Molecular Biology Exam test quiz
and answers graded A+
What are the main 2 differences between DNA and RNA polymerase? - ANS✅✅RNA contains an -
OH group attached. RNA polymerase also does not need a primer to begin.
TF2D - ANS✅✅general transcription factor that binds to TATA box, causing a large distortion in the
DNA which helps begin transcription. Binds to TBP subunit on transcription factor.
TF2H - ANS✅✅Uses ATP to pry apart DNA double helix at transcription start point, locally exposing
template strand.
Also phosphorylates serines on CTD tail of RNA polymerase II so polymerase is released from general
factors and begin elongation phase of transcription.
C terminal domain - ANS✅✅Contains sequence of amino acids that can accept phosphorylation
from TF2H using repeated serines.
Phosphorylation helps change RNA polymerase II conformation so elongation phase of transcription
can begin.
consensus sequence - ANS✅✅repeating sequence of nucleotides common for that function.
Location for general transcription factor binding point.
Where is everything located in proximity to transcription? - ANS✅✅All the proteins, DNA, and
even released RNA strand is kept in close environment within reach for convenience and efficiency
transcriptional activators - ANS✅✅gene regulatory proteins that bind to specific DNA sequences
to attract RNA polymerase II to start point of transcription.
mediator - ANS✅✅protein complex that allows activator proteins to communicate properly with
polymerase II and general transcription factors.
enhancer site - ANS✅✅binding site for activator protein - the DNA strand is looped around the
mediator so the binding site can be reached by the activator protein easily
,What are 4 ways to locally alter chromatin? - ANS✅✅Covalent histone modifications
nucleosome remodeling
nucleosome removal
nucleosome replacement
(all of the above help DNA become more accessible for transcription)
How does a specific regulatory protein assist in preparation of transcription at the histone level? -
ANS✅✅1) Regulatory protein bound to a regulatory sequence.
2) Recruits histone acetyl transferase, which attach acetyl groups to LYSINES exposed on some
exposed histone tails.
3) Acetylation negates charge interaction between positively charged lysine and negatively charged
carboxyl group, loosens up association.
4) Recruitment of protein kinase activity specific for histones.
5) Phosphorylation of serine residues on histone tails.
6) Previous phosphorylation and acetylation create the histone code (modification of histone) for
other regulatory proteins to "read" - chromatin remodeling complex attracted in this case.
7) Help move nucleosomes that facilitate attachment of transcription factor.
What is the general order of events leading to transcription initiation of a specific gene (example in
budding yeast) - ANS✅✅Gene activator protein binds to chromatin
Chromatin remodeling
covalent histone modification
addt'l activator proteins bind to gene regulatory region
assembly of pre-initiation complex and promoter
rearrangement of proteins in pre-initiation complex
transcription initiation
What are six ways in which eukaryotic gene repressor proteins can operate? - ANS✅✅1)
competitive DNA binding for repressor/activator
2) masking activation surface
3) repressor directly interacts with general transcription factors, preventing activator binding
, 4) recruitment of chromatin remodeling complex (makes chromatin more tightly bound so TATA
cannot be reached.)
5) recruitment of histone deacetylases (makes chromatin more tight and does not help binding of
transcription factors)
6) recruitment of histone methyl transferase (methyl group does not allow any other protein to bind
there)
histone deacetylase - ANS✅✅recruited by gene repressor proteins to prevent transcription. If
acetylation stimulates transcription initiation, de-acetylation reverses it.
histone methyl transferase - ANS✅✅causes methylation of histone tails on nucleosome, which
creates heterochromatin
What determines whether a gene is activated or not? - ANS✅✅the sum total of the regulation of
proteins in the environment.
Why is a methyl group important to the repression of transcription? - ANS✅✅Methyl group
attracts other protein that bind to other nucleosome regions.
When present, nothing else can come and bind. Shut down ability to activate any gene in that
region.
architectural protein - ANS✅✅protein that bends DNA to allow cooperative assembly of other
protein components to activate transcription.
What are 7 ways regulatory proteins are controlled? - ANS✅✅1) Control it at level of protein
synthesizing (make the protein or not, involves regulation gene that controls transcription factor)
2) Requirement binding of co-regulatory molecule
3) Phosphorylate/modify in some way
4) Assembly in which DNA binding subunit is separate from activation domain, requires it to come
together before activator protein can work
5) Un masking of inhibitor
6) Transcription factor stays in cytoplasm and can actually release inhibitor into nucleus after cell
signaling.
7) Release from nuclear membrane after cell signaling.
and answers graded A+
What are the main 2 differences between DNA and RNA polymerase? - ANS✅✅RNA contains an -
OH group attached. RNA polymerase also does not need a primer to begin.
TF2D - ANS✅✅general transcription factor that binds to TATA box, causing a large distortion in the
DNA which helps begin transcription. Binds to TBP subunit on transcription factor.
TF2H - ANS✅✅Uses ATP to pry apart DNA double helix at transcription start point, locally exposing
template strand.
Also phosphorylates serines on CTD tail of RNA polymerase II so polymerase is released from general
factors and begin elongation phase of transcription.
C terminal domain - ANS✅✅Contains sequence of amino acids that can accept phosphorylation
from TF2H using repeated serines.
Phosphorylation helps change RNA polymerase II conformation so elongation phase of transcription
can begin.
consensus sequence - ANS✅✅repeating sequence of nucleotides common for that function.
Location for general transcription factor binding point.
Where is everything located in proximity to transcription? - ANS✅✅All the proteins, DNA, and
even released RNA strand is kept in close environment within reach for convenience and efficiency
transcriptional activators - ANS✅✅gene regulatory proteins that bind to specific DNA sequences
to attract RNA polymerase II to start point of transcription.
mediator - ANS✅✅protein complex that allows activator proteins to communicate properly with
polymerase II and general transcription factors.
enhancer site - ANS✅✅binding site for activator protein - the DNA strand is looped around the
mediator so the binding site can be reached by the activator protein easily
,What are 4 ways to locally alter chromatin? - ANS✅✅Covalent histone modifications
nucleosome remodeling
nucleosome removal
nucleosome replacement
(all of the above help DNA become more accessible for transcription)
How does a specific regulatory protein assist in preparation of transcription at the histone level? -
ANS✅✅1) Regulatory protein bound to a regulatory sequence.
2) Recruits histone acetyl transferase, which attach acetyl groups to LYSINES exposed on some
exposed histone tails.
3) Acetylation negates charge interaction between positively charged lysine and negatively charged
carboxyl group, loosens up association.
4) Recruitment of protein kinase activity specific for histones.
5) Phosphorylation of serine residues on histone tails.
6) Previous phosphorylation and acetylation create the histone code (modification of histone) for
other regulatory proteins to "read" - chromatin remodeling complex attracted in this case.
7) Help move nucleosomes that facilitate attachment of transcription factor.
What is the general order of events leading to transcription initiation of a specific gene (example in
budding yeast) - ANS✅✅Gene activator protein binds to chromatin
Chromatin remodeling
covalent histone modification
addt'l activator proteins bind to gene regulatory region
assembly of pre-initiation complex and promoter
rearrangement of proteins in pre-initiation complex
transcription initiation
What are six ways in which eukaryotic gene repressor proteins can operate? - ANS✅✅1)
competitive DNA binding for repressor/activator
2) masking activation surface
3) repressor directly interacts with general transcription factors, preventing activator binding
, 4) recruitment of chromatin remodeling complex (makes chromatin more tightly bound so TATA
cannot be reached.)
5) recruitment of histone deacetylases (makes chromatin more tight and does not help binding of
transcription factors)
6) recruitment of histone methyl transferase (methyl group does not allow any other protein to bind
there)
histone deacetylase - ANS✅✅recruited by gene repressor proteins to prevent transcription. If
acetylation stimulates transcription initiation, de-acetylation reverses it.
histone methyl transferase - ANS✅✅causes methylation of histone tails on nucleosome, which
creates heterochromatin
What determines whether a gene is activated or not? - ANS✅✅the sum total of the regulation of
proteins in the environment.
Why is a methyl group important to the repression of transcription? - ANS✅✅Methyl group
attracts other protein that bind to other nucleosome regions.
When present, nothing else can come and bind. Shut down ability to activate any gene in that
region.
architectural protein - ANS✅✅protein that bends DNA to allow cooperative assembly of other
protein components to activate transcription.
What are 7 ways regulatory proteins are controlled? - ANS✅✅1) Control it at level of protein
synthesizing (make the protein or not, involves regulation gene that controls transcription factor)
2) Requirement binding of co-regulatory molecule
3) Phosphorylate/modify in some way
4) Assembly in which DNA binding subunit is separate from activation domain, requires it to come
together before activator protein can work
5) Un masking of inhibitor
6) Transcription factor stays in cytoplasm and can actually release inhibitor into nucleus after cell
signaling.
7) Release from nuclear membrane after cell signaling.
