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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<!-- CUSTOMIZE METADATA HERE -->
<title>Presentation</title>
<meta name="description" content="BI281H Discussion 4">
<meta name="author" content="Michael J. Harms">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
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<body>
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<div class="reveal">
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<div class="slides">
<section>
<h2>Proteins and Amino Acids</h2>
<h4>2017-10-02</h4>
<br/>
</section>
<section>
<p>What kinds of materials go into building a factory?</p>
<img src="https://upload.wikimedia.org/wikipedia/commons/7/71/Wolfsburg_VW-Werk.jpg" height="70%" width="70%"/>
<br/>
<small><a href="https://en.wikipedia.org/wiki/Factory">wikipedia</a></small>
</section>
<section>
<div class="row">
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/2.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/4.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/0.png" />
</div>
</div>
<div class="row">
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/3.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/5.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/1.png" />
</div>
</div>
</section>
<section>
<div class="row">
<div class="col-xs-6">
<img class="img-responsive" src="http://jcs.biologists.org/content/joces/122/10/1607/F1.medium.gif" height="100%" width="100%" />
</div>
<div class="col-xs-6">
<img class="fragment img-responsive" src="https://dm5migu4zj3pb.cloudfront.net/manuscripts/38000/38277/medium/JCI38277.f2.jpg" height="100%" width="100%" />
</div>
</div>
<small><a href="http://jcs.biologists.org/content/122/10/1607">Shi et al. (2009) JCS</a>, <a href="https://www.jci.org/articles/view/38277/figure/2"> Song et al. (2009)</a></small>
</section>
<section>
<img src="https://www.seeintl.org/wp-content/uploads/2013/12/cataracts-1.jpg" height="100%" width="100%" />
<small><a href="https://www.seeintl.org/cataracts/">See International</a></small>
</section>
<section>
<p>How does one chemical (protein) achieve such a vast array of functions?</p>
<div class="row">
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/2.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/4.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/0.png" />
</div>
</div>
<div class="row">
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/3.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/5.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/04/img/protein-diversity/1.png" />
</div>
</div>
</section>
<section>
<h4>Conceptual goals</h4>
<ul>
<li class="fragment">The sequence of a protein determines is structure, which determines its function</li>
<li class="fragment">Understand how concatenating relatively few amino acids can lead to a huge diversity of possible functional proteins. </li>
</ul>
<h4>Skill goals</h4>
<ul>
<li class="fragment">Identify the amino acids based on their chemical structure. </li>
<li class="fragment">Reason about how their individual chemistry leads to distinct biological roles. </li>
</ul>
</section>
<section>
<p>The power of combinatorics!</p>
<img src="http://www.planetdiecast.com/hwdphotos/originals/9141/1232/brio_010.jpg" height="100%" width="100%" />
<ul class="fragment">
<li>Directional (has front and back)</li>
<li>You can make it as long as you want</li>
<li>You can swap in any car at any point in the train</li>
</ul>
<small><a href="http://www.planetdiecast.com/index.php?%26option=com_content%26view=article%26id=86337:wooden-track-trains-part-1%26catid=13">Planet Diecast</a></small>
</section>
<section>
<h4>On your handout, circle amino acids whose <em>sidechain</em> participates in:</h4>
<ul>
<li>hydrophobic effect</li>
<li>Van der Waal's</li>
<li>hydrogen bonds</li>
<li>ionic interactions</li>
<li>covalent bonds (without enzymatic help)</li>
</ul>
</section>
<section data-transition="fade">
<img src="presentation-data/04/img/amino-acid-structures_0.png" />
</section>
<section data-transition="fade">
<img src="presentation-data/04/img/amino-acid-structures_1.png" />
</section>
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<img src="presentation-data/04/img/amino-acid-structures_2.png" />
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<img src="presentation-data/04/img/amino-acid-structures_3.png" />
</section>
<section data-transition="fade">
<img src="presentation-data/04/img/amino-acid-structures_4.png" />
</section>
<section data-transition="fade">
<img src="presentation-data/04/img/amino-acid-structures_5.png" />
</section>
<section>
<h3>Amino acids fill a large volume of "property space"</h3>
<div class="row">
<video data-autoplay mute loop height="55%" width="55%" loop>
<source src="presentation-data/04/video/amino-acid-properties.mp4" />
<source src="presentation-data/04/video/amino-acid-properties.mp4" />
</video>
</div>
</section>
<section>
<h4>Key points:</h4>
<ul>
<li>Proteins are formed from amino acids, arranged into a chain</li>
<li>Chain is formed by a series of peptide bonds</li>
<li>Because there are 20 naturally-occuring amino acids, a vast number of sequences are possible</li>
<li>These 20 amino acids cover a wide range of chemical properties</li>
</ul>
</section>
<section>
<h3>Big ideas</h3>
<h4 class="fragment">Amphipathic molecules lead to large-scale structure</h4>
<h4 class="fragment">Combinatorial polymers allow creation of a vast number of molecules</h4>
</section>
</div>
</div>
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