Molecular Biology Quiz: RNA and DNA Processes
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Questions and Answers

What is a primary role of small nucleolar RNAs (snoRNAs) in pre-rRNA processing?

  • They direct modification enzymes to specific rRNA sites. (correct)
  • They provide structural support to the nucleolus.
  • They carry out transcription of ribosomal proteins.
  • They are involved in the cleavage of pre-rRNA.
  • Which enzyme is responsible for the transcription of genes encoding ribosomal proteins?

  • DNA polymerase
  • RNA polymerase I
  • RNA polymerase II (correct)
  • RNA polymerase III
  • What occurs during the assembly of ribosomes?

  • 5S rRNA is exclusively synthesized in the nucleolus.
  • Ribosomal proteins are synthesized in the nucleolus.
  • Pre-rRNA associates with ribosomal proteins during its synthesis. (correct)
  • Ribosomal proteins first bind to the pre-rRNA after its processing.
  • What is NOT a modification that occurs during pre-rRNA processing?

    <p>Addition of phosphate groups to ribose residues (D)</p> Signup and view all the answers

    Where does the assembly of preribosomal particles primarily occur?

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

    Which DNA polymerases are responsible for nuclear DNA replication in eukaryotes?

    <p>DNA polymerases α, δ, and ε (C)</p> Signup and view all the answers

    What is a fundamental property shared by all DNA polymerases?

    <p>They synthesize DNA only in the 5' to 3' direction. (D)</p> Signup and view all the answers

    What initiates the separation of DNA strands at the origin of replication?

    <p>Initiator proteins recognizing specific nucleotide sequences (B)</p> Signup and view all the answers

    In prokaryotes, how many origins of replication are typically present?

    <p>One single origin of replication (A)</p> Signup and view all the answers

    How do eukaryotes differ from prokaryotes in terms of origins of replication?

    <p>Eukaryotes need multiple origins to replicate long chromosomes. (C)</p> Signup and view all the answers

    What effect would it have on replication time if a mammalian genome replicated from a single origin?

    <p>It would potentially take several weeks to replicate. (D)</p> Signup and view all the answers

    Which protein complex is involved in the molecular mechanism of DNA replication?

    <p>Replication complex or replisome (A)</p> Signup and view all the answers

    What role does helicase play at the origin of replication?

    <p>It unwinds the DNA strands. (D)</p> Signup and view all the answers

    Which type of RNA polymerase is responsible for transcribing the 5S rRNA?

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

    How many copies of the gene encoding the 5.8S, 18S, and 28S rRNAs are typically found in the human genome?

    <p>200 (B)</p> Signup and view all the answers

    Where are the genes encoding the 5S rRNA located in the human genome?

    <p>Chromosome 1 (B)</p> Signup and view all the answers

    Which components of the nucleolus reflect the progression of rRNA transcription and processing?

    <p>Fibrillar center, dense fibrillar component, granular component (C)</p> Signup and view all the answers

    What factor primarily influences the size of the nucleolus?

    <p>Metabolic activity of the cell (C)</p> Signup and view all the answers

    What is the significance of the 45S pre-rRNA in the cell?

    <p>It is processed into the functional forms of 5.8S, 18S, and 28S rRNAs. (B)</p> Signup and view all the answers

    What characteristic of rRNA transcription contributes to the high density of RNA chains?

    <p>High number of RNA polymerase molecules (A)</p> Signup and view all the answers

    Which of the following regions in the nucleolus is primarily involved in assembling ribosomal subunits?

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

    What is the primary function of the RNA-induced silencing complex (RISC) directed by miRNA?

    <p>To inhibit translation or stimulate mRNA degradation (B)</p> Signup and view all the answers

    How many different mRNAs can a single miRNA potentially target?

    <p>Up to 100 (B)</p> Signup and view all the answers

    Which type of non-coding RNA is over 200 nucleotides long and plays a role in gene expression regulation?

    <p>Long non-coding RNA (lncRNA) (A)</p> Signup and view all the answers

    What is the function of the nuclear pore complexes in the nuclear envelope?

    <p>To act as communication channels for selective exchange of molecules (C)</p> Signup and view all the answers

    What is a characteristic feature of satellite DNA?

    <p>It consists of repetitive DNA sequences (D)</p> Signup and view all the answers

    Which part of the nuclear envelope maintains the internal composition of the nucleus?

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

    What distinguishes AT-rich sequences from GC-rich sequences in the context of DNA density?

    <p>AT-rich sequences are less dense than GC-rich sequences (C)</p> Signup and view all the answers

    What is the primary role of the nuclear envelope in eukaryotic cells?

    <p>To act as a selective barrier regulating molecule traffic (B)</p> Signup and view all the answers

    What effect do deletions that affect residues 126 to 132 have on the T antigen?

    <p>They cause retention in the cytoplasm. (C)</p> Signup and view all the answers

    What is a characteristic feature of nuclear localization signals (NLS)?

    <p>Rich in Lys and Arg. (A)</p> Signup and view all the answers

    Which proteins are primarily involved in the transport of proteins to the nucleus?

    <p>Importins and Ran proteins. (C)</p> Signup and view all the answers

    What happens to the importin-Ran/GTP complex in the nucleus?

    <p>It releases the cargo protein. (D)</p> Signup and view all the answers

    What is the role of Ran-GAP in nuclear transport?

    <p>Hydrolyzes GTP in Ran to GDP. (C)</p> Signup and view all the answers

    What type of sequence does nucleoplasmin have for its nuclear localization signal?

    <p>Bipartite sequence separated by a short sequence. (A)</p> Signup and view all the answers

    How do importins transport cargo proteins through the nuclear pore complex?

    <p>By binding to cytoplasmic filaments of the nuclear pore complex. (C)</p> Signup and view all the answers

    What determines the directionality of nuclear transport?

    <p>High concentration of Ran/GTP in the nucleus. (A)</p> Signup and view all the answers

    What role do helicases play in DNA replication?

    <p>They catalyze the unwinding of parental DNA. (D)</p> Signup and view all the answers

    How do topoisomerases alleviate stress during DNA replication?

    <p>By creating transient breaks in the DNA strands. (B)</p> Signup and view all the answers

    What importance does the accuracy of DNA replication hold?

    <p>It ensures high fidelity for cell reproduction. (A)</p> Signup and view all the answers

    What unique activity do exonucleases of polymerase III and polymerase δ and ε provide?

    <p>They cleave incorrect bases from the growing DNA strand. (C)</p> Signup and view all the answers

    What is the function of single-stranded DNA-binding proteins during replication?

    <p>To stabilize uncoiled DNA strands. (B)</p> Signup and view all the answers

    How does telomerase differ from other DNA polymerases?

    <p>It can synthesize oligonucleotides with telomeric sequences. (C)</p> Signup and view all the answers

    What mechanism allows DNA polymerase to ensure high fidelity during replication?

    <p>Through double reading activity. (D)</p> Signup and view all the answers

    What is the role of DNA polymerase in relation to RNA primers?

    <p>It cleaves RNA primers post-replication. (C)</p> Signup and view all the answers

    Flashcards

    Helicases

    Enzymes that unwind the double helix of DNA during replication, separating the two strands. They use the energy from ATP hydrolysis to break the hydrogen bonds between the bases.

    Single-stranded DNA-binding proteins

    Proteins that bind to single-stranded DNA, preventing it from re-annealing and keeping it available for replication.

    Topoisomerases

    Enzymes that relieve the torsional stress caused by DNA unwinding during replication. They cut and re-ligate DNA strands to allow for rotation.

    DNA Replication

    The process of copying DNA, resulting in two identical DNA molecules. It involves unwinding the double helix, separating the strands, and using each strand as a template to synthesize a new complementary strand.

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    Telomerase

    A specialized DNA polymerase that adds repetitive sequences to the ends of chromosomes (telomeres) to protect them from degradation during replication.

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    Fidelity of DNA Replication

    The accuracy of DNA replication, measured as the number of incorrect bases incorporated per nucleotide.

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    Exonuclease Activity

    The ability of DNA polymerase to proofread its own work and remove incorrect bases, ensuring accurate replication.

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    Double Reading Activity

    A process where DNA polymerase checks the newly added base against the template strand, correcting any mismatches before moving on.

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    miRNA (microRNA)

    Small, non-coding RNA molecules involved in gene regulation. They bind to a protein complex called RISC to target and repress specific mRNAs.

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    lncRNA (Long non-coding RNA)

    Long, non-coding RNA molecules (over 200 nucleotides) with diverse roles in gene regulation, including X-chromosome inactivation in females.

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    Nuclear Envelope

    A double-layered membrane that encloses the nucleus, providing a barrier between the nucleus and cytoplasm.

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    Nuclear Pore Complex

    Complex protein structures embedded within the nuclear envelope, serving as the only communication channels between the nucleus and cytoplasm, allowing controlled transport of molecules.

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    Nuclear Lamina

    A protein meshwork lining the inner surface of the nuclear envelope, providing structural support and anchoring DNA.

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    Repetitive DNA Sequences

    Repeating sequences of DNA that are not transcribed and do not contain functional genetic information, but are important for chromosome structure.

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    Single Sequence Repeats

    Tandemly repeated short DNA sequences (1-500 nt) that are not transcribed and contribute to chromosome structure.

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    Satellite DNA

    DNA sequences enriched in A and T bases, which are less dense than GC-rich sequences, thus forming a separate band when separated by density gradient centrifugation.

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    DNA polymerase properties

    DNA polymerases are enzymes that synthesize new DNA strands during replication, with two essential properties: 1. They can only add nucleotides in the 5' to 3' direction. 2. They require a pre-existing primer strand to initiate synthesis. They cannot start a new strand from scratch.

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    Origin of replication

    The specific DNA sequence where DNA replication begins. It serves as the starting point for unwinding and separating the two DNA strands, creating two replication forks.

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    Initiator proteins

    Initiator proteins bind to specific sequences at the origin of replication, initiating the unwinding process.

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    Replisome

    A complex of proteins and enzymes that participate in DNA replication. It coordinates the process, including unwinding DNA, synthesizing new strands, and proofreading for errors.

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    Prokaryotic replication

    In prokaryotes, replication starts from a single origin and proceeds bidirectionally along the circular chromosome.

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    Eukaryotic replication

    In eukaryotes, multiple origins of replication are required to efficiently replicate the larger and more complex chromosomes. Each origin initiates independent replication bubbles, speeding up the entire process.

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    Nuclear Localization Signal (NLS)

    A short sequence of amino acids within a protein that acts as a signal for the protein to be transported into the nucleus.

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    Importin

    A protein that binds to the NLS of a cargo protein and facilitates its transport from the cytoplasm to the nucleus.

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    Ran

    A GTP-binding protein that plays a crucial role in nuclear transport by regulating the directionality of import and export.

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    Nuclear Pore Complex (NPC)

    The importin-cargo complex binds to the proteins of the cytoplasmic filaments of the nuclear pore complex and is transported through the pore.

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    Nuclear Import

    The process by which a protein with a NLS is recognized by importin and then transported through the nuclear pore complex into the nucleus.

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    Nuclear Export

    The importin-Ran/GTP complex is re-exported through the nuclear pore.

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    Ran-GAP

    A GTPase activating protein (Ran-GAP) associated with cytoplasmic filaments hydrolyzes GTP in Ran to GDP, releasing importin.

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    Ran Cycle

    The process where the Ran protein cycles between a GTP-bound state and a GDP-bound state, controlling the directionality of nuclear transport.

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    What are two important modifications in pre-rRNA processing?

    rRNA processing involves modifying the pre-rRNA molecule by adding methyl groups to certain ribose sugars. Conversion of uridine to pseudouridine. These modifications are crucial for proper rRNA function.

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    What is the role of snoRNPs in pre-rRNA processing?

    snoRNPs, composed of snoRNAs and proteins, play a crucial role in pre-rRNA processing by guiding enzymes to specific locations on the pre-rRNA molecule for modification.

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    How are ribosomes assembled?

    Ribosome assembly involves the association of pre-rRNA with ribosomal proteins and 5S rRNA. This assembly takes place in the nucleolus.

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    How are ribosomal proteins involved in ribosome assembly?

    Ribosomal proteins, synthesized outside the nucleolus by RNA polymerase II and translated in the cytoplasm, are transported to the nucleolus where they participate in ribosome assembly.

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    What is the role of 5S rRNA in ribosome assembly?

    Genes for 5S rRNA are transcribed by RNA polymerase III outside the nucleolus and transported to the nucleolus where they assemble along with pre-rRNA and ribosomal proteins.

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    rRNA Transcription

    The process of creating ribosomal RNA (rRNA) molecules.

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    45S pre-rRNA

    A large precursor molecule that contains all three rRNA components (28S, 5.8S, and 18S) before it is processed.

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    Nucleolus

    The site within the nucleus where rRNA is transcribed and ribosomes are assembled.

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    Nucleolar Organization Regions (NORs)

    Regions on chromosomes that contain the genes for 5.8S, 18S, and 28S rRNAs. These regions are essential for nucleolus formation.

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    RNA Polymerase I (RNApolI)

    The enzyme responsible for transcribing 45S pre-rRNA.

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    rRNA Processing

    The process of converting the 45S pre-rRNA into mature rRNA molecules.

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    Dense Fibrillar Component (DFC)

    A region within the nucleolus where pre-rRNA is processed.

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    Granular Component (G)

    A region within the nucleolus where ribosomal subunits are assembled.

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    Study Notes

    Unit 3: The Nucleus

    • The nucleus acts as a storehouse for genetic information, with DNA replication and RNA transcription and processing occurring within it.
    • It regulates gene expression by controlling the transport of transcription factors from the cytoplasm to the nucleus.

    3.1 The Cell Nucleus and DNA

    • Prokaryotes lack a nucleus, but eukaryotes have a nucleus that contains DNA.
    • DNA's primary function is storing genetic information.
    • DNA replication (creating identical copies) occurs at the genomic level within the nucleus.
    • RNA transcription and processing are also vital nuclear processes, creating RNA molecules from DNA templates.
    • Gene expression regulation involves controlling the movement of transcription factors from cytoplasm to the nucleus.

    Chromosomes and Chromatin

    • Eukaryotic genomes are complex, organized on multiple linear chromosomes.
    • DNA associates with proteins (histones), compacting it for fit within the cell nucleus. Human DNA unravels to 2 meters but has to fit in a 5-10µm area.
    • Chromosomes exist in two forms: highly condensed chromosomes (present during cell division) and uncondensed chromatin (found during interphase).
    • Heterochromatin and euchromatin are two major chromatin classes; heterochromatin is condensed and inactive, while euchromatin is less condensed and active in transcription. Chromatin at interphase is observed to be uncondensed throughout the nucleus while highly condensed regions are less prevalent.

    Levels of DNA Packaging

    • DNA exists in several levels of packaging, ranging from short 2nm regions of the DNA “beads on a string” to the coil condensed structures of 30nm chromatin fibres (interphase) to 300nm - 700nm structures.
    • Ultimately DNA is tightly wound into 1,400 nanometer chromatids.

    3.2 Nuclear Envelope

    • The nuclear envelope separates the nucleus from the cytoplasm.
    • It is a double membrane with an outer and inner membrane, with the outer membrane continuous with the endoplasmic reticulum.
    • The nuclear lamina provides structural support to the nucleus.
    • Nuclear pore complexes act as channels for regulating the passage of proteins, RNA's, and other molecules into and out of the nucleus.

    3.3 DNA Replication

    • DNA replication is a semi-conservative process where each new DNA molecule has one original strand and one newly synthesized strand.
    • DNA polymerase synthesizes DNA only in the 5' to 3' direction, adding to the 3′ OH- end of a growing strand.
    • Replication begins at replication origins recognized by initiator proteins, proceeding outward in both directions. Replicated segments may be hundreds of kb.
    • Eukaryotes have multiple origins to facilitate rapid genome replication.

    DNA Maintenance

    • DNA replication is highly accurate, with error frequencies less than one incorrect base for every 10^8 bases.
    • Mechanisms like proofreading (exonuclease activity of polymerases) and base selection by polymerases contribute to this accuracy. Mechanisms that aid in correcting an incorrect base are 3′ to 5′ exonuclease activity.

    3.4 DNA Transcription

    • DNA strands have different functions in transcription. The synthesis of RNA is carried out by RNA polymerase using the antisense strand as a template.
    • RNAP II synthesizes mRNA, which is pivotal in gene expression and protein synthesis.
    • Transcription is a multi-step process involving initiation, elongation, and termination. Initiation requires RNA polymerase binding to the promoter and unwinding DNA. During elongation, RNAP synthesizes RNA. Termination signals stop the process.
    • Eukaryotic cells contain three distinct polymerases with different targets and mechanisms.

    3.5 Traffic Between Nucleus and Cytoplasm

    • Selective transport of proteins and RNAs across the nuclear membrane.
    • Some proteins enter the nucleus because they have a nuclear localization signal (NLS).
    • Proteins are tagged with a nuclear export signal (NES) to leave the nucleus.
    • Specialized proteins like importins and exportins, along with Ran proteins (GTP), facilitate the selective transport.

    3.6 Nuclear Bodies

    • Specialized subnuclear compartments with diverse functions in RNA processing, DNA repair, and gene regulation.
    • Vary in number per nucleus; function frequently not fully understood. Examples include the nucleolus, Cajal bodies, nucleolar associated speckles and PML-bodies, which may play a role in gene expression and DNA repair.

    Genes and Genomes

    • Genome; the complete set of genetic instructions of an organism.
    • Gene: a DNA sequence that encodes a specific protein or RNA molecule.

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    Test your knowledge on the roles of small nucleolar RNAs, the enzymes involved in ribosomal protein transcription, and the assembly of ribosomes. This quiz also covers DNA replication in eukaryotes versus prokaryotes, including the mechanisms and proteins involved. Determine how these processes are fundamental to molecular biology.

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