Genetics Ch15
Select ways in which chromatin remodelers change chromatin structure. -Change in nucleosome position -Change in the composition of nucleosomes due to the exchange of RNA for DNA -Removal of histones from the DNA, creating nucleosome free gaps -Change in the composition of nucleosomes due to exchange of histones
-Change in nucleosome position -Removal of histones from the DNA, creating nucleosome free gaps -Change in the composition of nucleosomes due to exchange of histones
Select common factors that contribute to combinatorial control. -DNA methylation inhibits transcription. -Regulatory proteins alter the composition or arrangement of nucleosomes in the vicinity of a promoter. -Regulatory proteins change the sequence of the DNA in the vicinity of a promoter. -Activator proteins stimulate the ability of RNA polymerase to initiate transcription. -Activator and repressor activity is modulated by small effector molecules, protein-protein interactions, and covalent modifications. -Repressor proteins inhibit the ability of RNA polymerase to initiate transcription.
-DNA methylation inhibits transcription. -Regulatory proteins alter the composition or arrangement of nucleosomes in the vicinity of a promoter. -Activator proteins stimulate the ability of RNA polymerase to initiate transcription. -Activator and repressor activity is modulated by small effector molecules, protein-protein interactions, and covalent modifications. -Repressor proteins inhibit the ability of RNA polymerase to initiate transcription.
Select the locations where cis regulatory elements can be found relative to the gene of interest. -Downstream from the core promoter -Close to the core promoter -Upstream from the core promoter -Within introns -On a different chromosome -Far from the core promoter
-Downstream from the core promoter -Close to the core promoter -Upstream from the core promoter -Within introns -Far from the core promoter
Select the factors that are involved in activation of the CREB protein. -G protein -Mediator -Adenylyl cyclase -Protein kinase A -cAMP
-G protein -Adenylyl cyclase -Protein kinase A -cAMP
Select motifs that promote protein dimerization. -Zinc finger motif -Helix-loop-helix motif -Helix-turn-helix motif -Leucine zipper motif
-Helix-loop-helix motif -Leucine zipper motif
Select the common types of covalent modifications made to the amino-terminal tails of histones. -Methylation -Phosphorylation -Ubiquitination -Acetylation
-Methylation -Phosphorylation -Acetylation
Select the steps at which gene regulation can occur -DNA replication -RNA processing -Translation -Posttranslational modification -Transcription
-RNA processing -Translation -Posttranslational modification -Transcription
Select examples of how gene regulation benefits eukaryotic organisms. (select all that apply) -The ability to remove deleterious genes -The ability to respond to environmental stresses -The ability to respond to changes in nutrient availability
-The ability to respond to environmental stresses -The ability to respond to changes in nutrient availability
Select the most common ways that the functions of regulatory transcription factors are controlled. -Protein-RNA interactions -The binding of a small effector molecule -Protein-protein interactions -Protein-DNA interactions -Covalent modifications
-The binding of a small effector molecule -Protein-protein interactions -covalent modifications
Select the elements that compose a zinc finger motif. -Two β-sheet structures -Two zinc metal ions -Two α-helices -One α-helix -One β-sheet structure -A zinc metal ion
-Two β-sheet structures -One α-helix -A zinc metal ion
Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ________ (select multiple if needed) -controlling the switch from the initiation to the elongation stage of transcription -preventing DNA replication -regulating the unwinding of the double-stranded DNA at the promoter sequence -regulating the binding of the transcriptional complex to the core promoter -regulating RNA processing
-controlling the switch from the initiation to the elongation stage of transcription -regulating the binding of the transcriptional complex to the core promoter
Plants and animals require a greater level of gene regulation than single-celled eukaryotes because of _________ (select all that apply) -presence of multiple organelles -different tissue types -different developmental stages -more complex cell structure -multicellularity
-different tissue types -different developmental stages -more complex cell structure -multicellularity
The function of regulatory transcription factors must be modulated to ensure that genes are turned on ______. -all the time -in the correct cell type -at the proper time -under the appropriate environmental conditions -in growing cells only
-in the correct cell type -at the proper time -under the appropriate environmental conditions
Repressors inhibit TFIID by ______. -preventing the binding of TFIID to the TATA box -inhibiting the function of mediator -changing nucleosome organization near the promoter region -inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter
-preventing the binding of TFIID to the TATA box -inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter
DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called _________ (select all that apply) -regulatory sequences -regulatory elements -operator sequences -core promoters - control elements
-regulatory sequences -regulatory elements -control elements
Place the steps leading to the activation of the CREB protein in order from first to last
1. An extracellular signaling molecule binds to a plasma membrane receptor 2. A G protein is activated, that subsequently activates adenylyl cyclase 3. Andenylyl cyclase catalyzes the synthesis of cAMP 4. cAMP binds to protein kinase A 5. Protein kinase A travels to the nucleus and phosphorylates the CREB protein 6. The CREB protein binds to CBP, and RNA polymerase is activated
Place the steps in glucocorticoid hormone and receptor action in order from first to last
1. The glucocorticoid hormone diffuses through the plasma membrane 2. The glucocorticoid hormone binds to the glucocorticoid receptors 3. HSP90 is released from the glucocorticoid receptor 4. Two glucocorticoid receptors form a homodimer and travel through a nuclear pore into the nucleus
You are studying a bidirectional enhancer with the sequence 5'-CCTA-3'. Regulatory transcription factors that bind this sequence should also bind __________
3'-ATCC-5'
Which reaction is catalyzed by the DNA translocase enzyme found in all chromatin-remodeling complexes?
ATP hydrolysis
What affect does acetylation have on lysines in core histone protein tails?
Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone
T/F: Regulatory elements must be located within 200 base pairs upstream from the core promoter.
False
Select the histones for which variants have been identified. -H2A -H4 -H3 -H1 -H2B
H1 H2A H2B H3
Which histone variant is abundant on the inactivated X chromosome in female mammals?
MacroH2A
Activator proteins stimulate mediator to make what modification on RNA polymerase II?
Phosphorylation
General transcription factors are required for the binding of ___________ ____________ to the core promoter and its progression to the elongation stage.
RNA polymerase
TFIID binds to the _____________ box and helps recruit RNA polymerase II to the core ____________
TATA; promoter
Activator proteins might help ___________ bind to the ___________ box.
TFIID; TATA
The binding of a glucocorticoid receptor homodimer to a glucocorticoid response element ____________ the transcription of the nearby gene.
activates
A regulatory transcription factor that enhances the rate of transcription is called a(n) _____________
activator
What kind of protein is expected to enhance the ability of TFIID to initiate transcription?
activator proteins
Steroid hormones bind regulatory transcription factors called steroid receptors in order to ___________
affect gene transcription
In helix-turn-helix and helix-loop-helix motifs ___________ __________ side chains of the α-helix form _____________ bonds with nucleotide bases.
amino acid; hydrogen
Relative to the promoter for a gene of interest, regulatory elements are located _________
at various distances
A regulatory element that functions in the forward or reverse direction is said to be ____________________
bidirectional
The function of TFIID is to _________
bind to the TATA box and recruit RNA polymerase II to the core promoter
What effect can ATP-dependent chromatin remodeling have on transcription?
both activation and repression
The CREB protein is a regulatory transcription factor that is activated following an increase in ________
cAMP
Mediator phosphorylates the____________ -terminus of RNA polymerase II, stimulating progression to the ____________stage of transcription.
carboxyl; elongation
The SWI/SNF-family, the ISWI-family, the INO80-family, and the Mi-2 family are families of _________
chromatin-remodeling complexes
If chromatin is in a ____________ conformation, transcription may be difficult or impossible.
closed
A protein that increases the rate of transcription but does not directly bind to the DNA is called a __________
coactivator
Activator proteins often increase transcription through an interaction with _________
coactivators
The phenomenon in which the combination of many factors determines the expression of a given gene is known as ________________ _______________
combinatorial control
DNA sequences that are analogous to the operator sites found near bacterial promoters are called _____________ elements or _______________ sequences.
control; regulatory
In general, transcriptional regulation is aimed at _________
controlling the initiation of transcription at the promoter
ATP-______________ ______________ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.
dependent chromatin
Transcription factor proteins contain regions called __________ that have specific functions.
domains
Regulatory elements that inhibit transcription are called silencers and their effect on transcription is called ______ regulation.
down
You are studying a transcription factor that binds to DNA near a gene of interest. You discover that once the transcription factor binds, transcription of your gene of interest becomes undetectable. This is an example of ________
down regulation
Glucocorticoid response elements are located near ______ genes.
dozes of different
According to the histone code hypothesis, different patterns of covalent modifications to the amino-terminal tails of histones can __________ the degree of transcription of genes in the region.
either increase or decrease
Steroid hormones are synthesized by ____________ glands and secreted into the bloodstream, ultimately affecting the transcription or expression of genes in target cells.
endocrine
A glucocorticoid response element functions as a(n) _______
enhancer
Activators bind to ______.
enhancers
Gene regulation means that ___________
gene expression can be controlled so that genes can be expressed at high or low levels
Human nerve cells and muscle cells look quite different from each other due to differences in ___________
gene regulation
A domain called an α-______________ is often found in transcription factors because it is the proper width to fit into the ____________ groove of the DNA double helix.
helix; major
The dimerization of two different proteins leads to a ________
heterodimer
According to the ___________ ____________ hypothesis, the pattern of _______________modification acts like a language or code in specifying alterations in chromatin structure.
histone code; histone
The dimerization of two identical proteins results in a ______________
homodimer
If chromatin is in a closed conformation, nucleosome position and histone composition _________
make it difficult for transcription factors to gain access to and bind their target sequences in the promoter DNA
Most eukaryotic genes are regulated by ______ factor(s).
many
The uptake of glucocorticoid hormones usually stimulates the transcription of ______ genes.
many different
Activator proteins stimulate the ability of ________________ to phosphorylate the carboxyl-terminus of RNA polymerase II, which facilitates the switch between transcriptional initiation and elongation.
mediator
The protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors is called _____________
mediator
A repressor protein may stop _________________from allowing RNA polymerase to proceed to the _________________ phase of transcription.
mediators; elongation
A domain that has a very similar structure in many different proteins is called a(n) ____________
motif
A change in chromatin conformation from closed to open often involves the movement of ________
nucleosomes
The placement of ______________ at or near promoters often plays a key role in whether a gene is active or inactive.
nucleosomes
ATP-dependent chromatin remodeling is carried out by a protein complex that recognizes _______________ and uses ______________ to alter their configuration.
nucleosomes; ATP
When chromatin is accessible to transcription factors and RNA polymerase, it is referred to as being in the ______ conformation.
open
The function of a regulatory transcription factor can be modulated by covalent modifications, such as the attachment of a ___________________ group.
phosphate
The α-helix is often found in transcription factors because it is the __________
proper width to bind into the major groove of the DNA double helix
If gene regulation acts to prevent translation, what molecule will not be produced?
protein
The ability of humans to develop tans to protect their skin cells from UV rays by inducing genes that provide protection against UV radiation is an example of gene ___________
regulation
The phenomenon where the level of gene expression is controlled so that genes can be expressed at high or low levels is called gene ______________
regulation
Proteins that regulate the rate of transcription of target genes are called ______________ transcription factors.
regulatory
Variation in _______________ ____________ orientation and location makes it difficult to study all the regions of DNA that affect the expression of a given gene.
regulatory element
The binding of a regulatory transcription factor to a(n) _____________ can stimulate transcription 10- to 1000-fold, which is called _____________ regulation.
regulatory element; up
You are studying a region of DNA near a gene promoter. You notice that in some cases there is a nucleosome very close to the promoter, but in other cases, the nucleosome is gone. This move is most likely the result of chromatin __________
remodeling
Regulatory transcription factors that prevent transcription from occurring are called _________
repressors
The CREB protein binds to DNA at a sequence called the cAMP __________ __________
response element
The cAMP ____________ element-binding protein (_____________ protein) is a regulatory transcription factor that is activated in response to signaling molecules that increase cytoplasmic cAMP.
response; CREB
Repressors bind to _______
silencers
Generally, ____________ histones are incorporated into nucleosomes during S phase of the cell cycle. Later, histone ______________ are added by chromatin-remodeling complexes.
standard; variants
Regulatory transcription factors that respond to steroid hormones are called _____________ _____________
steroid receptor
What type of regulatory transcription factor utilizes the strategy depicted in the picture? picture-- The illustration shows an effector molecule which is a steroid hormone. It binds directly to the receptor of steroid in the protein which is shown as transcription factor. This hormone influences the ability of a transcription factor to bind to the DNA.
steroid receptor
A repressor interacting with mediator prevents _________
the phosphorylation of RNA polymerase
What is the purpose of histone variants?
to create functionally specialized regions of chromatin
Coactivators usually contain a _______________domain that promotes the activation of RNA polymerase, often interacting with general transcription factors
transactivation
A ________ _________ is a protein that influences the ability of RNA polymerase to transcribe a given gene.
transcription factor
The ATPase subunit of chromatin-remodeling complexes is called DNA __________
translocase
T/F: A transcription factor can have multiple domains.
true
T/F: The function of regulatory transcription factors is modulated
true
In helix-___________-helix and helix-____________-helix motifs, an α-helix recognizes a base sequence in the major groove of the DNA.
turn; loop
The cAMP response element (CRE) contains ______ of a consensus sequence bound by the CREB protein, which has ______.
two copies; two identical subunits
An enhancer is a DNA element that can be bound to a regulatory transcription factor, which leads to __________
up regulation
Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone _________
variants
Similarly to an α-helix, a ___________ finger motif can also recognize the ____________ groove of DNA.
zinc; major
Leucine ____________ motifs mediate dimerization between two _______________
zipper; proteins