02/13 transcription Flashcards
which strand is complementary to the mRNA transcript
the template strand
which strand matches the nucleotide sequence to the mRNA transcript
the coding strand
what are the general steps of initiation
The promoter is the recognition site for transcription factors that will bind with RNA po and form a closed promoter complex. This will later get opened to form an open promoter complex
what are the two main types of genes
structural- code for protein
non-structural- code for RNA type
how do transcription factors know when and where to bind
there are specific regulatory sequences that they “feel by braille” to and bind
which direction is downstream of a gene?
it is in the direction of the MRNA
what direction is upstream of a gene
it is away from the mRNA, these are generally regions where the promoter exists
for regions upstream of the +1 base, are they transcribed
no, these are not
is the first base in the mRNA transcript the start codon?
no, it is the 5’ UTR
is the promoter within the 5’ UTR region?
no it is not transcribed at all
what is the purpose of the -10 and -35 regions of the promoter
these are regions that reside within the major groove of the DNA, this is where transcription factor proteins will bind
what is a consensus sequence
A sequence with the most commonly occurring bases, they are essentially flexible recognition sequences
how do variations in the consensus sequence play a role?
they can affect the rate of RNA transcription
what is the sigma factor’s role?
it associates with RNA polymerase and scans the DNA for the consensus sequence of the promoter
at this consensus, it will synthesize a short spurt of RNA and then get released
how does RNA polymerase open the strand
it has a “helicase-like” activity and can break bonds
what is the primary difference between a DNA polymerase and an RNA polymerase
RNA polymerases do not require a primer to begin
does RNA polymerase have proofreading
no
what is rho dependent termination
it is a method of termination in bacteria
it requires the rho protein and a stem loop structure
what is rho independent termination
it is a method of termination in bacteria
it does not require rho protein but requires a stem loop and a U rich region
what do rho dependent and independent termination both depend on?
they depend on stem loop structures
what is a stem loop
it is a intramolecular secondary structure with complementary regions that form a loop
Describe the mechanism of rho dependent termination
rho protein recognizes its recognition sequence and binds to the RNA strand
the RNA polymerase is paused by the formation of a stem loop and the rho protein can catch up and dislodge it from the RNA transcript
without the formation of the stem loop, what would happen to the RNA polymerase
it wouldn’t know to stop and would continue transcribing
describe the mechanism of rho independent termination
it is facilitated by an allosteric binding site
another protein will bind to this site and cause the RNA polymerase to change shape and fall off of the template
why does the mechanism of rho independent termination have to be U rich?
if it is U rich, there will be a loose interaction between the template and polymerase
how do eukaryotes differ in terms of polymerases to prokaryotes
eukaryotes have more specialized types of polymerases
what is the core promoter
it is found in eukaryotes and includes the TATA box which determines the start point of transcription
what are regulatory elements
they are sequences that influence gene transcription
what is a constitutive gene
it is a gene that is always on
what is a facultative gene
it is a gene that oscillate between being on and off
what are enhancers
they are regulatory elements that stimulate transcription
what are silencers
they are regulatory elements that inhibit transcription
how can regulatory elements act on promoters that are far away?
through the use of radial loops which brings the regions closer
What are cis acting elements
they are DNA sequences that only affect nearby genes
What is a trans-acting element
they are regulatory proteins that bind to DNA sequences from any region
what is the role of TFIID
it binds to the TATA promoter by seeking out an AT rich area
how is TFIID different from the sigma binding protein in prokaryotes
the sigma binding protein travels down WITH the RNA polymerase to locate the promoter while TFIID acts alone and signals the other proteins when it finds the promoter
what is the role of TFIIH (2)
It has helicase activity that opens the complex
it phosphorylates the RNA polymerase, which gives it a negative charge and changes its structure via a covalent attachment of a phosphate group. This activates the RNA polymerase
what is the basal transcription apparatus comprised of
RNA pol II and 5 GTFS (general transcription factors)
what are GTFs
they are transcription factors necessary for all RNA transcription
What are STFs
they are specific transcription factors that bind to enhancers/ silencers that are specific to the gene
what is the primary 2 roles of a mediator protein
it acts to bridge signals and mediate interactions between STFs and RNA pol II
it also aids in TFIIH’s ability to phosphorylate RNA pol II
describe the role of the poly A sequence in eukaryotic termination
when the RNA polymerase moves downstream of the poly A sequence, it gets cleaved off by endonuclease activity, which separates the two RNA strands
What is the torpedo model of termination
an exonuclease enzyme degrades the remaining RNA in the 5’-3’ direction until it catches up to RNA polymerase and dislodges it
how is the torpedo model similar to rho dependent termination? how is it different?
it is similar since an enzyme follows the RNA polymerase and dislodges it
it is different since rho does NOT degrade the remaining RNA and it requires a stem loop
what is the allosteric model of termination
termination factors bind the the RNA polymerase and dislodges it
what termination process is the allosteric model of termination similar to?
it is similar to the rho independent model as they both involve the use of the allosteric binding site and termination by RNA polymerase dislodging
what is a key difference between eukaryotic and prokaryotic termination of transcription
the prokaryotic termination requires the use of a stem loop while the eukaryotic does not
when does the poly A tail get added
in post transcription
what does the pre-mRNA contain
start codon, introns, exons, stop codon
what does the pre-mRNA not contain
guanine cap, poly A tail, promoter
what are the three things that occur in post transcriptional processing
splicing of introns
addition of poly A tail
addition of guanine cap
true or false, nonstructural genes do not require post transcriptional processing
false, RNAs still need to undergo processing and splicing
describe RNA processing
nonstructural genes are often transcribed into larger RNA fragments and are then spliced by ribozymes to form smaller functional pieces
what is a ribozyme
it is an RNA that contains catalytic activity
what type of nuclease activity is used in RNA processing
endonuclease activity to internally cut the larger RNA
what are covalently modified bases
they are post-transcriptional modifications of RNA molecules
what does it mean when a bacteria has colinearity of gene expression
bacteria do not require additional processing steps as the coding strand directly codes for the mRNA sequence and the mRNA transcript directly codes for the polypeptide amino acid sequence
what are exons? introns?
exons are the codings sequences of the mRNA
introns are the intervening sequences that disrupt the exons and need to be spliced out
why does the nucleus play an important role in the transcription to translation pipeline in eukaryotes
the nucleus has a nuclear envelope that gives time for the mRNA transcript to be modified
bacteria cannot do this as they are immediate;y translated
what are the two types of introns?
self splicing and spliceosomes
what is the key difference between self-splicing and spliceosome introns
self-splicing introns will splice the same time everytime and do not require help from other proteins
spliceosomes can cut differently and perform alternative splicing
what is a spliceosome comprised of
it is comprised of RNA and protein (snRNPs)
what type of activity do both self splicing introns and spliceosome introns have?
they both have ribozyme activity
why is it important that not every cell has the same type of spliceosome
different spliceosomes will cut the mRNA in different ways, this will result in a different RNA strand which will code for different types of polypeptides
What is the role of RNaseP
it is an ribozyme endonuclease that cuts the tRNA in post transcriptional modifications
