L14: Gene Expression 2 Flashcards
What is the primary function of RNA polymerase in gene expression?
RNA polymerase transcribes DNA into RNA, initiating the first step of gene expression
What role does the core promoter play in transcription?
The core promoter contains sequences necessary for RNA polymerase binding, which initiates transcription
How do enhancer sequences affect gene expression?
Enhancer sequences increase the transcription rate by binding transcription factors that enhance RNA polymerase activity
What is the TATA box, and where is it located?
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
Describe the role of transcription factor IID (TFIID)
TFIID recognizes the core promoter and recruits RNA polymerase and other transcription factors to initiate transcription
What are the three types of RNA polymerase in eukaryotes, and their functions?
- RNA polymerase I transcribes rRNA genes
- RNA polymerase II transcribes mRNA
- RNA polymerase III transcribes tRNA and other small RNAs
How does chromatin structure impact transcription?
Chromatin structure, including DNA methylation and histone modifications, can repress or permit access to DNA for transcription
What is the function of the C-terminal domain (CTD) of RNA polymerase II?
The CTD becomes phosphorylated to recruit factors needed for mRNA processing, such as capping, splicing, and polyadenylation
How do transcription factors recognize specific DNA sequences?
Transcription factors bind to specific DNA motifs through their DNA-binding domains, enabling targeted gene regulation
What is alternative splicing, and why is it important?
Alternative splicing is the process by which different mRNA variants are produced from a single gene, allowing diverse protein functions
What are non-coding RNAs, and what roles do they play?
Non-coding RNAs do not encode proteins but are involved in gene regulation, through RNA interference and chromatin remodeling
Why is the assembly of the transcription initiation complex tightly regulated?
Tight regulation ensures genes are transcribed only when needed, preventing inappropriate gene expression that could harm the cell
What is the function of transcription factor II H (TFIIH)?
TFIIH has helicase activity that unwinds DNA, allowing RNA polymerase to access the DNA template for transcription
What is the significance of the TATA-binding protein (TBP) within TFIID?
TBP specifically binds to the TATA box, bending DNA to facilitate the recruitment of additional transcription machinery
How do silencer sequences function in gene regulation?
- 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
What is the holoenzyme in the context of transcription?
The holoenzyme is the fully assembled complex of RNA polymerase and its associated factors needed to initiate transcription
How do proximal promoter elements influence transcription?
Proximal promoter elements, located near the core promoter, bind transcription factors that modulate the rate of transcription initiation
What is the role of the mediator complex in transcription?
The mediator complex bridges transcription factors bound to enhancers with the RNA polymerase machinery at the promoter, facilitating transcription
Describe the function of small inhibitory RNAs (siRNAs) in gene regulation
siRNAs bind to target mRNAs to promote degradation or prevent translation, acting as a post-transcriptional regulatory mechanism
What is chromatin remodeling, and why is it necessary for transcription?
Chromatin remodeling adjusts nucleosome positioning to expose or conceal DNA sequences, making transcription sites accessible to transcription machinery like RNA polymerase
What are histone modifications, and how do they influence gene expression?
Histone modifications, such as acetylation and methylation, alter chromatin structure, either promoting or repressing transcriptional activity
Explain the concept of transcriptional silencing through DNA methylation
DNA methylation involves adding methyl groups to cytosine bases, typically silencing gene expression by blocking transcription factor binding or recruiting proteins that compact chromatin
What is the significance of enhancer-promoter looping in gene expression?
Enhancer-promoter looping brings distal enhancers into proximity with promoters, allowing enhancers to increase transcription of distant genes
Define alternative polyadenylation and its impact on mRNA
Alternative polyadenylation generates mRNA variants with different 3’ ends, influencing mRNA stability, localization, and translation efficiency
What are zinc finger motifs in transcription factors?
Zinc finger motifs are structural domains that stabilize DNA binding and enable transcription factors to recognize specific DNA sequences
How does the phosphorylation of RNA polymerase II’s C-terminal domain affect transcription?
Phosphorylation of the C-terminal domain is essential for transcription elongation and recruits processing factors for capping, splicing, and polyadenylation
What are general transcription factors, and why are they essential?
General transcription factors, like TFIID and TFIIH, are proteins that bind to promoters to initiate transcription by positioning RNA polymerase correctly
How do transcriptional activators and repressors influence gene expression?
Activators increase transcription by stabilizing the RNA polymerase complex, while repressors inhibit transcription by preventing complex assembly
What is the role of RNA polymerase III, and what does it transcribe?
RNA polymerase III transcribes tRNA, 5S rRNA, and other small RNAs involved in regulatory processes and protein synthesis
Describe the function of leucine zipper motifs in transcription factors
Leucine zipper motifs enable transcription factors to dimerize and bind DNA, enhancing specificity in gene regulation
How does RNA splicing contribute to protein diversity?
RNA splicing removes introns and can rearrange exons to produce different mRNA variants, leading to diverse protein isoforms from a single gene
What is the role of chromatin in gene regulation?
Chromatin organizes and compacts DNA, with its structure influencing gene accessibility and, consequently, transcriptional activity
How does transcriptional pausing regulate gene expression?
Transcriptional pausing temporarily halts RNA polymerase, allowing for timing adjustments and coordinated gene expression responses
What is the purpose of mRNA capping, and when does it occur?
mRNA capping occurs during transcription to protect mRNA from degradation and assist in ribosome recognition for translation
What are insulator elements in gene regulation?
Insulator elements block enhancer-promoter interactions to prevent inappropriate gene activation, maintaining distinct regulatory domains
Explain the function of transcription factor II B (TFIIB) in the transcription initiation complex
TFIIB stabilizes the transcription complex at the promoter and helps position RNA polymerase for accurate transcription start
How do transcription factors interact with co-factors in gene regulation?
Transcription factors bind DNA and recruit co-factors that either enhance or inhibit RNA polymerase activity, adjusting transcription rates
What is a gene promoter, and what key function does it serve?
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
What is the significance of the transcriptional start site (TSS)?
The TSS is the location where RNA polymerase begins transcribing DNA into RNA, marking the start of a gene’s expression
What is the function of TATA-binding protein (TBP) within TFIID?
TBP recognizes and binds to the TATA box, bending the DNA to facilitate assembly of the transcription initiation complex
How does the initiation complex prevent random gene transcription?
The complex requires specific DNA sequences and multiple transcription factors, ensuring genes are only transcribed under the right conditions
What are histone acetyltransferases (HATs), and what role do they play in transcription?
HATs add acetyl groups to histones, loosening chromatin structure and increasing transcriptional accessibility
Describe how TFIID stabilizes the transcription initiation complex
TFIID binds to the core promoter, helping anchor RNA polymerase and other transcription factors at the transcription start site
Why are transcriptional activators considered modular?
Transcriptional activators have separate DNA-binding and activation domains, allowing versatile combinations for targeted gene regulation
How do alternative promoter sequences provide regulatory flexibility?
Alternative promoters allow a gene to be expressed differently depending on cellular conditions, tissue type, or developmental stage
Explain how TATA-less promoters initiate transcription
TATA-less promoters use alternative core elements and transcription factors to recruit RNA polymerase, initiating transcription without a TATA box
What is the role of TFIIE in the transcription initiation complex?
TFIIE recruits TFIIH to the complex and helps regulate the helicase and kinase activities needed to begin transcription
How does transcriptional specificity arise among different cell types?
Cell type-specific transcription factors bind to unique enhancer or promoter regions, tailoring gene expression profiles to each cell type’s function
Why is the TATA box found in only a subset of genes?
The TATA box is a common but not universal promoter element, and many genes rely on alternative sequences for transcription initiation
