BCH5413 TEST 2 QUESTIONS AND CORRECT
ANSWERS 2025-2026
What is the use of the following factors: - sigma70 - sigma 32 - sigmaE - sigma54 - sigmaF - ANSWER --
sigma70: general - sigma 32: heat shock - sigmaE: heat shock - sigma54: nitrogen - sigmaF: flagellar
Prokaryotic transcription: overall steps - transcription unit is.. - during transcription.. - transcription
takes place in... - ANSWER -- transcription unit is a
sequence of DNA transcribed into a single RNA, starting at the promoter
and ending at the terminator - during transcription, the bubble is maintained within bacterial RNA
Pol, which unwinds and rewinds DNA, maintains the conditions of the
partner and template DNA strands, and synthesizes RNA - transcription takes place in a "bubble" in
which RNA is synthesized by
phase pairing with one strand of DNA in the transiently unwound
region. As the bubble progresses, the DNA duplex reforms behind it,
displacing the RNA in the form of a single polynucleotide chain
Prokaryotic RNA Pol Structure - ANSWER -- ribonucleotide
triphosphate tunnel (enter for elongation) - active site - RNA exit channel
*jaws in closed configuration
Structure of the Transcription Elongation complex - rudder - ANSWER -- contacts nascent RNA and
stabilizes elongation
complex
*dsDNA comes into Pol, non-template strand separated from template,
template used for RNA synthesis, exit of DNA and RNA out of Pol
Bacterial promoters - ANSWER -- sequence specific binding proteins
E. coli sigma 70 recognizes what two promoters - ANSWER -- For E.
,coli sigma 70, the two core promoters recognized are -10 box and -35
box
*these are considered 'core promoter elements'
UP promoter element - ANSWER -- sometimes in addition to core
promoter elements
Promoters and Promoter complexes - promoter definition - transcription initiation definition - position
+1
- synthesis of RNA in 5' -> 3' direction - ANSWER -- promoter: DNA
sequence that binds RNA Pol to initiate transcription - transcription initiation: synthesis of first
phosphodiester bond in
nascent RNA - position +1: position of nucleotide in DNA template that encodes the
fist nucleotide of mRNA - synthesis 5' -> 3': nucleotides added to 3' end form ribonucleotide
triphosphate precursors
Typical prokaryotic promoters recognized by E. coli sigma 70 - two regions and their sequences -
mutations within these regions alter... - what is important - strength of promoter determined by... -
region unwound by Pol is between.... - ANSWER -- -10 region
(Pribnow box): TATAAT consensus sequence - -35 region: TTGACA consensus sequence - different
promoters have similar but not identical -10 and -35 region
sequences - mutations within these regions alter promoter strength and function - distance between -10
and -35 regions important - strength of promoter mostly determined by affinity of RNA Pol for
promoter DNA sequences - region unwound by Pol appears to be between -9 and +3 (includes right
end of -10 sequence and extending to just downstream of transcription
initiation site)
How holoenzyme recognizes the promoter regulatory regions - what recognizes -10 and -35 regions -
what recognizes UP promoter
- which confers sequence specific binding to promoter - what subunits are involved in catalytic synthesis
of RNA - ANSWER -- sigma recognizes -10 and -35 regions - for UP (AT rich) promoter region, C terminal
domain of two alpha
subunits recognize this
,*sigma confers sequence specific binding to promoter
*beta and beta' subunits are involved in the catalytic synthesis of RNA
Where do sequence-specific interaction with the promoter occur? -
ANSWER -sigma subunit - sometimes alpha subunit if UP promoter is present
Sigma in holoenzyme recognizes -10 element via ____ with the non
template DNA strand of promoter - ANSWER -Sigma in holoenzyme
recognizes -10 element via base-specific interactions with the non
template DNA strand of promoter
Free sigma subunit (does/does not) recognize single stranded non
template strand - ANSWER -does not
*for sigma to recognize -10 and -35 regions, non-template strand has to
be in double stranded conformation
DNA Footprinting to identify that alpha-subunit recognizes UP
promoter element - ANSWER -- purified RNA Pol and DNA sequence
bound together - 5' end labeled with radioactive nucleotide (side protected by RNA Pol) - region bound
by RNA Pol protected from cleavage by DNase - after DNase treatment, purify DNA, run DNA on gel
- missing bands identify the binding site
Stages of transcription initiation - ANSWER -- holoenzyme recognizes
regulatory sequence in promoter and binds forming the closed promoter
complex - unwind dsDNA to form open promoter complex - transcription initiates (RNA Pol generates
short abortive transcripts
that are unstable and released) - at 10nt in length, the complex is stable and turns from initiation to
elongation
, Cycling of sigma during transcription - ANSWER -- as Pol transitions
to elongation, sigma factor is released - transcription proceeds with just core subunits until termination -
at termination, RNA Pol released - nascent RNA released - released core enzyme recycles back to bind
with sigma to form the
holoenzyme and repeats
Abortive transcription and initiation: RNA Pol at promoter - ANSWER -3 ideas:
1. movement of transient excursion: RNA Pol makes short movement
along DNA to make abortive transcripts, then goes back to its original
position
2. inch worming: back of RNA Pol stays stationary, as abortive
transcripts are made, front edge of RNA Pol stretches/inch worms, as
abortive transcript is released front of RNA Pol goes back to initial
position
3. scrunching: RNA Pol doesnt move but DNA compresses/scrunches in
promoter
How scientists determined which theory about RNA Pol and abortive
transcription is true - ANSWER -FRET - donor and acceptor used; donor can be stimulated and release
energy
which is transferred to acceptor and will fluoresce at different
wavelength - efficiency determined by proximity between donor and acceptor
How FRET would work concerning RNA Pol and abortive transcription - ANSWER -- linked acceptor to
DNA template and donor to back end
of sigma subunit - assembled open promoter complex - GTP and UTP added to start synthesis -
measured degree of energy transfer between donor and acceptor
(proximity)
What FRET would show for: - transient excursion - inchworming - scrunching - ANSWER -- transient
excursion: as Pol moves forward,
ANSWERS 2025-2026
What is the use of the following factors: - sigma70 - sigma 32 - sigmaE - sigma54 - sigmaF - ANSWER --
sigma70: general - sigma 32: heat shock - sigmaE: heat shock - sigma54: nitrogen - sigmaF: flagellar
Prokaryotic transcription: overall steps - transcription unit is.. - during transcription.. - transcription
takes place in... - ANSWER -- transcription unit is a
sequence of DNA transcribed into a single RNA, starting at the promoter
and ending at the terminator - during transcription, the bubble is maintained within bacterial RNA
Pol, which unwinds and rewinds DNA, maintains the conditions of the
partner and template DNA strands, and synthesizes RNA - transcription takes place in a "bubble" in
which RNA is synthesized by
phase pairing with one strand of DNA in the transiently unwound
region. As the bubble progresses, the DNA duplex reforms behind it,
displacing the RNA in the form of a single polynucleotide chain
Prokaryotic RNA Pol Structure - ANSWER -- ribonucleotide
triphosphate tunnel (enter for elongation) - active site - RNA exit channel
*jaws in closed configuration
Structure of the Transcription Elongation complex - rudder - ANSWER -- contacts nascent RNA and
stabilizes elongation
complex
*dsDNA comes into Pol, non-template strand separated from template,
template used for RNA synthesis, exit of DNA and RNA out of Pol
Bacterial promoters - ANSWER -- sequence specific binding proteins
E. coli sigma 70 recognizes what two promoters - ANSWER -- For E.
,coli sigma 70, the two core promoters recognized are -10 box and -35
box
*these are considered 'core promoter elements'
UP promoter element - ANSWER -- sometimes in addition to core
promoter elements
Promoters and Promoter complexes - promoter definition - transcription initiation definition - position
+1
- synthesis of RNA in 5' -> 3' direction - ANSWER -- promoter: DNA
sequence that binds RNA Pol to initiate transcription - transcription initiation: synthesis of first
phosphodiester bond in
nascent RNA - position +1: position of nucleotide in DNA template that encodes the
fist nucleotide of mRNA - synthesis 5' -> 3': nucleotides added to 3' end form ribonucleotide
triphosphate precursors
Typical prokaryotic promoters recognized by E. coli sigma 70 - two regions and their sequences -
mutations within these regions alter... - what is important - strength of promoter determined by... -
region unwound by Pol is between.... - ANSWER -- -10 region
(Pribnow box): TATAAT consensus sequence - -35 region: TTGACA consensus sequence - different
promoters have similar but not identical -10 and -35 region
sequences - mutations within these regions alter promoter strength and function - distance between -10
and -35 regions important - strength of promoter mostly determined by affinity of RNA Pol for
promoter DNA sequences - region unwound by Pol appears to be between -9 and +3 (includes right
end of -10 sequence and extending to just downstream of transcription
initiation site)
How holoenzyme recognizes the promoter regulatory regions - what recognizes -10 and -35 regions -
what recognizes UP promoter
- which confers sequence specific binding to promoter - what subunits are involved in catalytic synthesis
of RNA - ANSWER -- sigma recognizes -10 and -35 regions - for UP (AT rich) promoter region, C terminal
domain of two alpha
subunits recognize this
,*sigma confers sequence specific binding to promoter
*beta and beta' subunits are involved in the catalytic synthesis of RNA
Where do sequence-specific interaction with the promoter occur? -
ANSWER -sigma subunit - sometimes alpha subunit if UP promoter is present
Sigma in holoenzyme recognizes -10 element via ____ with the non
template DNA strand of promoter - ANSWER -Sigma in holoenzyme
recognizes -10 element via base-specific interactions with the non
template DNA strand of promoter
Free sigma subunit (does/does not) recognize single stranded non
template strand - ANSWER -does not
*for sigma to recognize -10 and -35 regions, non-template strand has to
be in double stranded conformation
DNA Footprinting to identify that alpha-subunit recognizes UP
promoter element - ANSWER -- purified RNA Pol and DNA sequence
bound together - 5' end labeled with radioactive nucleotide (side protected by RNA Pol) - region bound
by RNA Pol protected from cleavage by DNase - after DNase treatment, purify DNA, run DNA on gel
- missing bands identify the binding site
Stages of transcription initiation - ANSWER -- holoenzyme recognizes
regulatory sequence in promoter and binds forming the closed promoter
complex - unwind dsDNA to form open promoter complex - transcription initiates (RNA Pol generates
short abortive transcripts
that are unstable and released) - at 10nt in length, the complex is stable and turns from initiation to
elongation
, Cycling of sigma during transcription - ANSWER -- as Pol transitions
to elongation, sigma factor is released - transcription proceeds with just core subunits until termination -
at termination, RNA Pol released - nascent RNA released - released core enzyme recycles back to bind
with sigma to form the
holoenzyme and repeats
Abortive transcription and initiation: RNA Pol at promoter - ANSWER -3 ideas:
1. movement of transient excursion: RNA Pol makes short movement
along DNA to make abortive transcripts, then goes back to its original
position
2. inch worming: back of RNA Pol stays stationary, as abortive
transcripts are made, front edge of RNA Pol stretches/inch worms, as
abortive transcript is released front of RNA Pol goes back to initial
position
3. scrunching: RNA Pol doesnt move but DNA compresses/scrunches in
promoter
How scientists determined which theory about RNA Pol and abortive
transcription is true - ANSWER -FRET - donor and acceptor used; donor can be stimulated and release
energy
which is transferred to acceptor and will fluoresce at different
wavelength - efficiency determined by proximity between donor and acceptor
How FRET would work concerning RNA Pol and abortive transcription - ANSWER -- linked acceptor to
DNA template and donor to back end
of sigma subunit - assembled open promoter complex - GTP and UTP added to start synthesis -
measured degree of energy transfer between donor and acceptor
(proximity)
What FRET would show for: - transient excursion - inchworming - scrunching - ANSWER -- transient
excursion: as Pol moves forward,
