replication

  • Overview of DNA Replication

    • Replication: Synthesis of new DNA, occurs in the S phase of the cell cycle.
    • Key Concept: DNA replication is semi-conservative, meaning each new DNA molecule consists of one old and one new strand.

  • Strand Separation

    • The two strands of DNA are held together by hydrogen bonds between the bases, which are easier to break than the covalent bonds holding together a single strand.
    • Analogy: Think of it like Velcro, where the two strands can be peeled apart.
    • Each existing strand serves to produce its complementary strand without needing intelligence; the base pairs simply align correctly.

  • Proteins Involved in DNA Replication

    1. Helicase
    • Binds at the origins of replication and separates the two DNA strands, creating a replication fork and a replication bubble.
    1. Single-Strand Binding Proteins
    • Prevent the separated strands from reannealing (reforming hydrogen bonds).
    1. Primase
    • Synthesizes short RNA primers that are complementary to the template strand, allowing DNA polymerase III to begin synthesizing new DNA.
    1. DNA Polymerase III
    • Synthesizes the majority of new DNA, adding nucleotides in the 5’ to 3’ direction.
    • Can only extend a new strand by adding nucleotides to a pre-existing strand (the RNA primer).
    1. DNA Polymerase I
    • Removes RNA primers and replaces them with DNA.
    1. DNA Ligase
    • Joins the Okazaki fragments on the lagging strand by creating covalent bonds where gaps remain (nicks) after RNA removal.

  • Directionality of DNA Synthesis

    • DNA polymerase III synthesizes DNA in the 3' to 5' (template strand) direction to produce a new strand in the 5' to 3' (new strand) direction.
    • Continuous Replication: Occurs on the leading strand where DNA is synthesized in a straight line as helicase unwinds the DNA.
    • Discontinuous Replication: Occurs on the lagging strand where synthesis occurs in short segments (Okazaki fragments) due to the anti-parallel nature of DNA.

  • Continuous vs. Discontinuous Replication

    • On the leading strand:
    • One primer leads to a long continuous DNA fragment.
    • On the lagging strand:
    • Multiple primers are needed leading to short DNA segments called Okazaki fragments.
    • Leading Strand: Continuous replication.
    • Lagging Strand: Discontinuous replication.

  • Process of Lagging Strand Replication

    • Primase lays down RNA primers intermittently as helicase continues to unwind the DNA.
    • DNA polymerase synthesizes short DNA segments, then has to return to lay the next segment, leading to the discontinuous nature of replication on this strand.

  • Final Steps of DNA Replication

    • After the DNA strands are synthesized, DNA polymerase I removes the RNA primers from the Okazaki fragments, replacing them with DNA nucleotides.
    • Ligase connects fragments by forming the last covalent bond between the newly made DNA segments.

  • Key Terms

    • Replication Fork: The Y-shaped region where the DNA is split into two strands for replication.
    • Origin of Replication: The point where helicase initiates strand separation.
    • Okazaki Fragments: Short DNA sequences synthesized discontinuously on the lagging strand.
    • Leading Strand: The strand synthesized continuously in the direction of fork movement.
    • Lagging Strand: The strand synthesized in fragments opposite to fork direction.