Objectives II and III

We already know objective I based upon "Nucleic Acid" lecture

What is DNA-directed RNA Polymerase (RNA Pol)?

An enzyme that synthesizes RNA using DNA as a template. It catalyzes the formation of phosphodiester bonds between ribonucleotides.

What is a promoter region?

A specific DNA sequence where RNA polymerase binds to initiate transcription.

What is a terminator region in transcription?

A DNA sequence that signals the end of transcription, causing RNA polymerase to stop and release the RNA transcript.

What is a transcription bubble?

An unwound section of DNA where RNA polymerase reads the template strand and synthesizes RNA.

What is the direction of DNA reading versus RNA synthesis?

RNA polymerase reads the DNA template strand in the 3′ to 5′ direction, and synthesizes RNA in the 5′ to 3′ direction.

What is the structure of E. coli DNA-Directed RNA Polymerase?

It is a multi-subunit enzyme consisting of the core enzyme (α₂ββ′ω) and the σ (sigma) factor, which together form the holoenzyme.

What is the structure of the RNA Polymerase core enzyme in E. coli?

The core enzyme is made of subunits α₂ββ′ω. It can synthesize RNA but cannot initiate transcription without the σ factor.

What is the RNA Polymerase holoenzyme in E. coli?

The holoenzyme is composed of the core enzyme plus the σ factor. The σ factor enables the RNA polymerase to recognize and bind to promoter regions on DNA.

What is the promoter region in an E. coli gene?

It’s a DNA sequence located upstream of the transcription start site, containing conserved regions such as the -10 (Pribnow box) and -35 regions, which are recognized by the σ factor.

What is the Pribnow Box?

A conserved sequence at the -10 position (TATAAT) in bacterial promoters, essential for transcription initiation.

What is the consensus sequence in E. coli promoters?

Common sequences found at -35 (TTGACA) and -10 (TATAAT) that are optimal for σ factor binding and efficient transcription initiation.

What is the Template Strand (Antisense or Minus Strand)?

The DNA strand that RNA polymerase reads to synthesize RNA. It is complementary to the RNA product.

What is the Nontemplate Strand (Sense or Plus Strand)?

The DNA strand not used as a template. Its sequence is identical to the RNA transcript (except T is replaced with U).

What is NusA and what is its function?

NusA is a transcription elongation factor. It replaces the σ factor after initiation and helps regulate pausing and termination by stabilizing RNA structures.

What is intrinsic termination in E. coli transcription?

A termination mechanism that involves the formation of a GC-rich RNA hairpin followed by a U-rich sequence, causing RNA polymerase to detach from the DNA.

What is Rho-dependent termination?

A process where the Rho protein binds to the rut site on the RNA and uses ATP to translocate along the RNA, causing RNA polymerase to release the transcript and detach from DNA.

What is the Rho protein?

A helicase that binds to specific RNA sequences (rut sites), moves along the RNA, and unwinds the RNA-DNA hybrid at the transcription complex to terminate transcription.