RNA Processing and Capping
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Questions and Answers

What protects mRNA from 5' exonuclease degradation?

  • Intron splicing
  • 7-methylguanosine cap (correct)
  • Poly(A) tail
  • Secondary structures

    • What is the role of polyadenylate polymerase in mRNA processing?

  • Removes the 5' exon
  • Adds a 5' cap to the mRNA
  • Splices out introns from the mRNA
  • Synthesizes the poly(A) tail (correct)

    • Which sequence is highly conserved and involved in the addition of the poly(A) tail?

  • (3')UUUUU
  • (5')GGGCGG
  • (3')CCAUGG
  • (5')AAUAAA (correct)

    • In eukaryotes, which RNA polymerase synthesizes RNA that typically receives a poly(A) tail?

    <p>RNA Polymerase II</p> Signup and view all the answers

    When does the capping of the 5' end of mRNA occur?

    <p>Early in transcription</p> Signup and view all the answers

    What is the primary function of introns in pre-mRNA?

    <p>Non-coding sequences that are spliced out</p> Signup and view all the answers

    Which process is NOT involved in RNA processing in eukaryotes?

    <p>Conversion of RNA into DNA</p> Signup and view all the answers

    What is the purpose of splicing during RNA processing?

    <p>To remove introns</p> Signup and view all the answers

    Which RNA polymerase is responsible for the synthesis of mRNA in eukaryotes?

    <p>RNA polymerase II</p> Signup and view all the answers

    What is the role of TFIIH in the assembly of RNA polymerase?

    <p>Involvement in DNA melting and unwinding at the promoter</p> Signup and view all the answers

    During RNA strand initiation and promoter clearance, which transcription factors are released after the initial synthesis of 60-70 RNA nucleotides?

    <p>TFIIE and TFIIH</p> Signup and view all the answers

    What is the function of the TATA-binding protein (TBP) in the assembly of RNA polymerase?

    <p>Binding and interaction with the promoter</p> Signup and view all the answers

    Which RNA polymerase synthesizes pre-ribosomal RNA?

    <p>RNA polymerase I</p> Signup and view all the answers

    What remains attached to RNA polymerase II during the elongation phase of transcription?

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

    Which feature is characteristic of the Rho-independent terminator?

    <p>G-C rich stem</p> Signup and view all the answers

    Which subunit of the E. coli RNA polymerase is responsible for initiation of transcription?

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

    What activity does the Rho factor exhibit in the hot pursuit model?

    <p>Helicase activity</p> Signup and view all the answers

    What is the function of the Nus A protein during transcription in E. coli?

    <p>Clearing the promoter and preparing for elongation</p> Signup and view all the answers

    What kind of protein is the Rho factor?

    <p>46-kD protein, active as a hexamer</p> Signup and view all the answers

    Which process occurs when the RNA polymerase encounters a Rho-independent terminator?

    <p>Transcription stops and RNA disassociates from the DNA</p> Signup and view all the answers

    RNA synthesis occurs in three stages. Which stage is NOT one of them?

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

    What happens when RNA polymerase encounters a transcription-termination signal?

    <p>RNA synthesis stops</p> Signup and view all the answers

    The -10 sequence in E. coli promoters is also known as what?

    <p>Pribnow box</p> Signup and view all the answers

    What is the role of the β subunit in the E. coli RNA polymerase?

    <p>Ribonucleoside triphosphate binding site</p> Signup and view all the answers

    In the numbering of a transcription unit, what designation is given to the bases that follow the initiation site?

    <p>Downstream sequences</p> Signup and view all the answers

    What protects mRNA from 5' exonuclease degradation?

    <p>5' cap</p> Signup and view all the answers

    What happens during the RNA chain elongation stage?

    <p>Covalent extension of the RNA chain</p> Signup and view all the answers

    What is the function of introns in eukaryotic genes?

    <p>Intervene between coding sequences</p> Signup and view all the answers

    Which component is not part of the core enzyme of E. coli RNA polymerase?

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

    Which sequence is highly conserved and signals for the addition of the poly(A) tail?

    <p>(5')AAUAAA</p> Signup and view all the answers

    At which stage is the 5' cap added to the mRNA?

    <p>During transcription</p> Signup and view all the answers

    Which enzyme synthesizes RNA in eukaryotic cells up to and beyond the sequence AAUAAA?

    <p>RNA Polymerase II</p> Signup and view all the answers

    What happens to introns in the mRNA processing?

    <p>They are excised from the RNA transcripts</p> Signup and view all the answers

    Which of the following occurs first during mRNA processing?

    <p>Addition of 5' cap</p> Signup and view all the answers

    Which components remain in the mature mRNA after splicing?

    <p>Only exons</p> Signup and view all the answers

    Which type of RNA carries genetic information from DNA to the ribosomes?

    <p>Messenger RNAs (mRNAs)</p> Signup and view all the answers

    What is the primary function of transfer RNAs (tRNAs)?

    <p>They act as adaptors between amino acids and the codons in mRNA.</p> Signup and view all the answers

    Which structural form does RNA adopt due to its bulky 2'-OH group?

    <p>A-form geometry</p> Signup and view all the answers

    What component is Polyadenylated at the 3' end?

    <p>Messenger RNA</p> Signup and view all the answers

    What is the key role of ribosomal RNAs (rRNAs)?

    <p>Function as structural and catalytic components of ribosomes</p> Signup and view all the answers

    Which RNA type is specifically involved in RNA interference?

    <p>Small interfering RNAs (siRNAs)</p> Signup and view all the answers

    What is the primary transcript in eukaryotes?

    <p>pre-mRNA</p> Signup and view all the answers

    What is RNA synthesis also known as?

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

    What enzyme is responsible for RNA synthesis?

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

    Which direction does RNA synthesis proceed in?

    <p>5'-3'</p> Signup and view all the answers

    Which characteristic differentiates RNA synthesis from DNA synthesis?

    <p>RNA synthesis uses only one strand of DNA as a template</p> Signup and view all the answers

    In prokaryotes, which process starts immediately after transcription?

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

    What happens to the pre-mRNA before it becomes mRNA?

    <p>It is modified at both ends and undergoes intron removal</p> Signup and view all the answers

    What molecules will be identical to the DNA non-template (sense) strand?

    <p>RNA molecule</p> Signup and view all the answers

    What components make up a nucleotide?

    <p>Sugar + base + phosphate backbone</p> Signup and view all the answers

    Which nucleotide base pairs with thymine in DNA?

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

    What is the monophosphate form of guanine in RNA?

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

    What type of bonds link nucleotide subunits together in DNA and RNA?

    <p>Phosphodiester bonds</p> Signup and view all the answers

    In the helical structure of DNA, what extends into the centre at right angles to the acids of the helix?

    <p>Nitrogenous bases</p> Signup and view all the answers

    Which nucleotide function involves storing genetic information?

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

    How many hydrogen bonds are formed between cytosine and guanine?

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

    Which of the following is not a function of nucleotides?

    <p>Protein folding</p> Signup and view all the answers

    Study Notes

    RNA Processing

    • Almost all newly synthesized RNA molecules (primary transcripts) are processed to some degree in eukaryotic cells.
    • Three major modifications occur:
      • The 5'-end is capped with methylguanosine.
      • Introns are spliced out.
      • Poly-A tail is built at the 3' end.

    Capping the 5' of mRNA

    • Capping protects mRNA from 5' exonuclease degradation.
    • The cap is 7-methylguanosine linked to the 5' end of mRNA.
    • Formed by condensation of GTP with the 5' end of mRNA.
    • Guanine is then methylated.
    • Occurs early in transcription.

    Interrupted Genes in Eukaryotes: Exons & Introns

    • Most eukaryotic genes contain non-coding sequences called introns that interrupt the coding sequences (exons).
    • Introns are excised from the RNA transcripts prior to their transport to the cytoplasm.

    Introns

    • Introns are non-coding sequences located between coding sequences.
    • Introns are removed from the pre-mRNA and are not present in the mRNA.
    • Exons are composed of the sequences that remain in the mature mRNA after splicing.
    • Introns are variable in size and may be very large.

    Placing the Poly(A) Tail on the mRNA

    • Pol II synthesizes RNA up to and beyond the highly conserved sequence: (5')AAUAAA.
    • An endonuclease cleavage signal sequence is bound by an enzyme complex.
    • The RNA is cleaved by the endonuclease at a point 10-30 nucleotides 3' to the sequence AAUAAA.
    • The polyadenylate polymerase synthesizes a poly(A) tail.

    Key Points

    • Three different RNA polymerases are present in eukaryotes, and each polymerase transcribes a distinct set of genes.
    • Eukaryotic gene transcripts usually undergo three major modifications:
      • Addition of 7-methylguanosine caps to 5' termini.
      • Excision of non-coding intron sequences.
      • Addition of poly(A) tails to 3' ends.
    • All modifications occur in the nucleus prior to the transport to the cytoplasm.

    Transcription in Prokaryotes: E. coli RNA Polymerase

    Stages of Transcription

    • RNA chain initiation.
    • RNA chain elongation.
    • RNA chain termination.

    Promoters

    • In E. coli, must be > 12 bp to avoid occurrence by chance.
    • Promoters have only small conservation in sequence.
    • Four main regions:
      • Startpoint.
      • -10 sequence (Pribnow box).
      • -35 sequences.
      • The 17 nucleotide spacer sequence between -10 and -35 sequences.

    Numbering of a Transcription Unit

    • The transcript initiation site is +1.
    • Bases preceding the initiation site are given minus (-) prefixes and are referred to as upstream sequences.
    • Bases following the initiation site are given plus (+) prefixes and are referred to as downstream sequences.

    Starting Transcription

    • Binding of RNA polymerase holoenzyme to a promoter region in DNA.
    • Localized unwinding of both DNA strands (around -10 region) by RNA polymerase to provide a single-stranded template.
    • Formation of phosphodiester bonds between the first few ribonucleotides in the nascent RNA chain.
    • Conformational change in enzyme, promoter is cleared.
    • Sigma factor is released.
    • Nus A protein binds instead, ready for elongation "antitermination complex".

    Termination of Transcription

    • RNA polymerase transcribes until it meets a terminator.
    • Transcription then stops and the RNA product disassociates from the DNA template.
    • Many terminators are hairpin-forming sequences.
    • Two types of terminators:
      • Rho-dependent terminators - require a protein factor (p).
      • Rho-independent terminators - do not require p.

    E. coli RNA Polymerase

    • Core enzyme: α β β'ω.
    • Holoenzyme: α2 β β' ωσ.
    • Functions of the subunits:
      • α: assembly of the tetrameric core.
      • β: ribonucleoside triphosphate binding site.
      • β': DNA template binding region.
      • σ: initiation of transcription.

    Elongation

    • RNA polymerase is bound to DNA and is covalently extending the RNA chain.
    • Site for incoming ribonucleoside triphosphate.
    • Growing RNA chain.
    • Rewinding site.
    • Short region of DNA/RNA helix.
    • Unwinding site.
    • Movement of RNA polymerase.

    Transfer of Genetic Information: The Central Dogma

    • Information stored in the nucleotide sequences of genes is translated into the amino acid sequences of proteins through unstable intermediaries called messenger RNAs.
    • The mRNA codons on the mRNA are translated into an amino acid sequence by the ribosomes.

    Transcription and Translation in Eukaryotes

    • The primary transcript is pre-mRNA.
    • A precursor to the mRNA.
    • The pre-mRNA is modified at both ends, and introns are removed to produce the mRNA.
    • After processing, the mRNA is exported to the cytoplasm for translation by ribosomes.

    General Features of RNA Synthesis

    • Similar to DNA synthesis except:
      • The precursors are ribonucleoside triphosphates.
      • Only 1 strand of DNA is used as a template.
      • RNA chains can be initiated de novo (no primer required).
    • The RNA molecule will be complementary to the DNA template (antisense) strand and identical to the DNA non-template (sense) strand.
    • RNA synthesis is catalyzed by RNA polymerases and proceeds in the 5'-3' direction.

    The Central Dogma

    Prokaryotes

    • Gene
    • DNA
    • Transcription
    • mRNA
    • Translation
    • Protein

    Transcription vs. DNA Replication

    • RNA does not remain H-bonded to the DNA post-synthesis.
    • RNA molecules are selective copies of much shorter segments of the DNA.
    • Both employ polymerases.
      • to make phosphodiester linkages.
      • DNA ahead of synthesis is unwound.
      • Building blocks are very similar to each other.
      • RNA polymerase does not need a primer.

    The "Transcription Bubble"

    • DNA 3'
    • Rewinding
    • Template strand
    • Transcription bubble
    • Nontemplate strand
    • RNA
    • RNA-DNA hybrid, -8bp
    • Active site
    • Direction of transcription
    • Unwinding
    • NTP channel

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    Description

    Learn about the modifications that occur to RNA molecules in eukaryotic cells, including capping, splicing, and poly-A tailing. Understand the importance of capping in protecting mRNA from degradation.

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