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L3 Eukaryotic Transcription Factors
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L3 Eukaryotic Transcription Factors

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@TimeHonoredLimerick2759

Questions and Answers

What is the primary function of WT1 in mammals?

  • Producing hormones
  • Facilitating cell division
  • Controlling gene expression (correct)
  • Regulating protein synthesis

    • Mis-regulation of transcription factor expression can result in diseases and malformations.

    True

    Name one experimental method used to investigate transcription factors.

    ChiP or CUT and RUN

    Transcription factors can be purified by __________ chromatography, utilizing their ability to bind specific DNA sequences.

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

    Match the experimental method to its description:

    <p>Footprinting techniques = Detects binding of TFs to DNA Reporter gene assay = Measures the expression level of a gene Knock-down assays = Observes transcriptional alteration after TF deletion Machine learning approaches = Predicts DNA binding sites based on motifs</p> Signup and view all the answers

    Which of the following is NOT a method used to investigate transcription factors?

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

    What is the primary role of dimerization in transcription factors?

    <p>To increase sequence specificity</p> Signup and view all the answers

    The recognition helix in homeodomain proteins determines DNA binding specificity.

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

    Name one example of a transcription factor involved in muscle development.

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

    Homeodomain proteins form _____ alpha helices including the helix turn helix motif.

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

    What type of structure do zinc fingers utilize for their stability?

    <p>Zinc ions</p> Signup and view all the answers

    Leucine zippers can form both homodimers and heterodimers.

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

    What connects the zinc finger motifs in transcription factors?

    <p>Zn2+ ions</p> Signup and view all the answers

    Match the following elements with their descriptions:

    <p>Homeodomain proteins = Involved in embryonic patterning Zinc fingers = Stabilized by Zn2+ ions Leucine zippers = Form coiled coils for dimerization Helix-loop-helix = Involved in muscle and neurogenesis</p> Signup and view all the answers

    Which of the following activities do transcription factors NOT perform?

    <p>Directly synthesize mRNA</p> Signup and view all the answers

    Transcription factors have a fixed binding specificity and cannot change.

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

    Name one protein that has histone acetylase activity.

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

    Transcription factors activate and repress transcription by mediating contact with __________.

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

    Match the transcription factor activity with its description:

    <p>Recruitment of General TFs = Brings RNA polymerase to the promoter Altering histone structure = Changes chromatin configuration Blocking activator binding = Prevents transcription activation Recruiting histone deacetylase = Removes acetyl groups from histones</p> Signup and view all the answers

    What is one mechanism through which transcription factors can repress transcription?

    <p>Binding DNA to block activator binding</p> Signup and view all the answers

    Histone acetylases (HATs) increase transcription by loosening chromatin.

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

    What is the primary function of insulators in gene regulation?

    <p>Prevent interference to neighboring transcription units</p> Signup and view all the answers

    Identify the role of histone deacetylases (HDACs).

    <p>They remove acetyl groups from histones, leading to transcriptional repression.</p> Signup and view all the answers

    Housekeeping genes are only found in specific types of cells.

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

    Name one transcription factor motif classified as a structural motif.

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

    Cis-regulatory sequences include enhancers and ________.

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

    Match the transcription factors with their respective motifs:

    <p>Helix-turn-helix = C-Terminal recognition helix makes contact with DNA Zinc fingers = Classic DNA-binding motif containing zinc ions Leucine zippers = Form coiled-coil structural motifs Helix loop helix = Characteristics of protein interactions in dimers</p> Signup and view all the answers

    How do transcription factors boost transcription efficiency?

    <p>Each factor's action is additive in a non-linear way</p> Signup and view all the answers

    Tissue-specific genes contain binding sites only for tissue-specific transcription factors.

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

    What primarily determines when a specific gene is expressed?

    <p>The combination of binding sites for general and specialized transcription factors.</p> Signup and view all the answers

    Which of the following best defines a transcription factor?

    <p>A protein required to initiate or regulate transcription</p> Signup and view all the answers

    Specific transcription factors are involved in the formation of the basal transcription complex.

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

    How many human transcription factors have been identified?

    <p>1639</p> Signup and view all the answers

    Transcription factors often bind as ______ to modulate the binding frequency.

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

    Match the following types of transcription factors with their functions:

    <p>General factors = Forming the basal transcription complex Specific factors = Stimulating or repressing transcription of particular genes Chromatin remodellers = Affecting binding strength of transcription factors Transcription factors = Regulating gene expression</p> Signup and view all the answers

    What is a common mechanism used by transcription factors for gene activation?

    <p>Using multiple weak interactions in binding sites</p> Signup and view all the answers

    Transcription factors can access DNA easily because it is loosely wrapped around nucleosomes.

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

    What do transcription factors bind to in order to regulate transcription?

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

    Study Notes

    Definition and Types of Transcription Factors

    • Transcription factors (TFs) are proteins essential for initiating or regulating transcription, acting outside of RNA polymerase.
    • General (basal) transcription factors form the core transcription complex at the promoter (e.g., TFIID).
    • Specific transcription factors regulate the expression of particular genes by binding to regulatory sequences, leading to selective protein synthesis.
    • Approximately 1639 human transcription factors have been identified, indicating a complex transcriptional regulatory landscape.

    General Principles of TF Binding

    • TFs bind to DNA through weak interactions, requiring 10-20 such interactions to effectively stabilize DNA-protein interfaces.
    • DNA tightly wrapped around nucleosomes presents a barrier to TF access, necessitating specialized mechanisms for binding.
    • Higher specificity in binding is achieved through:
      • Multiple weak interactions within binding sites.
      • Chromatin remodelers that reposition nucleosomes.
      • Dimerization of TFs in solution to modulate binding frequency.

    Cis-Regulatory Sequences and Their Role

    • Cis-regulatory elements such as enhancers, silencers, and insulators influence gene expression.
    • Enhancers and silencers, located away from the promoter, regulate transcription by binding specific TFs.
    • Insulators prevent interference between neighboring genes, allowing precise gene regulation.

    Housekeeping Genes vs. Tissue-Specific Genes

    • Housekeeping genes are universally expressed and contain binding sites for ubiquitous TFs across all tissues.
    • Tissue-specific genes utilize both ubiquitous and tissue-specific TFs, dictating precise expression patterns based on binding site combinations.
    • Combinatorial control integrating multiple factors at the pre-initiation complex (PIC) determines final transcription outcomes.

    Structural Motifs of Transcription Factors

    • Four primary structural motifs classify TFs:
      • Helix-turn-helix: Common in various TFs, involves 2 α-helices connected by a turn; recognition helix binds in the major groove.
      • Zinc fingers: Structures stabilized by zinc ions, allowing interaction with DNA; diverse and can be combined in proteins for higher specificity.
      • Leucine zippers: Form coiled-coil dimers; allow dimerization through hydrophobic interactions and bind the major groove via basic amino acid stretches.
      • Helix-loop-helix: Dimerization enables DNA binding; involved in muscle development and neurogenesis.

    Mechanisms of Transcriptional Activation and Repression

    • TFs can activate transcription through:
      • Recruitment of general TFs or RNA polymerase II.
      • Modifying histone structures via chromatin remodeling enzymes.
      • Increasing RNA polymerase II activity to enhance transcription efficiency.
    • TF repression mechanisms include:
      • Directly blocking activators.
      • Binding to nearby sites and preventing effective activation by hindering the activation domain.

    Regulated Expression and Inducible Gene Expression

    • Spatio-temporal control of TF expression facilitates diverse gene expression patterns across cell types.
    • Misregulation of TF activity can result in disease and developmental malformations.

    Experimental Methods to Investigate TFs

    • Protein purification: Techniques such as affinity chromatography isolate TFs based on their DNA-binding properties.
    • Footprinting techniques: Identify gene-specific binding via detecting the physical presence of TFs on DNA.
    • Reporter gene assays: Analyze TF activity through genetic constructs linked to measurable reporter genes.
    • ChIP or CUT&RUN: Techniques to analyze TF binding to DNA in vivo.
    • Knock-down assays: Assess the impact of eliminating specific TFs on overall gene expression.
    • AI-based motif prediction: Utilize machine learning to predict TF binding sites by comparing against known motifs.

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    Description

    This quiz covers essential concepts related to eukaryotic transcription factors, including definitions and classifications. You'll explore experimental methods for studying these factors, their structural motifs, and mechanisms of activation and repression. Test your understanding of both general and specific transcription factors.

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