DNA Replication Mechanisms Quiz
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What role does DNA polymerase III play in relation to RNA primers on the lagging strand?

  • Synthesizes RNA primers necessary for initiation.
  • Extends RNA primers by incorporating deoxynucleotides. (correct)
  • Unwinds the double helix to facilitate replication.
  • Removes RNA primers and replaces them with DNA.

    • Which statement accurately describes the function of DNA polymerase I during DNA replication?

  • It synthesizes RNA primers to begin replication.
  • It removes RNA primers from Okazaki fragments and fills the gap with dNTPs. (correct)
  • It replaces DNA polymerase III in the elongation phase.
  • It facilitates the loop formation of the lagging strand.

    • What characteristic of the lagging strand during replication allows simultaneous activity of two DNA polymerases?

  • It is synthesized continuously in a single direction.
  • It forms a looped structure facilitating coordination. (correct)
  • It requires fewer RNA primers compared to the leading strand.
  • It has multiple origins of replication.

    • How does DNA polymerase III behave when it encounters an Okazaki fragment?

    <p>It detaches from the lagging strand template.</p> Signup and view all the answers

    What aspect of primase's function is specific to the lagging strand during DNA replication?

    <p>It creates multiple RNA primers in a discontinuous fashion.</p> Signup and view all the answers

    What is the key process in DNA replication that ensures each daughter duplex contains one strand from the parent structure?

    <p>Semi-conservative replication</p> Signup and view all the answers

    During which phase of the cell cycle does DNA replication take place in eukaryotic cells?

    <p>S Phase</p> Signup and view all the answers

    What structure is formed at the site where the parental double helix is undergoing strand separation?

    <p>Replication fork</p> Signup and view all the answers

    How many origins of replication can be found in human cells?

    <p>10,000-100,000</p> Signup and view all the answers

    What term describes the small portions of the eukaryotic genome that are replicated simultaneously during DNA replication?

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

    What type of DNA polymerase is essential for synthesizing daughter strands in prokaryotes?

    <p>DNA Polymerase III</p> Signup and view all the answers

    Approximately how many active replication forks can be found within a single replication focus in eukaryotic cells?

    <p>10-100</p> Signup and view all the answers

    Which of the following factors is NOT involved in DNA replication in prokaryotes?

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

    What is the function of a replication foci in the eukaryotic nucleus during DNA replication?

    <p>To concentrate multiple replicons for simultaneous replication</p> Signup and view all the answers

    What mechanism allows the gradual separation of the two strands of the double helix during DNA replication?

    <p>Hydrogen bond breaking</p> Signup and view all the answers

    What is the role of DNA ligase during DNA replication?

    <p>It covalently joins 3’ dNT to 5’ end of Okazaki fragments.</p> Signup and view all the answers

    Which statement about eukaryotic DNA replication is accurate?

    <p>Human cells have 10,000-100,000 different origins of replication.</p> Signup and view all the answers

    What happens to nucleosomes during DNA replication in eukaryotic cells?

    <p>Replication machinery displaces them but they quickly reassemble.</p> Signup and view all the answers

    What is the primary function of the 3'->5' exonuclease activity in DNA Polymerases?

    <p>To proofread and remove mispaired nucleotides.</p> Signup and view all the answers

    Which of the following accurately describes the spontaneous mutation rate during DNA replication?

    <p>It is influenced by the geometric fit of nucleotides.</p> Signup and view all the answers

    What is the significance of histone molecules during DNA replication?

    <p>They use parental histones for quick reassembly during replication.</p> Signup and view all the answers

    What mutation can lead to various genetic diseases related to DNA replication?

    <p>Deficiencies in the DNA polymerase proofreading ability.</p> Signup and view all the answers

    How do eukaryotic cells ensure accuracy during DNA repair?

    <p>Through the mismatch repair system employing various proteins.</p> Signup and view all the answers

    What is the primary function of DNA Polymerase I during DNA replication?

    <p>To replace RNA primers with DNA</p> Signup and view all the answers

    In prokaryotic cells, what is the role of DnaA during DNA replication initiation?

    <p>It recognizes the origin of replication</p> Signup and view all the answers

    What characterizes the lagging strand during DNA replication?

    <p>It requires multiple RNA primers for synthesis</p> Signup and view all the answers

    Which of the following is true about eukaryotic DNA replication initiation?

    <p>Helicase binds to the origin after the pre-replication complex forms</p> Signup and view all the answers

    What are Okazaki fragments?

    <p>Discontinuous DNA segments synthesized away from the replication fork</p> Signup and view all the answers

    Which enzyme is primarily responsible for unwinding DNA during replication in prokaryotes?

    <p>DnaB helicase</p> Signup and view all the answers

    What is the role of single-stranded DNA-binding (SSB) proteins in DNA replication?

    <p>To stabilize unwound DNA strands during replication</p> Signup and view all the answers

    Which type of topoisomerase relaxes DNA supercoiling in eukaryotic cells?

    <p>Type I topoisomerases</p> Signup and view all the answers

    What is the direction of new DNA synthesis by DNA Polymerase during replication?

    <p>5' to 3'</p> Signup and view all the answers

    In eukaryotes, when is the formation of new pre-replication complexes synchronized?

    <p>During the M and G1 phases of the cell cycle</p> Signup and view all the answers

    What role does DNA Gyrase play in prokaryotic DNA replication?

    <p>It introduces or removes supercoils.</p> Signup and view all the answers

    Which statement accurately describes the function of the γ-clamp loading complex?

    <p>It loads the sliding clamp onto DNA.</p> Signup and view all the answers

    How many core DNA polymerases are present in the DNA Polymerase III holoenzyme?

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

    During DNA replication in prokaryotes, what is the role of helicase?

    <p>To unwind the DNA double helix.</p> Signup and view all the answers

    In the context of DNA replication, what does 'replisome' refer to?

    <p>The entire complex of active proteins at the replication fork.</p> Signup and view all the answers

    What is the primary function of primase in prokaryotic DNA replication?

    <p>To synthesize RNA primers.</p> Signup and view all the answers

    What occurs to the DNA strands during the elongation phase of prokaryotic DNA replication?

    <p>Both strands are looped simultaneously.</p> Signup and view all the answers

    Which enzyme is primarily responsible for incorporating deoxynucleotides during DNA replication on the lagging strand?

    <p>DNA Polymerase III</p> Signup and view all the answers

    Study Notes

    HSS2305: Molecular Mechanisms of Disease

    • Lecture 13 covered DNA replication, DNA damage, and DNA repair.
    • A diagram of a cell's components was shown, labeling various organelles and structures.
    • DNA Replication: Reproduction relies on copying genetic material. DNA is copied during mitosis and meiosis. This copying is done by replication machinery, also used for repair. Human diploid cells have 46 chromosomes; gametes (haploid) have 23.

    DNA Replication

    • Semi-Conservative Replication: Watson and Crick described gradual strand separation of the double helix via breaking hydrogen bonds. Daughter strands are synthesized as complementary pairs to the parental templates. Each daughter duplex contains one strand from the parent.
    • Bacterial DNA Replication: Temperature sensitive bacterial mutants are heavily studied; these allow researchers to quickly turn gene expression on/off. In vitro culture systems, and more than 30 proteins are involved in the prokaryotic replication process. Bacterial and eukaryotic cell replication mechanisms are similar.
    • Eukaryotic DNA Replication: "Synthesis" phase (S-phase) of the cell cycle where DNA replicates. Many small portions of the eukaryotic genome (replicons) are replicated all at once. Human cells have 10,000 - 100,000 different replication origins. 10-15% of replicons are actively involved in S-phase.
    • Eukaryotic Replication: DNA replication proceeds in both directions (bi-directionally). Replication forks are areas where the double helix separates and new nucleotides are incorporated. 2 replication forks move in opposite directions

    DNA Replication: Nuclear Structure

    • Replication foci are localized sites within the nucleus. Several replicons become active within these foci. A typical replicating nucleus has ~50-250 foci. ~10-100 active replication forks (replicons)/replication foci occur in a cell.

    DNA Replication: Prokaryotes: DNA Polymerase

    • DNA polymerase holoenzyme is responsible for DNA synthesis. DNA Polymerase III dimer synthesizes daughter strands simultaneously with other proteins. DNA replication in prokaryotes requires a template DNA strand, primers, and appropriate nucleotides.

    DNA Replication: Semi-discontinuous

    • DNA replication is semi-discontinuous. This means the new DNA strands are not created continuously in a single direction; the leading strand is continuous, while the lagging strand is made in small fragments (Okazaki fragments) that require RNA primers to initiate.

    DNA Replication: Prokaryotes: Initiation

    • DnaA proteins recognize the origin of replication (OriC). DnaB helicase unwinds the DNA strands, and single-stranded DNA binding (SSB) proteins coat the unwound DNA. Primase synthesizes RNA primers, a necessary step before DNA polymerase can act.

    DNA Replication: Eukaryotes: Initiation

    • The origin recognition complex (ORC) recognizes replicon origins. Licensing factors (Cdc6 and Cdt1) and helicase are recruited to the origin.
    • Helicase is an unwinding protein comprised of minichromosome maintenance proteins (MCM2-7)

    DNA Replication: Eukaryotes: Pre-replication complex (pre-RC)

    • The pre-RC involves ORC, licensing factors, and helicase binding during the G1 phase. Protein kinases (Cdk and DDK) phosphorylate and activate the pre-RC. High activity in S-phase. The pre-RC is also responsible for inhibiting the formation of new complexes. Primase synthesizes RNA primers.

    DNA Replication: Supercoiling

    • DNA supercoiling arises during DNA unwinding; tension builds up. Topoisomerases relieve this tension. Type I topoisomerases relax DNA by nicking and closing one strand of the duplex. Type II topoisomerases change topology by breaking and rejoining double-stranded DNA to introduce or remove supercoils.

    DNA Replication: Prokaryotes: Elongation

    • Two core polymerases (DNA III) replicate DNA, assisted by at least two beta clamps. One clamp is associated with the leading strand, while one is associated with each lagging strand fragment. y-Clamp loading complex loads the sliding clamp onto DNA, also associated with helicase. The replisome refers to the replication fork complex.

    DNA Replication: Eukaryotes: Elongation

    • Eukaryotic replication fork proteins are homologous to related proteins in bacterial replication, but have slightly different nomenclature.

    DNA Repair: High Fidelity Mutation Rate

    • An error rate of incorporating incorrect nucleotides during DNA replication is low. DNA polymerases have extremely high fidelity.Only one correct orientation is geometrically proper to fit within the active site, insuring accurate incorporation of nucleotides. Proofreading capacity maintains accuracy.

    DNA Repair: Prokaryotes: Mismatch repair

    • DNA polymerases I and III have a 3'-5' exonuclease activity that removes wrongly incorporated nucleotides during DNA replication. Prokaryotic polymerases use a proofreading mechanism.

    DNA Repair: DNA Damage

    • DNA is susceptible to damage from ionizing radiation, chemicals, UV light, thermal energy from metabolism and from spontaneous lesions. Cells have mechanisms to repair damage. DNA repair mechanisms include:
    • accurate selection of nucleotides during replication
    • immediate proofreading
    • post-replicative mismatch repair

    DNA Repair: Nucleotide Excision Repair-Eukaryotes

    • Removes bulky lesions(pyrimidine dimers). Includes cut-and-patch repair.
      • Global genomic pathway (corrects lesions throughout genome)
      • Transcription-coupled pathway (repairs lesions on the DNA strand currently being transcribed by RNA polymerase II). Genes expressed most frequently are most likely to be repaired.
    • There are XPC and TFIIH complexes involved in repairing these lesions.

    DNA Repair: Base Excision Repair and Eukaryotes

    • Removes altered nucleotides(reactive chemicals/free radicals). Different types of alterations: Uracil, 8-oxoguanine, 3-methyladenine. Specific glycosylases identify and excise the base.
    • The AP endonuclease then cuts the sugar-phosphate backbone. DNA polymerase B adds the correct nucleotide and DNA ligase III seals the gap.
    • Alzheimer's disease is associated with increased oxidative DNA damage and deficiencies in base excision repair enzymes, leading to less effective repair which may contribute to disease development.

    DNA Repair: Double-strand Breakage Repair- Eukaryotes

    • Double-strand breaks occur from ionizing radiation and certain chemicals (such as those in chemotherapy). Nonhomologous end joining (NHEJ) repairs breaks quickly but may introduce errors. Homologous recombination (HR) is a more accurate method that requires an identical template strand, but is slower.

    Summary: DNA Replication, Damage and Repair

    • DNA replication is crucial for cell reproduction. DNA damage occurs frequently, and repair mechanisms play a key role in maintaining cell health and preventing disease.
    • Various types of errors or damage can be repaired.

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    HSS2305A Spring 2022 DNA Replication Lecture Notes PDF

    Description

    Test your knowledge on the intricacies of DNA replication, focusing on the roles of DNA polymerase III and I, the function of RNA primers, and the dynamics of lagging and leading strands. This quiz covers essential processes that ensure accurate DNA replication in eukaryotic cells.

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