Exam 2 Flashcards
what is a conservative mutation
a missense mutation (point mutation) that switches one AA to another AA with similar chemical properties
what are the functions of the phosphorylation of the CTD during transcription by RNA Pol II in eukaryotes
- promoter clearance/start of elongation
- recruitment of capping factors
- attachment of cap binding complex
- recruitment of splicing proteins
- recruitment of polyA complex
which strand is the template strand
the 3’ –> 5’ strand in the direction of transcription
where does transcription start
+1 is the first nucleotide
which pathway repairs an incorrect nucleotide incorporated by DNA pol
mismatch repair
which pathway repairs a crosslink generated by UV light
nucleotide excision repair
which pathway repairs an oxidation of guanines by a reactive oxygen species
base excision repair (can just remove the base)
which pathway repairs a damage base started to get repaired during replication, leading to conversion of a single strand break to a double strand break
homologous recombination
what genes are transcribed by pol I
rRNA
what genes are transcribed by pol II
mRNA
what genes are transcribed by pol III
other small RNAs
which pol transcribes the largest variety of genes
pol II
which pol transcribes the largest total amount of genes
pol I
where does synthesis of pol I occur
nucleolus
where does synthesis of pol II occur
nucleoplasm
where does synthesis of pol III occur
nucleoplasm
what are the steps of transcription initiation in bacteria
- sigma bound pol binds to promoter, sigma factor blocks active site to create closed complex state
- sigma factor moves away from active site, DNA enters active site, pin promotes opening of DNA (open state)
- the polymerase needs to hold the first nucleotides together (unstable) which leads to several cycles of abortive initiation until RNA chain is ~10nt
- structural transition at 10nt, sigma factor is cleared from RNA exit channel and falls off (called promoter clearance)
what is the function of primase
synthesizes RNA primers for replication
what are the functions of chromodomain and bromodomain proteins
binds methylated histone tails to maintain open/closed chromatin
what is the function of the mediator complex
binds to enhancer-bound transcription factors to promote transcription in eukaryotes
what is the function of guanylyltransferase
adds 5’ cap to mRNA in eukaryotes
what is the function of cas9
creat ds break
what kind of enzyme is cas9
bacterial enzyme
what is the function of gRNA in crispr/cas
bring cas9 to target on DNA (needs break on DNA not RNA)
what pathway will most likely repair the lesion in crispr/cas
NHEJ
if there is a gene knocked out during crispr/cas, what mutation will there be
indels
what is a knock in gene repaired by
HR
does a knock in or knock out need a donor sequence
knock in
is sigma70 or sigma34 spontaneous
sigma70
what is the role of a sigma factor in bacteria
brings RNA pol to a specific set of promoters
when splicing, what exons need to be included
first and last
what is the mechanism by which different mature mRNAs can be made from same pre mRNA
alternative splicing
what end is the cap added to
5’
what is the cap made of
7-methyl guanosine (7-MeG)
is 5’ cap attached at beginning or end of transcription
beginning
where is the capped mRNA attached to RNA pol II
c terminal domain
what are functions of the 5’ cap
inhibits 5’->3’ exonuclease
attaches to pol II
recruits ribosomes
what are the two different mechanisms of transcription termination in bacteria
rho-independent: without a protein
rho-dependent: uses protein
what is the order of splicing events
- U1 binds to 5’ splice site and U2 binds to branch point
- U1 brings the 5’ splice site and the A of branch point together
- binding of U4, U5, U6
- 2’ OH of A branch point serves as nu and attacks phosphodiester bond at 5’ exon
- formation of lariat on intron
- U5 base pairs w/ exons 1 and 2, maintaining them together
- 3’ OH of exon 1 serves as nu and attacks phosphodiester bond at 3’ splice site
- release of exon as lariat
