Gene Editing and CRISPR Developments

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Questions and Answers

What percentage of transcription in a typical human cell is associated with making non-coding RNAs?

  • 80% (correct)
  • 20%
  • 50%
  • 10%

Which of the following is NOT a function of non-coding RNAs?

  • Act as a scaffold
  • Serve as a template for protein synthesis (correct)
  • Block other RNA interactions
  • Guide molecules to a location

How do non-coding RNAs bind to other molecules?

  • Through electrostatic interactions
  • By covalent bonding
  • Via complementary base pairing (correct)
  • Using hydrogen bonds

Which role describes a non-coding RNA that binds to another RNA to prevent its function?

<p>Decoy (D)</p> Signup and view all the answers

In addition to guiding, what other roles can non-coding RNAs perform?

<p>Changing the structure of proteins (A)</p> Signup and view all the answers

Which of the following is a possible example of an interaction that non-coding RNAs can facilitate?

<p>Guiding DNA-cutting proteins to specific sequences (C)</p> Signup and view all the answers

Which statement about the functions of non-coding RNAs is accurate?

<p>They can act both as guides and blockers (B)</p> Signup and view all the answers

Which of these molecules can non-coding RNAs bind to?

<p>Small molecules and DNA (B)</p> Signup and view all the answers

What is the primary role of microRNAs (miRNAs) in RNA interference?

<p>Regulating gene expression by targeting mRNAs (D)</p> Signup and view all the answers

How do small-interfering RNAs (siRNAs) primarily interact with their target mRNA?

<p>They are perfectly complementary to their target mRNA. (C)</p> Signup and view all the answers

What is the primary function of telomeres in eukaryotic chromosomes?

<p>To protect chromosome ends from damage. (D)</p> Signup and view all the answers

What are the two sources of non-coding RNA (ncRNA) that can mediate RNA interference?

<p>Endogenous miRNAs and exogenous siRNAs (B)</p> Signup and view all the answers

What complex is responsible for mediating RNA interference in eukaryotic species?

<p>RNA-Induced Silencing Complex (RISC) (C)</p> Signup and view all the answers

What happens to telomeres as cells continue to divide?

<p>They become shorter. (C)</p> Signup and view all the answers

What is a key feature of the signal recognition particle (SRP)?

<p>It chaperones ribosomes to the ER. (A)</p> Signup and view all the answers

What role does telomerase play in cell division?

<p>It adds repeat sequences to the telomeres. (D)</p> Signup and view all the answers

Why can't DNA polymerase fully replicate the ends of chromosomes?

<p>It needs a primer to begin replication. (C)</p> Signup and view all the answers

What happens when the SRP binds to an SRP receptor?

<p>The ribosome is directed to the ER membrane. (D)</p> Signup and view all the answers

How is RNA interference different from traditional gene regulation mechanisms?

<p>It utilizes ncRNAs to specifically target mRNAs. (D)</p> Signup and view all the answers

What consequence occurs when telomeres become critically short?

<p>Cells enter a program of programmed cell death. (D)</p> Signup and view all the answers

What percentage of human protein-coding genes are estimated to be regulated by miRNAs?

<p>60% (B)</p> Signup and view all the answers

Which of the following sequences is the repeat found in human telomeres?

<p>5ʹ–GGGTTA–3ʹ (C)</p> Signup and view all the answers

What is the effect of rapidly dividing cells producing telomerase?

<p>Telomeres can be maintained or elongated. (D)</p> Signup and view all the answers

What occurs to the daughter strand during DNA replication when a primer is removed?

<p>It is left shorter than the complementary strand. (D)</p> Signup and view all the answers

What is one primary function of non-coding RNAs (ncRNAs) in the cell?

<p>They bind to multiple components acting as a scaffold for complex formation. (C)</p> Signup and view all the answers

How do ncRNAs guide one molecule to a specific location in the cell?

<p>Through binding to DNA or another RNA via complimentary base pairing. (D)</p> Signup and view all the answers

In what way can an ncRNA act as a blocker?

<p>By physically preventing a cellular process from occurring. (A)</p> Signup and view all the answers

What is a key difference between a decoy and a blocker ncRNA?

<p>A decoy binds an RNA molecule, while a blocker binds a non-RNA molecule. (D)</p> Signup and view all the answers

Which function describes an ncRNA that has catalytic activity?

<p>Ribozyme (A)</p> Signup and view all the answers

What effect does binding of an ncRNA have on proteins?

<p>It can alter their function or stability. (D)</p> Signup and view all the answers

Which of the following statements accurately describes scaffolding by ncRNAs?

<p>It facilitates the assembly of multiple proteins into a single complex. (C)</p> Signup and view all the answers

Which function of ncRNAs involves preventing their target from performing its intended role?

<p>Blocker (C)</p> Signup and view all the answers

What is the first step in the process of telomere lengthening?

<p>TERC acts as a guide, bringing telomerase to the end of the chromosome. (C)</p> Signup and view all the answers

How does HOTAIR influence gene expression?

<p>By forming a scaffold that binds two protein complexes. (A)</p> Signup and view all the answers

Which of the following accurately describes the role of TERC during telomere lengthening?

<p>It acts as a template for telomerase to extend DNA. (C)</p> Signup and view all the answers

Which of the following statements is true regarding the modifications made by protein complexes guided by HOTAIR?

<p>They silence the target genes through histone modification. (C)</p> Signup and view all the answers

What effect does double-stranded RNA have compared to antisense RNA?

<p>It is more potent at inhibiting mRNA. (C)</p> Signup and view all the answers

What is the main function of siRNAs in relation to mRNA?

<p>To promote mRNA degradation. (A)</p> Signup and view all the answers

Which component is involved in the telomere lengthening process?

<p>Telomerase (C)</p> Signup and view all the answers

Which of the following statements best distinguishes miRNAs from siRNAs?

<p>miRNAs regulate gene expression post-transcriptionally while siRNAs primarily induce degradation. (D)</p> Signup and view all the answers

What triggers the pause in translation when a polypeptide is being synthesized?

<p>Binding of SRP to an ER signal sequence (A)</p> Signup and view all the answers

Which component is critical for the adaptability of the type II CRISPR-Cas system?

<p>Cas proteins that recognize bacteriophage DNA (D)</p> Signup and view all the answers

During the expression phase of the CRISPR-Cas system, which of the following gets transcribed?

<p>The tracrRNA and Cas9 genes (B)</p> Signup and view all the answers

What is the primary role of the tracrRNA in the CRISPR-Cas system?

<p>To guide the Cas9 protein to the target sequence (B)</p> Signup and view all the answers

Which phase follows adaptation in the CRISPR-Cas defense mechanism?

<p>Expression phase (C)</p> Signup and view all the answers

What event characterizes the interference phase of the CRISPR-Cas system?

<p>Cleavage of bacteriophage DNA (B)</p> Signup and view all the answers

Which short sequences are interspersed in the Crispr gene?

<p>Unique spacers (A)</p> Signup and view all the answers

What happens to the GTP-binding proteins during the binding of SRP and the SRP receptor?

<p>They hydrolyze GTP, leading to SRP release (B)</p> Signup and view all the answers

What is the final outcome of the tracrRNA-crRNA complex forming with Cas9?

<p>The bacterial cell is prepared to destroy bacteriophage DNA (D)</p> Signup and view all the answers

What is the result of the bacterial cell's adaptation to a bacteriophage?

<p>It becomes resistant to further infections (D)</p> Signup and view all the answers

Flashcards

Non-coding RNA (ncRNA)

RNA molecules that do not code for proteins, but have various roles in cellular functions.

ncRNA binding

ncRNAs bind to other molecules like small molecules, DNA, RNA, and proteins.

ncRNA Functions

ncRNAs have diverse functions including scaffolding, guiding molecules, altering protein structure/function, possessing catalytic activity, blocking pathways, and acting as decoys.

RNA guide

An RNA molecule that directs a DNA cutting protein to specific location in DNA.

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Gene Deactivation

Cutting DNA by RNA-guided proteins to prevent a gene from creating a protein.

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Ribozyme

A catalytic RNA molecule that can cut or modify other RNA molecules or DNA.

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mRNA

messenger RNA; RNA that carries the genetic instructions for making proteins from the DNA.

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Human Cell ncRNA Percentage

In a typical human cell, 80% of RNA transcription involves non-coding RNAs.

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ncRNA function: Scaffold

ncRNA binds to multiple components (like proteins), forming a complex.

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ncRNA function: Guide

ncRNA directs a molecule (like protein) to a specific cell location.

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ncRNA function: Alter protein function/stability

ncRNA binding can change protein activity or how long it exists.

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ncRNA function: Ribozyme

ncRNA with catalytic function (like in ribosomes).

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ncRNA function: Blocker

ncRNA physically prevents a cellular process (e.g., translation).

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ncRNA interaction with DNA/RNA

ncRNAs bind DNA/RNA through complementary base pairing.

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ncRNA interaction with proteins/molecules

ncRNAs can bind/scaffold proteins or be a site for small molecule binding.

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ncRNA function: Decoy

ncRNA binds to & sequesters other ncRNAs, preventing their activity.

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Telomere Lengthening

The process of adding DNA to the ends of chromosomes, preventing their shortening during DNA replication.

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Telomerase

An enzyme that adds DNA to telomeres, using its RNA component as a template.

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TERC

The RNA component of telomerase, acting as a guide and template for DNA addition.

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HOTAIR Function

A non-coding RNA that binds to proteins and guides them to specific genes, silencing their expression.

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Chromatin Structure and Transcription

How the structure of DNA and its associated proteins affects gene expression.

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Double-Stranded RNA (dsRNA)

RNA molecules with two strands (like a ladder) that are more potent at inhibiting mRNA than single-stranded RNA.

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Small-Interfering RNA (siRNA)

Short, double-stranded RNA molecules that specifically target and degrade mRNA, stopping protein production.

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microRNA (miRNA)

Short, single-stranded RNA molecules that bind to mRNA, preventing its translation into protein.

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Telomere Shortening

Telomeres get shorter with each cell division, eventually limiting cell division and leading to cell death.

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DNA Polymerase and Telomeres

DNA polymerase cannot fully replicate the ends of chromosomes, leaving them shorter with each replication cycle.

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Telomerase Function

Telomerase adds repeating DNA sequences to the ends of chromosomes, compensating for the shortening caused by DNA polymerase.

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ncRNA Role in Telomere Replication

Non-coding RNA (ncRNA) plays a crucial role in telomere length regulation, guiding telomerase to the ends of chromosomes.

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How does telomerase know where to add DNA?

Non-coding RNA (ncRNA) molecules act as guides for telomerase, ensuring it adds DNA sequences to the correct location (telomeres) on the chromosomes.

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Why are telomeres important?

Telomeres protect chromosomes from degradation and prevent them from fusing with other chromosomes. They also regulate cell division and lifespan.

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RNA interference (RNAi)

A process where small non-coding RNAs (ncRNAs) like microRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression by targeting mRNA for degradation or blocking its translation.

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RNA-induced silencing complex (RISC)

A protein complex in eukaryotic cells involved in RNA interference. It binds to either miRNAs or siRNAs, leading to either mRNA degradation or translation inhibition.

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Signal recognition particle (SRP)

A complex of proteins and a small ncRNA that recognizes and binds to signal sequences on newly synthesized proteins, targeting them to the endoplasmic reticulum (ER).

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SRP-RNA function

The RNA component of SRP plays a critical role in binding the signal sequence and interacting with the SRP receptor on the ER membrane, ensuring proper protein targeting.

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Protein targeting to the ER

SRP-mediated targeting of proteins to the ER ensures that proteins destined for secretion or membrane localization reach their correct destination.

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SRP receptor

A protein complex located on the ER membrane that binds to SRP, facilitating the docking of ribosomes and the translocation of newly synthesized proteins into the ER lumen.

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CRISPR-Cas System

A bacterial defense mechanism against bacteriophages and transposons. It involves a gene called Crispr, tracrRNA ncRNA, and Cas proteins.

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CRISPR-Cas System: Adaptation

This phase occurs after a bacteriophage infection. Cas1 and Cas2 proteins recognize and cleave the bacteriophage DNA. A piece of the phage DNA (spacer) is then inserted into the Crispr gene.

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CRISPR-Cas System: Expression

This phase involves transcribing the Crispr, tracrRNA, and Cas9 genes. The tracrRNA binds to the pre-crRNA, which gets cleaved into small crRNAs. The complex of tracrRNA, crRNA, and Cas9 protein forms.

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CRISPR-Cas System: Interference

This phase involves using the tracrRNA-crRNA-Cas9 complex to destroy the bacteriophage DNA. Each spacer is complementary to a specific part of the phage DNA, guiding the complex to the target.

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What is tracrRNA?

A non-coding RNA (ncRNA) involved in the CRISPR-Cas system. It is complementary to the repeat sequences of the pre-crRNA and acts as a guide for the Cas9 protein.

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What does Cas9 do?

A protein in the CRISPR-Cas system that binds to the tracrRNA-crRNA complex. It acts as a DNA-cutting enzyme, using the crRNA as a guide to target and destroy specific phage DNA sequences.

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What is a spacer?

A short DNA sequence derived from bacteriophage DNA and inserted into the Crispr gene during the adaptation phase. It acts as a unique identifier for a specific phage.

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What is a crRNA?

A small non-coding RNA produced from the Crispr locus in the expression phase. It is complementary to a specific phage DNA sequence and guides the Cas9 protein to target and destroy the invader.

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Why is the CRISPR-Cas system important?

It provides bacteria with a powerful defense mechanism against bacteriophages. The ability to adapt and remember past infections makes the CRISPR-Cas system very effective.

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Study Notes

Chinese Scientist Claims to Use CRISPR to Make Genetically Edited Babies

  • A Chinese scientist, He Jiankui, claimed to have used CRISPR to edit the genes of human embryos
  • He offered no supporting data or evidence for his assertions
  • The claim sparked concern about the possibility of "designer babies"

Disgraced CRISPR-Baby Scientist Sentenced

  • He Jiankui, the scientist who claimed to have produced genetically edited babies, was found guilty of conducting illegal medical practices
  • He and two collaborators forged ethical review documents and misled doctors
  • The court sentenced him to three years in prison

Nobel Prize in Chemistry 2020

  • Jennifer Doudna and Emmanuelle Charpentier were awarded the Nobel Prize in Chemistry 2020
  • Awarded "for the development of a method for genome editing"
  • Shared the prize equally

Gene Expression- Non-Coding RNAs

  • In a typical human cell, only about 20% of transcription involves the production of mRNAs, whereas 80% is associated with making non-coding RNAs (ncRNAs)
  • ncRNAs perform a diverse set of functions
  • They can bind to small molecules, DNA, or RNA, or to proteins

ncRNA Functions

  • Scaffold: Bind to components like proteins, acting as a scaffold for complex formation
  • Guide: Guide one molecule to a specific location in the cell (like guiding a protein to a specific location on DNA)
  • Alteration of protein function or stability: ncRNA binding affects the protein's ability to be a catalyst or bind to other molecules.
  • Ribozyme: RNA molecule with catalytic function (like peptidyltransferase activity of ribosomes)
  • Blocker: ncRNA physically prevents or blocks a cellular process (e.g., blocks the binding of a ribosome to mRNA, inhibiting translation)
  • Decoy: Recognizes other ncRNAs and sequesters them to prevent them from working

Overview of Non-Coding RNAs

  • ncRNAs can bind to DNA or RNA molecules through complementary base pairing
  • ncRNAs can bind to proteins or small molecules
  • Stem-loop structures may bind or scaffold proteins, or form binding sites for small molecules

Role of ncRNAs in Eukaryotic DNA Replication

  • Telomeres are composed of repeat sequences that protect the ends of linear eukaryotic chromosomes from becoming tangled or broken
  • Telomeres shorten with each cell division, eventually leading to cell death
  • Some cells, like stem cells, express telomerase, which adds telomere sequences, preventing shortening of telomeres

Effects of ncRNAs on Chromatin Structure and Transcription

  • HOTAIR (Hox transcript antisense intergenic RNA) is an ncRNA that regulates transcription by acting as a scaffold
  • It binds to two proteins complexes and guides them to particular genes, covalently modifying histones and silencing these modifications

Effects of ncRNAs on Translation and mRNA Degradation

  • Double-stranded RNA (dsRNA) is more potent at inhibiting mRNA than antisense RNA
  • This phenomenon is called RNA interference
  • MicroRNAs (miRNAs) and small-interfering RNAs (siRNAs) are involved in RNA interference, regulating gene expression
  • miRNAs are partially complementary to mRNA targets, and siRNAs are usually perfectly complementary.

Non-Coding RNAs and Protein Sorting

  • Signal recognition particle (SRP) is a complex of protein and ncRNA that chaperones ribosomes to the ER
  • SRP binds to an ER signal sequence and pauses translation
  • SRP binds to an SRP receptor in the ER membrane, allowing the polypeptide to be threaded through a channel into the ER lumen.

Non-Coding RNAs and Genome Defense

  • Some bacteria and archaea use the CRISPR-Cas system for defense against bacteriophages and transposons
  • The type II CRISPR-Cas system contains genes for crRNAs, tracrRNA, and Cas proteins
  • These phases (adaptation, expression, and interference) allow the bacteria to recognize foreign DNA, cleave it, and prevent infection

Role of ncRNAs in Human Disease and Plant Health

  • Abnormal expression levels of miRNAs are found in almost all forms of human cancer. Some miRNAs are tumor suppressors, and others are oncogenes.
  • HOTAIR is highly expressed in several cancers and behaves as an oncogene when overexpressed.
  • Various ncRNAs are associated with neurological disorders.
  • ncRNAs play essential roles in plant health, including seed development, growth, and stress responses. This research is useful for agriculture.

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