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Mission: Immunity | Training Phase II
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After completing this page you may progress to your mission instructions, on the next page.
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<font face="Verdana, Arial, Helvetica, sans-serif" size="5" color="#FFFFFF"><strong>Training Phase II: Sequence A Peptide </strong></font>
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<td><img src="atomMainIdea.png" width="98" height="58"></td>
<td><font face="Verdana, Arial, Helvetica, sans-serif" size="4">Peptides are pieces of proteins, so, like proteins they too are chains of amino acids. On your mission, you will need to determine the amino acid sequences of peptides.</font></td>
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<strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="#5d6b86">Rover
Mission Training: Phase II</font></strong>
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<tr>
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<img width="18" height="6" src="rule.png">
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">The sequences
of the peptides held by MHCs determine whether a cell lives or dies. Based
on the sequences you record on your mission, you will decide whether the
cell has a virus, and if so, seal its fate.<br><br><b>Training Goal:
Sequence a peptide using the Rover's capabilities.</b><br><br><b>Step 1.
Find the beginning of the peptide.</b> Every protein and peptide has both
a positive and a negative end. To read the sequence of amino acids
correctly, you must start at the positive end.<b>You can use your
molecular rover to sense the charges along the peptide by giving the rover
a positive or negative charge using the controls below.</b></font>
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<strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif">The
Amino Acids</font><font size="3" face="Verdana, Arial, Helvetica, sans-serif"><br><br>Nonpolar
side chain<br></font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="ala.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">ALA</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="gly.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">GLY</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="ile.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">ILE</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="leu.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">LEU</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"> 
</font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="met.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">MET</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"><br></font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="phe.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">PHE</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="pro.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">PRO</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="trp.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">TRP</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
</font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="tyr.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3"> TYR</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="val.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">VAL</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
</font></strong>
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<strong><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Polar
side chain<br></font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="asn.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">ASN</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"> 
</font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="cys.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">CYS</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"> 
</font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="gln.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">GLN</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"> 
</font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="ser.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">SER</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="thr.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">THR</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"><br><br>Charged
side chain: (+)<br></font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="arg.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">ARG</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="his.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">HIS</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif">
 </font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="lys.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">LYS</font></a>
</strong>
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<p>
<strong><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Charged
side chain: (-)<br></font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="asp.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">ASP</font></a><font size="3" face="Verdana, Arial, Helvetica, sans-serif"> 
</font><a link_width="300" link_left="50 link_right=" link_menubar="false" link_toolbar="false" target="_blank" href="glu.cml" link_height="300"><font face="Verdana, Arial, Helvetica, sans-serif" size="3">GLU</font></a>
</strong>
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<font face="Verdana, Arial, Helvetica, sans-serif" size="4">But remember – <b>some
amino acid side chains are charged!</b> So if you drift to one of the side
chains, instead of to the actual beginning or end of the peptide, you will
need to accelerate the rover to escape the charge, and try again.<br><br><b>Step
2. Identify the amino acids.</b> Click the box marked "Identification
Mode". In this mode, when you allow the mouse cursor to stop for a moment
or two directly on top of an atom, the identity of that amino acid will
appear as a pop-up label. When you move the cursor again, the label
disappears. (Hint: experiment with the display controls to find a way to
know where one amino acid ends and the next begins.)<br><br><b>After
completing both steps, answer the questions below.</b></font>
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<b><font size="3" face="Verdana, Arial, Helvetica, sans-serif">Peptide
structure styles:</font></b>
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
<td>
<input type="radio" name="RadioGroup2" checked="checked" script="script:jmol:1:restrict none; select all; cpk; focus;" value="radio">
</td>
<td>
<font size="3" face="verdana, arial, sans-serif">spacefill</font>
</td>
<td>
<input type="radio" name="RadioGroup2" script="script:jmol:1:restrict none; select all; cpk 0.5; wireframe 0.3; focus;" value="radio">
</td>
<td colspan="4">
<font size="3" face="verdana, arial, sans-serif">ball & stick</font>
</td>
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<td>
 
</td>
<td>
<input type="radio" name="RadioGroup2" script="script:jmol:1:restrict none; select all; wireframe 0.3; focus;" value="radio">
</td>
<td>
<font size="3" face="verdana, arial, sans-serif">stick</font>
</td>
<td>
<input type="radio" name="RadioGroup2" script="script:jmol:1:restrict none; select backbone and not oxygen; trace; focus;" value="radio">
</td>
<td colspan="4">
<font size="3" face="verdana, arial, sans-serif">cartoon</font>
</td>
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<td colspan="8">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><strong>Color
Amino Acids By:</strong></font>
</td>
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<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"> </font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input type="radio" name="radioGroup3" checked="checked" script="script:jmol:1: select all; color atoms cpk; focus;" value="radiobutton">
</font>
</td>
<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="radioGroup3" script="script:jmol:1:select all; color atoms amino; #select backbone; #color atoms white; #select all; focus;" value="radiobutton">
</font>
</td>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif">amino
acid<!--<input value="radiobutton" script="script:jmol:2:select all; color gray; focus;" name="radioGroup3" type="radio"> -->
</font>
</td>
<td colspan="3">
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><!--by
structure -->
</font>
</td>
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<td>
 
</td>
<td>
 
</td>
<td>
 
</td>
<td align="right">
 
</td>
<td>
 
</td>
<td colspan="3">
 
</td>
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<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><strong>Keyboard
Flying:</strong><br><br>Forward=A   Reverse=S<br>Rotate =
Z or SHIFT-Z<br>Turning: arrow keys<br>Sideways/rise/drop:
SHIFT-arrow<br>Orbit: ALT-arrow </font>
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{value="1.0", label="positive"}{value="-1.0", label="negative"}{value="0.0", label="none"}
Execute Jmol script
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</font>
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<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">Identification
mode</font>
</td>
</tr>
<tr>
<td>
<font size="3" face="Verdana, Arial, Helvetica, sans-serif"><input type="checkbox" name="checkbox2" script_selected="script:jmol:1:set rover.visible off; focus;" script_deselected="script:jmol:1:set rover.visible on; focus;" value="checkbox">
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<font face="Verdana, Arial, Helvetica, sans-serif" size="3">Stealth
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</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3">Rover
Force Field </font><a link_width="300" link_left="100" link_menubar="false" link_toolbar="false" target="_blank" href="forcefield.cml" link_height="200" link_top="200"><font face="Verdana, Arial, Helvetica, sans-serif" size="2">(what's
this?)</font></a>
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<tr>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><!--
<input script_selected="script:jmol:1:set rover.visible off; focus;" type="checkbox" script_deselected="script:jmol:1:set rover.visible on; focus;" name="checkbox2" value="checkbox"> -->
</font>
</td>
<td>
<font face="Verdana, Arial, Helvetica, sans-serif" size="3"><!--Stealth
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<body marginwidth="5" bgcolor="rgb(230, 230, 230)" marginheight="5">
<strong><font size="4" face="Arial, Helvetica, sans-serif">Which of the
following is the correct sequence for the peptide above?</font></strong>
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true
PHE-ARG-VAL-GLY-VAL-ASP-ALA-VAL-THR
THR-VAL-ALA-ASP-VAL-VAL-ARG-PHE
THR-VAL-ALA-ASP-VAL-GLY-VAL-ARG-PHE
PHE-ARG-VAL-VAL-ASP-ALA-VAL-THR
THR-VAL-ASP-ASP-VAL-GLY-VAL-ARG-PHE
PHE-ARG-VAL-GLY-VAL-ASN-ALA-VAL-THR
2
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<body marginwidth="5" bgcolor="rgb(230, 230, 230)" marginheight="5">
<strong><font size="4" face="Arial, Helvetica, sans-serif">In addition to
the ends of a peptide, some amino acid side chains are also charged. Which
side chains in the peptide sequence are charged? Check all the correct
answers.</font></strong>
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true
true
ARG
HIS
GLU
ASN
ASP
0 4
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<a href="page2.cml"><font><img height="26" src="prev.jpg" border="0" width="60">
</font></a><font><a href="page4.cml"><img height="26" src="next.jpg" border="0" width="59">
</a></font>
</td>
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<img height="26" src="page.jpg" width="54">
<a href="index.cml"><font><img height="26" src="index.jpg" border="0" width="46">
</font></a><font><a href="page1.cml"><img height="26" src="page1.jpg" border="0" width="28">
</a><a href="page2.cml"><img height="26" src="page2.jpg" border="0" width="28">
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