BCHM 4360 Exam II Questions And
Correct Verified Answers
How many subunits are in the bacterial RNA Polymerase? - ANSWER -5
What shape do bacterial RNA Polymerase subunits assemble into? - ANSWER
jaw-like lobes
Between Pol I, II, and III, which subunits are common? - ANSWER -Rbp5, 6, 8,
10, and 12
What is an additional function of RNA Polymerase II? - ANSWER -couples
transcription to processing of RNA transcript
True or False: RNA core sequences can synthesize RNA, but cannot recognize
promoter sequences. - ANSWER -True
What does the core bacterial enzyme require in order to recognize promoter
sequences? - ANSWER -Sigma factor
Core polymerase (bacteria) + sigma factor =___________ - ANSWER
holoenzyme
Bacterial promoters generally have which two elements? - ANSWER --35 and -10
Are the -35 and -10 elements upstream or downstream of the TSS? - ANSWER
upstream
Why would having two contact points for sigma factors be beneficial to
transcription? - ANSWER -Makes a much more stable process than if just one
contact point
What is the main difference between the many bacterial sigma factors? -
ANSWER -Each has a preferred binding sequence and preferred spacing between
,the -35 and -10 elements
How do the sigma factor preferred spacings help regulate transcription? -
ANSWER -The closer the sequences and spacing are to the preference for a
particular sigma factor, the tighter the sigma factor will bind, giving higher
transcription rates
What are most common for strong promotion of expression of genes? - ANSWER -Consensus sequences
What does Domain 2 of the RNA Polymerase holoenzyme bind to and what is its
function? - ANSWER --10 region, helps separate duplex DNA (promoter melting)
What does Domain 3 of the RNA Polymerase holoenzyme bind to and what is its
function? - ANSWER -two bases of the extended -10 region
What does Domain 4 of the RNA Polymerase holoenzyme bind to and what is its
function? - ANSWER --35 element, attached to flexible part of core enzyme which
may let it accomodate different -35 to -10 spacings
What are pro and anti sigma factors? - ANSWER -Pro-sigma factors have
inhibitory domains that must be cleaved before the sigma can associate with the
core enzyme. Anti-sigma factors are proteins that bind to sigma factors and inhibit
their function
Explain the example of how anti-sigma factors are involved in the regulation of
flagellum assembly in S. typhimurium. - ANSWER -1. While the proteins that
form the flagellum base are being synthesized, the anti-sigma binds to the sigma
factor, preventing it from binding to the holoenzyme
2. The sigma factor promotes transcription of genes that are needed for completion
of flagellum assembly
3. In the late stages of flagellum protein synthesis, the anti-sigma factor is exported
from the cell so the sigma factor can promote assembly gene transcription,
allowing the flagellum to be put together.
Eukaryotic and archaeal promoters also need extra proteins to target the core
enzyme to promoters: _______ _____________ _______. - ANSWER -general
transcription factors
, The TFII complex works with RNA Polymerase ___ to form the ___-_________
complex. - ANSWER -II, pre-initiation
What is the function of TFIIA? - ANSWER -stabilizes binding of TBP and TFIIB
What is the function of TFIIB? - ANSWER -promoter recognition, stabilizes early
transcription complex
What is the function of TFIID? - ANSWER -promoter recognition, DNA bending
interacts with regulatory factors
What is the function of TFIIE? - ANSWER -recruits TFIIH
What is the function of TFIIF? - ANSWER -suppresses non-specific DNA
binding and captures non-template strand upon melting
What is the function of TFIIH? - ANSWER -unwinds promoter DNA,
phosphorylates CTD
True or False: All eukaryotic polymerases need the TATA binding protein (TBP)
to initiate transcription. - ANSWER -True
What are three other elements besides the TBP or TATA box that are often present
in eukaryotic transcription? - ANSWER -TFIIB recognition element (BRE),
initiator element (INR), and downstream promoter element (DPE)
True or False: A TATA box is required for every single transcription event. -
ANSWER -False, although it is found about 95% of the time
What is the first step in assembling the transcription initiation complex? -
ANSWER -Binding of TFIID to the TATA box
How does TFIID bind to the TATA box? - ANSWER -Via TBP, which binds to
the minor groove of DNA, which induces strong distortions in the DNA and causes
local DNA unwinding
Some other components of TFIID, called TBP-_________ factors (TAFs) mediate
recognition of other promoter elements like ___ and ___. - ANSWER -associated,
INR, DPE
What is the next step in transcription initiation after TFIID has associated with
DNA? - ANSWER -TFIIB is recruited. This recognizes the BRE promoter
Correct Verified Answers
How many subunits are in the bacterial RNA Polymerase? - ANSWER -5
What shape do bacterial RNA Polymerase subunits assemble into? - ANSWER
jaw-like lobes
Between Pol I, II, and III, which subunits are common? - ANSWER -Rbp5, 6, 8,
10, and 12
What is an additional function of RNA Polymerase II? - ANSWER -couples
transcription to processing of RNA transcript
True or False: RNA core sequences can synthesize RNA, but cannot recognize
promoter sequences. - ANSWER -True
What does the core bacterial enzyme require in order to recognize promoter
sequences? - ANSWER -Sigma factor
Core polymerase (bacteria) + sigma factor =___________ - ANSWER
holoenzyme
Bacterial promoters generally have which two elements? - ANSWER --35 and -10
Are the -35 and -10 elements upstream or downstream of the TSS? - ANSWER
upstream
Why would having two contact points for sigma factors be beneficial to
transcription? - ANSWER -Makes a much more stable process than if just one
contact point
What is the main difference between the many bacterial sigma factors? -
ANSWER -Each has a preferred binding sequence and preferred spacing between
,the -35 and -10 elements
How do the sigma factor preferred spacings help regulate transcription? -
ANSWER -The closer the sequences and spacing are to the preference for a
particular sigma factor, the tighter the sigma factor will bind, giving higher
transcription rates
What are most common for strong promotion of expression of genes? - ANSWER -Consensus sequences
What does Domain 2 of the RNA Polymerase holoenzyme bind to and what is its
function? - ANSWER --10 region, helps separate duplex DNA (promoter melting)
What does Domain 3 of the RNA Polymerase holoenzyme bind to and what is its
function? - ANSWER -two bases of the extended -10 region
What does Domain 4 of the RNA Polymerase holoenzyme bind to and what is its
function? - ANSWER --35 element, attached to flexible part of core enzyme which
may let it accomodate different -35 to -10 spacings
What are pro and anti sigma factors? - ANSWER -Pro-sigma factors have
inhibitory domains that must be cleaved before the sigma can associate with the
core enzyme. Anti-sigma factors are proteins that bind to sigma factors and inhibit
their function
Explain the example of how anti-sigma factors are involved in the regulation of
flagellum assembly in S. typhimurium. - ANSWER -1. While the proteins that
form the flagellum base are being synthesized, the anti-sigma binds to the sigma
factor, preventing it from binding to the holoenzyme
2. The sigma factor promotes transcription of genes that are needed for completion
of flagellum assembly
3. In the late stages of flagellum protein synthesis, the anti-sigma factor is exported
from the cell so the sigma factor can promote assembly gene transcription,
allowing the flagellum to be put together.
Eukaryotic and archaeal promoters also need extra proteins to target the core
enzyme to promoters: _______ _____________ _______. - ANSWER -general
transcription factors
, The TFII complex works with RNA Polymerase ___ to form the ___-_________
complex. - ANSWER -II, pre-initiation
What is the function of TFIIA? - ANSWER -stabilizes binding of TBP and TFIIB
What is the function of TFIIB? - ANSWER -promoter recognition, stabilizes early
transcription complex
What is the function of TFIID? - ANSWER -promoter recognition, DNA bending
interacts with regulatory factors
What is the function of TFIIE? - ANSWER -recruits TFIIH
What is the function of TFIIF? - ANSWER -suppresses non-specific DNA
binding and captures non-template strand upon melting
What is the function of TFIIH? - ANSWER -unwinds promoter DNA,
phosphorylates CTD
True or False: All eukaryotic polymerases need the TATA binding protein (TBP)
to initiate transcription. - ANSWER -True
What are three other elements besides the TBP or TATA box that are often present
in eukaryotic transcription? - ANSWER -TFIIB recognition element (BRE),
initiator element (INR), and downstream promoter element (DPE)
True or False: A TATA box is required for every single transcription event. -
ANSWER -False, although it is found about 95% of the time
What is the first step in assembling the transcription initiation complex? -
ANSWER -Binding of TFIID to the TATA box
How does TFIID bind to the TATA box? - ANSWER -Via TBP, which binds to
the minor groove of DNA, which induces strong distortions in the DNA and causes
local DNA unwinding
Some other components of TFIID, called TBP-_________ factors (TAFs) mediate
recognition of other promoter elements like ___ and ___. - ANSWER -associated,
INR, DPE
What is the next step in transcription initiation after TFIID has associated with
DNA? - ANSWER -TFIIB is recruited. This recognizes the BRE promoter
