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Four Levels of Protein Structure: Secondary Structure
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Proteins also have secondary structures called turns and loops. See them in this BioLink.
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<strong>Four Levels of Protein Structure:</strong> Secondary Structure
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<p class="mainidea">
Secondary structures are the shapes that form between neighboring
amino acids in a protein chain.
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<img width="33" src="chargeBullet.png" height="23">
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<p class="subhead">
The Alpha Helix and the Beta Sheet
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<b>Two easily recognized secondary structures occur over and over again
in most proteins. </b>An <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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<font color="#ff289d"><b>Alpha Helix</b></font>
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<font color="#dfbc00"><b>Beta Sheet</b></font>
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<p class="firstp">
<a href="script:page:0:message animControls.html"><b>Use the animation
controls</b></a><b> underneath the models</b> to see different ways
these structures can be drawn. Learn to recognize alpha helices and beta
sheets, so you will be able to find them in a whole protein (below).
</p>
<p>
Notice that the alpha helix is a made from single stretch of amino
acids, but the beta sheet is made from two separate pieces of a protein
chain.
</p>
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<p class="subhead">
Exploring Secondary Structures in a Protein Kinase
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<p class="firstp">
<b>A Kinase is a Type of Protein Switch</b>
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<p>
Kinase proteins are like molecular switches: they turn other molecules
on and off. Kinases do this by taking a phosphate from ATP and attaching
it to another molecule, which either activates (turns on) or deactivates
(turns off) the other molecule. There are hundreds of different kinases
and they regulate many important cellular functions. When they don't
work properly, cancer can result.
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<br>
<b>Use the controls beneath the model to highlight sections of this
kinase. Try the different display choices in the drop down menu to see
which ones illustrate different aspects of the structure. </b>
</p>
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<font size="2">Highlight 12 amino acids<br>starting at number</font>
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<select script4="script:jmol:3:script jmol-p2-cartoon.spt" script3="script:jmol:3:script jmol-p2-aminoAcidsBeads.spt" script2="script:jmol:3:script jmol-p2-allAtomsBallStick.spt" script1="script:jmol:3:script jmol-p2-allAtomsSpacefill.spt">
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<font size="3"><b>Hint: </b>To find the structures, use this menu
(at left) to change the way the structures are drawn. </font>
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<font size="2">Highlight 30 amino acids<br>starting at number</font>
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<font size="3">To highlight a whole beta sheet, use the 30-amino acid
highlighter control. </font>
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Take a snapshot of an alpha helix that shows how it folds.
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Take a snapshot of a beta sheet that shows how much space it occupies
within the protein. <a href="script:page:0:message hint-p3.html">Hint</a>.
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