Eukaryotic Gene Expression Quiz
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Questions and Answers

What is the primary role of RNA molecules in eukaryotic gene expression?

  • To carry genetic information from DNA to the ribosomes (correct)
  • To provide structural support to the cell
  • To replicate DNA
  • To digest cellular waste
  • Which process is crucial for the synthesis of RNA in eukaryotic cells?

  • Translation
  • Transcription (correct)
  • Replicative transcription
  • Protein folding
  • How does post-transcriptional control affect gene expression in eukaryotic cells?

  • It increases the number of chromosomes in the cell
  • It modifies RNA after synthesis, affecting the availability of mRNA for translation (correct)
  • It alters DNA structure to prevent replication
  • It blocks transcription entirely
  • What characteristic of eukaryotic DNA organization prevents tangling while allowing accessibility for gene expression?

    <p>Complex chromosomal packaging (A)</p> Signup and view all the answers

    Which types of regulatory molecules are essential for controlling transcription in eukaryotic cells?

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

    What role does TFIID play in the transcription initiation process?

    <p>It distorts local DNA structure allowing TFIIB to bind. (D)</p> Signup and view all the answers

    Which general transcription factor is responsible for exposing the template strand?

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

    What is required for RNA polymerase to be released from general transcription factors?

    <p>Phosphorylation of its polypeptide tail by TFIIH. (A)</p> Signup and view all the answers

    During transcription initiation, what happens after the formation of the transcription initiation complex?

    <p>Elongation factors load onto RNA polymerase for active transcription. (B)</p> Signup and view all the answers

    What is the significance of the energetically unfavorable reaction during transcription initiation?

    <p>It couples with ATP hydrolysis to facilitate strand separation. (B)</p> Signup and view all the answers

    What is the primary role of RNA polymerase in transcription?

    <p>It unwinds the DNA helix and catalyzes the formation of phosphodiester bonds. (D)</p> Signup and view all the answers

    Which of the following bases is found in RNA but not in DNA?

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

    Which RNA polymerase is primarily responsible for synthesizing most types of RNA?

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

    What is the function of the TATA box in transcription?

    <p>It is a promoter region that facilitates the binding of transcription factors and RNA polymerase. (C)</p> Signup and view all the answers

    How do ribose and deoxyribose differ?

    <p>Ribose contains one more oxygen atom than deoxyribose. (A)</p> Signup and view all the answers

    What role do transcription factors play in the initiation of transcription?

    <p>They assemble on the promoter to orient RNA polymerase and initiate transcription. (B)</p> Signup and view all the answers

    What is a key difference between the structure of RNA and DNA?

    <p>RNA contains uracil, whereas DNA contains thymine. (D)</p> Signup and view all the answers

    Which factor is NOT a role associated with RNA besides mRNA?

    <p>Storing genetic information. (D)</p> Signup and view all the answers

    What is the primary role of capping and polyadenylation in eukaryotic mRNA?

    <p>To increase stability of mRNA and facilitate export to cytosol (A)</p> Signup and view all the answers

    What are exons primarily known for in eukaryotic genes?

    <p>They are short protein-coding sequences scattered throughout the gene (B)</p> Signup and view all the answers

    Which of the following best describes the function of snRNAs in splicing?

    <p>They act as ribozymes that catalyze splicing reactions (C)</p> Signup and view all the answers

    What is the role of splice junction complexes?

    <p>They indicate successful completion of splicing (C)</p> Signup and view all the answers

    How are introns removed from pre-mRNA?

    <p>Through the formation of a lariat structure (B)</p> Signup and view all the answers

    What must occur before pre-mRNAs can be exported for protein translation?

    <p>Introns must be removed and exons stitched together (A)</p> Signup and view all the answers

    What signals the beginning and end of an intron in pre-mRNA?

    <p>snRNPs recognizing splice-site sequences (D)</p> Signup and view all the answers

    What is the consequence of failed mRNA export from the nucleus?

    <p>The mRNA will accumulate in the nucleus and degrade (B)</p> Signup and view all the answers

    What is the primary function of the nuclear pore complexes?

    <p>To mediate the export of mRNA to the cytosol (B)</p> Signup and view all the answers

    Which proteins are required for the export of mRNA from the nucleus?

    <p>Poly-A-binding proteins, cap-binding complex, and exon junction complexes (A)</p> Signup and view all the answers

    What role do transcription regulators play in gene expression?

    <p>They can either activate or repress transcription (C)</p> Signup and view all the answers

    How can regulatory DNA sequences influence gene expression?

    <p>Through integration of various environmental signals (C)</p> Signup and view all the answers

    What is a potential consequence of allowing aberrantly spliced transcripts to leave the nucleus?

    <p>They can become harmful (D)</p> Signup and view all the answers

    What mechanism facilitates interaction between transcriptional machinery and the promoter?

    <p>Formation of a Transcription Initiation Complex (TIC) (A)</p> Signup and view all the answers

    What is the role of repressor proteins in gene transcription?

    <p>To inhibit the assembly of the TIC or block RNA polymerase progression (C)</p> Signup and view all the answers

    What happens to waste RNAs that remain in the nucleus?

    <p>They are degraded and can be reused for transcription (C)</p> Signup and view all the answers

    What determines the transcription rate of eukaryotic genes?

    <p>Combinations of transcription regulators (D)</p> Signup and view all the answers

    What is a role of post-transcriptional controls in eukaryotic cells?

    <p>To fine-tune gene expression after transcription initiation (C)</p> Signup and view all the answers

    How does alternative RNA splicing benefit eukaryotic cells?

    <p>It allows for the production of different mRNAs and proteins from one gene (B)</p> Signup and view all the answers

    The presence of repressor proteins in the 5' UTR region primarily affects which process?

    <p>Ribosome access to mRNA (A)</p> Signup and view all the answers

    What is the significance of mRNA lifespan in protein expression levels?

    <p>Longer mRNA lifespan allows for multiple translations of the same mRNA (D)</p> Signup and view all the answers

    Which mechanism helps control mRNA degradation in eukaryotic cells?

    <p>The presence of specific binding sites for degradation factors (D)</p> Signup and view all the answers

    What is an outcome of combinatorial control in gene expression?

    <p>Specific gene expression in response to various signals (C)</p> Signup and view all the answers

    Which statement accurately describes the role of a single protein in gene expression?

    <p>It can coordinate the expression of multiple genes. (A)</p> Signup and view all the answers

    Flashcards

    Eukaryotic Gene Expression

    The process by which information encoded in DNA is used to synthesize functional products like proteins in eukaryotic cells.

    RNA molecules in gene expression

    Different types of RNA (like mRNA, tRNA, rRNA) play specific roles in translating DNA information into functional products.

    Transcription regulators

    Proteins that control the rate of gene expression by binding to specific DNA sequences, promoting or inhibiting transcription.

    Eukaryotic DNA packaging

    Organizing DNA into chromosomes involves multiple levels of packaging, making DNA accessible while preventing tangling.

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    RNA synthesis & processing

    Process of creating RNA from DNA (transcription) followed by modification of the RNA molecule (processing) before it is used.

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    Transcription Initiation Complex

    A group of proteins (transcription factors) that assemble at the start of a gene, enabling RNA polymerase to bind and begin transcription.

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    Role of TFIID

    TFIID binds specifically to DNA promoter regions, triggering a local DNA distortion that recruits other transcription factors like TFIIB.

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    TFIIH's Actions

    TFIIH plays dual roles: it unwinds the DNA double helix exposing the template strand, and it phosphorylates RNA polymerase tail to initiate transcription.

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    Transcription Release

    Once RNA polymerase is phosphorylated by TFIIH, it releases most general transcription factors, except for TFIID, to begin transcribing the gene.

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    Elongation Factors

    Elongation factors join actively transcribing RNA polymerase to help with the process of reading DNA and creating RNA. They are not part of the initial transcription initiation complex.

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    mRNA Capping

    Addition of a 5' cap (modified guanine nucleotide) to the mRNA molecule during transcription.

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    Polyadenylation

    Addition of a poly-A tail (a string of adenine nucleotides) to the 3' end of the mRNA molecule.

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    Why is mRNA capped?

    Capping protects the mRNA from degradation and helps it bind to the ribosome for translation.

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    Why is mRNA polyadenylated?

    Polyadenylation increases mRNA stability and facilitates its export from the nucleus.

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    Introns

    Non-coding sequences within a gene that are removed during RNA splicing.

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    Exons

    Coding sequences within a gene that are joined together during RNA splicing to form a mature mRNA.

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    RNA Splicing

    Process of removing introns and joining exons together to form a mature mRNA.

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    Spliceosome

    A complex of proteins and snRNAs that catalyzes RNA splicing.

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    RNA vs. DNA

    RNA carries genetic information from DNA, using a similar language but different chemical forms (ribose sugar, uracil base, single-stranded).

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    RNA polymerase

    An enzyme that makes RNA by unwinding DNA and then catalyzing the joining of nucleotides.

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    RNA polymerase II

    A specific type of RNA polymerase involved in transcribing genes to produce mRNA.

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    Transcription start site (+1)

    The point on DNA where RNA synthesis begins.

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    Promoter

    DNA sequences upstream of the transcription start site that tell RNA polymerase where and how to start transcription.

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    TATA box

    A common promoter sequence recognized by RNA polymerase II.

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    General transcription factors (GTFs)

    Proteins required for RNA polymerase binding to the promoter and initiating transcription.

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    TBP (TATA binding protein)

    A subunit of TFIID that binds to the TATA box and bends DNA.

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    mRNA Export

    The process of moving correctly processed mRNA from the nucleus to the cytoplasm for protein synthesis.

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    Nuclear Pore Complex

    A gate-like structure that controls the passage of molecules in and out of the nucleus.

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    Waste RNA

    Non-functional RNA molecules, such as excised introns, broken RNA, or aberrantly spliced transcripts, that are degraded within the nucleus.

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    Regulatory DNA Sequences

    Specific DNA sequences that transcription regulators bind to, often integrating information from various signals to control gene expression.

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    Mediator Complex

    A large protein complex that helps facilitate the assembly of the transcription initiation complex and RNA polymerase at the promoter.

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    Repressor Proteins

    Proteins that inhibit transcription by blocking the formation of the transcription initiation complex or preventing RNA polymerase from moving forward.

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    Transcription Initiation Complex (TIC)

    A group of proteins, including general transcription factors and RNA polymerase, that assemble at the promoter region of a gene to initiate transcription.

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    Combinatorial Control

    The process where multiple transcription regulators work together to control the expression of a gene. Each regulator binds to a specific DNA sequence, and their combined activity determines the transcription rate.

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    Post-Transcriptional Control

    Mechanisms that regulate gene expression after transcription has occurred. These mechanisms fine-tune protein production by controlling mRNA processing, stability, and translation.

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    Alternative Splicing

    A process where different combinations of exons within a gene are included in the final mRNA, leading to multiple protein isoforms from a single gene.

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    mRNA Degradation Control

    Mechanisms that regulate the lifespan of mRNA molecules. This influences the amount of protein produced from each mRNA.

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    How does mRNA lifespan affect protein expression?

    The longer an mRNA molecule survives, the more protein it can produce. Short-lived mRNAs result in lower protein levels.

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    What are the advantages of alternative splicing?

    Alternative splicing increases the diversity of proteins produced from a single gene. This allows cells to specialize and respond to different conditions.

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    How does mRNA degradation control protein expression?

    By regulating the rate at which mRNA molecules are broken down, cells can control the amount of protein produced. Degradation can either prevent an excessive amount of protein or allow for rapid production.

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    Study Notes

    Gene Expression in Eukaryotic Cells

    • Course: SBP3411
    • Instructor: Dr. Hanis H. Harith
    • Department of Biomedical Science, UPM

    Learning Outcomes

    • Identify the role of different types of RNA molecules in eukaryotic gene expression
    • Describe the key events and molecules involved in RNA synthesis and processing in eukaryotic cells
    • Discuss the role of transcription regulators in eukaryotic gene expression
    • Describe examples of mechanisms of post-transcriptional control at different levels

    Lecture Outline

    • Types of RNA & RNA polymerases
    • RNA synthesis and processing
    • Transcriptional controls
    • Post-transcriptional controls

    DNA Organization in Eukaryotic Cells

    • Storage of hereditary information
    • All cell types in a multicellular organism contain the same DNA content
    • Eukaryotic DNA is packaged into multiple chromosomes
    • Chromosome packing occurs on multiple levels, preventing tangling while remaining accessible for replication, repair, and gene expression.

    Flow of Genetic Information

    • Genetic information flows from DNA to RNA (transcription) and from RNA to protein (translation)
    • DNA is transcribed into RNA, which is then translated into a protein.
    • The sequence of DNA determines the sequence of RNA, which in turn determines the sequence of amino acids in the protein.
    • Segments of DNA that are transcribed into RNA are called genes.
    • Non-coding sequences (introns) are spliced out from pre-mRNA.

    RNA Transcripts or Molecules

    • RNA carries information from the DNA
    • RNA has different chemical forms (ribose vs. deoxyribose; uracil vs. thymine).
    • RNA polymerase unwinds DNA, creating phosphodiester bonds between nucleotides.
    • Different types of RNA have different functions, such as messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).

    RNA Synthesis in Eukaryotic Cells: Initiation

    • General transcription factors (TFs) are assembled on the promoter region of a gene.
    • Promoter: DNA sequences upstream of transcription start site (+1).
    • TFIID binds to the TATA box (located at -30).
    • TATA box is common on promoters used by RNA polymerase II.
    • Local DNA distortion by TFIID allows adjacent binding of TFIIB.

    RNA Synthesis: Formation of Transcription Initiation Complex

    • Assembly of other general TFs exposes the template strand (ATP hydrolysis required).
    • Binding of RNA polymerase completes the formation of the transcription initiation complex.
    • RNA polymerase needs to be released from most general TFs (phosphorylation of RNA polymerase by TFIIH occurs).

    RNA Synthesis: Elongation & Termination

    • Elongation factors facilitate movement of RNA polymerase.
    • Polynucleotide synthesis is driven by ATP hydrolysis.
    • Incoming ribonucleoside triphosphates react with the 3' end of the RNA chain.
    • Hydrolysis of pyrophosphate drives overall reaction towards polynucleotide synthesis.
    • When transcription ends, RNA polymerase is dephosphorylated by protein phosphatases and released from DNA.

    Eukaryotic RNA Processing: RNA Capping & Polyadenylation

    • RNA processing (capping, splicing, polyadenylation) occurs as RNA is synthesized.
    • Facilitated by enzymes on the phosphorylated tail of RNA polymerase.
    • RNA capping: attachment of a guanine nt with a methyl group at the 5' end when RNA transcript is about 25 nts long
    • Polyadenylation: addition of adenine nucleotides to form poly-A tail at the 3' end.
    • Significance of capping and polyadenylation increases mRNA stability and facilitates export.

    Organization of Eukaryotic Genes and Pre-mRNA

    • Exons are short protein-coding sequences.
    • Introns are long, non-coding sequences.
    • Both exons and introns are transcribed into pre-mRNA.
    • RNA splicing removes introns and joins exons.
    • RNA splicing and processing are required for pre-mRNAs to become functional mRNA.

    RNA Splicing by Spliceosome

    • The core of the spliceosome is composed of snRNAs and proteins (snRNPs).
    • snRNAs act as ribozymes that catalyze the splicing reactions.
    • Successful splicing is marked by exon junction complexes.
    • snRNPs recognize splice-site sequences signaling the beginning and end of introns by complementary base pairing.
    • Introns are spliced out by forming a lariat structure, then degraded.

    mRNA Export

    • Only correctly processed mRNAs are exported to the cytosol.
    • Bound to poly-A-binding proteins, a cap-binding complex, and exon junction complexes.
    • Mediated by nuclear pore complexes.
    • Waste RNAs remain and are degraded.

    Gene Expression is Mainly Controlled by Transcription Regulators

    • Transcription regulators switch transcription on/off (activator/repressor).
    • Proteins recognize specific regulatory DNA sequences and form noncovalent interactions.
    • Regulatory DNA sequences integrate information from many signals.

    Transcription Regulators can Recruit Chromatin-Modifying Proteins

    • DNA packaging (e.g., nucleosomes) can physically block assembly of the transcription initiation complex (TIC).
    • Chromatin structure needs modification to access promoters.
    • Gene activators enhance transcription initiation efficiency by recruiting enzymes that covalently modify histone proteins (e.g., HATs).
    • Proteins including general transcription factors promote transcription.
    • Chromatin remodeling complexes increase accessibility to nearby DNA (e.g., TATA box).
    • Gene repressors reduce transcription initiation efficiency by recruiting enzymes that modify histone proteins (e.g., HDACs).

    Transcriptional Control in a Multicellular Organism

    • Some proteins are commonly expressed across cell types.
    • Distinctive cell properties are determined by expression of specialized proteins.
    • Expression of eukaryotic genes is controlled by combinations of transcription regulators (combinatorial control).
    • Multiple transcription regulators bind to respective regulatory DNA sequences.
    • Regulatory DNA sequences integrate information from various signals to determine transcription rate.
    • A single protein can coordinate the expression of multiple genes.

    Post-transcriptional Controls in Eukaryotic Cells

    • Mechanisms operate after transcription initiation to fine-tune gene expression.
    • Alternative RNA splicing: Exons may be skipped or included by spliceosome, but their order in the DNA sequence is maintained.
    • Presence of binding sites for repressor proteins in the 5' UTR region.
    • Mechanisms control mRNA degradation or sequestering from mRNA.

    Mechanisms of mRNA Degradation Control

    • mRNA lifespan determines protein expression level.
    • mRNA stability varies depending on nucleotide sequence (e.g., 3' UTR, which may contain binding sites for proteins involved in RNA degradation).
    • mRNAs are eventually degraded by RNases in the cytosol.
    • mRNA degradation can also be regulated by miRNAs.
    • miRNAs form RNA-induced silencing complex (RISC) in the cytosol and target specific mRNA with complementary sequences.
    • Target mRNA is rapidly degraded by RISC, or sequestered and degraded by nucleases.

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    Test your knowledge on the critical roles of RNA molecules in eukaryotic gene expression. This quiz covers topics such as transcription initiation, post-transcriptional control, and regulatory mechanisms essential for controlling transcription. Check your understanding of key components involved in these processes!

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