BCH 5413 COMPREHENSIVE EXAM
QUESTIONS AND CORRECT ANSWERS
STUDY GUIDE
●● low glucose
Answer: high cAMP- CAP binding occurs, stablizes UPE region and
increases rate of transcription
●● low lactose
Answer: repressor binding
●● high lacotose
Answer: allolactose inducer binds repressor preventing repressor
binding, allows transcription
●● Low trp
Answer: ribosome stalls, Seq 2 binds Seq3 forming non-terminating
hairpin
●● -10
Answer: Pribnow box, TATAAT
,●● Core promoters
Answer: -10 and -35 (TTGACA)
●● Operon
Answer: collection of genes involved in regulation protein synthesis
●● Repressor
Answer: negative regulator
●● UP region
Answer: recognized by alpha subunit of RNA polymerase, -40 to -60, AT
rich , stimulates rrnBP1 gene
●● CTD
Answer: 7 AA sequence repeated 52x in mammals, Ser 2, Ser 5, Ser 7.
Binds to components of capping, splicing, and polyadenlyation systems
●● Steps of initiation
Answer: 1. PIC formation
2. Closed promoter is converted to open promoter by melting.
3. Abortive initiation (scrunching)
4. Early elongation (promoter escape
5. Productive elongation
,●● DSIF
Answer: (DRB sensitivity-inducing factor), once phosphorylated by
NELF it converts from negative elongation factor to positive elongation
factor
●● Transcriptional pausing
Answer: mediated by NELF and DSIF at around +30
●● TFIIH
Answer: phosphorylates Ser 5, TEC is arrested at checkpoint for pre-
mRNA capping. P-TEBb phosphorylates Ser 2 which allows further
elongation. Phosphatases dephosphorylate the CTD at Ser 5 so at end of
transcription almost exclusively Ser 2
●● mRNA 5' capping
Answer: 5'-5' phosphodiester bond resistant to 5'-3' exonuclease activity
●● mRNA 5' cap roles
Answer: 1. required for splicing
2. CBP binds to cap to facilitate tranport of MRNA into cytoplasm
3. CBP binds to facilitates translation of mRNA
4. Stimulates polyadenylation
, 5. decapping is involved in regulation of mRNA turnover
●● Polyadenylation (poly a tail)
Answer: NOT synonymous with transcription termination
Hofer and Darnell experiment showed that transcription terminates
downstream of Poly-A site.
●● Torpedo Model
Answer: Cleavage of poly A site to make tail creates an unprotected 5'
end which is degraded by exonuclease and digests RNA until it reaches
polymerase which destabilizes complex and transcription stops
●● Poly A Signal
Answer: AAUAAA, and G/U
●● CSPF
Answer: Cleavage and polyadenylation specificity factor
●● CSPF 160
Answer: binds AAUAAA site
●● CstF64 (cleavage stimulating factor)
Answer: binds GU rich area
QUESTIONS AND CORRECT ANSWERS
STUDY GUIDE
●● low glucose
Answer: high cAMP- CAP binding occurs, stablizes UPE region and
increases rate of transcription
●● low lactose
Answer: repressor binding
●● high lacotose
Answer: allolactose inducer binds repressor preventing repressor
binding, allows transcription
●● Low trp
Answer: ribosome stalls, Seq 2 binds Seq3 forming non-terminating
hairpin
●● -10
Answer: Pribnow box, TATAAT
,●● Core promoters
Answer: -10 and -35 (TTGACA)
●● Operon
Answer: collection of genes involved in regulation protein synthesis
●● Repressor
Answer: negative regulator
●● UP region
Answer: recognized by alpha subunit of RNA polymerase, -40 to -60, AT
rich , stimulates rrnBP1 gene
●● CTD
Answer: 7 AA sequence repeated 52x in mammals, Ser 2, Ser 5, Ser 7.
Binds to components of capping, splicing, and polyadenlyation systems
●● Steps of initiation
Answer: 1. PIC formation
2. Closed promoter is converted to open promoter by melting.
3. Abortive initiation (scrunching)
4. Early elongation (promoter escape
5. Productive elongation
,●● DSIF
Answer: (DRB sensitivity-inducing factor), once phosphorylated by
NELF it converts from negative elongation factor to positive elongation
factor
●● Transcriptional pausing
Answer: mediated by NELF and DSIF at around +30
●● TFIIH
Answer: phosphorylates Ser 5, TEC is arrested at checkpoint for pre-
mRNA capping. P-TEBb phosphorylates Ser 2 which allows further
elongation. Phosphatases dephosphorylate the CTD at Ser 5 so at end of
transcription almost exclusively Ser 2
●● mRNA 5' capping
Answer: 5'-5' phosphodiester bond resistant to 5'-3' exonuclease activity
●● mRNA 5' cap roles
Answer: 1. required for splicing
2. CBP binds to cap to facilitate tranport of MRNA into cytoplasm
3. CBP binds to facilitates translation of mRNA
4. Stimulates polyadenylation
, 5. decapping is involved in regulation of mRNA turnover
●● Polyadenylation (poly a tail)
Answer: NOT synonymous with transcription termination
Hofer and Darnell experiment showed that transcription terminates
downstream of Poly-A site.
●● Torpedo Model
Answer: Cleavage of poly A site to make tail creates an unprotected 5'
end which is degraded by exonuclease and digests RNA until it reaches
polymerase which destabilizes complex and transcription stops
●● Poly A Signal
Answer: AAUAAA, and G/U
●● CSPF
Answer: Cleavage and polyadenylation specificity factor
●● CSPF 160
Answer: binds AAUAAA site
●● CstF64 (cleavage stimulating factor)
Answer: binds GU rich area
