Ch. 15 Assessment Genetics

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

* Acetylation * Methylation * Phosphorylation

Select all that apply Select the histones for which variants have been identified.

* H1, H2A, H2B, H3

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

* In the correct cell type * Under the appropriate environmental conditions * At the proper time

Repressors inhibit TFIID by ______.

* Inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter * Preventing the binding of TFIID to the TATA box

Select all that apply: 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

Select ways that nucleosomes can change.

* change in location * change in histones to variants with specialized roles * covalent modifications to the amino-acid terminal tails of histones.

Select all that apply Mapping the locations of nucleosomes in the genomes allows for the determination of ______.

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

Select all that apply Select the strategies used by ENCODE investigators to identify functional elements in the human genome.

** identify sites where DNase I can cleave DNA ** identify DNA binding sites for transcription factors ** Isolate and sequence RNA molecules transcribed by the human genome. ** Identify sites of histone modification. ** Map DNA methylation sites.

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 ______.

*control elements *regulatory sequences *regulatory elements

Place these steps in a simplified model for transcriptional activation of a eukaryotic gene in order from first to last, putting the first step at the top.

1) Binding of an activator to an enhancer in the NFR 2) recruitment of a chromatin-remodeling complex and a histone-modifying enzyme 3) Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of preinitiation complex. 4) Eviction of destabilization of histone octamers, allowing RNA polymerase II to pass, and elongation to occur.

Place the steps in glucocorticoid hormone and receptor action in order from first to last.

1) Hormone enters the cytosol of a cell by diffusing through the plasma membrane 2) The hormone specifically binds to glucocorticoid receptor 3) HSP90 is released from the glucocorticoid receptor 4) Two glucocorticoid receptors form a homodimer and travel through a nuclear pore into the nucleus.

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

150bp

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 DNA sequence is methylated?

5'-CG-3'

DNA methyltransferase is an enzyme that attaches a methyl group to the _____________ position of the _______________ base

5; cytosine

What is a motif?

A domain that has a very similar structure in many different proteins.

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

ATP hydrolysis

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

Activator proteins

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

Both activation and repression

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

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 ________________________.

DNase; histones

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.

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 ______________

H2A.Z; H2A

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

H2B ubiquitination H3 methylation Histone acetylation

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.

Which of the following regulates iron assimilation in mammalian cells?

RNA binding proteins

TFIID binds to the_____________________ box and helps recruit RNA polymerase II to the core ____________________.

TATA; core

Activator proteins might help ___________________________ bind to the _____________________ box

TFIID; TATA

Which statement accurately describes the location of iron response elements (IREs) in mRNAs for ferritin and transferrin receptor?

The IRE is in the 5'-UTR end of ferritin mRNA but in the 3'-UTR of transferrin receptor mRNA.

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

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

True

An enhancer is a DNA element that can be bound to a regulatory transcription factor, which leads to ______.

Up regulation

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

In helix-turn-helix and helix-loop-helix motifs ______________________ __________________side chains of the α-helix form ___________________ bonds with nucleotide bases.

amino acid; 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

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

chaperones

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

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

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

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

Iron response elements (IREs) can be found in the 5'-UTR of ____________________ mRNA and in the 3'-UTR of ____________________ __________________ mRNA

ferritin; transferrin receptor

Methylation of the cytosine in both strands is called ______________________ methylation, and methylation of only one strand is called ____________________.

full; hemimethylation

he 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

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

general transcription factors

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

The dimerization of two identical proteins results in a

homodimer

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

housekeeping genes

The central goal of the Encyclopedia of DNA Elements (ENCODE) Consortium is to make a comprehensive list of functional elements in the ____________________ _____________________, including those that control gene expression.

human genome

A sequence found in both ferritin and transferrin receptor mRNAs that is recognized by an RNA-binding protein is called the ______.

iron response element

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 __________________________.

lysines; acetyltransferase

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

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

mediator

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

methylated

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

motif

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

nucleosome; region

A change in chromatin confirmation 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

______________________ 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

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

nucleosomes; histone

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

Regulatory transcription factors that prevent transcription from occurring are called

repressors

The function of TFIID is inhibited by _____________________, which prevent the binding of TFIID to the _________________ box.

repressors; TATA

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

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

steroid receptor

Regulatory transcription factors that respond to steroid hormones are called _____________________ ___________________.

steroid receptors

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

tissue-specific

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

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

When a fully methylated DNA segment of DNA is replicated, the newly made daughter strand contains __________________________ cytosines. This DNA is said to be___________________________.

unmethylated; hemimethylated

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

Select the organism with the highest amount of DNA methylation.

vertebrates