Molecular Mechanisms of Disease - HSS2305
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Questions and Answers

What role does the proximal promoter play in gene transcription?

  • It enhances transcriptional activity and influences initiation frequency. (correct)
  • It functions independently from transcription factors.
  • It solely initiates transcription by itself.
  • It decreases the binding efficiency of RNA polymerase II.

    • Which of the following elements is associated with recruiting transcription factors to the promoter?

  • Enhancer region
  • CRE
  • HRE
  • CAAT Box (correct)

    • Which statement about enhancers is correct?

  • They solely initiate transcription without the involvement of transcription factors.
  • Enhancers have a fixed length of 50 base pairs.
  • Enhancers can only function within 100 base pairs of the promoter.
  • They can operate at distances up to 50,000 base pairs upstream of the start site. (correct)

    • What is the function of the GC Box within the proximal promoter?

    <p>It serves as a binding site for transcription factors like SP1. (D)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of Specific Response Elements?

    <p>They bind only to transcription factors. (D)</p> Signup and view all the answers

    What is the role of the Pre-Initiation Complex (PIC) in eukaryotic transcription?

    <p>To facilitate the transcription of protein-coding genes. (D)</p> Signup and view all the answers

    Which of the following proteins first binds to the TATA box during the formation of the PIC?

    <p>TFIID (B)</p> Signup and view all the answers

    What is the primary function of TFIIH within the PIC?

    <p>Phosphorylates RNA polymerase II. (B)</p> Signup and view all the answers

    Which transcription factor stabilizes the Pre-Initiation Complex?

    <p>TFIIA (A)</p> Signup and view all the answers

    What defines transcription initiation in eukaryotes?

    <p>The formation of a phosphodiester bond between the first two nucleotides. (D)</p> Signup and view all the answers

    What is the primary function of RNA polymerase II during transcription?

    <p>To synthesize RNA from a DNA template (C)</p> Signup and view all the answers

    Which strand of DNA has a sequence identical to the newly synthesized RNA strand?

    <p>Sense strand (A)</p> Signup and view all the answers

    What is the end product of transcription?

    <p>Messenger RNA (A)</p> Signup and view all the answers

    During translation, which molecules are primarily involved in the synthesis of proteins?

    <p>mRNA, ribosomal RNA, and tRNAs (A)</p> Signup and view all the answers

    What role does TFIIH play in RNA polymerase II activity?

    <p>It triggers the uncoupling of RNA Pol II from the pre-initiation complex. (B)</p> Signup and view all the answers

    At what site does RNA polymerase initiate transcription?

    <p>At the transcription start site (B)</p> Signup and view all the answers

    What is the function of TFIID in the transcription process?

    <p>It remains bound to the TATA box to initiate the formation of a new pre-initiation complex. (A)</p> Signup and view all the answers

    What structural characteristic is unique to the carboxyl-terminal domain (CTD) of RNA polymerase II?

    <p>It consists of a 7 amino acid repeating sequence. (D)</p> Signup and view all the answers

    How does the phosphorylation of Serine-5 affect the carboxyl-terminal domain of RNA Polymerase II?

    <p>It enhances the hydrophilicity of the CTD. (C)</p> Signup and view all the answers

    What happens to the transcription factors associated with the pre-initiation complex during elongation?

    <p>They dissociate from RNA polymerase II. (A)</p> Signup and view all the answers

    What is the initial starting material required for transcription?

    <p>DNA (A)</p> Signup and view all the answers

    What is the end product of transcription after processing?

    <p>Messenger RNA (mRNA) (B)</p> Signup and view all the answers

    Which enzyme is responsible for initiating transcription in eukaryotes?

    <p>RNA polymerase II (A)</p> Signup and view all the answers

    During translation, which molecules are primarily responsible for synthesizing proteins?

    <p>Ribosomal RNA (rRNA) and transfer RNA (tRNAs) (B)</p> Signup and view all the answers

    What replaces thymine (T) in the RNA strand during transcription?

    <p>Uracil (U) (C)</p> Signup and view all the answers

    What is the primary role of transcription factors in eukaryotic transcription?

    <p>They initiate transcription and regulate gene expression. (D)</p> Signup and view all the answers

    Which of the following is true about RNA polymerase in eukaryotes?

    <p>Three different RNA polymerases perform distinct functions in transcription. (D)</p> Signup and view all the answers

    Which components uniquely make up the TFIID complex?

    <p>TATA-binding protein and TBP-Associated Factors. (C)</p> Signup and view all the answers

    In what direction is RNA synthesized during transcription?

    <p>5’-to-3’ direction. (D)</p> Signup and view all the answers

    What is the function of the promoter region in transcription?

    <p>To provide a template for polymerase binding. (D)</p> Signup and view all the answers

    What does the phosphorylation of Serine-5 in the carboxyl-terminal domain (CTD) of RNA Polymerase II trigger?

    <p>Uncoupling of RNA Polymerase II from the Pre-Initiation Complex (A)</p> Signup and view all the answers

    Which transcription factors remain associated with the TATA box during the transcription process?

    <p>TFIID (D)</p> Signup and view all the answers

    What is the characteristic sequence of the phosphorylated carboxyl-terminal domain of RNA Polymerase II?

    <p>Tyr-Ser*-Pro-Thr-Ser*-Pro-Ser (C)</p> Signup and view all the answers

    What structural characteristic is associated with the RNA Polymerase II during transcription elongation?

    <p>It has a repeating domain that is polar. (C)</p> Signup and view all the answers

    Which factor is responsible for phosphorylating Serine-5 in RNA Polymerase II's CTD?

    <p>TFIIH (D)</p> Signup and view all the answers

    What is the main function of the Pre-Initiation Complex (PIC) in eukaryotic transcription?

    <p>It facilitates the binding of RNA polymerase II and opens the DNA. (C)</p> Signup and view all the answers

    Which protein complex first interacts with the TATA box during the formation of the PIC?

    <p>TFIID (D)</p> Signup and view all the answers

    What is the function of TFIIH within the Pre-Initiation Complex?

    <p>It phosphorylates the RNA polymerase II tail to promote elongation. (B)</p> Signup and view all the answers

    What occurs during the initiation phase of transcription?

    <p>The formation of a phosphodiester bond between the first two nucleotides. (A)</p> Signup and view all the answers

    Which factor is responsible for providing a specific binding site for RNA polymerase II within the PIC?

    <p>TFIIB (C)</p> Signup and view all the answers

    Flashcards

    Gene Transcription

    The process of creating a complementary RNA molecule from a DNA template in the nucleus.

    RNA Polymerase

    An enzyme that binds to DNA, starts transcription at a specific site (promoter), and synthesizes RNA.

    mRNA (messenger RNA)

    The processed RNA molecule that carries the genetic code from DNA to the ribosomes for protein synthesis.

    Transcription factors

    Proteins that help RNA polymerase bind to the DNA and initiate transcription.

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    Central Dogma of Molecular Biology

    The fundamental concept in molecular biology stating that information flows from DNA to RNA to protein.

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    Proximal Promoter

    A DNA region near the core promoter that helps regulate transcription initiation frequency. It enhances the core promoter's activity and influences how often transcription starts.

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    CAAT Box

    A DNA sequence within the proximal promoter that helps recruit specific transcription factors, boosting RNA polymerase II binding efficiency.

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    GC Box

    A GC-rich DNA sequence in the proximal promoter that binds transcription factors like SP1, activating a wide range of genes, especially housekeeping genes.

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    Specific Response Elements

    DNA sequences within the proximal promoter that respond to specific hormones, growth factors, or signaling molecules, allowing for gene regulation in response to external cues.

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    Enhancer Region

    A DNA region located up to 50,000 base pairs away from the start site, influencing gene transcription by interacting with the promoter region.

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    What is the PIC?

    The Pre-Initiation Complex (PIC) is a group of around 100 proteins that are essential for the transcription of protein-coding genes in eukaryotic cells. It helps position RNA polymerase II at the right spot on the DNA, denatures the DNA, and sets it up for the transcription process.

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    What does TFIID do?

    TFIID is a key component of the PIC. It binds to the TATA box, a DNA sequence located upstream of the transcription start site. This binding is crucial for positioning the PIC correctly on the DNA.

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    What does TFIIB do?

    TFIIB works in the PIC by providing a specific binding site for RNA polymerase II, the enzyme that builds the RNA molecule from DNA. This helps to ensure that RNA polymerase II is correctly positioned and ready to begin transcription.

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    What is TFIIH's role?

    TFIIH is another important protein in the PIC. It has three main jobs: 1) It phosphorylates RNA polymerase II to start elongation, 2) It contains DNA helicases to unwind the DNA at the promoter start site, and 3) It helps form the transcription bubble.

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    What is the role of transcription activators?

    Transcriptional activators, also known as specific transcription factors, bind to coactivators, which then bind to the PIC. This interaction helps to regulate and control the transcription process, ensuring genes are expressed appropriately.

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    TFIIH

    A transcription factor that helps initiate transcription by phosphorylating the CTD of RNA Polymerase II. This phosphorylation triggers the uncoupling of RNA Polymerase II from the PIC, allowing it to begin transcription.

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    CTD (Carboxyl-terminal Domain)

    A repeating sequence of amino acids found at the tail of the largest subunit of RNA Polymerase II. This domain undergoes phosphorylation, which triggers the transition from initiation to elongation during transcription.

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    Phosphorylation of CTD

    The process of adding a phosphate group to specific serine residues within the CTD of RNA Polymerase II. This modification is crucial for the transition from initiation to elongation during transcription.

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    PIC (Pre-Initiation Complex)

    A complex formed at the promoter region of a gene, consisting of RNA Polymerase II and several general transcription factors (including TFIIB, TFIIE, TFIIH) that are required for initiation of transcription.

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    Elongation

    The process of RNA synthesis where RNA Polymerase II moves along the DNA template, adding nucleotides to the growing RNA chain. This phase follows initiation and continues until a termination signal is reached.

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    What is the Central Dogma?

    The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein.

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    What is Transcription?

    Transcription is the process of creating a messenger RNA (mRNA) molecule from a DNA template in the nucleus.

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    What is Translation?

    Translation is the process of synthesizing a protein using the genetic code carried by mRNA in the cytoplasm.

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    What is RNA Polymerase?

    RNA polymerase is an enzyme that binds to DNA and creates a complementary RNA strand.

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    What is the Promoter Region?

    The promoter region is a specific DNA sequence where RNA polymerase binds to initiate transcription.

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    Template Strand

    The DNA strand that is used as a template for RNA synthesis. It is read in the 3'-to-5' direction while RNA is synthesized in the 5'-to-3' direction.

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    Transcription Factors (TFs)

    Proteins that bind to DNA and help RNA polymerase initiate transcription. They regulate gene expression by controlling how often a specific gene is transcribed.

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    General Transcription Factors (GTFs)

    A group of transcription factors that are essential for RNA polymerase II to initiate transcription. They bind to the core promoter and help position RNA polymerase II correctly.

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    TFIIH's role

    TFIIH plays a crucial role in the initiation of transcription by phosphorylating the CTD of RNA Polymerase II, unwinding DNA, and forming the transcription bubble.

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    CTD phosphorylation

    The addition of a phosphate group to specific serine residues within the CTD of RNA Polymerase II, triggered by TFIIH, marks the transition from initiation to elongation.

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    How does RNA Polymerase II transition from initiation to elongation?

    Phosphorylation of the RNA Polymerase II CTD by TFIIH makes the polymerase more hydrophilic, triggering its uncoupling from the PIC and allowing it to begin elongating the RNA.

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    Study Notes

    Molecular Mechanisms of Disease

    • HSS2305 course covers molecular mechanisms of disease.
    • Course materials include diagrams, videos, and notes on lectures about gene transcription and translation.

    Eukaryotic Gene Transcription and Translation

    • Eukaryotic gene transcription and translation are complex processes.
    • Transcription involves copying DNA into mRNA.
    • Translation involves using mRNA to synthesize proteins.

    Central Dogma of Molecular Biology

    • DNA undergoes transcription to create RNA.
    • RNA undergoes translation to create proteins.
    • This sequence is the central dogma of molecular biology.
    • DNA is transcribed to RNA
    • RNA is translated into proteins

    Gene Transcription (Complex)

    • Pre-mRNA is formed with introns.
    • Exons are joined.
    • Post-transcriptional modifications occur (cap added, poly-A tail).
    • mRNA is now finished

    Protein Synthesis (DNA Transcription, Translation and Folding)

    • Protein synthesis includes DNA transcription, translation, and folding.
    • Process is involved in building proteins from DNA information

    Transcription

    • Synthesis of complementary RNA from a DNA template in the nucleus.
    • Starting material is DNA.
    • Required machinery includes RNA polymerase II and transcription factors.
    • End product is messenger RNA (mRNA) after processing.

    Translation

    • Synthesis of proteins in the cytoplasm using information encoded by mRNA.
    • Starting material is mRNA.
    • Required machinery includes ribosomal RNA (rRNA) and ribosomal proteins, transfer RNA (tRNAs).
    • End product is a polypeptide.

    Sense vs Antisense DNA Strands

    • Coding strand's sequence is identical to the newly synthesized RNA strand, except that thymine (T) in DNA is replaced by uracil (U) in RNA.
    • Template strand (antisense strand) is the one that is used to make RNA copy.

    Transcription (Both strands encode genes)

    • Both strands of DNA encode genes.
    • DNA is 3.6 x 104 base pairs long.
    • RNA transcripts are produced/formed.
    • Gene replication occurs.

    RNA Polymerase

    • Enzyme that binds to DNA.
    • Initiates transcription at a specific site (promoter region).
    • Incorporates nucleotides into a strand of RNA whose sequence is complementary to one of the DNA strands (template).
    • Prokaryotes have one RNA polymerase.
    • Eukaryotes have three slightly different RNA polymerases (I, II, and III).

    Eukaryote Transcription - RNA Polymerase

    • RNA polymerase is also known as DNA-dependent RNA polymerase.
    • RNA is synthesized in the 5′-to-3′ direction.
    • 3′ to 5′ strand in DNA is called template strand.
    • Transcription start site is at +1.
    • Enhancer sites are at -50,000 to +50,000.
    • Proximal elements are at -40 to -2007.
    • Core promoter is at -40 to +40

    Eukaryotic Transcription - Transcription Factors

    • General transcription factors assemble at the core promoter.
    • Necessary for RNA polymerase II to begin transcription.
    • Consist of TFII A, B, D, E, F, and H (TF +roman numerals II).
    • TFIID uniquely consists of TATA-binding protein (TBP) and TBP-Associated Factors (TAFs).

    Eukaryotic Transcription- Gene Promoter

    • Site on DNA to which RNA polymerase binds prior to transcription initiation.
    • Determines which strand is template (anti-sense).
    • Has specific sequences (elements) called core and proximal promoter elements.

    Eukaryotic Transcription- Core Promoter

    • Contains key elements like the TATA box.
    • Site of preinitiation complex formation.
    • Present in ~20% of eukaryotic promoters.
    • Has elements like TATA box, BRE, Inr, DPE.

    Eukaryotic Transcription- Core Promoter Elements

    • Contains initiator elements (INR), BRE, TATA box, initiator (Inr), DPE
    • Role in initiation of gene transcription by RNA polymerase II
    • Location is around the transcription start site.

    Proximal Promoter Elements

    • Includes binding sites for specific transcription factors.
    • Regulates gene expression levels and timing.
    • Important elements include CAAT box and GC box.
    • Can include hormone response elements (HREs) and cAMP response elements (CREs).

    Eukaryote Transcription – Enhancer Regions

    • Enhancer regions are long (50-1500 base pairs).
    • Function differently than promoters.
    • Can be located far from the start site (up to 50,000 base pairs).
    • Transcription factors (TFs) bind to enhancers and interact with the pre-initiation complex.

    Eukaryote Transcription - Pre-Initiation Complex (PIC)

    • Complex of approximately 100 proteins.
    • Necessary for protein-coding gene transcription in eukaryotes.
    • Positions RNA polymerase II at gene transcription start sites.
    • Denatures the DNA and positions the DNA in the RNA polymerase II.
    • Transcriptional activators (specific TFs) bind to coactivators that then bind to the PIC.

    Eukaryote Transcription- Formation of the Pre-Initiation Complex (PIC)

    • TFIID binds to the TATA box upstream Transcription start site.
    • Binding of TFIIA and TFIIB to the complex.
    • TFIIA stabilizes the complex.
    • TFIIB provides specific binding site for RNA Pol II.

    Eukaryote Transcription – Elongation

    • Extension of mRNA transcript using DNA template.
    • RNA polymerase II can incorporate ~20-50 nucleotides per second.
    • The transcription bubble area is unwound.
    • DNA-RNA hybrid stabilizes elongation complex (~ 8-9 bp).

    Eukaryote Transcription – Elongation – Carboxyl-terminal Domain (CTD)

    • Repeating 7 amino acid domain in RNA polymerase II.
    • Serine-5 phosphorylation by TFIIH triggers uncoupling of RNA pol II from PIC.
    • Promotes elongation, 5 prime capping of mRNA.
    • TFIID remains bound to TATA, initiating more PIC complexes.

    Eukaryote Transcription – Elongation – Transcription Factors

    • P-TEFb phosphorylates CTD at Ser 2
    • Recruits factors that help elongation/RNA modifications/splicing/polyadenylation.
    • Eleven-Nineteen-Lysine-rich Leukemia (ELL) protein and TFIIF weaken interactions between RNA pol II and nonspecific DNA binding sites.
    • Suppresses transient pausing of polymerase.

    Eukaryote Transcription- Termination

    • No well-defined termination sequence in eukaryotes.
    • Transcription termination often involves a polyadenylation signal sequence (PAS).
    • PAS sequence (AAUAAA) typically appears in RNA transcript upstream.
    • Ultimate mRNA length determined by processing steps including cleavage and addition of Adenosines.
    • Polyadenylation forms a poly-A tail.

    Biological Molecules – Proteins – Polar Uncharged

    • R groups are weakly acidic or basic.
    • Do not form fully charged molecules.
    • Can form H bonds with other molecules..

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    HSS2305A 2024 Lecture 8 PDF

    Description

    This quiz covers the molecular mechanisms of disease as taught in the HSS2305 course. It includes key concepts like gene transcription and translation, alongside the central dogma of molecular biology. You will test your knowledge on the processes that convert DNA into functional proteins.

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