Gene Transcription and Regulation Quiz
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Questions and Answers

What is the role of the TATA binding protein (TBP)?

  • It modifies chromatin structure to make DNA accessible for transcription.
  • It recruits RNA polymerase II to the promoter.
  • It binds to the TATA box in the core promoter, causing DNA bending and unwinding. (correct)
  • It binds to the TATA box in the regulatory promoter.

    • Which of the following is NOT a characteristic of eukaryotic RNA polymerases?

  • They can transcribe different genes.
  • They require accessory proteins for transcription initiation.
  • They can recognize DNA sequences on their own. (correct)
  • They are multisubunit enzymes.

    • What component of the basal transcription apparatus directly interacts with the TATA box in the core promoter?

  • RNA polymerase II
  • TFIID (correct)
  • Mediator complex
  • General transcription factors

    • What is the primary function of regulatory proteins in transcription initiation?

    <p>To modify chromatin structure and make DNA accessible. (D)</p> Signup and view all the answers

    What is the significance of the promoter region in gene transcription?

    <p>It provides information about the frequency and level of transcription. (B)</p> Signup and view all the answers

    What is the function of the promoter region in a gene?

    <p>It binds to proteins that initiate transcription. (C)</p> Signup and view all the answers

    What is the difference between an intron and an exon?

    <p>Introns are removed from the RNA transcript during splicing, while exons are retained. (C)</p> Signup and view all the answers

    What is the relationship between genes and proteins?

    <p>One gene always encodes for one protein. (D)</p> Signup and view all the answers

    Where does transcription occur in eukaryotic cells?

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

    What is the process of gene expression?

    <p>All of the above. (D)</p> Signup and view all the answers

    What is the function of the termination region in a gene?

    <p>It signals the end of transcription. (D)</p> Signup and view all the answers

    What is the significance of regulatory regions in gene expression?

    <p>They can increase or decrease the rate of gene expression. (C)</p> Signup and view all the answers

    What does the term "albinism" refer to?

    <p>A genetic disorder resulting in the absence of melanin pigment. (A), A genetic disorder resulting in the absence of melanin pigment. (B)</p> Signup and view all the answers

    Which of the following components is NOT part of the transcription machinery?

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

    What is the role of the regulatory promoter in transcription?

    <p>Regulates the speed of transcription initiation. (D)</p> Signup and view all the answers

    Enhancers and silencers are regulatory elements that can be located ____ from the gene they regulate.

    <p>very far upstream or downstream of the gene (B)</p> Signup and view all the answers

    What is the function of the 'open complex' in transcription?

    <p>It allows the DNA to unwind and expose the template strand for RNA polymerase. (A)</p> Signup and view all the answers

    Which of the following statements about transcription is TRUE?

    <p>Transcription uses a DNA template to produce RNA. (D)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of alternative splicing?

    <p>It is a process that occurs in the cytoplasm. (D)</p> Signup and view all the answers

    What happens to the intron after it is removed during splicing?

    <p>It is degraded. (D)</p> Signup and view all the answers

    What is the role of the 5' splice site in RNA splicing?

    <p>It is the site where the intron is cleaved. (A)</p> Signup and view all the answers

    What is the primary function of the nuclear export receptor?

    <p>It facilitates the movement of mRNA from the nucleus to the cytoplasm. (C)</p> Signup and view all the answers

    Which of the following is NOT an example of a disease that can arise from a mutation in a splice site?

    <p>Alzheimer's disease (B)</p> Signup and view all the answers

    What is the approximate length of the RNA transcript when RNA polymerase II detaches from the promoter region?

    <p>30 nucleotides (D)</p> Signup and view all the answers

    Which of the following statements accurately describes the movement of DNA during the elongation phase of transcription?

    <p>DNA moves through a channel in RNA polymerase in a 3' to 5' direction. (B)</p> Signup and view all the answers

    What is the role of the "protein wall" in RNA polymerase during elongation?

    <p>It forces DNA to make a sharp turn at the active site. (B)</p> Signup and view all the answers

    How does the process of transcription termination differ from the process of DNA replication?

    <p>Transcription termination involves the degradation of a portion of the RNA transcript, while DNA replication does not. (B)</p> Signup and view all the answers

    What is the primary function of Rat1 in transcription termination?

    <p>It degrades the extra RNA transcript in the 5' to 3' direction. (B)</p> Signup and view all the answers

    What is the role of RNA in the context of gene expression?

    <p>RNA acts as a messenger, carrying genetic information from DNA to ribosomes for protein synthesis. (C)</p> Signup and view all the answers

    What is the primary function of genes? Explain the difference between coding and regulatory regions.

    <p>Genes are responsible for encoding and regulating essential cellular functions. (D)</p> Signup and view all the answers

    What is the major difference between eukaryotic genes and prokaryotic genes in terms of their structure?

    <p>Eukaryotic genes are significantly larger and more complex than prokaryotic genes, with introns and exons. (C)</p> Signup and view all the answers

    What is the process by which genetic information is transferred from DNA to RNA called?

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

    What are the roles of promoters and enhancers/silencers in the regulation of gene expression?

    <p>Promoters initiate transcription, while enhancers/silencers regulate the rate of transcription. (A)</p> Signup and view all the answers

    What is the main difference between RNA polymerase I, II, and III in eukaryotic cells?

    <p>RNA polymerase I transcribes ribosomal RNA, RNA polymerase II transcribes messenger RNA, and RNA polymerase III transcribes transfer RNA. (C)</p> Signup and view all the answers

    What is the significance of alternative splicing in gene expression?

    <p>Alternative splicing increases the number of different protein products that can be produced from a single gene. (D)</p> Signup and view all the answers

    What is the importance of the discovery of ribozymes in the understanding of the evolution of life?

    <p>It challenged the prevailing belief that only proteins could act as catalysts and suggested that RNA could have played a key role in the origin of life. (B)</p> Signup and view all the answers

    Flashcards

    Eukaryotic Genes

    Segments of DNA that encode RNA or proteins in eukaryotes.

    RNA Classes

    Different types of RNA molecules, including mRNA, tRNA, rRNA, and ribozymes.

    Transcription

    The process of synthesizing RNA from a DNA template.

    Promoters

    Regions of DNA that initiate transcription of a gene.

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    Enhancers/Silencers

    DNA sequences that increase or decrease gene transcription.

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    RNA Processing

    Modifications made to RNA after transcription, including capping and splicing.

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    Alternative Splicing

    A process that allows a single gene to produce multiple RNA variants by splicing differently.

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    Intergenic Regions

    Non-coding DNA between genes that does not encode for proteins.

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    Transcription termination

    The process where RNA polymerase releases RNA at the end of the transcription unit.

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    Key players in transcription

    Factors involved in transcription include RNA polymerase, transcription factors, and mediator complex.

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    RNA polymerase II

    An enzyme that transcribes protein-coding genes in eukaryotes.

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    TATA box

    A specific sequence in the core promoter recognized by TFIID for transcription initiation.

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    Basal transcription apparatus

    A complex formed by RNA pol II, general transcription factors, and a mediator for initiating transcription.

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    Regulatory Regions

    Nucleotide sequences that regulate gene expression by increasing or decreasing it, often located far from the gene.

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    Termination Region

    The region that signifies the end of transcription in gene expression.

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    Introns

    Noncoding regions of RNA that are removed during splicing before translation into protein.

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    Exons

    Coding regions of a gene that remain in the final mRNA and are translated into proteins.

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    Gene Expression

    The process of producing RNA and proteins from a gene, occurring in the nucleus.

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    One Gene One Polypeptide

    The modified hypothesis that each gene encodes one polypeptide, though some genes produce non-protein RNA.

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    Phenotype Discovery

    The realization that major physical differences in organisms are due to differences in specific proteins.

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    Regulatory Promoter

    A DNA region that binds transcription factors to control transcription speed.

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    Transcription Factors (TFs)

    Proteins that bind to promoters and enhancers to regulate gene expression.

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    Open Complex

    The formation when RNA polymerase unwinds DNA and separates strands.

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    Mediator Complex

    A group of proteins that help regulate transcription by connecting DNA and RNA polymerase.

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    Abortive initiation

    A process where RNA pol II synthesizes a short RNA strand before elongation begins.

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    Elongation in transcription

    RNA pol II moves downstream, adding nucleotides to the growing RNA strand during transcription.

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    RNA-DNA hybrid

    A complex formed when the RNA strand remains bound to the DNA during transcription elongation.

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    Termination of transcription

    The process where RNA pol II stops RNA synthesis and releases the RNA molecule, often influenced by Rat1 enzyme.

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    Role of Rat1

    An enzyme that degrades excess RNA after transcription, signaling the termination of transcription by reaching RNA pol II.

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    5' Splice Site

    The region on an intron at the 5' end that is cleaved during splicing.

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    Lariat Formation

    The structure formed when a branch point A attaches to the 5' splice site, looping the intron.

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    mRNA Nuclear Export

    The process of transporting mature mRNA from the nucleus to the cytoplasm.

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    Haemophilia and Splicing

    A disease caused by intronic mutations in factor IX affecting splicing process, leading to bleeding disorders.

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    Study Notes

    Gene Expression: From DNA to RNA

    • Gene expression is the process of producing RNA and proteins from a gene
    • DNA stores and transmits genetic information
    • Proteins catalyse essential chemical reactions
    • RNA has a catalytic function, ribozymes, in cutting/binding sequences and replication
    • RNA's role has shifted from catalyst to primarily information storage and transfer, but different types of RNA play diverse roles

    Intended Learning Outcomes (ILOs)

    • Describe the structure of eukaryotic genes
    • List and compare the main RNA classes and RNA polymerases
    • Outline the stages of eukaryotic transcription
    • Explain the function of promoters and enhancers/silencers
    • Define RNA processing and the concept of alternative splicing

    The Flow of Information

    • DNA synthesis (DNA replication)
    • RNA synthesis (transcription)
    • Protein synthesis (translation)
    • This is the central dogma of molecular biology

    The Transcription Unit

    • Regions of a gene include a promoter, RNA coding region and a terminator.
    • The first transcribed nucleotide is numbered +1.
    • Promoter region contains information on frequency/level of transcription.

    The Basis of Transcription

    • Transcription copies DNA to RNA
    • All three major RNA classes (mRNA, tRNA, rRNA) are involved in protein synthesis
    • Gene expression in eukaryotes is a multistage and compartmentalised process

    Three Main RNA Classes

    • Messenger RNA (mRNA)
    • Ribosomal RNA (rRNA)
    • Transfer RNA (tRNA)

    The Toolkit of Transcription

    • Starting DNA template
    • Transcription unit (promoter, RNA sequences)
    • Machinery for transcription (enzymes, proteins)
    • Transcription starts in a bubble and occurs in the 5' to 3' direction.
    • The template strand is used to produce the RNA transcript.

    RNA Polymerase - An Enzyme

    • RNA polymerase synthesizes RNA using a DNA template.
    • Transcription proceeds from 5' to 3' on the template strand (3' to 5' on the non-template strand).

    The Transcription "Christmas Tree"

    • The image displays a complex molecular structure in transcription.

    Transcription Unit

    • Promoter, RNA coding region, and terminator regions make up a transcription unit.
    • Transcription starts at +1 nucleotide. The template strand and non-template strand are identified.

    Stages of Transcription

    • Initiation involves recognizing and binding to the promoter.
    • DNA unwinds
    • Elongation involves polymerase moving along the template strand synthesizing RNA.
    • Termination involves polymerase dissociating at the end of the transcription unit.

    Key Players in Transcription

    • Chromatin structure modification (by regulatory proteins near the promoter) makes DNA accessible.
    • RNA polymerase is an enzyme for transcription
    • Transcription factors, mediator complex, and cis DNA elements (promoters, regulatory DNAs) are involved.

    Regulation of Transcription Initiation (i and ii)

    • Eukaryotic RNA polymerase cannot recognize DNA sequence on its own; regulatory proteins are required.
    • Regulatory proteins bind to DNA to change chromatin structure
    • RNA polymerase II + general transcription factors + mediator = basal apparatus
    • Regulatory promoters (up/down stream) bind transcription factors, allowing enhancers/silencers to regulate transcription.
    • Many proteins are involved in the entire transcription machine
    • DNA/RNA pol II conformational change exposes single-strand DNA and unwinds a short stretch.

    Different Types of RNA Polymerases

    • Three main RNA polymerases in eukaryotes: I, II, and III
    • Different polymerases bind to different promoters/transcribe different genes.
    • RNA polymerase II transcribes genes encoding proteins.

    RNA Polymerase II Promoters

    • Core promoter and a regulatory promoter.
    • Special sequences such as: TATA box, BRE, INR, DPE etc., are recognized by TFs
    • Transcription factors bind to these initiation sequences facilitating RNA polymerase positioning to start point/transcription.

    The Intervening Sequences: Introns

    • Introns are non-coding regions within genes, absent in mature mRNA.
    • Introns are typically present in eukaryotes
    • Intron size/number correlates with complexity of the organism.

    The Structure of mRNA

    • 5' cap (modified guanine nucleotide)
    • Coding regions / Exons
    • Poly(A) tail (adenine nucleotides)
    • Modification after transcription, e.g., 5' cap, poly(A) tail, splicing
    • mRNA stability / translation regulation

    Alternative Splicing

    • The same DNA molecule can be spliced in various ways, producing different mRNA products and proteins.

    RNA Transport from Nucleus to Cytoplasm

    • mRNA processing, maturation, and assembly with export factors occurs.
    • Proteins escort mRNA from nucleus for translation in cytoplasm

    Nuclear Export of mRNA

    • mRNA export is a complex process requiring multiple regulatory proteins.

    Splicing

    • The process that removes introns before mRNA translation.
    • Introns are removed and exons joined.
    • Spliceosome (RNA and proteins) facilitates the splicing process.
    • Splicing is a two-step process.

    The Royal Disease (Haemophilia)

    • An intronic mutation in factor IX leading to incorrect splicing can cause haemophilia.

    DNA Replication Analogy (with transcription) and differences

    • Analogy with DNA replication involves use of DNA template to generate a copy.
    • Differences exist in the enzymes, substrates/products.

    Colinear or not colinear?

    • Colinearity suggests a DNA sequence proportional to a protein's amino acid sequence.
    • Evidence from studies contradict this, implying non-colinearity in some cases.

    Abortive Initiation

    • Likely to be a rate-limiting control on gene activation
    • After synthesis of a ~9-12nt long strand, elongation begins.
    • When the transcript is around 30 nt long, RNA polymerase II leaves the promoter region.

    Termination

    • RNA Pol II lacks specific termination sequences and may continue after stopping transcription.
    • mRNA is degraded (e.g., by Rat1) once it forms after reaching a sequence.

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    Description

    Test your knowledge on the processes of gene transcription and the regulatory mechanisms involved. This quiz covers topics such as the TATA binding protein, RNA polymerases, gene expression, and the role of different regulatory elements. Perfect for students studying molecular biology or genetics.

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