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Protein Folding: Page 10
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<p class="pagetitle"><strong>Protein Folding:</strong> Tertiary Structure </p>
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<td><img src="chargeMainIdea.png" width="98" height="58"></td>
<td><p class="mainidea">The third level of protein structure is the folding of the secondary structures together to take on the final shape. Several forces are at work to encourage and stabilize this level, called tertiary protein structure.</p></td>
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Tertiary Structure and Disease
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<p class="firstp">
The fully folded shape of a protein chain, known as its<b> tertiary
(meaning “third level”) structure</b>, is strongly tied to
its function. If a protein does not fold correctly, it will not work
correctly, because it will not have the shape needed to perform its job.
This can have some serious consequences.
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At right are brain scans of a two people, one without Alzheimer's
disease, showing normal brain activity, and one with Alzheimer's,
showing a loss of brain activity. Alzheimer's disease is caused by
incorrect folding of proteins in brain cells. Other mis-folding
diseases include Huntington’s and mad cow disease.
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<img src="alzheimers.gif">
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<p class="subhead">
Stabilizing Tertiary Structure
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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 with side chains
</li>
</ul>
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<td><input checked="checked" id="RadioGroup1_5" name="RadioGroup1" 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" value="radio"></td>
<td>original view </td>
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<td><input selfscript="selectcomponent 2 true; selectcomponent 3 false" id="RadioGroup1_4" name="RadioGroup1" script="script:jmol:1:restrict none; select all; labels off; set echo off; isosurface off; cpk; select polar; color [x00dddd]; select hydrophobic; color [xfeaeae]; color atoms translucent; 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>hydrophobic core</td>
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<td><input script_selected="script:jmol:1:select hydrophobic; color atoms translucent;" name="checkbox3" script_deselected="script:jmol:1:select hydrophobic; color atoms opaque;" type="checkbox" value="checkbox"></td>
<td>make hydrophobic translucent </td>
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<td><input script_selected="script:jmol:1:select polar; color atoms translucent;" name="checkbox2" script_deselected="script:jmol:1:select polar; color atoms opaque;" type="checkbox" value="checkbox"></td>
<td>make hydrophilic translucent </td>
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<td><input selfscript="selectcomponent 2 true; selectcomponent 3 false" id="RadioGroup1_11" name="RadioGroup1" script="script:jmol:1:restrict none; select all; labels off; set echo off; isosurface off; cpk; select polar; color [x00dddd]; select hydrophobic; color [xfeaeae]; color atoms translucent; 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>hydrophobic core</td>
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<td><input id="RadioGroup1_2" name="RadioGroup1" 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} 109.3 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2; delay 0.3;; delay 0.3; moveto 2.5 { 965 -33 259 69.2} 1788.0 0.0 0.0 {8.344 36.030083 45.891502} 39.8; delay 0.3; select 4 and (sidechain or *.ca); wireframe 0.3; cpk 0.5; delay 0.2; select (4.ca); label a cysteine side chain; set labeloffset 1 10; color label white; delay 0.8; moveto 2.0 { -937 185 -298 32.6} 1788.0 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 { 228 653 722 26.2} 1682.1 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; select all; " type="radio" value="radio"></td>
<td>disulfide bond </td>
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<td><input id="RadioGroup1_3" name="RadioGroup1" 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} 109.3 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>salt bridge </td>
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<tr>
<td><input id="RadioGroup1_7" name="RadioGroup1" 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 { 358 -786 -505 36.5} 109.3 0.0 0.0 {7.0289993 32.1175 32.2415} 28.2; delay 0.3; moveto 2.0 { -891 -130 -435 70.9} 1517.6 6.1 12.1 {20.789701 22.939697 21.8956} 39.7; delay 0.3; 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; select all" type="radio" value="radio"></td>
<td>side chain hydrogen bond </td>
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<tr>
<td> </td>
<td> </td>
</tr>
<tr>
<td> </td>
<td><font size="3"><b>To center your view on an atom: click the checkbox below, then click a visible atom.</b></font></td>
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<td><input script_selected="script:jmol:1:set picking center" name="checkbox" script_deselected="script:jmol:1:set picking ident" type="checkbox" value="checkbox"></td>
<td>center clicked atom</td>
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<td> </td>
<td> </td>
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<td> </td>
<td> </td>
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<td> </td>
<td><input id="button1" name="button1" script="script:jmol:1:snapshot" type="submit" value="Take a Snapshot"></td>
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<p> </p>
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org.concord.modeler.ImageQuestion350300<html>
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<p class="question">
Show an interaction that stabilizes an alpha helix and a loop:
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Show an interaction that stabilizes two alpha helices:
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org.concord.modeler.ImageQuestion350300<html>
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Show an interaction that stabilizes a loop and a beta sheet:
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Show the hydrophobic core:
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<b>Double-click each image above, and in the space below the image,
describe the type of interaction or bond that stabilizes the structures. For example "disulfide bond". </b>
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