Chp. 11 - Exam 3 Bio 190
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Questions and Answers

What is the primary function of TERC in relation to telomerase?

  • It serves as a guide for telomerase binding. (correct)
  • It acts as a primer for DNA replication.
  • It helps in the degradation of mRNA.
  • It silences target genes.

HOTAIR is an ncRNA that enhances gene expression by modifying histones.

False (B)

What does telomerase add to the end of the chromosome, and what is its purpose?

Excess DNA, to create room for future primer.

The ncRNA known as ______ regulates transcription by forming a scaffold for protein complexes.

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

Match the following terms with their definitions:

<p>Double-stranded RNA = More potent at inhibiting mRNA Antisense RNA = Less effective than double-stranded RNA miRNAs = Regulate gene expression post-transcriptionally siRNAs = Target specific mRNA for degradation</p> Signup and view all the answers

What percentage of transcription in a typical human cell is associated with making ncRNAs?

<p>80% (C)</p> Signup and view all the answers

Non-coding RNAs can only bind to DNA.

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

What is a ribozyme?

<p>A ribozyme is an RNA molecule capable of acting as an enzyme to catalyze biochemical reactions.</p> Signup and view all the answers

NcRNAs can affect processes of __________, transcription, and translation.

<p>DNA replication</p> Signup and view all the answers

Match the following functionalities of ncRNAs with their respective roles:

<p>Bind to DNA = Affects DNA replication Scaffold proteins = Supports protein assembly Bind small molecules = Forms binding sites Affects transcription = Regulates gene expression</p> Signup and view all the answers

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

<p>Providing genetic information (D)</p> Signup and view all the answers

Only a small portion of ncRNAs have roles in human diseases.

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

What is the primary difference between coding and non-coding RNAs?

<p>Coding RNAs carry the genetic information for protein synthesis, while non-coding RNAs do not code for proteins but serve other functions.</p> Signup and view all the answers

What is the repeat sequence found in human telomeres?

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

As cells divide, telomeres become longer.

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

What enzyme is responsible for adding repeating sequences to telomeres?

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

The ends of the chromosomes cannot be fully replicated by __________.

<p>DNA polymerase</p> Signup and view all the answers

What happens to a cell when its telomeres become too short?

<p>The cell undergoes programmed cell death. (A)</p> Signup and view all the answers

What is the function of telomeres?

<p>To protect the ends of chromosomes from becoming tangled or broken.</p> Signup and view all the answers

Telomere lengthening occurs in _______ steps.

<p>3</p> Signup and view all the answers

What is one primary function of the Signal Recognition Particle (SRP)?

<p>To guide the ribosome to the endoplasmic reticulum (ER) (B)</p> Signup and view all the answers

SRP is composed solely of protein.

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

What must bind GTP for SRP to bind to its receptor in the ER membrane?

<p>Proteins within SRP and the SRP receptor</p> Signup and view all the answers

The SRP changes a protein's function to open a __________ for the polypeptide.

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

What is the result of GTP hydrolysis in the SRP and SRP receptor complex?

<p>It releases SRP, allowing translation to resume (A)</p> Signup and view all the answers

During translation, SRP pauses the process upon binding to an ER signal __________.

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

What is the relationship between SRP and non-coding RNA (ncRNA)?

<p>SRP is composed of ncRNA and protein.</p> Signup and view all the answers

Match the following components with their roles in the SRP pathway:

<p>SRP = Guides ribosome to ER GTP-binding proteins = Cause SRP release ER receptor = Binds SRP ncRNA = Part of SRP structure</p> Signup and view all the answers

What is the role of the Cas9 protein in the interference phase?

<p>It cleaves bacteriophage DNA (C)</p> Signup and view all the answers

NcRNAs have no impact on human diseases.

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

Name one type of cancer where abnormal expression levels of certain miRNAs have been found.

<p>Breast cancer</p> Signup and view all the answers

HOTAIR behaves as an ______ when overexpressed.

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

Match the following roles of ncRNAs with their applications:

<p>Tumor suppressor = Reduces cancer progression Oncogene = Promotes cancer development miRNA = Regulates gene expression HOTAIR = Associated with cancer</p> Signup and view all the answers

What is the primary function of the CRISPR-Cas system in bacteria?

<p>Defense against bacteriophages (B)</p> Signup and view all the answers

The type II CRISPR-Cas system contains multiple types of CRISPR-associated genes.

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

What proteins form a complex to recognize and cleave foreign bacteriophage DNA during the adaptation phase?

<p>Cas1 and Cas2</p> Signup and view all the answers

In the interference phase, the tracrRNA-crRNA-Cas9 complex binds to the __________ protein.

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

Match the following stages of the CRISPR-Cas system with their descriptions:

<p>Adaptation = Insertion of bacteriophage DNA into the Crispr gene Expression = Transcription of Crispr, tracr, and Cas9 genes Interference = Cleavage of bacteriophage DNA by the Cas9 protein</p> Signup and view all the answers

Which non-coding RNA is involved in the CRISPR-Cas system's defense mechanism?

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

The expression phase occurs after the bacterial cell has been exposed to a bacteriophage for the first time.

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

What happens to the pre-crRNA during the expression phase?

<p>It is cleaved into many small crRNA molecules.</p> Signup and view all the answers

Flashcards

Non-coding RNA (ncRNA)

RNA molecules that do not code for proteins.

mRNA

RNA that carries genetic information for protein synthesis from DNA to ribosomes.

ncRNA binding

ncRNAs bind to other molecules through complementary base pairing & other methods, affecting processes such as replication, transcription, & translation.

Ribozyme

RNA molecules with enzymatic activity. ncRNAs can be ribozymes.

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Gene silencing

Deactivation of a gene, preventing the production of its protein by cutting and deactivating the gene's DNA.

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Base Pairing

Complementary pairing of DNA or RNA nucleotides, for example, A with T/U and G with C.

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DNA cutting

A method used for silencing genes by cutting the DNA, inactivating the gene's instructions

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ncRNA function

ncRNAs perform a wide range of functions, including regulating DNA replication, transcription, and translation, and protein sorting, genome defense, and impacting human/plant health.

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Telomerase action

Telomerase adds extra DNA to chromosome ends, creating space for future replication primers. TERC guides telomerase to the end.

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HOTAIR function

HOTAIR, an ncRNA, forms a scaffold to bind protein complexes and direct them to specific genes for gene silencing through histone modification.

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dsRNA potency

Double-stranded RNA (dsRNA) is more effective at inhibiting mRNA than antisense RNA in experiments.

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MicroRNA (miRNA) vs. siRNA

Both miRNAs and siRNAs are small RNA molecules involved in gene regulation. They have differences in function (e.g., miRNAs tend to reduce gene expression rather than block translation entirely).

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Chromosome Replication Primers

DNA primers are needed for DNA synthesis. Adding "excess" DNA lengthens the template strand available for primer attachment; allowing the DNA replication process to extend across the new end.

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Telomeres

Repeating sequences at the ends of eukaryotic chromosomes that protect them from damage and shortening during cell division.

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Telomere shortening

The progressive loss of telomere repeat sequences during cell division, eventually leading to cell death.

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Telomerase

An enzyme that can add telomere repeat sequences to the ends of chromosomes to compensate for shortening during replication.

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DNA polymerase

An enzyme that synthesizes new DNA strands by adding nucleotides to an existing primer.

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Primer

A short sequence of nucleotides that provides a starting point for DNA polymerase during DNA replication.

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Eukaryotic chromosome replication

The process of duplicating a eukaryotic chromosome's DNA.

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ncRNA in telomere replication

Some non-coding RNA molecules (ncRNA) may be involved in the process of telomere replication, but specific details are not clear from the provided content.

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3 Steps of telomere lengthening

The process of lengthening telomeres involves three stages:1. Preparation, 2. addition of repeated sequences, and 3. stabilization of the telomere.

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SRP function in protein sorting

SRP binds to an ER signal sequence on a polypeptide, causing translation to pause. It then escorts the ribosome to the ER membrane.

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SRP receptor

A protein in the ER membrane that binds to SRP, bringing the ribosome close to the ER channel.

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ER channel

A protein channel in the ER membrane that allows the polypeptide to enter the ER lumen during translation.

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GTP hydrolysis role in SRP

GTP hydrolysis by SRP and the SRP receptor releases SRP, allowing translation to resume and the polypeptide to enter the ER lumen.

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CRISPR-Cas system

A bacterial immune system that protects against bacteriophages (viruses that infect bacteria) by using CRISPR sequences and Cas proteins.

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CRISPR sequences

Short, repeated DNA sequences in bacterial genomes that store information about past phage infections.

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Cas proteins

Enzymes that use CRISPR sequences to identify and destroy invading phage DNA.

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CRISPR spacers

Short DNA sequences within CRISPR that serve as a record of past bacteriophage infections. Each spacer is complementary to a fragment of bacteriophage DNA.

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ncRNA roles in cancer

Abnormal expression of certain non-coding RNAs (ncRNAs), like microRNAs (miRNAs), is found in many types of cancer. Some miRNAs act as tumor suppressors, while others act as oncogenes (cancer-promoting genes).

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ncRNA roles in plant health

Abnormal expression of certain ncRNAs can disrupt plant health, impacting seed development, growth, and stress responses. Understanding these roles is crucial for agriculture.

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Adaptation Phase

The first phase of the CRISPR-Cas system where the bacteria encounters a bacteriophage, the Cas1 and Cas2 proteins cleave the phage DNA, and a piece of phage DNA is inserted into the CRISPR gene.

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Expression Phase

The second phase where the CRISPR, tracr, and Cas9 genes are transcribed, and the tracrRNA guides the pre-crRNA to be cleaved into smaller crRNA molecules.

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Interference Phase

The third phase where the tracrRNA-crRNA-Cas9 complex binds to the bacteriophage DNA, the Cas9 protein cleaves the phage DNA, preventing its replication.

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tracrRNA

A non-coding RNA molecule that interacts with the pre-crRNA during the CRISPR system's expression phase, guiding the cleavage of the pre-crRNA into smaller crRNA molecules.

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Cas9

A protein encoded by the Cas9 gene, acting as a molecular scissor that cuts the target DNA identified by the crRNA.

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Spacer

Short, unique sequences within the CRISPR gene that are derived from bacteriophage or transposon DNA, providing a memory of past infections.

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Study Notes

CRISPR-Cas System

  • Chinese scientist He Jiankui claimed to use CRISPR to genetically edit babies.
  • He offered no evidence or data to support his claims.
  • This act could open the door to "designer babies."

RNA Interference (RNAi)

  • Double-stranded RNA is more potent at inhibiting mRNA than antisense RNA.
  • The phenomenon was termed RNA interference.
  • microRNAs (miRNAs): transcribed from endogenous eukaryotic genes and regulate gene expression. miRNAs are partially complementary to their mRNA targets.
  • Small interfering RNAs (siRNAs): come from exogenous sources, and are usually perfectly complementary to their target mRNA. They play a role in preventing viral infections.

Non-coding RNAs (ncRNAs) and Gene Regulation

  • ncRNAs bind to other molecules and macromolecules.
  • ncRNAs have several common functions:
    • Scaffold: bind to multiple components, act as scaffold for formation of a complex.
    • Guide: guide one molecule to a specific location in the cell.
    • Alteration of protein function or stability: bind to ncRNA to affect protein function/stability.
    • Ribozyme: RNA molecule with catalytic function, for example peptidyltransferase activity of ribosome.
    • Blocker: prevents or blocks a cellular process (binding to ribosomes inhibiting translation).
    • Decoy: recognizes other ncRNAs and sequesters them, preventing them from working.

ncRNAs and Human Disease

  • Abnormal expression levels of miRNAs have been found in nearly all forms of human cancer.
  • Some miRNAs are tumor suppressors, some are oncogenes.
  • HOTAIR is expressed in several cancers, behaving as an oncogene when overexpressed.
  • Various ncRNAs are associated with neurological disorders (Alzheimer's disease) and cardiovascular diseases (arrhythmias).

ncRNAs in Plant Health

  • Abnormalities in ncRNAs play essential roles in plant health.
  • Their study is important for agriculture.
  • Examples of ncRNAs involved in plant health include miRNA-156, COOLAIR, and IPS1.

Telomeres and DNA Replication

  • The ends of linear eukaryotic chromosomes have telomeres composed of repeat sequences (e.g. 5' - GGGTTA-3' in humans)
  • Telomeres protect the ends of chromosomes from entanglement and breakage.
  • Telomeres shorten with each cell division; when they are too short, the cell can no longer successfully divide, leading to programmed cell death.
  • Some cells express telomerase, an enzyme that adds repeating sequence and extends the telomeres.
  • Telomeres cannot be fully replicated by DNA polymerase due to the 5' overhang of DNA.
  • RNA primers are required for DNA polymerase to begin replication; primers are removed.
  • Telomerase is the solution for synthesizing the full length of the top strand, which counteracts the problem of limited DNA replication at the end of DNA strands.
  • Telomere length is regulated through TERC, an ncRNA that facilitates the binding of telomerase.

HOTAIR

  • HOTAIR is an ncRNA in humans and other mammals
  • It regulates transcription by forming a scaffold that binds two protein complexes and guides them to particular genes.
  • The protein complexes covalently modify histones, leading to the silencing of target genes.

Signal Recognition Particle (SRP)

  • SRP is composed of protein and ncRNA.
  • It chaperones the ribosome to the ER.
  • As a polypeptide is being made, SRP binds to the ER signal sequence, causing translation to pause.
  • SRP binds to an SRP receptor in the ER membrane.
  • GTP molecules bound to SRP and the SRP receptor are hydrolyzed, thereby releasing SRP.
  • Translation resumes, and the polypeptide is threaded through a channel into the ER lumen.

CRISPR-Cas System (in detail)

  • Some bacteria and archaea have a system called the CRISPR-Cas system that defends against bacteriophages (and transposons).
  • The type II CRISPR-Cas system was described.
  • The system involves three main components:
    • Crispr genes (with repeats and spacers)
    • TracrRNA (a noncoding RNA)
    • Cas genes (encoding associated proteins, e.g., Cas9).
  • Defense occurs in three phases:
    • Adaptation: after bacterial exposure to a bacteriophage. Cas1 and Cas2 proteins cleave the bacteriophage DNA, and a piece of that DNA is added to the Crispr gene.
    • Expression: tracrRNA bonds to complementary sequences of pre-crRNA; pre-crRNA is then cleaved into small crRNA molecules; each tracrRNA-crRNA complex binds to the Cas9 proteins.
    • Interference: the tracrRNA-crRNA- Cas9 complex binds to bacteriophage DNA due to complementary base pairing. The Cas9 protein cleaves the bacteriophage DNA, thereby inactivating it.

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Chapter 11 Notes - Exam 3 PDF

Description

This quiz explores the functions and characteristics of non-coding RNAs (ncRNAs) and telomerase, including their roles in gene expression and chromosome maintenance. Test your knowledge on the differences between coding and non-coding RNAs, the significance of telomerase, and how ncRNAs regulate various cellular processes.

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