DNA Replication Fork
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Questions and Answers

What is the replication fork responsible for?

  • Creating a junction for DNA repair
  • Simultaneously replicating both strands of DNA (correct)
  • Initiating RNA synthesis
  • Separation of DNA strands for transcription

    • Which statement is true regarding the leading strand during DNA replication?

  • It is synthesized in a discontinuous manner.
  • It requires the synthesis of Okazaki fragments.
  • It is synthesized simultaneously with the lagging strand.
  • It is synthesized continuously as the replication fork moves. (correct)

    • What is the primary challenge in synthesizing the lagging strand?

  • It must be synthesized in the opposite direction of the replication fork. (correct)
  • It is only initiated once replication is completed.
  • It can only be synthesized during RNA transcription.
  • It has no template available for synthesis.

    • What are Okazaki fragments?

    <p>Discontinuous segments of lagging strand DNA</p> Signup and view all the answers

    When can DNA synthesis on the lagging strand be initiated?

    <p>When a substantial length of template is exposed</p> Signup and view all the answers

    What does the anti-parallel nature of DNA imply for replication at the fork?

    <p>Only one strand can be synthesized continuously.</p> Signup and view all the answers

    How does the leading strand direction relate to the replication fork?

    <p>It follows the movement of the fork.</p> Signup and view all the answers

    Which statement accurately describes the role of DNA polymerase at the replication fork?

    <p>It operates by chasing the replication fork for the leading strand.</p> Signup and view all the answers

    What do the proteins at the replication fork primarily interact with?

    <p>The structure of the phosphate backbone</p> Signup and view all the answers

    Which DNA polymerase is primarily responsible for chromosome replication in E. coli?

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

    What characteristic distinguishes DNA polymerase I from DNA polymerase III?

    <p>It has a 5' exonuclease activity.</p> Signup and view all the answers

    What is a primary feature of DNA polymerase III that aids in its function?

    <p>It forms a complex known as DNA Pol III holoenzyme.</p> Signup and view all the answers

    What function does the 5' exonuclease of DNA polymerase I serve?

    <p>To remove RNA or DNA upstream of DNA synthesis.</p> Signup and view all the answers

    Which property does NOT describe DNA polymerase III?

    <p>It removes RNA primers effectively.</p> Signup and view all the answers

    What type of interactions do DNA polymerases exploit during DNA replication?

    <p>Physical and electrostatic interactions with the DNA backbone</p> Signup and view all the answers

    How many DNA polymerases does E. coli have that are distinguished by their enzymatic properties?

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

    What role do topoisomerases play during DNA replication?

    <p>They remove the supercoils produced by DNA unwinding.</p> Signup and view all the answers

    What is the primary function of single-stranded binding protein (SSB)?

    <p>To bind to single-stranded DNA and prevent re-annealing.</p> Signup and view all the answers

    Which statement best describes how topoisomerases function during DNA replication?

    <p>They temporarily break and rejoin DNA strands without releasing them.</p> Signup and view all the answers

    Which enzyme can initiate new DNA strands on single-stranded DNA?

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

    What happens to the DNA strands as DNA helicase unwinds the double helix?

    <p>The strands accumulate positive supercoils.</p> Signup and view all the answers

    Which of the following statements is NOT true about DNA helicase?

    <p>It synthesizes RNA primers for replication.</p> Signup and view all the answers

    How do SSB proteins interact with ssDNA?

    <p>They interact through electrostatic interactions.</p> Signup and view all the answers

    Why is it necessary to remove supercoils during DNA replication?

    <p>To allow for efficient unwinding of DNA at the replication fork.</p> Signup and view all the answers

    What occurs to the linking number as DNA helicase unwinds the DNA strands?

    <p>It decreases gradually.</p> Signup and view all the answers

    Which function do both type I and type II topoisomerases share?

    <p>They both relieve DNA supercoiling.</p> Signup and view all the answers

    What is the main limitation of DNA polymerase with respect to primer usage?

    <p>It can only extend 3'OH primers annealed to ssDNA templates.</p> Signup and view all the answers

    In the process of DNA replication, what does topoisomerase achieve by passing strands through breaks?

    <p>It removes knots and tangles in the DNA.</p> Signup and view all the answers

    What is a major consequence of SSB coating on ssDNA?

    <p>More extended conformation of the ssDNA.</p> Signup and view all the answers

    Which organism's replication machinery does NOT use gyrase or topo 1?

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

    What type of interaction do SSBs primarily utilize to contact ssDNA?

    <p>Electrostatic interactions</p> Signup and view all the answers

    What are Okazaki fragments composed of?

    <p>Short fragments of new DNA</p> Signup and view all the answers

    How does primase initiate the synthesis of a new DNA strand?

    <p>By synthesizing RNA primers</p> Signup and view all the answers

    What is the role of RNAse H during DNA replication?

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

    How often is a new RNA primer required on the leading strand during DNA replication?

    <p>Once per replication cycle</p> Signup and view all the answers

    What prevents DNA polymerases from initiating a new DNA strand without a primer?

    <p>Their requirement for a free 3'OH</p> Signup and view all the answers

    What is the main function of DNA helicases during replication?

    <p>To separate the two strands of the DNA double helix</p> Signup and view all the answers

    What occurs after RNA primers are removed during DNA replication?

    <p>DNA ligase seals the nicks in the DNA</p> Signup and view all the answers

    How many RNA primers are needed for the synthesis of the lagging strand?

    <p>Hundreds to thousands for each Okazaki fragment</p> Signup and view all the answers

    In what manner do DNA helicases interact with single-stranded DNA?

    <p>By moving directionally along ssDNA</p> Signup and view all the answers

    What unique feature distinguishes DNA helicases from DNA polymerases?

    <p>Their structural configuration as hexameric proteins</p> Signup and view all the answers

    What happens when the last ribonucleotide of an RNA primer is removed?

    <p>DNA polymerase fills the gap with nucleotides</p> Signup and view all the answers

    What activates primase to initiate RNA primer synthesis?

    <p>Association with other DNA replication proteins</p> Signup and view all the answers

    Which component is responsible for sealing nicks in the DNA during replication?

    <p>DNA ligase</p> Signup and view all the answers

    What is the polarity of DNA helicases when functioning on the lagging strand template of the replication fork?

    <p>5'—&gt;3'</p> Signup and view all the answers

    Why do DNA helicases require chemical energy during their movement along ssDNA?

    <p>For ATP hydrolysis</p> Signup and view all the answers

    What role do single-stranded binding proteins (SSBs) play after the DNA helicase has separated the strands?

    <p>They bind to and stabilize single-stranded DNA</p> Signup and view all the answers

    How does cooperative binding of SSBs enhance the stabilization of ssDNA?

    <p>By enabling interaction between adjacent SSBs</p> Signup and view all the answers

    In the assay for DNA helicase activity, what indicates that the helicase has successfully displaced the short ssDNA?

    <p>Change in the electrophoretic mobility of the short ssDNA</p> Signup and view all the answers

    What results from the cleavage of the DNA substrate using a restriction enzyme in the context of helicase polarity determination?

    <p>It generates asymmetrically sized ssDNA fragments</p> Signup and view all the answers

    What indicates the movement direction of the DNA helicase during the polarity determination assay?

    <p>The size of the displaced ssDNA fragment</p> Signup and view all the answers

    What is the primary function of DNA helicases in the context of DNA replication?

    <p>To unwind double-stranded DNA</p> Signup and view all the answers

    When DNA helicases move along ssDNA, what type of DNA do they bind to?

    <p>Single-stranded DNA (ssDNA)</p> Signup and view all the answers

    Why does the substrate in the helicase assay need to include a labeled ssDNA?

    <p>To enable detection of the displacement</p> Signup and view all the answers

    What is required for the movement of helicases along single-stranded DNA?

    <p>Chemical energy from ATP</p> Signup and view all the answers

    How does boiling act as a control in the DNA helicase activity assay?

    <p>It completely denatures the DNA molecules</p> Signup and view all the answers

    What is the role of SSB molecules when they first bind to separated ssDNA?

    <p>They stabilize the ssDNA and promote cooperative binding</p> Signup and view all the answers

    What does the size difference between displaced ssDNA demonstrate in helicase polarity experiments?

    <p>The direction of the DNA helicase movement</p> Signup and view all the answers

    Study Notes

    DNA Replication Fork

    • DNA replication involves the simultaneous synthesis of both DNA strands at a replication fork.
    • The replication fork is the junction between separated template strands and the unreplicated DNA.
    • It moves along the unreplicated DNA, producing two template strands for new DNA synthesis.

    Leading and Lagging Strands

    • DNA is synthesized by elongating the 3' end, only one strand can be continuously replicated (leading strand) as the fork moves.
    • The other strand (lagging strand) is synthesized discontinuously in short fragments called Okazaki fragments.
    • The direction of lagging strand synthesis is opposite the replication fork's movement.
    • Okazaki fragments typically range from 100-1,000 bases in eukaryotes and 1000-2000 in bacteria.

    RNA Primers

    • DNA polymerases cannot initiate DNA synthesis de novo; they require an existing 3'-OH group.
    • RNA primers (5-10 nucleotides long) are synthesized by primase (a specialized RNA polymerase).
    • Leading strands need only one RNA primer, while lagging strands require a new primer for each Okazaki fragment.
    • These primers are then replaced with DNA.

    RNA Primer Removal

    • RNAse H removes most of the RNA primer.
    • This enzyme specifically degrades RNA base-paired with DNA, leaving a ribonucleotide attached to the DNA.
    • An exonuclease removes the last ribonucleotide.
    • The gap left by RNA primer removal is filled by DNA polymerase.
    • DNA ligase seals the remaining nick in the DNA backbone.

    DNA Helicases

    • DNA helicases unwind the DNA double helix ahead of the replication fork.
    • They use ATP hydrolysis to separate the DNA strands.
    • Helicases are often ring-shaped hexamers, which encircle one strand and move directionally.

    Single-Stranded Binding Proteins (SSBs)

    • SSBs bind to separated strands immediately after helicase to prevent them from re-annealing.
    • This binding is cooperative, making nearby binding sites more favorable.
    • SSBs stabilize and extend single strands of DNA, preparing them for replication.

    Topoisomerases

    • Topoisomerases relieve the positive supercoiling that builds up ahead of the replication fork due to DNA unwinding.
    • They break and rejoin DNA strands. This process changes the linking number to accommodate the unwinding.
    • Topoisomerases prevent replication machinery from stalling.

    DNA Polymerase Specialization

    • Cells have multiple DNA polymerases with distinct roles and properties.
    • For example, DNA polymerase III is highly processive and crucial for chromosome replication.
    • DNA polymerase I, on the other hand, is less processive and specialized for removing RNA primers.

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    Description

    This quiz covers the process of DNA replication, focusing on the replication fork's role and the synthesis of leading and lagging strands. Learn about RNA primers and the critical differences in how each strand is replicated during this fundamental biological process.

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