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Genetics > Chapter 16.2: Control of Transcription Initiation Through Enhancers > Flashcards

Chapter 16.2: Control of Transcription Initiation Through Enhancers Flashcards

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1
Q

Do activators act in cis or trans?

A

trans

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2
Q

What is the function of RNA pol III in transcription in eukaryotes?

A

o RNA polymerase III transcribes genes that encode the tRNAs as well as certain other small RNA molecules

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3
Q

What is the leucine zipper?

A

o Leucine zipper is a helix with leucines at regular intervals

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4
Q

What is the function of insulators?

A

 DNA elements called insulators organize chromatin so that enhancers have access only to particular promoters
 Insulators are characterized as DNA elements located between a promoter and an enhancer that block the enhancer from activating transcription from that promoter

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5
Q

What is the a domain in the leucine zipper?

A

basic domain

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6
Q

Does an enhancer act in cis or trans?

A

cis

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7
Q

How do insulators work?

A

 Insulators bind a protein called CTCF (CCCTC-binding factor) that facilitates the formation of DNA loops
• A promoter and an enhancer will be in separate loops and cannot interact with each other if an insulator lies between them

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8
Q

What is the sub-domain of the dimerization domain in activators?

A

leucine zipper

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9
Q

What are the 3 domains in repressors in eukaryotes?

A
  • DNA-binding motifs
  • Repression domains for interacting with corepressors
  • Dimerization domains
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10
Q

Do repressors act in cis or trans?

A

trans

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11
Q

How can phosphorylation modify transcription factors?

A

• Can either activate or deactivate a transcription factor by: influencing movement of the factor into the nucleus, the factor’s DNA-binding properties, its ability to multimerize, or its ability to interact with other proteins, including coactivators or corepressors

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12
Q

How does indirect repression work in eukaryotes?

A

o Some repressors can compete with activators for access to an enhancer because the binding sites of the repressor and the activator overlap
o In quenching, a protein can bind the activation domain of an activator bound to an enhancer and thereby prevent the activator from functioning
o Some indirect repressors bind to activators and hold them in the cytoplasm; posttranslational modification of the indirect repressor causes it to release the activator, which can enter the nucleus and bind its target enhancers
o Some indirect repressors can form heterodimers with activators; if only activator homodimers can bind DNA, the indirect repressors can titrate the activators so that few homodimers are able to form

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13
Q

What is a TATA box and where is it located?

A

TATA box (or initiation box), consisting of roughly seven nucleotides of the sequence TATA(A or T)A(A or T), located just upstream of the transcription initiation site (in the promoter)

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14
Q

What is the function of the mediator?

A

 Mediator does not bind DNA directly but instead serves as a bridge between the RNA pol II complex at the promoter, and activator or repressor proteins bound at the enhancer

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15
Q

Where do basal factors bind?

A

to the promoter

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16
Q

Does a promoter act in cis or trans?

A

cis

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17
Q

Where do repressors bind in eukaryotes?

A

to the enhancers

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18
Q

Do basal factors act in cis or trans?

A

trans

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19
Q

What is the function of basal factors?

A

 Basal factors assist in the binding of RNA polymerase II to the promoter

20
Q

What is the function of RNA pol II in transcription in eukaryotes?

A

o RNA polymerase II (pol II) transcribes genes that encode all proteins

21
Q

What are the 3 domains of activators?

A

• DNA-binding domain
• Activation domain
Dimerization domain

22
Q

What allows for a basal level of transcription?

A

• Binding of RNA polymerase to the TATA box allows a low, so called basal level of transcription

23
Q

What is the function of RNA pol I in transcription in eukaryotes?

A

o RNA polymerase I (pol I) transcribes genes that encode the major components of ribosomes (rRNAs)

24
Q

What are the two types of coactivators that open chromatin?

A

histone acetyl transferase (HAT) enzyme and chromatin remodelers

25
Q

What are transcription factors?

A

o Transcription factors are all sequence-specific DNA binding proteins that influence transcription

26
Q

What is the function of repressors in eukaryotes?

A

• Eukaryotic repressors generally recruit corepressor proteins to enhancers

27
Q

Define o Chromatin immunoprecipitation-sequencing (ChIPSeq)

A

o Chromatin immunoprecipitation-sequencing (ChIPSeq) is a powerful new technology for finding all the target genes of a particular transcription factor within the entire genome of a particular type of cell

28
Q

What is the function of the dimerization domain in activators?

A

enables activators to interact with other transcription factor subunits to form multimeric proteins

29
Q

What can binding of proteins to enhancers cause?

A

 Binding of proteins to enhancers can augment or repress basal levels of transcription

30
Q

What is the function of activators?

A
  • Activators help “recruit” the basal factors and pol II to core promoter sequences by interacting directly with the components of this complex
  • Activators recruit coactivators
31
Q

How do chromatin remodelers open chromatin?

A

 Chromatin remodelers contain ATPase subunits an use the energy from ATP hydrolysis to displace nucleosomes from the promoter

32
Q

What are proteins that open local chromatin structure to allow gene transcription?

A

coactivators

33
Q

Where do activators bind?

A

to the enhancers

34
Q

What are coactivators?

A

these are proteins that open local chromatin structure to allow gene transcription

35
Q

How do histone acetyl transferase enzymes open chromatin?

A

 Histone acetyl transferase (HAT) enzymes acetylate particular amino acid residues of histone tails

36
Q

What is the key component of basal factors?

A

 The key component of the basal factor complex that forms on most promoters is the TATA box-binding protein, or TBP

37
Q

What are the 2 sub-domains of the DNA-binding domain in activators?

A

o Helix-turn-helix domains

o Zinc fingers

38
Q

Where is the enhancer located in eukaryotes?

A

o An enhancer is a regulatory site that can be quite distant from the promoter

39
Q

What is the function of indierect repressors?

A

• Indirect repressors prevent transcription by interfering with the function of activators

40
Q

Define bioinfomatics

A

o Bioinformatics is a field of science in which biology, computer science, and information technology merge to form a single discipline

41
Q

What is the function of corepressor proteins in eukaryotes?

A

o Corepressor proteins on their own cannot bind to DNA, so they associate with enhancers only if a repressor with which they can associate is already there
o Two Functions
 Some corepressors can interact directly with the RNA pol II basal complex and prevent it from binding the promoter
 Other corepressors are enzyme that modify histone tail amino acids, resulting in closed chromatin

42
Q

Where is the promoter located in eukaryotes?

A

o A promoter is always very close to the gene’s protein-coding region

43
Q

What is the function of the TATA box-binding protein, or TBP?

A

• This protein recruits other proteins called TBP-associated factors, or TAFs, to the promoter in an ordered pathway of assembly

44
Q

What is quenching?

A

o In quenching, a protein can bind the activation domain of an activator bound to an enhancer and thereby prevent the activator from functioning

45
Q

Define phosphorylation

A

the addition of a phosphate group to a protein by action of an enzyme called a kinase

Genetics (62 decks)

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