Mid-term Flashcards
Transcription Definition
The process by which regions of DNA are copied into RNA molecules
What are Cis-Acting elements
features embedded in the DNA that regulate transcription
What are some examples of cis-acting elements
promoters, regulatory sequences, terminator
What are trans-acting elements
features that bind to the cis-acting element of a gene to control its expression
what are some examples of trans-acting elements
RNA polymerase, transcription factors, gene regulatory proteins.
What direction is the template strand read
3’ to 5’
What direction are transcripts made in
5’ to 3’
What is the non-coding strand
The template strand used for transcription
What is the coding strand
the non-template strand is the coding because it is almost identical to RNA
RNA polymerase definition
catalyzes phosphodiester bond between NTPS
What are some differences between prokaryotic transcription and eukaryotic transcription
prokaryotes have no membrane-bound organelles (aka no nucleus), circular genome, transcription and translation occur at the same time, there are no post transcriptional modifications like introns, extrons, 5’ cap, or poly-a tail
What is the holoenzyme
core enzyme + sigma factor
What is the core enzyme
No sigma factor
What is the sigma factor
a specificity factor that tells the polymerase which strand to use.
How did we figure out the purpose of sigma factor
core enzyme created double-stranded RNA by using both strands of DNA as a template. Holoenzyme only created one strand of RNA
Why is the sigma important for initiation of transcription
it recognizes the promoter at the -10 and -35 box, weakly binds to the double stranded DNA, then binds strongly to the single stranded DNA
How does sigma recognize the promoter
at the -35 and -10 box. there is always a conserved TT at the -35 box.
After sigma binds to the promoter, what happens?
The RNA polymerase moves to the right elongating the RNA and sigma dissociates. It can now rejoin with a different core, thereby creating another holoenzyme
How can sigma factors change in response to the different needs of the cell
There are multiple sigma factors and they each have different sequence specificities for promoters so they can bind to different promoters. The -10 and -35 box are still important for all sigma factors.
How does prokaryotic transcription terminate
Via Rho-independent or Rho-dependent termination
Explain Rho-independent termination
There is an inverted repeat in DNA followed by string of A residues that creates a hairpin structure. This structure helps pull apart the weak dA-rU interaction and RNA polymerase falls off
Explain Rho-dependent termination
RNA is thought to be threaded through Rho center and then when the polymerase stalls at the termination signal, Rho may break apart the DNA-RNA interaction
What is Rho
a protein that reduces ability of RNA polymerase to transcribe
Operon
a group of genes involved in the same response pathway that are regulated together
How are operons regulated
by specialized proteins (repressors) binding to specific DNA elements (operators)
Explain the lac operon with glucose only
LacI gene encodes the repressor monomer which binds to the operator blocking transcription
Explain the lac operon with lactose only
allolactase binds to the repressor tetramer which blocks the repressor from binding to the operator. cAMP-CAP which rises when glucose levels fall, helps the RNA polymerase bind to the promoter.
Explain the lac operon with glucose and lactose
only medium level of transcription of lac genes
What is the trp operon
codes for protein that the bacterium needs to make the amino acid tryptophan
Explain the trp operon with high tryptophan
trpR encodes the repressor. When tryptophan is bound to the repressor, it is able to interact with the operator and block it from transcribing but not 100%. There is an attenuator sequence that forms a stable hairpin causing ribosome to fall if transcription occurs.
Explain the trp operon with low tryptophan
trpR encodes the repressor but no tryptophan can activate the repressor so transcription occurs and forms an unstable hairpin and ribosome stalls.
Difference between operons and sigma factors
operons only control a handful of genes while alternative sigma factors change a lot more.
anti-sigma factors
proteins that can bind to sigma factors and control their activity
anti-anti sigma factors
promote sigma factors
What helps regulation of sigma factors
anti-sigma factors, anti-anti sigma factors, transcription factors (assist sigma factor recognition of promoter elements)
Difference between eukaryotic RNA polymerase II and prokaryotic polymerase II
eukaryotic polymerase cant recognize promoters without general transcription factors
What binds to the TATA box
TBP (TFIID)
What binds to BRE (B recognition element)
TFIIB
What is the purpose of the Inr
Together with TATA and BRE promotes basal transcription of any gene
what is the purpose of DCE
can replace TATA in TATA-less promoters
What is the order of binding
TFIID binds to DNA via TBP at TATA box, TFIIA stabilizes binding of TFIIB and TBP, TFIIB binds to BRE and recruits RNA polymerase, TFIIF binds polymerase II and TFIIB, TFIIE recruits TFIIH, TFIIH unwinds promoter DNA and phosphorylates C-terminal domain of polymerase
What are the two forms of RNA polymerase II
hypo-phosphorylated which can join the pre-initiation complex, hyper-phosphorylated which can mediate RNA synthesis initiation and elongation
What transcription factors remain at the promoter
TBP and TFIIB
What transcription factors remain at the promoter
TBP and TFIIB
What transcription factors remain at the promoter
TBP and TFIIB
What transcription factors that dissociate from the elongation complex
TFIIE and TFIIH
What are activators
bind upstream of the promoter
What are repressors
bind to silencers and inhibit transcription
what are co-activators
aid activators by serving as a bridge
How does acetylation of histones affect transcription
cause DNA to loosen up
HATs
writer enzymes, they add acetylation
HDACs
Eraser enzymes, that remove acetylation making DNA not active
What is the purpose of polyadenylation
stability / protection from degradation, translation, gene expression regulation
