Lec.13: Bacterial Transcription

Gene-Specific Transcription

Process where only specific DNA genes within the genome are transcribed into RNA rather than copying the entire genome at once

Template Strand

The 3' to 5' DNA strand read directly by RNA polymerase to synthesize a complementary RNA transcript

Coding Strand

The 5' to 3' non-template DNA strand with the same sequence as the RNA product except thymine is replaced by uracil

Direction of RNA Synthesis

Occurs exclusively in the 5' to 3' direction

Messenger RNA (mRNA)

Transcripts that serve as coding templates translated into polypeptide chains

Transfer RNA (tRNA)

Small structural RNAs featuring a conserved 3'-CCA acceptor terminus that deliver specific amino acids to ribosomes during translation

16S rRNA

Ribosomal RNA component of the small 30S subunit that base-pairs with the Shine-Dalgarno sequence during translation initiation

23S and 5S rRNA

Ribosomal RNA components that form structural and catalytic parts of the large 50S subunit

Bacterial Transcription Rate

Synthesis of RNA by RNA polymerase at a rate of 40 nucleotides per second at 37 degrees Celsius in E. coli

Transcription Bubble

A temporary localized 12 -20 bp unwound DNA region where RNA polymerase copies a single RNA transcript before DNA re-anneals

Transcription Bubble vs Replication Fork

A transcription bubble is a localized temporary unwinding producing a single RNA transcript while a replication fork generates two double-stranded DNA daughter molecules

RNA Sugar Structure

Contains ribose with a 2'-hydroxyl group unlike the 2'-deoxyribose in DNA

RNA Nitrogenous Bases

Uses adenine cytosine guanine and uracil with A-U forming 2 hydrogen bonds and C-G forming 3 hydrogen bonds

Stem-Loop Hairpin Structure

Secondary RNA structure formed when single-stranded RNA folds back on itself with base-paired stems and unpaired loops

3'-CCA Terminus

Conserved sequence at the 3' acceptor arm of all functional tRNAs where amino acids are covalently attached

Promoter -35 Region

Consensus sequence TTGACA recognized by RNA polymerase for transcription initiation

Promoter -10 Region

Consensus sequence TATAAT or Pribnow box where RNA polymerase binds and unwinds DNA to form an open complex

+1 Transcription Start Site

The exact nucleotide position where RNA polymerase initiates RNA synthesis

5' Triphosphate Retention

The first ribonucleotide incorporated at the +1 position retains its 5'-triphosphate group because it is not linked to an upstream nucleotide

Leader Region

Transcribed untranslated mRNA sequence preceding the coding region that contains the Shine-Dalgarno sequence

Shine-Dalgarno Sequence

Ribosome binding site located in the mRNA leader region that base-pairs with 16S rRNA to align the ribosome over the AUG start codon

Coding Region

Transcribed mRNA region starting at an AUG initiation codon and ending at a nonsense stop codon

Nonsense Stop Codons

The three codons UAA UAG and UGA that signal translation termination

Rho-Independent Termination

Intrinsic termination mechanism triggered by a GC-rich stem-loop hairpin followed immediately by a poly-U tract that causes RNA polymerase to stall and dissociate

Poly-U Tract Function

Weak A-U hydrogen bonding between the RNA poly-U tract and DNA poly-A template that destabilizes the transcription complex

Rho Factor

An accessory protein with RNA/DNA helicase activity that unwinds the RNA-DNA hybrid to terminate transcription

Rho-Dependent Termination

Mechanism where Rho helicase binds mRNA travels 5' to 3' and unwinds the RNA-DNA hybrid when RNA polymerase stalls at a terminator hairpin

Christmas Tree Structure

Electron microscopy visual of active rRNA transcription with central DNA trunk and emerging RNA branches increasing in length from promoter to terminator

Compact rRNA Branching

Phenomenon where emerging rRNA branches appear short because newly synthesized rRNA rapidly folds into compact tertiary stem-loop structures

Polycistronic mRNA

A single bacterial mRNA transcript controlled by one promoter that codes for multiple distinct functional proteins

Operon

A cluster of bacterial genes controlled by a single promoter encoding enzymes of the same metabolic pathway

Intergenic Spacer Regions

Non-coding sequences separating cistrons on polycistronic mRNA that each contain a Shine-Dalgarno sequence for independent translation

Coupled Transcription and Translation

Simultaneous transcription and translation occurring in the bacterial cytoplasm due to the absence of a nuclear membrane

Polysome (Polyribosome)

An array of multiple ribosomes spaced about 80 nucleotides apart translating a single mRNA simultaneously from N-terminus to C-terminus

Direction of Translation

mRNA is read 5' to 3' and polypeptides are synthesized from the N-terminus to the C-terminus

Translational Rate in E. coli

Ribosomes synthesize 15 amino acids per second corresponding to 900 residues per minute

Initiator tRNA

Specialized tRNA loaded with N-formylmethionine (fMet) that recognizes the AUG start codon in bacteria

Specialized enzymes that covalently attach specific amino acids to the 3'-CCA acceptor end of their corresponding tRNAs

Aminoacyl-tRNA Synthetases