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<h2 class="hd hd-2 unit-title">Question 1</h2>
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<p> Question 1 is worth a total of 7 points. <br /> There is a codon chart and an amino acid reference table at the bottom of this page. </p>
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<p>The following is the line angle drawing of <b>Molecule 1</b>.</p>
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<p>This schematic shows the interaction between Molecule 1 (shown in blue) and Enzyme X at dotted circles #1-#4. <br /><i>For simplicity, only the side-chains of the amino acids of Enzyme X that interact with the Molecule 1 are shown.</i></p>
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Question 1b
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<p>Give the STRONGEST interaction at... </p>
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<option value="hydrogen"> hydrogen</option>
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<option value="hydrophobic"> hydrophobic</option>
<option value="VDW"> VDW</option>
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<span class="status unanswered" id="status_1f4d70879b18410eaa0c60a78c24ca6c_2_1" data-tooltip="Not yet answered.">
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<option value="option_1f4d70879b18410eaa0c60a78c24ca6c_3_1_dummy_default">Select an option</option>
<option value="hydrogen"> hydrogen</option>
<option value="ionic"> ionic</option>
<option value="hydrophobic"> hydrophobic</option>
<option value="VDW"> VDW</option>
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<span class="status unanswered" id="status_1f4d70879b18410eaa0c60a78c24ca6c_3_1" data-tooltip="Not yet answered.">
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<p class="answer" id="answer_1f4d70879b18410eaa0c60a78c24ca6c_3_1"/>
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<label class="problem-group-label" for="input_1f4d70879b18410eaa0c60a78c24ca6c_4_1" id="label_1f4d70879b18410eaa0c60a78c24ca6c_4_1">Position #3</label>
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<option value="option_1f4d70879b18410eaa0c60a78c24ca6c_4_1_dummy_default">Select an option</option>
<option value="hydrogen"> hydrogen</option>
<option value="ionic"> ionic</option>
<option value="hydrophobic"> hydrophobic</option>
<option value="VDW"> VDW</option>
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<span class="status unanswered" id="status_1f4d70879b18410eaa0c60a78c24ca6c_4_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
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<p class="answer" id="answer_1f4d70879b18410eaa0c60a78c24ca6c_4_1"/>
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<label class="problem-group-label" for="input_1f4d70879b18410eaa0c60a78c24ca6c_5_1" id="label_1f4d70879b18410eaa0c60a78c24ca6c_5_1">Position #4</label>
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<option value="option_1f4d70879b18410eaa0c60a78c24ca6c_5_1_dummy_default">Select an option</option>
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<option value="hydrophobic"> hydrophobic</option>
<option value="VDW"> VDW</option>
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<span class="status unanswered" id="status_1f4d70879b18410eaa0c60a78c24ca6c_5_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
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<p class="answer" id="answer_1f4d70879b18410eaa0c60a78c24ca6c_5_1"/>
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<p>You identify four mutant versions (A-D) of the Enzyme X, each of which has mutation in one of the codons corresponding to amino acids shown above at positions 1–4.<b> Please note that each interaction is critical for the Enzyme X - Molecule 1 binding.</b></p>
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Question 1c
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<p>Which <b>TWO mutants</b> are likely to bind to Molecule 1?</p>
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<h2 class="hd hd-2 unit-title">Question 2</h2>
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<p> Question 2 is worth a total of 8 points. </p>
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Question 2a
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<p>Enzyme X catalyzes the conversion of Molecule 1 (S) into a specific product (P) with a &#916;G &lt; 0.</p>
<p>Which energy profile represents an anabolic (energy requiring) reaction with a &#916;G &lt; 0? Select the best answer.</p>
<p><img src="/assets/courseware/v1/23cc724896bd58c9fc24deb02e61eae6/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ex_q2a.png" width="500" style="float: center;" alt="Two energy diagrams, with course of reaction on the x axis and G on the y axis. The left diagram starts at a low value, rises to a hill, then ends at a higher value. The right diagram starts at a high value, rises to a hill, then ends at a lower value. Both have blank boxes for later labeling."/></p>
<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><div class="choicegroup capa_inputtype" id="inputtype_831b48eb78714ac6be8f6b495501391a_2_1">
<fieldset aria-describedby="status_831b48eb78714ac6be8f6b495501391a_2_1">
<div class="field">
<input type="radio" name="input_831b48eb78714ac6be8f6b495501391a_2_1" id="input_831b48eb78714ac6be8f6b495501391a_2_1_choice_0" class="field-input input-radio" value="choice_0"/><label id="831b48eb78714ac6be8f6b495501391a_2_1-choice_0-label" for="input_831b48eb78714ac6be8f6b495501391a_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_831b48eb78714ac6be8f6b495501391a_2_1"> Left energy profile
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<input type="radio" name="input_831b48eb78714ac6be8f6b495501391a_2_1" id="input_831b48eb78714ac6be8f6b495501391a_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="831b48eb78714ac6be8f6b495501391a_2_1-choice_1-label" for="input_831b48eb78714ac6be8f6b495501391a_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_831b48eb78714ac6be8f6b495501391a_2_1"> Right energy profile
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<p>On the right energy profile only (reproduced below), use the dropdown options to label the diagram.</p>
<p><img src="/assets/courseware/v1/ed5f910603fddd28a6e4af2e7bf1c8cc/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ex_q2a_fig.png" width="300" style="float: center;" alt="One energy diagram, with course of reaction on the x axis and G on the y axis. The diagram starts at a higher value (labeled 1) and rises to a hill, then ends at a higher value (labeled 4). The difference between the top of the hill and the high value is labeled 3 and the difference between the high value and low value is labeled 2."/></p>
<ul>
<li>&#916;G (free energy) is at location <div class="inline" tabindex="-1" aria-label="Question 2" role="group"><div class="inputtype option-input inline">
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<option value="option_831b48eb78714ac6be8f6b495501391a_3_1_dummy_default">Select an option</option>
<option value="1"> 1</option>
<option value="2"> 2</option>
<option value="3"> 3</option>
<option value="4"> 4</option>
</select>
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</div></div></li>
<li>EA (energy of activation) is at location <div class="inline" tabindex="-1" aria-label="Question 3" role="group"><div class="inputtype option-input inline">
<select name="input_831b48eb78714ac6be8f6b495501391a_4_1" id="input_831b48eb78714ac6be8f6b495501391a_4_1" aria-describedby="status_831b48eb78714ac6be8f6b495501391a_4_1">
<option value="option_831b48eb78714ac6be8f6b495501391a_4_1_dummy_default">Select an option</option>
<option value="1"> 1</option>
<option value="2"> 2</option>
<option value="3"> 3</option>
<option value="4"> 4</option>
</select>
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<span class="status unanswered" id="status_831b48eb78714ac6be8f6b495501391a_4_1" data-tooltip="Not yet answered.">
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<p class="answer" id="answer_831b48eb78714ac6be8f6b495501391a_4_1"/>
</div></div></li>
<li>Molecule 1 (S) is at location <div class="inline" tabindex="-1" aria-label="Question 4" role="group"><div class="inputtype option-input inline">
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Question 2b
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<p>The mutant version of Enzyme X is less active than the wildtype. The &#916;G of the reaction catalyzed by a mutant version of Enzyme X would be ____________ the &#916;G of the normal/original Enzyme X catalyzed reaction.</p>
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Question 2c, part i
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<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><p>The following biochemical pathway shows how Molecule 1 is metabolized within a cell. The enzymes catalyzing different steps of the biochemical pathways are shown as E1-E4 and Enzyme X.</p>
<p><img src="/assets/courseware/v1/dbcf2f4a817d2d3b91fe79c38ea00743/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ex_q2c_NEW.png" style="float:center;" alt="A multi-step pathway from Molecule 1 to products D and N. In order: Molecule 1 is made into P by enzyme X. P is made into C by E 1. C is made into D by E 2. In the other path: Molecule 1 is made into M by E 3. M is made into N by E 4. Product c inhibits E 3."/></p>
<p>Which step represents the <b>inhibitory feedback loop</b> in the pathway? Select the best answer.</p>
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<input type="radio" name="input_2d102584500c419d8b9117943e81ecb1_2_1" id="input_2d102584500c419d8b9117943e81ecb1_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="2d102584500c419d8b9117943e81ecb1_2_1-choice_2-label" for="input_2d102584500c419d8b9117943e81ecb1_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_2d102584500c419d8b9117943e81ecb1_2_1"> C made into D
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Question 2c, part ii
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Question 2d
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<p><b>Gene X encodes</b> Enzyme X that is a <b>glycoprotein (protein that has a carbohydrate covalently added to it).</b> Use the dropdown options to complete the table below.</p>
<table class="chart" summary="Given five organelles, determine if they played a role in the creation and processing of Enzyme X." label="Three columns. First column gives the organelle. Second column asks if the organelle played a role in synthesizing Enzyme X. Third column asks what role was played by that organelle, if any." width="100%">
<tbody>
<tr><th scope="col" style="text-align: center; border: 1px solid black;"><b>Organelle</b></th>
<th scope="col" style="text-align: center; border: 1px solid black;"><b>Involved in Enzyme X synthesis?</b></th>
<th scope="col" style="text-align: center; border: 1px solid black;"><b>If yes, what process is involved?</b></th>
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<td style="text-align: center; border: 1px solid black;">Cytoskeleton</td>
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<option value="Yes"> Yes</option>
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<select name="input_d9c7cb8b144b4fd3a59b774217655d85_3_1" id="input_d9c7cb8b144b4fd3a59b774217655d85_3_1" aria-describedby="status_d9c7cb8b144b4fd3a59b774217655d85_3_1">
<option value="option_d9c7cb8b144b4fd3a59b774217655d85_3_1_dummy_default">Select an option</option>
<option value="protein modification"> protein modification</option>
<option value="replication"> replication</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
<option value="no involvement"> no involvement</option>
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<td style="text-align: center; border: 1px solid black;">Nucleus</td>
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<option value="option_d9c7cb8b144b4fd3a59b774217655d85_5_1_dummy_default">Select an option</option>
<option value="protein modification"> protein modification</option>
<option value="replication"> replication</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
<option value="no involvement"> no involvement</option>
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<td style="text-align: center; border: 1px solid black;">Endoplasmic Reticulum</td>
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<option value="option_d9c7cb8b144b4fd3a59b774217655d85_6_1_dummy_default">Select an option</option>
<option value="Yes"> Yes</option>
<option value="No"> No</option>
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<option value="option_d9c7cb8b144b4fd3a59b774217655d85_7_1_dummy_default">Select an option</option>
<option value="protein modification"> protein modification</option>
<option value="replication"> replication</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
<option value="no involvement"> no involvement</option>
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<td style="text-align: center; border: 1px solid black;">Ribosomes</td>
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<option value="Yes"> Yes</option>
<option value="No"> No</option>
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<option value="protein modification"> protein modification</option>
<option value="replication"> replication</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
<option value="no involvement"> no involvement</option>
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<td style="text-align: center; border: 1px solid black;">Golgi body</td>
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<option value="Yes"> Yes</option>
<option value="No"> No</option>
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<option value="option_d9c7cb8b144b4fd3a59b774217655d85_11_1_dummy_default">Select an option</option>
<option value="protein modification"> protein modification</option>
<option value="replication"> replication</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
<option value="no involvement"> no involvement</option>
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<h2 class="hd hd-2 unit-title">Question 3</h2>
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<p>The following pedigree shows a disease that is caused by the <b>ABSENCE</b> of Enzyme X. Individual 6 has a genotype (Aa) and is unaffected. <br /><i><b>NOTE:</b> Filled circles represent affected females, open circles represent unaffected females, filled boxes represent affected males and open boxes represent unaffected males.</i> </p>
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Question 3a, part i
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Question 3a, part ii
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<p>Using &#8220;A&#8221; for the allele associated with the dominant phenotype and &#8220;a&#8221; for the allele associated with recessive phenotype, give <b>ALL</b> the possible genotypes of Individual #3.</p>
<p>Please separate each answer with a comma followed by a space, e.g. "M, N, L".</p>
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Question 3a, part iii
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<p><b>Individual #9</b> marries a female (Genotype: aa). What is the probability that their daughter will have the disease?</p>
<p>Please give your answer in terms of a percent rounded to the nearest whole number, e.g. "91" for 90.5%. Do not include a percent sign (%) in your answer.</p>
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<p>You want to study body color (grey or cream) that is regulated by an autosomal gene, Gene D in fruit flies. Gene D can exist as “Allele D” (regulates the dominant phenotype) or “Allele d” (regulates the recessive phenotype). Cream is the recessive phenotype.</p>
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Question 3b, part i
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<p>You mate a <b>homozygous grey fly (P1)</b> with <b>homozygous cream fly (P2)</b> and get 1000 grey F1 flies. Give the genotype of the following flies in terms of D and d.</p>
<br/>
<h3>P1:</h3>
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<br/>
<h3>P2:</h3>
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<p id="answer_f00a8f29f858433bacafe754ee95f9fa_3_1" class="answer"/>
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<br/>
<h3>F1:</h3>
<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 3" role="group"><div id="inputtype_f00a8f29f858433bacafe754ee95f9fa_4_1" class=" capa_inputtype textline">
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<h3 class="hd hd-3 problem-header" id="3e9dd4f65c644e9abc7f22ff7e20617c-problem-title" aria-describedby="block-v1:OCW+Pre-7.01+1T2020+type@problem+block@3e9dd4f65c644e9abc7f22ff7e20617c-problem-progress" tabindex="-1">
Introduction
</h3>
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<p>You mate two F1 flies and get 1000 F2 flies. Complete the Punnett Square provided below and use it to answer the following questions. <br/><b>NOTE: This is a tool to assist you. The Punnett Square itself will not be graded, only the questions below!</b></p>
<table class="chart" summary="A Punnett Square to represent an F 1 cross. The header is the gametes of one parent and the first column is the gametes of the other, with offspring results in the second and third column." label="Three columns. The first column indicates the gametes of one F 1 parent. The second and third columns give the offspring resulting from the F 1 cross." width="100%"><caption>Complete the Punnett Square</caption>
<tbody>
<tr><th scope="col" style="text-align: center; border: 1px solid black;"><img src="/assets/courseware/v1/015929758d3cd89d108d6a207619ec44/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q4c_gametes_arrow.png" style="float:center;" alt="Figure labeling the header and first column as the F 1 gametes."/></th>
<th scope="col" style="text-align: center; border: 1px solid black;"><b>D</b></th>
<th scope="col" style="text-align: center; border: 1px solid black;"><div class="inline" tabindex="-1" aria-label="Question 1" role="group"><div class="inputtype option-input inline">
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<option value="option_3e9dd4f65c644e9abc7f22ff7e20617c_2_1_dummy_default">Select an option</option>
<option value="D"> D</option>
<option value="d"> d</option>
<option value="DD"> DD</option>
<option value="Dd"> Dd</option>
<option value="dd"> dd</option>
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<tr>
<td style="text-align: center; border: 1px solid black;"><b>D</b></td>
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<option value="D"> D</option>
<option value="d"> d</option>
<option value="DD"> DD</option>
<option value="Dd"> Dd</option>
<option value="dd"> dd</option>
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<option value="option_3e9dd4f65c644e9abc7f22ff7e20617c_4_1_dummy_default">Select an option</option>
<option value="D"> D</option>
<option value="d"> d</option>
<option value="DD"> DD</option>
<option value="Dd"> Dd</option>
<option value="dd"> dd</option>
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<option value="D"> D</option>
<option value="d"> d</option>
<option value="DD"> DD</option>
<option value="Dd"> Dd</option>
<option value="dd"> dd</option>
</select>
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<td style="text-align: center; border: 1px solid black;"><div class="inline" tabindex="-1" aria-label="Question 5" role="group"><div class="inputtype option-input inline">
<select name="input_3e9dd4f65c644e9abc7f22ff7e20617c_6_1" id="input_3e9dd4f65c644e9abc7f22ff7e20617c_6_1" aria-describedby="status_3e9dd4f65c644e9abc7f22ff7e20617c_6_1">
<option value="option_3e9dd4f65c644e9abc7f22ff7e20617c_6_1_dummy_default">Select an option</option>
<option value="D"> D</option>
<option value="d"> d</option>
<option value="DD"> DD</option>
<option value="Dd"> Dd</option>
<option value="dd"> dd</option>
</select>
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<select name="input_3e9dd4f65c644e9abc7f22ff7e20617c_7_1" id="input_3e9dd4f65c644e9abc7f22ff7e20617c_7_1" aria-describedby="status_3e9dd4f65c644e9abc7f22ff7e20617c_7_1">
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<option value="D"> D</option>
<option value="d"> d</option>
<option value="DD"> DD</option>
<option value="Dd"> Dd</option>
<option value="dd"> dd</option>
</select>
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Question 3b, part ii
</h3>
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<h3>How many F2 flies would have the genotype &#8221;Dd&#8221;? (Enter your answer as a whole number integer.)</h3>
<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><div id="inputtype_f284f8e5e34840f3a73b5dd9655f9f42_2_1" class=" capa_inputtype textline">
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<br/>
<h3>How many F2 flies would have the cream body color? (Enter your answer as a whole number integer.)</h3>
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Question 3c, parts i-ii
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<p>You identify a <b>red eye fly</b> (Fly #3) that is regulated by Gene R. (White is the recessive phenotype.) You perform a <b>test cross</b> to analyze if the genotype of <b>Fly #3</b> is &#8220;Rr&#8221; or &#8220;RR&#8221;.</p>
<h3>(i) Give the genotype of the fly with which you will mate Fly #3 for the test cross.</h3>
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<h3>(ii) Give the ratios of the phenotypes and genotypes of the resulting flies if <b>Fly #3</b> was <b>heterozygous</b> for Gene R.</h3>
<h3>Phenotype ratio:<br/><i>Please give your answer in lowercase and without spaces in the following format: #red:#white</i></h3>
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<h3>Genotype ratio:</h3>
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</div></div>RR out of 4</li>
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<p>Please take a look at Cell #1 (Genotype: Qq) below that has a single pair of chromosome.</p>
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Question 3d, parts i-iii
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<h3>(i) What is the ploidy of cell #1?</h3>
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<i>Choose from: haploid, diploid, triploid, tetraploid</i>
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<p>(ii) If cell #1 divides by mitosis, what is the ploidy of...</p>
<h3>cell #2?</h3>
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<h3>cell #3?</h3>
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<h3>(iii) Cell #2 divides to eventually form four gametes as shown. What type of division is this?</h3>
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Question 3d, part iv
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<p>Considering the diagram and your answer to <b>Question 3d, part iii</b>, use the dropdown options to determine the chromosome content of the resulting gametes.</p>
<ul> <li>There are<div class="inline" tabindex="-1" aria-label="Question 1" role="group"><div class="inputtype option-input inline">
<select name="input_79b9115c35164483917c6917114e34f0_2_1" id="input_79b9115c35164483917c6917114e34f0_2_1" aria-describedby="status_79b9115c35164483917c6917114e34f0_2_1">
<option value="option_79b9115c35164483917c6917114e34f0_2_1_dummy_default">Select an option</option>
<option value="0"> 0</option>
<option value="1"> 1</option>
<option value="2"> 2</option>
<option value="3"> 3</option>
<option value="4"> 4</option>
</select>
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<span class="status unanswered" id="status_79b9115c35164483917c6917114e34f0_2_1" data-tooltip="Not yet answered.">
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<p class="answer" id="answer_79b9115c35164483917c6917114e34f0_2_1"/>
</div></div>gamete(s) with a single "Q" chromosome.</li>
<li>There are<div class="inline" tabindex="-1" aria-label="Question 2" role="group"><div class="inputtype option-input inline">
<select name="input_79b9115c35164483917c6917114e34f0_3_1" id="input_79b9115c35164483917c6917114e34f0_3_1" aria-describedby="status_79b9115c35164483917c6917114e34f0_3_1">
<option value="option_79b9115c35164483917c6917114e34f0_3_1_dummy_default">Select an option</option>
<option value="0"> 0</option>
<option value="1"> 1</option>
<option value="2"> 2</option>
<option value="3"> 3</option>
<option value="4"> 4</option>
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<div class="indicator-container">
<span class="status unanswered" id="status_79b9115c35164483917c6917114e34f0_3_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
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<p class="answer" id="answer_79b9115c35164483917c6917114e34f0_3_1"/>
</div></div>gamete(s) with a single "q" chromosome.</li>
<li>There are<div class="inline" tabindex="-1" aria-label="Question 3" role="group"><div class="inputtype option-input inline">
<select name="input_79b9115c35164483917c6917114e34f0_4_1" id="input_79b9115c35164483917c6917114e34f0_4_1" aria-describedby="status_79b9115c35164483917c6917114e34f0_4_1">
<option value="option_79b9115c35164483917c6917114e34f0_4_1_dummy_default">Select an option</option>
<option value="0"> 0</option>
<option value="1"> 1</option>
<option value="2"> 2</option>
<option value="3"> 3</option>
<option value="4"> 4</option>
</select>
<div class="indicator-container">
<span class="status unanswered" id="status_79b9115c35164483917c6917114e34f0_4_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
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<p class="answer" id="answer_79b9115c35164483917c6917114e34f0_4_1"/>
</div></div>gamete(s) with both a "Q" and "q" chromosome.</li>
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<h2 class="hd hd-2 unit-title">Question 4</h2>
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<p> Question 4 is worth a total of 10 points. <br /> There is a codon chart at the bottom of this page. </p>
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Question 4b, part i
</h3>
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<p>The following is the schematic of a nucleotide triphosphate with an unusual pentose sugar.</p>
<p><img src="/assets/courseware/v1/f09fbb4f5eb0d332c319d053cd2c0952/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ex_q4b_v2.png" width="600" style="float:center;" alt="The line angle diagram of a nucleotide triphosphate with a pentose sugar. The triphosphate group is on the left, covalently bound to the sugar, which has no hydroxide (O H) groups. The base is covalently bound to the right side of the sugar."/></p>
<p>Use the dropdown options to label each carbon atom of the sugar as 1 prime - 5 prime.</p>
<ul>
<li>Carbon A:<div class="inline" tabindex="-1" aria-label="Question 1" role="group"><div class="inputtype option-input inline">
<select name="input_8e306cc6520d4b7da066f6e35ab97183_2_1" id="input_8e306cc6520d4b7da066f6e35ab97183_2_1" aria-describedby="status_8e306cc6520d4b7da066f6e35ab97183_2_1">
<option value="option_8e306cc6520d4b7da066f6e35ab97183_2_1_dummy_default">Select an option</option>
<option value="1 prime"> 1 prime</option>
<option value="2 prime"> 2 prime</option>
<option value="3 prime"> 3 prime</option>
<option value="4 prime"> 4 prime</option>
<option value="5 prime"> 5 prime</option>
</select>
<div class="indicator-container">
<span class="status unanswered" id="status_8e306cc6520d4b7da066f6e35ab97183_2_1" data-tooltip="Not yet answered.">
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</span>
</div>
<p class="answer" id="answer_8e306cc6520d4b7da066f6e35ab97183_2_1"/>
</div></div></li>
<li>Carbon B:<div class="inline" tabindex="-1" aria-label="Question 2" role="group"><div class="inputtype option-input inline">
<select name="input_8e306cc6520d4b7da066f6e35ab97183_3_1" id="input_8e306cc6520d4b7da066f6e35ab97183_3_1" aria-describedby="status_8e306cc6520d4b7da066f6e35ab97183_3_1">
<option value="option_8e306cc6520d4b7da066f6e35ab97183_3_1_dummy_default">Select an option</option>
<option value="1 prime"> 1 prime</option>
<option value="2 prime"> 2 prime</option>
<option value="3 prime"> 3 prime</option>
<option value="4 prime"> 4 prime</option>
<option value="5 prime"> 5 prime</option>
</select>
<div class="indicator-container">
<span class="status unanswered" id="status_8e306cc6520d4b7da066f6e35ab97183_3_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
</span>
</div>
<p class="answer" id="answer_8e306cc6520d4b7da066f6e35ab97183_3_1"/>
</div></div></li>
<li>Carbon C:<div class="inline" tabindex="-1" aria-label="Question 3" role="group"><div class="inputtype option-input inline">
<select name="input_8e306cc6520d4b7da066f6e35ab97183_4_1" id="input_8e306cc6520d4b7da066f6e35ab97183_4_1" aria-describedby="status_8e306cc6520d4b7da066f6e35ab97183_4_1">
<option value="option_8e306cc6520d4b7da066f6e35ab97183_4_1_dummy_default">Select an option</option>
<option value="1 prime"> 1 prime</option>
<option value="2 prime"> 2 prime</option>
<option value="3 prime"> 3 prime</option>
<option value="4 prime"> 4 prime</option>
<option value="5 prime"> 5 prime</option>
</select>
<div class="indicator-container">
<span class="status unanswered" id="status_8e306cc6520d4b7da066f6e35ab97183_4_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
</span>
</div>
<p class="answer" id="answer_8e306cc6520d4b7da066f6e35ab97183_4_1"/>
</div></div></li>
<li>Carbon D:<div class="inline" tabindex="-1" aria-label="Question 4" role="group"><div class="inputtype option-input inline">
<select name="input_8e306cc6520d4b7da066f6e35ab97183_5_1" id="input_8e306cc6520d4b7da066f6e35ab97183_5_1" aria-describedby="status_8e306cc6520d4b7da066f6e35ab97183_5_1">
<option value="option_8e306cc6520d4b7da066f6e35ab97183_5_1_dummy_default">Select an option</option>
<option value="1 prime"> 1 prime</option>
<option value="2 prime"> 2 prime</option>
<option value="3 prime"> 3 prime</option>
<option value="4 prime"> 4 prime</option>
<option value="5 prime"> 5 prime</option>
</select>
<div class="indicator-container">
<span class="status unanswered" id="status_8e306cc6520d4b7da066f6e35ab97183_5_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
</span>
</div>
<p class="answer" id="answer_8e306cc6520d4b7da066f6e35ab97183_5_1"/>
</div></div></li>
<li>Carbon E:<div class="inline" tabindex="-1" aria-label="Question 5" role="group"><div class="inputtype option-input inline">
<select name="input_8e306cc6520d4b7da066f6e35ab97183_6_1" id="input_8e306cc6520d4b7da066f6e35ab97183_6_1" aria-describedby="status_8e306cc6520d4b7da066f6e35ab97183_6_1">
<option value="option_8e306cc6520d4b7da066f6e35ab97183_6_1_dummy_default">Select an option</option>
<option value="1 prime"> 1 prime</option>
<option value="2 prime"> 2 prime</option>
<option value="3 prime"> 3 prime</option>
<option value="4 prime"> 4 prime</option>
<option value="5 prime"> 5 prime</option>
</select>
<div class="indicator-container">
<span class="status unanswered" id="status_8e306cc6520d4b7da066f6e35ab97183_6_1" data-tooltip="Not yet answered.">
<span class="sr">unanswered</span><span class="status-icon" aria-hidden="true"/>
</span>
</div>
<p class="answer" id="answer_8e306cc6520d4b7da066f6e35ab97183_6_1"/>
</div></div></li>
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<span id="solution_8e306cc6520d4b7da066f6e35ab97183_solution_1"/>
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Question 4b, part ii
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<p>The following is the sequence of a double stranded DNA.</p>
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Question 4c
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<p>Give the 5 base sequence that could serve as primer to synthesize most of the molecule shown if the bottom strand was used as template strand for transcription. <br/> <i>Please give you answer without spaces in the following format: X'NNNNNX' </i></p>
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Question 4d
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<p>You can also amplify the DNA in a test tube in vitro (in a test tube) using Polymerase chain reaction (PCR).</p>
<p>Select all the <b>similarities</b> between PCR and DNA replication.</p>
<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><div class="choicegroup capa_inputtype" id="inputtype_2c98ec4efa184772863d016995578964_2_1">
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<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_2_1[]" id="input_2c98ec4efa184772863d016995578964_2_1_choice_0" class="field-input input-checkbox" value="choice_0"/><label id="2c98ec4efa184772863d016995578964_2_1-choice_0-label" for="input_2c98ec4efa184772863d016995578964_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_2_1"> Both require template DNA.
</label>
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<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_2_1[]" id="input_2c98ec4efa184772863d016995578964_2_1_choice_1" class="field-input input-checkbox" value="choice_1"/><label id="2c98ec4efa184772863d016995578964_2_1-choice_1-label" for="input_2c98ec4efa184772863d016995578964_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_2_1"> Both use DNA polymerase.
</label>
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<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_2_1[]" id="input_2c98ec4efa184772863d016995578964_2_1_choice_2" class="field-input input-checkbox" value="choice_2"/><label id="2c98ec4efa184772863d016995578964_2_1-choice_2-label" for="input_2c98ec4efa184772863d016995578964_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_2_1"> Both use RNA primers.
</label>
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<div class="field">
<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_2_1[]" id="input_2c98ec4efa184772863d016995578964_2_1_choice_3" class="field-input input-checkbox" value="choice_3"/><label id="2c98ec4efa184772863d016995578964_2_1-choice_3-label" for="input_2c98ec4efa184772863d016995578964_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_2_1"> Both require nucleotides to make new DNA.
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<p>Select all the <b>differences</b> between PCR and DNA replication.</p>
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<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_3_1[]" id="input_2c98ec4efa184772863d016995578964_3_1_choice_0" class="field-input input-checkbox" value="choice_0"/><label id="2c98ec4efa184772863d016995578964_3_1-choice_0-label" for="input_2c98ec4efa184772863d016995578964_3_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_3_1"> One is regulated by cellular process and the other is regulated by temperature.
</label>
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<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_3_1[]" id="input_2c98ec4efa184772863d016995578964_3_1_choice_1" class="field-input input-checkbox" value="choice_1"/><label id="2c98ec4efa184772863d016995578964_3_1-choice_1-label" for="input_2c98ec4efa184772863d016995578964_3_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_3_1"> One process amplifies DNA once and the other amplifies it many times.
</label>
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<div class="field">
<input type="checkbox" name="input_2c98ec4efa184772863d016995578964_3_1[]" id="input_2c98ec4efa184772863d016995578964_3_1_choice_2" class="field-input input-checkbox" value="choice_2"/><label id="2c98ec4efa184772863d016995578964_3_1-choice_2-label" for="input_2c98ec4efa184772863d016995578964_3_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_2c98ec4efa184772863d016995578964_3_1"> One process requires a DNA primer and the other requires a RNA primer.
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Question 4e
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<p>If the Top strand in part c (displayed again above for your convenience) was used as a template for transcription&#8230;</p>
<br/>
<p>(i) give the sequence of the newly transcribed <b>RNA</b>.<br/>Please give your answer without spaces in the following format: X'NNNX'<br/><i>The Xs should indicate polarity.</i></p>
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<p>(ii) give the <b>amino acid sequence</b> of the newly translated peptide.<br/>Please give your answer without spaces in the following format: X-Aaa-Aaa-X<br/><i>The Xs should indicate polarity.</i></p>
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<p>(iii) give the sequence of the 3 base <b>anti-codon (on the tRNA)</b> that corresponds to the 2nd codon.<br/>Please give your answer without spaces in the following format: X'NNNX'<br/><i>The Xs should indicate polarity.</i></p>
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<p>(iv) give the <b>amino acid sequence</b> of the newly translated peptide if the bold and highlighted <b>&#8220;T/A (Top/ Bottom)" base pair</b> is changed to an <b>&#8220;A/T (Top/ Bottom)" base pair</b>.<br/>Please give your answer without spaces in the following format: X-Aaa-Aaa-X<br/><i>The Xs should indicate polarity.</i></p>
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<h2 class="hd hd-2 unit-title">Question 5</h2>
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<p> Question 5 is worth a total of 3 points. </p>
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<p>You want to clone part of Gene X that encodes Enzyme X. The following is the partial sequence of Gene X. It has recognition sites (shown in the grey boxes) for the restriction enzyme SalI, which cuts it at the positions shown by arrows.</p> <img src='/assets/courseware/v1/7c97d9da770247ac77e9e65ab9e90267/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5.png'>
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Question 5a
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<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><p>Select the sequence of Gene X AFTER it has been cut with SalI at Site A and Site B.</p>
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<input type="radio" name="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1" id="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_0" class="field-input input-radio" value="choice_0"/><label id="fa0a13ab27464ec4842c6c33487fb8a1_2_1-choice_0-label" for="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_fa0a13ab27464ec4842c6c33487fb8a1_2_1"> <img src="/assets/courseware/v1/22b36acb6afa0016998801453a4bebf7/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5a_a.png" width="300" style="float:center;" alt="A possible product of the restriction cut site by S A L 1. The top strand reads 5 prime T C G A C A T gap G T A 3 prime. The bottom strand reads 3 prime G T A space T A C A G C T 5 prime. The gaps are the same size and aligned so a 5 prime overhang exists on each strand."/>
</label>
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<input type="radio" name="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1" id="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="fa0a13ab27464ec4842c6c33487fb8a1_2_1-choice_1-label" for="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_fa0a13ab27464ec4842c6c33487fb8a1_2_1"> <img src="/assets/courseware/v1/0a306c3cc3736d61e704716c4b8c68ab/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5a_b.png" width="300" style="float:center;" alt="A possible product of the restriction cut site by S A L 1. The top strand reads 3 prime T C G A C T C gap G A G 5 prime. The bottom strand reads 5 prime G A G space C T C A G C T 3 prime. The gaps are the same size and aligned so a 3 prime overhang exists on each strand."/>
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<input type="radio" name="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1" id="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="fa0a13ab27464ec4842c6c33487fb8a1_2_1-choice_2-label" for="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_fa0a13ab27464ec4842c6c33487fb8a1_2_1"> <img src="/assets/courseware/v1/84e6140fd7a37ff872fa5f9be6564195/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5a_c.png" width="300" style="float:center;" alt="A possible product of the restriction cut site by S A L 1. The top strand reads 3 prime T C G A C A T gap G T A 5 prime. The bottom strand reads 5 prime G T A space T A C A G C T 3 prime. The gaps are the same size and aligned so a 3 prime overhang exists on each strand."/>
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<input type="radio" name="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1" id="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_3" class="field-input input-radio" value="choice_3"/><label id="fa0a13ab27464ec4842c6c33487fb8a1_2_1-choice_3-label" for="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_fa0a13ab27464ec4842c6c33487fb8a1_2_1"> <img src="/assets/courseware/v1/ac531c7e30fd2924e0a395026098a97e/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5a_d.png" width="300" style="float:center;" alt="A possible product of the restriction cut site by S A L 1. The top strand reads 5 prime T C G A C A T gap G A G 3 prime. The bottom strand reads 3 prime G T A space C T C A G C T 5 prime. The gaps are the same size and aligned so a 5 prime overhang exists on each strand."/>
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<input type="radio" name="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1" id="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_4" class="field-input input-radio" value="choice_4"/><label id="fa0a13ab27464ec4842c6c33487fb8a1_2_1-choice_4-label" for="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_4" class="response-label field-label label-inline" aria-describedby="status_fa0a13ab27464ec4842c6c33487fb8a1_2_1"> <img src="/assets/courseware/v1/1d615d850e31af7bc23e1f2a6bd2b9b0/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5a_e.png" width="300" style="float:center;" alt="A possible product of the restriction cut site by S A L 1. The top strand reads 5 prime T C G A C T C gap G A G 3 prime. The bottom strand reads 3 prime G A G space C T C A G C T 5 prime. The gaps are the same size and aligned so a 5 prime overhang exists on each strand."/>
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<input type="radio" name="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1" id="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_5" class="field-input input-radio" value="choice_5"/><label id="fa0a13ab27464ec4842c6c33487fb8a1_2_1-choice_5-label" for="input_fa0a13ab27464ec4842c6c33487fb8a1_2_1_choice_5" class="response-label field-label label-inline" aria-describedby="status_fa0a13ab27464ec4842c6c33487fb8a1_2_1"> <img src="/assets/courseware/v1/bf0f6d1658aff3fb2edf3614a12b1dca/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q5a_f.png" width="300" style="float:center;" alt="A possible product of the restriction cut site by S A L 1. The top strand reads 3 prime T C G A C A T gap G A G 5 prime. The bottom strand reads 5 prime G T A space C T C A G C T 3 prime. The gaps are the same size and aligned so a 3 prime overhang exists on each strand."/>
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<h3 class="hd hd-3 problem-header" id="72e5dd022e094e28af9d5597b95b87c8-problem-title" aria-describedby="block-v1:OCW+Pre-7.01+1T2020+type@problem+block@72e5dd022e094e28af9d5597b95b87c8-problem-progress" tabindex="-1">
Question 5b
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<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><p>Select the enzyme that would generate a base sequence which can ligate with SalI digested base sequence at Site A of Gene X.</p>
<img src="/assets/courseware/v1/3e2d5ca273782971b06162bafcf949b7/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/RE_ex_q5b.png" style="float:center;" alt="Three different restriction enzyme sites are shown. The 6 base pair sequence is the same for all three enzymes with varying cut sites. For enzyme 1, the top strand reads 5' C T C G A cut G 3 prime and the bottom strand reads 3 prime G cut A G C T C 5 prime. For enzyme 2, the top strand reads 5' C T C cut G A G 3 prime and the bottom strand reads 3 prime G A G cut C T C 5 prime. For enzyme 3, the top strand reads 5' C cut T C G A G 3 prime and the bottom strand reads 3 prime G A G C T cut C 5 prime."/>
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Question 5c
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<p>Ligation of the base sequences involves the formation of 3' to 5' phosphodiester bonds. This is an example of a...</p>
<div class="wrapper-problem-response" tabindex="-1" aria-label="Question 1" role="group"><div class="choicegroup capa_inputtype" id="inputtype_05656cd4a1a94cca885aee808e3e529f_2_1">
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