DNA to RNA synthesis Flashcards
Which way are strands read/synthesized
read 3’ to 5’, sun 5’ to 3’-ASK SOMEONE
RNA polymerase structure
5 subunits with sigma cofactor at top, reads with sequence specificity, not gene specificity-holoenzyme
template strand vs coding strand
coding strand is nontemplate
initiation
holoenzyme bindsto promoter
RNAP begins RNA synthesis
Sigma/promoter dependent
Principal start site for trx
Elongation
Lengthens transcript by addition of nucleotides to 3 end of
RNA located in active site of RNA pol II.
Sigma dissociates from RNAP and promoter.
Termination
RNA synthesis stops
Release of RNA Transcript
Dissociation of RNAP from the DNA template
Depends of DNA-encoded, RNA signals
Structure of bac promoter
tss, 7bp, pribnow box, 19bp, ~35 sequence
pribnow and 35 sequence are recognized by holoenzyme
rho dependent termnation
rho follows behind polymerase and when it catches termination occurs-uses ATP
Rho independent term
Creates stem loop that pinches off polymerase, this mechanism is encoded in DNA
RNA poly subunits
two beta are the pincers for the claws, alpha and omega are structural
Rifampicin
binds to bacterial polymerase and inhibits (tuberculosis)
Euk vs Prok polymerases
Pro only has one polymerase-has many different sigma factors though
DNA sequence elements
Promoter (where RNA polymerase binds)-TATA box-DS seq-just after the TSS
Proximal Promoer (CpG islands) (where regulatory/housekeepings proteins bind)-cell metabolism-roughly 120 bps upstream TSS
Enhancer-way upstream- DS sea-regulatory proteins
Pol II
Can have more promoters downstream
Pol II Core Promoter Elements
BRE-TFIIB Recognition Element
TATA Box-Binds TBP
INR-Initiator
DPE-downstream promoter element binding site
TFIID
TBP +14 other factors-nucleates assembly of trx pre initiation complex
Different factors of TFIID bind to other locations (TATA, INR, DPE)
Most responsible for recognition site where RNA Pol II should bind
RNA Pol II vs Prok RNA poly
Bigger and more complicated-no sigma factor in Euk
TFIIH
Helicase activity
How does pol II know where to go
Bunch of promoters are recognized by proteins
GTFs
analgous to sigma factor
euk promoter with different sequence elements that recognize where to place Pol 2
5’ cap
7-methylguanosine
Added as soon as part leaves pol 2
5’ to 5’ triphosphate linkage
ONLY IN EUKS-proks have coupled trx/trans so no need to protect
Poly A tail
Only in EUKS
Not encoded in DNA
Uses ATP
Similarities between Rep and Trx
- DNA template-dependent
- Chemical mechanism 3’OH attacks alpha phosphate of NTP
- 5’ to 3’ synthesis
- Energy requirement from NTP or dNTP substrates
Dif between Rep and Trx
- no primer requirement
- trx utilizes small segments of DNA (genes)
- only one of two strands serve as template in try
- trx is conservative, replication is semi conservative
- NTP and UTP is trx, dNTP and DTTP in replication
Dif between euk and pro try
- 1 poly vs 3
- sigma factor binds to promoter as subunit or RNA Poly, TFIID (TBP) binds to promoter and TBP, TFIIB, TFIIF bind RNA poly 2
- core and reg are close vs far
- Polycistronic vs monocistronic transcripts
- COupled vs uncouped trx/trans
- No histones vs histones
RNA poly
TBP binds to promoter, then TFIIB, TFIIF bind, whole thing is called TFIID
Mono vs polycistronic
1 gene in mRNA vs multiple genes in mRNA
alpha-amanitin
bind to RNA pol II and inhibits trx, mushroom toxin
FEN1
5’ end removal
Okazaki-rna primer off
