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Protein Folding: Page 8
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<p class="pagetitle"><strong>Protein Folding:</strong> Secondary Structure</p>
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<td><img src="chargeMainIdea.png" width="98" height="58"></td>
<td><p class="mainidea">Proteins weave beautiful patterns as they fold. Two shapes made by the folds are very common. They occur due to the repeating nature of the amino acid backbone.</p></td>
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<p class="subhead">
Secondary Structures: The Alpha Helix and the Beta Sheet
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<b>Two easily recognized folding patterns occur over and over again in most
proteins. </b>They are referred to as 'secondary' structures (remember
that the primary structure is the order of the amino acids in the string
of protein). The <b>alpha helix</b> is formed when the protein curls
around into a spiral shape, and a <b>beta sheet</b> is formed when
extended parts of the protein line up next to each other, defining a
flattened shape. Below are models of the alpha helix and beta sheet.
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Notice that the beta sheet is made up of more than one strand, and the
strands need not be directly connected to each other.
</p>
<p>
<a href="script:page:0:message animControls.html"><b>Use the animation
controls</b></a><b> underneath the models to take a tour</b>. Each
"stop" on the tour emphasizes a different, important property of
proteins. <b>Be prepared to find alpha helices and beta sheets in a
whole protein, below.</b>
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<p class="subhead">
Secondary Structures: The Turn and the Loop
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<img src="turn.gif" width="180" height="166">
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<p class="firstp">
What about the parts of the protein that connect the alpha helices
and beta sheets? There are two structures that can connect them, <b>turns
and loops</b>. A <b>turn</b> is how a protein backbone makes a
short, sharp "U" turn, changing direction by 180 degrees. <b>Loops</b>
are longer with no particular pattern to them, meandering between
helices and sheets. (Although they are called "loops," they do not
usually form an actual loop).
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<img src="loop.gif" width="180" height="166">
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<p class="subhead">
Exploring Secondary Structures in a Protein Kinase
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<b>A Protein Switch</b><br>At left is a model of a protein
kinase. There are hundereds of different kinases, all of which take a
phosphate from ATP and transfer it to another molecule, activating or
deactivating it. Kinases can switch other proteins on and off, and they
regulate many important cellular functions. When they don't work
properly, cancer can result.
</p>
<p>
Many kinases have very simlar <a href="script:page:0:message primaryStructure.html">primary
structures</a>, which causes them to fold into the same <b>secondary
structures</b>, and the same overall shape, enabling them to perform the
same sort of function.
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<b>Use the controls beneath the model to explore the folds of this
kinase. Then, take snapshots to illustrate the descriptions in the image
questions below. </b>
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<font size="2">Highlight 12 amino acids<br>starting at number</font>
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<!-- <b>Molecule Style and Color: </b><br>-->
<select script4="script:jmol:3:script jmol-p2-aminoAcidsBeads.spt" script3="script:jmol:3:script jmol-p2-allAtomsBallStick.spt" script2="script:jmol:3:script jmol-p2-allAtomsSpacefill.spt" script1="script:jmol:3:select none;" name="select" script5="script:jmol:3:script jmol-p2-cartoon.spt">
<option selected>Select a style
<option>all atoms spacefill
<option>all atoms ball & stick
<option>string of beads
<option>cartoon
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<font size="2">Highlight 30 amino acids<br>starting at number</font>
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Snapshot of an alpha helix:
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Snapshot of a beta sheet:
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A loop between a beta sheet and an alpha helix:
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