Ashley Rhoades Week 8

Week 8 Journal

• (p. 110) Choose two genes from Figure 4.6 https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_57614_1%26url%3D(PDF of figures on MyLMUConnect)] and draw a graph to represent the change in transcription over time. *Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.
• (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.
  • For genes X, Y, and Z is the first hour the color for the 1:1 ratio would be black for all three genes. For gene X in the third hour it would be dim red, back to black for the 5th hour, and then bright green in the 9th hour. For gene Y it would be medium red in the 3rd hour, dim green in the 5th hour, and bright green in the 9th. For gene Z it would be dim red the 3rd, 5th and 9th hours.
• (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
  • Gene X and Y were transcribed similarly in that they point increased and peaked at the 3rd hour and then went back down to a ratio lower than the 1st hour.
• (p. 118) Why would most spots be yellow at the first time point?
  • Most spots would be yellow at the first time point because that indicates little change in expression. The yeast cells are going to respond immediately to changes in environmental conditions so it makes sense that expression has not yet changed and the spots are therefore yellow.
• (p. 118) 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).
  • The TEF4 spot is light green and therefore the expression was repressed over the course of the experiment. TEF4 stimulates amino-acyl tRNA binding and therefore translation. This gene would be repressed with a reduction in glucose because making those proteins requires energy and glucose is the provider of that energy. The cell isn’t going to want to make more proteins if it is low on food.
• (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
  • The genome can have different promoters for each of the isozymes. Having different promoters for the enzymes rather than one promoter and multiple transcription factors allows the isozymes to be more specifically regulated.
• (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?
  • The control population is red and the experimental population is green. So when a gene involved in repression like TUP1 is deleted we are going to see more red because the experimental population is not be repressed and therefore expression is going to be greater than that of the control. Meaning we are going to have a larger number for the experimental expression in our numerator than the control expression in the data and the red is going to trump the green.
• (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
  • Yap1p is related to the environmental stress response. Overexpression of this transcription factor is going to turn on more genes related to the stress response. Since expression is increasing we are going to see more red spots.
• (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
  • Yes. Genes work together or oppositely so loss of repressor can cause some genes to be expressed more, so other genes may be repressed due to this. In the case of a transcription factor, some transcription factors cause certain genes to be pressed. So more of that transcription factor will lead to gene repression in some cases.
• (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 want the control spots to be consistent and reasonable to the conditions. Then you can verify if you truly deleted a gene by the color changes. The color spots are going to be dependent on what the gene does as we saw in the case of TUP1 and Yap1p.

Survey of Biomathematics

• Ashley Rhoades
• Loyola Marymount University
• Email me through OpenWetWare
• BIOL398-03/S13

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Ashley Rhoades