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Protein Conservation 9
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Explore a Conserved Protein
page 11 of 11
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<font face="Verdana, Arial, Helvetica, sans-serif" size="5">All life on
earth requires DNA in order to reproduce, and the building blocks of DNA
are the same in all organisms. It is because of this universal need that
many of the protein enzymes that make and repair DNA are very similar,
even in very different organisms. We've seen how closely related thymidine
synthase is in three species. Now we'll compare it in 100 different
organisms.</font>
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<font face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)" size="5"><strong>Coloring
by Side Chain Similarity</strong></font>
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<br>
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<table width="96%">
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<p>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif">We've
compared the amino acid sequences of thymidine synthase from 100
different species. Each of its amino acids has been given a
score, from most conserved (similar) to least conserved across
the 100 species, and colored according to the score. The most
conserved amino acids are a deep red, and the least conserved
(most variable) are blue. </font>
</p>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><b>Use
the checkboxes below the 3D model</b> to toggle the display of
the amino acids of each color (conservation level). </font>
</p>
</td>
</tr>
<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><strong>Fly
Through the Molecule:</strong><br>- 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 will
appear to the left</strong> of the molecule to "fly" around and
through it<br>- <strong>take snapshots</strong> to answer the
questions below </font>
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</tr>
</table>
</center>
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<table cellpadding="5" cellspacing="0" border="0" width="95%">
<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">All:<br><input value="Off" type="submit" script="script:jmol:1:select protein; cpk off; script:textbox:3:load consurf_controls_unchecked.htm" name="button1"><input value="On" type="submit" script="script:jmol:1:select protein; cpk; script:textbox:3:load consurf_controls_checked.htm" name="button2"></font>
</td>
<td>
 
</td>
</tr>
</table>
<table width="96%">
<tr>
<td colspan="3">
<center>
<table width="100%">
<tr>
<td bgcolor="black">
<center>
<table border="0" cellpadding="2" height="35" noshade="" width="100%">
<tr>
<td bgcolor="#10c8d1">
<input type="checkbox" script_selected="script:jmol:1:select ~grade01; spacefill on;" name="g1" script_deselected="script:jmol:1:select ~grade01; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 1">
<b>1</b>
</td>
<td bgcolor="#8cffff">
<input type="checkbox" script_selected="script:jmol:1:select ~grade02; spacefill on;" name="g2" script_deselected="script:jmol:1:select ~grade02; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 2">
<b>2</b>
</td>
<td bgcolor="#d7ffff">
<input type="checkbox" script_selected="script:jmol:1:select ~grade03; spacefill on;" name="g3" script_deselected="script:jmol:1:select ~grade03; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 3">
<b>3</b>
</td>
<td bgcolor="#eaffff">
<input type="checkbox" script_selected="script:jmol:1:select ~grade04; spacefill on;" name="g4" script_deselected="script:jmol:1:select ~grade04; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 4">
<b>4</b>
</td>
<td bgcolor="#ffffff">
<input type="checkbox" script_selected="script:jmol:1:select ~grade05; spacefill on;" name="g5" script_deselected="script:jmol:1:select ~grade05; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 5">
<b>5</b>
</td>
<td bgcolor="#fcedf4">
<input type="checkbox" script_selected="script:jmol:1:select ~grade06; spacefill on;" name="g6" script_deselected="script:jmol:1:select ~grade06; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 6">
<b>6</b>
</td>
<td bgcolor="#fac9de">
<input type="checkbox" script_selected="script:jmol:1:select ~grade07; spacefill on;" name="g7" script_deselected="script:jmol:1:select ~grade07; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 7">
<b>7</b>
</td>
<td bgcolor="#f07dab">
<input type="checkbox" script_selected="script:jmol:1:select ~grade08; spacefill on;" name="g8" script_deselected="script:jmol:1:select ~grade08; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 8">
<b>8</b>
</td>
<td bgcolor="#a02560">
<input type="checkbox" script_selected="script:jmol:1:select ~grade09; spacefill on;" name="g9" script_deselected="script:jmol:1:select ~grade09; spacefill off;" checked="checked" alt="toggle display of amino acids at conservation grade 9">
<b>9</b>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
</center>
</td>
</tr>
<tr>
<td width="33%">
<b><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Variable</font></b>
</td>
<td align="center" width="32%">
<b><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Average</font></b>
</td>
<td align="right" width="35%">
<b><font face="Verdana, Arial, Helvetica, sans-serif" size="3">Conserved</font></b>
</td>
</tr>
</table>
</center>
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<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><b>In every
species, thymidine sythase starts with the same precursor, and converts
it to thymidine. So every thymidine synthase protein, whether in humans,
rats, bacteria, or any other organism, must grab and hold onto the same
starting material. </b></font>
</p>
<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><b>1. Find a
region of thymidine synthase that you think is likely to perform this
essential function. Take a snapshot of the region and use the draw
rectangle button <img src="drawbox.gif"> to show the exact region you
are choosing. </b></font>
</p>
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<p>
<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><b>2. In the
space below, explain why you chose this region. </b></font>
</p>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><b>3. Where
are the most conserved amino acids in the protein? Take a snapshot to
illustrate your choice below:</b></font>
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distributed evenly throughout the protein
mostly in the core of the protein
mostly on the outside of the protein
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4"><b>4. Where
are the least conserved (most variable) amino acids in the protein? Take a
snapshot to illustrate your choice below:</b></font>
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distributed evenly throughout the protein
mostly in the core of the protein
mostly on the outside of the protein
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