BCH 5413 Exam 2 Questions with Verified Solutions Graded A+
high glucose - Answers low cAMP-no CAP binding
low glucose - Answers high cAMP- CAP binding occurs, stablizes UPE region and increases rate
of transcription
low lactose - Answers repressor binding
high lacotose - Answers allolactose inducer binds repressor preventing repressor binding,
allows transcription
Low trp - Answers ribosome stalls, Seq 2 binds Seq3 forming non-terminating hairpin
-10 - Answers Pribnow box, TATAAT
Core promoters - Answers -10 and -35 (TTGACA)
Operon - Answers collection of genes involved in regulation protein synthesis
Repressor - Answers negative regulator
UP region - Answers recognized by alpha subunit of RNA polymerase, -40 to -60, AT rich ,
stimulates rrnBP1 gene
CTD - Answers 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 - Answers 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 - Answers (DRB sensitivity-inducing factor), once phosphorylated by NELF it converts from
negative elongation factor to positive elongation factor
Transcriptional pausing - Answers mediated by NELF and DSIF at around +30
TFIIH - Answers 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 - Answers 5'-5' phosphodiester bond resistant to 5'-3' exonuclease activity
,mRNA 5' cap roles - Answers 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) - Answers NOT synonymous with transcription termination
Hofer and Darnell experiment showed that transcription terminates downstream of Poly-A site.
Torpedo Model - Answers 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 - Answers AAUAAA, and G/U
CSPF - Answers Cleavage and polyadenylation specificity factor
CSPF 160 - Answers binds AAUAAA site
CstF64 (cleavage stimulating factor) - Answers binds GU rich area
CSPF 73 - Answers endonuclease
Polymerase of Poly A - Answers templated-INdependent RNA synthesis,
slow polyadenylation (1-2 A sec) converted to rapid polyadenylation (25 A sec) with hydrolysis
of ATP
Typical poly A-tail - Answers 100-200 bases
Multiple polyadenylation sites - Answers possible, helps regulate gene expression altering
stability and turnover
CHIP analysis - Answers 1. Formaldehyde cross-linking,
2. lyse cells, shear chromatin
3. immunoprecipitate with appropriate antibody
4. reverse cross-links
5. PCR analysis
Phosphorylation of pol II CTD on Ser 2 and Ser 5 _____ - Answers recruits the capping apparatus
, to mRNA
Ser 2 remains attached to - Answers ABD1
Splicing mechanism - Answers 1. First transesterification: 2 OH of branch site adenine attacks
the phosphodiester bond at the 5' splice sit forming lariat of introns
2. Second transesterificaton: 3-OH on 5' exon attacks the phosphodiester at the 3' splice site
Splice site consensus sequenes - Answers 5' end of intron is GU
3' end of intron is AG
Branch point - Answers A (20-50 bp upstream 3' splice site)
Spliceosome - Answers nuclear complexes responsible for removing intron-derived sequences
from hnRNA
*contains 8 common snRNP
U1 - Answers snRNP binds to 5' splice site
U2 - Answers snRNP binds the branch site
U4 - Answers binds and sequesters snRNP6
U5 - Answers aligns hnRNA for splicing
U6 - Answers promotes RNA splicing reaction
Splicesome assembly - Answers A complex (U2 recruited to branch point by U2FA)
B complex ( U4, U5, U6 recruited)
C complex (Dynamic rearrangement, U1 and U4 exit, now catalytically active, U2 and U6 position
the branch site A for attack on 5' splice site)
Linearizes the lariat for intron degradation - Answers debranching enzyme
SR protiens - Answers (Serine/Arginine-rich proteins) bind to ESE's to regulate splicing to
enhance interactions with U1 and U2
Each cell type expresses different levels of SR proteins - Answers modified by cell cycle
dependent phosphorylation/dephosphorylation
SR protein functions - Answers 1. Exon definitions
2. Intron bridging
high glucose - Answers low cAMP-no CAP binding
low glucose - Answers high cAMP- CAP binding occurs, stablizes UPE region and increases rate
of transcription
low lactose - Answers repressor binding
high lacotose - Answers allolactose inducer binds repressor preventing repressor binding,
allows transcription
Low trp - Answers ribosome stalls, Seq 2 binds Seq3 forming non-terminating hairpin
-10 - Answers Pribnow box, TATAAT
Core promoters - Answers -10 and -35 (TTGACA)
Operon - Answers collection of genes involved in regulation protein synthesis
Repressor - Answers negative regulator
UP region - Answers recognized by alpha subunit of RNA polymerase, -40 to -60, AT rich ,
stimulates rrnBP1 gene
CTD - Answers 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 - Answers 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 - Answers (DRB sensitivity-inducing factor), once phosphorylated by NELF it converts from
negative elongation factor to positive elongation factor
Transcriptional pausing - Answers mediated by NELF and DSIF at around +30
TFIIH - Answers 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 - Answers 5'-5' phosphodiester bond resistant to 5'-3' exonuclease activity
,mRNA 5' cap roles - Answers 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) - Answers NOT synonymous with transcription termination
Hofer and Darnell experiment showed that transcription terminates downstream of Poly-A site.
Torpedo Model - Answers 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 - Answers AAUAAA, and G/U
CSPF - Answers Cleavage and polyadenylation specificity factor
CSPF 160 - Answers binds AAUAAA site
CstF64 (cleavage stimulating factor) - Answers binds GU rich area
CSPF 73 - Answers endonuclease
Polymerase of Poly A - Answers templated-INdependent RNA synthesis,
slow polyadenylation (1-2 A sec) converted to rapid polyadenylation (25 A sec) with hydrolysis
of ATP
Typical poly A-tail - Answers 100-200 bases
Multiple polyadenylation sites - Answers possible, helps regulate gene expression altering
stability and turnover
CHIP analysis - Answers 1. Formaldehyde cross-linking,
2. lyse cells, shear chromatin
3. immunoprecipitate with appropriate antibody
4. reverse cross-links
5. PCR analysis
Phosphorylation of pol II CTD on Ser 2 and Ser 5 _____ - Answers recruits the capping apparatus
, to mRNA
Ser 2 remains attached to - Answers ABD1
Splicing mechanism - Answers 1. First transesterification: 2 OH of branch site adenine attacks
the phosphodiester bond at the 5' splice sit forming lariat of introns
2. Second transesterificaton: 3-OH on 5' exon attacks the phosphodiester at the 3' splice site
Splice site consensus sequenes - Answers 5' end of intron is GU
3' end of intron is AG
Branch point - Answers A (20-50 bp upstream 3' splice site)
Spliceosome - Answers nuclear complexes responsible for removing intron-derived sequences
from hnRNA
*contains 8 common snRNP
U1 - Answers snRNP binds to 5' splice site
U2 - Answers snRNP binds the branch site
U4 - Answers binds and sequesters snRNP6
U5 - Answers aligns hnRNA for splicing
U6 - Answers promotes RNA splicing reaction
Splicesome assembly - Answers A complex (U2 recruited to branch point by U2FA)
B complex ( U4, U5, U6 recruited)
C complex (Dynamic rearrangement, U1 and U4 exit, now catalytically active, U2 and U6 position
the branch site A for attack on 5' splice site)
Linearizes the lariat for intron degradation - Answers debranching enzyme
SR protiens - Answers (Serine/Arginine-rich proteins) bind to ESE's to regulate splicing to
enhance interactions with U1 and U2
Each cell type expresses different levels of SR proteins - Answers modified by cell cycle
dependent phosphorylation/dephosphorylation
SR protein functions - Answers 1. Exon definitions
2. Intron bridging
