Vkuehn Week 7

Week 7 Individual Journal Assignment

1. Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
   • Drawn graph
2. 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. ( Represented in order of 1 hour, 3 hours, 5 hours, 9 hours passed.
   • X: black, dark red, black, medium green
   • Y: black, medium red, dark green, bright green
   • Z: black, dark red, dark red, dark red
3. Were any of the genes in Figure 4.7b transcribed similarly?
   • X and Y were transcribed similarly because they both were first induced and later repressed in a similar pattern.
4. Why would most spots be yellow at the first time point?
   • At frist both would be yellow because they were just starting transcription and there would be little variation between the experimental and control.
5. Go to http://www.yeastgenome.org 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 would be repressed because it would no longer need to bind the factor to the ribosomal complex for transcription because it is not needed at as high of a rate.
6. Why would TCA cycle genes be induced if the glucose supply is running out?
   • If glucose is running low in TCA cycle the cycle genes would be induced because you would want to use those remaining glucose molecules for energy. Since there are less available it would need to induce the TCA cycle genes so that this process can still occur.
7. What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
   • The expression of the genes responsible for producing those enzymes could be codependent on one transcription factor so they are transcribed simultaneously.
8. Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
   • If you delete Tup1 you will see red spots on the assay.
9. What color spots would you expect to see on the chip when the transcription factor Yap1p is over expressed?
   • If Yap1p is overexposed you would also expect to see red spots.
10. Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
    • Yes, if you lose a transcription factor it could repress the gene because it would not be transcribed without the this as one of the starting indicators.
11. 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 need an experimental and control of both the Tup1 and Yap1p genes, then you would need to compare the results and check that the chips are different in color in comparison to the control.

Vkuehn (talk) 23:35, 9 October 2013 (PDT)

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