Genetics Ch 17

What structural difference limits gene regulation in bacteria?

Bacteria do not have chromatin, making their DNA more accessible for transcription.

What role does the nuclear membrane play in eukaryotic gene regulation?

It separates transcription and translation, allowing for more levels of control.

What is the effect of chromatin structure on gene expression?

Tightly packed chromatin represses gene expression by limiting access to transcription machinery.

How do chromatin-remodeling complexes regulate gene expression?

They reposition nucleosomes to expose or hide regulatory DNA regions.

What are three histone modifications that influence gene expression?

Acetylation, methylation, phosphorylation.

What is the function of histone acetylation?

Acetylation loosens DNA-histone interaction, making genes more accessible for transcription.

How does DNA methylation affect transcription?

Methylation of CpG islands inhibits transcription, often by recruiting proteins that compact chromatin.

What is the role of transcription factors in eukaryotic transcription?

They regulate initiation by binding to enhancers and promoters to activate or repress transcription.

How do enhancers regulate transcription from a distance?

They cause DNA to loop so bound transcription factors can interact with the basal transcription apparatus.

What is an insulator sequence?

A DNA sequence that blocks the action of an enhancer in a position-dependent manner.

What is a response element?

A regulatory DNA sequence shared by multiple genes that responds to the same transcription factor.

Why do eukaryotic genes respond to the same stimulus despite being scattered across the genome?

They share response elements activated by the same transcription factors.

How does RNA splicing influence gene expression?

Alternative splicing allows one gene to produce different proteins in different tissues or conditions.

What is the role of the 5′ cap and poly(A) tail in RNA stability?

They protect mRNA from degradation and help regulate translation efficiency.

What mRNA regions affect RNA stability besides the ends?

Sequences in the 5′ UTR, coding region, and 3′ UTR influence mRNA stability and translation.

How would a nonfunctional poly(A)-binding protein affect gene expression?

mRNA would be degraded faster due to poly(A) tail shortening and cap removal, reducing protein production.

Why is RNA degradation a form of gene regulation?

It determines how long mRNA is available for translation, controlling the level of protein production.

What is RNA interference (RNAi)?

A gene regulation mechanism where small RNAs (siRNA, miRNA) bind mRNA and suppress gene expression.

How do siRNAs and miRNAs differ?

siRNAs often cause direct cleavage of mRNA; miRNAs usually inhibit translation or destabilize mRNA without cleavage.

What protein complex do siRNAs/miRNAs bind to regulate mRNA?

The RNA-induced silencing complex (RISC).

How can RNA interference affect transcription?

Small RNAs can also recruit proteins that modify chromatin and silence transcription.

What is the purpose of competing endogenous RNAs (ceRNAs)?

They share miRNA binding sites and compete for limited miRNAs, indirectly regulating gene expression.

How do chromatin structure and histone modifications work together to regulate gene expression?

Chromatin structure limits access to DNA, and histone modifications like acetylation or methylation alter that structure to permit or prevent transcription.

How can a single stimulus activate multiple unrelated genes in eukaryotes?

By activating transcription factors that bind shared response elements found in each gene’s regulatory region.

Why is RNA splicing considered a regulatory mechanism rather than just processing?

It allows cells to produce different proteins from the same gene, varying the protein output based on context.

How does RNA interference allow cells to rapidly silence genes?

siRNAs/miRNAs are quickly produced and directly inhibit translation or degrade specific mRNAs, preventing protein synthesis without altering DNA.

Why is gene regulation considered multilayered in eukaryotes?

It occurs at multiple levels: chromatin remodeling, transcription initiation, RNA processing, RNA stability, translation, and post-translational modification.

How does gene regulation differ between prokaryotes and eukaryotes?

Eukaryotes lack operons, have chromatin, and compartmentalize transcription within the nucleus, unlike prokaryotes.

Why does the absence of operons in eukaryotes affect gene regulation?

Eukaryotic genes are typically regulated individually rather than in clusters like operons in bacteria.

How does chromatin structure influence gene expression in eukaryotes?

Tightly packed chromatin represses transcription; open chromatin allows transcription machinery access.

What are DNase I hypersensitive sites?

Regions of chromatin that are more open and accessible to enzymes, often located near active genes.

What do chromatin-remodeling complexes do?

They reposition nucleosomes to expose promoter regions and enable transcription.

What are the main types of histone modification?

Acetylation, methylation, and phosphorylation.

How does histone acetylation affect transcription?

It loosens chromatin structure, making DNA more accessible for transcription.

What is the histone code?

A hypothesis that specific combinations of histone modifications influence gene expression patterns.

What is DNA methylation and how does it affect gene expression?

Addition of methyl groups (usually at CpG sites), which inhibits transcription.

What are CpG islands and why are they important?

Stretches of DNA rich in CpG sites, often near gene promoters; methylation here silences genes.

What are general transcription factors?

Proteins that assemble at the promoter to form the basal transcription apparatus.

What are enhancers and how do they regulate transcription?

DNA sequences that increase transcription by binding transcription factors; can act at a distance via DNA looping.

How do transcription factors affect enhancers?

They bind to enhancers and interact with the basal transcription apparatus to increase transcription levels.

What is an insulator in eukaryotic gene regulation?

A DNA sequence that blocks the effect of enhancers in a position-dependent manner.

What is the function of a mediator complex?

It bridges transcription factors and RNA polymerase in the basal transcription apparatus.

What is transcriptional pausing or stalling?

When RNA polymerase begins transcription but pauses downstream of the promoter, often requiring additional signals to continue.

How can multiple eukaryotic genes be co-regulated?

By sharing common response elements that bind the same transcription factors.

What is alternative splicing?

A process by which different combinations of exons are joined to produce multiple mRNAs from a single pre-mRNA.

How does alternative splicing regulate gene expression?

It allows a single gene to produce different protein products in different conditions or cell types.

How does mRNA stability affect gene expression?

Longer-lived mRNAs produce more protein; unstable mRNAs degrade quickly, reducing protein levels.

What factors influence mRNA stability in eukaryotes?

The 5′ cap, poly(A) tail, UTR sequences, and RNA-binding proteins.

What role do proteins at the 5′ and 3′ ends of mRNA play?

They regulate translation and degradation by interacting with each other and the ribosome.

What is RNA interference (RNAi)?

A regulatory mechanism in which small RNAs (siRNAs or miRNAs) guide proteins to complementary mRNAs to repress gene expression.

How do siRNAs and miRNAs regulate gene expression?

They bind to target mRNA and lead to degradation, inhibit translation, or silence transcription.

What is RISC and how does it function?

The RNA-induced silencing complex, which uses a small RNA guide to target specific mRNAs for silencing or cleavage.

How can competing endogenous RNAs regulate miRNA availability?

They share miRNA binding sites and act as "sponges," limiting miRNA action on other targets.