Mbalducc Week 6 - Revision history

Mbalducc: changed an answer

2017-10-09T22:54:48Z

changed an answer

2017-10-09T22:22:46Z

added answers

2017-10-09T22:17:13Z

added answers

2017-10-09T21:56:09Z

added acknowledgements

2017-10-09T16:43:24Z

added my responses

2017-10-09T16:32:39Z

added references

2017-10-06T16:51:40Z

added references

2017-10-06T16:49:05Z

added response

2017-10-06T16:47:11Z

added response

2017-10-06T16:24:29Z

added graph

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 #Over the course of the experiment, the TEF4 was repressed. This could have happened due to the lack of glucose, which may be necessary for the transcription of this gene.
 #TCA cycles would be induced if glucose is running out because the genes in these cycles help to preserve the glucose that is remaining.
-#A mechanism that the genome could use to ensure that genes for enzymes in a common pathway are induced simultaneously is by having conserved promoter sequence for the transcription of those genes. If one gene is induced, that means that all the genes with the same or similar promoter sequences would also be induced.
+#A mechanism that the genome could use to ensure that genes for enzymes in a common pathway are induced simultaneously is by using the guilt by association mechanism. This is because if one known gene is repressed or induced a certain way, then the other genes that are related will also be repressed or induced.
 #I would expect the glucose-repressed genes to be labelled bright red in the later times of this experiment, since they are no longer repressed by glucose or TUP1.
 #In the later times of this experiment, I would expect the spots to be bright red, since the yap1 gene is over expressed.

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 #A mechanism that the genome could use to ensure that genes for enzymes in a common pathway are induced simultaneously is by having conserved promoter sequence for the transcription of those genes. If one gene is induced, that means that all the genes with the same or similar promoter sequences would also be induced.
 #I would expect the glucose-repressed genes to be labelled bright red in the later times of this experiment, since they are no longer repressed by glucose or TUP1.
 = Acknowledgements =

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 #Over the course of the experiment, the TEF4 was repressed. This could have happened due to the lack of glucose, which may be necessary for the transcription of this gene.
 #TCA cycles would be induced if glucose is running out because the genes in these cycles help to preserve the glucose that is remaining.
-#A mechanism that the genome could use to ensure that genes for enzymes in a common pathway are induced simultaneously is
+#A mechanism that the genome could use to ensure that genes for enzymes in a common pathway are induced simultaneously is by having conserved promoter sequence for the transcription of those genes. If one gene is induced, that means that all the genes with the same or similar promoter sequences would also be induced.
 = Acknowledgements =
 I worked with my homework partner, [[User:johnllopez616|John Lopez]], on this assignment. We met in person and spoke over text about how to answer the questions.
 While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

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 #A mechanism that the genome could use to ensure that genes for enzymes in a common pathway are induced simultaneously is
 = Acknowledgements =
 = References =

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 #Gene X and Gene Y transcribed similarly. They both increased in the first 3 hours, then came back down to about a 1:1 ratio, then reduced transcription to 0.15-0.05.
 #The spots would be yellow at the first time point because they have both the red and green dyes, they have not had a chance to transcribe based on oxygen or not yet. The yellow comes from the mix of red and green dyes because of the 1:1 ratio of each gene. The biological reason that most spots resulted in being yellow would be that the same gene is transcribed whether or not oxygen is present.
-#Over the course of the experiment, the TEF4 was repressed. This could have happened due to the lack of glucose, which is necessary for
+#Over the course of the experiment, the TEF4 was repressed. This could have happened due to the lack of glucose, which may be necessary for the transcription of this gene.
+#TCA cycles would be induced if glucose is running out because the genes in these cycles help to preserve the glucose that is remaining.
 = Acknowledgements =

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 #'''Gene X''': 1 hour: Black, 3 hours: Dark Red, 5 hours: Black, 9 hours: Dark Green. '''Gene Y''': 1 hour: Black, 3 hours: Red, 5 hours: Black, 9 hours: Dark Green. '''Gene Z''': 1 hour: Black, 3 hours: Black, 5 hours: Dark Red, 9 hours: Dark red.
 #Gene X and Gene Y transcribed similarly. They both increased in the first 3 hours, then came back down to about a 1:1 ratio, then reduced transcription to 0.15-0.05.
+#The spots would be yellow at the first time point because they have both the red and green dyes, they have not had a chance to transcribe based on oxygen or not yet. The yellow comes from the mix of red and green dyes because of the 1:1 ratio of each gene. The biological reason that most spots resulted in being yellow would be that the same gene is transcribed whether or not oxygen is present.
 = Acknowledgements =
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 = References =
   LMU BioDB 2017. (2017). Week 6. Retrieved October 6, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6
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 #Here is the graph I created of two genes, DIT1 and SPS100 and their transcription rates over time. [[File:balduccitranscriptiongraph.png|400px]]
 #'''Gene X''': 1 hour: Black, 3 hours: Dark Red, 5 hours: Black, 9 hours: Dark Green. '''Gene Y''': 1 hour: Black, 3 hours: Red, 5 hours: Black, 9 hours: Dark Green. '''Gene Z''': 1 hour: Black, 3 hours: Black, 5 hours: Dark Red, 9 hours: Dark red.
+#