BCHM 4360 EXAM 2
What is transcriptional silencing? - ANSWERS-where large
chromosomal regions are not transcribed for long periods of time,
perhaps many cell divisions
What is the function of Sir proteins? - ANSWERS-Silencing
Information Regulator proteins, establish and maintain
heterochromatin
What is the genomic cause of Rett Syndrome? - ANSWERS-MeCP2
binds to methylated DNA and recruits Sin3A, a transcriptional co-
repressor that represses a number of important human genes, only on
X chromosome though
What is the genomic cause for Beckwith-Wiedemann syndrome? -
ANSWERS-Failure of correct imprinting with regards to IGF2(off)
maternal and H19 (off) paternal and looping of DNA caused by
enhancer-bound proteins
What did Bonas and colleagues discover and do about plant
pathogens? - ANSWERS-They noticed that the amino acid sequences
of each repeat in transcription activator-like proteins (TAL) was
highly conserved so they used bioinformatics to align the sequences
and a consensus binding sequence was identified
,What did Stoddard and colleagues examine and find? - ANSWERS-
They examined crystal structures of TAL proteins bound to DNA,
found that these repeats are arranged in a right-handed spiral that
follows the major groove of DNA. Found that each TAL repeat forms
a pair of alpha-helices. Found that the residues between the alpha-
helices are inserted in the major groove and recognize and interact
with a single base pair.
TAL is being used for engineering of proteins with specific binding
affinities.
What did Johnson, Meyer, and Ptashne discover? - ANSWERS-They
discovered that the switch between lysis and lysogeny in phage
lambda is regulated by cooperative binding of cI to DNA, and this
depends on the C-terminal. Using nuclease protection assays, they
determined that, with increasing amounts of cI, cI binds first to OR1
and OR2, then OR3 - this allowed equilibrium constants to be
calculated for each site. Data showed cooperative binding.
What is the alternate pairwise cooperation model? - ANSWERS-
Under wild-type conditions, the pair binds to OR1 and OR2, and OR3
only binds at much higher concentrations. When OR1 is mutated, the
pair binds to OR2 and OR3.
What did Dodd and colleagues find with regards to the alternate
pairwise cooperation model? - ANSWERS-They found that cI binding
to OR3 is helped by cooperative interaction with OL3. Repression of
Prm by cI requires OL, probably due to DNA looping around so cI
can interact with both operators, mediated by octamer formation at
high cI concentrations.
,Which experiment produced results by accident? - ANSWERS-
Ferruccio Ritossa discovered the increase in transcription that occurs
with increased temperature due to an accidental increase in
temperature of the incubators. Puffs were observed to be different in
the different temperatures.
What did Pelham and colleagues find with regards to heat-shock
proteins? - ANSWERS-They deleted different parts of the promoter to
see which regions were important for transcription and found that the
sequences between -10 and -66 were enough for heat-shock induction.
Promoters smaller than -66 from the transcription start site resulted in
no transcript.
How were microarrays used by Brown, Davis, and colleagues to
describe heat-shock proteins? - ANSWERS-Human cells were either
subjected to heat-shock or grown normally. RNA from each type of
cell was labeled with a different colored dye and put on a microarray.
Differences in the ratio of the dyes indicated differences in
transcription between normal growth and heat-shock for certain
genes.
What are the three steps of translation? - ANSWERS-initiation,
elongation, termination
True or False: The transcription bubble is just as big as the replication
bubble. - ANSWERS-False, replication bubble is much larger because
it requires two machines at once.
, When does transcription officially start? - ANSWERS-when RNA
Polymerase binds to the promoter
What is the first base to be transcribed known as and how is it
denoted? - ANSWERS-the transcription start site (TSS) and +1
Which direction is RNA transcribed in? - ANSWERS-5' to 3'
On RNA, bases 3' of a site are __________ while bases 5' of a site are
_________. - ANSWERS-downstream, upstream
When the RNA is a sufficient size, the RNA Polymerase moves past
the ________ and changes ____________ to be more stably
associated with the DNA. - ANSWERS-promoter, conformation
How does the RNA Polymerase maintain the transcription bubble
along the DNA? - ANSWERS-unwinds the DNA ahead of the bubble
and the DNA re-pairs behind the enzyme
Elongation continues until the polymerase meets a DNA sequence
called a __________. - ANSWERS-terminator
What are the three additional types of enzymes besides RNA
Polymerase that are required in eukaryotic transcription? -
ANSWERS-1. Nucleosome remodeling enzymes
2. Histone chaperones
What is transcriptional silencing? - ANSWERS-where large
chromosomal regions are not transcribed for long periods of time,
perhaps many cell divisions
What is the function of Sir proteins? - ANSWERS-Silencing
Information Regulator proteins, establish and maintain
heterochromatin
What is the genomic cause of Rett Syndrome? - ANSWERS-MeCP2
binds to methylated DNA and recruits Sin3A, a transcriptional co-
repressor that represses a number of important human genes, only on
X chromosome though
What is the genomic cause for Beckwith-Wiedemann syndrome? -
ANSWERS-Failure of correct imprinting with regards to IGF2(off)
maternal and H19 (off) paternal and looping of DNA caused by
enhancer-bound proteins
What did Bonas and colleagues discover and do about plant
pathogens? - ANSWERS-They noticed that the amino acid sequences
of each repeat in transcription activator-like proteins (TAL) was
highly conserved so they used bioinformatics to align the sequences
and a consensus binding sequence was identified
,What did Stoddard and colleagues examine and find? - ANSWERS-
They examined crystal structures of TAL proteins bound to DNA,
found that these repeats are arranged in a right-handed spiral that
follows the major groove of DNA. Found that each TAL repeat forms
a pair of alpha-helices. Found that the residues between the alpha-
helices are inserted in the major groove and recognize and interact
with a single base pair.
TAL is being used for engineering of proteins with specific binding
affinities.
What did Johnson, Meyer, and Ptashne discover? - ANSWERS-They
discovered that the switch between lysis and lysogeny in phage
lambda is regulated by cooperative binding of cI to DNA, and this
depends on the C-terminal. Using nuclease protection assays, they
determined that, with increasing amounts of cI, cI binds first to OR1
and OR2, then OR3 - this allowed equilibrium constants to be
calculated for each site. Data showed cooperative binding.
What is the alternate pairwise cooperation model? - ANSWERS-
Under wild-type conditions, the pair binds to OR1 and OR2, and OR3
only binds at much higher concentrations. When OR1 is mutated, the
pair binds to OR2 and OR3.
What did Dodd and colleagues find with regards to the alternate
pairwise cooperation model? - ANSWERS-They found that cI binding
to OR3 is helped by cooperative interaction with OL3. Repression of
Prm by cI requires OL, probably due to DNA looping around so cI
can interact with both operators, mediated by octamer formation at
high cI concentrations.
,Which experiment produced results by accident? - ANSWERS-
Ferruccio Ritossa discovered the increase in transcription that occurs
with increased temperature due to an accidental increase in
temperature of the incubators. Puffs were observed to be different in
the different temperatures.
What did Pelham and colleagues find with regards to heat-shock
proteins? - ANSWERS-They deleted different parts of the promoter to
see which regions were important for transcription and found that the
sequences between -10 and -66 were enough for heat-shock induction.
Promoters smaller than -66 from the transcription start site resulted in
no transcript.
How were microarrays used by Brown, Davis, and colleagues to
describe heat-shock proteins? - ANSWERS-Human cells were either
subjected to heat-shock or grown normally. RNA from each type of
cell was labeled with a different colored dye and put on a microarray.
Differences in the ratio of the dyes indicated differences in
transcription between normal growth and heat-shock for certain
genes.
What are the three steps of translation? - ANSWERS-initiation,
elongation, termination
True or False: The transcription bubble is just as big as the replication
bubble. - ANSWERS-False, replication bubble is much larger because
it requires two machines at once.
, When does transcription officially start? - ANSWERS-when RNA
Polymerase binds to the promoter
What is the first base to be transcribed known as and how is it
denoted? - ANSWERS-the transcription start site (TSS) and +1
Which direction is RNA transcribed in? - ANSWERS-5' to 3'
On RNA, bases 3' of a site are __________ while bases 5' of a site are
_________. - ANSWERS-downstream, upstream
When the RNA is a sufficient size, the RNA Polymerase moves past
the ________ and changes ____________ to be more stably
associated with the DNA. - ANSWERS-promoter, conformation
How does the RNA Polymerase maintain the transcription bubble
along the DNA? - ANSWERS-unwinds the DNA ahead of the bubble
and the DNA re-pairs behind the enzyme
Elongation continues until the polymerase meets a DNA sequence
called a __________. - ANSWERS-terminator
What are the three additional types of enzymes besides RNA
Polymerase that are required in eukaryotic transcription? -
ANSWERS-1. Nucleosome remodeling enzymes
2. Histone chaperones
