Protein content is regulated by?
1) Tx and Translation frequency
2) Protein life
How does RNA polymerase link to ribonucleotides?
What are the functions non-coding RNAs?
enzymatic, structural, regulatory
What are the sequences necessary for transcription?
promoter, RNA-coding sequence, terminator
mono - eukaryote and poly in prokaryotes
What specifies promoter strength?
Which is more varied? Bacterial terminators or promoters? Explain why.
Terminators are more varied because they encode a hair-loop
What are the 3 types of RNA polymerases in Eukaryotes? How are they similar/different?
similar structure, share subunits, but different functions
RNA polymerase II requires what to initiate transcription?
general transcription factor (TFII)
general transcription factor required by RNA polymerase II, recognizes promoter to open DNA and release DNA from promoter
TFIID with subunit TBP recognizes what?
TATA box for transcription initiation
General transcription factors form what?
transcription initiation complex
What starts elongation phase?
Role of elongation factors ?
associate with RNA polymerase during elongation to 1) enhance RNA polymerase processing or
2) to help move it along the genome
How does negative/positive supercoiling dictate DNA opening?
- supercoiling: helix opening facilitated
+ supercoiling: hinders opening
What introduces supercoils? What enzyme removes suprcoils?
Big enzymes introduces supercoils, topoisomerases removes them
What happens to Eukaryotic RNA before nuclear export?
Primary RNA transcript is processed: 5’ capping, RNA splicing 3’ polyadelynation
mRNA export from nucleus is blocked if?
end modifications aren’t present or mRNA binding proteins are absent/present
RNA splicing removes?
introns from newly transcribed pre-mRNA
pre-mRNA splicing reaction mechanism
spiceosome recognizes: 5’ and 3’ splice site, branch point of lariat structure.
spliceosome catalyzes transesterification reaction
core spliceosome comprises of?
5 small nuclear snRNAS which forms a small RNP with other proteins
how are splice sites identified?
base pairing between snRNA and pre-mRNA consensus sites?
RNA splicing mistakes
exon skipping, cryptic splice site selection
2 mechanisms to enhance splicing fidelity?
1) mark splice sites with spliceosome subunits as they occur on nascent RNA chain
2) exon definition hypothesis
What effect does chromatin structure have on splicing?
1) tight chromatin slows down RNA polymerase (more time for splice site recognition to reduce exon skipping) 2) histone modifications recruit splice components which affects splice site selection
hOW IS 3’ END generated?
RNA-processing enzymes make the 3’ end through polyadenylation signals that lead to transcription termination in mammals
What are 2 RNA binding proteins that recognize polyadenylation signals?
Cleavage and Polyadenylation Specificity Factor (AUAAA) and Cleavage stimulation factor (GU-rich)
What happens after RNA cleavage?
RNA pol. II keeps elongation until it is destabilized by exonuclease (5–>3)
How is mRNA synthesis made to be more efficient?
combining active genes in mRNA production factories
degrades nuclear junk RNA, processes rRNA, determines RNA life time in cytosol
What happens to mature mRNA?
BINDS to exportins and exported to cytosol
5’ –> 3’ splice site and branch point of lariat