Chapter 15 Gene Regulation in Eukaryotes I

Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ______.

-regulating the binding of the transcriptional complex to the core promoter -controlling the switch from the initiation to the elongation stage of transcription

Mapping the locations of nucleosomes in the genomes allows for the determination of ______.

-where covalent modifications of histones occur -where histone variants are found -where nucleosomes are located

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'

What kind of protein is expected to enhance the ability of TFIID to initiate transcription?

Activator proteins

Select ways that nucleosomes can change.

-Change in location -Change in histones to variants with specialized roles -Covalent modifications to the amino-terminal tails of histones

The function of regulatory transcription factors must be modulated to ensure that genes are turned on ______.

-at the proper time -under the appropriate environmental conditions -in the correct cell type

Which enzyme catalyzes the formation of 5-methylcytosine?

DNA methyltransferase

A protein called _____ usually cleaves DNA at sites where regulatory transcription factors bind, but does not usually cleave DNA that is wrapped around _____.

DNase1 histone

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

Select the common types of covalent modifications made to the amino-terminal tails of histones.

Phosphorylation Methylation Acetylation

What type of regulatory transcription factor utilizes the strategy depicted in the picture?

Steroid receptor

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

Which of the following represents de novo methylation?

The methylation of DNA that was previously unmethylated

True or false: A transcription factor can have multiple domains.

True

True or false: The function of regulatory transcription factors is modulated.

True

Select the organism with the highest amount of DNA methylation.

Vertebrates

A regulatory transcription factor that enhances the rate of transcription is called a(n)

activator

Steroid hormones bind regulatory transcription factors called steroid receptors in order to ______.

affect gene transcription

Activator proteins often increase transcription through an interaction with ______.

coactivators

Methylation of the cytosine in both strands is called ______ methylation, and methylation of only one strand is called ______

full, hemimethylation

In order to regulate the translation of both ferritin and transferrin receptor mRNAs, the iron regulatory protein (IRP) binds to the _____ of the mRNAs.

iron response element

Positively charged ____ within core histone proteins can be acetylated by histone _____.

lysine acetyltransferases

The protein complex that mediates the interaction between RNA polymerase II and regulatory transcription factors is called

mediator

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

Following the binding of a hormone, two glucocorticoid ______ form a dimer and travel to the ______

receptors nucleus

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

In helix- ____ -helix and helix- ____ -helix motifs, an α-helix recognizes a base sequence in the major groove of the DNA.

turn; loop

The cytosines in CpG islands near housekeeping genes are

unmethylated

In general ______ CpG islands correlate with active genes, and _____ CpG islands correlate with suppressed genes.

unmethylated methylated

What DNA sequence is methylated?

5'-CG-3'

Which reaction is catalyzed by the DNA translocase enzyme found in all chromatin-remodeling complexes?

ATP hydrolysis

A protein that increases the rate of transcription but does not directly bind to the DNA is called a

coactivator

DNA sequences that are analogous to the operator sites found near bacterial promoters are called______ elements or _____ sequences.

control; regulatory

DNA methylation is the ______ attachment of methyl groups to DNA.

covalent

The methylation of DNA that was previously unmethylated is called ________ _________ methylation.

de novo

Transcription factor proteins contain regions called ______ that have specific functions.

domains

The dimerization of two identical proteins results in a

homodimer

Repressors bind to ______.

silencers

Regulatory transcription factors that respond to steroid hormones are called

steroid receptors

Coactivators usually contain a _____ domain that promotes the activation of RNA polymerase.

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

Repressors inhibit TFIID by ______.

-preventing the binding of TFIID to the TATA box -inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter

What is the size of the nucleosome-free region found at the core promoter of active genes?

150 bp

DNA methyltransferase is an enzyme that attaches a methyl group to the _____ position of the ______ base.

5; cytosine

What effect can ATP-dependent chromatin remodeling have on transcription?

Both activation and repression

Select the histones for which variants have been identified.

H1 H2B H2A H3

How does iron regulatory protein exert its effect on ferritin mRNA?

Iron regulatory protein (IRP) binds to the iron response element (IRE) in the 5' UTR, and thus inhibits ferritin translation.

_________ can change in location along a DNA molecule, by replacement of a standard histone with a histone variant, and through covalent modifications on histone tails.

Nucleosomes

In helix-turn-helix and helix-loop-helix motifs _____ side chains of the α-helix form _____ bonds with nucleotide bases.

amino; acids; hydrogen

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

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

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

Steroid hormones are synthesized by ______ glands and secreted into the bloodstream, ultimately affecting the transcription or expression of genes in target cells.

endocrine

The binding of a regulatory transcription factor to a(n)_____ can stimulate transcription 10- to 1000-fold, which is called _____ regulation.

enhancer; up

Activators bind to ______.

enhancers

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

Core _______ proteins contain a globular domain and a flexible amino-terminal tail. DNA wraps around the globular domains, and the amino-terminal tails protrude from the chromatin.

histone

Genes that code for proteins that are required in most cells of a multicellular organism are called ______.

housekeeping genes

When fully methylated DNA is replicated, it is initially hemimethylated. The hemimethylated DNA is recognized by DNA methyltransferase, which makes it fully methylated. This process is called ______ methylation.

maintenance

CpG islands near the promoters of tissue-specific genes are often ______.

methylated

Regulatory transcription factors that prevent transcription from occurring are called

repressors

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

Histone _______ are proteins that bind histones and aid in the assembly of histone octamers.

chaperones

Genes that are highly regulated and may be expressed only in certain cell types are called ______ - ______ genes.

tissue specific

What is the name for stretches of DNA of 1000-2000 bp in length containing a high number of CpG sites that are found near gene promoters?

CpG islands

Enzymes that carry out what functions travel along with RNA polymerase II?

H3 methylation H2B ubiquitination Histone acetylation

True or false: The methylation state of DNA is inherited during cell division.

True

If chromatin is in a _____ conformation, transcription may be difficult or impossible.

closed

The core promoter of active genes is found in _______ a(n) -free _______ , which is a segment of DNA that is missing histones.

nucleosome region

ATP- ______ ______ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.

dependant chromatin

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

The transactivation domain of coactivators promotes the activation of RNA polymerase, often by interacting with ______.

general transcription factors

The placement of ________ at or near promoters often plays a key role in whether a gene is active or inactive.

nucleosome

The ENCODE Consortium is attempting to list all ______.

functional elements in the human genome

Gene regulation means that ______.

gene expression can be controlled so that genes can be expressed at high or low levels

If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be _____. If the same sequence of nonmethylated DNA is introduced into a cell, it will be _____ in daughter cells.

methylated nonmethylated

A change in chromatin confirmation from closed to open often involves the movement of ______.

nucleosomes

The mapping ______ of allows researchers to understand their location, to understand where ______ variants are found, and to learn where covalent modifications of histones occur.

nucleosome histones

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 ______.

regulatory sequences regulatory elements control elements

Nucleosomes containing the histone variant _______ which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone _______.

H2AZ; H2A

A domain that has a very similar structure in many different proteins is called a(n)

motif

The function of TFIID is inhibited by ____ , which prevent the binding of TFIID to the _____ box.

repressor; TATA