molecular chapter9_2

What is the role of MerR-family activators in transcription?

They alter promoter DNA structure to optimize spacing between -10 and -35 regions (from 19bp to ideal ~17bp), enhancing RNA polymerase binding.

How does NtrC activate transcription?

By binding enhancer elements, undergoing phosphorylation and oligomerization, looping DNA, and stimulating RNA polymerase (σ54) via ATP hydrolysis.

What are the components of a two-component signal transduction system?

A sensor kinase that autophosphorylates and a response regulator that receives the phosphate and binds DNA to regulate transcription.

How does the PhoR-PhoB system respond to low phosphate?

PhoR becomes active, phosphorylates PhoB, which then binds DNA to activate gene transcription related to phosphate acquisition.

What determines the lytic or lysogenic fate in bacteriophage λ?

The balance of transcriptional regulators cI, cII, and Cro, and environmental conditions such as DNA damage.

What is the role of cI in λ phage?

Stimulates PRM (its own promoter), represses PR and PL (lytic genes), and promotes lysogeny.

What is the role of cII in λ phage?

Stimulates transcription at PRE, increasing cI production and promoting lysogeny.

What is the role of Cro in λ phage?

Represses PRM, reducing cI levels and enabling expression of lytic genes.

What is the sequence of events for lysogeny?

cII → PRE → cI → PRM → integrase ↑, PR and PL ↓ → lysogeny

What triggers lytic growth in λ phage?

Low cII levels or DNA damage that deactivates cI via RecA cleavage, derepressing PR and PL promoters.

How does DNA damage promote lytic growth in lysogens?

RecA is activated and cleaves cI, preventing it from repressing lytic genes.

What is the DNA binding structure of cI?

It has a helix-turn-helix domain and forms dimers, tetramers, and octamers to cooperatively bind operators and regulate gene expression.

What is the DNA binding structure of Cro?

A helix-turn-helix motif forming dimers that bind DNA, especially OR3 to suppress cI.

What is autoregulation of cI?

High cI levels bind OR3 and OL3, suppressing PRM and preventing overexpression of cI to maintain lysogeny balance.

What is autoregulation of Cro?

Cro binds OR3 to repress PRM and enhance its own expression, promoting lytic growth.

What is anti-termination in transcription?

A mechanism preventing normal transcription termination to allow expression of downstream genes.

How does N protein mediate anti-termination?

It binds nut sites in RNA, recruits Nus proteins, and modifies RNA polymerase to read through terminators tL and tR.

What is the function of Q protein in λ phage?

Q binds QBE in DNA and interacts with σ70 to prevent early termination at PR’, enabling transcription of late lytic genes.

What is attenuation in bacterial transcription?

A mechanism that uses alternative RNA secondary structures in the leader region to either terminate or continue transcription based on metabolite availability.

How does the trp operon use attenuation?

High tryptophan leads to 3

What are riboswitches?

RNA structures that bind small molecules via an aptamer domain, altering RNA folding to regulate transcription or translation.

What are the components of a riboswitch?

An aptamer (binds metabolite) and an expression platform (changes gene expression).

How does the B. subtilis adenine riboswitch regulate transcription?

Low adenine → 2