RNA Interference (RNAi) Quiz
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Questions and Answers

Which enzyme is involved in processing precursor microRNAs into mature microRNAs?

  • Dicer (correct)
  • Lentivirus
  • Argonaute
  • Drosha

    • What is the function of gRNA in the CRISPR-Cas system?

  • It prevents the binding of Cas protein to the target DNA sequence
  • It cleaves the target DNA sequence
  • It synthesizes the target DNA sequence
  • It guides the Cas protein to the target DNA sequence (correct)

    • What was the rationale behind using antisense mRNA in attempts to reduce gene expression in the 1980s and 1990s?

  • To enhance translation and increase mRNA stability
  • To prevent translation and lead to mRNA degradation (correct)
  • To promote gene overexpression
  • To induce random mutations in the target gene

    • Which molecule is endogenous and involved in gene silencing?

    <p>miRNA</p> Signup and view all the answers

    Where does Drosha function in the cell during the production of siRNA?

    <p>Nucleus</p> Signup and view all the answers

    What is the role of RNA-dependent RNA Polymerases (rdRP) in nematodes?

    <p>Amplify siRNA to strengthen gene silencing</p> Signup and view all the answers

    What is the function of Dicer in the RNA-induced silencing complex (RISC)?

    <p>Cleavage of dsRNA to produce siRNA</p> Signup and view all the answers

    What is the method of gene silencing that prevents mRNA translation using siRNA or miRNA?

    <p>RNA interference (RNAi)</p> Signup and view all the answers

    What is the function of antisense RNA in gene silencing?

    <p>Producing sense and antisense mRNA that impede translation</p> Signup and view all the answers

    What is the role of miRNA in natural gene silencing?

    <p>Promoting mRNA degradation</p> Signup and view all the answers

    What does RNAi control in nature?

    <p>Developmental timing, protection against RNA viruses, and regulation of transposon activity</p> Signup and view all the answers

    What is the structure of RNAi gene and transcript?

    <p>Identical and complementary to the mRNA target</p> Signup and view all the answers

    What is the function of Dicer in the regulation of gene expression?

    <p>Recognizing and cleaving externally supplied dsRNAs to produce siRNA</p> Signup and view all the answers

    How can RNAi be induced in human cells?

    <p>By introducing shRNA that is identical/homologous to the target gene</p> Signup and view all the answers

    What is the role of cosuppression in plants?

    <p>Suppressing gene expression using siRNA</p> Signup and view all the answers

    What is the function of the tracrRNA in the CRISPR/Cas system?

    <p>Provides the stem loop structure that binds Cas nucleases</p> Signup and view all the answers

    What is the role of the guiding RNA (gRNA) in the CRISPR/Cas system?

    <p>Guides the complex to the target location within the DNA</p> Signup and view all the answers

    What is the main function of a nuclease in the CRISPR/Cas system?

    <p>Makes a double stranded break in the chromosome</p> Signup and view all the answers

    What is the purpose of the CRISPR repeat-spacer array in the CRISPR/Cas system?

    <p>Transcribed into precrRNA, and processed into crRNAs</p> Signup and view all the answers

    What is the function of Cas genes in the CRISPR/Cas system?

    <p>Encode a large and heterogeneous family of proteins</p> Signup and view all the answers

    What is the purpose of the leader end of the CRISPR locus in the CRISPR/Cas system?

    <p>Integrates a novel repeat-spacer unit</p> Signup and view all the answers

    What is the primary function of the tracrRNA in the CRISPR/Cas system?

    <p>Provides the stem loop structure that binds Cas nucleases</p> Signup and view all the answers

    What is the role of the crRNA in the CRISPR/Cas system?

    <p>Used as a guide by a Cas complex to interfere with the corresponding invading nucleic acid</p> Signup and view all the answers

    CRISPR/Cas system provides bacteria with immunity against invading RNA

    <p>False</p> Signup and view all the answers

    The loop length of the stem in an RNA molecule is typically 7-20 pairs

    <p>True</p> Signup and view all the answers

    The CRISPR repeat-spacer array is transcribed into precrRNA, and processed into crRNAs

    <p>True</p> Signup and view all the answers

    The leader end of the CRISPR locus is involved in the immunization process

    <p>True</p> Signup and view all the answers

    The CRISPR/Cas system is designed to introduce a gene construct in a precise location via heterologous recombination

    <p>False</p> Signup and view all the answers

    Type II restriction endonucleases are highly specific and do not lead to off-target cleavage

    <p>False</p> Signup and view all the answers

    TALENs are a fusion of Fok1 and Zinc Finger Nucleases (ZFNs)

    <p>False</p> Signup and view all the answers

    Type II restriction endonucleases are more suitable for genome engineering compared to CRISPR/Cas due to their widespread availability and cost-effectiveness

    <p>False</p> Signup and view all the answers

    The non-specific nature of Type II restriction endonucleases limits their utility in genome engineering applications due to the risk of off-target effects

    <p>True</p> Signup and view all the answers

    TALE proteins are secreted by Xanthomonas bacteria during plant infections and are known for their precision in recognizing single base pairs through repeat variable residues.

    <p>True</p> Signup and view all the answers

    Zinc-Finger Nucleases (ZFNs) consist of zinc-finger modules or motifs and a FokI-derived cleavage domain, allowing for independent manipulation of binding and cleavage domains.

    <p>True</p> Signup and view all the answers

    The CRISPR system utilizes a bacterial defense mechanism against viral infections, where specific fragments of the invader's genetic material are captured as 'spacers' between identical 'repeats' to form a memory bank.

    <p>True</p> Signup and view all the answers

    The CRISPR/Cas9 complex patrols the bacterial cell, searching for target DNA sequences that match the guide RNA, recognizing a specific region called PAM (protospacer adjacent motif) in the DNA to ensure specificity.

    <p>True</p> Signup and view all the answers

    The key advantage of CRISPR lies in its adaptability and efficiency in guiding cleavage, allowing for the production of a single RNA molecule that guides cleavage in conjunction with Cas9, offering a straightforward and effective way to edit genes.

    <p>True</p> Signup and view all the answers

    TALEs are combined with Fok1 endonuclease to create TALENs, which enable targeted DNA cleavage at specific locations.

    <p>True</p> Signup and view all the answers

    TALENs induce double-strand breaks with sticky ends, providing advantages in ease of design for new genomic targets and higher specificity compared to other technologies.

    <p>True</p> Signup and view all the answers

    ZFNs are considered broad editors, but some zinc-finger modules display unreliable binding or off-target effects, posing challenges in their application with standardized plasmids.

    <p>True</p> Signup and view all the answers

    The CRISPR/Cas9 complex introduces a double-strand break in the DNA, activating the cell's natural repair mechanisms, which include non-homologous end joining (NHEJ) or homology-directed repair (HDR).

    <p>True</p> Signup and view all the answers

    CRISPR's simplicity allows for the production of a single RNA molecule that guides cleavage in conjunction with Cas9, offering a straightforward and effective way to edit genes.

    <p>True</p> Signup and view all the answers

    The CRISPR/Cas9 system is a more precise genome editing tool compared to TALENs and ZFNs.

    <p>False</p> Signup and view all the answers

    The CRISPR system, particularly the type II CRISPR system, employs the Cas9 protein and a guiding RNA molecule to induce precise DNA cleavage.

    <p>True</p> Signup and view all the answers

    Which of the following is a disadvantage of using Type II restriction endonucleases in genome engineering applications?

    <p>Risk of off-target effects due to non-specific cleavage</p> Signup and view all the answers

    Which technology is a fusion of Fok1 and Transcriptional Activator-Like Effectors (TALEs) for precise DNA cutting at specific recognition sites?

    <p>TALENs</p> Signup and view all the answers

    What is the primary reason for the limited suitability of Type II restriction endonucleases for genome engineering compared to CRISPR/Cas?

    <p>Non-specific cleavage leading to off-target effects</p> Signup and view all the answers

    What is the advantage of using TALENs over Zinc Finger Nucleases (ZFNs) for genomic cleavage?

    <p>Increased specificity in recognizing single base pairs</p> Signup and view all the answers

    Which enzyme is used in tandem with engineered nucleases like TALENs and ZFNs for genomic cleavage?

    <p>Fok1</p> Signup and view all the answers

    Which gene editing tool utilizes a bacterial defense mechanism against viral infections to induce precise DNA cleavage?

    <p>Transcription Activator-Like Effector Nucleases (TALENs)</p> Signup and view all the answers

    Which gene editing tool consists of zinc-finger modules or motifs and a FokI-derived cleavage domain, allowing for independent manipulation of binding and cleavage domains?

    <p>Transcription Activator-Like Effector Nucleases (TALENs)</p> Signup and view all the answers

    Which gene editing tool induces double-strand breaks with sticky ends, providing advantages in ease of design for new genomic targets and higher specificity compared to other technologies?

    <p>Zinc-Finger Nucleases (ZFNs)</p> Signup and view all the answers

    Which gene editing tool employs the Cas9 protein and a guiding RNA molecule to induce precise DNA cleavage?

    <p>RNA-dependent RNA Polymerases (rdRP)</p> Signup and view all the answers

    Which gene editing tool is known for its precision in recognizing single base pairs through repeat variable residues?

    <p>CRISPR/Cas9</p> Signup and view all the answers

    Study Notes

    RNA Interference: Mechanisms and Applications

    • Gene silencing via antisense involves inserting a copy of the target gene in reverse orientation, producing sense and antisense mRNA that base pair and impede translation.
    • In plants, antisense RNA was less efficient in suppressing gene expression than sense RNA, leading to the discovery of cosuppression mediated by short interfering RNA (siRNA) molecules.
    • RNA interference (RNAi) is a gene silencing method that prevents mRNA translation using siRNA or microRNA (miRNA), with miRNA being endogenous and siRNA being introduced into the cell.
    • miRNA and siRNA are small RNA molecules involved in natural gene silencing by inhibiting translation or promoting mRNA degradation.
    • In nature, RNAi controls developmental timing, protects against RNA viruses, and regulates transposon activity.
    • miRNA synthesis involves transcription by RNA Polymerase II/III, processing to produce mature miRNA, and subsequent binding to promote target mRNA degradation.
    • Drosha and Dicer are ribonucleases that produce siRNA from pri- and pre-miRNA, with Drosha functioning in the nucleus and Dicer in the cytosol as part of the RNA-induced silencing complex (RISC).
    • Eukaryotic genomes contain miRNAs that target mRNAs for gene silencing.
    • The structure of RNAi gene and transcript includes portions identical and complementary to the mRNA target, allowing for identification and degradation of the target mRNA.
    • RNAi is a powerful tool in molecular biology, used in biotechnology for gene silencing and regulation of gene expression.
    • Dicer can recognize and cleave externally supplied dsRNAs to produce siRNA, which regulates gene expression through degradation or translation impeding of targeted mRNA.
    • In nematodes, RNA-dependent RNA Polymerases (rdRP) can amplify siRNA to strengthen gene silencing, while in human cells, RNAi can be induced by introducing shRNA that is identical/homologous to the target gene.

    Gene Editing Tools: TALENs, ZFNs, and CRISPR/Cas9

    • Transcription Activator-Like Effector (TALE) proteins are secreted by Xanthomonas bacteria during plant infections and are known for their precision in recognizing single base pairs through repeat variable residues.
    • TALEs are combined with Fok1 endonuclease to create TALENs, which enable targeted DNA cleavage at specific locations.
    • TALENs induce double-strand breaks with sticky ends, providing advantages in ease of design for new genomic targets and higher specificity compared to other technologies.
    • Zinc-Finger Nucleases (ZFNs) play a crucial role in genome editing by inducing double-strand breaks at precise genomic locations, allowing targeted mutations or insertion of desired sequences during repair mechanisms.
    • ZFNs consist of zinc-finger modules or motifs and a FokI-derived cleavage domain, allowing for independent manipulation of binding and cleavage domains.
    • ZFNs are considered broad editors, but some zinc-finger modules display unreliable binding or off-target effects, posing challenges in their application with standardized plasmids.
    • The CRISPR system, particularly the type II CRISPR system, employs the Cas9 protein and a guiding RNA molecule to induce precise DNA cleavage.
    • The CRISPR system utilizes a bacterial defense mechanism against viral infections, where specific fragments of the invader's genetic material are captured as "spacers" between identical "repeats" to form a memory bank.
    • The CRISPR/Cas9 complex patrols the bacterial cell, searching for target DNA sequences that match the guide RNA, recognizing a specific region called PAM (protospacer adjacent motif) in the DNA to ensure specificity.
    • When the complex locates its target, the Cas protein introduces a double-strand break in the DNA, activating the cell's natural repair mechanisms, which include non-homologous end joining (NHEJ) or homology-directed repair (HDR).
    • The key advantage of CRISPR lies in its adaptability and efficiency in guiding cleavage, allowing for the production of a single RNA molecule that guides cleavage in conjunction with Cas9, offering a straightforward and effective way to edit genes.
    • CRISPR's simplicity allows for the production of a single RNA molecule that guides cleavage in conjunction with Cas9, offering a straightforward and effective way to edit genes.

    Gene Editing Tools: TALENs, ZFNs, and CRISPR/Cas9

    • Transcription Activator-Like Effector (TALE) proteins are secreted by Xanthomonas bacteria during plant infections and are known for their precision in recognizing single base pairs through repeat variable residues.
    • TALEs are combined with Fok1 endonuclease to create TALENs, which enable targeted DNA cleavage at specific locations.
    • TALENs induce double-strand breaks with sticky ends, providing advantages in ease of design for new genomic targets and higher specificity compared to other technologies.
    • Zinc-Finger Nucleases (ZFNs) play a crucial role in genome editing by inducing double-strand breaks at precise genomic locations, allowing targeted mutations or insertion of desired sequences during repair mechanisms.
    • ZFNs consist of zinc-finger modules or motifs and a FokI-derived cleavage domain, allowing for independent manipulation of binding and cleavage domains.
    • ZFNs are considered broad editors, but some zinc-finger modules display unreliable binding or off-target effects, posing challenges in their application with standardized plasmids.
    • The CRISPR system, particularly the type II CRISPR system, employs the Cas9 protein and a guiding RNA molecule to induce precise DNA cleavage.
    • The CRISPR system utilizes a bacterial defense mechanism against viral infections, where specific fragments of the invader's genetic material are captured as "spacers" between identical "repeats" to form a memory bank.
    • The CRISPR/Cas9 complex patrols the bacterial cell, searching for target DNA sequences that match the guide RNA, recognizing a specific region called PAM (protospacer adjacent motif) in the DNA to ensure specificity.
    • When the complex locates its target, the Cas protein introduces a double-strand break in the DNA, activating the cell's natural repair mechanisms, which include non-homologous end joining (NHEJ) or homology-directed repair (HDR).
    • The key advantage of CRISPR lies in its adaptability and efficiency in guiding cleavage, allowing for the production of a single RNA molecule that guides cleavage in conjunction with Cas9, offering a straightforward and effective way to edit genes.
    • CRISPR's simplicity allows for the production of a single RNA molecule that guides cleavage in conjunction with Cas9, offering a straightforward and effective way to edit genes.

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