# (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.

#*The genome could induce or repress genes in a common pathway simultaneously if the different genes all contained equivalent regulatory sequences in their promotor regions that bound to the same regulatory protein (transcription factor). In this case, the transcription factor would have be specific in that it only would act on genes present in that pathway (or associated processes). If so, genes involved in the same pathway could be regulated by controlling the synthesis of just one protein, regardless of their diverse positions in the genome.

#*The genome could induce or repress genes in a common pathway simultaneously if the different genes all contained equivalent regulatory sequences in their promotor regions that bound to the same regulatory protein (transcription factor). In this case, the transcription factor would have be specific in that it only would act on genes present in that pathway (or associated processes). If so, genes involved in the same pathway could be regulated by controlling the synthesis of just one protein, regardless of their diverse positions in the genome.

# (Question 13, p. 121)  Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red.  What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?

# (Question 13, p. 121)  Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red.  What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?