Transcription - Bio 112 Unit 3 Slide 10

Vocabulary practice flashcards covering gene architecture, transcription initiation, elongation, and termination mechanisms in bacteria and eukaryotes.

Gene (transcription unit)

A sequence of DNA that produces a single RNA molecule, typically containing a promoter, a coding region, and a transcription terminator sequence.

Promoter

A regulatory DNA sequence where transcription factors or sigma ($\sigma$) factor bind to recruit RNA polymerase to start transcription.

Coding region

The region of a gene that contains the DNA sequence that corresponds to and is transcribed into the RNA transcript.

Transcription terminator sequence

A DNA sequence that is copied into RNA, after which transcription stops and the RNA transcript is released.

Template strand

The DNA strand read by RNA polymerase in the $3' \rightarrow 5'$ direction, serving as the blueprint to synthesize a complementary and antiparallel RNA transcript.

Coding strand (non-template strand)

The DNA strand that is complementary to the template strand; its sequence and directionality match the RNA transcript, except it contains thymine ($\text{T}$) instead of uracil ($\text{U}$).

Upstream

The relative position along a gene situated in the direction opposite to the movement of transcription (towards the promoter relative to the transcription start site).

Downstream

The relative position along a gene situated in the direction that transcription proceeds (towards the terminator relative to the transcription start site).

$+1$ site

The transcription start site, representing the first DNA base used as a template to make the first base of the synthesized RNA transcript.

$-10$ box and $-35$ box

Two conserved bacterial promoter sequences that orient RNA polymerase and serve as binding sites for the sigma ($\sigma$) factor; the $+1$ site is approximately $10$ bases downstream of the $-10$ box.

Sigma ($\sigma$) factor

A bacterial protein that binds specifically to the $-35$ and $-10$ boxes of the promoter to recruit RNA polymerase and initiate transcription.

RNA polymerase

A large multi-subunit enzyme complex that unwinds DNA, reads the template strand in the $3' \rightarrow 5'$ direction, and synthesizes new RNA in the $5' \rightarrow 3'$ direction.

RNA Polymerase I

The eukaryotic RNA polymerase dedicated to transcribing genes that encode ribosomal RNA (rRNA), specifically the two large ribosomal RNAs ($18\text{S}$ and $28\text{S}$).

RNA Polymerase II

The eukaryotic RNA polymerase that transcribes protein-coding genes into messenger RNA (mRNA), as well as small nuclear RNA and microRNA.

RNA Polymerase III

The eukaryotic RNA polymerase responsible for transcribing transfer RNA (tRNA) genes and the $5\text{S}$ ribosomal RNA (rRNA) gene.

Core promoter

The minimum DNA region in eukaryotes near the transcription start site where general transcription factors and RNA polymerase assemble to initiate transcription.

TATA box

A conserved eukaryotic core promoter sequence located approximately $25$ base pairs upstream of the transcription start site, recognized by the TATA-binding protein (TBP).

TATA-binding protein (TBP)

A general transcription factor subunit that specifically recognizes and binds to the eukaryotic TATA box to facilitate recruitment of the RNA polymerase complex.

General transcription factors

A set of eukaryotic proteins that bind to core promoter elements to assemble the minimum complex required to initiate transcription and position RNA polymerase II.

Enhancer sequence

A regulatory DNA sequence located far from the core promoter that binds transcriptional activator proteins; DNA folding brings this sequence near the promoter to stimulate transcription.

Transcriptional activator proteins

Regulatory proteins that bind to enhancer sequences in DNA and interact with the transcription machinery to stimulate or increase transcription.

Mediator complex

A multiprotein eukaryotic complex that interacts with general transcription factors, RNA polymerase, and regulatory proteins bound to enhancers or silencers to coordinate transcription.

Hairpin loop

A folded secondary structure formed by bacterial mRNA after the terminator sequence is transcribed, which causes RNA polymerase to dissociate from the DNA template.

Pre-mRNA processing

A series of eukaryotic nuclear modifications applied to precursor mRNA before export to the cytoplasm, including the addition of a $5'$ cap, a $3'$ poly(A) tail, and intron splicing.