Transcriptional Regulation Turning Genes On and Off in Both Normal and Pathological Conditions.

What is the trp operon, and what does the Trp repressor do?

A set of bacterial genes encoding tryptophan biosynthesis enzymes. The Trp repressor shuts off their transcription when tryptophan is plentiful.

What is the Trp repressor’s structure and DNA-binding motif?

A homodimer with a helix-turn-helix (HTH) motif in each subunit. Each dimer binds two tryptophans.

How does tryptophan activate the Trp repressor?

It causes a conformational change that aligns the HTH recognition helices with the operator.

Low tryptophan: what happens to the repressor, operator, and operon?

The repressor is inactive because its helices are misaligned (low operator affinity). The operator stays unoccupied, RNA polymerase transcribes the operon, and tryptophan is synthesized.

High tryptophan: what happens after the repressor binds the operator?

It blocks RNA polymerase from transcribing the operon, so enzyme production and tryptophan synthesis fall.

What is the lac operon, and which sugars affect it?

Genes for lactose uptake and metabolism. Glucose is preferred, and lactose induces the operon. Expression is highest when glucose is low and lactose is present.

What does the Lac repressor do, and how does allolactose affect it?

It binds the operator and blocks RNA polymerase. Allolactose (made from lactose) causes a conformational change that lowers its operator affinity, so it releases.

What are CAP and the CAP-binding site?

CAP is an activator that helps RNA polymerase bind and initiate transcription. It binds a site upstream of the lac promoter.

How does glucose affect cAMP and CAP?

High glucose gives low cAMP, so little active CAP-cAMP forms. Low glucose gives high cAMP, which binds CAP and promotes its DNA binding.

Does removing the Lac repressor guarantee maximal transcription? Can CAP activate with the repressor bound?

No to both. Maximal transcription needs the repressor released and CAP-cAMP bound. A bound repressor blocks transcription even when CAP is active.

Glucose + lactose ? →

Allolactose releases the repressor, but cAMP is low so CAP is inactive. Result: low (basal) transcription.

Glucose, no lactose ? →

The repressor stays bound and CAP is inactive. Result: OFF/basal.

No glucose, no lactose ? →

-cAMP-CAP is active, but the repressor stays bound. Result: very low/OFF.

No glucose, lactose present ? →

The repressor is released and CAP-cAMP is bound. Result: high transcription.

Negative vs. positive regulation?

Negative: a repressor decreases transcription. Positive: an activator increases it.

How can a ligand control a repressor?

It can remove the repressor from DNA, as when allolactose releases the Lac repressor. Or it can promote repressor binding, as when tryptophan promotes Trp repressor binding. Ligand binding changes conformation and DNA affinity.

How can a ligand control an activator?

It can promote binding (cAMP → CAP, increasing transcription) or cause release (decreasing transcription).

Why is eukaryotic regulation more complex than bacterial?

DNA is packaged into chromatin, and nucleosomes can cover promoters and transcription factor sites.

Why does DNA wrap around histones?

Negatively charged DNA is attracted to positively charged histone regions.

Three higher-order control mechanisms and their purposes?

Chromatin remodeling (changes nucleosome organization to expose DNA). DNA bending/looping (brings enhancers and promoters together). Synergism (a combined response greater than the sum of individual effects).

What are chromatin remodeling complexes (CRCs), and how do they work?

ATP-dependent complexes (e.g., SWI/SNF) that slide nucleosomes, alter their structure, or remove or exchange histones, exposing regulatory DNA.

How does lysine acetylation affect chromatin?

It neutralizes lysine’s positive charge, weakening histone-DNA attraction and making chromatin more accessible.

HATs vs. CRCs?

HATs chemically modify histones (e.g., SAGA, a HAT-containing coactivator complex). CRCs physically rearrange nucleosomes.

HATs, bromodomains, HDACs?

HATs are “writers” (add acetyl groups). Bromodomains are “readers” (bind acetyl-lysine) and help stabilize SWI/SNF on acetylated chromatin. HDACs are “erasers” (remove acetyl groups, restoring positive charge and reducing access).

Steps of the cooperative HAT/CRC model?

Activator binds DNA → recruits a HAT complex (SAGA) → histones are acetylated → bromodomains recruit SWI/SNF → ATP-dependent nucleosome remodeling exposes the promoter → GTFs and RNA Pol II assemble → transcription.

How are HDACs recruited to genes?

DNA-binding repressors recruit HDAC-containing corepressor complexes.

What is DNA looping, and why does it matter?

A loop that brings distant DNA regions (e.g., enhancer and promoter) together, so activator-associated proteins can contact coactivators and machinery at the promoter.

How can two activators act synergistically?

They recruit complementary factors, e.g., one recruits a HAT and the other a CRC, or one recruits Mediator, which helps recruit GTFs and Pol II to assemble the PIC.

TATA box and preinitiation complex (PIC)?

The TATA box is a promoter sequence recognized by TATA-binding protein. The PIC is Pol II plus GTFs assembled at a promoter before initiation.

Two functional domains of an activator?

A DNA-binding domain and an activation domain.

How do eukaryotic repressors often differ from bacterial ones?

They often act indirectly, by interfering with activators or GTFs, rather than only blocking DNA.

Three repression mechanisms?

Competitive DNA binding (repressor occupies an overlapping site, so the activator can’t bind).

Masking the activation surface (repressor binds the activator and blocks its interactions).

Direct repression of GTFs (repressor contacts machinery such as TFIID and impairs PIC assembly).

Masking vs. direct GTF inhibition?

Masking targets the activator. Direct inhibition targets the transcription machinery

What is a gene regulatory circuit, and why do cells use them?

A network in which gene products regulate other genes. It coordinates the timing and amount of expression in response to signals.

Transcriptional cascade?

Signal → Gene A → activator A → Gene B → activator B → Gene C.

Negative autoregulation?

A protein accumulates and inhibits transcription of its own gene, preventing overproduction.

Combinatorial activation?

Multiple signals produce different activators that bind separate sites on the same gene. Their combined action increases transcription.

Why are transcription factors “multiprotein hubs,” and what are the coactivator and corepressor sequences?

They interact with many regulators. Coactivator: TF binds DNA → recruits coactivator → chromatin or machinery is regulated → transcription increases. Corepressor: the same path, ending in decreased transcription.

Promoter as a “molecular summing junction”?

It attracts multiple regulatory proteins simultaneously, and the gene's final response—whether it turns on or off—depends entirely on the combined binding strength of the activators pushing the gas pedal versus the repressors stepping on the brakes.

Enhanceosome?

a molecular team of proteins—including transcription factors and structural scaffolds—that snaps together cooperatively like a puzzle on an enhancer to turn a gene on

Cooperative assembly?

Protein-protein interactions favor formation or stabilization of a complex, so one factor can help another bind.

DNA-bending protein vs. cohesin?

HMGB1 is an architectural protein that bends DNA locally, helping bring factors together on otherwise straight DNA. Cohesin is a ring-shaped complex that organizes larger chromatin loops via loop extrusion.

What is epigenetic regulation, and what are its three major types?

Heritable, persistent control of gene activity without changing DNA sequence. Types: DNA methylation, histone modifications, and RNA-mediated silencing.

Euchromatin vs. heterochromatin?

Euchromatin is open and accessible (active). Heterochromatin is compact (repressed).

DNA methylation: how established, and how does it repress?

DNMTs add methyl groups to cytosine at CpG sites, forming 5-methylcytosine. It blocks transcription factor binding or recruits readers such as MeCP2, which brings corepressors and HDACs.

H3K4me3 vs. H3K9me3 vs. H3K27me3?

H3K4me3 marks active promoters. H3K9me3 and H3K27me3 mark repression.

What is EZH2?

A histone methyltransferase in PRC2. Overactivity raises H3K27me3 and silences tumor suppressors.

Promoter hypermethylation?

Excess CpG methylation at a promoter blocks transcription factors and recruits repressors, silencing the gene.

How do epigenetic changes contribute to cancer?

They silence tumor suppressors (via promoter hypermethylation, repressive histone marks, or deregulated histone-modifying enzymes) without changing DNA sequence.

α-KG, TET2, and IDH1/2 normally?

IDH1/2 convert isocitrate to α-KG. α-KG is a citric acid metabolite required by TET enzymes and histone demethylases. TET2 oxidizes 5-mC, initiating DNA demethylation.

What happens with IDH1/2 cancer mutations?

The mutant enzyme converts α-KG to D-2-HG, which inhibits TET enzymes and histone demethylases. Result: DNA hypermethylation, accumulation of histone methyl marks, silenced protective genes, and blocked differentiation.

Other influences on epigenetics?

Viral proteins can alter DNA methylation. Inflammation and differentiation signals change transcription factor activity and epigenetic marks. Metabolism acts through α-KG (supports demethylation) vs. 2-HG (inhibits it)

XIST?

A lncRNA that coats the X chromosome it is transcribed from and recruits chromatin-regulatory machinery to initiate X inactivation.

miRNA?

A small RNA that guides silencing complexes to target mRNAs, causing translational repression, deadenylation, and decay.

What are long noncoding RNAs (lncRNAs)?

RNAs longer than 200 nucleotides that generally do not encode proteins but can regulate gene expression.

How are lncRNAs similar to mRNAs?

Many are transcribed by RNA polymerase II and undergo 5′ capping, splicing, and polyadenylation.

What are intergenic lncRNAs (lincRNAs)?

lncRNAs transcribed from regions between protein-coding genes it can recruit chromatin-modifying enzymes right to that spot. This chemically alters the local DNA packaging—either opening it up to activate the neighboring protein-coding gene or locking it down to silence

What are natural antisense transcripts (NATs)?

RNAs transcribed from the opposite DNA strand of another gene,

What are enhancer RNAs (eRNAs)?

RNAs transcribed from enhancer regions that may contribute to gene regulation.

What are PROMPTs?

short, unstable RNA molecules made as a byproduct just before a gene's starting point that are usually destroyed by the cell almost immediately instead of making proteins.

What are circular RNAs (circRNAs), and how are they formed?

are closed-loop RNA molecules they are completely resistant to exonucleases

What are sno-lncRNAs?

long, non-protein-making RNA molecules wrapped in specialized cell signals (snoRNAs) that protect them from being destroyed so they can help regulate cell activities.

What are the four major functional mechanisms of lncRNAs?

Transcriptional activator, transcriptional repressor, guide, and scaffold.

How does a guide lncRNA function?

It helps direct regulatory proteins or complexes to specific DNA or RNA targets.

How does a scaffold lncRNA function?

It binds multiple proteins and brings them together into a functional complex