GENE REGULATION (OPERONS, EUKARYOTIC REGULATION, EPIGENETICS)

What is the function of a promoter?

A DNA sequence where RNA polymerase binds to initiate transcription.

What are the -10 and -35 elements in bacteria?

Consensus promoter sequences recognized by the sigma factor for transcription initiation.

What is the operator in bacterial operons?

A regulatory DNA sequence where repressors bind to block RNA polymerase.

What is an operon?

A cluster of genes under the control of a single promoter and operator, producing polycistronic mRNA.

What is the function of the lac operon?

Allows E. coli to metabolize lactose when glucose is scarce.

What molecule inactivates the lac repressor?

Allolactose, an isomer of lactose.

Why is the lac operon normally “off”?

The lac repressor binds the operator, blocking transcription.

When is CAP–cAMP activated?

When glucose levels are low, increasing transcription of the lac operon.

What does CAP–cAMP do?

Enhances RNA polymerase binding at the lac promoter, boosting transcription.

What happens to lac operon expression when glucose is high and lactose is present?

Low expression because CAP–cAMP is inactive (catabolite repression).

What happens when both glucose is low and lactose is present?

High expression; repressor released and CAP–cAMP activated.

Why do prokaryotes rarely use enhancers?

Their genomes are compact and transcription–translation are coupled, reducing spatial regulatory complexity.

What are general transcription factors (GTFs)?

Proteins required for all RNA Pol II transcription initiation in eukaryotes.

What does TFIID do?

Binds the TATA box and helps recruit RNA Pol II.

What is the function of TFIIH?

Unwinds DNA and phosphorylates RNA Pol II to trigger elongation.

What are specific transcription factors?

Regulatory proteins that bind enhancers or silencers to control transcription of particular genes.

What is an enhancer?

A DNA sequence that increases transcription when bound by activators.

What is a silencer?

A DNA sequence that decreases transcription when bound by repressors.

Can enhancers act from far away?

Yes—upstream, downstream, or within introns; DNA looping brings them to the promoter.

Why do eukaryotes require many transcription factors?

Their gene regulation is combinatorial and highly context-dependent across tissues and conditions.

What is chromatin remodeling?

Changing nucleosome positioning to alter access to DNA for transcription factors.

What does histone acetylation do to transcription?

Increases transcription by loosening chromatin.

What enzyme acetylates histones?

Histone acetyltransferase (HAT).

What enzyme removes histone acetylation?

Histone deacetylase (HDAC).

What is DNA methylation?

Addition of methyl groups to cytosines, commonly at CpG sites, usually reducing gene expression.

Is DNA methylation heritable?

Yes—maintenance methylases copy methylation patterns to daughter strands after replication.

What are CpG islands?

GC-rich promoter regions that are often regulated by methylation.

What does heavy promoter methylation do?

Silences transcription by blocking TF binding and tightening chromatin.

What is alternative splicing?

A mechanism that yields multiple mRNAs (and proteins) from a single gene by rearranging exon inclusion.

How do miRNAs regulate gene expression?

Bind partially complementary mRNA sequences to degrade them or block translation.

How do siRNAs regulate gene expression?

Bind perfectly complementary mRNA to induce cleavage and degradation.

What is RNA interference (RNAi)?

Post-transcriptional gene silencing using miRNA or siRNA.

What is the 5' UTR?

The untranslated region upstream of the start codon; regulates translation initiation efficiency.

What is the 3' UTR?

The untranslated region downstream of the stop codon; contains regulatory elements for stability and translation.

What are zinc-finger, helix-turn-helix, and leucine zipper motifs?

DNA-binding structural motifs in transcription factors.

What is epigenetics?

Heritable changes in gene expression not caused by changes in DNA sequence.

Why is methylation considered reversible?

Demethylase enzymes can remove methyl groups and reactivate genes.

What is cross-kingdom RNA interference?

The phenomenon where RNAs from one organism can regulate gene expression in another organism.

What determines the total amount of a protein in the cell?

Protein = rate of production – rate of degradation.

What is ubiquitination?

Tagging a protein for degradation by the proteasome.

What are distal control elements?

Enhancers or silencers located far from the promoter.

How do activators increase transcription?

Bind enhancers → recruit coactivators → increase RNA Pol II activity.

What is the mediator complex?

A multiprotein complex that links activators to RNA Pol II and integrates regulatory signals.

What does chromatin compaction do to transcription?

Decreases transcription by limiting access to DNA.

What is imprinting?

When only one allele (maternal or paternal) is expressed due to epigenetic marks.

What is the role of nucleosomes in regulation?

They physically block transcription factors unless remodeled.

How does environmental stress affect epigenetics?

It can induce methylation or acetylation changes that alter gene expression.

Why do multicellular organisms need complex gene regulation?

To generate distinct cell types and respond to internal/external signals.

What is the difference between basal and regulated transcription?

Basal transcription uses GTFs alone; regulated transcription uses activators/silencers for modulation.

What happens if enhancer-binding proteins mutate?

Transcription of target genes changes dramatically, often affecting development.

Why is eukaryotic gene regulation slower than prokaryotic?

Transcription and translation are separated by the nuclear membrane; chromatin must be remodeled first.