lecture 10
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Questions and Answers

What does RNA polymerase synthesize using a DNA template?

  • Single stranded RNA (correct)
  • Double stranded DNA
  • Single stranded DNA
  • Double stranded RNA
  • Which sequences in DNA are essential for RNA polymerase to know where to start and stop transcription?

  • Promoter and terminator sequences (correct)
  • Repressor and enhancer sequences
  • Start codons and stop codons
  • Introns and exons
  • Which statement is true regarding the transcription of the promoter sequence?

  • It is transcribed last.
  • It is transcribed first. (correct)
  • It is transcribed in segments.
  • It is never transcribed.
  • What key feature distinguishes E.coli RNA polymerase from E.coli DNA polymerase?

    <p>It does not need a primer sequence to initiate.</p> Signup and view all the answers

    How many general transcription factors are minimally required for transcription by RNA pol-II?

    <p>5</p> Signup and view all the answers

    What do eukaryotic promoters contain that allows for the recruitment of RNA polymerase?

    <p>Core promoter elements</p> Signup and view all the answers

    What distinguishes eukaryotic RNA polymerases from each other?

    <p>They recognize different promoters and transcribe various classes of genes.</p> Signup and view all the answers

    What is primarily required for RNA pol-II to initiate transcription?

    <p>General transcription factors</p> Signup and view all the answers

    What is the role of the kinase subunit in TFIIH?

    <p>To phosphorylate the C-terminal domain of RNA pol-II</p> Signup and view all the answers

    Which complex is essential for linking general transcription factors to gene-specific transcription factors?

    <p>Mediator complex</p> Signup and view all the answers

    If a yeast cell cannot produce TFIIF, which of the following would not occur?

    <p>Successful transcription initiation</p> Signup and view all the answers

    What type of protein does the BCL11A gene encode?

    <p>A transcriptional repressor of fetal hemoglobin</p> Signup and view all the answers

    What is the primary function of enhancers in gene expression?

    <p>To facilitate robust transcription beyond basal levels</p> Signup and view all the answers

    When BCL11A function is removed from an adult mouse, which type of hemoglobin is produced?

    <p>Fetal hemoglobin</p> Signup and view all the answers

    What allows distant regulatory elements to interact effectively during transcription regulation?

    <p>DNA looping facilitated by Mediator</p> Signup and view all the answers

    What aspect is characteristic of gene-specific transcription factors?

    <p>They can be either activators or repressors</p> Signup and view all the answers

    What is the primary function of the promoter sequence in transcription?

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

    Which stage of transcription follows the initiation phase?

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

    How does bacterial RNA polymerase initiate transcription compared to eukaryotic RNA polymerase?

    <p>Bacterial initiation involves a sigma factor, whereas eukaryotic initiation involves general transcription factors.</p> Signup and view all the answers

    What role do enhancer sequences play in transcription?

    <p>They can amplify the activity of transcription factors.</p> Signup and view all the answers

    What do the terms 'template strand' and 'coding strand' refer to in the context of transcription?

    <p>The template strand serves as the one from which RNA is synthesized.</p> Signup and view all the answers

    Which of the following correctly describes the difference between eukaryotic and prokaryotic transcription?

    <p>Prokaryotic requires only RNA polymerase, while eukaryotic requires general transcription factors and RNA polymerase II.</p> Signup and view all the answers

    What is the direction of mRNA synthesis during transcription?

    <p>From 5’ to 3’</p> Signup and view all the answers

    What is the significance of transcriptional termination?

    <p>It signals the end of RNA synthesis.</p> Signup and view all the answers

    Study Notes

    Transcription Learning Objectives

    • Compare and contrast DNA replication and transcription
    • Explain how E. coli RNA polymerase initiates transcription
    • Diagram a bacterial promoter sequence
    • Describe the processes of transcriptional elongation and termination
    • Summarize the roles of different eukaryotic RNA polymerases
    • Distinguish between the binding of bacterial and eukaryotic RNA polymerases to promoters
    • Describe the functions of the general transcription factors for RNA polymerase II
    • Compare and contrast promoters and enhancers
    • Describe how activators and repressors affect transcription

    Transcription Key Concepts

    • Transcription begins at a promoter sequence
    • Transcription ends at a terminator sequence
    • Transcription occurs in three stages: initiation, elongation, and termination
    • Prokaryotic initiation involves a sigma factor and RNApol holoenzyme
    • Eukaryotic initiation involves general transcription factors, RNApol II, and a mediator complex
    • Additional gene-specific transcription factors that bind to enhancer sequences may be required
    • Gene-specific transcription factors may activate or repress gene transcription

    Replication vs. Transcription

    • DNA Replication makes a complete copy of the chromosome
    • During transcription, only portions of DNA sequence are transcribed into RNA
    • Both DNA and RNA are synthesized in the 5’ to 3’ direction

    Coding Strand vs. Template Strand

    • Transcription produces RNA that is complementary to one strand of DNA
    • The template strand is different for different genes

    RNA polymerase carries out transcription

    • RNA Polymerase synthesizes single-stranded RNA using DNA as a template
    • New RNA strand is synthesized in the 5’ to 3’ direction

    E. coli RNA polymerase

    • Has a core enzyme (two alpha subunits, one beta subunit, one beta prime subunit)
    • Has a sigma subunit

    Sequences in DNA tell RNA pol where to start and stop transcription

    – Promoter: sequence of DNA that signals the start of a gene – Terminator: sequence of DNA that signals the end of a gene

    E. coli promoters contain -10 and -35 consensus sequences

    • The -10 sequence is called the Pribnow box
    • The -35 sequence is the -35 box

    Bacterial transcription stops at the terminator sequence

    • Termination occurs when RNA polymerase encounters a terminator sequence
    • Terminator sequences are often rich in GC content
    • Termination can be rho-dependent or rho-independent

    Eukaryotic RNA Polymerases

    • Recognize different promoters
    • Transcribe different classes of genes
    • All consist of 12-17 different subunits, 9 conserved subunits, 5 are related to bacterial subunits

    _____________________ are required for eukaryotic RNA pol

    • General transcription factors (GTFs)
    • Additional gene-specific transcription factors

    5 general transcription factors are minimally required for transcription by RNA pol-II

    • TFIID (large protein complex): binds to the TATA box
    • TFIIB: recruits RNA Polymerase II
    • TFIIF: stabilizes RNA polymerase II and helps it move along the DNA
    • TFIIE: helps TFIIH bind to RNA polymerase II
    • TFIIH: contains a kinase subunit that phosphorylates the C-terminal domain of RNA pol-II, causing a conformational change that separates RNA polymerase II from the pre-initiation complex and allows it to move downstream

    RNA polymerase II/Mediator complexes and transcription initiation

    • Large (>20 protein) complex called Mediator is also required
    • Plays a key role in linking general transcription factors to gene-specific transcription factors

    Eukaryotic Promoters …and Enhancers

    • Promoters are regions of DNA that are located upstream of the gene they regulate
    • Enhancers are regions of DNA that can be located upstream, downstream, or within the gene they regulate
    • An individual gene may have multiple cell- or time-specific enhancers

    Enhancers are required for anything beyond “basal” transcription

    • Basal transcription is the minimal level of transcription that occurs in the absence of any enhancers or other regulatory elements
    • Enhancers can increase the level of transcription by 10- to 100-fold

    Distant regulatory elements are united by DNA looping and Mediator

    • DNA looping allows enhancers to interact with promoters, even if they are located far apart
    • Mediator acts as a bridge between enhancers and promoters

    Gene-specific TFs can be activators or repressors

    • Activators bind to enhancers and increase the rate of transcription
    • Repressors bind to enhancers and decrease the rate of transcription

    Mini-Case Study: Sickle Cell Anemia

    • Sickle cell anemia is a genetic disorder that causes red blood cells to become sickle-shaped
    • The disease is caused by a mutation in the beta-globin gene, which affects the production of hemoglobin
    • Fetal hemoglobin is produced in fetuses and is not affected by the sickle cell mutation
    • BCL11A is a gene that is not expressed in fetuses, but is expressed in adults
    • When BCL11A function is removed from an adult mouse, fetal hemoglobin is now produced in the blood cells of the adult mouse
    • BCL11A encodes a transcriptional repressor of fetal hemoglobin
    • Scientists have generated BCL11A-deficient hematopoietic stem cells (bone marrow!) that can be transplanted into mice, resulting in red blood cells (RBC) that lack BCL11A and produce fetal hemoglobin

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