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Four Levels of Protein Structure: The "Glue" in Secondary Structures
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Using the controls above create what you think are the best images showing
how hydrogen bonds stabilize secondary structures, and place them below.
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<p class="pagetitle">
<strong>Four Levels of Protein Structure:</strong> The "Glue" in
Secondary Structures
</p>
</body>
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<img width="98" src="chargeMainIdea.png" height="58">
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<p class="mainidea">
Secondary structures are stable because hidden in the repeating
pattern of the protein backbone are the makings of hundreds of
hydrogen bonds.
</p>
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<p class="subhead">
Why do secondary structures form?
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<p class="firstp">
On the right are two amino acids. As you can see from the red and
blue molecular surface, both the side chains and backbone atoms of
these amino acids are polar. A hydrogen bond is shown between the
backbone atoms of the two amino acids.
</p>
<p>
Hydrogen bonds are a form of polar attraction. <b>When a protein
chain remains folded as an alpha helix or a beta sheet, it is
doing so because it is stabilized by hydrogen bonds between the
atoms of the backbone.</b> Since the backbone is a repeating
structure, the hydrogen bonds form repeatedly as long as the fold
follows certain patterns.
</p>
<p>
Explore the molecule below to see what overall affect hydrogen
bonds have on protein shape.
</p>
<p>
</p>
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<td>
<img width="309" src="polarAmino.jpg" height="315">
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<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Your
Goal:</strong></font> <font face="Verdana, Arial, Helvetica, sans-serif" size="3">Explore
the protein and take snapshots of secondary structures with emphasis on
seeing how hydrogen bonds help to stabilize these structures (alpha helix
and beta sheet).<br><br></font>
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<td colspan="7">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Show:</strong>
</font>
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<td width="12">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
<td width="24">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:hbonds calculate; hbonds 0.15; color hbonds violet;" value="checkbox" script_deselected="script:jmol:1:hbonds off;" name="checkbox3" checked="checked">
</font>
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<td width="72">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">hydrogen
bonds </font>
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<td width="31" align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:trace on; color trace structure;" value="checkbox" script_deselected="script:jmol:1:trace off;" name="checkbox4">
</font>
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<td width="75">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">backbone
trace </font>
</td>
<td width="30" align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:cartoon on; color cartoon structure;" value="checkbox" script_deselected="script:jmol:1:cartoon off;" name="checkbox5">
</font>
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<td width="71">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">cartoons</font>
</td>
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<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:select sidechain; spacefill 20%; select sidechain or *.CA; wireframe 0.2; select sidechain or nitrogen; wireframe 0.2; select all;" value="checkbox" script_deselected="script:jmol:1:select sidechain; spacefill off; select sidechain or *.CA; wireframe off; select sidechain or nitrogen; wireframe off; select all;" name="checkbox32" checked="checked">
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">side
chains </font>
</td>
<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:select backbone; spacefill 20%; wireframe 0.2;select all;" value="checkbox" script_deselected="script:jmol:1:select backbone; spacefill off; wireframe off; select all;" name="checkbox33" checked="checked">
</font>
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<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">backbone</font>
</td>
<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
</tr>
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<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="radio" value="radiobutton" script="script:jmol:1:display all;moveto 1.0 { 802 -64 -593 140.2} 121.5 0.0 0.0 {-0.5722567 0.7668621 -0.8663576} 20.0; select all;" name="radiobutton2" checked="checked">
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">entire
protein </font>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="radio" value="radiobutton" script="script:jmol:1:display all; moveto 1.0 { 306 465 -831 110.0} 194.9 0.0 0.0 {-5.3386426 -1.1175412 2.8080368} 22.1; select helix; display selected; select all;" name="radiobutton2">
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">alpha
helix </font>
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<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="radio" value="radiobutton" script="script:jmol:1:display all;moveto 1.0 { 761 -551 343 136.4} 157.2 0.0 0.0 {-0.5722567 0.7668621 -0.8663576} 20.0; select sheet; display selected; select all;" name="radiobutton2">
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<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">beta
sheet </font>
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<tr>
<td colspan="7">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Translucency:</strong></font>
</td>
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<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:select sidechain; color atoms translucent; select all;" value="checkbox" script_deselected="script:jmol:1:select sidechain; color atoms opaque; select all;" name="checkbox">
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">side
chains </font>
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<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:select backbone; color atoms translucent; select all;" value="checkbox" script_deselected="script:jmol:1:select backbone; color atoms opaque; select all;" name="checkbox6">
</font>
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<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">backbone</font>
</td>
<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="checkbox" script_selected="script:jmol:1:color cartoons translucent; select all;" value="checkbox" script_deselected="script:jmol:1:color cartoons opaque; select all;" name="checkbox7">
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">cartoons</font>
</td>
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<td colspan="7">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Color
Atoms By :</strong></font>
</td>
</tr>
<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="radio" value="radiobutton" script="script:jmol:1:color atoms cpk;" name="radiobutton3" checked="checked">
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</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">element</font>
</td>
<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="radio" value="radiobutton" script="script:jmol:1:select sidechain; color atoms amino; select backbone; color atoms gray; select all;" name="radiobutton3">
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<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">amino
acid </font>
</td>
<td align="right">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><input type="radio" value="radiobutton" script="script:jmol:1:color atoms structure;" name="radiobutton3">
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">structure</font>
</td>
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<tr>
<td colspan="7">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><strong>Fly
Through the Molecule :</strong></font>
</td>
</tr>
<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">  </font>
</td>
<td colspan="6">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">-
select <strong>navigation mode</strong> from the <strong>view</strong>
menu<br>- <strong>choose front</strong> when the dialog comes up<br>-
<strong>use the controls that appear to the left</strong> of the
molecule to "fly" around and through it </font>
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org.concord.modeler.ImageQuestion371371<html>
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<body class="question">
<p class="question">
The hydrogen bonds that stabilize an alpha helix.
</p>
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false
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org.concord.modeler.ImageQuestion371371<html>
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The hydrogen bonds that stabilize a beta sheet.
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Hydrogen bonds stabilizing alpha helices and beta sheets form between
the atoms of which part(s) of the amino acids involved?
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the side chains
the side chains and backbone
the backbone
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Place a snapshot here that illustrates your answer to the previous
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