McGraw Ch. 15

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

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

- Binding of an activator to an enhancer in the NFR - Recruitment of a Chromatin- Remodeling complex and a histone- modifying enzyme - Recruitment of general transcription factors and RNA Pol II to the core promoter, allowing the formation of a preinitiation complex - Eviction or destabilization of histone octamers, allowing RNA Pol II to pass, and elongation to occur

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 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

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

Activators

The methylation of DNA that was previously unmethylated is called ____ ____ methylation.

De Novo

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

Which of the following are terms used to describe eukaryotic DNA sequences that can be bound by regulatory transcription factors, and which then affect the ability of RNA polymerase to transcribe a particular gene?

Regulatory sequences Regulatory elements Control elements

Regulatory transcription factors that respond to steroid hormones are called

Steroid, Receptor

TFIID binds to the ____ box and helps recruit RNA polymerase II to the core ____

TATA, Promoter

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

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

Tissue Specific Genes

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

Transactivation

A protein that influences the ability of RNA polymerase to transcribe a given gene is termed a(n)

Transcription factor

The ATPase subunit of chromatin-remodeling complexes is called DNA

Translocase

A transcription factor can have multiple domains.

True

Cells modulate the function of their regulatory transcription factors.

True

Gene regulation means that

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

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

Covalent

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

Nucleosome, Region

The methylation state of DNA is inherited during cell division.

True

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

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

Up Regulation

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.

C/ Carboxy/ Carboxyl Elongation

Select ways that nucleosomes can change.

Change in Location Covalent modifications to the amino=terminal tails of histones Change in histones to variants with specialized roles

Transcription may be difficult or impossible, if chromatin is in a(n) ____ conformation

Closed

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

Coactivator

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

Control, Regulatory

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

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

Dependent, Chromatin

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

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

Enhancer, up

Activators are proteins that 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

The ENCODE Consortium is attempting to list all ______.

Functional Elements in a human genome

The phenomenon where the level of gene expression is controlled so that genes can be expressed at high or low levels is called gene

Gene regulation

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

General Transcription Factors

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

Name the histones for which variants have been identified.

H2A, H2B, H1, H3

The dimerization of two different proteins leads to a

Heterodimer

The dimerization of two identical proteins results in a(n)

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

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

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

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 Blank______ of the mRNAs.

Iron Response Element

Positively charged within core histone proteins can be acetylated by histone

Lysine, Acetyltransferase

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)

Motifs

____ 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

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

Activator proteins often increase transcription through an interaction with

With coactivators

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

Domains

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