AP Bio unit 6.2

DNA and DNA Replication

Overview of DNA Structure

  • DNA (Deoxyribonucleic Acid): The molecule that carries genetic information.

  • Chromosome: Structure made of DNA and proteins that contains genetic information.

  • Free Nucleotides: The building blocks of DNA, comprising adenine (A), thymine (T), cytosine (C), and guanine (G).

Key Molecular Components

  • DNA Polymerase: Enzyme responsible for synthesizing new DNA strands by adding nucleotides.

  • Adenine (A): One of the four nucleotides, pairs with thymine.

  • Thymine (T): One of the four nucleotides, pairs with adenine.

  • Cytosine (C): One of the four nucleotides, pairs with guanine.

  • Guanine (G): One of the four nucleotides, pairs with cytosine.

Process of DNA Replication

  • When does it occur?: DNA replication occurs during the S phase of the cell cycle.

  • Directionality: Strands of DNA are oriented in opposite directions (5′ to 3′ and 3′ to 5′).

  • RNA Primer and Okazaki Fragments: RNA primers initiate DNA synthesis; Okazaki fragments are short DNA sequences on the lagging strand.

Models of DNA Replication

Three Alternative Models

  1. Conservative Model

    • The parental strands direct the synthesis of an entirely new double-stranded molecule.

    • The parental strands are completely conserved.

  2. Semi-Conservative Model

    • Each of the two parental strands serves as a template for a new strand, resulting in daughter molecules each containing one parental and one new strand after replication.

  3. Dispersive Model

    • The material in the parental strands is randomly distributed between the two daughter molecules, leading to a mix of old and new DNA.

Meselson-Stahl Experiment (1954)

  • Goal: To determine which model of DNA replication is correct.

  • Process:

    1. Bacteria were cultured with a heavy nitrogen isotope, 15N^{15}N.

    2. Bacteria were then transferred to a medium containing a light nitrogen isotope, 14N^{14}N.

    3. DNA was centrifuged and analyzed after each replication round.

Conclusions of the Meselson-Stahl Experiment

  • Analyzed samples pointed to the semi-conservative model being accurate, as the behavior of nitrogen isotopes in replicated DNA indicated parental strands were conserved across generations.

Steps of DNA Replication

  1. Helicase: Unwinds the parental double helix at origins of replication.

    • Forms replication forks from the open DNA.

  2. Single-Strand Binding Proteins (SSBP): Stabilize and prevent re-pairing of separated strands.

  3. Topoisomerase: Relieves strain ahead of the replication fork by breaking, swiveling, and rejoining DNA strands.

  4. Primase: Synthesizes short RNA primers necessary for DNA polymerases to begin synthesis.

  5. DNA Polymerase III: Synthesizes the leading strand continuously in the 5' to 3' direction toward the replication fork.

    • On the lagging strand, synthesizes in chunks (Okazaki fragments).

  6. DNA Polymerase I: Removes RNA primers and replaces them with DNA nucleotides.

  7. DNA Ligase: Joins Okazaki fragments by connecting the sugar-phosphate backbones into a continuous DNA strand.

  8. Error Checking: DNA polymerases also function as proofreading enzymes for replication accuracy.

Shortened Mnemonics of DNA Replication Steps

  • OPLACE:

    • Open and unwind (Origin, Helicase, Topoisomerase)

    • Prime (Primase)

    • PLLL-ace (Polymerase, Leading vs. Lagging, Ligase, Little Error checking)

Addressing the 5' End Problem

  • Issue: DNA polymerase cannot complete replication at the 5' end of the lagging strand, risking gradual shortening of DNA strands.

  • Solution: Telomeres, repeating units of non-coding DNA sequences at the ends of chromosomes, protect genes from erosion.

  • Telomerase: An enzyme that adds telomeres to DNA, preventing loss during replication.

Proofreading and Repair Mechanisms

  • Role of DNA Polymerase: Proofreads bases during nucleotide addition.

  • Mismatch Repair: If errors occur, specific enzymes remove and replace incorrectly paired nucleotides.

  • Nuclease: Capable of removing damaged DNA segments, followed by the functions of DNA polymerase and ligase to repair the DNA.

Quick Review

  • Complementary Strand Synthesis: If a parental strand is 5'-ACGTAC-3', the complementary strand will read 3'-TGCATG-5'.

  • Roles:

    • Helicase: Unzips DNA.

    • Topoisomerase: Relieves strain during unwinding.

    • DNA Polymerase III: Adds nucleotides to the growing strand.

  • Direction of DNAP III: It moves along the parental strand from 3' to 5'.

  • Okazaki Fragments: Occur on the lagging strand because DNA polymerase III must replicate in segments moving away from the replication fork.

  • Key Terms:

    • Leading Strand: Continuously synthesized in the direction of the replication fork.

    • Lagging Strand: Synthesized discontinuously, forming Okazaki fragments due to the needfor backward processing.

    • Primase: An enzyme that synthesizes short RNA primers, which are necessary for the initiation of DNA replication on both leading and lagging strands.

    • DNA Polymerase:

    • Primer: Short segments of RNA that serve as starting points for DNA synthesis, providing the necessary 3' hydroxyl group for DNA polymerase to add DNA nucleotides.

    • heliocase: An enzyme that unwinds the DNA double helix at the replication fork, allowing the strands to be separated for replication.