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Protein Conservation 3
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Hydrophobic and Hydrophilic Side Chains
Change solvent:
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<font face="verdana, arial, sans-serif" size="5">Each of the twenty
different amino acids has a chemical "personality" based on the
characteristics of its side chain. Some "personalities" are similar, some
quite different. One of the most far-reaching personality traits of the
amino acid side chains is their response to water, the polar solvent in
all our cells - mostly, they either love it or hate it.</font>
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org.concord.modeler.text.LineIcon710.0305515<html><body align="center"><strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)">Simple Representations of Amino Acids</font></strong></body></html>-46544255
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<font face="verdana, arial, sans-serif" size="4">Before we look at how
side chains react to water, <b>check out this chart</b>, which shows you a
couple of ways we will be symbolizing different amino acids.<br><br>The
simplest way to show different amino acids is with a single letter code
that is accepted worldwide. Three-letter abbreviations are also very
common, but take up more space.<br><br>It's important to remember that
each symbol actually stands for a complex little molecule that has a
unique personality.<br><br></font>
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<map name="Map">
<area title="the chemical structure of alanine" shape="rect" href="#" coords="28,53,140,143"></area>
<area shape="rect" alt="a graphic of alanine" href="#" coords="214,77,246,113"></area>
<area shape="rect" alt="abbreviations for alanine" href="#" coords="307,60,355,137"></area>
<area shape="rect" alt="the chemical structure of phenylalanine" href="#" coords="5,176,151,292"></area>
<area shape="rect" alt="a graphic of phenylalanine" href="#" coords="212,214,248,252"></area>
<area shape="rect" alt="abbreviations for phenylalanine" href="#" coords="308,196,356,281"></area>
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<img height="300" src="simplifiedAminoacids2.gif" border="0" width="361">
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org.concord.modeler.text.LineIcon710.0305515<html><body align="center"><strong><font size="5" face="Verdana, Arial, Helvetica, sans-serif" color="rgb(051, 051, 051)">Hydrophobic and Hydrophilic Side Chains</font></strong></body></html>-46544255
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<b><font size="4" face="verdana, arial, sans-serif">Water - love it or
(try to) leave it</font></b><font size="4" face="verdana, arial, sans-serif"><br>When
it comes to water, amino acid side chains come in two "flavors", based on
whether they are content to be surrounded by it, or cluster to shield
themselves from it.<br><br><b>Click "Run" and watch the model.</b><br>1.
You should notice that the two amino acids ("A" for alanine and "T" for
threonine) behave differently in water and oil.<br><br>2. Make sure to
change the solvent from water (polar) to oil (non-polar) to observe the
behavior of the amino acids in each. </font>
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<b>Observation and Deduction Challenges: <BR><br>
1. How do alanine and threonine behave differently in water and in oil? <br>
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<b>2. Molecules that are polar are called hydrophilic, which means "loves water". Non-polar molecules are hydrophobic, which means that they "fear water". Can you deduce whether alanine and threonine are polar or non-polar, based on their behavior in water and oil? Support your conclusions with your observations from part 1 of this question.</b>
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<font face="verdana, arial, helvetica, sans-serif" size="2">Note: the
model above considers only side chain interactions with solvent.
Individual amino acids have amino and acid groups that would influence
their behavior in solvent, but we ignore these for the purpose of focusing
on the side chains. </font>
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