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