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Questions and Answers

What does the primary transcript (mRNA precursor) contain?

  • Exons
  • Ribosomes
  • Nucleotides
  • Introns (correct)

    • Which machinery is responsible for removing introns from the primary transcript?

  • Endoplasmic reticulum
  • Golgi apparatus
  • Ribosome
  • Splicesome (correct)

    • U6 is classified as what type of molecule?

  • Protein Enzyme
  • Liposome
  • Ribozyme (correct)
  • Carbohydrate

    • What is defined as multiple ribosomes bound to a single mRNA?

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

    What provide mechanical support and chromatin anchoring within the nuclear envelope?

    <p>Lamin proteins</p> Signup and view all the answers

    What is the process by which RNA products are transported out of the nucleus?

    <p>Nuclear trafficking</p> Signup and view all the answers

    What structure is the site of transcription in eukaryotic cells?

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

    What is the role of the 5' and 3' untranslated regions (UTRs) of mRNA?

    <p>Affects the initiation and progression of translation</p> Signup and view all the answers

    What occurs when eIF2 is phosphorylated?

    <p>Initiating tRNA cannot bind to mRNA</p> Signup and view all the answers

    What stress conditions can inhibit translation through phosphorylation of initiation factors?

    <p>Viral infection</p> Signup and view all the answers

    Which of the following processes is specifically affected by the global regulation of translation?

    <p>Translation of all mRNAs</p> Signup and view all the answers

    Which of the following can lead to inhibition of translation?

    <p>Stress conditions such as heat shock</p> Signup and view all the answers

    What primarily determines the transcriptional state of myofibers and skin fibroblasts?

    <p>Genetic expression</p> Signup and view all the answers

    Which type of transcription factor is responsible for stimulating transcription?

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

    What percentage of the genome is estimated to encode transcription factors?

    <p>5-10%</p> Signup and view all the answers

    Which domain of a transcription factor promotes binding with another protein of similar structure?

    <p>Dimerization domain</p> Signup and view all the answers

    Which type of motif binds to DNA through ionic bonds and hydrogen bonds?

    <p>DNA-binding motif</p> Signup and view all the answers

    Which type of transcription factor can interact directly with specific DNA sequences?

    <p>Sequence-specific transcription factors</p> Signup and view all the answers

    What role do nucleoporins play in the nuclear pore complex?

    <p>Forming a hydrophobic mesh that blocks free diffusion</p> Signup and view all the answers

    What are the signaling sequences involved in the transport of proteins across the nuclear envelope?

    <p>Nuclear Localization Signal (NLS) and Nuclear Export Signal (NES)</p> Signup and view all the answers

    Which statement best describes the nature of transcription factors?

    <p>Each gene is regulated by multiple transcription factors.</p> Signup and view all the answers

    What type of DNA-binding domain is known for its zinc ions and recognition helix?

    <p>Zinc fingers</p> Signup and view all the answers

    Which proteins are responsible for ferrying proteins across the nuclear envelope for import?

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

    Which of the following best describes how transcription factors interact with DNA?

    <p>Through Van der Waals forces and ionic bonds</p> Signup and view all the answers

    What characterizes the structure of the nuclear pore complex?

    <p>Features octagonal symmetry with a diameter of 20-40 nm</p> Signup and view all the answers

    What is the function of repressors in gene regulation?

    <p>They inhibit transcription.</p> Signup and view all the answers

    Which of the following statements about mRNA export across the nuclear envelope is true?

    <p>Only mature mRNAs are exported as ribonucleoproteins (RNPs)</p> Signup and view all the answers

    What is the primary function of importin α/β in the transport process?

    <p>Binding to nuclear localization signals</p> Signup and view all the answers

    What is the distinction between mRNA export and protein transport across the nuclear envelope?

    <p>mRNA transport is not exportin or RanGTP dependent, while protein transport is</p> Signup and view all the answers

    Which components are necessary for binding nuclear export signals?

    <p>Exportins and RanGTP</p> Signup and view all the answers

    Which statement about the genetic information in cells is accurate?

    <p>Every cell contains the same genetic information despite potential differences in appearance and function</p> Signup and view all the answers

    What is the role of histone acetyltransferases (HATs) in transcription?

    <p>They transfer acetyl groups to lysine residues of histones.</p> Signup and view all the answers

    How does the addition of an acetyl group affect the binding of histones to DNA?

    <p>It reduces the binding to negatively charged DNA.</p> Signup and view all the answers

    What is the impact of chromatin remodeling complexes on transcription?

    <p>They increase the accessibility of the promoter to transcription machinery.</p> Signup and view all the answers

    Which of the following coactivators is mentioned as having the ability to acetylate and initiate transcription?

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

    What type of modification do histone acetyltransferases perform on histones?

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

    Which transcription factor is highlighted in the example provided?

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

    What is the primary effect of reducing the binding of histones to DNA?

    <p>Increased transcriptional activity.</p> Signup and view all the answers

    Which complex is known to enhance the accessibility of chromatin for transcription?

    <p>SWI/SNF</p> Signup and view all the answers

    What characterizes the function of coactivators in transcription?

    <p>They assist in the recruitment of transcription factors.</p> Signup and view all the answers

    What effect does acetylation typically have on histones?

    <p>It reduces histone-DNA binding affinity.</p> Signup and view all the answers

    What role do acetyl groups play when transferred to histone lysine residues?

    <p>They reduce the binding affinity of histones to DNA.</p> Signup and view all the answers

    Which of the following best describes the function of chromatin remodeling complexes?

    <p>They increase the accessibility of the promoter to transcription machinery.</p> Signup and view all the answers

    Which coactivator is known for both acetylating histones and initiating transcription?

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

    What effect does the acetylation of histones have on chromatin structure?

    <p>It allows greater accessibility to DNA for transcription.</p> Signup and view all the answers

    Which interaction is primarily facilitated by the action of histone acetyltransferases (HATs)?

    <p>Exposure of binding sites for chromatin remodeling complexes.</p> Signup and view all the answers

    What role does the nuclear envelope play in the transport of molecules?

    <p>Contains transmembrane proteins that facilitate selective transport.</p> Signup and view all the answers

    Which of the following is a function of the nucleolus?

    <p>Assembly of ribosomal RNA and ribosome subunits.</p> Signup and view all the answers

    What characterizes the structure of chromatin?

    <p>It is tightly packed DNA associated with protein complexes.</p> Signup and view all the answers

    How does the outer membrane of the nuclear envelope relate to the endoplasmic reticulum?

    <p>The outer membrane is continuous with the rough endoplasmic reticulum.</p> Signup and view all the answers

    What happens to RNA products after transcription in the nucleus?

    <p>They are transported out of the nucleus through nuclear pores.</p> Signup and view all the answers

    Which statement about the mechanical support provided by the nuclear envelope's inner membrane is accurate?

    <p>It contains proteins that anchor chromatin and offer structural support.</p> Signup and view all the answers

    What is the purpose of the poly(A) tail in eukaryotic mRNA?

    <p>It assists in the binding of mRNA to ribosomes during translation.</p> Signup and view all the answers

    What is primarily responsible for regulating the transcriptional state of different cell types?

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

    Which type of transcription factor binds specifically to regulatory sites of particular genes?

    <p>Sequence-specific transcription factors</p> Signup and view all the answers

    Which domain of a transcription factor is responsible for its interaction with other proteins?

    <p>Activation domain</p> Signup and view all the answers

    What type of binding do transcription factors use to attach to DNA?

    <p>Van der Waals forces, ionic bonds, hydrogen bonds</p> Signup and view all the answers

    Which transcription factor structure is characterized by the presence of zinc ions?

    <p>Zinc fingers</p> Signup and view all the answers

    How do activators function in relation to transcription?

    <p>They stimulate transcription</p> Signup and view all the answers

    Which of the following best describes the regulation of gene expression by transcription factors?

    <p>Transcription factors can regulate multiple genes, and multiple factors can regulate a single gene</p> Signup and view all the answers

    What is the role of repressors in transcriptional regulation?

    <p>They inhibit the transcription of specific genes</p> Signup and view all the answers

    What is the primary role of nuclear pore complexes (NPCs) in cellular function?

    <p>Transporting RNAs and proteins across the nuclear envelope</p> Signup and view all the answers

    Which feature of nucleoporins is crucial for their function in the nuclear pore complex?

    <p>The presence of FG domains which create a hydrophobic mesh</p> Signup and view all the answers

    What specific signal indicates that a protein should be transported into the nucleus?

    <p>Nuclear Localization Signal (NLS)</p> Signup and view all the answers

    What distinguishes the export of mRNA from the export of proteins across the nuclear envelope?

    <p>Only mature mRNAs are recognized for export</p> Signup and view all the answers

    Which of the following pairs of receptors is involved in the transport of proteins across the nuclear envelope?

    <p>Exportins and RanGTP</p> Signup and view all the answers

    What is the diameter of the central channel within the nuclear pore complex?

    <p>20-40 nm</p> Signup and view all the answers

    How do importins interact with proteins meant for nuclear transport?

    <p>They recognize specific amino acid sequences known as NLS</p> Signup and view all the answers

    What is the structural symmetry characteristic of nuclear pore complexes?

    <p>Octagonal symmetry</p> Signup and view all the answers

    Which of the following accurately describes the relationship between the nuclear genetic content and cellular function?

    <p>All cells contain the same genetic information but have different functions</p> Signup and view all the answers

    What is a common characteristic of Helix-Loop-Helix (HLH) transcription factors?

    <p>HLH transcription factors always exist in dimers.</p> Signup and view all the answers

    Which amino acids are primarily responsible for the DNA binding capabilities of Helix-Loop-Helix transcription factors?

    <p>Lysine, arginine, and histidine.</p> Signup and view all the answers

    What is the role of enhancers in relation to transcription factors?

    <p>Enhancers increase the frequency of transcription by mediating TF interactions.</p> Signup and view all the answers

    Which statement accurately describes the function of co-activators in transcription control?

    <p>Co-activators enhance transcription by modifying chromatin structure.</p> Signup and view all the answers

    What distinguishes proximal promoter elements from distal promoter elements?

    <p>Proximal promoters typically contain fixed consensus sequences.</p> Signup and view all the answers

    What is a characteristic function of transcription factors (TFs)?

    <p>TFs bind to specific DNA sequences to regulate transcription.</p> Signup and view all the answers

    What defines the Leucine Zipper motif in transcription factors?

    <p>It incorporates leucine every third amino acid along the α-helices.</p> Signup and view all the answers

    Which of the following correctly identifies the role of response elements?

    <p>They are DNA sites where transcription factors bind to regulate transcription.</p> Signup and view all the answers

    How do distal promoter elements affect gene expression?

    <p>They may include enhancers that mediate responses based on cellular conditions.</p> Signup and view all the answers

    What is a key feature distinguishing basic Helix-Loop-Helix (bHLH) from Leucine Zipper transcription factors?

    <p>bHLH factors often have basic amino acids at their helices for DNA recognition.</p> Signup and view all the answers

    What is the function of the nucleolus?

    <p>Site of ribosomal RNA synthesis</p> Signup and view all the answers

    Which protein complex is crucial for nuclear import of proteins?

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

    Which adaptation of chromatin affects accessibility for transcription?

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

    What role do nucleoporins play in nuclear trafficking?

    <p>Constitute the nuclear pore complex</p> Signup and view all the answers

    Which factor is most likely to inhibit gene expression by modifying chromatin structure?

    <p>Histone deacetylases</p> Signup and view all the answers

    In the context of gene expression, what does a polysome refer to?

    <p>Multiple ribosomes translating a single mRNA</p> Signup and view all the answers

    What is the significance of the 5’-Cap in mRNA?

    <p>Regulation of mRNA degradation</p> Signup and view all the answers

    What role do sequence-specific transcription factors play in gene regulation?

    <p>They bind to regulatory sites and can act as activators or repressors.</p> Signup and view all the answers

    Which domain is directly responsible for interaction with other proteins in transcription factors?

    <p>Activation domain</p> Signup and view all the answers

    What type of interaction is primarily involved in the binding of DNA-binding motifs to DNA?

    <p>Ionic bonds and hydrogen bonds</p> Signup and view all the answers

    Which structural feature of zinc fingers allows them to interact with DNA?

    <p>Zinc ion coordination with cysteines and histidines</p> Signup and view all the answers

    What is a characteristic of the transcription factors’ regulatory capabilities?

    <p>Each gene can be regulated by multiple transcription factors.</p> Signup and view all the answers

    Why is the transcriptional state of cells not considered fixed?

    <p>It varies under different cellular conditions and influences.</p> Signup and view all the answers

    What structural characteristic allows transcription factors to form dimers?

    <p>Heterodimerization potential</p> Signup and view all the answers

    Which transcription factor type is known for stimulating transcription?

    <p>Sequence-specific transcription factors</p> Signup and view all the answers

    What role do general transcription factors play in the transcription process?

    <p>They associate with RNA polymerase at core promoter sites.</p> Signup and view all the answers

    How do transcription factors vary across different cell types?

    <p>Cell types express unique sets of transcription factors based on their specific needs.</p> Signup and view all the answers

    What mechanism do coactivators use to alter nucleosome structure for transcriptional activation?

    <p>By ATP hydrolysis leading to histone displacement</p> Signup and view all the answers

    Which action is NOT performed by histone acetyltransferases (HATs)?

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

    Which of the following alterations may result from chromatin remodeling complexes?

    <p>Increased accessibility of the promoter region</p> Signup and view all the answers

    What is a characteristic effect of coactivators during transcriptional regulation?

    <p>Interact with histones to enhance chromatin relaxation</p> Signup and view all the answers

    Which of the following statements about the role of coactivators is correct?

    <p>They include factors like the Mediator complex interacting with RNA Pol II.</p> Signup and view all the answers

    What mechanism do Nxf1 and Nxt1 utilize for mRNA export?

    <p>They transport mRNA as ribonucleoproteins (RNPs).</p> Signup and view all the answers

    What structural feature distinguishes Helix-Loop-Helix (HLH) transcription factors?

    <p>Two α-helical segments separated by a loop</p> Signup and view all the answers

    What is the primary function of the FG domain in nucleoporins?

    <p>To form a hydrophobic mesh that regulates diffusion.</p> Signup and view all the answers

    Which proteins are necessary for transporting proteins with a Nuclear Localization Signal (NLS)?

    <p>Importins α/β</p> Signup and view all the answers

    Which amino acids are specifically mentioned as basic residues that play a role in DNA binding?

    <p>Lysine, Arginine, and Histidine</p> Signup and view all the answers

    What is a primary function of transcription factors (TFs) when bound to response elements?

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

    What characteristic is unique to the structure of the nuclear pore complex (NPC)?

    <p>It possesses octagonal (8-sided) symmetry.</p> Signup and view all the answers

    What distinguishes a Nuclear Export Signal (NES) from a Nuclear Localization Signal (NLS)?

    <p>NLS is recognized by importins exclusively.</p> Signup and view all the answers

    Which component is commonly found in proximal promoters that serves as a consensus sequence for general transcription factors?

    <p>CAAT box</p> Signup and view all the answers

    What defines enhancer sites in gene regulation?

    <p>They can be positioned up to 50,000 base pairs upstream from the transcription start site.</p> Signup and view all the answers

    Why are only mature mRNAs exported from the nucleus?

    <p>Only fully processed mRNAs are recognized by transport receptors.</p> Signup and view all the answers

    What role do transport receptors like importins and exportins play in nuclear trafficking?

    <p>They facilitate the movement of RNAs and proteins across the nuclear envelope.</p> Signup and view all the answers

    What function do co-activators serve in transcription?

    <p>Increase gene expression without binding directly to DNA</p> Signup and view all the answers

    How do nucleoporins contribute to the functionality of the nuclear pore complex?

    <p>They form the transport channel and regulate macromolecule movement.</p> Signup and view all the answers

    What characteristic is shared by both basic Helix-Loop-Helix (bHLH) and basic Leucine Zipper (bZIP) transcription factors?

    <p>They both contain regions that bind to specific nucleotide sequences in DNA.</p> Signup and view all the answers

    What type of dimer is formed by Helix-Loop-Helix (HLH) transcription factors?

    <p>Both homo- and hetero-dimers</p> Signup and view all the answers

    What indication do proteins have for their transport to the nucleus?

    <p>A Nuclear Localization Signal (NLS).</p> Signup and view all the answers

    How do distal promoter elements typically differ from proximal promoters?

    <p>They may include enhancers or silencers that modulate gene expression.</p> Signup and view all the answers

    Which statement accurately describes how transcription factors interact with DNA?

    <p>Transcription factors recognize and bind to specific DNA sequences.</p> Signup and view all the answers

    Study Notes

    HSS2305: Molecular Mechanisms of Disease

    • The course covers molecular mechanisms of disease.
    • Lecture 11 focused on the control of gene expression.

    Lecture Outline

    • Announcements
    • Sample questions
    • Control of gene expression
    • Midterm and assignment reminders
    • Important topics covered in this semester included rare disease assignments, topics emailed out, deadlines, reminders about plagiarism, reference managers, and APA formatting.

    Lecture 10 Review Questions

    • Question 1: The primary transcript (mRNA precursor) contains:

      • Poly(A) tail
      • Introns
      • 5'-Cap
      • Amino acids

    • Question 2: What is the machinery that removes introns?

      • Spliceosome
      • Proteasome
      • Autophagosome
      • Ribosome

    • Question 3: U6 is an example of what?

      • Carbohydrate
      • Protein enzyme
      • Ribozyme
      • Inorganic catalyst

    • Question 4: A polysome is:

      • A single ribosome bound to a single mRNA
      • A transcriptional machine
      • Multiple ribosomes bound to a single mRNA
      • A single ribosome bound to multiple mRNAs

    Nucleus

    • Site of transcription
    • Tightly packed DNA and protein complex (chromatin)
    • Nuclear envelope
    • Nuclear pores
    • Nucleolus
    • Proteins for transcription transported into nucleus
    • RNA products transported out of nucleus

    Nuclear Envelope

    • Double membrane
    • Outer membrane continuous with rough endoplasmic reticulum (RER)
    • Inner membrane with lamina for support and chromatin anchoring
    • ~60 transmembrane proteins

    • 1000 nuclear pore complexes

    Nuclear Pore Complex (NPC)

    • Composed of nucleoporins (~30 different)
    • Gateway for RNAs and proteins
    • Octagonal symmetry
    • Central channel ~20-40nm in diameter
    • Nucleoporins line the channel with FG domains (phenylalanine-glycine repeats)
    • Hydrophobic mesh blocks free diffusion of large macromolecules

    Nuclear Trafficking: Transport of Proteins Across Nuclear Envelope

    • Proteins with specific amino acid sequences (NLS) are transported.
    • Nuclear export signal (NES)
    • Transport receptors (importins and exportins)
    • Heterodimeric receptor (importin α/β) binds NLS
    • Exportins and RanGTP
    • Proteins transported across the nuclear envelope via nuclear pores

    Nuclear Trafficking: Transport of mRNA Across Nuclear Envelope

    • mRNAs transported as ribonucleoproteins (RNPs)
    • Associated proteins interact with FG domains of nucleoporins
    • Only mature mRNAs (fully processed) are exported
    • Nxf1 and Nxt1-dependent
    • Not exportin or RanGTP dependent

    Genetic Blueprint and Transcriptional State

    • Every cell in an organism has the same DNA, but not every cell looks or acts the same.
    • Gene expression and the transcriptional state determine cell types (e.g. myofibers vs. skin fibroblasts)
    • Cell type-specific gene expression is tightly controlled and varies between cell types and conditions.

    Overview of Gene Regulation

    • There are 4 levels of gene regulation:
      • Transcriptional
      • Processing
      • Translational
      • Post-translational
    • These processes can be regulated independently or in conjunction to achieve a wide range of cellular outcomes.

    2 - mRNA Processing Control

    • RNA transcripts undergo processing.
    • Only processed mRNA can exit the nucleus.
    • Splicing via action of snRNPs in the nucleus.
    • Different splice sites can be repressed or activated.
    • SR proteins activate splice sites (e.g., exon/intron splicing enhancers). hnRNPs repress.

    3 - Translational control

    • Initiation and progression of translation.
    • Global regulation affects all mRNAs (phosphorylation of initiation factors like eIF2 inhibits translation).
    • Specific regulation affects the translation of specific mRNAs (e.g. Ferritin) with stem loops in the mRNA's 5' and 3' UTR and other regulatory factors like microRNAs (miRNAs)
    • mRNA localization to specific cellular sites.
    • mRNA stability within the cytoplasm.

    4 - Post-Translational Control

    • Protein degradation (proteasomes)
    • Proteasomes degrade proteins within the nucleus and cytosol.
    • Ubiquitin ligases (e1, e2, e3) attach ubiquitin to proteins to be degraded.
    • Polyubiquinated proteins bind to the proteasome.
    • Proteasome unfolds target proteins and degrades them to smaller peptides and amino acids.

    RNA interference (RNAi)

    • Some types of RNA inhibit gene expression via destruction of specific mRNA molecules (small interfering RNAs (siRNAs) in plants and microRNAs (miRNAs) in mammals)

    MicroRNAs (miRNAs)

    • Important regulators in biological processes.
    • Abnormalities in miRNA can play a major role in the development of diseases.
    • miRNAs bind to sites in the 3' UTR of mRNAs and have multiple target mRNAs

    siRNAs

    • Unknown if naturally occurring in mammals but found in plants.
    • Clinical applications using designed siRNAs to silence disease-related genes.
    • Strategies being developed for diseases like HIV, Hepatitis, and Cancer.

    siRNAs - Clinical Applications

    • Techniques are promising, but delivery complications and immune responses can be obstacles.

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    HSS2305A - Spring 2022 - Lecture Notes PDF

    Description

    This quiz focuses on Lecture 11 of the HSS2305 course, which discusses the control of gene expression. Key concepts such as mRNA processing, spliceosomes, and polysomes are covered. Test your understanding of molecular mechanisms involved in gene expression.

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