L3 Eukaryotic Transcription Factors
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Questions and Answers

What is the primary role of general (basal) transcription factors?

  • To participate in the formation of the basal transcription complex (correct)
  • To repress transcription
  • To bind exclusively to enhancer regions
  • To stimulate transcription of specific genes

    • Specific transcription factors can bind to regulatory sequences of any gene.

    False

    Define a transcription factor.

    Any protein required to initiate or regulate transcription, other than RNA polymerase.

    Transcription factors are identified to interact through specific amino acid side chains and base __________.

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

    Approximately how many human transcription factors have been identified?

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

    Match the following transcription factor types with their functions:

    <p>General transcription factors = Form the basal transcription complex Specific transcription factors = Stimulate or repress transcription of specific genes Chromatin remodelers = Alter nucleosome positioning to facilitate binding Transcription factor dimers = Modulate binding frequency</p> Signup and view all the answers

    It takes approximately 10-20 weak interactions for a stable DNA-protein interface to form.

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

    What is one mechanism by which transcription factors can achieve tissue-specific gene expression?

    <p>Regulated expression or activity of transcription factors.</p> Signup and view all the answers

    What is the purpose of spatio-temporal control of transcription factor expression?

    <p>To allow diversification of gene-expression patterns in different cell types</p> Signup and view all the answers

    Mis-regulation of transcription factor expression does not impact health.

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

    Name one method used to identify transcription factors.

    <p>Footprinting techniques</p> Signup and view all the answers

    Transcription factors can be purified by affinity __________, using their property of binding specific DNA sequences.

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

    Match the methods with their functions in studying transcription factors:

    <p>Footprinting techniques = Detects transcription factor binding to DNA Reporter gene assay = Assesses the activity of transcription factors Knock-down assays = Observes changes in transcriptional profile ChIP or CUT and RUN = Identifies protein-DNA interactions</p> Signup and view all the answers

    Which approach uses machine learning for binding site prediction?

    <p>Structure-homology motif prediction</p> Signup and view all the answers

    What is the primary function of homeodomain proteins?

    <p>To enhance sequence-specificity through dimerization</p> Signup and view all the answers

    Zinc fingers consist of a structure maintained by Zn2+ ions.

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

    What determines the DNA binding specificity of homeodomain proteins?

    <p>Amino acid sequence of helix 3</p> Signup and view all the answers

    The leucine zipper forms a ____ helix due to the hydrophobic interactions among leucine residues.

    <p>coiled coil</p> Signup and view all the answers

    Match the following protein motifs with their functions:

    <p>Homeodomain = Regulation of hox genes Zinc Finger = Diverse transcriptional activators Leucine Zipper = Protein dimerization and DNA positioning bHLH = Muscle development and neurogenesis</p> Signup and view all the answers

    Which of the following correctly describes the structure of zinc fingers?

    <p>A finger loop of 12 amino acids with two Cys and two His</p> Signup and view all the answers

    Substitution of leucine in the leucine zipper structure does not affect dimerization or DNA binding.

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

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

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

    What role do enhancers and silencers play in gene regulation?

    <p>They are cis-regulatory sequences that modulate transcription.</p> Signup and view all the answers

    Housekeeping genes are only found in specific tissues.

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

    What determines the expression timing of tissue-specific genes?

    <p>The combination of binding sites for ubiquitous and tissue-specific transcription factors.</p> Signup and view all the answers

    The _____ is a DNA-binding motif found in many transcription factors.

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

    Match the structural motifs with their characteristics:

    <p>Helix-turn-helix = Two alpha helices connected by a turn Zinc fingers = Bind DNA through interactions with zinc ions Leucine zippers = Facilitate dimerization of transcription factors Helix loop helix = Involved in protein-protein interactions</p> Signup and view all the answers

    How does the action of multiple transcription factors typically affect transcription?

    <p>Their actions are additive in a non-linear way.</p> Signup and view all the answers

    Insulators serve to promote interference to neighboring transcription units.

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

    What are ubiquitous transcription factors?

    <p>Transcription factors present in all tissues that bind to promoter regions.</p> Signup and view all the answers

    What is the primary role of transcription factors (TFs)?

    <p>To regulate gene expression</p> Signup and view all the answers

    Transcription factors can only activate transcription but cannot repress it.

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

    Name one enzyme that has histone acetylase activity.

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

    Transcription factors can also recruit __________ to the promoter to assist with transcription.

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

    Match the transcriptional regulators with their functions:

    <p>CBP = Histone acetylase activity HDAC = Histone deacetylase activity Transcriptional activators = Recruit RNA polymerase Repressors = Block activation domains</p> Signup and view all the answers

    Which activity is NOT a mechanism used by transcription factors to influence transcription?

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

    Histone acetylation typically promotes transcription.

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

    What is one effect of transcriptional repressors binding to DNA?

    <p>They block activator binding.</p> Signup and view all the answers

    Study Notes

    Transcription Factors Overview

    • Transcription factors (TFs) are proteins essential for initiating or regulating transcription, excluding RNA polymerase.
    • Two categories:
      • General (basal) factors contribute to the formation of the basal transcription complex at the transcription start site.
      • Specific factors modulate transcription of particular genes through binding to regulatory sequences, influencing protein synthesis variability.
    • Approximately 1,639 human transcription factors have been identified.

    TF Binding and Mechanism

    • Transcription factors bind to DNA via specific amino acid interactions, involving weak associations; a stable complex requires 10-20 interactions.
    • Access to DNA is restricted due to nucleosome wrapping; TFs utilize chromatin remodelers to facilitate binding.
    • Binding sites may contain multiple weak interactions; synergy exists when multiple TFs interact to activate genes.
    • TFs often function as dimers to enhance binding specificity; they primarily exist as monomers in solution.

    Cis-Regulatory Sequences

    • Key elements include enhancers and silencers located far from promoters, which facilitate or inhibit transcriptional activity.
    • Insulators are present to prevent unintended interactions between nearby transcription units.

    Housekeeping Genes

    • Housekeeping genes exhibit consistent expression across all cell types, featuring binding sites for ubiquitous TFs.
    • Activators work additively in non-linear fashion; e.g., if TF A increases transcription two-fold and TF B ten-fold, their combined effect can boost transcription significantly.

    Tissue-Specific Genes

    • Feature binding sites for both ubiquitous and tissue-specific TFs, example: globin genes interact with factors like SP1 and GATA-1.
    • The context determines binding specificity; combinatorial control at the pre-initiation complex (PIC) decides gene expression outcomes.

    Structural Motifs Classifying TFs

    • Four primary structural motifs used to classify TFs:
      • Helix-turn-helix: Found in both prokaryotic and eukaryotic TFs; recognition helix binds in major groove.
      • Zinc fingers: Stabilized by Zn2+; diverse with multiple variations; example includes nuclear receptors.
      • Leucine zippers: Characterized by leucine every seventh amino acid; forms dimers for specific DNA positioning.
      • Helix-loop-helix: Involves dimerization; plays significant roles in muscle development and neurogenesis.

    Mechanisms of TF Activation and Repression

    • Activators interact with general TFs or RNA polymerase II to initiate transcription.
    • Some TFs remodel chromatin structure via recruitment of histone-modifying enzymes (HATs and HDACs).
    • Repression can occur by blocking activators or interfering with transcriptional complexes.

    Regulated Expression of TFs

    • Spatial and temporal control over TF expression is crucial for diverse gene-expression patterns across cell types.
    • Misregulation can lead to diseases or malformations in development.

    Experimental Methods for Investigating TFs

    • Protein purification: Uses affinity chromatography to isolate TFs based on their DNA-binding capabilities.
    • Footprinting techniques: Identify where TFs bind DNA by observing protected regions against nucleases.
    • Reporter gene assays: Measure transcriptional activity in response to specific TFs.
    • ChIP or CUT and RUN: Techniques for analyzing TF binding across the genome.
    • Knock-down assays: Analyze transcriptional changes following the deletion of specific TFs.
    • Machine learning and AI: Used for predicting TF DNA-binding motifs and their functions based on structural homology.

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    L3 Eukaryotic Transcription Factors PDF

    Description

    This quiz assesses your understanding of eukaryotic transcription factors, including their definitions and classifications. You'll explore the differences between general and specific transcription factors, learn about experimental methods used to study them, and recognize structural motifs and mechanisms of action. Test your knowledge on key examples and concepts in this essential field of molecular biology.

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