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What is the primary function of the Dicer enzyme in RNA interference?

  • To facilitate binding of mRNA to the RISC complex
  • To recruit RISC to the targeted mRNA
  • To unwind double-stranded RNA
  • To cleave larger dsRNAs into smaller fragments (correct)
  • What is the main difference between the effects of miRNA and siRNA?

  • miRNA prevents translation of mRNA, while siRNA degrades mRNA (correct)
  • miRNA is derived from exogenous sources, while siRNA is derived from endogenous sources
  • miRNA is involved in transcriptional gene regulation, while siRNA is involved in post-transcriptional gene regulation
  • miRNA is a perfect match for the mRNA target, while siRNA is not
  • What is the purpose of the RNA-induced silencing complex (RISC)?

  • To unwind double-stranded RNA and select the antisense strand (correct)
  • To cleave larger dsRNAs into smaller fragments
  • To recruit Dicer to the targeted mRNA
  • To translate mRNA into protein
  • What is the role of the Argonaut protein in RNA interference?

    <p>To guide the RISC complex to the targeted mRNA and facilitate binding</p> Signup and view all the answers

    What is the characteristic of the pre-miRNA that is transcribed directly from a gene?

    <p>The presence of a hairpin loop</p> Signup and view all the answers

    Why is RNA silencing believed to be an evolutionarily conserved process?

    <p>Because it is a mechanism to fight off foreign invaders such as viruses and transposons</p> Signup and view all the answers

    What is the outcome when siRNA is a perfect match for the mRNA target?

    <p>The mRNA is degraded by the Argonaut protein</p> Signup and view all the answers

    What is the result of creating strains of mice that lacked the proteins that make miRNA?

    <p>The mice developed a variety of health problems, including heart disease and cancer</p> Signup and view all the answers

    What is the purpose of the ATP-dependent process in RISC?

    <p>To unwind double-stranded RNA and select the antisense strand</p> Signup and view all the answers

    What is the main function of RNA interference?

    <p>To defend against foreign invaders such as viruses and transposons</p> Signup and view all the answers

    What is the estimated percentage of the transcriptional output of our genomes that is comprised of non-coding RNAs (ncRNA)?

    <p>98%</p> Signup and view all the answers

    What is the primary function of micro RNAs (miRNA) and small interfering RNA (siRNA)?

    <p>Control of gene expression</p> Signup and view all the answers

    What is the source of small interfering RNAs (siRNA)?

    <p>From exogenous sources, such as a viral infection, a transposable element, or a molecule supplied by a scientist</p> Signup and view all the answers

    What is the length of micro RNAs (miRNA)?

    <p>22 nucleotides</p> Signup and view all the answers

    What is the enzyme responsible for cutting micro RNAs (miRNA) from a larger RNA?

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

    What is the significance of the discovery of let-7 miRNA in many species, including humans?

    <p>It is a fundamental process of gene regulation</p> Signup and view all the answers

    What is the role of non-coding RNAs (ncRNA) in gene regulation?

    <p>They regulate many processes, including gene silencing, replication, RNA processing, and more</p> Signup and view all the answers

    What is the significance of the transcription of non-coding RNAs (ncRNA) in higher organisms?

    <p>It is responsible for the complexity of higher organisms</p> Signup and view all the answers

    What is the role of miRNA-101 in prostate cancer?

    <p>It leads to the overexpression of a particular histone methyltransferase</p> Signup and view all the answers

    What is the implication of micro RNAs in heart conditions?

    <p>They influence the production of alpha and beta myosin heavy chain</p> Signup and view all the answers

    What is RNA activation (RNAa)?

    <p>A process of activating a gene</p> Signup and view all the answers

    What type of interactions do proteins that bind to DNA use during transcription?

    <p>Hydrogen bonding, electrostatic attractions, and hydrophobic interactions</p> Signup and view all the answers

    What is the function of the DNA-binding domain in proteins?

    <p>To bind to DNA during transcription</p> Signup and view all the answers

    What is the most common motif found in DNA-binding proteins?

    <p>Helix-turn-helix (HTH)</p> Signup and view all the answers

    What is the role of the major groove in DNA-binding proteins?

    <p>It is the site of binding for proteins that recognize DNA with specific base sequences</p> Signup and view all the answers

    What is the role of glycine in the HTH motif?

    <p>It is involved in the beta-turn</p> Signup and view all the answers

    What is the role of glutamine and arginine in DNA-binding proteins?

    <p>They interact favorably with adenine and guanine</p> Signup and view all the answers

    What is the effect of A-T rich areas on the structure of DNA?

    <p>It causes local variations in helix structure</p> Signup and view all the answers

    What is the purpose of the zinc-finger domain in DNA-binding proteins?

    <p>To recognize the shape of the bases protruding into the grooves</p> Signup and view all the answers

    What is the characteristic of the basic-region leucine zipper motif?

    <p>The motif has a series of leucines every seven residues</p> Signup and view all the answers

    What is the function of the acidic domains in transcription factors?

    <p>To recognize other transcription factors</p> Signup and view all the answers

    What is the purpose of the glutamine-rich domains in transcription factors?

    <p>To recognize other transcription factors</p> Signup and view all the answers

    What is the primary function of the polyadenylate tail at the 3' end of a message?

    <p>To protect the mRNA from nucleases and phosphatases</p> Signup and view all the answers

    What is the function of the proline-rich domain in the activator CTF-1?

    <p>To bind to histone proteins via the proline repeats</p> Signup and view all the answers

    What is the term for the DNA sequences that are expressed in the final mRNA product?

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

    What is the characteristic of the zinc-finger domain in DNA-binding proteins?

    <p>The motif has two closely spaced cysteines and two closely spaced histidines</p> Signup and view all the answers

    What is the function of the basic region in the basic-region leucine zipper motif?

    <p>To bind to DNA</p> Signup and view all the answers

    What is the result of the splicing reaction in eukaryotic genes?

    <p>The removal of introns and the linking of exons</p> Signup and view all the answers

    How many introns are present in the pro a-2 collagen gene in chickens?

    <p>51</p> Signup and view all the answers

    What is the purpose of the transcription-activation domains?

    <p>To recognize other transcription factors</p> Signup and view all the answers

    What is the characteristic of the protein TFIIIA?

    <p>It has nine repeating structures of 30 amino acids each</p> Signup and view all the answers

    What is the term for the process of removing intervening sequences from a primary transcript?

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

    What is the function of the C-terminal end of the activator CTF-1?

    <p>To bind to histone proteins</p> Signup and view all the answers

    What is the function of the 5' cap in mRNA?

    <p>To protect the mRNA from exonuclease degradation</p> Signup and view all the answers

    What is the characteristic of the genes of eukaryotes?

    <p>They are not necessarily continuous</p> Signup and view all the answers

    What is the purpose of the poly-T tail in affinity chromatography?

    <p>To isolate mRNA from a cell lysate</p> Signup and view all the answers

    What is the consequence of inaccurate splicing in eukaryotic genes?

    <p>The formation of abnormal proteins</p> Signup and view all the answers

    What is the term for the ribonucleoprotein particles that form through association with a set of nuclear proteins?

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

    What is the conserved sequence at the branch site within the intron in higher eukaryotes?

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

    What is the result of the nucleophilic attack on the phosphodiester backbone at the 5' splice site?

    <p>Formation of a lariat structure and release of exon 1</p> Signup and view all the answers

    What is the function of small nuclear ribonucleoproteins (snRNPs) in the splicing process?

    <p>To mediate the splicing process</p> Signup and view all the answers

    What is the characteristic of the RNA portion of snRNPs in higher eukaryotes?

    <p>It is between 100 and 200 nucleotides in length</p> Signup and view all the answers

    What is the function of the spliceosome in the splicing process?

    <p>To mediate the splicing process</p> Signup and view all the answers

    What is the estimated percentage of proteins in humans that have isoforms based on alternative splicing?

    <p>5% of proteins</p> Signup and view all the answers

    What is the primary function of the motifs described in the transcription factors section?

    <p>To determine the role of a new protein as a transcription factor</p> Signup and view all the answers

    What is the role of regulatory proteins in alternative splicing?

    <p>To direct the alternative splicing</p> Signup and view all the answers

    What is the result of differential splicing of the human troponin T gene?

    <p>Sixty-four possible isoforms of the protein</p> Signup and view all the answers

    What is the purpose of the leader and trailer sequences in RNA transcripts?

    <p>To facilitate the trimming process</p> Signup and view all the answers

    What is the enzyme responsible for generating the 5' ends of all E. coli tRNAs?

    <p>RNase P</p> Signup and view all the answers

    What is the characteristic of the Tau protein in people with Alzheimer's disease?

    <p>It has six isoforms</p> Signup and view all the answers

    What type of modification takes place in eukaryotic tRNA and is not found in prokaryotes?

    <p>Addition of a 2'-O-methylribosyl group</p> Signup and view all the answers

    What is the mechanism by which the splice sites are brought together in both self-splicing and ribonucleoprotein-mediated splicing?

    <p>A lariat mechanism</p> Signup and view all the answers

    What is the purpose of the CCA sequence at the 3' end of tRNA molecules?

    <p>To provide a binding site for amino acids</p> Signup and view all the answers

    What is the primary difference between the processing of rRNA in prokaryotes and eukaryotes?

    <p>The degree of trimming</p> Signup and view all the answers

    What is the purpose of capping the 5' end of eukaryotic mRNA?

    <p>To increase the stability of the mRNA</p> Signup and view all the answers

    What is the purpose of polyadenylating the 3' end of eukaryotic mRNA?

    <p>To increase the stability of the mRNA</p> Signup and view all the answers

    Why is mRNA modified after initial transcription in eukaryotes?

    <p>To increase the stability of the mRNA</p> Signup and view all the answers

    What is the primary difference between the processing of mRNA in prokaryotes and eukaryotes?

    <p>The presence of a poly-A sequence</p> Signup and view all the answers

    What is a characteristic of Group I ribozymes?

    <p>They require an external guanosine, which becomes covalently bonded to the splice site</p> Signup and view all the answers

    What is the significance of the discovery of RNAs that catalyze their own self-splicing?

    <p>It provides evidence for the existence of an RNA-based world</p> Signup and view all the answers

    What is a characteristic of hammerhead ribozymes?

    <p>They can be catalytically active with as few as 43 nucleotides</p> Signup and view all the answers

    What is the role of the folded conformation of RNA in ribozymes?

    <p>It is crucial for the catalytic activity of the ribozyme</p> Signup and view all the answers

    What is the significance of the discovery of RNA that catalyzes its own self-splicing in relation to the splicing of mRNA by snRNPs?

    <p>It is easy to see a connection between the two processes</p> Signup and view all the answers

    What is the role of divalent cations in the catalytic activity of ribozymes?

    <p>They stabilize the folded structure of the RNA by neutralizing some of the negative charges on the phosphate groups</p> Signup and view all the answers

    What is a characteristic of the transesterification reaction that takes place in self-splicing RNA?

    <p>It releases one end of the intron</p> Signup and view all the answers

    What is the significance of the discovery of RNA that catalyzes its own self-splicing in relation to the origin of life?

    <p>It suggests that RNA may have been the original genetic molecule and the original catalytic molecule</p> Signup and view all the answers

    What is the characteristic of the catalytic efficiency of catalytic RNAs compared to protein enzymes?

    <p>It is lower than that of protein enzymes</p> Signup and view all the answers

    What is the requirement for the catalytic activity of Group II ribozymes?

    <p>The 2'-OH of an internal adenosine</p> Signup and view all the answers

    What is the primary function of RNA polymerase in transcription?

    <p>To catalyze the process of nucleotide incorporation</p> Signup and view all the answers

    What is the role of the s-subunit in RNA polymerase?

    <p>To recognize promoters</p> Signup and view all the answers

    What is the direction of RNA synthesis during transcription?

    <p>5' to 3' on the coding strand</p> Signup and view all the answers

    What is the function of the Pribnow box in prokaryotic transcription?

    <p>To recognize promoters</p> Signup and view all the answers

    What is the role of enhancers in transcriptional regulation?

    <p>To stimulate transcription above basal levels</p> Signup and view all the answers

    What is the difference between a promoter and an enhancer?

    <p>A promoter is a DNA sequence near the transcription start site, while an enhancer is a DNA sequence farther away from the start site</p> Signup and view all the answers

    How does repression work in the lac operon?

    <p>The repressor binds to the operator and blocks RNA polymerase</p> Signup and view all the answers

    What is the role of RNA secondary structures in transcription attenuation?

    <p>To regulate transcription through secondary structures</p> Signup and view all the answers

    What is the difference between the template strand and the coding strand?

    <p>The template strand is the strand that is transcribed, while the coding strand is the strand that is not transcribed</p> Signup and view all the answers

    What is the function of Mg2+ in RNA synthesis?

    <p>To facilitate the binding of RNA polymerase to the template strand</p> Signup and view all the answers

    What is the role of chromatin remodeling complexes in eukaryotic transcription?

    <p>To allow RNA polymerase to access the promoter region and begin transcription</p> Signup and view all the answers

    What is the function of the TATA box in eukaryotic promoters?

    <p>To aid in promoter recognition and binding</p> Signup and view all the answers

    What is the role of general transcription factors in transcription initiation?

    <p>To aid in promoter recognition and binding</p> Signup and view all the answers

    What is the function of response elements in transcription?

    <p>To increase the rate of transcription above basal levels</p> Signup and view all the answers

    What is the difference between micro RNA and small interfering RNA?

    <p>Micro RNA is produced by transcription of the cell’s genes, while small interfering RNA is from exogenous sources</p> Signup and view all the answers

    What is the role of RNA-induced silencing complex (RISC) in RNA interference?

    <p>To bind to the mRNA with the target sequence</p> Signup and view all the answers

    What is the function of DNA-binding domains in transcription factors?

    <p>To bind to the DNA and aid in promoter recognition</p> Signup and view all the answers

    What is the role of histone modifying enzymes in eukaryotic transcription?

    <p>To allow RNA polymerase to access the promoter region and begin transcription</p> Signup and view all the answers

    What is the outcome when the sequence of the siRNA is perfect?

    <p>The mRNA is degraded before it gets a chance to be translated</p> Signup and view all the answers

    What is the role of transcription-activation domains in transcription factors?

    <p>To bind to other proteins and increase the rate of transcription</p> Signup and view all the answers

    What is the primary function of the 5' cap in mRNA?

    <p>To protect the mRNA from degradation</p> Signup and view all the answers

    What is the term for the process of removing intervening sequences from a primary transcript?

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

    What is the characteristic of a ribozyme?

    <p>It is a RNA molecule with catalytic ability</p> Signup and view all the answers

    What is the role of the branch point in the splicing reaction?

    <p>It is the site where the lariat shape is formed</p> Signup and view all the answers

    What is the function of the 3' polyadenylation in mRNA?

    <p>To stabilize the mRNA</p> Signup and view all the answers

    What is the characteristic of the genes of eukaryotes?

    <p>They are non-continuous</p> Signup and view all the answers

    What is the role of snRNP in the splicing reaction?

    <p>It is the ribonucleoprotein molecule that facilitates the reaction</p> Signup and view all the answers

    What is the consequence of inaccurate splicing in eukaryotic genes?

    <p>The mRNA is degraded</p> Signup and view all the answers

    Study Notes

    Non-Coding RNAs (ncRNAs)

    • 98% of transcribed RNA does not make protein
    • ncRNAs linked to processes like transcription, gene silencing, replication, RNA processing, modification, translation, protein stabilization, and translocation

    Micro RNAs (miRNAs) and Small Interfering RNAs (siRNAs)

    • small double-stranded RNAs involved in controlling gene expression
    • miRNAs:
      • Produced by transcription of cell's genes
      • About 22 nucleotides long
      • Cut from larger RNA by enzyme Dicer
      • Not a perfect match for mRNA target, preventing translation
    • siRNAs:
      • From exogenous sources (viral infection, transposable element, or supplied by scientist)
      • Cut by Dicer to 21-25 nucleotides
      • Guides RISC complex to targeted mRNA, facilitating binding and silencing

    RNA Interference (RNAi)

    • Process by which miRNA and siRNA decrease gene expression
    • RISC complex mediates RNAi
    • Extent of sequence matching controls effect on gene expression

    Where miRNA Fits into Gene Expression

    • Similar process to RNA interference, using same enzymes
    • miRNA loaded onto RISC complex, interacting with mRNA target
    • No cleavage of mRNA, preventing translation

    Evolutionary Significance of RNA Silencing

    • Protects genome from foreign invaders (viruses, transposons)
    • Conserved process in higher organisms
    • Importance demonstrated in mouse studies (health problems without miRNA) and human studies (miRNA and cancer)

    DNA-Binding Proteins

    • Bind to DNA during transcription using interactions like hydrogen bonding, electrostatic attractions, and hydrophobic interactions
    • Two functional domains: DNA-binding domain and transcription-activation domain

    Structural Motifs in DNA-Binding Proteins

    • Helix-turn-helix (HTH), zinc fingers, and basic-region leucine zipper (bZIP) motifs
    • Interact with DNA in major or minor groove
    • HTH motif: a-helix fits into major groove
    • Zinc fingers: looped out from intersection of cysteines and histidines with zinc ion
    • Basic-region leucine zipper: basic region binds to DNA in major groove, leucine zipper interacts with second analogous protein fragment

    Transcription-Activation Domains

    • Involved in binding of transcription factors to other proteins, not DNA
    • Motifs like acidic domains, glutamine-rich domains, and proline-rich domains

    Posttranscriptional RNA Modification

    • Modification of RNA after transcription
    • Trimming, addition of terminal sequences, and base modification occur
    • tRNA, rRNA, and mRNA undergo modification
    • tRNA:
      • Trimming of precursor sequence
      • Addition of terminal sequences (C CA at 3' end)
      • Base modification (methylation, sulfur substitution)
    • mRNA:
      • Capping of 5' end with guanylate residue
      • Polyadenylating 3' end
      • Splicing of coding sequences (in eukaryotes)### Intron and Exon Structure
    • Intron: a sequence of DNA that is removed from the primary RNA transcript to produce mature RNA
    • Exon: a sequence of DNA that is retained in the mature RNA
    • The pro-alpha2 collagen gene in chickens has 51 exons, with the coding regions spread out over 40,000 base pairs

    Splicing Mechanisms

    • Splicing occurs in the nucleus and involves the formation of ribonucleoprotein particles (RNPs) with a set of nuclear proteins
    • The substrate for splicing is the capped, polyadenylated pre-mRNA
    • Splicing requires cleavage at the 5' and 3' ends of introns and the joining of the two ends
    • Specific sequences make up the splice sites, with GU at the 5' end and AG at the 3' end of introns in higher eukaryotes
    • A branch site within the intron also has a conserved sequence, with PyNPyPuAPy (where Py is any pyrimidine and Pu is any purine) and an invariant A

    Alternative RNA Splicing

    • Many proteins are always spliced in the same way, but some can be spliced in different ways to give different isoforms of the protein
    • In humans, 5% of proteins produced have isoforms based on alternative splicing
    • Alternative splicing is regulated by specific proteins that affect the recognition of splice sites
    • The human troponin T gene produces a muscle protein with many isoforms due to differential splicing

    Ribozymes

    • Ribozymes are RNA molecules with catalytic activity
    • The discovery of ribozymes has had a profound impact on the way biochemists think about catalysis
    • Ribozymes can catalyze their own self-splicing, as well as other reactions involved in protein synthesis
    • The catalytic efficiency of ribozymes is less than that of protein enzymes
    • Ribozymes have been found to stimulate transcription elongation

    Characteristics of Ribozymes

    • Several groups of ribozymes are known to exist, including Group I and Group II ribozymes
    • Group I ribozymes require an external guanosine and use a transesterification mechanism
    • Group II ribozymes display a lariat mechanism of operation, similar to the mechanism seen in splicing facilitated by snRNPs
    • Hammerhead ribozymes are the smallest known ribozymes, with as few as 43 nucleotides

    Basics of Transcription

    • RNA synthesis is the transcription of the base sequence of DNA to that of RNA
    • All RNAs are synthesized on a DNA template
    • The enzyme that catalyzes the process is DNA-dependent RNA polymerase
    • The RNA chain grows from the 5' to the 3' end
    • The enzyme uses one strand of the DNA (the antisense strand, or template strand) as the template for RNA synthesis

    RNA Polymerase Subunits

    • In prokaryotes, the subunits of RNA polymerase (α, β, β', and ω) make up the core of the enzyme and are responsible for the enzymatic activity
    • The σ-subunit is used for promoter recognition
    • In eukaryotes, the opposite strand is often used to produce small noncoding RNAs

    Transcription Control

    • Frequency of transcription is controlled by the promoter sequence
    • Additional sequences upstream can also be involved in regulating transcription
    • Proteins called transcription factors can bind to these sequences and stimulate or inhibit transcription
    • Many prokaryotic genes are controlled in groups called operons, and expression of some genes is controlled by transcription attenuation

    Repression and Induction

    • Repression involves the binding of a repressor protein to the operator portion of the promoter, preventing transcription
    • Induction involves the binding of an inducer molecule to the repressor, allowing transcription to occur

    RNA Secondary Structures

    • In prokaryotes, transcription and translation are linked
    • RNA secondary structures can form during transcription, affecting the speed of translation
    • Depending on the speed of translation, the RNA produced can form different hairpin loop structures that can act as terminators or allow transcription to proceed

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    Test your knowledge of RNA interference, a process of gene silencing that involves the degradation of specific mRNA molecules. This quiz covers the functions of Dicer, miRNA, siRNA, RISC, and Argonaut proteins.

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