Taur.vil Week 7
Week 7 Individual Journal
5) Microarray graph representing the change in transcription over time for SPS1 and DIT1.
6b) Gene X:
- 1 Hour: Black
- 3 Hours: Dim Red
- 5 Hours: Black
- 9 Hours: Med. Green
Gene Y:
- 1 Hour: Black
- 3 Hours: Med. Red
- 5 Hours: Very Dim Green
- 9 Hours: Bright Green
Gene Z:
- 1 Hour: Black
- 3 Hours: Dim Red
- 5 Hours: Dim Red
- 9 Hours: Dim Red
7) Genes X and Y followed the same pattern of transcription. For each, expression was the same after one hour, was increased at three hours, decreased by hour 5, and stayed repressed through hour 9.
9) Most spots would be yellow because both red and green tagged mRNA would be bound at the same percentage. We can tell this is the case because all expression levels in the microarray were equal (microarray level of 1.0) to those of the control cells with unlimited oxygen. A biological reason for this could be the initially high levels of oxygen (as can be observed in Figure 4.7a).
10) Over the course of the experiment, the TEF4 site went from yellow in OD3.7 to green in OD6.9 indicating that it was repressed. TEF4 is a translation elongation factor and the metabolism likely slows in the absence of glucose the cells energy source. The need for TEF4 may be reduced as the cell reacts to starvation conditions, reducing the amount of translation taking place and therefore the amount of TEF4 required.
11) TCA cycle genes would be induced as glucose runs out because the cell is metabolizing existing cellular components such as lipids through the TCA/glyoxalate cycle. By doing so, it is able to gain energy for essential cellular function, but only at the cost of non-essential cellular components.
12) The cell could ensure that enzymes of the same pathway are simultaneously expressed or repressed by using the same set of transcription factors for all genes in the pathway.
13) Because a repressor was removed from the cell, transcription would be greater in the experimental condition, producing a red color on the DNA chip.
14) If the trancription factor Yap1p is overexpressed, the increased transcription would result in many red spots.
15) Yes it could. The loss of a repressor or over expression of an inducer could facilitate increase transcription of a down stream repressor, thereby decreasing the overall transcription.
16) I would like to see clear, yellow control spots for this type of experiment as there would be no change between control and experimental groups. I could verify if a gene had been overexpressed if the color appeared to be green after normalization. Alternately, if a gene was completely deleted it would appear black on the microarray plate, meaning no protein was detected, or bright red when combined with the control condition.
- As part of Biological Databases
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