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Protein Folding: Page 5
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<p class="pagetitle"><strong>Protein Folding:</strong>Most Proteins Fold in Water</p>
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<td><img src="chargeMainIdea.png" width="98" height="58"></td>
<td><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></td>
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<p class="subhead">
Water, Water Everywhere
</p>
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<p class="firstp">
The inside of a cell is a watery environment. Water surrounds most
protein molecules as they are made and start to fold. A water molecule is shown below.
</p>
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<p class="firstp">
<img width="365" src="water_surface2Comp.png" height="201">
</p>
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<link rel="stylesheet" href="bioStyles.css" type="text/css">
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<body class="question">
<p class="question">
Is water a polar or non-polar molecule? Explain your answer by writing
about the bonds in water.
</p>
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<p class="firstp">
Molecules that
prefer to associate with water are called <b>hydrophilic</b>, which
means "loves water". Molecules that prefer NOT to associate with water
are <b>hydrophobic</b>, which means that they "fear water". Protein
folding is influenced greatly by interactions of hydrophobic and
hydrophilic amino acids with water.
</p>
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<p class="firstp">
<b>Which amino acids are <a href="script: page:0:message p5-hydrophobic.html">hydrophobic</a>,
and which are <a href="script: page:0:message p5-hydrophilic.html">hydrophilic</a>?</b>
Explore the answer using the model to the right, which contains a few
water molecules and one amino acid.
</p>
<p>
<b>In reality, liquid water surrounds enerything in the cell - there is
no empty space.</b> But in the model to the right, we only show a few
water molecules so you can see the interactions more clearly.
</p>
<p>
<b>Click the Run button on the model to observe how water and amino
acids "get along" together. Use the buttons below the model to compare
non-polar and polar amino acids. Then answer the questions below.</b>
</p>
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Polar amino acid
Click to load a model with water and a polar amino acid
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Nonpolar amino acid
Click to load a model with water and a nonpolar amino acid
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<body class="question">
<p class="question">
Which type of amino acid is hydrophobic?
</p>
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true
polar
non-polar
neither - they both avoid water
neither - they both stay near water
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Use your knowledge of positive and negative charge to explain why polar
molecules attract water and other polar molecules.
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<img width="33" src="chargeBullet.png" height="23">
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<p class="subhead">
Protein Folding Starts in Water
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<p class="firstp">
When amino acids are bonded together, creating a protein, both polar and
non-polar amino acids make up the chain. As the surrounding water
interacts with the protein, the protein chain collapses on itself. This part of
protein folding is called <b>"hydrophobic
collapse"</b>.
</p>
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<p class="firstp">
In the model on the right, each amino acid in a protein chain is a
represented as a bead:<br>
</p>
<p>
<img src="aaBeads2D.gif">
</p>
<p>
Use the model to explore how a protein chain behaves in water and in a
non-polar solvent, oil.
</p>
<p>
<b>Click Run to see the protein chain interact with the solvent. Be sure
to change the solvent using the buttons underneath the model. </b>Then
answer the questions below.
</p>
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</p>
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Water
Protein interacts with polar solvent
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Oil
Protein interacts with nonpolar solvent
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<body class="question">
<p class="question">
Which solvents lead to the collapse 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 nonpolar amino acids end up when the protein chain
collapses?
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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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<p class="firstp" align="center"><strong>You have reached the end of Part 1.<BR><a href="script:page:0:message endPartOne.html">CLICK HERE BEFORE REPORTING.</a></strong></p>
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