Chapter 15.2 Connect Questions - Concept, Comprehensive, and Conceptual Questions

nucleosomes

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

D. do all of the above.

A chromatin-remodeling complex may... A. change the locations of nucleosomes. B. evict histones from DNA. C. replace standard histones with histone variants. D. do all of the above.

yeast

A gene you are studying has an NFR flanked by a -1 and +1 nucleosome. Its transcriptional start site is located at the boundary between the NFR and the +1 nucleosome. This gene is likely found in ______.

H3.3

A histone variant found in the transcribed regions of genes is ______.

Blank 1: standard or normal Blank 2: variants or variant

Generally, ___________ histones are incorporated into nucleosomes during S phase of the cell cycle. Later, histone __________ are added by chromatin-remodeling complexes.

Blank 1: chaperones

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

transcribed; silent

Histone variant H3.3 is often found in the ______ regions of genes but is less common in ______ genes.

Blank 1: Seq or sequencing Blank 2: nucleosomes or nucleosome

Scientists use computer software to match sequences obtained from ChIP- __________ to sequences on a genome map. In this way they can determine the positions of _________ in relation to genes of interest.

Blank 1: translocase

The ATPase subunit of chromatin-remodeling complexes is called DNA __________

Blank 1: promote, activate, enhance, increase, or induce Blank 2: inhibit, repress, silence, or decrease

The pattern of covalent modifications to histone tails provides binding sites for proteins that affect the degree of transcription. Certain patterns can either __________ or __________ transcription.

Blank 1: nucleosomes or nucleosome

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

Blank 1: 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.

Blank 1: nucleosomes or nucleosome Blank 2: ATP

ATP-dependent chromatin remodeling is carried out by a protein complex that recognizes __________ and uses ___________ to alter their configuration.

Blank 1: histone or histones

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.

A. H1 B. H2B C. H2A E. H3

Select all that apply Select the histones for which variants have been identified. Multiple select question. A. H1 B. H2B C. H2A D. H4 E. H3

True

True or false: The ChIP-Seq method is used on species whose entire genome has been sequenced already.

1. Histone modifications may directly affect the interaction between histones and the DNA, or 2. they may affect the binding of other proteins to the chromatin.

CONCEPT CHECK: Describe two different ways that histone modifications may alter chromatin structure.

Blank 1: variants or variant

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 __________

chromatin-remodeling complexes

The SWI/SNF-family, the ISWI-family, the INO80-family, and the Mi-2 family are families of ______.

To create functionally specialized regions of chromatin

What is the purpose of histone variants?

Transcriptional initiation might occur at multiple points in a gene

What would happen if nucleosomes did not re-form behind RNA polymerase II?

B. The core promoter is found in a nucleosome-free region.

Which of the following characteristics is typical of a eukaryotic gene that can be transcribed? A. The core promoter is wrapped around a nucleosome. B. The core promoter is found in a nucleosome-free region. C. The terminator is wrapped around a nucleosome. D. None of the above characteristics is typical of a eukaryotic gene.

Blank 1: nucleosome or nucleosomes Blank 2: region

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

Eliminates the positive charge on lysine, disrupting the electrostatic attraction between the histone and the negatively charged DNA backbone

What affect does acetylation have on lysine in core histone protein tails?

Both activation and repression

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

transcriptional termination

At the end of many eukaryotic genes, a well-positioned nucleosome is followed by an NFR. This arrangement may be important for ______.

Eviction of histone octamers may allow certain proteins to access particular sites in the DNA and bind there, which could affect transcription.

CONCEPT CHECK: How might eviction of histone octamers affect transcription?

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 a preinitiation complex 4. Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur

Click and drag on elements in order 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. Eviction or destabilization of histone octamers, allowing RNA pol II to pass, and elongation to occur 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

1. One result of ATP-dependent chromatin remodeling is a change in the positions of nucleosomes (Figure 15.9a). This may involve shifts in nucleosomes to new locations or changes in the relative spacing of nucleosomes over a long stretch of DNA. 2. A second effect is that remodelers may evict histone octamers from the DNA, thereby creating gaps where nucleosomes are not found (Figure 15.9b). 3. A third possibility is that remodelers may change the composition of nucleosomes by removing standard histones and replacing them with histone variants (Figure 15.9c). The functions of histone variants are described next.

How do chromatin remodeling complexes change chromatin structure? Three effects are possible:

B. where covalent modifications of histones occur C. where histone variants are found D. where nucleosomes are located

Select all that apply Mapping the locations of nucleosomes in the genomes allows for the determination of ______. Multiple select question. A. where DNA mutations occur B. where covalent modifications of histones occur C. where histone variants are found D. where nucleosomes are located E. whether genes will be active or not

A. Acetylation B. Phosphorylation D. Methylation

Select all that apply Select the common types of covalent modifications made to the amino-terminal tails of histones. Multiple select question. A. Acetylation B. Phosphorylation C. Ubiquitination D. Methylation

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

Select all that apply Select ways that nucleosomes can change. Multiple select question. A. Covalent modifications to the carboxyl-terminal tails of histones B. Change in histones to variants with specialized roles C. Covalent modifications to the amino-terminal tails of histones D. Change in location E. Change from DNA to RNA within nucleosomes

150 bp

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

Histone eviction is needed for elongation because RNA polymerase II cannot transcribe through nucleosomes. It needs to unwind the DNA for transcription to take place.

CONCEPT CHECK: Explain why histone eviction is needed for the elongation phase of transcription to occur.

An NFR is needed at the core promoter so that activators can recognize enhancers and then the preinitiation complex can form.

CONCEPT CHECK: Why is an NFR needed at the core promoter for transcription to occur?

closed

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

Blank 1: dependent or dependent Blank 2: chromatin

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

DNA gel electrophoresis DNA sequencing PCR Immunoprecipitation

Select the procedures that are used in chromatin immunoprecipitation sequencing (ChIP-Seq). DNA gel electrophoresis DNA sequencing Protein gel electrophoresis PCR Immunoprecipitation

make it difficult for transcription factors to gain access to and bind their target sequences in the promoter DNA

If chromatin is in a closed conformation, nucleosome position and histone composition ______.

ATP hydrolysis

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

Blank 1: lysines or lysine Blank 2: acetyltransferases or acetyltransferase

Positively charged _________ within core histone proteins can be acetylated by histone __________

Blank 1: histone Blank 2: code Blank 3: histone

According to the ________ ________ hypothesis, the pattern of ________ modification acts like a language or code in specifying alterations in chromatin structure.

Blank 1: deacetylase Blank 2: DNA or dna

As RNA polymerase II progresses over the DNA, histone ________ removes acetyl groups behind it, favoring the binding of histones to the ________

H3 methylation H2B ubiquitination Histone acetylation

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

Blank 1: H2A.Z, H2AZ, or H2A Z Blank 2: H2A or h2a

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 ________

D. All of the above

Transcriptional activation of eukaryotic genes involves which of the following events? A. Changes in nucleosome locations B. Changes in histone composition within nucleosomes C. Histone modifications D. All of the above

A. influences chromatin structure.

According to the histone code hypothesis, the pattern of histone modifications acts like a language that... A. influences chromatin structure. B. promotes transcriptional termination. C. inhibits the elongation of RNA polymerase. D. does all of the above