Transcriptional Regulation of Gene Expression
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Questions and Answers

Which statement is true regarding Type I zinc finger motifs?

  • They possess internal inverted repeats in their DNA binding site.
  • They function predominantly as dimers.
  • They require no metal ions for DNA binding.
  • They stabilize the DNA binding domain using one Zn2+ ion. (correct)

    • What is the primary role of zinc fingers in engineered nucleases such as ZFNs?

  • To enhance RNA packaging during protein folding.
  • To bind specifically to DNA sequences. (correct)
  • To cleave DNA directly without needing a linker.
  • To stabilize the FokI cleavage domain.

    • What distinguishes TALENs from ZFNs in their structure?

  • TALENs use single Zn2+ ions for DNA binding.
  • TALENs utilize transcription activator-like effectors as part of their design. (correct)
  • TALENs are formed by fusing proteins that are not derived from bacteria.
  • TALENs require only two fingers for DNA targeting.

    • Which of the following correctly describes the binding characteristics of Type II zinc finger motifs?

    <p>They bind DNA primarily as dimers and use a leucine zipper.</p> Signup and view all the answers

    What is the minimum number of zinc fingers required in a ZFN to provide adequate DNA affinity?

    <p>Three zinc fingers are necessary for sufficient binding affinity.</p> Signup and view all the answers

    What distinguishes eukaryotic promoters from bacterial promoters?

    <p>Eukaryotic promoters are regulated by numerous regulatory proteins.</p> Signup and view all the answers

    Which motif is NOT mentioned as being a common DNA-binding domain in transcription factors?

    <p>Structural zinc motif</p> Signup and view all the answers

    How do transcription factors recognize DNA sequences?

    <p>Through specific amino acid side chains of an α helix referred to as the recognition helix.</p> Signup and view all the answers

    What is one critical function of transcription factors in gene expression?

    <p>They affect regulation and transcription initiation by binding to regulatory sequences.</p> Signup and view all the answers

    Which statement regarding bacterial regulators is true?

    <p>Bacterial promoters are usually regulated by one or two regulatory proteins.</p> Signup and view all the answers

    What characteristic is unique to eukaryotic gene regulation compared to bacterial gene regulation?

    <p>Eukaryotic genes may have regulatory sites located within the coding sequence.</p> Signup and view all the answers

    Which of the following is NOT a function of transcription factors?

    <p>Inducing mutations in the DNA sequence.</p> Signup and view all the answers

    Which type of regulatory protein would likely be involved in the repression of gene expression?

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

    Which motif is characterized by two short α helices connected by a β turn?

    <p>Helix-turn-helix motif</p> Signup and view all the answers

    What structural feature is unique to the homeodomain type of helix-turn-helix motif?

    <p>It contains three α-helices.</p> Signup and view all the answers

    In which organisms was the homeodomain DNA-binding motif first identified?

    <p>Fruit fly</p> Signup and view all the answers

    What type of amino acid arrangement is found in the basic leucine zipper motif?

    <p>Hydrophobic residues concentrated on one side</p> Signup and view all the answers

    Which function is associated with the proteins containing the homeodomain motif?

    <p>Body pattern development</p> Signup and view all the answers

    How many amino acids typically comprise the basic leucine zipper motif?

    <p>60 – 80 amino acids</p> Signup and view all the answers

    In which part of the DNA do the N-terminal residues of the homeodomain interact?

    <p>Minor groove</p> Signup and view all the answers

    Which motif is specifically associated with transcription factors in plants for floral organ development?

    <p>Homeodomain motif</p> Signup and view all the answers

    Which of the following motifs is commonly utilized by bacterial regulatory proteins for DNA binding?

    <p>Helix-turn-helix motif</p> Signup and view all the answers

    Which term describes a distinctive type of α helix that plays a role in the DNA-binding motif of several proteins?

    <p>Amphipathic helix</p> Signup and view all the answers

    What is the primary function of the leucine zipper motif in proteins?

    <p>Dimerization of subunits</p> Signup and view all the answers

    In the basic helix-loop-helix (b-hlh) motif, what role do the basic residues play?

    <p>They facilitate DNA binding</p> Signup and view all the answers

    How do zinc ions contribute to the function of the zinc finger motif?

    <p>By stabilizing the protein structure</p> Signup and view all the answers

    What characteristic distinguishes the two helices in the basic helix-loop-helix motif?

    <p>One helix contains basic residues while the other does not</p> Signup and view all the answers

    Which statement about the zinc finger motif is true regarding its presence in proteins?

    <p>Multiple zinc fingers can enhance DNA-binding strength</p> Signup and view all the answers

    What is a common feature found in c-Myc and HIF-1 proteins?

    <p>Presence of leucine zipper motif</p> Signup and view all the answers

    What is the approximate length of the zinc finger domain?

    <p>30 amino acids</p> Signup and view all the answers

    What structural feature is essential for the dimerization of leucine zipper proteins?

    <p>Hydrophobic interactions between leucine residues</p> Signup and view all the answers

    Which of the following statements best describes the basic helix-loop-helix motifs?

    <p>They are often involved in cell cycle or developmental processes</p> Signup and view all the answers

    What is a notable feature of zinc finger motifs in relation to gene editing?

    <p>Proteins with multiple zinc fingers have been engineered for enhanced specificity</p> Signup and view all the answers

    Study Notes

    Transcriptional Regulation of Gene Expression

    • Eukaryotic promoters have more regulators than bacterial promoters.
    • Bacterial promoters are typically near or overlap the coding region and usually regulated by one or two regulatory proteins.
    • Eukaryotic genes have multiple regulator-binding sites that can span a large region (more than 50 kb), and can be upstream, downstream, or even within the coding sequence of the gene itself.

    Transcription Factors (TFs)

    • Gene activation and repression in both bacteria and eukaryotes require transcription factors.
    • TFs are proteins that affect gene regulation and transcription initiation by binding to regulatory sequences near or within the gene and interacting with RNA polymerase.
    • TF binding sites usually contain inverted repeats.

    The Recognition Helix

    • DNA recognition by a TF typically occurs through amino acid side chains in an alpha helix, called the recognition helix.
    • This helix interacts with the major groove of DNA.

    Classification of Transcription Factors

    • TFs are classified by the presence of specific conserved motifs.
    • These motifs include:
      • helix-turn-helix DNA-binding motif
      • leucine zipper motif
      • basic helix-loop-helix motif
      • zinc finger motif

    The Helix-Turn-Helix (HTH) Motif

    • Many bacterial and eukaryotic regulatory proteins use the HTH motif for DNA binding.
    • The HTH motif is made up of approximately 20 amino acids (aa) that form two short alpha helices connected by a beta turn.
    • The HTH motif is often part of a larger DNA-binding domain.

    The Homeodomain

    • The homeodomain is a unique HTH-type motif.
    • It's composed of three alpha-helices, with two of these helices corresponding to the well-known helix-turn-helix motif.
    • The N-terminal residues of the homeodomain reach around the DNA duplex and interact with the minor groove.
    • The homeodomain is found in proteins that regulate body pattern development, including in fruit flies, plants, and humans.

    The Basic Leucine Zipper (bZIP) Motif

    • bZIP motifs are made up of 60-80 amino acids, depending on the species.
    • They're amphipathic alpha helices with hydrophobic amino acid residues concentrated on one side.
    • bZIP motifs are found in many eukaryotic and a few bacterial regulatory proteins.
    • They primarily function for dimerization, with separate motifs used for DNA binding.
    • A striking feature is Leucine residues at every seventh position, creating a hydrophobic surface for dimerization.

    The Basic Helix-Loop-Helix (bHLH) Motif

    • bHLH motifs are made up of approximately 50 amino acids.
    • They contain two amphipathic alpha helices connected by a loop of variable length.
    • One helix contains basic residues and mediates DNA binding.
    • The other helix does not have basic residues but mediates dimer formation.
    • bHLH motifs are often involved in development and cell cycle activity.

    The Zinc Finger Motif

    • Zinc finger domains consist of about 30 amino acids.
    • The domain forms an elongated loop stabilized by zinc ions.
    • Zinc ions do not directly interact with the DNA.
    • Zinc fingers are found in eukaryotic and some bacterial proteins.
    • There are various types, with Type I and Type II being common.
    • Single zinc figure interactions are weak, however, multiple zinc fingers strengthen binding to DNA.

    Type I Zinc Finger Motif

    • These motifs function as monomers and contain a long DNA binding site with no inverted repeats.
    • They utilize one zinc ion to stabilize the DNA binding domain.

    Type II Zinc Finger Motif

    • These motifs combine a zinc-binding and helix-turn-helix motif.
    • They use two zinc ions to stabilize their DNA binding domain, which has an HTH motif.
    • They bind DNA as dimers using a leucine zipper.

    Zinc Finger Motif Summary

    • Proteins with this domain perform diverse roles in DNA recognition, RNA packaging, transcriptional activation, protein folding, and lipid binding.

    Zinc Finger Nucleases (ZFNs)

    • ZFNs are engineered nucleases where zinc fingers are fused to a FokI domain for DNA cleavage.
    • FokI is a type II restriction endonuclease found in the bacterium Flavobacterium okeanokoites.
    • Each zinc finger binds three consecutive base pairs.
    • A minimum of three fingers is needed for sufficient DNA affinity.

    Transcription Activator-Like Effector Nucleases (TALENs)

    • TALENs are transcription activator-like effectors fused to FokI nucleases.
    • TALEs are secreted by Xanthomonas bacteria, and bind plant DNA sequences via 34 amino acid central repeat domains.
    • TALENs direct the nuclease complex to a specific DNA site for cleavage.
    • FokI then cleaves the target DNA.
    • Each TALE module binds a single base pair.
    • The linker to the FokI domain is longer in TALENs than in ZFNs and contains additional TALE-derived sequences.
    • TALEN design is simpler than that of ZFNs.

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    Related Documents

    BIOL 366 Lecture 12: Transcriptional Regulation of Gene Expression PDF

    Description

    Explore the complex mechanisms of transcriptional regulation in eukaryotes and bacteria. This quiz covers the roles of promoters, transcription factors, and the recognition helix in gene expression. Test your understanding of how gene regulation varies across different organisms.

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