Transcription and RNA Processing Flashcards
Lectures 4-7
what are the differences between DNA and RNA?
URACIL
RNA has a ribose sugar (-OH group on 2’ C)
RNA has a tertiary structure, since it is single stranded (ex. tRNAs) and quaternary structure (functional units in the ribosome)
REMEMBER: if I had to pick between DNA and RNA, I would pick RNA since it has U in it
which nucleotide is PROMISCUOUS?
GUNANINE
pairs with C and U
REMEMBER: promiscuous Girl (begins with G)
which molecule is more stable, DNA or RNA?
DNA
what are some basic features of RNA?
unstable
easier to regulate
not segregated to nucleus
evolved first
can have many conformations
what are the types of RNA?
coding: mRNA
noncoding: tRNA, rRNA
how is RNA synthesized?
TRANSCRIPTION
5’ to 3’ direction, using 3’ to 5’ DNA template
complementary and antiparallel to DNA template
RNA strand wil MATCH noncoding strand
how is an rNTP added to the strand?
two phosphates cleaved off INCOMING rNTP, attaches to the 3’ OH group of the last rNTP in strand
nucleophilic attack
ALWAYS synthesized 5’ to 3’
what the subunits of the RNA holoenzyme?
alpha –> assembly of tetrameric core
beta –> rNTP bonding site
beta prime –> DNA template binding region
omega –> stabilize tertameric core
sigma –> binds to RNA polymerase tertrameric core and assists in correct initiation of transcription
PROKARYOTES
REMEBER: B - Beta - Binding site
what does the sigma factor bind to?
-35 and -10 consensus sequences
properly positions RNA polymerase to begin transcription
describe initiation in prokaryotes
once the holoenzyme is bound to the promoter, RNA polymerase is positioned over the transcription start site
unwinds DNA
NO PRIMER needed
describe elongation in prokaryotes
sigma factor released
rNTPs added 5’ to 3’ by RNA polymerase
transcription bubble moves with RNA polymerase and unwound DNA rewinds behind it
describe TERMINATION in prokaryotes
RNA polymerase reaches terminator region
upstream of where termination will take place
newly synthesized RNA and RNA polymerase released
can be rho dependent or independent
describe RHO DEPENDENT termination
rho binds to the RUT site (C-rich) and moves towards 3’ end of RNA
RNA polymerase encounters termination sequence and pauses, rho catches up
rho unwinds DNA-RNA hybrid and terminates transcription
describe RHO INDEPENDENT termination
2 common features: inverted repeates, 6-9 As
string of Us cause RNA polymerase to pause and the inverted repeats fold into a hairpin
DNA-RNA pairing is destabilized
separates from template, terminating sequence
how many RNA polymerases do eukaryotes have?
at least THREE
plants have FIVE
for reference: prokaryotes have 1
describe the elements of the mRNA stand during INITIATION in EUKARYOTES
-35 consensus sequence, -25 consensus sequence, +1 initiator element, +30 core-promotor element
regulatory promotor up to 100 NT upstream
describe the proteins involved in INITIATION in EUKARYOTES
TFII A, B, D, E, F, H
TFIID contains TATA BP and assembles to TATA box, followed by the rest of the TFs and RNA polymerase II
TFs bind to ENHANCER (upstream)
TFs bind to promotor forming PREINITIATION COMPLEX –> initiates basal transcription
MEDIATOR permits interactions with activator/repressor proteins
describe ELONGATION is EUKARYOTES
POLYMERASE II moves along template strand
TFs stay at promotor
DNA enters polymerase downstream through a CLEFT, BENDS at a 90 degree angle and separates
template strand enters pore
rNTPs added to 3’ end of chain
synthesized 5’ to 3’
RNA is separated from DNA through another cleft
what does it mean if two amino acids are COLINEAR?
in prokaryotes, the coding region of a gene is uninterrupted
number of NUCLEOTIDES is proportional to the number of AMINO ACIDS (3:1)
what are the primary regions in mature prokaryotic mRNA?
5’ untranslated region –> does not code for AAs, binds to ribsomal complex
shine-dalgarno sequence
protein coding region –> begins with start codon, ends with stop codon
3’ UTR –> does not code for AAs, affects stability of the mRNA and regulates translation
when does translation happen in prokaryotes?
simultaneously to transcription (no processing in between)
what modifications are made to eukaryotic pre-mRNA?
removal of introns
addition of 5’ cap
addition of poly A tail
where are introns spliced? by what?
in the nucleus, by splicosomes
the order of exons is always kept in mature mRNA
what are introns?
influence how genes are expressed
present in eukaryotic DNA
can have self splicing capabilities
removed from pre-mRNA
