BCH5413 TEST 2 QUESTIONS AND ANSWERS ALL
REVISED AND UPDATED
What happens after phosphodiester bond formation? - ANSWER Release
of PPi
- synthesis 5' -> 3'
Does RNA synthesis require a primer? - ANSWER -RNA synthesis and
transcription does not require primer
- can initiate de novo
RNA transcription -
carried out by..
- what does it do
- separation of two DNA strands? - ANSWER -transcription carried out
by RNA Pol
- Pol catalyzes synthesis of nascent RNA
- separation of two DNA strands creates transcription bubble
Rate of transcription - ANSWER -eukaryotes: 15-30 nt/sec
Bacteria: 50-100 nt/sec
Mechanisms of bacterial transcription initiation: RNA Pol
- synthesizes what from what
- in E. coli how many Pol synthesize most of the DNA - ANSWER --
synthesizes RNA from one strand of dsDNA template
- in E. coli a single RNA Pol synthesizes most mRNA, tRNA, rRNA
Holoenzyme subunits - ANSWER -4 subunits: alpha, beta, beta', sigma
,- Core enzyme: alpha, beta, beta' (synthesizes RNA randomly on
dsDNA templates)
- sigma factor: confers promoter binding and specificty
Sigma factor(s) with Pol
- most E. coli promoters bound by...
- allows for...
- sigma is released upon.... what continues transcription elongation? -
alternative sigma factors recognize... - ANSWER -- most E. coli
promoters bound by sigma 70 associated RNA Pol
- allows correct binding and transcription initiation at specific promoters
- sigma is released upon transcription initiation; core enzyme continues
transcription elongation
- alternative sigma factors recognize different promoters
Corresponding gene to holoenzyme subunit
- subunit functions - ANSWER -rpoA: 2 alpha subunits (enzyme
assembly, promoter recognition, binds some activators)
rpoB: beta subunit (catalytic center)
rpoC: Beta' subunit (catalytic center)
rpoD: sigma subunit (promoter specificity)
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
REVISED AND UPDATED
What happens after phosphodiester bond formation? - ANSWER Release
of PPi
- synthesis 5' -> 3'
Does RNA synthesis require a primer? - ANSWER -RNA synthesis and
transcription does not require primer
- can initiate de novo
RNA transcription -
carried out by..
- what does it do
- separation of two DNA strands? - ANSWER -transcription carried out
by RNA Pol
- Pol catalyzes synthesis of nascent RNA
- separation of two DNA strands creates transcription bubble
Rate of transcription - ANSWER -eukaryotes: 15-30 nt/sec
Bacteria: 50-100 nt/sec
Mechanisms of bacterial transcription initiation: RNA Pol
- synthesizes what from what
- in E. coli how many Pol synthesize most of the DNA - ANSWER --
synthesizes RNA from one strand of dsDNA template
- in E. coli a single RNA Pol synthesizes most mRNA, tRNA, rRNA
Holoenzyme subunits - ANSWER -4 subunits: alpha, beta, beta', sigma
,- Core enzyme: alpha, beta, beta' (synthesizes RNA randomly on
dsDNA templates)
- sigma factor: confers promoter binding and specificty
Sigma factor(s) with Pol
- most E. coli promoters bound by...
- allows for...
- sigma is released upon.... what continues transcription elongation? -
alternative sigma factors recognize... - ANSWER -- most E. coli
promoters bound by sigma 70 associated RNA Pol
- allows correct binding and transcription initiation at specific promoters
- sigma is released upon transcription initiation; core enzyme continues
transcription elongation
- alternative sigma factors recognize different promoters
Corresponding gene to holoenzyme subunit
- subunit functions - ANSWER -rpoA: 2 alpha subunits (enzyme
assembly, promoter recognition, binds some activators)
rpoB: beta subunit (catalytic center)
rpoC: Beta' subunit (catalytic center)
rpoD: sigma subunit (promoter specificity)
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
