L14: Gene Expression 2 Flashcards

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1
Q

What is the primary function of RNA polymerase in gene expression?

A

RNA polymerase transcribes DNA into RNA, initiating the first step of gene expression

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2
Q

What role does the core promoter play in transcription?

A

The core promoter contains sequences necessary for RNA polymerase binding, which initiates transcription

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3
Q

How do enhancer sequences affect gene expression?

A

Enhancer sequences increase the transcription rate by binding transcription factors that enhance RNA polymerase activity

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4
Q

What is the TATA box, and where is it located?

A

The TATA box is a DNA sequence within the core promoter, around 25-30 base pairs upstream of the transcription start site, and helps position RNA polymerase
- Only found in 24% of genes - regulated by alternative promoter sequences or mechanisms

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5
Q

Describe the role of transcription factor IID (TFIID)

A

TFIID recognizes the core promoter and recruits RNA polymerase and other transcription factors to initiate transcription

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6
Q

What are the three types of RNA polymerase in eukaryotes, and their functions?

A
  • RNA polymerase I transcribes rRNA genes
  • RNA polymerase II transcribes mRNA
  • RNA polymerase III transcribes tRNA and other small RNAs
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7
Q

How does chromatin structure impact transcription?

A

Chromatin structure, including DNA methylation and histone modifications, can repress or permit access to DNA for transcription

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8
Q

What is the function of the C-terminal domain (CTD) of RNA polymerase II?

A

The CTD becomes phosphorylated to recruit factors needed for mRNA processing, such as capping, splicing, and polyadenylation

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9
Q

How do transcription factors recognize specific DNA sequences?

A

Transcription factors bind to specific DNA motifs through their DNA-binding domains, enabling targeted gene regulation

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10
Q

What is alternative splicing, and why is it important?

A

Alternative splicing is the process by which different mRNA variants are produced from a single gene, allowing diverse protein functions

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11
Q

What are non-coding RNAs, and what roles do they play?

A

Non-coding RNAs do not encode proteins but are involved in gene regulation, through RNA interference and chromatin remodeling

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12
Q

Why is the assembly of the transcription initiation complex tightly regulated?

A

Tight regulation ensures genes are transcribed only when needed, preventing inappropriate gene expression that could harm the cell

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13
Q

What is the function of transcription factor II H (TFIIH)?

A

TFIIH has helicase activity that unwinds DNA, allowing RNA polymerase to access the DNA template for transcription

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14
Q

What is the significance of the TATA-binding protein (TBP) within TFIID?

A

TBP specifically binds to the TATA box, bending DNA to facilitate the recruitment of additional transcription machinery

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15
Q

How do silencer sequences function in gene regulation?

A
  • Silencer sequences are DNA regions that repress transcription, often located upstream or downstream of the regulated gene
  • Silencers bind repressors to decrease gene expression by inhibiting transcription initiation
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16
Q

What is the holoenzyme in the context of transcription?

A

The holoenzyme is the fully assembled complex of RNA polymerase and its associated factors needed to initiate transcription

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17
Q

How do proximal promoter elements influence transcription?

A

Proximal promoter elements, located near the core promoter, bind transcription factors that modulate the rate of transcription initiation

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18
Q

What is the role of the mediator complex in transcription?

A

The mediator complex bridges transcription factors bound to enhancers with the RNA polymerase machinery at the promoter, facilitating transcription

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19
Q

Describe the function of small inhibitory RNAs (siRNAs) in gene regulation

A

siRNAs bind to target mRNAs to promote degradation or prevent translation, acting as a post-transcriptional regulatory mechanism

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20
Q

What is chromatin remodeling, and why is it necessary for transcription?

A

Chromatin remodeling adjusts nucleosome positioning to expose or conceal DNA sequences, making transcription sites accessible to transcription machinery like RNA polymerase

21
Q

What are histone modifications, and how do they influence gene expression?

A

Histone modifications, such as acetylation and methylation, alter chromatin structure, either promoting or repressing transcriptional activity

22
Q

Explain the concept of transcriptional silencing through DNA methylation

A

DNA methylation involves adding methyl groups to cytosine bases, typically silencing gene expression by blocking transcription factor binding or recruiting proteins that compact chromatin

23
Q

What is the significance of enhancer-promoter looping in gene expression?

A

Enhancer-promoter looping brings distal enhancers into proximity with promoters, allowing enhancers to increase transcription of distant genes

24
Q

Define alternative polyadenylation and its impact on mRNA

A

Alternative polyadenylation generates mRNA variants with different 3’ ends, influencing mRNA stability, localization, and translation efficiency

25
Q

What are zinc finger motifs in transcription factors?

A

Zinc finger motifs are structural domains that stabilize DNA binding and enable transcription factors to recognize specific DNA sequences

26
Q

How does the phosphorylation of RNA polymerase II’s C-terminal domain affect transcription?

A

Phosphorylation of the C-terminal domain is essential for transcription elongation and recruits processing factors for capping, splicing, and polyadenylation

27
Q

What are general transcription factors, and why are they essential?

A

General transcription factors, like TFIID and TFIIH, are proteins that bind to promoters to initiate transcription by positioning RNA polymerase correctly

28
Q

How do transcriptional activators and repressors influence gene expression?

A

Activators increase transcription by stabilizing the RNA polymerase complex, while repressors inhibit transcription by preventing complex assembly

29
Q

What is the role of RNA polymerase III, and what does it transcribe?

A

RNA polymerase III transcribes tRNA, 5S rRNA, and other small RNAs involved in regulatory processes and protein synthesis

30
Q

Describe the function of leucine zipper motifs in transcription factors

A

Leucine zipper motifs enable transcription factors to dimerize and bind DNA, enhancing specificity in gene regulation

31
Q

How does RNA splicing contribute to protein diversity?

A

RNA splicing removes introns and can rearrange exons to produce different mRNA variants, leading to diverse protein isoforms from a single gene

32
Q

What is the role of chromatin in gene regulation?

A

Chromatin organizes and compacts DNA, with its structure influencing gene accessibility and, consequently, transcriptional activity

33
Q

How does transcriptional pausing regulate gene expression?

A

Transcriptional pausing temporarily halts RNA polymerase, allowing for timing adjustments and coordinated gene expression responses

34
Q

What is the purpose of mRNA capping, and when does it occur?

A

mRNA capping occurs during transcription to protect mRNA from degradation and assist in ribosome recognition for translation

35
Q

What are insulator elements in gene regulation?

A

Insulator elements block enhancer-promoter interactions to prevent inappropriate gene activation, maintaining distinct regulatory domains

36
Q

Explain the function of transcription factor II B (TFIIB) in the transcription initiation complex

A

TFIIB stabilizes the transcription complex at the promoter and helps position RNA polymerase for accurate transcription start

37
Q

How do transcription factors interact with co-factors in gene regulation?

A

Transcription factors bind DNA and recruit co-factors that either enhance or inhibit RNA polymerase activity, adjusting transcription rates

38
Q

What is a gene promoter, and what key function does it serve?

A

A gene promoter is a DNA region that includes the transcription start site and core promoter, essential for the binding and initiation of RNA polymerase

39
Q

What is the significance of the transcriptional start site (TSS)?

A

The TSS is the location where RNA polymerase begins transcribing DNA into RNA, marking the start of a gene’s expression

40
Q

What is the function of TATA-binding protein (TBP) within TFIID?

A

TBP recognizes and binds to the TATA box, bending the DNA to facilitate assembly of the transcription initiation complex

41
Q

How does the initiation complex prevent random gene transcription?

A

The complex requires specific DNA sequences and multiple transcription factors, ensuring genes are only transcribed under the right conditions

42
Q

What are histone acetyltransferases (HATs), and what role do they play in transcription?

A

HATs add acetyl groups to histones, loosening chromatin structure and increasing transcriptional accessibility

43
Q

Describe how TFIID stabilizes the transcription initiation complex

A

TFIID binds to the core promoter, helping anchor RNA polymerase and other transcription factors at the transcription start site

44
Q

Why are transcriptional activators considered modular?

A

Transcriptional activators have separate DNA-binding and activation domains, allowing versatile combinations for targeted gene regulation

45
Q

How do alternative promoter sequences provide regulatory flexibility?

A

Alternative promoters allow a gene to be expressed differently depending on cellular conditions, tissue type, or developmental stage

46
Q

Explain how TATA-less promoters initiate transcription

A

TATA-less promoters use alternative core elements and transcription factors to recruit RNA polymerase, initiating transcription without a TATA box

47
Q

What is the role of TFIIE in the transcription initiation complex?

A

TFIIE recruits TFIIH to the complex and helps regulate the helicase and kinase activities needed to begin transcription

48
Q

How does transcriptional specificity arise among different cell types?

A

Cell type-specific transcription factors bind to unique enhancer or promoter regions, tailoring gene expression profiles to each cell type’s function

49
Q

Why is the TATA box found in only a subset of genes?

A

The TATA box is a common but not universal promoter element, and many genes rely on alternative sequences for transcription initiation