Chapter 17.3 and 17.5 Connect Conceptual, Comprehensive, and Concept Questions

Blank 1: clustered Blank 2: interspaced Blank 3: palindromic

CRISPR stands for _________ , regularly _________ , short, ____________ repeats

tracr Cas9 Cas1 Cas2 Crispr

Click and drag on elements in order Order the genes commonly found in the CRISPR-Cas type II system. Start with tracr at the top. tracr Cas9 Cas2 Crispr Cas1

Blank 1: nonhomologous Blank 2: joining Blank 3: recombination Blank 4: repair

In gene mutagenesis by CRISPR-Cas, a DNA break can be repaired by ____________ end ______________ or by homologous _______________ _______________

B. 24-31

When pre-piRNA is processed, the resulting piRNAs are ______ nucleotides in length. Multiple choice question. A. 3-4 B. 24-31 C. 100-150 D. 300-400

Blank 1: single or s Blank 2: guide or g

When the CRISPR-Cas system is used for gene mutagenesis, tracrRNA and crRNA are linked together in a molecule called the ___________ ___________ RNA

D. Germ-line cells

Where are PIWI proteins primarily expressed? Multiple choice question. A. Neural cells B. Epidermal cells C. Gastrointestinal cells D. Germ-line cells

A. Cas9

Which component in the CRISPR-Cas9 system makes a double-strand break in DNA? Multiple choice question. A. Cas9 B. tracrRNA C. crRNA

B. Adaptation

Which phase of the CRISPR-Cas defense system is depicted in this figure? Multiple choice question. A. Termination B. Adaptation C. Interference D. Expression

C. Expression

Which phase of the CRISPR-Cas defense system is depicted in this figure? Multiple choice question. A. Termination B. Interference C. Expression D. Adaptation

B. crRNA

During the interference phase of the CRISP-Cas defense system, each spacer within a ______ is complementary to one of the strands of the bacteriophage DNA. Multiple choice question. A. piRNA B. crRNA C. tracrRNA D. snoRNA

B. The RNA that is transcribed from a particular transposable element.

What is each piRNA complementary to? Multiple choice question. A. The DNA from a particular bacteriophage. B. The RNA that is transcribed from a particular transposable element. C. The RNA that is transcribed from a region found in all transposable elements. D. A region of DNA that is found in all bacteriophages.

D. Directing the methylation of DNA and histones to stop transcription of the TE

What is the mechanism used by a piRITS to inhibit the movement of a transposable element? Multiple choice question. A. Cleaving TE DNA B. Cleaving TE RNA C. Directing the acetylation of DNA and histones to stop transcription of the TE D. Directing the methylation of DNA and histones to stop transcription of the TE

B. Spacer

Which region in the crRNA is complementary to a strand of bacteriophage DNA? Multiple choice question. A. tracr gene B. Spacer C. Repeats

Blank 1: living, live, or alive

A major advantage of CRISPR-Cas technology over site-directed mutagenesis is that it can be used directly on ______________ cells

Blank 1: nucleus Blank 2: methylation Blank 3: H3

A piRITS complex enters the cell __________ and directs the _____________ of DNA and the trimethylation of histone ________________ , leading to inactivation of the chromatin that contains DNA from a transposable element.

C. piRISC

A piRNA-containing complex that acts in the cytosol to direct the cleavage of TE RNA is called ______. Multiple choice question. A. miRNA B. piRITS C. piRISC D. snoRNP

Blank 1: transposable Blank 2: element

A segment of DNA that can become integrated into chromosomes is called a(n) _______________ _____________

Blank 1: CRISPR Blank 2: Cas or Cas9

An immune type system in prokaryotes that protects against foreign invaders is called the ____________________ - __________________ system.

C. adaptive defense system

Because a bacterial cell must first be exposed to an agent to elicit a response, the CRISPR-Cas system is called a(n) ______. Multiple choice question. A. prolonged defense system B. interference defense system C. adaptive defense system D. acute defense system

Blank 1: PIWI

Because they are expressed in germ-line cells, _____________ proteins prevent unwanted TE insertions from being passed from parent to offspring.

D. The genes encoding pre-crRNA and tracrRNA are transcribed C. tracrRNAs bind to pre-crRNA due to complementary base pairing A. pre-cRNA cleaved into many small molecules B. Each tracrRNA-cRNA complex binds to a Cas9 protein

Click and drag on elements in order Place the steps in the expression phase of the CRISPR-Cas system in order. Start with the first step at the top. A. pre-cRNA cleaved into many small molecules B. Each tracrRNA-cRNA complex binds to a Cas9 protein C. tracrRNAs bind to pre-crRNA due to complementary base pairing D. The genes encoding pre-crRNA and tracrRNA are transcribed

A. The pre-piRNA is transcribed in the nucleus and exported to the cytosol C. The pre-piRNA is cleaved into several piRNAs B. Each piRNA associates with a PIWI protein to form a piRISC D. piRISC binds to TE RNA in the cytosol E. piRISC directs the cleavage of TE RNA

Click and drag on elements in order Place the steps in transposable element silencing by piRISCs in order from first to last, with the first step at the top. A. The pre-piRNA is transcribed in the nucleus and exported to the cytosol B. Each piRNA associates with a PIWI protein to form a piRISC C. The pre-piRNA is cleaved into several piRNAs D. piRISC binds to TE RNA in the cytosol E. piRISC directs the cleavage of TE RNA

D. The pre-piRNA is transcribed in the nucleus, exported to the cytosol and cleaved into several piRNAs B. Each piRNA associates with a PIWI protein to form a piRITS E. piRITS travels to the nucleus and binds to RNA that is being transcribed from a TE A. piRITS directs the methylation of DNA and trimethylation of lysine 9 on histone H3 C. Proteins that convert euchromatin to heterochromatin are recruited to the TE region F. Transcription of the TE is prevented by increased chromatin compaction

Click and drag on elements in order Place the steps in transposable element silencing by piRITS complexes in order from first to last, with the first step at the top. A. piRITS directs the methylation of DNA and trimethylation of lysine 9 on histone H3 B. Each piRNA associates with a PIWI protein to form a piRITS C. Proteins that convert euchromatin to heterochromatin are recruited to the TE region D. The pre-piRNA is transcribed in the nucleus, exported to the cytosol and cleaved into several piRNAs E. piRITS travels to the nucleus and binds to RNA that is being transcribed from a TE F. Transcription of the TE is prevented by increased chromatin compaction

B. Cas9

During the interference phase, which protein in the CRISPR-Cas system cleaves bacteriophage DNA? Multiple choice question. A. Cas2 B. Cas9 C. Cas1 D. Crispr E. tracr

B. several different piRNA sequences separated by sequences that are not complementary to TE RNA

Genes that encode piRNAs are organized into clusters that contain ______. Multiple choice question. A. a single piRNA sequence B. several different piRNA sequences separated by sequences that are not complementary to TE RNA C. several copies of an identical piRNA sequence separated by sequences that are not complementary to TE RNA D. several different piRNA sequences directly adjacent to each other

B. The mutated gene can be introduced into a living organism to see how the mutation affects the organism.

How is site-directed mutagenesis useful in the study of genes and proteins? Multiple choice question. A. Since site-directed mutagenesis introduces random mutations, new genes can be identified. B. The mutated gene can be introduced into a living organism to see how the mutation affects the organism. C. The mutated gene can be studied in vitro only.

C. Site-directed mutagenesis

If a scientist wanted to determine how a specific mutation in a gene of interest affected an organism, what technique would be most useful? Multiple choice question. A. Real-time PCR B. DNA sequencing C. Site-directed mutagenesis D. Reverse transcriptase PCR

C. A subsequent bacteriophage infection

In the CRISPR-Cas defense system, what triggers the expression phase? Multiple choice question. A. Bacterial lysis B. An initial bacteriophage infection C. A subsequent bacteriophage infection D. Bacterial conjugation

A. Spacer region

In the CRISPR-Cas system, what part of the sgRNA is designed to be complementary to the gene to be mutated? Multiple choice question. A. Spacer region B. Linker region C. tracrRNA D. Repeat region

A --> 1. crRNA B --> 3. tracrRNA C --> 2. Cas9

Match each component from the expression phase of the CRISPR-Cas system with the letters shown in the figure. 1. crRNA 2. Cas9 3. tracrRNA A --> B --> C -->

A. Can be used to make a specific point mutation. B. Researcher includes donor DNA that is homologous to the region where the break occurs.

Select all that apply After Cas9 makes a double strand break, which characteristics are observed for repair of the break by homologous recombination repair (HRR)? Multiple select question. A. Can be used to make a specific point mutation. B. Researcher includes donor DNA that is homologous to the region where the break occurs. C. Frameshift mutation may occur in the coding sequence of the gene. D. The break region may incur a small deletion.

A. bacteriophages B. plasmids C. transposons

Select all that apply CRISPR-Cas systems provide a defense against ______. Multiple select question. A. bacteriophages B. plasmids C. transposons D. bacteria

A. adult mice B. plant cells C. mouse embryos D. roundworms E. human cell lines

Select all that apply CRISPR-Cas technology has been used to mutate genes in ______. Multiple select question. A. adult mice B. plant cells C. mouse embryos D. roundworms E. human cell lines F. human embryos

B. Cas1 E. Cas2

Select all that apply During adaptation, what proteins in the CRISPR-Cas system are involved in recognizing and cleaving bacteriophage DNA into small pieces? Multiple select question. A. Cas9 B. Cas1 C. tracr D. Crispr E. Cas2

C. Interference D. Expression E. Adaptation

Select all that apply Select the three phases of the CRISPR-Cas response. Multiple select question. A. Termination B. Initiation C. Interference D. Expression E. Adaptation

A. Trimethylation of histone H3 catalyzed by piRITS D. Methylation of DNA catalyzed by piRITS

Select all that apply Which chemical modifications recruit proteins that convert a TE-containing region from euchromatin to heterochromatin? Multiple select question. A. Trimethylation of histone H3 catalyzed by piRITS B. Acetylation of histone H3 catalyzed by piRITS C. Cleavage of TE DNA catalyzed by piRISC D. Methylation of DNA catalyzed by piRITS

B. at a specific sequence of DNA

Site-directed mutagenesis allow a researcher to make a mutation ______. Multiple choice question. A. in the vector DNA B. at a specific sequence of DNA C. at the ends of chromosomes D. in the DNA flanking the gene of interest

Blank 1: oligonucleotide

Site-directed mutagenesis is sometimes referred to as _____________ -directed mutagenesis.

A. to provide defense against bacteriophages

The natural function of the CRISPR-Cas system in bacteria is to ______. Multiple choice question. A. to provide defense against bacteriophages B. to make changes throughout the bacterial chromosome C. to provide defense against other bacteria

A. transposition

The process by which a transposable element is integrated into a new site in the genome is called ______. Multiple choice question. A. transposition B. silencing C. interference D. adaptation

A. piRISCs can direct the cleavage of TE RNA.

What is the mechanism used by piRISCs to inhibit the movement of transposable elements? Multiple choice question. A. piRISCs can direct the cleavage of TE RNA. B. piRISCs can direct the acetylation of DNA and histones to stop the transcription of the TE. C. piRISCs can direct the cleavage of TE DNA. D. piRISCs can direct the methylation of DNA and histones to stop the transcription of the TE.

C. It contains a region that is not complementary to the template.

What is the most important feature of a primer used in site-directed mutagenesis? Multiple choice question. A. It is exactly complementary to the template DNA. B. It is 20 nucleotides long. C. It contains a region that is not complementary to the template. D. It comes from a natural source.

D. Interference

What phase of the CRISPR-Cas defense system is depicted in this figure? Multiple choice question. A. Termination B. Expression C. Adaptation D. Interference

B. Argonaute

When piRISC directs the degradation of TE RNA, what protein cleaves the TE RNA? Multiple choice question. A. Cas1 B. Argonaute C. Cas9 D. Dicer

D. piRITS

Which type of complex caused the chemical modifications in the TE region shown in the figure? Multiple choice question. A. CRISPR-Cas B. piRISC C. snoRNP D. piRITS E. miRNAs

Blank 1: Site Blank 2: Directed Blank 3: Mutagenesis

________________ - _________________ _______________ allows a researcher to produce a mutation at a specific sequence.

Blank 1: PIWI or p Blank 2: interacting or i

ncRNAs that inhibit the integration of TEs into new sites are called _____________ - ___________ RNAs

C. the integration of transposable elements into new sites

piRNAs prevent ______. Multiple choice question. A. bacteriophage infection B. the excision of transposable elements from the genome C. the integration of transposable elements into new sites