# (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.

# (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.

#*[[File:Bklein7 Week7 Question1.png]]

#*[[File:Bklein7 Week7 Q1small.png]]

#*Disclaimer: I am red-green colorblind, so assessing the red-green color scale for changes in transcription (Figure 4.5) proved difficult. In correlating the colors from Figure 4.6b to values, I made my best guesses using the aid of pixel color analysis tools.

#*Disclaimer: I am red-green colorblind, so assessing the red-green color scale for changes in transcription (Figure 4.5) proved difficult. In correlating the colors from Figure 4.6b to values, I made my best guesses using the aid of pixel color analysis tools.

# (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.)

# (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.)

#*[[File:Bklein7 Week7 Question2.png]]

#*[[File:Bklein7 Week7 Q2small.png]]

# (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?

# (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?

#*The transcription of genes X and Y from Figure 4.7b exhibited similar patterns in response to the gradual loss of oxygen. The transcription of both genes was induced at the 3 hour mark (90% of normal oxygen level), showed very little or no change when compared to the control at the 5 hour mark (~62% of normal oxygen level), and finally was repressed at the 9 hour mark (10% of normal oxygen level). Despite these similar patterns of up and down-regulation, the magnitudes of the transcriptional changes did vary between the two genes. Gene Y was both more dramatically induced at the 3 hour mark and more dramatically repressed at the 9 hour mark. Additionally, gene Y was very slightly down-regulated at the 5 hour mark whereas gene X showed no change from its transcription at a normal oxygen level.

#*The transcription of genes X and Y from Figure 4.7b exhibited similar patterns in response to the gradual loss of oxygen. The transcription of both genes was induced at the 3 hour mark (90% of normal oxygen level), showed very little or no change when compared to the control at the 5 hour mark (~62% of normal oxygen level), and finally was repressed at the 9 hour mark (10% of normal oxygen level). Despite these similar patterns of up and down-regulation, the magnitudes of the transcriptional changes did vary between the two genes. Gene Y was both more dramatically induced at the 3 hour mark and more dramatically repressed at the 9 hour mark. Additionally, gene Y was very slightly down-regulated at the 5 hour mark whereas gene X showed no change from its transcription at a normal oxygen level.

#*''Saccharomyces cerevisiae releases chemical energy from glucose through anaerobic respiration (fermentation) in glucose-rich environments, despite it being the energetically inefficient pathway when compared to aerobic respiration. However, in glucose-limited environments, yeast cells switch to the aerobic pathway. Upon switching pathways, ethanol is converted to acetyl-CoA, which enters the TCA cycle (aerobic pathway), and glucose is converted into storage sugars. This diauxic shift is captured in the microarray experiment. In the glucose-limited experimental group, TCA cycle genes are induced to shift from fermentation to the aerobic respiration pathway. This shift happens in response to glucose depletion, because it enables the cell to produce more ATP through the more energetically productive TCA cycle and conserve glucose. Thus, the cell is essentially preparing for survival in a glucose-limited environment by freeing up higher levels of chemical energy to sustain cellular processes and storing glucose for emergency use.

#*''Saccharomyces cerevisiae releases chemical energy from glucose through anaerobic respiration (fermentation) in glucose-rich environments, despite it being the energetically inefficient pathway when compared to aerobic respiration. However, in glucose-limited environments, yeast cells switch to the aerobic pathway. Upon switching pathways, ethanol is converted to acetyl-CoA, which enters the TCA cycle (aerobic pathway), and glucose is converted into storage sugars. This diauxic shift is captured in the microarray experiment. In the glucose-limited experimental group, TCA cycle genes are induced to shift from fermentation to the aerobic respiration pathway. This shift happens in response to glucose depletion, because it enables the cell to produce more ATP through the more energetically productive TCA cycle and conserve glucose. Thus, the cell is essentially preparing for survival in a glucose-limited environment by freeing up higher levels of chemical energy to sustain cellular processes and storing glucose for emergency use.

# (Question 12, p. 120)  What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

# (Question 12, p. 120)  What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?