Lodish Ch 9: Transcriptional Control of Gene Expression
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In bacteria, an operon:

  • is a region of DNA that is transcribed as a single mRNA encoding several proteins. (correct)
  • encodes for miRNAs.
  • contains a promoter unique for each individual gene in the operator.
  • none of the above

    • Sigma factors present in bacteria are proteins required to:

  • allow translation to proceed.
  • initiate transcription. (correct)
  • terminate DNA replication.
  • terminate DNA replication and initiate transcription.

    • Operator constitutive mutants of the lac operon would

  • express β-galactosidase constitutively. (correct)
  • prevent the inducer from binding to the repressor.
  • express the lac repressor constitutively.
  • block the binding of RNA polymerase to the promoter.

    • How does binding of the lac repressor to the lac operator block transcription initiation?

    <p>lac repressor binding blocks RNA polymerase from interacting with DNA at the start site.</p> Signup and view all the answers

    Which of the following proteins does not "Footprint" the lac operon control region?

    <p>β-galactosidase</p> Signup and view all the answers

    You are studying the expression of the gene that appears to be under the control of three different transcription-control regions during mouse embryonic development. Which one of the following is the BEST method to use to determine when each of these regions are active in the developing mouse embryo?

    <p>reporter gene assay</p> Signup and view all the answers

    Reporter genes employ fragments of DNA encoding proteins that when translated do not have any obvious effects in the cells and tissues. Which one of the following is NOT a reporter protein?

    <p>RNA polymerase 1</p> Signup and view all the answers

    You are studying the effects of α-amanitin, a poisonous cyclic octapeptide, on eukaryotic cells and have noticed that following treatment, there is no miRNA transcription. Based on this evidence you conclude that α-amanitin must be inhibiting:

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

    Which of the following is a fundamental difference between gene regulation in bacteria compared with eukaryotes?

    <p>In eukaryotes, but not bacteria, transcription can be influenced by how effectively the DNA sequence of a promoter region interacts with histone octamers.</p> Signup and view all the answers

    All of the following statements about the essential carboxy terminal domain (CTD) of RNA polymerase are true except:

    <p>The CTD is present in RNA polymerase I, II, and III.</p> Signup and view all the answers

    You have identified a transcription factor and hypothesize that it binds to the promoter region of a gene that encodes a protein that causes cells to stop dividing. In order to test the interaction between the transcription factor and the DNA you will need to do a specific assay. Which one of the following would you use to test your hypothesis?

    <p>chromatin immunoprecipitation</p> Signup and view all the answers

    The human genome encodes transcription factors that contain an acidic activation domain that is phosphorylated in response to increased levels of the second messenger cAMP. Which one of the following contains one of these activation domains?

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

    Enhancers are considered transcription-control elements that regulate the expression of eukaryotic genes. Which one of the following is true regarding these elements?

    <p>They generally range in length from about 50-200 base pairs.</p> Signup and view all the answers

    Which one of the following terms is used to describe the protein:DNA complex containing several transcription factors bound to a single enhancer?

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

    The TATA box

    <p>acts to position RNA polymerase II for transcription initiation.</p> Signup and view all the answers

    All the following elements can function as eukaryotic promoters except

    <p>an enhancer.</p> Signup and view all the answers

    Which of the following is the correct order of binding of general transcription factors to initiate transcription at RNA polymerase II promoters?

    <p>TFIID, TFIIB, Pol II, TFIIH</p> Signup and view all the answers

    What is the function of TFIIH in the transcription initiation complex?

    <p>all of the above</p> Signup and view all the answers

    This serves as the promoter for 70% of eukaryotic genes and typically serves as a control region for genes that are transcribed at relatively low rates.

    <p>CpG islands</p> Signup and view all the answers

    An enhancer

    <p>is a DNA element that stimulates transcription of eukaryotic promoters.</p> Signup and view all the answers

    Which of the following is not used in the electrophoretic mobility shift assay (EMSA)?

    <p>DNase I</p> Signup and view all the answers

    A leucine-zipper motif contains

    <p>a leucine residue at every seventh position.</p> Signup and view all the answers

    Which of the following is not a structural motif found in a DNA-binding domain?

    <p>random-coil acidic domain</p> Signup and view all the answers

    Bromodomains are found in chromosome-associated proteins that contribute to transcriptional activation. To facilitate this activation, the bromodomains bind to histones, specifically their lysine residues that have been post-translationally modified by:

    <p>acetylation.</p> Signup and view all the answers

    Which of the following is NOT true regarding the chromatin-remodeling SWI/SNF complex?

    <p>It can stabilize DNA-histone interactions.</p> Signup and view all the answers

    All the following statements about heterochromatin are true except:

    <p>Heterochromatin is more susceptible to DNasel than is euchromatin.</p> Signup and view all the answers

    All of the following events play a role in yeast-mating type switching except

    <p>methylation of the silent-mating-type locus.</p> Signup and view all the answers

    The mediator complex

    <p>has histone acetylase activity.</p> Signup and view all the answers

    Transcriptionally inactive genes

    <p>often are methylated.</p> Signup and view all the answers

    The nuclear-receptor superfamily consists of several proteins that bind to consensus sequences of DNA response elements. Which of the following is NOT considered a member of this superfamily?

    <p>acetylcholine receptor</p> Signup and view all the answers

    Which one of the following techniques would be best suited to follow how a thyroxine-bound receptor translocates from the cytoplasm to its DNA response element?

    <p>fluorescence microscopy and a GFP-tagged receptor fusion protein</p> Signup and view all the answers

    Lipid soluble hormones activate transcription by

    <p>binding to a nuclear receptor.</p> Signup and view all the answers

    Which protein domains are found in nuclear-receptor family members?

    <p>variable region, DNA-binding domain, ligand-binding domain</p> Signup and view all the answers

    Regulation of transcription by steroid hormones

    <p>involves cytoplasmic hormone receptors that can move to the nucleus.</p> Signup and view all the answers

    Epigenetics marks refer to modifications to DNA and proteins that in turn regulate gene expression. Which statement is true regarding these specific types of modifications?

    <p>All of the above</p> Signup and view all the answers

    What family of proteins plays an essential role in the repression of genes that help to direct the formation of specific tissues and organs in a developing embryo?

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

    X chromosome inactivation in mammals is mediated by

    <p>long non-coding RNAs (ncRNA).</p> Signup and view all the answers

    Which of the following statement(s) regarding transcription initiation and RNA Pol III is (are) true?

    <p>all of the above</p> Signup and view all the answers

    Study Notes

    Transcriptional Control of Gene Expression

    • Bacterial operons are DNA regions, transcribed as a single mRNA, encoding several proteins.
    • Sigma factors are proteins in bacteria that initiate transcription.
    • Operator constitutive mutants of the lac operon result in constitutive expression of β-galactosidase.
    • Lac repressor binding to the lac operator blocks transcription initiation by preventing RNA polymerase interaction with the DNA.
    • Reporter genes are DNA fragments encoding proteins with no obvious effects in cells/tissues and used to study gene expression.
    • Luciferase, green fluorescent protein, and β-galactosidase are examples of reporter proteins.
    • In eukaryotes, but not bacteria, transcription can be influenced by how effectively the DNA sequence of a promoter region interacts with histone octamers.
    • DNA affinity chromatography and polymerase chain reaction determine when regions in developing mouse embryos are active (using specific experiments for this type of determination).

    Eukaryotic RNA Polymerases

    • Eukaryotes possess three RNA polymerases, each responsible for a different type of RNA synthesis(i.e., RNA polymerase I synthesizes ribosomal RNA, RNA polymerase II synthesizes messenger RNA, and RNA polymerase III synthesizes tRNA and other small RNAs)
    • Eukaryotic RNA polymerases are more complex than bacterial ones and contain more subunits.
    • The CTD of RNA polymerase II is critical for viability and has multiple repeats of a heptapeptide.
    • The CTD of RNA polymerase II is involved in the assembly of the transcription initiation complex. Phosphorylation is crucial for the transition from transcriptional initiation to elongation.

    Transcriptional Control Elements (eukaryotes)

    • Promoters and enhancers are regions of DNA that play crucial roles in controlling transcription.
    • Enhancers are cis-acting DNA sequences that stimulate transcription from promoters located tens of thousands of base pairs away; they are not found only upstream of the transcription start site. Enhancers are typically 50–200 base pairs in length.
    • Promoters are located close to the transcription start site and usually lose their ability to stimulate transcription when moved tens of base pairs away.
    • The TATA box is a promoter sequence for genes transcribed by RNA polymerase II, it is present in 70% of eukaryotic promoters and acts as a control region. The initiator element is also crucial for transcription initiation.
    • CpG islands are also found near promoters and are characterized by repeated CpG dinucleotides.
    • The enhanceosome is a large nucleoprotein complex, formed by the assembly of proteins to multiple binding sites in an enhancer.
    • Transcription factors are proteins that bind to DNA to regulate gene expression.
    • Specific examples include the leucine-zipper motif (that contains a stretch of leucine residues at every seventh position), zinc-finger motif (forming a compact domain), and helix-loop-helix motif.
    • Electrophoretic mobility shift assays (EMSAs) and DNase I footprinting techniques are used to identify protein-DNA interactions.

    Gene Regulation in Eukaryotes

    • Chromatin remodeling complexes help regulate gene expression by modifying histone interactions to allow for access for gene's expression.
    • They can involve the methylation or acetylation of cytosine bases or histones.
    • Heat-shock genes have a mechanism of stalling RNA polymerase II, pausing transcription and then rapidly re-initiating with transcription factor interactions, which imparts an advantage in cells facing unusual stress.
    • Nuclear receptors, such as the glucocorticoid receptor (GR), regulate gene transcription in response to steroid hormones.
    • The process typically involves the translocation of receptor to the nucleus and then interacts with glucocorticoid response elements (GRE) controlling transcription of responsive genes.

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    Description

    Explore the mechanisms of transcriptional control in gene expression, focusing on bacterial operons and eukaryotic transcription factors. Understand the roles of sigma factors, operators, and reporter genes in regulating gene activity. This quiz will test your knowledge on how these processes differ between prokaryotes and eukaryotes.

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