Kwrigh35 Week 6

Assignment Answers

Question 1

See figure 1

Figure 1. The numbers on the y axis represent the amount the gene is expressed relative to the microarray taken at time 0. Negative numbers indicate that the gene was repressed X-Fold times.

Question 2

Table 1 Transcriptional Response of Three Genes to the Gradual Loss of Oxygen

Gene	1 hour	3 hour	5 hour	9 hour
Gene X	Black	Dim Red	Black	Medium Green
Gene Y	Black	Medium Red	Black	Bright Green
Gene Z	Black	Dim Red	Dim Red	Dim Red

Question 3

Genes X and Y were transcribed similarly. We can tell because their transcription rates have both increased at hour 3, but then have decreased through hours 5 and 9.

Question 4

• Spots occur yellow when RNA is expressed an equal amount in both of the samples. This is because green light mixed with red light appears yellow when present in equal amounts.
• Most spots appear yellow at the first time point because there has not been enough time for the change in environment to affect gene transcription.

Question 5

TEF4 was repressed during this experiment. When there are low levels of glucose (food) in the environment, cells need to conserve energy. TEF4 is repressed in the absence of glucose because the cell needs to use available energy for other processes, not translation.

Question 6

TCA cycle genes would be induced if glucose supply is running out because the TCA cycle by itself does not consume any glucose molecules. A cell would use TCA cycle as its primary source of energy in order to conserve glucose.

Question 7

The genome could use the same transcription factor for all of the genes associated in in a common pathway in order to ensure that the enzymes are induced or repressed simultaneously.

Question 8

If a microarray were produced using cells where the repressor TUP1 were deleted, then gene repression would not occur, even when glucose levels are high. I would expect the genes normally repressed by TUP1 to be present at the same level during the entire experiment. That means that spots represented at all time points would be red, because the gene is never repressed.

Question 9

YAP1 is a transcription factor that aids the cell in resisting environmental stresses. This implies that the depletion of glucose would not affect the cell as much when YAP1 is over-expressed. Therefore, I would expect the spots at later times in the experiment to stay green, even if glucose is depleted.

Question 10

The micro array slide should also contain spots for the DNA segments that code for the mRNA that is translated into TUP1p and YAP1p. Therefore, hybridization of the DNA and cDNA should occur in these spots. If TUP1 is deleted, then there should be no fluoresced cDNA bound to the microarray plate; the TUP1 spot should be black. If YAP1 is over-expressed, then the mRNA that codes for YAP1p should be abundantly present; the spot should be black/yellow because there should be the same amount of YAP1 present at all times.

Acknowledgments

Wiki Syntax

• For help formatting the table in question 2, I referenced this Wikipedia help page devoted to wiki tables.

References

LMU BioDB 2017. (2017). Week 6. Retrieved October 9, 2017, from Week 6

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