James P. McDonald Week 8

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Discovery Questions from Chapter 4

5. On paper

6. At 1 hour X, Y, and Z are all black because they had ratios at 1. At 3 hours X, Y, and Z are all a dim red each with a ratio between 1.5-4.5x increase. At 5 hours X and Y go back to black because they are both around a ratio of 1. Z stays at a dim red with a 2x increase. At 9 hours X is a dim/medium green with about a 6x decrease, Y is bright green with about a 20x decrease and Z is still a dim red remaining at a 2x increase.

7. All three of the genes were transcribed similarly up to the 3 hour mark. They all started at a ratio of one and had similar increases. After 3 hours X and Y continued to behave similar at the 5 hour mark as they went back to a ratio around 1. At the 9 hour mark both the X and Y ratios decreased but the Y decreased a lot more than X. Gene Z did not behave anything like X and Y after the 3 hour mark.

9. Initially, the control and experimental cultures have an abundance of glucose so regulation remains constant. Therefore there is no change in the expression of the gene, resulting in the yellow spot. Later in the experiment the glucose is depleted and regulation changes.

10. In the beginning of the experiment the TEF4 expression is constant but over the course of the experiment TEF4 expression was reduced as glucose supplies declined. The glucose is the only available food for the cell so when it was depleted the cell must have sensed that it may starve. It is stated in DeRisi's paper that the cells respond to this by repressing genes involved in protein synthesis. Since TEF4 is a gene used in translation, it is an important part of protein synthesis. I would hypothesize that the cell would repress TEF4 expression and other genes involved in protein synthesis when it detects starvation because the cell needs to save energy.

11. The TCA cycle produces energy in the form of ATP. When glucose runs lows the cell is able to sense that it will starve. The TCA cycle genes are induced because the cell wants to produce as much energy as it can before the glucose runs out. This is a way the cell can prepare itself to live in the absence of a food source for a period of time.

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