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<h2 class="hd hd-2 unit-title">Reference Summary</h2>
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<h3><b>The PCR Process</b></h3>
<p>The following diagram depicts the process of <b>PCR (Polymerase Chain Reaction)</b>, which has 3 main steps:</p>
<ol>
<li> denaturation </li>
<li> primer annealing </li>
<li> extension (synthesis of new DNA by the DNA polymerase, Taq Polymerase) </li>
</ol>
<br/><br/>
<img src='/assets/courseware/v1/8b444a0dddbe81d52f2bb75c32ddd187/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/w0_newBW.png' alt="This diagram illustrates the process of P C R described above. The process starts with 1 molecule of double stranded D N A, which is shown as a pair of lines. Each line has a 5 prime or 3 prime label at each end. The top line is black and and the complementary sequence of the bottom strand is gray. An arrow labelled cycle 1 feeds into step 1, which is annotated Denature at 95 degrees Celsius. The subsequent illustration shows that the previously paired D N A strands are now separated. Step 2 is annotated Anneal primers at 55 degrees Celsius. The corresponding illustration shows that smaller D N A fragments, or primers, have paired with the orignal D N A strands. The 5 prime end of each primer is paired at the 3 prime end of the D N A strand. The top black D N A strand is paired with a gray primer. The gray primer follows the same complementary sequence as the bottom, gray D N A strand. Similarly, the bottom gray D N A strand is paired with a black primer, which follows the sequence of the top, black strand. Step 3 is annotated Extend D N A at 65 degrees Celsius. The corresponding illustration shows that each of the primers has been extended to the full length of the D N A strand that it paired with. Therefore, the end products are 2 double stranded D N A molecules, where each is composed of one black and one gray strand. This molecule is the same as the starting double stranded D N A molecule. Next, there is an arrow that circles from the prodcuts of the cycle back up to step 1. This arrow is labelled cycle 2 and indicates that steps 1 through 3 will be repeated. After cycle 2, there will be 4 molecules of double stranded D N A. Another circling arrow is labelled cycle 3, which will result in 8 molecules of double stranded D N A. A final, dashed arrow indicates that after 30 cycles, there will be greater than 10 to the ninth double stranded D N A molecules.">
<br /> <br />
<p> It is important to note that this reaction, while based off of the principle of DNA replication, happens in a test tube (not a cell!) with the <b>goal of amplifying a DNA sequence</b>.</p>
<br /><h3><b> Notes about PCR Primers </b></h3>
<p>The primers used in this reaction are <b>DNA primers</b>, not RNA primers, because they are synthetically made and added to the test tube. The primers should <b>anneal to the outermost region</b> of the sequence that you would like to amplify. For each reaction, you should have <b>two types of primers</b>: one to extend along the top strand of the DNA sequence and one to extend along the bottom strand.</p>
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<h2 class="hd hd-2 unit-title">Exercise 1 (Understanding PCR)</h2>
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<p>If you start with 1 piece of double-stranded DNA, how many double-stranded DNAs will you have after 4 cycles of PCR? (Enter your answer as an integer.)</p>
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<p>The figure above shows one strand (long strand on top) of a piece of double-stranded DNA. Which of the small primers underneath it (A, B, and C) in the figure can be used to successfully <b>amplify the gray region</b> of the DNA strand in a PCR reaction?<br/>Check all that apply.</p>
<p>(Remember: DNA is synthesized 5' to 3' off of a free 3' end.)</p>
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<div class="submission-feedback" id="submission_feedback_cdf498a8a19c413d97c5aee983ee96aa">
<span class="sr">Some problems have options such as save, reset, hints, or show answer. These options follow the Submit button.</span>
</div>
</div>
<div class="problem-action-buttons-wrapper">
<span class="problem-action-button-wrapper">
<button type="button" class="reset problem-action-btn btn-default btn-small" data-value="Reset"><span class="icon fa fa-refresh" aria-hidden="true"></span><span aria-hidden="true">Reset</span><span class="sr">Reset your answer</span></button>
</span>
</div>
</div>
<div class="notification warning notification-gentle-alert
is-hidden"
tabindex="-1">
<span class="icon fa fa-exclamation-circle" aria-hidden="true"></span>
<span class="notification-message" aria-describedby="cdf498a8a19c413d97c5aee983ee96aa-problem-title">
</span>
<div class="notification-btn-wrapper">
<button type="button" class="btn btn-default btn-small notification-btn review-btn sr">Review</button>
</div>
</div>
<div class="notification warning notification-save
is-hidden"
tabindex="-1">
<span class="icon fa fa-save" aria-hidden="true"></span>
<span class="notification-message" aria-describedby="cdf498a8a19c413d97c5aee983ee96aa-problem-title">None
</span>
<div class="notification-btn-wrapper">
<button type="button" class="btn btn-default btn-small notification-btn review-btn sr">Review</button>
</div>
</div>
<div class="notification general notification-show-answer
is-hidden"
tabindex="-1">
<span class="icon fa fa-info-circle" aria-hidden="true"></span>
<span class="notification-message" aria-describedby="cdf498a8a19c413d97c5aee983ee96aa-problem-title">Answers are displayed within the problem
</span>
<div class="notification-btn-wrapper">
<button type="button" class="btn btn-default btn-small notification-btn review-btn sr">Review</button>
</div>
</div>
</div>
"
data-graded="False">
<p class="loading-spinner">
<i class="fa fa-spinner fa-pulse fa-2x fa-fw"></i>
<span class="sr">Loading…</span>
</p>
</div>
</div>
</div>
</div>
</div>