Anthony J. Wavrin Week 8

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#*You would like to see a control spot that has a different amount of color (expression) than your experimental spot, this would indicate that there was a change in expression levels, so not yellow dots.  To truly verify that a particular gene has been deleted or overexpressed, a northern blot (for overexpressed) or southern blot (for deleted) can be performed.
#*You would like to see a control spot that has a different amount of color (expression) than your experimental spot, this would indicate that there was a change in expression levels, so not yellow dots.  To truly verify that a particular gene has been deleted or overexpressed, a northern blot (for overexpressed) or southern blot (for deleted) can be performed.
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[http://openwetware.org/wiki/BIOL398-03/S13:Week_8 | Original Assignment]
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[[BIOL398-03/S13:Week_8| Original Assignment]]
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Assignment 8

  1. (p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
    • Gene X – Black, Dim Red, Black, Medium Green
    • Gene Y – Black, Medium Red, Dim Green, Bright Green
    • Gene Z – Black, Dim Red, Dim Red, Dim Red
  2. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
    • For hour 1 and hour 3 the three genes were transcribed similarly but, after hour 3 Gene Z stays induced while Gene X and Y are repressed. Overall, Gene X and Y are transcribed “similarly”.
  3. (p. 118) Why would most spots be yellow at the first time point?
    • This is because there has not been sufficient time for the cell to react to the system and reach its “equilibrium” to the new environment. Thus, there are more yellow spots than would be expected.
  4. (p. 118) Go to Yeast Genome and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
    • TEF4 is repressed, this is because translation requires energy. If glucose, its energy source, was depleting, the cell would want to only allocate its resources to surviving, thus expressing a gene involved in translation would not be sufficient because it won’t be spending a lot of energy making proteins.
  5. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • This is because respiration is much more efficient than fermentation. So, if glucose supply is running out, the cell will want to make the most out of the rest of the supply. By inducing the genes for the TCA cycle repress the genes for fermentation. Thus, this will maximize the amount of energy it can get from the glucose.
  6. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
    • One way of doing this is to have the genes for the enzymes have the same repressor or promoter sequences. Then, the cell would make one universal promoter, or repressor, to induce or repress an entire pathway.
  7. (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
    • Red, because it would no longer be repressed and thus it would be more induced in the experimental
  8. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
    • Yes, if Yap1p is over expressed, there would be a red spot because it would induce transcription, since it is a transcription factor.
  9. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
    • Yes, because some genes have repressors that are activated due to concentrations of other proteins. Thus, if a repressor is removed, and a gene is induced, it could increase the concentration of a protein that causes another gene to be repressed.
  10. (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?
    • You would like to see a control spot that has a different amount of color (expression) than your experimental spot, this would indicate that there was a change in expression levels, so not yellow dots. To truly verify that a particular gene has been deleted or overexpressed, a northern blot (for overexpressed) or southern blot (for deleted) can be performed.

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