Gene Structure and Prokaryotic Transcription (2.1–2.2)

Vocabulary flashcards covering key terms and definitions from gene structure, promoters, transcription initiation/elongation/termination, and prokaryotic transcription concepts.

Gene

The basic unit of genetic information: the nucleic acid sequence that codes for a functional product (polypeptide, tRNA, or rRNA); a linear sequence with a fixed start and end.

Coding region

The part of a gene that begins with DNA TAC on the template strand and ends with a stop codon; yields codons for amino acids (on the coding strand it corresponds to ATG at the start).

Start codon (AUG)

The codon that signals translation initiation in mRNA; in bacteria the coding region begins with TAC on the template, corresponding to AUG in mRNA.

Stop codon (RNA: UAA/UAG/UGA; DNA: TAA/TAG/TGA)

Codon that terminates translation; marks the end of the coding region.

Promoter

DNA sequence at the start of a gene where RNA polymerase binds; includes signals to orient the polymerase and indicate where transcription should begin; typically contains -35 and -10 elements.

-35 sequence

Promoter element about 35 bases upstream of the start site; consensus TTGACA; recognized by sigma factor.

-10 sequence (Pribnow box)

Promoter element about 10 bases upstream of the start site; consensus TATAAT; site where DNA strands separate.

Pribnow box

Another name for the -10 promoter element in bacterial promoters.

Shine-Dalgarno sequence

Ribosome binding site in prokaryotic mRNA; pairs with 16S rRNA to initiate translation.

Leader sequence

Region transcribed into mRNA but not translated; contains the Shine-Dalgarno sequence and precedes the coding region.

Trailer sequence

Downstream sequence after the coding region that helps prepare RNA polymerase for termination.

Terminator

DNA/RNA sequence signaling transcription termination; two types: intrinsic (rho-independent) and rho-dependent.

Trailer

Downstream RNA segment following the coding region that can be involved in transcription termination preparation.

Intrinsic termination (rho-independent)

Terminating transcription via RNA hairpin (stem-loop) followed by a run of uracils in RNA, causing RNA polymerase to dissociate.

Rho-dependent termination

Termination requiring the Rho factor, which binds mRNA and moves with RNA polymerase to the terminator, unwinding the RNA–DNA hybrid.

RNA polymerase

Enzyme that synthesizes RNA from a DNA template; core enzyme plus sigma factor forms holoenzyme for initiation.

Core enzyme

The catalytic part of RNA polymerase (five subunits) capable of elongation but unable to initiate on its own.

Sigma factor

Regulatory subunit that enables RNA polymerase to recognize promoters; has no catalytic activity and dissociates after initiation.

Holoenzyme

RNA polymerase core enzyme bound to a sigma factor; capable of initiating transcription.

Open complex / transcription bubble

Region where DNA is unwound to expose the template strand for transcription.

Transcription elongation

Phase where RNA polymerase moves along the template, synthesizing RNA in 5'→3' direction and maintaining the open complex.

Transcription initiation

Phase when RNA polymerase binds the promoter, forms the open complex, and begins RNA synthesis.

Template strand

DNA strand used by RNA polymerase to synthesize RNA; read 3'→5' during transcription.

Coding (sense) strand

DNA strand whose sequence is identical to the RNA transcript (with T instead of U); read 5'→3'.

mRNA

Messenger RNA; carries the genetic message from DNA to the ribosome for protein synthesis.

tRNA

Transfer RNA; carries amino acids during translation; often encoded by genes with promoters and spacers; undergoes posttranscriptional modifications.

rRNA

Ribosomal RNA; component of ribosomes; encoded by multiple rRNA genes with promoters, spacers, and terminators.

16S rRNA

Ribosomal RNA component of the small subunit that interacts with the Shine-Dalgarno sequence during initiation.

Polycistronic mRNA

mRNA that encodes more than one polypeptide; common in bacteria and produced from operons.

Operon

Cluster of genes transcribed from a single promoter into a polycistronic mRNA; typical in bacteria; enables coordinated expression.

Monocistronic

mRNA that encodes a single polypeptide; typical in eukaryotes.

Polypeptide start in bacteria (N-formylmethionine)

Initiator amino acid coded by the start codon AUG in bacteria; typically N-formylmethionine in protein synthesis.

Consensus sequence

Typical promoter sequences recognized by a sigma factor (e.g., -35 TTGACA and -10 TATAAT for sigma-70); variations exist with different sigma factors.

Sigma factor diversity

Different sigma factors recognize different promoter sequences, enabling regulation of transcription in response to conditions.

Promoter strength

Relative efficiency with which a promoter is recognized by RNA polymerase; influences transcription level.