Question 1

You have discovered a novel factor that you think is involved in facilitating transcription through nucleosome arrays. You propose that the factor displaces a histone dimer from the core octamer, leaving a core hexamer on the DNA. Design an experiment to test your hypothesis and show sample positive results.

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Question 2

Draw a diagram illustrating the three key steps in the nuclear import of proteins. Which step requires the conversion of GTP to GDP?

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Question 3

Draw a rough sketch of the structure of a nuclear pore complex.

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Question 4

Discuss how Ran functions as a "molecular switch" in both nuclear import and export.

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Question 5

Describe two models for translocation of cargo through the nuclear pore complex.

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Question 6

Assume that you find in Q. 90 that the zinc finger protein is sometimes in the nucleus and sometimes in the cytoplasm. Describe one possible mechanism for cytoplasmic retention and subsequent signal-mediated import of this transcription factor.

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Question 7

Diagram the key steps in the regulated nuclear import of NF-$\kappa$B.

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Question 8

Diagram the key steps in the regulated nuclear import of the glucocorticoid receptor (GR).

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Question 9

You suspect that a sequence upstream of a transcriptional start site is acting as an enhancer and not as a promoter. Describe an experiment you would run to test your hypothesis. Predict the results.

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Question 10

A team of molecular biologists has made transgenic mice using a viral promoter and a cDNA coding for a human protein called p45. In most of the transgenic mice, they observe position-dependent expression of the human gene. They seek your advice. Suggest regulatory regions that you could link to the promoter- p45 DNA construct that might confer position-independent expression. Explain your choice of regulatory regions.

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Question 11

You have purified a transcription factor that has a leucine-rich region. You perform an electrophoretic mobility shift assay (EMSA) using a double-stranded oligonucleotide that you know from other studies contains the site recognized by this transcription factor in vivo. However, the transcription factor does not bind to the labeled oligonucleotide in your EMSA. Provide an explanation for this result.

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Question 12

You are studying a new class of eukaryotic promoters recognized by a novel RNA polymerase. You discover two general transcription factors that are required for transcription of these promoters. You suspect that one has helicase activity and that the other is required to recruit the helicase and the RNA polymerase to the promoter. Describe experiments you would perform to test your hypothesis. Provide sample results of your experiments.

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Question 13

You include an inhibitor of the protein kinase activity of TFIIH in an in vitro transcription assay. What step in transcription would you expect to see blocked? Describe an experiment you would run to test your hypothesis. Predict the results.

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The answer of You include an inhibitor of the protein...

Question 14

Assume that you are studying a transcription factor (TF). You have constructed a plasmid vector for expression of GFP-tagged TF. You discover that TF is sometimes in the nucleus and sometimes in the cytoplasm. Describe a possible mechanism for its cytoplasmic retention and subsequent signal-mediated import. Design an experiment to test your hypothesis and provide sample results.

Accepted Answer

The answer of Assume that you are studying a transcription...

Quiz 11: Transcription in Eukaryotes

Draw a diagram illustrating the three key steps in the nuclear import of proteins. Which step requires the conversion of GTP to GDP?

Draw a rough sketch of the structure of a nuclear pore complex.

Discuss how Ran functions as a "molecular switch" in both nuclear import and export.

Describe two models for translocation of cargo through the nuclear pore complex.

Assume that you find in Q. 90 that the zinc finger protein is sometimes in the nucleus and sometimes in the cytoplasm. Describe one possible mechanism for cytoplasmic retention and subsequent signal-mediated import of this transcription factor.

Diagram the key steps in the regulated nuclear import of NF- $\kappa$ B.

Diagram the key steps in the regulated nuclear import of the glucocorticoid receptor (GR).

You suspect that a sequence upstream of a transcriptional start site is acting as an enhancer and not as a promoter. Describe an experiment you would run to test your hypothesis. Predict the results.

You include an inhibitor of the protein kinase activity of TFIIH in an in vitro transcription assay. What step in transcription would you expect to see blocked? Describe an experiment you would run to test your hypothesis. Predict the results.

Quiz 11: Transcription in Eukaryotes

Draw a diagram illustrating the three key steps in the nuclear import of proteins. Which step requires the conversion of GTP to GDP?

Draw a rough sketch of the structure of a nuclear pore complex.

Discuss how Ran functions as a "molecular switch" in both nuclear import and export.

Describe two models for translocation of cargo through the nuclear pore complex.

Assume that you find in Q. 90 that the zinc finger protein is sometimes in the nucleus and sometimes in the cytoplasm. Describe one possible mechanism for cytoplasmic retention and subsequent signal-mediated import of this transcription factor.

Diagram the key steps in the regulated nuclear import of NF- κ\kappaκ B.

Diagram the key steps in the regulated nuclear import of the glucocorticoid receptor (GR).

You suspect that a sequence upstream of a transcriptional start site is acting as an enhancer and not as a promoter. Describe an experiment you would run to test your hypothesis. Predict the results.

You include an inhibitor of the protein kinase activity of TFIIH in an in vitro transcription assay. What step in transcription would you expect to see blocked? Describe an experiment you would run to test your hypothesis. Predict the results.

Diagram the key steps in the regulated nuclear import of NF- $\kappa$ B.