RNA Flashcards
types of RNA (5) and associated rna polymerase
II
- mRNA: messenger - amino acid sequences
- rRNA - ribosomal - ribosomal proteins, make up ribosomes
- miRNA - micro - non-coding, regulate gene expression
III
- tRNA : transfer - brings aminos to ribosome during translation
- snRNA - small nuclear, with proteins, form complexes for processing (splicing)
how are rna pols isolated
enhancers
bound by transcription factors
regulate gene expression
elements that regulate gene expression
- TATA box: promoter sequence
- CpG island promoter
- Enhancer
Core promoter elements
help initiate transcription
- site for binding
core promoter element vs proximal promoter elements
Core: site for binding
proximal: regulation of expression
Tata box binding protein
c-terminal binds to TATA
- bends double helix
- aids in uncoiling so RNApol can bind
gene specific transcription factor binding elements
- Activate transcription
- can repress it
- Recruited in certain situations
‘Regulatory”
general transcription factors (TFII)
Always needed for rna ii
Bind DNA or other proteins
“housekeeping”
preinitiation complex (PIC)
Composed of
- TFIIs
- Mediator
- RNA pol ii
formation of pic
- TFIID recruited
- TAFs bind elements on promoter - TFIIB recruited
- binds TBP - TFIIB binds RNAPII and TFIIF
- TFIIE and TFIIH bind
- H brings 2 helicases and 1 kinase
TFIIs
TFIID: TBP and TBP-associated factors (TAFs)
TFIIB
TFIIF
TFIIE: 2 subunits
TFIIH: 10 subunits
Describe the effects the following would have on
transcription of mRNA and tRNA genes.
a. Loss of TBP
TBP binds to TATA box AND binds TFIIB
No TBP = no complex
Describe the effects the following would have on
transcription of mRNA and tRNA genes.
b. Loss of TFIIB
TFIIB binds to TBP, then allows RNA pol, TFIIF, TFIIE, TFIIH to bind
No TFIIB = only TFIID = no function
Describe the effects the following would have on
transcription of mRNA and tRNA genes.
c. Loss of TFIID
TFIID = TBP and TAFS
No TFIID = no binding to dna = no complex
mediator in PIC
20 subunits
flexible
stimulated transcription
binds RNAPII and TFs
what could be an advantage to using weak interactions to hold together complimentary dna strands and the PIC
Allows them to easily come apart when needed
recycle pic components
replicate dna
To make DNA and RNA, phosphodiester bonds are
formed between which two chemical groups on the
deoxyribose sugar? (select all that apply)
1. H 2 O
2. 5’ hydroxyl group
3. 3’ hydroxyl group
4. 5’ phosphate
5. 3’ phosphate
6. pyrophosphate
- 3’ Hydroxyl group
- 5’ phosphate
transcriptional activators
- interact w mediated and TFs
- mod chromatin structure
transcriptional repressors
- competitive dna binding
- binding site overlaps (downstream) binding site for activator = activator can’t bind - masking activation surface
- repressor binding site downstream
- binds to activator (inhibits) - direct interaction w TFs
- binds so activator can’t
how do transcriptional repressors work
recruit histone deacetyltransferases
- affects chromatin remodelling
overview of mrna processing
- 5’ capping after transcription
- cleavage at polyA site via endonuclease (remove junk after site)
- polyadenylation (add poly a tail to site)
- splicing
what doe sit mean that mRNA processing occurs co-transcriptionally
The processing of mrna happens while transcription is occuring
c terminal domain (CTD) of rnapolii
a coordinator of mrna processing
bidning site for modifications
What is the role of Cet1 and is its spatial
distribution consistent with that function?
- peaks at TSS
- climbs back slightly after processing
- lower than TFIIB
At beginning before/during start = 5’ end = 5’ capping
What is the role of Pcf11 and is its special
distribution consistent with that function?
- Starts low
- peaks after poly a site
At poly a site = cleavage
how does CTD phosphorylation cycle regulate transcriptional processing
different patterns of phosphorylation recruit different factors
The enzymes bind to the residues of phosphorylation areas
You discover a new protein and show it is important for transcription termination and can
bind the RNAPII-CTD. Based on what you know about the RNAPII-CTD phosphorylation
cycle,
which CTD modification state is this new protein likely to recognize and bind?
What do you expect to see if you remove the kinases and phosphatases responsible for
depositing or removing that the relevant modifications?
- recognize the dephosphorylation of Ser2
- Ser2 stays phosphorylated
- protein can’t bind
- termination can’t occur
ctd phosphorylation patterns
Initiation:
- CDK7 : Ser5 Ser7
Elongation:
- CDK9: Ser2
- Ser 5 and Ser 7 dephosphorylated
Near termination
- Fcp1 dephosphorylates Ser2-P
how are locations of exons and introns determined
- comparing the genomic sequence (has introns) with a global mRNA sequence (only has exons)
- look at seq before and after splice sites
- predict where splice sites are
- highest frequency of 5’ GU and 3’ AG
Describe the effect the following would have
on splicing
1. A deletion mutation removing the
section highlighted in yellow (splice site between exon 1 and intron)
There would be no splicing between exon 1 and intron, but it would splice between intron and exon 2
Intron would not be removed
Describe the effect the following would have
on splicing
- Changing all the adenines in the section
highlighted in yellow to guanine (splice site between exon 1 and intron, AGGUAAGUA)
–> GGGUGGGUG
dna repair - photoreactivation
uv induced thymine dimers repaired via photoreactivation
light used by enzymjes to break bonds that form cyclobutane ring
dna repair - nucleotide excision repair of thymine dimers
dmamged dna unwound by helicase
cleaved on either side of dimer
gap filled by pol
dna repair - base excision
uracil paired with guanine by accident
bond between uracil and deoxyribose cleaved
leaves sugar w no base
dna chain cleaved
gap filled
