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Proteins and Nucleic Acids: Amino Acid Sequence and Protein Shape
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Amy: some introduction here....
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Proteins and Nucleic Acids</strong>: Amino Acid Sequence and Protein Shape
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The structure of a protein solely depends on the sequence of its amino acids.
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Sequence and structure
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<font face="Verdana, Arial, Helvetica, sans-serif"><b>Challenge: Half and
half</b><br><br>Suppose the amino acids on the left side of the protein
were hydrophobic, and the ones on the right were hydrophilic. What would
happen? Follow these steps.<br></font>
<ol>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif">Reset the model. </font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif"><b>Hold down the
ALT key and click on an amino acid</b>. This brings up the amino acid
menu. It lets you choose one of the 20 amino acids. </font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif">Select an amino
acid. Pink ones are hydrophobic, and the rest are hydrophilic (polar
or charged).</font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif">Repeat for the
other amino acids, until all 10 on the left side of the protein are
pink and all 10 on the right are cyan. </font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif">When you're done,
click Run. </font>
</li>
<li>
<font face="Verdana, Arial, Helvetica, sans-serif">Once the protein
has folded up, take a snapshot.</font>
</li>
</ol>
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<b>Color key</b><br><br><b>Polarity:</b><br>
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<font size="3"><i>Positively charged </i></font>
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<td width="16" bgcolor="green">
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<font size="3"><i>Negatively charged </i></font>
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<font size="3"><i>Neutral </i></font>
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<br>
<b>Hydrophobicity:</b><br>
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<font size="3"><i>Hydrophilic </i></font>
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<font size="3"><i>Hydrophoblic </i></font>
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Take a snapshot
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Take a snapshot
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Randomize initially
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Generate a random self-avoided polypeptide conformation
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Place the snapshot of the protein after it has folded in the box below.
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<p class="question">
Create an amino acid with a different shape by changing the location of
the hydrophobic and hydrophilic amino acids. Take a snapshot and drag it
here.
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Proteins and Nucleic Acids
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