BMSC 708
BMSC 708 EXAM II 2025
Transcription Initiation (3 Steps) - Correct Ans-1. Polymerase binds to promoter
sequence in duplex DNA. "closed complex" 2. Polymerase melts duplex DNA near
transcription start site, forming a transcription bubble. "open complex" 3. Polymerase
catalyzes phosphodiester linkage of two initial rNTPs.
Elongation - Correct Ans-Polymerase advances 3'--> 5' down template strand, melting
duplex DNA and adding rNTPs to growing RNA.
Termination - Correct Ans-At transcription stop site, polymerase releases completed
RNA and dissociates from DNA.
transcription steps - Correct Ans-initiation, elongation, termination
RNA polymerase binds to specific ___________ to initiate transcription - Correct Ans-
promoter sequences
RNA polymerase subunits - Correct Ans-Beta- polymerization
Alpha- interact with other regulatory proteins
Sigma- specificity and identification of start site
promoter - Correct Ans-- A site on DNA to which the enzyme RNA polymerase can bind
initiate the transcription of DNA into RNA
- upstream of transcription start site
- 35 region and -10 region "consenus sequences"
consensus sequences - Correct Ans-short stretches of DNA that appear with little
variation, in many different genes
pribnow box - Correct Ans-the TATAAT sequence that is often found at the -10 region
of bacterial promoters,
promoter consensus sequences - Correct Ans--35bp TTGACA
-10bp TATAAT (prinbow box)
alternative sigma factors - Correct Ans-recognize different sets of promoters to control
expression of specific groups of genes
sigma 70 - Correct Ans-- RNA polymerase subunit
- repressors or activators bind to DNA near a region to which RNA polymerase binds
- repressors bind between +30 and -50
- activators bind between -30 and -65
operon - Correct Ans-cluster of genes under the control of a single promoter
sigma 54 - Correct Ans-- RNA polymerase subunit
- activators bind generally between -80 and -160
- active transcription even when their enhancers (binding sites) are moved more than a
kilobase away from the start site
enhancers - Correct Ans-- A DNA sequence that recognizes certain transcription
factors that can stimulate transcription of nearby genes
- binds to specific TF
- acts in an orientation and position independent manner
DNase I footprinting assays - Correct Ans-- identify protein-DNA interactions
- identifies specific sequence location where polymerase binds
Lac repressor - Correct Ans-a protein that binds to the operator site of the lac operon
and inhibits transcription
BMSC 708
, BMSC 708
_____________ and ___________ on the lac control region - Correct Ans-foorprint of
RNA polymerase, lac repressor
Gel-shift assays - Correct Ans-- identify protein-DNA interactions
- detect protein binding to DNA. DNA migrates through the gel according to size. protein
binding to DNA slows it down
Jacob-Monod model - Correct Ans-- model of repressors and activators
- bacterial gene control
- RNA polymerase, lac repressor, lactose, medium, Nascent polypeptide chains, B-
galactosidase, lactose permease, thiogalactoside transacetylase
induction of lac operon - Correct Ans-leads to increase synthesis of lac mRNA
three critical cis-acting sites on lac control region - Correct Ans-1. cAMP-CAP footprint
2. RNA polymerase footprint
3. Repressor footprint
Isopropyl-B-D- thiogalactoside - Correct Ans-- inducer of galactosidase activity by
binding and inhibiting the repressor
- induce lac operon: increase synthesis of lac mRNA
operator - Correct Ans-- DNA sequence where regulatory molecules bind to regulate
gene expression
- only found in prokaryotes
- often times short inverted repeats
bacterial repressor structure - Correct Ans-most are dimers containing alpha helices
that insert into adjacent major grooves of operator DNA
cAMP-CAP - Correct Ans-binds CAP site and assists RNA polymerase bind to
promoter to transcribe lac operon in the absence of glucose
CAP - Correct Ans-- catabolite activator protein
- glucose sensor: activates transcription of lac operon, but only when glucose is low
- helps RNA polymerase bind to promoter
- requires binding with cAMP
glucose present (cAMP low); no lactose - Correct Ans-repressor binds operator; no lac
mRNA
glucose present (cAMP low), lactose present - Correct Ans-lactose binds repressor,
very little mRNA transcribed
glucose present (cAMP high), lactose present - Correct Ans-lactose binds repressor,
cAMP binds promoter, abundant lac mRNA transcribed
cAMP - Correct Ans-- "hunger signal" produced when glucose levels are low
- binds to CAP, then binds to CAP site to help RNA polymerase bind to promoter
lactose (lac operon) - Correct Ans-lac operon inducer molecule that binds lac repressor
and prevents binding to the operator
lac operon - Correct Ans-- gene system responsible for the metabolism of lactose
- expressed in the presence of lactose and the absence of glucose
- contains the three genes: LacZ, LacY, LacA
lac repressor - Correct Ans-- represses transcription of lac operon in the absence of
lactose
- when lactose is present, it binds the lac repressor and prevent its binding to the
operator - catabolic operon
trp operon - Correct Ans-- anabolic operon
BMSC 708
BMSC 708 EXAM II 2025
Transcription Initiation (3 Steps) - Correct Ans-1. Polymerase binds to promoter
sequence in duplex DNA. "closed complex" 2. Polymerase melts duplex DNA near
transcription start site, forming a transcription bubble. "open complex" 3. Polymerase
catalyzes phosphodiester linkage of two initial rNTPs.
Elongation - Correct Ans-Polymerase advances 3'--> 5' down template strand, melting
duplex DNA and adding rNTPs to growing RNA.
Termination - Correct Ans-At transcription stop site, polymerase releases completed
RNA and dissociates from DNA.
transcription steps - Correct Ans-initiation, elongation, termination
RNA polymerase binds to specific ___________ to initiate transcription - Correct Ans-
promoter sequences
RNA polymerase subunits - Correct Ans-Beta- polymerization
Alpha- interact with other regulatory proteins
Sigma- specificity and identification of start site
promoter - Correct Ans-- A site on DNA to which the enzyme RNA polymerase can bind
initiate the transcription of DNA into RNA
- upstream of transcription start site
- 35 region and -10 region "consenus sequences"
consensus sequences - Correct Ans-short stretches of DNA that appear with little
variation, in many different genes
pribnow box - Correct Ans-the TATAAT sequence that is often found at the -10 region
of bacterial promoters,
promoter consensus sequences - Correct Ans--35bp TTGACA
-10bp TATAAT (prinbow box)
alternative sigma factors - Correct Ans-recognize different sets of promoters to control
expression of specific groups of genes
sigma 70 - Correct Ans-- RNA polymerase subunit
- repressors or activators bind to DNA near a region to which RNA polymerase binds
- repressors bind between +30 and -50
- activators bind between -30 and -65
operon - Correct Ans-cluster of genes under the control of a single promoter
sigma 54 - Correct Ans-- RNA polymerase subunit
- activators bind generally between -80 and -160
- active transcription even when their enhancers (binding sites) are moved more than a
kilobase away from the start site
enhancers - Correct Ans-- A DNA sequence that recognizes certain transcription
factors that can stimulate transcription of nearby genes
- binds to specific TF
- acts in an orientation and position independent manner
DNase I footprinting assays - Correct Ans-- identify protein-DNA interactions
- identifies specific sequence location where polymerase binds
Lac repressor - Correct Ans-a protein that binds to the operator site of the lac operon
and inhibits transcription
BMSC 708
, BMSC 708
_____________ and ___________ on the lac control region - Correct Ans-foorprint of
RNA polymerase, lac repressor
Gel-shift assays - Correct Ans-- identify protein-DNA interactions
- detect protein binding to DNA. DNA migrates through the gel according to size. protein
binding to DNA slows it down
Jacob-Monod model - Correct Ans-- model of repressors and activators
- bacterial gene control
- RNA polymerase, lac repressor, lactose, medium, Nascent polypeptide chains, B-
galactosidase, lactose permease, thiogalactoside transacetylase
induction of lac operon - Correct Ans-leads to increase synthesis of lac mRNA
three critical cis-acting sites on lac control region - Correct Ans-1. cAMP-CAP footprint
2. RNA polymerase footprint
3. Repressor footprint
Isopropyl-B-D- thiogalactoside - Correct Ans-- inducer of galactosidase activity by
binding and inhibiting the repressor
- induce lac operon: increase synthesis of lac mRNA
operator - Correct Ans-- DNA sequence where regulatory molecules bind to regulate
gene expression
- only found in prokaryotes
- often times short inverted repeats
bacterial repressor structure - Correct Ans-most are dimers containing alpha helices
that insert into adjacent major grooves of operator DNA
cAMP-CAP - Correct Ans-binds CAP site and assists RNA polymerase bind to
promoter to transcribe lac operon in the absence of glucose
CAP - Correct Ans-- catabolite activator protein
- glucose sensor: activates transcription of lac operon, but only when glucose is low
- helps RNA polymerase bind to promoter
- requires binding with cAMP
glucose present (cAMP low); no lactose - Correct Ans-repressor binds operator; no lac
mRNA
glucose present (cAMP low), lactose present - Correct Ans-lactose binds repressor,
very little mRNA transcribed
glucose present (cAMP high), lactose present - Correct Ans-lactose binds repressor,
cAMP binds promoter, abundant lac mRNA transcribed
cAMP - Correct Ans-- "hunger signal" produced when glucose levels are low
- binds to CAP, then binds to CAP site to help RNA polymerase bind to promoter
lactose (lac operon) - Correct Ans-lac operon inducer molecule that binds lac repressor
and prevents binding to the operator
lac operon - Correct Ans-- gene system responsible for the metabolism of lactose
- expressed in the presence of lactose and the absence of glucose
- contains the three genes: LacZ, LacY, LacA
lac repressor - Correct Ans-- represses transcription of lac operon in the absence of
lactose
- when lactose is present, it binds the lac repressor and prevent its binding to the
operator - catabolic operon
trp operon - Correct Ans-- anabolic operon
BMSC 708
