l4 Flashcards
transcriptome
The sum of all RNA molecules produced by the genome machinery
● Prokaryotes only have 1 RNA polymerase complex
● Eukaryotes have 3 RNA polymerases + two organelle ones
rna polymerase
RNA is based on ribose
RNA synthesis has 3 phases (no primer needed)
● Initiation (most regulated)
● Elongation
● Termination
mrna
code for proteins
rrna
part of ribosome
trna
carries amino acids and puts the in right place for mrna and translates itno amino acid
frequent transcriptase
Frequent one used is a leukemia variant, RT needs a primer with an OH group,
the copy RT makes can be called copy DNA (cDNA)
rna poly where transcribe prokayotes?
● Subunits
1. 𝜶: Binds starting codon
2. 𝛽: Actually adds the nucleotides
3. 𝛽’: Binds the DNA template (so it doesn’t fall off)
4. ⍵: folds the 𝛽’ subunit
5. σ: Recognizes DNA promoter
● This subunit enables regulation of multiple gene sets.
● There are also anti-sigma factors that inactivate one or several
of them
● There are also anti-anti-sigma factors that can activate the
sigmas by inactivating the anti-sigma factors
intiations
● Ribosome subunit 30S binds to the DNA strand at the initiation codon
thanks to two factors
● Initiation factor 2 accompanies methionine to the start codon
● IF1, 2 and 3 unbind from the complex, allowing the 50S subunit to
associate
termination rho independant
Hair pin is made (on 5’ side)
● The hair pin slows down the RNA polymerase
● If paired with A=U rich DNA, the poly falls off
termination rho dependant
● RNA still makes hairpins, this calls a rho factor
● The rho factor forms a ring shaped translocase
● Threads the RNA along the ring, when it catches up to polymerase,
it “kills” it
rna ploly where dna transcribed eukaryotes?
rnap1, rnap3, rnap2
rnap 1
● Makes rRNA, which lies in the nucleus, transcribing genes, and
makes up ribosomes.
● rDNA is a lot of repeated sequences
rnap 3
● Makes tRNA, which needs to be spliced and matured after
transcribing DNA
● Also transcribes one type of rRNA genes
rnap 2
● Makes primary RNA (RNA not matured yet)
● TBP and “General transcription initiation factors” look for promoters
and help binding
enhancers
promote binding to promoter, but van be far away
transcription factors
influence inhancers, promoters and loops
introns
useless, non coidng
exons
coding
polyadenylate tail
aaaaaaaaaaaaaaaaaa is added to make sure its stable, if short rna can degrade
splicing
● Splicing happens while RNA is being made
● After the cap is added, a collection of splicing enzymes (spliceosome) look
for a splice donor site(end of first exon), when found, looks for a splice
acceptor site(start of next exon).
● It will then glue these sites together
● The order of exons is determined by proteins that obscure the acceptor site
capping
● Cap synthesizing complex makes the cap, due to this Cap binding complex
(CBC) is activated
● When CBC is activated, this is the first sign that splicing should happen
● The cap is a guanosine methylated in the 7th C
prokayrote initioation
The 30S ribosome attaches to the RBS or Shine-Dalgarno sequence (just a
sequence of a lotta purines). Once bound, it scans for the start codon where all
the good stuff happens.
eukaryotic intiation
There is no RBS, instead, the ribosome recognizes the 5’ cap structure of the
mRNA. The 40S ribosome binds to the 5’ cap with IF. After binding, the ribosome
scans for the start codon.
TATA binding protein TBP
a transcription initiation factor, it is part of the ‘loaders’
of each of the three eukaryotic RNA polymerases, somewhat analogously to the sigma
subunit of the bacterial RNA polymerase
eukaryotic rna polymerase II
makes primary rna transcripts that become mrna, starts at gene promoters,
polyadenylase
elongates 3”OH cleaved rna, adds 80 to 250 A’s to 3’ end of mrna
