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Protein Conservation 9
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Explore a Conserved Protein
page 11 of 11
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<font size="5" face="Verdana, Arial, Helvetica, sans-serif">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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Raised Bevel
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<br>
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<table width="96%">
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<td>
<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 size="4" face="Verdana, Arial, Helvetica, sans-serif"><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>
<strong><font size="4" face="Verdana, Arial, Helvetica, sans-serif">Fly
Through the Molecule:</font></strong><font size="4" face="Verdana, Arial, Helvetica, sans-serif"><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>
</td>
</tr>
</table>
</center>
</body>
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<table cellpadding="5" cellspacing="0" border="0" width="95%">
<tr>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">All:<br><input value="Off" name="button1" script="script:jmol:1:select protein; cpk off; script:textbox:3:load consurf_controls_unchecked.htm" type="submit"><input name="button2" value="On" script="script:jmol:1:select protein; cpk; script:textbox:3:load consurf_controls_checked.htm" type="submit"></font>
</td>
<td>
 
</td>
</tr>
</table>
<table width="96%">
<tr>
<td colspan="3">
<center>
<table width="100%">
<tr>
<td bgcolor="black">
<center>
<table noshade="" height="35" border="0" cellpadding="2" width="100%">
<tr>
<td bgcolor="#10c8d1">
<input name="g1" script_selected="script:jmol:1:select ~grade01; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade01; spacefill off;" alt="toggle display of amino acids at conservation grade 1" checked="checked">
<b>1</b>
</td>
<td bgcolor="#8cffff">
<input name="g2" script_selected="script:jmol:1:select ~grade02; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade02; spacefill off;" alt="toggle display of amino acids at conservation grade 2" checked="checked">
<b>2</b>
</td>
<td bgcolor="#d7ffff">
<input name="g3" script_selected="script:jmol:1:select ~grade03; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade03; spacefill off;" alt="toggle display of amino acids at conservation grade 3" checked="checked">
<b>3</b>
</td>
<td bgcolor="#eaffff">
<input name="g4" script_selected="script:jmol:1:select ~grade04; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade04; spacefill off;" alt="toggle display of amino acids at conservation grade 4" checked="checked">
<b>4</b>
</td>
<td bgcolor="#ffffff">
<input name="g5" script_selected="script:jmol:1:select ~grade05; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade05; spacefill off;" alt="toggle display of amino acids at conservation grade 5" checked="checked">
<b>5</b>
</td>
<td bgcolor="#fcedf4">
<input name="g6" script_selected="script:jmol:1:select ~grade06; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade06; spacefill off;" alt="toggle display of amino acids at conservation grade 6" checked="checked">
<b>6</b>
</td>
<td bgcolor="#fac9de">
<input name="g7" script_selected="script:jmol:1:select ~grade07; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade07; spacefill off;" alt="toggle display of amino acids at conservation grade 7" checked="checked">
<b>7</b>
</td>
<td bgcolor="#f07dab">
<input name="g8" script_selected="script:jmol:1:select ~grade08; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade08; spacefill off;" alt="toggle display of amino acids at conservation grade 8" checked="checked">
<b>8</b>
</td>
<td bgcolor="#a02560">
<input name="g9" script_selected="script:jmol:1:select ~grade09; spacefill on;" type="checkbox" script_deselected="script:jmol:1:select ~grade09; spacefill off;" alt="toggle display of amino acids at conservation grade 9" checked="checked">
<b>9</b>
</td>
</tr>
</table>
</center>
</td>
</tr>
</table>
</center>
</td>
</tr>
<tr>
<td width="33%">
<b><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Variable</font></b>
</td>
<td align="center" width="32%">
<b><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Average</font></b>
</td>
<td align="right" width="35%">
<b><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Conserved</font></b>
</td>
</tr>
</table>
</center>
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<p>
<font size="4" face="Verdana, Arial, Helvetica, sans-serif"><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 size="4" face="Verdana, Arial, Helvetica, sans-serif"><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 size="4" face="Verdana, Arial, Helvetica, sans-serif"><b>2. In the
space below, explain why you chose this region. </b></font>
</p>
</body>
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<font size="4" face="Verdana, Arial, Helvetica, sans-serif"><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 size="4" face="Verdana, Arial, Helvetica, sans-serif"><b>4. Where
are the least conserved (most variable) amino acids in the protein? Take a
snapshot to illustrate your choice below:</b></font>
</body>
</html>
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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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