15 | Transcription Flashcards
Transcription
The enzymatic production of an exact complementary strand of RNA upon a DNA template
Discrete Steps of Transcription
(1) Binding
(2) Formation
(3) Initiation
(4) Elongation
(5) Termination (& Recycling)
mRNA
(Messenger RNA)
Encode the amino acid sequence of one or more polypeptides specified by a gene or a set of genes
tRNA
(Transfer RNA)
Read information encoded in mRNA and provide the appropriate amino acid to a growing polypeptide chain during protein synthesis
rRNA
(Ribosomal RNA)
Constituents of ribosomes, the intricate cellular machines of protein synthesis
RNA Polymerase
Specialized enzymes that catalyze transcription in cells and viruses
How does RNA transcription differ from DNA replication?
(1) No primer required to begin
(2) Involves sections not entirety of DNA
(3) Only one strand serves as template
Transcriptome
Entire set of transcripts within a cell
RNA polymerase core
Subunits of the enzyme necessary to catalyze a reaction carried out by a polymerase
sigma (σ) factor
Transient subunit of RNA polymerase that direct enzyme to specific site upon DNA
E.coli RNA Polymerase Structure
Five polypeptide subunits:
β’ / β / α (2-copies) / ω
RNA polymerase holoenzyme
The six subunits of the polymerase core plus the sigma factor
RNA Polymerase I
Transcribes genes encoding large rRNA precursors
RNA Polymerase II
Encodes nearly all protein-coding genes to make mRNA
RNA Polymerase III
Transcribes genes encoding smaller functional RNAs (tRNA, snRNA, 5S rRNA)
How were the structure of bacterial and yeast RNA polymerases determined?
Via x-ray crystallography
Initiation
When RNA polymerase binds to specific sequence on DNA
Promoter
Specific sequence on DNA at which initiation occurs
Elongation
Addition of nucleotides to growing RNA strand
Termination
Release of product RNA when polymerase reaches end of gene
Template strand
Complement of the coding strand
Coding strand
Identical in nucleotide sequence to the RNA transcribed on the gene
Closed complex
Formed during first step of transcription when polymerase binds the promoter and DNA remains intact
Open complex
Formed during the second step of transcription when the bound DNA is partially unwound ~10bp upstream from the transcription start site
Initiation
Conformational change in transcriptional complex occurs that is required for elongation to take place
Promoter clearance
Movement of transcription complex away from promoter
Elongation complex
End result of promoter clearance.
Tightly bound, highly efficient transcript synthesis complex
Why is RNA synthesis processive?
Once elongation begins the kinetics of the polymerization reaction favor the addition of a nucleotide over the premature release of the transcript
Actinomycines
A class of polypeptide antibiotics isolated from soil bacteria of the genus Streptomyces.
(e.g. Actinomycin D, Acridine, Rifampicin)
Actinomycin D Mechanism of Action
Inhibits transcription elongation by RNA polymerase
α-amanitin
Naturally bio-defense antibiotic of a mushroom
RNA polymerase binds to the DNA of E. coli within what range?
A 100bp range between ~70bp before start site to ~30bp after
σ70
The most common sigma factor in E.coli
Consensus sequence
Sequence of nucleotides statistically determined to be most commonly found at a particular position on DNA.
Critical in the identification of promoter regions.
Upstream promoter (UP) element
AT-rich recognition element found between -40 and -60 of the promoters in certain highly expressed genes
Abortive initiation
When, within the first 8-10 phosphodiester bonds, a transcript is released prior to completion and the assembled polymerase holoenzyme begins RNA synthesis upon the same template again.
Pyrophosporolysis
Reverse polymerization reaction
Kinetic proofreading
Catalytic, accuracy ensuring result of stalling by polymerase during transcription
Nucleolytic proofreading
Hydrolytic, accuracy ensuring nuclease activity inherent to RNA polymerase
Termination sequence
Occurs when transcription stops at a certain sequence and the haloenzyme disassociates from the DNA template.
ρ-dependent
Termination of transcription at the “rut”: a CA-rich sequence
ρ-independent
Termination involving a hair-pin loop followed a sequence of A-U interactions
TBP
(TATA-binding protein)
A transcription factor shared by all eukaryotic RNA polymerases that binds to the “TATA” box at initiation
Preinitiation complex
Association of transcription factors, promoter DNA and Poly I
Steps of Transcription at Poly II promoters
(1) Recruitment
(2) Formation
(3) Phosphorylation
(4) Elongation
(5) Dephosphorylation [termination]
Mediator complex
Multi-protein that acts as intermediary between specific transcription factors as a coactivator.
aka: Transcriptional Coactivator
Keys of Eukaryotic Transcription
(1) Takes place in nucleus
(2) Three RNA-polymerases recognize three sets of promoters
(3) Additional proteins required for promoter recognition
(4) Transcripts require processing (removal of RNA seq.) to make a mature product (final product)
