Bio 181 CH. 20 Questions 1-8

5 September 2022
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Part A The unpaired nucleotides produced by the action of restriction enzymes are referred to as _____.
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Sticky ends
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Part B The sticky end of the DNA restriction fragment shown here will pair with a DNA restriction fragment with the sticky end _____.
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-ACGT
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Part A - Using restriction enzymes to cut DNA The ability of restriction enzymes to cut DNA at specific sites makes DNA cloning possible. The diagram below shows a section of human DNA that contains an imaginary gene for video game proficiency (the vgp gene), shown in red. Shaded areas mark the restriction sites (also called recognition sites) of four restriction enzymes: EcoRI, HaeIII, BamHI, and HindIII. Arrows indicate where each enzyme cuts the two DNA strands. Which enzyme(s) will produce a DNA fragment that contains the entire vgp gene (shown in red) and has "sticky ends"? Select all that apply.
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BamHI HindIII
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Part B - Inserting the vgp gene into a cloning vector In the second step of the cloning procedure, DNA fragments produced by a restriction enzyme are inserted into a cloning vector that has been cut by the same enzyme. The vector used in this tutorial is a plasmid. To clone the vgp gene into the plasmid below, a restriction enzyme must do all of the following: cut the human DNA on both sides of the vgp gene, but not inside the gene cut the plasmid without cutting inside the ampicillin resistance gene (ampR ), shown in blue (The importance of the ampR gene will be explained in Part C.) produce sticky ends when it cuts both the human DNA and the plasmid, so that the human DNA fragments can combine with the plasmid The questions below will help determine which restriction enzyme should be used to make a plasmid that contains both an intact vgp gene and a functional ampR gene. Answer questions 1-4 by selecting from the answer choices on the left. Drag the correct answer to the right of each question.
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1) BamHI, HaeIII and HindIII 2)BamHI, EcoRI and HaeIII 3)BamHI, EcoRI and HindIII 4)BamHI only
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Part C - Transformation and selection of recombinant bacteria In the third step of the cloning procedure,all of the plasmids that were created in the second step are incubated with bacteria. The bacteria do not have an ampR gene on their own chromosome. As shown below, at least four classes of bacteria result. Notice that only one class contains the vgp gene To help sort out those bacteria that have the vgp gene, scientists first attempt to grow the bacteria both in a medium with ampicillin and in a medium without ampicillin. Demonstrate your understanding of this step by sorting the four bacterial classes based on where they will grow. Drag the icon for each bacterial class to the appropriate bin.
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Will grow only in meadium without ampicillin: no plasmid none in second box Will grow in both media: nonrecombinant plasmid, recombinant plasmid but no vgp gene, recombinant plasmid with vgp gene
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Part D - Screening the plasmid library The final step of the cloning procedure is to screen the plasmid library for clones that carry the vgp gene, shown in red below. To accomplish the screening, researchers synthesize a single-stranded DNA probe using vgp mRNA as a template. What will be the sequence of nucleotides in the probe? Drag the labels to their appropriate locations in the probe. Labels can be used once, more than once, or not at all.
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T C A C A C T G...G A A T T C A T
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Part A - Reading the figure There is a lot of information in the figure shown here.
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The wild-type mouse
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Part B - Interpreting the figure The hypothesis was that all three segments of the regulatory region are required for highest expression of the Hoxd13 gene. Is this hypothesis supported by the results?
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Yes; when any of the segments were deleted, the expression level dropped to less than 100% of the control.
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Part C What was the effect on the amount of Hoxd13 mRNA when segments B and C were both deleted?
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Only about 35% of the control amount of Hoxd13 mRNA was produced.
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Part D- Look at the blue stain in the in situ hybridization for the transgenic mouse lacking segments B and C. How would you describe the spatial pattern of gene expression in the embryo paw as compared to the control?
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The blue stain is generally lighter than in the control, but all four digit zones are still visible.
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Part E What was the effect on the amount of Hoxd13 mRNA when just segment C was deleted?
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Only about 60% of the control amount of Hoxd13 mRNA was produced.
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Part F How would you describe the spatial pattern of gene expression in the embryo paw lacking segment C as compared to the control and to the paw lacking segments B and C?
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The digit zones are not visibly stained as they are in the control and the paw lacking B and C.
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Part G - Evaluating the experimental design Suppose the researchers had only measured the amount of Hoxd13 mRNA and not done the in situ hybridizations. What important information about the role of the regulatory segments would have been missed?
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The spatial patterns of Hoxd13 gene expression in the paws would have been missed.
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Part H Suppose the researchers had only done the in situ hybridizations and not measured the amount of Hoxd13 mRNA. What important information would have been missed?
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Quantitative data about Hoxd13 mRNA levels would have been missed.
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Part A What information can not be obtained from the sequence of a gene?
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Whether the gene is methylated.
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Part B What is the polymerase chain reaction (PCR)?
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A method to amplify a fragment of DNA.
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Part C True or false? Comparison of the sequences of the same gene across species can give some insight into the existence of a common ancestor with that gene.
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True
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Part D True or false? The Taq enzyme is a type of DNA polymerase that allows researchers to separate the DNA strands during the annealing step of the PCR cycle without destroying the polymerase.
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False
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Part E How many DNA molecules would there be after four rounds of PCR if the initial reaction mixture contained two molecules?
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32
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Part F During which step in the PCR cycle are nucleotides used?
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Extension
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Part G During which step in the PCR cycle do primers form bonds with a single-stranded template?
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Annealing
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Part A If cells from a carrot are removed and placed in a culture medium, they can develop into a normal adult plant. This demonstrates that carrot cells _____.
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retain all the genes that were in the zygote that developed into the original plant
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Part A Which of the following is true of stem cells?
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All of the above.
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Part A This is a DNA fingerprint exhibiting samples from a victim, two suspects, and the crime scene. Which of these DNA fragments is common to both the victim and Suspect 1?
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B
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Part B This is a DNA fingerprint exhibiting samples from a victim, two suspects, and the crime scene. Which of these DNA fragments is common to both the victim and Suspect 2?
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C
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Part C Why is Suspect 1 considered more likely to have committed the crime than Suspect 2?
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The crime scene sample contains DNA fragments from both the victim and Suspect 1.
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Part A Why is golden rice pale yellow in color?
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It is rich in beta-carotene.
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Part B Which of these is a symptom of vitamin A deficiency?
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blindness
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Part C Which of these is a vitamin A precursor?
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beta-carotene
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Part D The transfer of antibiotic-resistant genes from genetically engineered bacteria to disease-causing bacteria _____.
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seems unlikely