Introduction to Gene Regulation
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Questions and Answers

What is the role of histone modifications in gene regulation?

  • They influence the accessibility of DNA for transcription. (correct)
  • They directly synthesize RNA molecules.
  • They permanently alter the DNA sequence.
  • They prevent the binding of RNA polymerase.

    • Where are nucleosome-free regions (NFR) typically located in gene structure?

  • In the middle of exons.
  • Randomly distributed throughout the gene.
  • Only within introns.
  • At the beginning and end of many genes. (correct)

    • How does acetylation affect gene expression?

  • It causes DNA to be tightly packed.
  • It enhances the binding of transcription factors. (correct)
  • It inhibits the formation of nucleosomes.
  • It increases DNA methylation levels.

    • What is the characteristic distribution of nucleosomes across a protein-encoding gene?

    <p>Precisely positioned at the beginning and end, less so elsewhere.</p> Signup and view all the answers

    Which chemical groups are examples of histone modifications?

    <p>Phosphate, acetyl, and methyl groups.</p> Signup and view all the answers

    What is the primary function of DNA methylation in eukaryotic organisms?

    <p>To inhibit gene transcription</p> Signup and view all the answers

    In which organisms is DNA methylation most commonly observed?

    <p>Plants and vertebrates</p> Signup and view all the answers

    What percentage of DNA is methylated in mammals?

    <p>2 to 7%</p> Signup and view all the answers

    What are CpG islands primarily associated with?

    <p>Promoter regions of many genes</p> Signup and view all the answers

    What occurs to the expression of tissue-specific genes when their CpG islands become methylated?

    <p>The genes are silenced</p> Signup and view all the answers

    Which component is often recruited by methyl-CpG-binding proteins?

    <p>Factors promoting chromatin compaction</p> Signup and view all the answers

    What is most likely to happen to methylated CpG islands in housekeeping genes?

    <p>They remain unmethylated</p> Signup and view all the answers

    Which of the following describes a characteristic of fully methylated DNA?

    <p>Inhibition of transcription</p> Signup and view all the answers

    What is the typical length of CpG islands found near the promoters of genes?

    <p>1,000 to 2,000 nucleotides</p> Signup and view all the answers

    Which of the following correctly describes a scenario involving the binding of an activator protein?

    <p>Methylation inhibits the binding of activator proteins.</p> Signup and view all the answers

    What is the primary role of regulatory transcription factors?

    <p>To regulate the rate of transcription of target genes</p> Signup and view all the answers

    How do enhancers affect transcription?

    <p>They can increase the transcription rate by 10- to 1,000-fold</p> Signup and view all the answers

    What is the function of general transcription factors?

    <p>To assist RNA polymerase in binding to the core promoter</p> Signup and view all the answers

    Which of the following statements about gene regulation is true?

    <p>Nerve and muscle cells exhibit differences due to gene regulation</p> Signup and view all the answers

    What term describes the decrease in transcription resulting from the binding of a transcription factor?

    <p>Down-regulation</p> Signup and view all the answers

    In combinatorial control, which factors can influence transcription?

    <p>Both activators and repressors</p> Signup and view all the answers

    Which of the following best describes the function of silencers?

    <p>Elements that decrease the rate of transcription</p> Signup and view all the answers

    What is a key feature of regulatory transcription factors?

    <p>They can be modulated to enhance or inhibit transcription</p> Signup and view all the answers

    What aspect of gene expression does timing relate to in gene regulation?

    <p>Developmental stages and cell type diversity</p> Signup and view all the answers

    Which of the following is NOT a way to modulate regulatory transcription factor functions?

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

    What role do glucocorticoids primarily influence in cells?

    <p>Nutrient metabolism</p> Signup and view all the answers

    Which type of chromatin conformation is difficult for transcription to occur?

    <p>Closed conformation</p> Signup and view all the answers

    What are GREs (Glucocorticoid Response Elements) primarily characterized as?

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

    What effect does covalent modification, such as phosphorylation, primarily have?

    <p>It alters the protein-protein interactions.</p> Signup and view all the answers

    What is one way chromatin remodeling complexes can change chromatin structure?

    <p>Evicting histone octamers</p> Signup and view all the answers

    Which enzymes are known to modify the amino terminal tails of histones?

    <p>Acetyltransferases, methyltransferases, and kinases</p> Signup and view all the answers

    What is the primary function of histone variants in relation to nucleosomes?

    <p>They create specialized chromatin.</p> Signup and view all the answers

    What is a common consequence of the histone code on chromatin structure?

    <p>It dictates the binding of specific proteins.</p> Signup and view all the answers

    What role do chromatin remodeling machines primarily play?

    <p>They reposition and restructure nucleosomes.</p> Signup and view all the answers

    How many histone genes does the human genome contain?

    <p>More than 70</p> Signup and view all the answers

    Which of the following is a method by which ATP-dependent chromatin remodeling occurs?

    <p>Change in the position of nucleosomes</p> Signup and view all the answers

    What is the primary function of the protein called DNA translocase?

    <p>It functions as an ATPase subunit in remodeling complexes.</p> Signup and view all the answers

    Which modification on histones is primarily associated with enhancing transcription?

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

    What aspect of chromatin is dynamically altered to affect gene expression?

    <p>The three-dimensional packing of chromatin</p> Signup and view all the answers

    Study Notes

    Introduction to Gene Regulation

    • Gene expression is regulated to ensure accurate timing of gene expression during development and distinct cell types.
    • All organisms regulate gene expression, but eukaryotes have more complex mechanisms than prokaryotes.
    • The mechanisms of gene regulation enable specific genes to be expressed in specific cell types at the right time.

    Regulatory Transcription Factors

    • Transcription factors are proteins that influence the ability of RNA polymerase to transcribe a given gene.
    • There are two main types of transcription factors: general and regulatory.
    • General transcription factors are required for the binding of RNA polymerase to the core promoter and progression to the elongation stage.
    • Regulatory transcription factors regulate the rate of transcription of target genes.
    • Enhancers are DNA sequences that increase the rate of transcription (up-regulation) when transcription factors bind to them.
    • Silencers decrease the rate of transcription (down-regulation) when transcription factors bind to them.
    • Most eukaryotic genes are regulated by many factors, so the regulation is complex and involves multiple factors working together.
    • Combinatorial control refers to the combined action of multiple transcription factors to regulate gene expression.

    Modulation of Regulatory Transcription Factor Functions

    • Transcription factors can be modulated in three common ways:
      • Binding of a small effector molecule: Examples include steroid hormones.
      • Protein-protein interactions: Interactions between proteins can activate or inhibit transcription factors.
      • Covalent modification: Modifications such as phosphorylation can alter the activity of transcription factors.

    Steroid Hormones and Regulatory Transcription Factors

    • Steroid hormones influence gene expression by binding to specific receptors.
    • The hormone-receptor complex acts as a transcription factor and regulates target genes.
    • Glucocorticoids are steroid hormones that influence nutrient metabolism.
    • Gonadocorticoids, such as estrogen and testosterone, influence the growth and function of the gonads.
    • Glucocorticoid response elements (GRE) function as enhancers and are located near dozens of different genes, allowing the hormone to activate many genes.

    Chromatin Remodeling and Histones

    • ATP-dependent chromatin remodeling refers to dynamic changes in chromatin structure that are essential for gene expression.
    • Chromatin remodeling complexes can alter the positions of nucleosomes, evict histone octamers, or change the composition of nucleosomes.
    • Chromatin can exist in two conformations:
      • Closed conformation is tightly packed and inaccessible to transcription factors.
      • Open conformation is more accessible to transcription factors and allows for transcription.
    • Histone modifications play a vital role in chromatin structure and function.
    • Histone variants are incorporated into nucleosomes to create specialized chromatin.
    • The histone code refers to the pattern of histone modifications that provide binding sites for proteins that regulate chromatin structure and gene expression.

    DNA Methylation

    • DNA methylation is a common modification in eukaryotes, where a methyl group is covalently attached to cytosine bases.
    • DNA methylation usually inhibits eukaryotic gene transcription by preventing the binding of transcription factors.
    • CpG islands are regions of DNA with a high concentration of CpG dinucleotides.
    • Unmethylated CpG islands are typically found in housekeeping genes and genes that are essential for survival.
    • Methylated CpG islands are found in tissue-specific genes, and methylation can lead to silencing of these genes.

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    Description

    This quiz explores the mechanisms of gene expression regulation in eukaryotes. It covers the roles of transcription factors, including general and regulatory types, and the functions of enhancers and silencers in transcription. Understand the complexities of gene regulation critical for development and cell type differentiation.

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