Molecular Biology

Robert F. Weaver

Chapter 12 Transcription Activators in Eukaryotes - all with Video Answers

Educators

Chapter Questions

00:36

Problem 1

List three different classes of DNA-binding domains found in eukaryotic transcription factors.

Sam Limsuwannarot

Numerade Educator

Problem 1

Design an experiment to show that TFIID binds directly to an acidic activating domain. Show sample positive results.

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00:36

Problem 2

List three different classes of transcription-activation domains in eukaryotic transcription factors.

Sam Limsuwannarot

Numerade Educator

02:10

You are studying the human $B L U$ gene, which is under the control of three enhancers. You suspect that the proteins that bind to these enhancers interact with each other to form an enhanceosome that is required for activation. What spacing among these enhancers is optimal for such interaction? What changes in this spacing could you introduce to test your hypothesis? What results would you expect?

Yifan Zhou

Numerade Educator

00:45

Problem 3

Draw a diagram of a zinc finger. Point out the DNA-binding motif of the finger.

Rabeya Zahid

Numerade Educator

00:55

Problem 3

Consider Figure 12.22a. What primers would you use in a 3C experiment to show association between the ICR insulator and each of the $I g f 2$ promoters $P 1, P 2$, and $P 3$, on the maternal chromosome.

Josee Pacheco

Numerade Educator

05:48

Problem 4

You are going to create a human activator (eA1) that controls a set of genes responsible for academic success. You aim to create an activator that includes the components deemed essential through the study of other activators.
What is the composition of your activator? In the process you also create two additional distinct activators (eA2, eA3). What experiments would you run to determine which activator works best? Suppose you wanted the activator to work in women students but not in men. How might you arrange that? What kind of activator would you have to design to make that work?

Eric Tran

Numerade Educator

02:28

Problem 4

List one important similarity and three differences between a typical prokaryotic helix-turn-helix domain and the Zif2 68 zinc finger domain.

Dennis Howard

Numerade Educator

02:22

Problem 5

Draw a diagram of the dimer composed of two molecules of the N-terminal 65 amino acids of the GAL4 protein, interacting with DNA. Your diagram should show clearly the dimerization domains and the motifs in the two DNAbinding domains interacting with their DNA-binding sites. What metal ions and coordinating amino acids, and how many of each, are present in each DNA-binding domain?

Jessica Wooten

Numerade Educator

01:24

Problem 6

In general terms, what is the function of a nuclear receptor?

Rehana Riaz

Numerade Educator

05:41

Problem 7

Explain the difference between type I and II nuclear receptors and give an example of each.

Rabeya Zahid

Numerade Educator

02:28

Problem 8

What metal ions and coordinating amino acids, and how many of each, are present in each DNA-binding domain of a nuclear receptor? What part of the DNA-binding domain contacts the DNA bases?

Dennis Howard

Numerade Educator

01:38

Problem 9

What is the nature of the homeodomain? What other DNA-binding domain does it most resemble?

Rabeya Zahid

Numerade Educator

02:20

Problem 10

Draw a diagram of a leucine zipper seen from the end. How does this diagram illustrate the relationship between the structure and function of the leucine zipper?

Dennis Howard

Numerade Educator

Problem 11

Draw a diagram of a bZIP protein interacting with its DNA-binding site.

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Problem 12

Describe and show the results of an experiment that illustrates the independence of the DNA-binding and transcription-activating domains of an activator.

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Problem 13

Present two models of recruitment of the class II preinitiation complex, one involving a holoenzyme, the other not.

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Problem 14

Describe and give the results of an experiment that shows that an acidic transcription-activating domain binds to TFIID.

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Problem 15

Present evidence that favors the holoenzyme recruitment model.

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05:46

Problem 16

Present two lines of evidence that argue against the holoenzyme recruitment model.

Eric Goldman

Numerade Educator

02:05

Problem 17

Why is a protein dimer (or tetramer) so much more effective than a monomer in DNA binding? Why is it important for a transcription activator to have a high affinity for specific sequences in DNA?

Vivek Singh

Numerade Educator

00:45

Problem 18

Present three models to explain how an enhancer can act on a promoter hundreds of base pairs away.

Eleanor Behling

Numerade Educator

00:45

Problem 19

Describe and give the results of an experiment that shows the effect of isolating an enhancer on a separate circle of DNA intertwined with another circle of DNA that contains the promoter. Which model(s) of enhancer activity does this experiment favor? Why?

Eleanor Behling

Numerade Educator

Problem 20

Describe how you would perform a hypothetical 3C experiment. Describe the results you would get, and give an interpretation.

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05:05

Problem 21

What advantage do complex enhancers confer on a gene?

Sana Riaz

Numerade Educator

Problem 22

Describe how you would identify transcription factories in a cell nucleus. Why are both in vitro and in vivo transcription essential parts of the procedure? Why does the existence of transcription factories imply that chromatin loops occur in the nucleus?

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05:48

Problem 23

LEF-1 is an activator of the human T-cell receptor $\alpha$-chain, yet LEF-1 by itself does not activate this gene. How does LEF-1 act? Describe and show the results of an experiment that supports your answer.

Eric Tran

Numerade Educator

01:34

Problem 24

Does LEF-1 bind in the major or minor groove of its DNA target? Present evidence to support your answer.

Jessica Wooten

Numerade Educator

01:49

Problem 25

What do insulators do?

Pankaj Jain

Numerade Educator

00:45

Problem 26

Diagram a model to explain the following results:
(a) Having one insulator between an enhancer and a promoter partially blocks enhancer activity. (b) Having two insulators between an enhancer and a promoter does not block enhancer activity. (c) Having one insulator on either side of an enhancer strongly blocks enhancer activity.

Eleanor Behling

Numerade Educator

Problem 27

What is the effect of three copies of an insulator between an enhancer and a promoter? How do you explain this phenomenon?

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00:45

Problem 28

Present evidence for the hypothesis that an insulator blocks enhancement by interacting with nearby enhancers and promoters. What are the difficulties in generalizing this hypothesis to all insulators?

Eleanor Behling

Numerade Educator