RNA processing Flashcards
RNA synthesis initiation
uses RNA pol 2, a large complex comprised of multiple subunits
the initiation requires the sigma co enzyme along side all the other core subunits. sigma decreases the affininity the complex has for DNA allowing it to glide along to locate the TATA box.
What are the sub units of pol2 core
alpha-
beta- cata of RNA
beta’- binds to the DNA
gamma- needed to restore the activity of the denatured enzyme
RNA elongation
rna pol will read the template in a 3-5 but the RNA is sythed in the 5-3.
The 3’OH of the last attached NTP will act as a nuc and attack the inner most PO4. this will hydrolysed the NTP and create a phosphate bridge.
what is the role of the MG+ in the pol2?
to help stabilize the charge of the oxygen.
RNA termination.
my occur intrinsically or through the presence of another protein.
intrinsic= formation of the hairpin loop, followed by a string of Us. this causes pol2 to pause and will eventually fall off
the roh protein will rec a sequence of the RNA strand, attach to it, and travel up the strand to know RNA pol off.
how does RNA pol 2 know where to start and stop transcription
by the use of cis acting element. these factors re conserved sequences in the DNA strands, and when they are coded they act as binding sites for transcription factors.
what are common cis acting elements
TATA box w/ The transcription start site
DEP 9downstream promoter element
enhancer site which can be wayyy upstream for the initiator elements
CAAt and box for the cis-acting elements
what is the preinitiation complex
a complex of subunits that assembles to signal for the RNA pol 2 to come.
TFIID binds to the TBP (tata binding protein)
this little unit summons TFIIH, the POl2 and helicase to come and pry the DNA strand open AND phosphorylates in C terminus of the POL2. the phosphorylation triggers the recruitment of the processing enzymes for editing.
how do TF regulate the process of transcription
PIC is able to regulate at low []
in most cases though, many TF will need to assemble to make a lrg enough impact. this is called combinatorial control
how is the 5’ cap added
the RNA 5’ end will have a NTP attached. phospphatatse will removed a phos
the generate 5” NDP will attach the phosphate of a GTP.
the GTP unit is phosphorylated and is added as a GMP unit to the 5’ end by guanylyltransfease.
this 5’Gppp5’A… is methylates at the N7 location by guanylmethyltrasnferase.
this protect degradation of the RNA by nucleases (exonuc)
how is the poly A tail added
the protein CPSF recognizes a conserved RNA sequence AAUAAA and an endonuc will make a cut 30bp downstream from the signal. a polymerase will then add about 250 A via ATP hydrolysis.
which sequences are used un RNA splicing
start= GU
end= AG
what is a splicesome
is a unit sompirsed of RNA and proteins
how is RNA spliced
an 2’OH grup will nuc attack the G phosphate bridge of the 5’ GU splice site, exposing a 3’ OH group. This forms a 2’-5’ ester linkage, displacing the exon from the RNA unit. The free 3’OH group will then attach the 5’ G phosphate of the 3’ AG splice site, forming yet another ester linkage between the 2 exons.
these are called transesterification reactions
what are transesterification reactions?
the splicing of pre mRNA by the splicesome, by forming ester linings between exons and exons and intron and introns.
how does the presence of inosine contribute to degeneracy?
inosine is able to bp with A, C or U. The presence of I in the third location allows for many codons to code for the same AA
what does aminoacyl -tRNA synthase do?
catalyzes the charging of tRNA moles. AA is attached to the corresponding tRNA vis adenylation. this is accomplished by the COO- unit on the AA attacks the internal PO4 ATP. this forms a high E ester bond that is esilty cleaved. the3’ OH group on the CCA arm attacks the AA and breaks the ester bond.
how do aminoacyl-tRNA transferases achieve specificity
They contain co-enzymes which interact with the side chain residues of a particular AA. if the AA is not a perfect match, it will either not fit or be slightly too small (or miss a critical component) to which the CCA arm will swing the AA from the Acitve site into the editing site where it is removed.
aminoacyl-tRNA specificity example
how is inosine formed
the deamination of adenine
what is another term used for degeneracy
wobble
what are the charged intermediates used in translation
aminoacyl- tRNA
what is adenylation
the addition of an AMP unit via hydrolysis. this actives the AA and promotes the transfer of the AA to the corresponding tRNA
