Kmeilak Week 7
Discovery Questions from Chapter 4
5. Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
6b. 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 hour): black
- Gene X (3 hours): dim red
- Gene X (5 hours): black
- Gene X (9 hours): medium green
- Gene Y (1 hour): black
- Gene Y (3 hours): medium red
- Gene Y (5 hours): dim green
- Gene Y (9 hours): bright green
- Gene Z (1 hour): black
- Gene Z (3 hours): dim red
- Gene Z (5 hours): dim red
- Gene Z (9 hours): dim red
7. Were any of the genes in Figure 4.7b transcribed similarly?
Yes, Gene X and Gene Y begin at 1.0, were induced at the 3 hour mark, and then were repressed at the 5 hour mark and was further repressed at the 9 hour mark.
9. Why would most spots be yellow at the first time point?
Most spots would be yellow at the first time point because of a delayed transcriptional reaction to changed environmental conditions. Initially, the gene expression would be the same as the control because not enough time had passed for significant gene expression changes.
10. Go to [1] 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 was repressed over the course of this experiment. It is most likely that this repression occurred with a reduction in available glucose because TEF4 helps bind AA-tRNA to ribosomes. With less glucose, and therefore less energy available, the cell would most likely become more conservative in gene expression and express fewer genes, lessening the need to expend energy transcribing a gene whose product aids in the binding of tRNA because there is less translation in the cell with reduced energy available.
11. Why would TCA cycle genes be induced if the glucose supply is running out?
TCA cycle genes are induced if the glucose supply is running out because the glyoxylate cycle breaks down cellular components which then need to be put through the TCA cycle to provide energy to the cell. By doing this, the cell is able to continue to obtain energy through catabolism of its own components.
12. What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
Common transcription factors.
13. Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
The DNA chip would be red because the removal of a repressor would increase transcription rates.
14. What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
The color spots would be red due to increased transcription from the increased levels of transcription factor Yap1p.
15. Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
It is possible if the increased transcription and translation of the gene resulted in increased downstream expression of a repressor for that gene.
16. 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 like to see yellow control spots for the transcription factor gene as well as the gene for the repressor. It is possible to verify a particular gene was deleted or overexpressed by looking at mRNA expression levels. If the gene is gone, the mRNA will be as well, and if it is overexpressed, then there will be more mRNA.
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