Emilysimso Week 7

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  1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it in hard copy and turn it in in class.
  2. (Question 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, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
    • X: 1 - black, 3 - dim red, 5 - dimmer red, 9 - dim green
    • Y: 1 - black, 3 - red, 5 - bright green, 9 - dim green
    • Z: 1 - black, 3 - red, 5 - bright green, 9 - bright green
  3. (Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
    • Genes X and Y were transcribed similarly, as they both started as emitting more red light and then moved to green as time passed
  4. (Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
    • A yellow color appears when there has been no change in gene expression. Therefore, it makes sense that many of the genes would be yellow at the first time point, as they haven't had time to express the genes.
    • In the experiment, many of the genes would be yellow because the genes remained the same and were not effected by the variables introduced. Some of these could also have been controls.
  5. (Question 10, p. 118) Go to the Saccharomyces Genome Database 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 change in expression 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 repressed due to the bright green color.
    • If there was less glucose available, there was less available energy for the cell to go through translation, as the cell needs to use glucose to initiate translation. Therefore, there would be less TEF4 produced, because the cell didn't need to "turn on" that gene as part of translation.
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • The TCA cycle provides energy to cells by oxidizing acetate to produce ATP molecules. If glucose levels were low, a cell may use the TCA cycle to crate extra energy so that the cell could continue its normal processes.
  7. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
    • The genes can cluster together so that they respond at the same time.
  8. (Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?
    • Tup1p is responsible for the repression of glucose repressed genes. So, if a cell doesn't have TUP1, it would function normally in a low glucose situation. Therefore, I would expect the spots to be red because if they are glucose-repressed they are unable to take in glucose, and thus are glucose depleted.
  9. (Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?
    • Yap1p helps cells resist environmental stress. If cells overexpress Yap1p, one could expect that they would appear green in later stages of this experiment because they would be better able to adapt to the decrease in glucose.
  10. (Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?
    • If all of the TUP1 and overexpressed YAP1 were deleted, all of the spots would be yellow in the microarray because they would be able to regulate their pathways more efficiently.

Weekly Assignment Information

User: Emilysimso

Assignments

Individual Journal Entries

Class Journal Entries

Group Project

Heavy Metal HaterZ

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