Biology Quiz: RNA Transcription Concepts
48 Questions
0 Views

Choose a study mode

Play Quiz
Study Flashcards
Spaced Repetition
Chat to lesson

Podcast

Play an AI-generated podcast conversation about this lesson

Questions and Answers

What role does TBP play in the formation of the preinitiation complex?

  • It binds to the TATA box forming a saddle shape. (correct)
  • It phosphorylates the CTD of Pol II.
  • It interacts with the major groove of DNA.
  • It unwinds DNA during transcription initiation.

    • Which factor is primarily responsible for the helicase activity during the initiation of transcription?

  • TFIIF
  • TFIIA
  • TFIIB
  • TFIIH (correct)

    • What stabilizes the core PIC near the transcription start site?

  • Phosphorylation of Pol II by TFIIH.
  • Binding of TFIIE to the template DNA.
  • The docking of TBP onto the TATA box.
  • The insertion of the N-terminal of TFIIB into the RNA channel exit. (correct)

    • Which of the following is a unique feature of TFIIH in the transcription initiation process?

    <p>It has both helicase and kinase activities.</p> Signup and view all the answers

    What happens to the N-terminal of TFIIB as transcription progresses?

    <p>It is released from the RNA exit channel.</p> Signup and view all the answers

    What is one of the first steps to study the DNA binding of proteins?

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

    What does increased transcription typically correlate with in a gene?

    <p>Frequent initiation events and bursts</p> Signup and view all the answers

    What is the main significance of the 5’ region sequence added to the gene of interest in transcription studies?

    <p>It is recognized by a protein fused to a reporter</p> Signup and view all the answers

    Which of the following techniques is NOT used to analyze DNA-protein interactions?

    <p>Western Blot</p> Signup and view all the answers

    Which hypothesis is supported by the observation that transcription expression changes over time?

    <p>Burst Hypothesis</p> Signup and view all the answers

    What is the main role of RNA Pol II in transcription?

    <p>Synthesize messenger RNA and regulatory RNAs</p> Signup and view all the answers

    What is the function of the TATA box in gene transcription?

    <p>Serve as a consensus sequence for polymerase binding</p> Signup and view all the answers

    Which element can influence transcription from a promoter located tens of thousands of base pairs away?

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

    Which complex interacts directly with RNA Pol II to enhance transcriptional initiation?

    <p>Multisubunit Co-activator Complex</p> Signup and view all the answers

    What role do general transcription factors (TFs) play in transcription?

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

    Which of the following proteins is critical for binding to the TATA box in the transcription process?

    <p>TBP (TATA-box Binding Protein)</p> Signup and view all the answers

    In what phase of transcription does the RNA polymerase move away from the transcription start site?

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

    Which part of the DNA is responsible for influencing transcription when close to the promoter?

    <p>Promoter Proximal Elements</p> Signup and view all the answers

    What is the role of TAFs within TFIID?

    <p>Initiate transcription from promoters that lack a TATA box</p> Signup and view all the answers

    Which statement about the preinitiation complex (PIC) is true?

    <p>It includes RNA polymerase and general transcription factors.</p> Signup and view all the answers

    What is the primary function of the recognition helix in specific DNA-protein interactions?

    <p>To contact DNA bases through non-covalent interactions</p> Signup and view all the answers

    Which of the following is true about the zinc finger motif?

    <p>The C2H2 variant is the most common DNA binding motif in the human genome.</p> Signup and view all the answers

    What is a distinguishing characteristic of leucine zippers?

    <p>Contain hydrophobic residues at every 7th position.</p> Signup and view all the answers

    How do bZIPs and bHLHs enhance regulatory diversity through their structure?

    <p>By allowing the formation of heterodimeric combinations.</p> Signup and view all the answers

    What is the primary purpose of linker scanning mutagenesis?

    <p>To assess the importance of DNA regulatory regions.</p> Signup and view all the answers

    What cannot be determined using the Electrophoretic Mobility Shift Assay (EMSA)?

    <p>The identity of the bound protein complex.</p> Signup and view all the answers

    What does chromatin immunoprecipitation (ChIP) primarily assess?

    <p>DNA-protein binding interactions in vivo</p> Signup and view all the answers

    In in vivo transfections, what is typically tested?

    <p>The ability of altered proteins to repress transcription</p> Signup and view all the answers

    What key feature characterizes the basic helix-loop-helix motif?

    <p>There are two alpha helices connected by a loop</p> Signup and view all the answers

    What type of proteins typically contain a 60-residue DNA binding motif and are involved in development?

    <p>Transcription factors</p> Signup and view all the answers

    Which of the following best describes the function of homeodomains in transcription factors?

    <p>To bind specifically to DNA sequences</p> Signup and view all the answers

    Identify the primary role of proteins that contain the 60-residue DNA binding motif during development.

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

    Which family of transcription factors is notably characterized by the presence of homeodomains?

    <p>HOX family</p> Signup and view all the answers

    What is a significant characteristic of proteins with DNA binding motifs such as the homeodomain?

    <p>They are often involved in regulating developmental processes</p> Signup and view all the answers

    What structural characteristic defines a Zinc finger motif?

    <p>It is a domain formed by folding a polypeptide chain around a Zinc ion.</p> Signup and view all the answers

    Which amino acid side chains are primarily involved in the most common DNA binding Zinc finger motif ($C_{2}H_{2}$)?

    <p>Two cysteines and two histidines</p> Signup and view all the answers

    How many Zinc ions are bound by the $C_{6}$ type Zinc finger motif?

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

    In terms of structural configuration, what is the primary role of the polypeptide chain in a Zinc finger?

    <p>To form a compact domain around a Zinc ion that interacts with DNA.</p> Signup and view all the answers

    What is the typical number of cysteines present in the $C_{4}$ type Zinc finger motif?

    <p>Four cysteines</p> Signup and view all the answers

    What is the function of the hydrophobic residues in the leucine zipper structure?

    <p>They promote protein dimerization.</p> Signup and view all the answers

    How many helical turns are formed by the leucine zipper segment?

    <p>8 turns</p> Signup and view all the answers

    Which region of the leucine zipper is responsible for binding to specific DNA sequences?

    <p>N-terminal region</p> Signup and view all the answers

    Which sequence is commonly recognized by the DNA binding domain of leucine zippers?

    <p>5'-ACGT-3'</p> Signup and view all the answers

    What distinguishes the Helix-Loop-Helix (HLH) motif structurally from the helix-turn-helix (HTH) motif?

    <p>HLH has two alpha helices connected by a short loop, while HTH has a different arrangement.</p> Signup and view all the answers

    What is a key characteristic of the hydrophobic amino acids in the C-terminus of the Helix-Loop-Helix structure?

    <p>They have a specific arrangement with hydrophilic residues at every 2nd/3rd position.</p> Signup and view all the answers

    Which region of the Helix-Loop-Helix protein interacts with DNA?

    <p>N-terminus alpha helix</p> Signup and view all the answers

    How does the helix-turn-helix (HTH) motif typically function in proteins?

    <p>By enabling proteins to bind to DNA for gene regulation.</p> Signup and view all the answers

    What commonality exists between the Helix-Loop-Helix and helix-turn-helix motifs?

    <p>Both motifs are characterized by two alpha helices connected by a loop.</p> Signup and view all the answers

    Study Notes

    Housekeeping

    • Midterm results will be available soon
    • Quiz 4 opens Saturday, November 2nd, and closes Tuesday, November 5th
    • No class on Monday
    • Email [email protected] for quiz grading questions
    • SciLearn TAs cannot provide answers
    • Students should attend post-tutorial office hours if they can't attend the scheduled review sessions

    Transcription

    • Initiation: RNA polymerase binds to the promoter, denatures DNA locally, and catalyzes the first phosphodiester linkage
    • Elongation: RNA polymerase moves away from the start site, changing to a processive configuration
    • Termination: RNA polymerase recognizes a stop site, releases the completed RNA, and dissociates from DNA

    Transcription (From Last Week)

    • Transcription Start Site (+1): The starting point of transcription
    • Promoter: Region of DNA where transcription factors bind to initiate transcription
    • Enhancers: DNA elements influencing the ability of RNA polymerase to transcribe a gene.
    • Upstream/Downstream: Upstream is in the opposite direction of transcription from the start point, downstream is in the same direction.
    • Proximal/Distal: Proximal elements are close to the promoter, distal elements are further away.

    Eukaryotic RNA Polymerases

    • Eukaryotes have 3 RNA polymerases (I, II, and III)
    • RNA polymerase I is responsible for most ribosomal RNA
    • RNA polymerase II synthesizes mRNA, snRNAs, siRNAs, and miRNAs
    • RNA polymerase III synthesizes tRNAs and ribosomal components.

    Promoters

    • TATA box: Region rich in Ts and As, located 10-35 bases upstream of the transcription start site.
    • TBP (TATA-box binding protein): Binds to the minor groove, disrupting the DNA double helix, crucial for efficient pol I/III transcription.

    Proximal Promoter Elements & Enhancers

    • Proximal promoter elements: Short (6-10bp) elements near the promoter that control transcription
    • Enhancers: Elements (50-200bp) that can stimulate transcription from regions of DNA thousands of bases away from the promoter.

    Mediators

    • Multisubunit co-activator complex
    • Bridges chromatin sections to enhance transcription initiation
    • Interacts directly with RNA polymerase II
    • Binds to activation domains
    • Communicates regulatory signals from DNA binding TFs to RNA polymerase II

    RNA Pol II General Transcription Factors (TFs)

    • TFIID is the largest general transcription factor essential for RNA polymerase II-mediated transcription.
    • Made up of TBP and TBP-associated factors
    • TAFs initiate transcription from promoters lacking TATA box

    Preinitiation Complex (PIC)

    • TBP binds to the TATA box forming a saddle shape and interacting with the minor DNA groove
    • TFIIA associates with TBP and DNA upstream.
    • TFIIB clamps onto TBP, contacting the major groove on both sides of the TATA box.
    • Complex of RNA polymerase II and TFIIF associate with TATA-TFIIA-TFIIB complex to form the core PIC
    • N-terminal of TFIIB is inserted into the RNA channel
    • TFIIE encloses the template DNA.
    • TFIIH docks onto TFIIE, forming the closed PIC

    Initially Transcribing Complex

    • Helicase activity in TFIIH unwinds DNA at the TSS, enabling the formation of an open complex
    • N-term of TFIIB is released as transcription progresses
    • TFIIH Kinases phosphorylate RNA polymerase II's CTD

    TFIIH

    • Only transcription factor with enzymatic activity.
    • Helicase is essential for initiation.
    • XPB proteins are kinases.
    • Kinases in TFIIH phosphorylate the CTD.
    • Necessary for elongation.
    • Involved in nucleotide excision DNA repair.

    TFs are Modular!

    • Transcription factors have discrete domains for DNA binding, activation/repression, chromatin remodeling, nuclear import, and protein interaction.

    TFs Recognize Specific DNA Motifs!

    • Recognition Helix: An alpha helix from which most of the amino acid side chains that contact DNA bases extend, primarily interacting through non-covalent interactions in the major groove

    Homeodomains

    • 60-amino acid DNA binding motif important in development (ex: Pax3, HOX family).

    Zinc Fingers

    • Polypeptide chain folds around a zinc ion.
    • Most common DNA binding motif.
    • C2H2: 2 Cysteines and 2 HIstidine side chains bind one Zinc ion.
    • C4: 4 Cysteines bind to zinc
    • C6: 6 Cysteines bind to two separate zinc ions

    Leucine Zippers (bZip)

    • Hydrophobic residue every 7th position.
    • Coiled-coil dimerization in C terminus.
    • DNA binding in N terminus.

    Basic Helix-Loop-Helix

    • Similar to bZip.
    • Two alpha helices connected by a short loop.
    • N terminus alpha helix: Basic residues interacting with DNA
    • Middle loop region
    • C terminus: hydrophobic AAs spaced out like amphipathic helices (h-philic every 2nd/3rd, h-phobic every 3rd/4th position)

    Combinatorial Diversity & Cooperative Binding

    • TFs (bZIPs and bHLHs) can exist as heterodimers (combinations of monomers)
    • Dimer formation brings together activation domains.
    • Protein-protein interactions between unrelated TFs can affect protein-binding affinity.

    Linker Scanning Mutagenesis

    • Method to determine the importance of different parts of regulatory DNA sequences.
    • Introducing overlapping mutations into a DNA region.
    • Assessing the effect of mutation on gene expression.

    EMSA (Electrophoretic Mobility Shift Assay)

    • Detects protein-DNA complexes using radiolabeled DNA probes and fractionated protein samples.
    • Cannot determine the bound protein sequence.

    In Vivo Transfections

    • Testing the ability of a protein to activate/repress transcription in living cells.
    • Typically conducted after identifying, isolating, and purifying a transcription factor.

    ChIP (Chromatin Immunoprecipitation)

    • Antibody-based method for assessing DNA-protein binding interactions in vivo.
    • Crosslinking DNA with formaldehyde, shearing the DNA, immunoprecipitating bound DNA, sequencing the DNA, and determining the binding sites.

    What does increased transcription look like?

    • In-vivo technique looks at actively transcribed RNA, not degraded RNA
    • Sequence added to the 5' region of interest, recognized by a reporter protein
    • Transcribed gene region will also be bound by the reporter protein

    Transcription occurs in bursts!

    • Transcriptional initiation from highly transcribed genes occurs in bursts
    • Experiment looked at the SNAIL gene in Drosophila, which had a strong enhancer (sna) downstream of its promoter.

    P-granules

    • Proteins involved in transcription often colocalize in puncta (dots)
    • Liquid-liquid condensate formation.
    • Examples of factors involved: concentration of macromolecules, valency, electrostatic interactions, post-translational modifications, intrinsically disordered proteins, transient expression

    Know the Difference!

    • Distinguish between RNA polymerases I, II, and III
    • Differentiate between Northern, Southern, and Western Blots
    • Compare ChIP and EMSA
    • Distinguish between PCR and qRT-PCR

    Studying That Suits You

    Use AI to generate personalized quizzes and flashcards to suit your learning preferences.

    Quiz Team

    Related Documents

    Proteins That Regulate Transcription RR9-11 PDF

    Description

    Test your knowledge on the key concepts of RNA transcription with this quiz. From the roles of RNA polymerase to the significance of promoters and enhancers, enhance your understanding of this essential biological process.

    More Like This

    Use Quizgecko on...
    Browser
    Open
    Browser
    Browser