BIMM 112 Midterm 2 questions well
answered already passed
Why do chromatin remodeling factors exist? - correct answer ✔✔ Nucleosomes are intrinsically
immobile on a biological timescale at physiological conditions.
What cofactor is used by chromatin remodeling factors? - correct answer ✔✔ ATP
All known chromatin remodeling factors have a subunit from the ----- family of proteins. (fill in
the blank) - correct answer ✔✔ SNF2-like
Explain how the restriction enzyme accessibility assay can be used to monitor chromatin
remodeling. - correct answer ✔✔ In the restriction enzyme accessibility assay, a bacterial
restriction enzyme, such as HaeIII, is added to chromatin. If the DNA containing a HaeIII
restriction site is packaged into a nucleosome (not in the linker DNA), the HaeIII is not able to
cut the DNA. In other words, digestion of DNA by HaeIII is blocked by nucleosomes. [HaeIII can
cut DNA in the linker DNA.] If, however, a chromatin remodeling factor is added, then the
nucleosomes will move and HaeIII will be able to cut its sites (when they are transiently in the
linker DNA between nucleosome cores). Thus, chromatin remodeling activity is monitored by
the increased HaeIII digestion of DNA packaged into chromatin.
Explain how the nucleosome "sliding" assay with differently positioned nucleosomes can be
used to demonstrate chromatin remodeling. - correct answer ✔✔ The nucleosome 'sliding'
assay monitors the change in nucleosome positioning on a mononucleosome. If you have a
mononucleosome (on, e.g., a DNA fragment of about 200 bp) with the nucleosome at the edge
of the DNA fragment, it will migrate faster on a gel than a mononucleosome with the
nucleosome positioned in the center of the same (in this case, 200 bp) DNA fragment. Thus, the
'sliding' assay monitors the chromatin-remodeling-factor-catalyzed shift of an edge-positioned
nucleosome to the center of the DNA fragment, or the shift of a center-positioned nucleosome
to the edge of the DNA fragment.
,Give one example of the regulation of the activity of a chromatin remodeling enzyme, such as
one of those discussed in class. - correct answer ✔✔ (i). The chromatin remodeling activity of
Rad54 is regulated by Rad51. Specifically, the Rad51 protein activates chromatin remodeling
activity by Rad54. It appears that Rad54 has an autoinhibitory region that is depressed upon the
binding of Rad51 to Rad54. or,
(ii). The recruitment of HARP (SMARCAL1) to sites of DNA damage is dependent upon the
binding of RPA (replication protein A) to the conserved N-terminal protein motif in HARP. or,
(iii). The conserved N-terminal Leucine Latch motif in CSB (also known as Rhp26 and ERCC6)
autoinhibits the ATPase and chromatin remodeling activities of CSB.
What general lesson about the evolution of eukaryotic enzymes with chromatin was learned in
the studies of homologous strand pairing by Rad54 and Rad51 in chromatin? - correct answer
✔✔ Over the course of evolution, eukaryotic DNA-directed enzymes have been optimized to
function more efficiently with chromatin (their natural substrate) than with naked DNA. In the
specific case of Rad54 and Rad51, homologous strand pairing by Rad54 and Rad51 works better
with chromatin than with naked DNA.
What are the primary functions of each of the three major eukaryotic RNA polymerases? -
correct answer ✔✔ 1. RNA polymerase I - synthesizes ribosomal RNA (rRNA except for 5S rRNA)
2. RNA polymerase II - synthesizes mRNA
3. RNA polymerase III - synthesizes tRNA and 5S rRNA
What is the biochemical activity of the HARP protein? - correct answer ✔✔ HARP is an ATP-
driven DNA rewinding motor protein (an annealing/reverse helicase)
From a theoretical standpoint, what are the properties of a pure boundary (insulator) element?
- correct answer ✔✔ A 'pure' boundary element is transcriptionally neutral, and acts as a cis-
acting barrier across which neither positive transcriptional activation (such as by enhancers) nor
negative transcriptional repression (such as by heterochromatin) can occur
Which basal transcription factor recognizes the TATA, Inr, MTE, DPE, and DPR core promoter
elements? What is the name of the subunit that binds to the TATA box? - correct answer ✔✔
, TFIID recognizes the TATA, Inr, MTE, DPE, and DPR TBP (TATA box-binding protein) binds to the
TATA box.
What is the name of the unique repeated amino acid sequence at the C-terminus of the largest
subunit of RNA polymerase II? What are its two most commonly studied post-translational
modifications, and where are they generally located on gene bodies? - correct answer ✔✔ CTD
(C-terminal domain). It is extensively modified with different modifications. The best-
characterized post-translational modifications are phosphorylation at Serine 2 and Serine5.
Phosphorylated Ser5 is commonly found at the 5' end of gene bodies. Phosphorylated Ser2 is
commonly found at the 3' end of gene bodies.
What basal transcription factor unwinds the DNA during transcription initiation? Aside from
transcription, in what basic molecular process does this factor participate? - correct answer ✔✔
TFIIH
TFIIH participates in transcription and in nucleotide excision repair (NER).
What is a TRF? Which TRF is present in all bilateria? - correct answer ✔✔ TRF = TBP-related
factor. TRFs are related to TBP.
TRF2 is present in all bilateria.
Which RNA polymerase II transcription system complements the RNA polymerase I and RNA
polymerase III transcription systems? Why? - correct answer ✔✔ -TCT motif (also known as the
polypyrimidine initiator) system.
-The RNA polymerase I system is dedicated to the synthesis of the 18S, 5.8S, and 28S rRNAs.
-The RNA polymerase III system synthesizes the 5S rRNA as well as tRNAs. The TCT system is
dedicated to the synthesis of ribosomal proteins. Thus, all combined, the three transcription
systems generate the ribosomal RNAs and proteins.
What is the name of the fungal toxin that inhibits RNA polymerase II at 1 microgram/mL
concentration? Does it affect other eukaryotic RNA polymerases? - correct answer ✔✔ α-
amanitin
answered already passed
Why do chromatin remodeling factors exist? - correct answer ✔✔ Nucleosomes are intrinsically
immobile on a biological timescale at physiological conditions.
What cofactor is used by chromatin remodeling factors? - correct answer ✔✔ ATP
All known chromatin remodeling factors have a subunit from the ----- family of proteins. (fill in
the blank) - correct answer ✔✔ SNF2-like
Explain how the restriction enzyme accessibility assay can be used to monitor chromatin
remodeling. - correct answer ✔✔ In the restriction enzyme accessibility assay, a bacterial
restriction enzyme, such as HaeIII, is added to chromatin. If the DNA containing a HaeIII
restriction site is packaged into a nucleosome (not in the linker DNA), the HaeIII is not able to
cut the DNA. In other words, digestion of DNA by HaeIII is blocked by nucleosomes. [HaeIII can
cut DNA in the linker DNA.] If, however, a chromatin remodeling factor is added, then the
nucleosomes will move and HaeIII will be able to cut its sites (when they are transiently in the
linker DNA between nucleosome cores). Thus, chromatin remodeling activity is monitored by
the increased HaeIII digestion of DNA packaged into chromatin.
Explain how the nucleosome "sliding" assay with differently positioned nucleosomes can be
used to demonstrate chromatin remodeling. - correct answer ✔✔ The nucleosome 'sliding'
assay monitors the change in nucleosome positioning on a mononucleosome. If you have a
mononucleosome (on, e.g., a DNA fragment of about 200 bp) with the nucleosome at the edge
of the DNA fragment, it will migrate faster on a gel than a mononucleosome with the
nucleosome positioned in the center of the same (in this case, 200 bp) DNA fragment. Thus, the
'sliding' assay monitors the chromatin-remodeling-factor-catalyzed shift of an edge-positioned
nucleosome to the center of the DNA fragment, or the shift of a center-positioned nucleosome
to the edge of the DNA fragment.
,Give one example of the regulation of the activity of a chromatin remodeling enzyme, such as
one of those discussed in class. - correct answer ✔✔ (i). The chromatin remodeling activity of
Rad54 is regulated by Rad51. Specifically, the Rad51 protein activates chromatin remodeling
activity by Rad54. It appears that Rad54 has an autoinhibitory region that is depressed upon the
binding of Rad51 to Rad54. or,
(ii). The recruitment of HARP (SMARCAL1) to sites of DNA damage is dependent upon the
binding of RPA (replication protein A) to the conserved N-terminal protein motif in HARP. or,
(iii). The conserved N-terminal Leucine Latch motif in CSB (also known as Rhp26 and ERCC6)
autoinhibits the ATPase and chromatin remodeling activities of CSB.
What general lesson about the evolution of eukaryotic enzymes with chromatin was learned in
the studies of homologous strand pairing by Rad54 and Rad51 in chromatin? - correct answer
✔✔ Over the course of evolution, eukaryotic DNA-directed enzymes have been optimized to
function more efficiently with chromatin (their natural substrate) than with naked DNA. In the
specific case of Rad54 and Rad51, homologous strand pairing by Rad54 and Rad51 works better
with chromatin than with naked DNA.
What are the primary functions of each of the three major eukaryotic RNA polymerases? -
correct answer ✔✔ 1. RNA polymerase I - synthesizes ribosomal RNA (rRNA except for 5S rRNA)
2. RNA polymerase II - synthesizes mRNA
3. RNA polymerase III - synthesizes tRNA and 5S rRNA
What is the biochemical activity of the HARP protein? - correct answer ✔✔ HARP is an ATP-
driven DNA rewinding motor protein (an annealing/reverse helicase)
From a theoretical standpoint, what are the properties of a pure boundary (insulator) element?
- correct answer ✔✔ A 'pure' boundary element is transcriptionally neutral, and acts as a cis-
acting barrier across which neither positive transcriptional activation (such as by enhancers) nor
negative transcriptional repression (such as by heterochromatin) can occur
Which basal transcription factor recognizes the TATA, Inr, MTE, DPE, and DPR core promoter
elements? What is the name of the subunit that binds to the TATA box? - correct answer ✔✔
, TFIID recognizes the TATA, Inr, MTE, DPE, and DPR TBP (TATA box-binding protein) binds to the
TATA box.
What is the name of the unique repeated amino acid sequence at the C-terminus of the largest
subunit of RNA polymerase II? What are its two most commonly studied post-translational
modifications, and where are they generally located on gene bodies? - correct answer ✔✔ CTD
(C-terminal domain). It is extensively modified with different modifications. The best-
characterized post-translational modifications are phosphorylation at Serine 2 and Serine5.
Phosphorylated Ser5 is commonly found at the 5' end of gene bodies. Phosphorylated Ser2 is
commonly found at the 3' end of gene bodies.
What basal transcription factor unwinds the DNA during transcription initiation? Aside from
transcription, in what basic molecular process does this factor participate? - correct answer ✔✔
TFIIH
TFIIH participates in transcription and in nucleotide excision repair (NER).
What is a TRF? Which TRF is present in all bilateria? - correct answer ✔✔ TRF = TBP-related
factor. TRFs are related to TBP.
TRF2 is present in all bilateria.
Which RNA polymerase II transcription system complements the RNA polymerase I and RNA
polymerase III transcription systems? Why? - correct answer ✔✔ -TCT motif (also known as the
polypyrimidine initiator) system.
-The RNA polymerase I system is dedicated to the synthesis of the 18S, 5.8S, and 28S rRNAs.
-The RNA polymerase III system synthesizes the 5S rRNA as well as tRNAs. The TCT system is
dedicated to the synthesis of ribosomal proteins. Thus, all combined, the three transcription
systems generate the ribosomal RNAs and proteins.
What is the name of the fungal toxin that inhibits RNA polymerase II at 1 microgram/mL
concentration? Does it affect other eukaryotic RNA polymerases? - correct answer ✔✔ α-
amanitin
