Paul Magnano: Week 8 Individual Journal

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Paul Magnano BIOL398-03/S13 User: Paul Magnano

Class Journals

Assignments/Individul Journals

Questions from ch 4

  • 5. (p. 110) Choose two genes from Figure 4.6 (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.
  • 6b. (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: 1.0 > black, 2.2 > medium red, 1.0 > black, 0.15 > bright green
    • gene Y: 1.0 > black, 4.5 >bright red, 0.95 > dim green, 0.05 > bright green
    • gene Z: 1.0 > black, 1.5 > dim red, 2.0 > medium red, 2.0 > medium red
  • 7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
    • All three genes transcribed similarly up to hour three, showing an increase. Genes X and Y transcribed similarily after hour 3 showing an overall decrease, although gene Y was more drastic in the reduction. Gene Z was transcribed differently after 3 hours, showing a continued increase.
  • 9. (p. 118) Why would most spots be yellow at the first time point?
    • because the response to oxygen depletion would take time to come into effect
  • 10. (p. 118) Go to 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).
    • Over the course of the experiment, TEF4 was reduced as glucose levels decreased. TEF4 is an important part in protien synthesis, so I would hypothesize that when the glucose levels decreased, the yeast cells would show reduction in TEF4 to reduce the rate of protein synthesis. This would save energy, and would allow the yeast cells to survive longer if they were continually deprived of glucose (food).
  • 11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • Because the TCA cycle allows energy production without glucose. Its the yeast response to sensing they "might starve". By activating the TCA cycle when they sense glucose is low, they can produce as much ATP as possible through the cycle, before glucose runs out.
  • 12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
    • The cells could use the same repressors or promoters to control the pathway, that way the control of the pathway is through one promoter or repressor.
  • 13. (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?
    • If the gene TUP1 was deleted the chip would show green, because the gene would not be present in the experimental cells. Since the gene is a repressor, any genes it repressed in the experimental cells would show red, as their activity would increase due to a lack of repression by TUP1.
  • 14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
    • Increased activity is shown by a red color, so if Yap1p was overexpressed I would expect to see a red color, with brightness dependant on the magnitude of over expression.
  • 15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
    • Yes it could. If the initial repressor was repressing a gene that represses a 3rd gene, then the 3rd gene would be repressed. If the initial transcription factor activated a gene that represses a 3rd gene, then over expression of the first gene would greatly repress the 3rd gene.
  • 16. (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?
    • I would want control spots that would be completely unnaffected by any manipulations of the experiment. The microarray should accurately determine if a gene is repressed or over expressed, over expression would be shown by a red color, and repression should be shown by a green color.