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Protein Folding: Primary Structure
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<p class="pagetitle"><strong>Protein Folding:</strong> Primary Structure </p>
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<td><img src="chargeMainIdea.png" width="98" height="58"></td>
<td><p class="mainidea">The primary structure of a protein is the sequence of its amino acids. The sequence refers to the order of the amino acids, one after another, in the protein string or chain.</p></td>
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<p class="firstp">
To function as a protein, a string of amino acids must fold into a
specific shape. Following the chain of amino acids from beginning to end
helps determine why it folded into its shape, how it works, and how it
is held together.
</p>
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<p class="firstp">
<b>Like all proteins, parvalbumin (at left) is a string of amino acids
folded into a three-dimensional shape.</b> Parvalbumin is primarily
found in muscle cells, where it helps your muscles to relax after
contracting.
</p>
<p>
<b>1. Play the movie </b>to see the folds and other properties of
parvalbumin.<br><input name="button1" type="submit" script="script:jmol:1:select image all; remove; script jmol-p2-movie1.spt; script jmol-p2-colorInSeq.spt; script jmol-p2-movie2.spt; script jmol-p2-movie3.spt;" value="Play Movie" id="button1">
</p>
<p>
<b>2. After playing the movie, use the mouse and the controls below</b>
to explore:<br><b>- Rotate:</b> Click & drag the mouse on the molecule <b>-
Zoom:</b> Hold down SHIFT and drag
</p>
<div align="center">
<p>
<b>Molecule Style and Color: </b><br><!--
-- Try all the views in these menus --<br>
-->
<select
script5="script:jmol:1:set echo off; select image all; remove; add image displayBoxSpacefill.gif (60,5);script jmol-p2-allAtomsSpacefill.spt"
script4="script:jmol:1:set echo off; select image all; remove; add image displayBoxBackbone.gif (60,5);script jmol-p2-foldsProtein.spt"
script3="script:jmol:1:set echo off; select image all; remove; add image displayBoxBeads.gif (60,5);script jmol-p2-aminoAcidsBeads.spt"
script2="script:jmol:1:set echo off; select image all; remove; add image displayBoxBallAndStick.gif (60,5);script jmol-p2-allAtomsBallStick.spt"
script1="script:jmol:1:select none;">
<option selected>Select a style
<option>all atoms ball & stick
<option>amino acid beads
<option>protein folds
<option>all atoms spacefill
</select>
<input name="button1" type="submit" script="script:jmol:1:script jmol-p2-buildAnything.spt" value="Build it!" id="button1">
<select
script1="script:jmol:1:select none;"
script2="script:jmol:1:set echo off; isosurface off; select image all; remove; add image colorsBoxAminoSimple.gif (60,5);select all; color shapely;"
script3="script:jmol:1:set echo off; isosurface off; select image all; remove; add image colorsBoxRainbow.gif (60,5);select all; color monomer;"
script4="script:jmol:1:set echo off; isosurface off; select image all; remove; add image colorsBoxElementProtein.gif (60,5); select all; color cpk"
script5="script:jmol:1:set echo off; isosurface off; select image all; remove; add image colorsBoxPolaritySimple.gif (60,5); select protein and hydrophobic; color [xfeaeae]; select not hydrophobic; color [x00ffff];"
script6="script:jmol:1:set echo off; isosurface off; select image all; remove; add image colorsBoxMonocolor.gif (60,5);select all; color [x9ab9a4];"
>
<option selected>Select color(s)
<option>by amino acid
<option>end-to-end rainbow
<option>element
<option>polarity
<option>monocolor
</select>
</p>
<table>
<tr>
<td align="right">
<input name="checkbox" type="checkbox" script_selected="script:jmol:1:set echo off; select image all; remove; isosurface parvsurface sasurface; color isosurface [x9ab9a4]; isosurface on" script_deselected="script:jmol:1:set echo off; select image all; remove; select all; isosurface off" id="checkbox">
</td>
<td>
Show protein surface
</td>
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</table>
</div>
<p>
<b>3. Take some snapshots</b> to illustrate the views described in each
box below.
</p>
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Take a snapshot
Take snapshots to illustrate your answers to the questions below.
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org.concord.modeler.ImageQuestion362400<html>
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<p class="question">
Put a snapshot of the surface of the protein here.
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<p class="question">
Create an image that clearly shows both ends of the string of amino
acids. In the snapshot, use the text annotation tool <img src="annotation-text.gif">
to mark both ends.
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