Transcription Flashcards
Creation of complementary mRNA sequences from short strands of DNA
Transcription
Which strand of DNA is transcribed and in what direction
Template strand; 5’ to 3’
3 major components need in transcription
- a DNA template
- Raw materials or substrates for RNA
- Transcription apparatus consisting of enzymes to catalyze RNA synthesis
Transcription starts when enzymes recognize the _________ and ends at the _________. In between is the ______ of the gene which is copied into an RNA molecule
Promoter region; Terminator region; RNA-coding region
In terms of direction, upstream refers to the what end of the DNA
5’-end
The mRNA is complementary and antiparallel to the ____ strand
Template
Bacterial RNA polymerase has _ alpha, _ beta, _beta prime, and _ omega
2,1,1,1
It joins and leaves the core enzymes as it is needed forming a holoenzyme. It recognizes a specific promoter region for every particular gene
Sigma factor
_______ are antibiotics that target bacterial RNA polymerases. Commonly used as cures against______
Rifamycins; Tubercolosis
True or False: An RNA polymerase without a sigma factor will not bind to any part of the genome
False
Define the mechanistic action of rifamycin
Binds to the part where the RNA polymerase should bind to the DNA
Enumerate the phases of transcription
- Initiation phase
- Elongation Phase
- Termination Phase
Enumerate the phases of initiation
-Promoter recognition
-Formation of the transcription bubble
-Creation of first bonds between rNTPs
-Escape of transcription apparatus from the promoter
Promoters have different affinities for RNA polymerase. Give a consequence/advantage of these differences
These differences lead to variations on frequency and prioritization of expression of genes.
Are short sequences of considerable similarity found in promoter regions
Consensus sequence
The most common consensus sequence in prokaryotes
Pribnow box or -10 consensus sequence
Give an example of a specific sequence in Pribnow box/ -10 consensus sequence
TATAAT
True or False: Pribnow box is always TATAAT
False
A consensus sequence in prokaryotes that control the rate of transcription
-35 consensus sequence
Difference between down mutation and up mutation
Rate of transcription (Down= Reduce, Up=Increase)
Unwinding of gene beings at the ___ consensus sequence and extends downstream covering ___ to ___ sites
-10; -12: +12
How much nucleotides are transcribed as initial abortive attempts before proceeding to the elongation phase?
2-6 nucleotides
True or False: During elongation, the sigma subunit should always be released regardless of the type of RNA
False; Should be either depending on the type of RNA
During elongation phase, the leading edge is found in what direction. In what direction does the trailing edge found?
Downstream= Leading edge
Upstream= Trailing edge
Which is faster, the transcription of bacteria or eukaryotes? Describe the magnitude of their difference
Eukaryotes are faster having 1000-2000 nucleotides per second while prokaryotes have 40 nucleotides per second
In Elongation phase, it is around 18 nucleotides in length of unwound DNA where the mRNA is continuously synthesized
Transcription bubble
Negative supercoiling is found upstream of downstream?
Upstream
Enzyme that relieves the stress associated with unwinding and rewinding of DNA
Topoisomerase
True or False. Termination phase is an abrupt stop
False
Enumerate the process of termination phase
-RNA polymerase stops synthesizing RNA
-RNA molecules is released from RNA polymerase
-Newly made RNA dissociates from the DNA
-The RNA polymerase detaches from DNA
Enumerate the process of Rho-dependent termination
-Rho protein binds to the binding site of the unstructured RNA and moves toward its 3’-end
-Rho protein has helicase activity that unwinds RNA-DNA hybrid in the transcription bubble
The RNA polymerase pauses when it encounters the terminator site, then the rho protein to catches up
Type of terminators in prokaryotes that contains inverted repeats that form hairpins when transcribed into mRNA
Rho-independent terminators
Explain the process of Rho-independent terminators
-Inverted repeats are followed by 7-9 A positions that convert to a string of U
-The hairpins serve as blocks to destabilize the DNA-RNA pairings
-The weak A-U string pairing facilitates the separation of DNA and RNA
Polycistronic mRNA is common in _____ while monocistronic is common in _______
Prokaryotes; Eukaryotes
Define the functions of the following bacterial RNA polymerase:
-RNA Polymerase I
-RNA Polymerase II
-RNA Polymerase III
-RNA polymerase IV and V
-For RNA transcription
-For transcribing pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs
-Transcribing other small RNA molecules (tRNAs, small rRNA, and some miRNAs and snRNAs)
-Transcribe RNAs that play roles in DNA methylation and chromatic structure in plants
In Eukaryote Transcription, they assemble near the start site of a gene to initiate minimal levels of transcription together with the RNA polymerase
General Transcription Factors
This is the combination of general transcription factor and RNA polymerase in eukaryote transcription
Transcriptional Activator Apparatus
In eukaryote transcription, this stimulates formation of the basal transcription apparatus at the start site of a gene
Transcriptional Activator Proteins
In eukaryote transcription, this is where the basal transcription apparatus binds and located upstream of the gene
Core promoter
In eukaryote transcription, it is composed of TATAAA and is found -25 to -30bp upstream of the start site
TATA box
in eukaryote transcription, these are located immediately upstream to core promoters and where transcriptional activator proteins binds. These mostly affect rate of transcription
Regulatory Promoters
More distant upstream sequences in eukaryote transcription; These sites often loop out so that these can directly connect to the basal activator protein at the core promoter
Enhancers
Where do the protein complex attach?
Basal Transcription Apparatus:
Transcriptional Activator Proteins:
Basal Transcription Apparatus: Core promoters
Transcriptional Activator Proteins: Regulatory promoters and Enhancers
Sigma factor of prokaryotes is what of eukaryotes?
Transcription factors
What trasncription factor recognizes the TATA box with its TATA-binding protein?
TFIID
In eukaryote transcription, this is formed when the single-stranded DNA is positioned within the active site of the RNA polymerase
Open complex
Elongation starts at ___bp from the start site when the transcription factors separate for re-use in other transcription events
30bp
True or False. RNA Polymerase I in Eukaryote Transcription is similar to rho-dependent termination in Bacteria
True
In RNA polymerase I termination, it requires a _________ but it binds to a sequence ________ of the stop site
Termination Factor; Downstream
True or False. RNA Polymerase III termination is similar to the Rho-dependent termination in bacteria
False
Difference between RNA polymerase III and the Rho-independent termination of Bacteria
Lack of hairpin structure after string of U
Describe the series of event in RNA polymerase II termination
-Transcription continues well beyond the termination site producing a pre-mRNA
-The pre-mRNA is cleaved at a consensus site which separates from the excess non-coding part by the Rat1
-Rat 1 proceeds to degrade until it reaches the transcription machinery
Archaea RNA polymerase recognizes TATA-box using what transcription factor?
TFIIB
