RNA Polymerases and Transcription Processes
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Questions and Answers

Which RNA polymerase is primarily responsible for transcribing pre-mRNAs?

  • RNA polymerase IV
  • RNA polymerase I
  • RNA polymerase III
  • RNA polymerase II (correct)

    • What is the main function of RNA polymerase IV in some eukaryotic cells?

  • Silencing transposons (correct)
  • Transcribing tRNAs
  • Transcribing rRNAs
  • Assisting in DNA methylation

    • What is the effect of α-amanitin on RNA polymerase II?

  • It causes a misincorporation of nucleotides by RNA polymerase II.
  • It enhances the activity of RNA polymerase II.
  • It breaks down RNA polymerase II.
  • It inhibits the movement of RNA polymerase II along the DNA template. (correct)

    • Which of the following correctly lists the three main stages of bacterial transcription?

    <p>Initiation, Elongation, Termination (A)</p> Signup and view all the answers

    During the elongation stage of bacterial transcription, what occurs?

    <p>DNA is threaded through RNA polymerase and new nucleotides are added to the 3’ end of the RNA strand. (D)</p> Signup and view all the answers

    Which of the following is NOT a function performed by RNA Polymerase III?

    <p>Transcribes pre-mRNAs (B)</p> Signup and view all the answers

    In bacterial transcription, what happens during the termination stage?

    <p>The RNA molecule is released from the DNA template. (A)</p> Signup and view all the answers

    Which of the following characteristics is true of all eukaryotic RNA polymerases?

    <p>They are all large multimeric enzymes with more than a dozen subunits. (B)</p> Signup and view all the answers

    What action does RNA polymerase undertake when it incorporates an incorrect nucleotide?

    <p>It backtracks and cleaves the last two nucleotides. (B)</p> Signup and view all the answers

    What primarily determines the direction of transcription on a DNA strand?

    <p>The locations of the consensus sequences in the promoter and their orientation (B)</p> Signup and view all the answers

    What must happen to fully stop transcription at a terminator site?

    <p>The RNA polymerase must stop RNA synthesis, the RNA molecule must be released from polymerase, the RNA molecule and polymerase must detach from the DNA. (A)</p> Signup and view all the answers

    What is required for Rho-dependent termination?

    <p>The presence of the Rho factor and a rut site upstream of the terminator. (B)</p> Signup and view all the answers

    How does RNA polymerase recognize the start site?

    <p>By its alignment based on the consensus sequences in the promoter (C)</p> Signup and view all the answers

    What is the role of the rut site in Rho-dependent termination?

    <p>It is a binding site for the Rho factor on the RNA molecule. (C)</p> Signup and view all the answers

    What is the role of rNTPs in RNA synthesis?

    <p>They provide the necessary substrate for transcription and are paired to the template strand (C)</p> Signup and view all the answers

    What is the function of the Rho factor's helicase activity during transcription termination?

    <p>To unwind the DNA-RNA hybrid within the transcription bubble. (A)</p> Signup and view all the answers

    Why does the 5' end of a newly synthesized RNA molecule have three phosphate groups?

    <p>Because the 5' end of the first rNTP does not form a phosphodiester bond in its first interaction (A)</p> Signup and view all the answers

    What is 'abortive initiation' in RNA transcription?

    <p>The process where RNA polymerase repeatedly synthesizes and releases short RNA transcripts (D)</p> Signup and view all the answers

    What is a key characteristic of Rho-independent terminators?

    <p>They contain inverted repeats. (C)</p> Signup and view all the answers

    How does the timing of transcription termination relate to the terminator sequence in DNA?

    <p>Transcription stops only after the terminator has been transcribed by the RNA polymerase. (D)</p> Signup and view all the answers

    What event allows RNA polymerase to move beyond the promoter and begin elongation?

    <p>A conformational change in RNA polymerase that reduces its affinity for the consensus sequences (B)</p> Signup and view all the answers

    What is the primary role of sigma factor during transcription?

    <p>To help RNA polymerase attach to the consensus sequences in the promoter. It may be released after initiation. (C)</p> Signup and view all the answers

    What sequence feature of the RNA transcript is usually found at the Rho utilization site?

    <p>Rich in cytosine nucleotides and devoid of secondary structures. (B)</p> Signup and view all the answers

    What are the two primary functions that are essential for life according to the provided text?

    <p>Information storage and catalyzing chemical reactions (C)</p> Signup and view all the answers

    How does RNA polymerase maintain transcription efficiency during elongation?

    <p>By continuously unwinding DNA ahead of the transcription bubble and rewinding DNA behind it (B)</p> Signup and view all the answers

    Prior to the discovery of ribozymes, what was the assumed relationship between nucleic acids and proteins?

    <p>Nucleic acids were considered solely responsible for storing genetic information, while proteins were in charge of catalyzing chemical reactions (D)</p> Signup and view all the answers

    What key finding resolved the apparent paradox of which came first, nucleic acids or proteins?

    <p>The identification of ribozymes, RNA molecules capable of catalysis. (B)</p> Signup and view all the answers

    What is the function of a ribozyme, as mentioned in the text?

    <p>To cut, connect, and replicate RNA molecules (C)</p> Signup and view all the answers

    What is the main idea behind the 'RNA world' hypothesis?

    <p>RNA served as both genetic information carrier and catalyst in early life. (C)</p> Signup and view all the answers

    Why did DNA eventually become the primary carrier of genetic information over RNA?

    <p>Because DNA has greater chemical stability and more faithful replication. (A)</p> Signup and view all the answers

    Which feature of archaeal RNA polymerase is most similar to that of eukaryotic RNA polymerase II?

    <p>The number of subunits (D)</p> Signup and view all the answers

    What is meant by the term 'biochemical dichotomy' as used in the provided text?

    <p>The belief that information storage and catalytic functions are handled by two different types of molecules. (A)</p> Signup and view all the answers

    What is the primary function of the TATA-binding protein (TBP) in archaea?

    <p>To bind to the promoter sequence (B)</p> Signup and view all the answers

    What is the significance of the discovery of ribozymes for our understanding of early life?

    <p>It showed a plausible way for a single type of molecule to carry out both information storage and catalytic functions. (D)</p> Signup and view all the answers

    Which regulatory protein assists the archaeal TATA-binding protein (TBP) and is also found in eukaryotes?

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

    What structural feature of archaea is similar to that of eukaryotes involving the compaction of DNA but is absent in bacteria?

    <p>The use of histones to form nucleosome-like structures (C)</p> Signup and view all the answers

    What is the significance of the consensus sequence in the archaeal promoter, in relation to transcription?

    <p>It determines the location of the transcription start site (A)</p> Signup and view all the answers

    What is the function of the string of uracil nucleotides in rho-independent transcription termination?

    <p>To destabilize the DNA-RNA pairing, promoting separation. (D)</p> Signup and view all the answers

    In rho-independent termination, what immediately precedes the string of uracil nucleotides in the transcribed RNA?

    <p>An inverted repeat sequence that has formed a hairpin (C)</p> Signup and view all the answers

    What is a polycistronic mRNA?

    <p>An mRNA molecule transcribed from a group of genes. (C)</p> Signup and view all the answers

    In which domains of life are polycistronic mRNA molecules most commonly found?

    <p>Both bacteria and some eukaryotes. (B)</p> Signup and view all the answers

    What is the sequence of events in rho-independent transcription termination?

    <p>Inverted repeat is transcribed into RNA, hairpin forms, string of uracils destabilizes the DNA-RNA pairing, RNA separates (A)</p> Signup and view all the answers

    What is a key difference between bacterial and eukaryotic transcription regarding polycistronic mRNA?

    <p>Bacteria use it extensively, eukaryotes do not. (D)</p> Signup and view all the answers

    Which of the following best describes the evolutionary relationship between bacteria, archaea, and eukaryotes?

    <p>Bacteria, archaea, and eukaryotes are equally distantly related to each other. (B)</p> Signup and view all the answers

    What is the role of adenine-uracil (A-U) base pairings in rho-independent transcription termination?

    <p>To destabilize the DNA-RNA pairing, promoting separation. (D)</p> Signup and view all the answers

    Study Notes

    Early RNA World

    • Life requires storing and transmitting genetic information, and catalyzing chemical transformations.
    • Initially, it was believed that nucleic acids stored information, and proteins catalyzed reactions.
    • This created a "chicken and egg" problem: How could one emerge without the other?
    • RNA was discovered to act as a biological catalyst (ribozyme).
    • Ribozymes can perform various functions like cutting RNA, connecting RNA molecules, replicating RNA, and catalyzing peptide bond formation between amino acids.
    • This suggests that early life may have been an "RNA world," where RNA served both as genetic material and catalyst.
    • RNA may have eventually evolved the ability catalyze reactions to create protein-based enzymes which would be more efficient.
    • RNA gave way to DNA for genetic storage due to DNA's stability and faithful replication.
    • RNA remains important in many biological processes today.

    RNA Structure

    • RNA, like DNA, is a polymer of nucleotides.
    • RNA nucleotides contain ribose sugar, while DNA nucleotides contain deoxyribose sugar.
    • Uracil replaces thymine in RNA.
    • RNA is usually single-stranded but secondary structures can form due to complementary regions in the strand.
    • Secondary structures are crucial to the function of RNA molecule

    Classes of RNA

    • Ribosomal RNA (rRNA): Ribosomes (sites of protein synthesis)
    • Messenger RNA (mRNA): Carries coding instructions for a polypeptide chain from DNA to ribosomes
    • Transfer RNA (tRNA): Serves as a link between mRNA codons and amino acids

    Bacterial RNA polymerase

    • Bacteria have one type of RNA polymerase for all types of RNA synthesis.
    • RNA polymerase consists of a core enzyme (with two alpha (α), one beta (β), one beta prime (β'), and one omega(ω) ), which catalyzes the elongation of the RNA molecule.
    • Sigma (σ) factor enables RNA polymerase to bind to a promoter.
    • Promoters have consensus sequences, important for promoter recognition.
      • The -10 consensus sequence is usually TATAAT, and near -35 nucleotides there is a sequence called TTGACA.
    • Different types of sigma factors allow RNA polymerase to initiate transcription at different promoters.

    Eukaryotic RNA polymerases

    • Eukaryotes have three major types of RNA polymerase (I, II, and III).
    • RNA polymerase I transcribes rRNA.
    • RNA polymerase II transcribes pre-mRNAs, some snRNA and miRNAs.
    • RNA polymerase III transcribes other small RNA molecules (rRNA, snRNA, miRNAs, and tRNA)

    Eukaryotic Promoters

    • Eukaryotic promoters typically consist of a core promoter and a regulatory promoter
    • The core promoter contains conserved sequences (like the TATA box) where general transcription factors bind, positioning RNA polymerase II over the start site.
    • The regulatory promoter contains sequences where regulatory transcription factors can bind and enhance or repress the rate of transcription.

    Transcription Initiation

    • Initiation involves promoter recognition, and formation of a transcription bubble, creation of the first bonds between rNTPs, and release of sigma factor.
    • The transcription apparatus (consisting of RNA polymerase and accessory proteins), recognizes and binds to a promoter which determines the transcription start site.

    Transcription Elongation

    • Elongation involves DNA unwinding by RNA polymerase, adding nucleotides to the growing RNA chain in a 5'→3' direction.
    • The resulting RNA molecule is antiparallel and complementary to the DNA template strand.

    Transcription Termination

    • Termination involves the recognition of the termination sequence and release of the RNA molecule and RNA polymerase.
    • Eukaryotes have three different RNA polymerases each with distinct termination mechanisms.
    • Bacterial cells can have rho-dependent or rho-independent terminators.
    • Rho-dependent terminators are regulated by the protein rho, which moves along the RNA molecule and separates the RNA from the template.
    • Rho-independent terminators contain inverted repeats that form hairpin loops in the RNA, and a stretch of adenines, which cause the RNA to detach from the template DNA.

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    An early RNA world (Chapter 13) PDF

    Description

    Test your understanding of RNA polymerases, their functions, and the stages of transcription in both prokaryotic and eukaryotic cells. This quiz covers key details such as the effects of inhibitors and mechanisms of termination. Challenge yourself on your knowledge of the transcription process and RNA polymerase roles.

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