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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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<strong>Four Levels of Protein Structure:</strong> The "Glue" in
Secondary Structures
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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.
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Why do secondary structures form?
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Hydrogen bonds (see <a link_width="850" link_left="100" link_resizable="false" link_menubar="false" link_toolbar="false" href="chemlink_hbonds_water_protein.cml" target="_blank" link_statusbar="false" link_top="100"><font>ChemLink:
Hydrogen bonds</font></a>) are a form of polar attraction found in
proteins as well as in water and other polar substances. Each
hydrogen bond is a weak attraction, but many of them together are
powerful.
</p>
<p>
<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.
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<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Your
Goal:</font></strong> <font face="Verdana, Arial, Helvetica, sans-serif" size="3">Explore
how hydrogen bonds help to stabilize the alpha helix and beta sheet
structures. Use the checkboxes to turn on and off different aspects of
this protein.<br><br></font>
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<td colspan="7">
<strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Show:</font></strong><font face="Verdana, Arial, Helvetica, sans-serif" size="3">
</font>
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<td width="12">
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"> </font>
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<td width="24">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="checkbox3" type="checkbox" value="checkbox" script_selected="script:jmol:1:hbonds calculate; hbonds 0.15; color hbonds violet;" script_deselected="script:jmol:1:hbonds off;" checked="checked">
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<td width="72">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">hydrogen
bonds </font>
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<td align="right" width="31">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="checkbox4" type="checkbox" value="checkbox" script_selected="script:jmol:1:trace on; color trace structure;" script_deselected="script:jmol:1:trace off;">
</font>
</td>
<td width="75">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">backbone
trace </font>
</td>
<td align="right" width="30">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="checkbox5" type="checkbox" value="checkbox" script_selected="script:jmol:1:cartoon on; color cartoon structure;" script_deselected="script:jmol:1:cartoon off;">
</font>
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<td width="71">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">cartoons</font>
</td>
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="checkbox32" type="checkbox" value="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;" script_deselected="script:jmol:1:select sidechain; spacefill off; select sidechain or *.CA; wireframe off; select sidechain or nitrogen; wireframe off; select all;" checked="checked">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">side
chains </font>
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<td align="right">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="checkbox33" type="checkbox" value="checkbox" script_selected="script:jmol:1:select backbone; spacefill 20%; wireframe 0.2;select all;" script_deselected="script:jmol:1:select backbone; spacefill off; wireframe off; select all;" checked="checked">
</font>
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<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">backbone</font>
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<td align="right">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="radiobutton2" 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;" checked="checked">
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<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">entire
protein </font>
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<td align="right">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input type="radio" name="radiobutton2" 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;">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">alpha
helix </font>
</td>
<td align="right">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input type="radio" name="radiobutton2" 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;">
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<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">beta
sheet </font>
</td>
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<tr>
<td colspan="7">
<strong><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Color
Atoms By :</font></strong>
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<tr>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input name="radiobutton3" type="radio" value="radiobutton" script="script:jmol:1:color atoms cpk;" checked="checked">
</font>
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<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">element</font>
</td>
<td align="right">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input type="radio" name="radiobutton3" value="radiobutton" script="script:jmol:1:select sidechain; color atoms amino; select backbone; color atoms gray; select all;">
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif">amino
acid </font>
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<td align="right">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input type="radio" name="radiobutton3" value="radiobutton" script="script:jmol:1:color atoms structure;">
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<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">structure</font>
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Hydrogen bonds stabilizing an alpha helix. Use the arrow tool to point
out the hydrogen bonds.
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Hydrogen bonds stabilizing a beta sheet. Use the arrow tool to point out
the hydrogen bonds.
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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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