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<h2 class="hd hd-2 unit-title">Question 1</h2>
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You are working with two double helical DNA molecules that are of the same length (in base pairs): <b>DNA double helix 1</b> contains 25% Guanine (G) whereas <b>DNA double helix 2</b> has 30% Adenine (A).
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Question 1a, part i
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<p>Give the % of each of the following bases in<b> DNA double helix 1</b>.</p>
<p>Please type your answer in terms of a percent rounded to the nearest whole number, e.g. "91" for 90.5%.</p>
<br/>
<h3>%T=</h3>
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<h3>%A=</h3>
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<h3>%C=</h3>
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Question 1a, part ii
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<p>Give the % of each of the following bases in<b> DNA double helix 2</b>.</p>
<p>Please type your answer in terms of a percent rounded to the nearest whole number, e.g. "91" for 90.5%.</p>
<br/>
<h3>%T=</h3>
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<h3>%G=</h3>
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<h3>%C=</h3>
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Question 1b
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<p>Use the dropdown boxes to explain the relationship between proteins and the major classes of nucleic acids (DNA and RNA).</p>
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First, the process of<div class="inline" tabindex="-1" aria-label="Question 1" role="group"><div class="inputtype option-input inline">
<select name="input_a6c25afa47cd45799bf06b03f0cb78b2_2_1" id="input_a6c25afa47cd45799bf06b03f0cb78b2_2_1" aria-describedby="status_a6c25afa47cd45799bf06b03f0cb78b2_2_1">
<option value="option_a6c25afa47cd45799bf06b03f0cb78b2_2_1_dummy_default">Select an option</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
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<select name="input_a6c25afa47cd45799bf06b03f0cb78b2_3_1" id="input_a6c25afa47cd45799bf06b03f0cb78b2_3_1" aria-describedby="status_a6c25afa47cd45799bf06b03f0cb78b2_3_1">
<option value="option_a6c25afa47cd45799bf06b03f0cb78b2_3_1_dummy_default">Select an option</option>
<option value="DNA"> DNA</option>
<option value="RNA"> RNA</option>
<option value="proteins"> proteins</option>
</select>
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<select name="input_a6c25afa47cd45799bf06b03f0cb78b2_4_1" id="input_a6c25afa47cd45799bf06b03f0cb78b2_4_1" aria-describedby="status_a6c25afa47cd45799bf06b03f0cb78b2_4_1">
<option value="option_a6c25afa47cd45799bf06b03f0cb78b2_4_1_dummy_default">Select an option</option>
<option value="DNA."> DNA.</option>
<option value="RNA."> RNA.</option>
<option value="proteins."> proteins.</option>
</select>
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<p/>
Next, the process of<div class="inline" tabindex="-1" aria-label="Question 4" role="group"><div class="inputtype option-input inline">
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<option value="option_a6c25afa47cd45799bf06b03f0cb78b2_5_1_dummy_default">Select an option</option>
<option value="transcription"> transcription</option>
<option value="translation"> translation</option>
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<option value="option_a6c25afa47cd45799bf06b03f0cb78b2_6_1_dummy_default">Select an option</option>
<option value="DNA"> DNA</option>
<option value="RNA"> RNA</option>
<option value="proteins"> proteins</option>
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</div></div>to make <b>proteins</b>.
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Question 1c, part ii
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<legend id="c3ed7e7297644204aac430bdef2687fe_2_1-legend" class="response-fieldset-legend field-group-hd">Which of the following statements about replication of double-stranded DNA are TRUE?</legend>
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<input type="checkbox" name="input_c3ed7e7297644204aac430bdef2687fe_2_1[]" id="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_2" class="field-input input-checkbox" value="choice_2"/><label id="c3ed7e7297644204aac430bdef2687fe_2_1-choice_2-label" for="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_c3ed7e7297644204aac430bdef2687fe_2_1"> The parental strand is read 3' to 5'.
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<input type="checkbox" name="input_c3ed7e7297644204aac430bdef2687fe_2_1[]" id="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_3" class="field-input input-checkbox" value="choice_3"/><label id="c3ed7e7297644204aac430bdef2687fe_2_1-choice_3-label" for="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_c3ed7e7297644204aac430bdef2687fe_2_1"> The new strand is made 3' to 5'
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<input type="checkbox" name="input_c3ed7e7297644204aac430bdef2687fe_2_1[]" id="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_4" class="field-input input-checkbox" value="choice_4"/><label id="c3ed7e7297644204aac430bdef2687fe_2_1-choice_4-label" for="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_4" class="response-label field-label label-inline" aria-describedby="status_c3ed7e7297644204aac430bdef2687fe_2_1"> The parental and newly synthesized strand of the DNA duplex are complementary and anti-parallel.
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<input type="checkbox" name="input_c3ed7e7297644204aac430bdef2687fe_2_1[]" id="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_5" class="field-input input-checkbox" value="choice_5"/><label id="c3ed7e7297644204aac430bdef2687fe_2_1-choice_5-label" for="input_c3ed7e7297644204aac430bdef2687fe_2_1_choice_5" class="response-label field-label label-inline" aria-describedby="status_c3ed7e7297644204aac430bdef2687fe_2_1"> The 3&#8217; end of the newly synthesized strand is the receiving end for the incoming base.
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<h2 class="hd hd-2 unit-title">Question 2</h2>
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<p>The following is the sequence of a double stranded DNA that you want to amplify using Polymerase chain reaction (PCR).</p><p>
<b>5’ATGCCTAAC----------------------------------------------CCCGTACAT3’ TOP<br />
3’TACGGATTG---------------------------------------------GGGCATGTA5’ BOTTOM</b>
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Question 2a, part i
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<p>Give the sequence of a 9-bases long primer that would bind to the BOTTOM strand and can be elongated to make a new TOP strand.</p>
<p> Please type your answer this format: X'NNNNX'
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Question 2a, part ii
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<p>Give the sequence of a 9-bases long primer that would bind to the TOP strand and can be elongated to make a new BOTTOM strand.</p>
<p> Please type your answer this format: X'NNNNX'
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Question 2b
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<legend id="131a5918502040ebbc039cf0f509ed7c_2_1-legend" class="response-fieldset-legend field-group-hd">Check three components that are common to both replication of DNA within a cell and amplification of DNA using PCR.</legend>
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Question 2c
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<p>Starting with one molecule of DNA duplex, approximately how many molecules of DNA would you get at the end of 30 PCR reaction cycles?</p>
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<h2 class="hd hd-2 unit-title">Question 3</h2>
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<p>The following is the sequence of one strand of a double stranded DNA.</p>
<p><b>5’ ATTTCTAGCTTGGGCCAT3' </b></p>
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<p>If the sequence above was used as a <b>template strand for replication</b>&#8230;</p>
<p>Give the sequence of the new strand and label its 5' and 3' ends.<br/>Please give your answer without spaces in the form of: X'NNNNX'</p>
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<p>In which direction would the new strand be synthesized? <br/> Please give your answer in the form of: X' to X'</p>
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Question 3b
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<p>If the sequence above (given at the start of the question) used as a <b>template strand for transcription</b>&#8230;</p>
<p>Give the sequence of the newly transcribed RNA, label its 5' and 3' ends, <b>AND</b> separate each codon with a forward slash.<br/>Please give your answer without spaces in the form of: X'NN/NNX'</p>
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<p>In which direction would the new strand be transcribed? <br/> Please give your answer in the form of: X' to X'</p>
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<p>Give the <b>amino acid </b>sequence coded for by the newly transcribed RNA.<br/>Please give your answer without spaces in the form of: X-Aaa-Aaa-X<br/><i>Note: A codon chart has been provided at the bottom of this page.</i></p>
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<p> Which of these two processes requires primer to make the new strand?</p>
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Question 3d
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<p> The same sequence is repeated here for you.</p>
<p>5&#8217; ATTTCTAGCTT<b><u>G</u></b>GGCCAT3&#8217;</p>
<p>If the bold and underlined &#8220;G&#8221; in the above sequence was changed to &#8220;A&#8221; &#8230;
</p>
<p>Give the sequence of the newly transcribed RNA, label its 5' and 3' ends, <b>AND</b> separate each codon with a forward slash.<br/>Please give your answer without spaces in the form of: X'NN/NNX'</p>
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<br/>
<p>Give the sequence of the anti-codon corresponding to the 2nd codon and label its 5' and 3' ends. <br/> Please give your answer without spaces in the form of: X'NNNX'</p>
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<p>Give the <b>amino acid </b>sequence of the newly translated polypeptide.<br/>Please give your answer without spaces in the form of: X-Aaa-Aaa-X</p>
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<h2 class="hd hd-2 unit-title">Question 4</h2>
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<p>You want to study wing length (long or short) that is regulated by an autosomal Gene, Gene A, in fruit flies. Gene A can exist in the form of two different alleles; Allele A regulates the dominant phenotype whereas “Allele a” regulates the recessive phenotype.</p>
<p>You perform the following mating experiment.</p> <img src='/assets/courseware/v1/b677a574c5d85dab868606e01419ec16/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q4.png'>
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Question 4a
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<option value="option_b9d8ae6c6a5248038f66bc676db5ed1f_2_1_dummy_default">Select an option</option>
<option value="Long wings"> Long wings</option>
<option value="Short wings"> Short wings</option>
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Question 4b
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<p>In the mating experiment, the genotypes of parent 1 (P1), parent 2 (P2), and off-spring (F1) are unknown. Use the dropdown boxes to determine the correct genotype of P1, P2, and F1 flies.</p>
<p><img src="/assets/courseware/v1/3450c1ea063961047bcee54ff149a574/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_q4b.png" width="600" style="float:center;" alt="A fly mating experiment scheme with phenotypes given but genotypes unknown. The phenotype of P1 is long winged. The phenotype of P2 is short winged. F1 consists of one thousand flies that all have long wings."/></p>
<ul> <li>Genotype of P1:<div class="inline" tabindex="-1" aria-label="Question 1" role="group"><div class="inputtype option-input inline">
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<option value="option_56261bdb70d34f93b7103586dee1eeeb_2_1_dummy_default">Select an option</option>
<option value="A"> A</option>
<option value="a"> a</option>
<option value="AA"> AA</option>
<option value="Aa"> Aa</option>
<option value="aa"> aa</option>
</select>
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<li>Genotype of P2:<div class="inline" tabindex="-1" aria-label="Question 2" role="group"><div class="inputtype option-input inline">
<select name="input_56261bdb70d34f93b7103586dee1eeeb_3_1" id="input_56261bdb70d34f93b7103586dee1eeeb_3_1" aria-describedby="status_56261bdb70d34f93b7103586dee1eeeb_3_1">
<option value="option_56261bdb70d34f93b7103586dee1eeeb_3_1_dummy_default">Select an option</option>
<option value="A"> A</option>
<option value="a"> a</option>
<option value="AA"> AA</option>
<option value="Aa"> Aa</option>
<option value="aa"> aa</option>
</select>
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<li>Genotype of F1:<div class="inline" tabindex="-1" aria-label="Question 3" role="group"><div class="inputtype option-input inline">
<select name="input_56261bdb70d34f93b7103586dee1eeeb_4_1" id="input_56261bdb70d34f93b7103586dee1eeeb_4_1" aria-describedby="status_56261bdb70d34f93b7103586dee1eeeb_4_1">
<option value="option_56261bdb70d34f93b7103586dee1eeeb_4_1_dummy_default">Select an option</option>
<option value="A"> A</option>
<option value="a"> a</option>
<option value="AA"> AA</option>
<option value="Aa"> Aa</option>
<option value="aa"> aa</option>
</select>
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<h3 class="hd hd-3 problem-header" id="400080871ecb46c7af84ba260ed778a1-problem-title" aria-describedby="block-v1:OCW+Pre-7.01+1T2020+type@problem+block@400080871ecb46c7af84ba260ed778a1-problem-progress" tabindex="-1">
Question 4c, part i
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<p>You mate two F1 flies to obtain 1000 flies in F2 generation.</p>
<p>Use the dropdown options to fill in the Punnett Square for this cross. Some information has been provided for you.</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>A</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="Aa"> Aa</option>
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<option value="A"> A</option>
<option value="a"> a</option>
<option value="AA"> AA</option>
<option value="Aa"> Aa</option>
<option value="aa"> aa</option>
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<option value="AA"> AA</option>
<option value="Aa"> Aa</option>
<option value="aa"> aa</option>
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Question 4c, part ii
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<p>Give the <b>phenotypes and corresponding ratios</b> of the F2 flies based on the Punnett Square.</p>
<p>Please give your answers without spaces in the following format: <br/>#long:#short</p>
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Question 4c, part iii
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<p>Give the <b>genotypes and corresponding ratios</b> of the F2 flies based on the Punnett Square.</p>
<p>Please give your answers without spaces in the following format: <br/>#NN:#NN:#NN </p>
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<h3 class="hd hd-3 problem-header" id="da0eb3b97a084e4d8d55aed1ab7a163f-problem-title" aria-describedby="block-v1:OCW+Pre-7.01+1T2020+type@problem+block@da0eb3b97a084e4d8d55aed1ab7a163f-problem-progress" tabindex="-1">
Question 4d, part i
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<p>Using the Punnett Squares in the next two parts, design a mating experiment that can help you identify if a fly having long wings is homozygous or heterozygous for the alleles of Gene A.</p>
<p>Fill in the Punnett Square for this cross with the result of your designed experiment if the fly was <b>homozygous</b> for the alleles of Gene A. (The gametes for the long-winged fly that is homozygous have been given to you in the top row of the Punnett Square.)</p>
<table class="chart" summary="A Punnett Square to represent a test cross for a fly homozygous for Gene A." label="Three columns. The header is the gametes for the homozygoug long winged fly. The first column indicates the gametes of the other test parent. The second and third columns give the offspring resulting from the cross." width="100%"><caption>Complete the Punnett Square</caption>
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<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>A</b></th>
<th scope="col" style="text-align: center; border: 1px solid black;"><b>A</b></th>
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Question 4d, part ii
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<p>Fill in the punnett square for this cross with the result of your designed experiment if the fly was <b>heterozygous</b> for the alleles of Gene A. (The gametes for the long-winged fly that is heterozygous have been given to you in the top row of the Punnett Square.)</p>
<table class="chart" summary="A Punnett Square to represent a test cross for a fly homozygous for Gene A." label="Three columns. The header is the gametes for the homozygoug long winged fly. The first column indicates the gametes of the other test parent. The second and third columns give the offspring resulting from the cross." width="100%"><caption>Complete the Punnett Square</caption>
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<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>A</b></th>
<th scope="col" style="text-align: center; border: 1px solid black;"><b>a</b></th>
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<h2 class="hd hd-2 unit-title">Question 5</h2>
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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_1057b8cc53804256b8d56914c11b8914_2_1" id="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_0" class="field-input input-radio" value="choice_0"/><label id="1057b8cc53804256b8d56914c11b8914_2_1-choice_0-label" for="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_0" class="response-label field-label label-inline" aria-describedby="status_1057b8cc53804256b8d56914c11b8914_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."/>
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<input type="radio" name="input_1057b8cc53804256b8d56914c11b8914_2_1" id="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_1" class="field-input input-radio" value="choice_1"/><label id="1057b8cc53804256b8d56914c11b8914_2_1-choice_1-label" for="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_1" class="response-label field-label label-inline" aria-describedby="status_1057b8cc53804256b8d56914c11b8914_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_1057b8cc53804256b8d56914c11b8914_2_1" id="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_2" class="field-input input-radio" value="choice_2"/><label id="1057b8cc53804256b8d56914c11b8914_2_1-choice_2-label" for="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_2" class="response-label field-label label-inline" aria-describedby="status_1057b8cc53804256b8d56914c11b8914_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_1057b8cc53804256b8d56914c11b8914_2_1" id="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_3" class="field-input input-radio" value="choice_3"/><label id="1057b8cc53804256b8d56914c11b8914_2_1-choice_3-label" for="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_3" class="response-label field-label label-inline" aria-describedby="status_1057b8cc53804256b8d56914c11b8914_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_1057b8cc53804256b8d56914c11b8914_2_1" id="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_4" class="field-input input-radio" value="choice_4"/><label id="1057b8cc53804256b8d56914c11b8914_2_1-choice_4-label" for="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_4" class="response-label field-label label-inline" aria-describedby="status_1057b8cc53804256b8d56914c11b8914_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_1057b8cc53804256b8d56914c11b8914_2_1" id="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_5" class="field-input input-radio" value="choice_5"/><label id="1057b8cc53804256b8d56914c11b8914_2_1-choice_5-label" for="input_1057b8cc53804256b8d56914c11b8914_2_1_choice_5" class="response-label field-label label-inline" aria-describedby="status_1057b8cc53804256b8d56914c11b8914_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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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/a4130fb271d8b3b265038893553d4a70/asset-v1:OCW+Pre-7.01+1T2020+type@asset+block/ps2_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>
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