>
</tr>
<tr>
<td colspan="2" align="right">
<input name="checkbox" script_selected="script:jmol:1:set picking center" script_deselected="script:jmol:1:set picking ident" type="checkbox" value="checkbox">
</td>
<td colspan="4">
center clicked atom
</td>
</tr>
<tr>
<td colspan="6">
<p>
<b><font size="3">Next, take snapshots to answer the questions
below.</font></b>
</p>
</td>
</tr>
</table>
<input name="button1" id="button1" script="script:jmol:1:snapshot" type="submit" value="Take a Snapshot">
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<body class="question">
<p class="question">
Show an interaction that stabilizes two alpha helices to each other. Use
the annotation tool to label the type of interaction you are showing.
</p>
</body>
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false
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org.concord.modeler.ImageQuestion372300<html>
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<body class="question">
<p class="question">
Create a view that shows both the amino acids at the surface and those
that fold into the inside the protein. Use the annotation tools to label
the part that is more attracted to water.
</p>
</body>
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