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Four Levels of Protein Structure: Water Helps Shape Proteins
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<p class="pagetitle">
<strong>Four Levels of Protein Structure:</strong> Water Helps Shape
Proteins
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<img src="chargeMainIdea.png" width="98" height="58">
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<p class="mainidea">
As proteins are made, they generally fold spontaneously into
compact structures. Why don't they remain unfolded, as long,
flexible strings of amino acids?
</p>
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<p class="subhead">
Water, Water Everywhere
</p>
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A key reason that proteins fold is the way that side chains interact
with water. The inside of a cell is a watery environment, and water
molecules surround most proteins as they are being made and start to
fold. A water molecule is shown below. <font size="3"><b>Need a review
of polarity? See <a href="chemlink_polarity.html">ChemLink: Polarity</a>.</b>
</font>
</p>
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<p class="question">
Is water a polar or non-polar molecule? Explain your answer by writing
about the bonds in water.
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Polar molecules are attracted to water, so they are called <b>hydrophilic</b>,
which means "water-loving." The attractions between hydrophilic
molecules and water cause them to crowd in next to each other. Molecules
that are less attracted to water get crowded out of the way. They are
called <b>hydrophobic</b> ("water fearing") as a result.
</p>
<p>
<b>Which amino acids are hydrophobic, and which are hydrophilic? To find
out, </b><br>  1. Click "Run" to see the polar amino acid in water.<br> 
2. <b>Select the non-polar amino acid</b> and compare its behavior to
the polar amino acid.
</p>
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Polar amino acid
Click to load a model with water and a polar amino acid
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Execute MW script
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Nonpolar amino acid
Load a model with water and a nonpolar amino acid
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Which type of amino acid is hydrophobic?
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<html>polar
<html>non-polar
<html>neither - they both don't attract water very well
<html>neither - they attract the water molecules equally
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<p class="question">
Which of the following correctly describe the interactions of the amino
acids with water? (Check ALL that apply.)
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true
<html>non-polar amino acids are repelled by water
<html>non-polar amino acids are weakly attracted to water
<html>water molecules are attracted to each other more than to <b>non-polar</b> amino acids
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Use your knowledge of positive and negative charge to explain why polar
molecules attract each other better than non-polar molecules.
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Protein Folding in Water
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In the model on the right, each amino acid in a protein chain is shown
as a bead. The color of each bead corresponds to the polarity of its
side chain:<br>
</p>
<p>
<img src="aaBeads3D.gif">
</p>
<p>
Use the model to explore what happens to a protein chain in water, and
what happens in oil (a non-polar solvent).
</p>
<p>
<img src="listBullet.png">
<b> Click Run. </b><br><img src="listBullet.png"><b> Be sure to
change the solvent using the buttons underneath the model. </b>
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<html>
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<p class="question">
Which solvent(s) leads to folding of the protein?
</p>
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true
both water and oil
neither water nor oil
water
oil
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Where do the amino acids with polar side chains end up when the protein
chain folds?
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true
evenly throughout the folded protein
mostly inside the folded protein
mostly on the outside of the folded protein
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