BCHM 4360 EXAM 2 2025 WITH ACTUAL
CORRECT QUESTIONS AND VERIFIED
DETAILED ANSWERS |FREQUENTLY TESTED
QUESTIONS AND SOLUTIONS|ALREADY
GRADED A+|BRAND NEW!!!|GUARANTEED
PASS|LATEST UPDATE
In eukaryotes, intrinsic terminator sites are recognized by which RNA Polymerase?
Pol III
Eukaryotic intrinsic terminators have a stretch of which nucleotide? Also what is the function of
this?
As, which is thought to destabilize the DNA-RNA hybrid the same way as bacterial intrinsic
terminators
Termination for which RNA Polymerase requires additional proteins? What are these proteins in
yeast and mice?
Pol I, DNA binding proteins such as Reb1p in yeast and TTF1 in mice
True or False: RNA Pol II continues to transcribe after the polyadenylation signal, but the mRNA
is cleaved at the poly(A) signal and the 3' end of the mRNA is processed.
True
What are the two main models of transcription termination by RNA Pol II?
allosteric and torpedo
Describe the allosteric model of transcription termination by RNA Pol II.
1. RNA Pol II transcribes through the polyA and 3' processing signals
2. RNA processing proteins associate with the processing signals and the CTD
3. Cleavage or recognition of processing proteins causes conformation changes that lead to
dissociation of Pol II from DNA
1|Page
,True or False: The polyA tail is a timing mechanism, so the longer the tail is, the shorter the
transcript is going to be around to get translated.
False, the longer the tail is, the longer the transcript is going to be around to get translated
Describe the torpedo model of transcription termination by RNA Pol II.
1. After cleavage, the RNA downstream of the polyA site is digested by a 5' to 3' endonuclease
2. This endonuclease is the torpedo. It continues to degrade the nascent RNA until it runs into
the RNA Polymerase
3. This disrupts polymerization and causes the enzyme to dissociate from the DNA.
What did Pugh and Rhee do?
Used a ChIP-exo technique to find out how eukaryotic transcription is initiated from promoters
without TATA boxes. They mapped the occupancy of general transcription factors and RNA
Polymerase II in yeast.
What was the main conclusion from the research done by Pugh and Rhee?
Showed that all promoters in yeast has a TATA or TATA-like sequence where TBP could bind and
promote initiation.
What did Kornberg help discover that explained and fixed the squelching problem previously
observed?
Mediator
How did Joan and Ron Conway and others continue to discover Mediator?
They used Multidimensional Protein Identification Technology, immunoprecipitation, and mass
spectrometry to identify the components of Mediator.
How did Carpousis and Gralla discover abortive initiation in bacteria?
DNA containing the promoter was incubated with radioactive nucleotides (at different
concentrations) and RNA Polymerase holoenzyme. There were a number of short products as
well as longer ones.
Who else, besides Carpousis and Gralla, discovered abortive products in cells and how did they
do it?
Goldman, Ebright, and Nickels found abortive products by using phage promoters. A probe was
used (made out of special nucleotides that hybridize with high affinity and specificity) that
would match the first 15 nucleotides of any abortive products.
2|Page
, True or False: One level of regulation is the promoter strength, but most regulation comes from
targeted gene regulation.
True
What are regulatory proteins that decrease the level of transcripts for certain genes called?
repressors
What are proteins that increase transcription called?
activators
What are regulatory sequences?
specific DNA regions to which regulatory proteins bind
True or False: Regulatory sequences must be a short distance away or directly adjacent to the
promoter to work effectively.
False, regulatory sequences can be directly upstream of the promoter or can be many kb away
In bacteria, sequences recognized by regulators are called _________ sites, and are typically
_____ to the promoter or _____________ it.
operator, close, overlapping
If operators are distal to the gene, the DNA must ____ around for the regulatory protein to
interact with the polymerase, sometimes aided by ____________ DNA binding proteins.
loop, architectural
True or False: Eukaryotic genes are more often controlled by distal regulatory sequences than
bacterial genes.
True
What is an enhancer?
A distal regulatory sequence of DNA that can be several thousand base pairs away
What are locus control regions?
combination of enhancer and insulator elements that are found in more complex eukaryotes
Regulatory proteins are often modular, and can have additional domains that (3 things):
3|Page
CORRECT QUESTIONS AND VERIFIED
DETAILED ANSWERS |FREQUENTLY TESTED
QUESTIONS AND SOLUTIONS|ALREADY
GRADED A+|BRAND NEW!!!|GUARANTEED
PASS|LATEST UPDATE
In eukaryotes, intrinsic terminator sites are recognized by which RNA Polymerase?
Pol III
Eukaryotic intrinsic terminators have a stretch of which nucleotide? Also what is the function of
this?
As, which is thought to destabilize the DNA-RNA hybrid the same way as bacterial intrinsic
terminators
Termination for which RNA Polymerase requires additional proteins? What are these proteins in
yeast and mice?
Pol I, DNA binding proteins such as Reb1p in yeast and TTF1 in mice
True or False: RNA Pol II continues to transcribe after the polyadenylation signal, but the mRNA
is cleaved at the poly(A) signal and the 3' end of the mRNA is processed.
True
What are the two main models of transcription termination by RNA Pol II?
allosteric and torpedo
Describe the allosteric model of transcription termination by RNA Pol II.
1. RNA Pol II transcribes through the polyA and 3' processing signals
2. RNA processing proteins associate with the processing signals and the CTD
3. Cleavage or recognition of processing proteins causes conformation changes that lead to
dissociation of Pol II from DNA
1|Page
,True or False: The polyA tail is a timing mechanism, so the longer the tail is, the shorter the
transcript is going to be around to get translated.
False, the longer the tail is, the longer the transcript is going to be around to get translated
Describe the torpedo model of transcription termination by RNA Pol II.
1. After cleavage, the RNA downstream of the polyA site is digested by a 5' to 3' endonuclease
2. This endonuclease is the torpedo. It continues to degrade the nascent RNA until it runs into
the RNA Polymerase
3. This disrupts polymerization and causes the enzyme to dissociate from the DNA.
What did Pugh and Rhee do?
Used a ChIP-exo technique to find out how eukaryotic transcription is initiated from promoters
without TATA boxes. They mapped the occupancy of general transcription factors and RNA
Polymerase II in yeast.
What was the main conclusion from the research done by Pugh and Rhee?
Showed that all promoters in yeast has a TATA or TATA-like sequence where TBP could bind and
promote initiation.
What did Kornberg help discover that explained and fixed the squelching problem previously
observed?
Mediator
How did Joan and Ron Conway and others continue to discover Mediator?
They used Multidimensional Protein Identification Technology, immunoprecipitation, and mass
spectrometry to identify the components of Mediator.
How did Carpousis and Gralla discover abortive initiation in bacteria?
DNA containing the promoter was incubated with radioactive nucleotides (at different
concentrations) and RNA Polymerase holoenzyme. There were a number of short products as
well as longer ones.
Who else, besides Carpousis and Gralla, discovered abortive products in cells and how did they
do it?
Goldman, Ebright, and Nickels found abortive products by using phage promoters. A probe was
used (made out of special nucleotides that hybridize with high affinity and specificity) that
would match the first 15 nucleotides of any abortive products.
2|Page
, True or False: One level of regulation is the promoter strength, but most regulation comes from
targeted gene regulation.
True
What are regulatory proteins that decrease the level of transcripts for certain genes called?
repressors
What are proteins that increase transcription called?
activators
What are regulatory sequences?
specific DNA regions to which regulatory proteins bind
True or False: Regulatory sequences must be a short distance away or directly adjacent to the
promoter to work effectively.
False, regulatory sequences can be directly upstream of the promoter or can be many kb away
In bacteria, sequences recognized by regulators are called _________ sites, and are typically
_____ to the promoter or _____________ it.
operator, close, overlapping
If operators are distal to the gene, the DNA must ____ around for the regulatory protein to
interact with the polymerase, sometimes aided by ____________ DNA binding proteins.
loop, architectural
True or False: Eukaryotic genes are more often controlled by distal regulatory sequences than
bacterial genes.
True
What is an enhancer?
A distal regulatory sequence of DNA that can be several thousand base pairs away
What are locus control regions?
combination of enhancer and insulator elements that are found in more complex eukaryotes
Regulatory proteins are often modular, and can have additional domains that (3 things):
3|Page
