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Proteins and Nucleic Acids: Protein Interactions and Conformations
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<p class="pagetitle"><strong>Proteins and Nucleic Acids:</strong> Protein Interactions and Conformations</p>
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<td><p class="mainidea"> How do the interactions among the amino acids and their environment relate to the structure a protein and by extension its function?</p></td>
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<p class="firstp">
In the model on a previous page, you saw that linear polymers can curl
and bend. In that model, they just seemed to pivot around the bonds.
However, most molecules have distinct shapes and structures. What
determines the structures? In proteins, the flexibility of the amino
acids around the bonds allows the long chains to curl. The amino acids
can also interact with each other and the environment they are in. On
this page you will explore how interactions between amino acids, their
polarities and hydrophobicities relate to the conformation of a protein.
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Interactions between amino acids
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Amino acids form certain structures because of the interactions between
them. On the right is a model that shows a fictitious protein. With the
red ellipical area is a beta sheet that is formed by a number of hydrogen bonds
between the strands. De-select and re-select the check box below and observe how the protein's conformation relates to the presence of these hydrogen bonds.
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Water's final touches
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Proteins fold in water. Therefore, an important property of each amino
acid is its interaction with water.<br><br>Some amino acids are <b>hydrophillic</b>.
They tend to be attracted to water, because they are either polar or
charged. Others are <b>hydrophobic</b>. They are neither polar nor
charged, and tend not to be attracted to water.<br><br><b>How
Hydrophobicity Works:</b> When you put hydrophobic molecules in water,
they tend to clump together. This is because they have no charge and
little or no polarity. Water molecules are polar, so they are attracted
much more strongly to each other than to the hydrophobic molecules.
Water excludes other molecules that aren't polar. This is true for the
amino acids too. In the model below we will explore how the amino acids
interact with the water they encounter in cells.
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The model on the right starts with a completely hydrophobic chain. Run the
model and observe its shape. Then select "Completely hydrophilic chain"
and "Half hydrophobic/half hydrophilic", respectively, and run them to see
what shape the chain will take.<br><br>Take a snapshot of what the protein chain becomes after it is set to be half hydrophobic and half hydrophilic and run for a while.
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Completely hydrophobic chain
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Completely hydrophilic chain
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Half hydrophilic/half/hydrophobic
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<font face="Arial, Helvetica, sans-serif" size="4"><strong>Run the model,
and imagine you are one of the hydrophobic amino acids. What do you
experience as the chain folds in water? Describe your interactions with
other amino acids and with water molecules.</strong></font>
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Place the snapshot of the protein with half hydrophobic and half
hydrophilic amino acids. Point out how the amino acids help determine
the shape of the folded protein.
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