Semester 2 2026 Revision: Gene Expression and Transcription

Vocabulary-style revision flashcards covering E. coli transcription, operon regulation (lac and trp), bacteriophage lambda life cycles, and relevant molecular biology techniques.

E. coli Genome Size

$4,639,675\,bp$ coding for $4254$ proteins.

Central Dogma

The flow of genetic information: DNA $\rightarrow$ RNA $\rightarrow$ Protein.

RNA Polymerase Core Enzyme

The complex $\alpha_2\beta\beta'\omega$ which can elongate RNA but cannot initiate transcription.

RNA Polymerase Holoenzyme

The complex $\alpha_2\beta\beta'\omega\sigma$ which is capable of initiating transcription.

$\sigma$-factor

A subunit that helps RNA polymerase find the promoter and dissociates after transcription initiation begins.

$\beta$ and $\beta'$ subunits

Subunits of RNA polymerase that form the catalytic center.

Rifampicin (Rifamycin)

An antibiotic that kills E. coli by blocking transcription initiation; resistant mutants often have altered $\beta$-subunits.

$-35$ box

A consensus promoter element with the sequence TTGACA.

$-10$ box (Pribnow box)

A consensus promoter element with the sequence TATAAT where DNA strand separation occurs.

Closed complex ($RP_c$)

The initial stage where RNA polymerase binds to promoter DNA without separating the strands.

Open complex ($RP_o$)

A very stable complex ($K_d = 10^{14}\,M$) where DNA strands separate at the $-10$ box to expose the template.

Rho-independent (intrinsic) termination

Termination caused by a G:C-rich stem-hairpin loop followed by a run of U residues in the mRNA.

Rho ($\rho$)

A $46\,kDa$ hexameric protein with ssRNA-dependent ATPase and helicase activity that unwinds the DNA:RNA hybrid to terminate transcription.

$rut$ sequence

The 'rho utilisation' sequence on mRNA where the Rho protein binds.

lacZ

A gene encoding $\beta$-galactosidase, which hydrolyses lactose into galactose and glucose and isomerises lactose into allolactose.

Allolactose

The natural inducer of the lac operon, produced by the isomerisation of lactose.

IPTG

A synthetic inducer of the lac operon that is not a substrate for $\beta$-galactosidase.

Crp-cAMP Activator

A complex that provides positive regulation by binding upstream of the $-35$ box when glucose levels are low and cAMP levels are high.

Lac Repressor (LacI)

A tetrameric protein with a helix-turn-helix (HTH) motif that binds operator DNA to block transcription in the absence of an inducer.

trpL

The leader mRNA sequence in the tryptophan operon that contains the attenuator and four regions capable of forming alternative hairpins.

Attenuation

A regulatory mechanism in the trp operon where ribosome stalling at tandem Trp codons controls the formation of a terminator or anti-terminator hairpin.

Tryptophan (as a co-repressor)

A small molecule that binds to the Trp repressor to tighten its interaction with the operator DNA (trpO).

CI ($\lambda$ repressor)

A protein that maintains lysogeny by repressing $P_L$ and $P_R$ while activating $P_{RM}$; it binds $O_R1$ with the highest affinity.

Cro

A protein that drives lysis by repressing $P_{RM}$ (shuts off CI) and later repressing $P_L$ and $P_R$; it binds $O_R3$ with the highest affinity.

CII

A regulatory protein whose stability determines the lysis/lysogeny decision; it is degraded by proteases in rich media, leading to lysis.

RecA

A protein activated by UV damage that facilitates the cleavage of the CI repressor and LexA, triggering the SOS response and prophage induction.

DNase I Footprinting

A technique used to identify the specific DNA region protected by a bound protein by observing 'gaps' in a cleavage pattern on a denaturing gel.

S1 Nuclease Mapping

An experimental technique used to infer the position of a transcription start site by digesting single-stranded DNA not protected by mRNA hybridization.