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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
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<title>Presentation</title>
<meta name="description" content="BI281H Discussion 2">
<meta name="author" content="Michael J. Harms">
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<body>
<!-- CUSTOMIZE SLIDES HERE -->
<div class="reveal">
<!-- Any section element inside of this container is a slide -->
<div class="slides">
<section>
<div class="row">
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/02/img/protein-diversity/2.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/02/img/protein-diversity/4.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/02/img/protein-diversity/0.png" />
</div>
</div>
</section>
<section>
<iframe width="560" height="315" src="https://www.youtube.com/embed/oimU652RB1w" frameborder="0" allowfullscreen></iframe>
</section>
<section>
<div class="row">
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/02/img/protein-diversity/2.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/02/img/protein-diversity/4.png" />
</div>
<div class="col-xs-4">
<img class="img-responsive" src="presentation-data/02/img/protein-diversity/0.png" />
</div>
</div>
</section>
<section>
<h2>Players and Forces</h2>
<h4>2017-09-27</h4>
<br/>
</section>
<section>
<h4>Conceptual goals</h4>
<ul>
<li class="fragment">Know the main chemical forces that undergird life</li>
<li class="fragment">Understand the basis of the hydrophobic effect</li>
<li class="fragment">Know how the four main classes of biomolecules differ in these properties.</li>
</ul>
<h4>Skill goals</h4>
<ul>
<li class="fragment">Reason about the relative importance of different molecular forces in an aqueous environment</li>
<li class="fragment">Identify the ability to participate in different interactions from structure.</li>
</ul>
</section>
<section>
<p>If $\Delta G < 0$ for $A \rightleftarrows B$, the reaction favors:</p>
<ol>
<li>$A$</li>
<li>$B$</li>
<li>Neither</li>
<li>It depends</li>
</ol>
<p style="color:blue" class="fragment">$B$</p>
</section>
<section>
<p>At equilibrium, $[A] > [B]$ for $A \rightleftarrows B$. This implies:</p>
<ol>
<li>$\Delta G ^{\circ}> 0$</li>
<li>$\Delta G ^{\circ}< 0$</li>
<li>Neither</li>
</ol>
<p style="color:blue" class="fragment">$\Delta G > 0$</p>
</section>
<section>
<p>Explain what this equation means:</p>
<p>$\Delta G = \Delta H - T \Delta S$</p>
<div class="fragment" style="color:blue">
<p>Where a reaction ends up ($\Delta G$) depends on:</p>
<ul>
<li>Changes in the bonds formed (enthalpy, $\Delta H$)</li>
<li>Change in the disorder (entropy, $T\Delta S$)</li>
</ul>
</div>
</section>
<section>
<h3>Road map</h3>
<h4>What are the important molecular interactions?</h4>
<h4>What about water?</h4>
<h4>Biological molecules and these interactions</h4>
</section>
<section>
<p>What is the ratio of formed to unformed for covalent bonds at equlibrium?</p>
<p>$A + B \rightleftharpoons AB$</p>
<p class="fragment">$K = \frac{[AB]}{[A][B]}$</p>
<p class="fragment">Useful info: $R = 0.0083\ kJ \cdot mol^{-1} K^{-1}$, $T = 300\ K$</p>
<div class="fragment" style="color:blue">
<p>Ratio of formed to unformed is given by:</p>
<p>$\Delta G = -RTln(K)$</p>
<p>$K = \frac{[AB]}{[A][B]} = e^{--\Delta G/RT}$</p>
<p>$K = e^{--400/(300*0.0083)} = 6 \times 10^{69}$</p>
</div>
</section>
<section>
<h4>Question:</h4>
<p>The energy of a $Na^{+}$ + $Cl^{-1}$ bond in vacuum is $\approx -400\ kJ\cdot mol^{-1}$, but the book says ionic interactions are $\approx -70 kJ \cdot mol^{-1}$ in proteins. What is the origin of this difference?</p>
</section>
<section>
<h3>Protip: water is 55 M and should never be ignored</h3>
<div class="row">
<video data-autoplay mute loop height="55%" width="55%" loop>
<source src="presentation-data/02/video/water-solution.mp4" />
<source src="presentation-data/02/video/water-solution.mp4" />
</video>
</div>
</section>
<section>
<h4>Question:</h4>
<p>The energy of a $Na^{+}$ + $Cl^{-1}$ bond in vacuum is $\approx -400\ kJ\cdot mol^{-1}$, but the book says ionic interactions are $\approx -70 kJ \cdot mol^{-1}$ in proteins. What is the origin of this difference?</p>
<p style="color:blue">Water competes the partners in an ion pair, this (effectively) weakens the bond.</p>
<p class="fragment"><span style="color:red">Key point:</span> The strength of an interaction depends on its context!</p>
</section>
<section>
<h3>What happens if you jam a random molecule into water</h3>
<div class="row">
<video data-autoplay mute loop height="55%" width="55%" loop>
<source src="presentation-data/02/video/water-solution.mp4" />
<source src="presentation-data/02/video/water-solution.mp4" />
</video>
</div>
<p class="fragment">Disrupts smooth handoff of one water to another</p>
</section>
<section>
<p>Solutes throw off a water molecule's "groove".</p>
<p>Fewer degrees of freedom means drop in entropy.</p>
<p>Drop in entropy makes the dissolving the compound less favorable.</p>
<p>$$\Delta G = \Delta H - T \color{red}{\Delta S}$$</p>
</section>
<section>
<h4>Uber nerds:</h4>
<small>$V_{old} = \frac{4}{3} \pi r_{old}^{3} $</small><br/>
<small>After merging, you have a sphere of $2 \times V_{old}$ with a radius:</small><br/>
<small>$(2 \times V_{old}) = \frac{4}{3} \pi r_{new}^{3} $</small><br/>
<small>$(2 \times \frac{4}{3} \pi r_{old}^3) = \frac{4}{3} \pi r_{new}^{3} $</small><br/>
<small>$(2 \times r_{old}^3) = r_{new}^{3} $</small><br/>
<small>$r_{new} = 2^{1/3} \times r_{old}$</small><br/>
<small>Now compare surface areas:</small><br/>
<small>$2 \times 4 \pi r_{old}^2 \stackrel{?}{>} 4 \pi r_{new}^{2}$</small><br/>
<small>$2 \times r_{old}^2 \stackrel{?}{>} (2^{1/3} r_{old})^{2}$</small><br/>
<small>$2 > {2}^{2/3}$</small><br/>
</section>
<section>
<p>What happens when you create a molecule with both hydrophobic and polar character?</p>
<div class="fragment">
<img src="https://upload.wikimedia.org/wikipedia/commons/thumb/c/c6/Phospholipids_aqueous_solution_structures.svg/450px-Phospholipids_aqueous_solution_structures.svg.png" height="35%" width="35%"/>
<br/>
<small><a href="https://en.wikipedia.org/wiki/Lipid_bilayer">wikimedia</a></small>
</div>
</section>
<section>
<font size=6>
<p>How hydrophobic is the molecule?</p>
<p>What interactions can it make?</p>
<p>What sorts of biological functions might it fulfill?</p>
</font>
<div class="panel fragment">
<div class="row" align="middle">
<div class="col-xs-1"> <h4>A</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/glucose.png" class="img-responsive" height="50%" width="50%"></img>
</div>
<div class="col-xs-1"> <h4>B</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/adenosine.png" class="img-responsive" height="70%" width="70%"></img>
</div>
</div>
<div class="row" align="middle">
<div class="col-xs-1"> <h4>C</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/glutamic-acid.png" class="img-responsive" height="50%" width="50%"></img>
</div>
<div class="col-xs-1"> <h4>D</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/cholesterol.png" class="img-responsive" height="80%" width="80%"></img>
</div>
</div>
</div>
</section>
<section>
<div class="panel">
<div class="row" align="middle">
<div class="col-xs-1"> <h4>A</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/glucose.png" class="img-responsive" height="50%" width="50%"></img>
<br/>sugars
</div>
<div class="col-xs-1"> <h4>B</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/adenosine.png" class="img-responsive" height="70%" width="70%"></img>
<br/>nucleic acids
</div>
</div>
<div class="row" align="middle">
<div class="col-xs-1"> <h4>C</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/glutamic-acid.png" class="img-responsive" height="50%" width="50%"></img>
<br/>amino acids
</div>
<div class="col-xs-1"> <h4>D</h4> </div>
<div class="col-xs-5">
<img src="presentation-data/02/img/cholesterol.png" class="img-responsive" height="80%" width="80%"></img>
<br/>lipids
</div>
</div>
</div>
</section>
<section>
<h3>Summary</h3>
<ul>
<li>Biomolecules are built (mostly) from CHNOPS</li>
<li>These atoms participate in covalent, ionic, hydrogen-bond, and van der Waals interactions</li>
<li>Water can change the net strength of these interactions</li>
<li>The "hydrophobic effect" works to minimize the amount of solute surface interacting with water</li>
<li>Most biomolecules are "amphipathic," leading to self-organization</li>
<li>The four main molecular building blocks (sugars, nucleic acids, amino acids, and lipids) differ in these properties allowing them to fulfill different roles</li>
</ul>
</section>
</div>
</div>
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