DNA Structure and Replication

Basic DNA Structure

  • DNA is composed of two polynucleotide strands connected by:
    • Nucleotides (the monomers)
    • Each nucleotide consists of:
      • Sugar (deoxyribose in DNA)
      • Phosphate
      • Nitrogenous base
  • Phosphodiester bonds hold nucleotides together in strands.
  • Structure features:
    • Antiparallel: Strands run in opposite directions.
    • Complementarity: Specific nitrogenous bases pair together.
    • Double helix: Twisted ladder shape.

Storage of Genetic Information

  • Information in DNA is encoded in the sequence of nitrogenous bases, specifically:
    • Purines: Adenine (A) and Guanine (G)
    • Pyrimidines: Thymine (T) and Cytosine (C)
  • Pairing rules:
    • A pairs with T (connected by 2 hydrogen bonds)
    • G pairs with C (connected by 3 hydrogen bonds)

Organization of DNA

  • DNA exists in cells as chromosomes:
    • Chromosomes: Long pieces of DNA containing many genes.
    • Prokaryotic DNA: Loop structure.
    • Eukaryotic DNA:
    • Multiple linear chromosomes, supercoiled during cell division.
    • Humans have 46 chromosomes in 23 pairs (diploid, 2n).
  • Gene: Section of DNA that encodes for a protein.
  • Alleles: Different forms of the same gene.
  • Locus: Specific position of a gene on a chromosome.
  • Gene families: Groups of closely related genes.

What is a Genome?

  • Genome: Collection of all DNA in an organism across its chromosomes.
  • Differences in genomes of prokaryotes vs. eukaryotes.

Historical Discoveries of DNA

  • 1869: Johann Friedrich discovered "nuclein."
  • 1920s-1940s: Experiments by Griffith & Avery suggested DNA as an information-carrying molecule.
  • 1952: Hershey & Chase demonstrated DNA stored hereditary information.
  • 1950s: Chargaff discovered base pairing rules (A=T, G=C).
  • 1953: Rosalind Franklin used X-ray diffraction to capture DNA images; Watson & Crick built molecular models based on collected knowledge.

DNA Replication Hypotheses

  • Three models proposed:
    • Conservative: Original strands separate and remain intact.
    • Dispersive: New DNA molecules are a mix of old and new DNA.
    • Semiconservative: Each new molecule consists of one original and one new strand.
  • 1958: Meselson & Stahl supported the semiconservative model using isotopes in bacterial experiments.

Overview of DNA Replication

  • Requires:
    • DNA molecule to copy (parental DNA).
    • Enzymes to perform the copying.
    • Nucleotides (deoxynucleoside triphosphates, or dNTPs) to build the copy.
    • Nucleotides consist of deoxyribose, a nitrogenous base (A, T, G, C), and 3 phosphate groups for energy.
  • Stages of replication:
    1. Initiation: Begins at the origin of replication.
    2. Elongation: New strands are synthesized.
    3. Termination: Replication finishes.

Prokaryotic vs. Eukaryotic Replication

  • Eukaryotes have:
    • More DNA and multiple origins of replication.
    • More enzymes involved.
    • A complex initiation phase.
    • Specific enzymes for linear chromosomes.

Enzymes and Proteins in Replication

  • Helicase: Unwinds the DNA strands using ATP.
  • Gyrase: Topoisomerase that relieves strain from unwinding.
  • Primase: Lays down RNA primer to signal where to start extension.
  • DNA Polymerases: Synthesizes new DNA strands in the 5’ to 3’ direction:
    • DNA Polymerase III: Principal replication enzyme.
    • DNA Polymerase I: Replaces RNA primer with DNA.
  • DNA Ligase: Joins fragments of DNA.
  • Single-strand binding proteins: Prevent strands from re-annealing.
  • Sliding clamps: Hold DNA polymerase in place.
  • Replisome: Complex formed by multiple enzymes for DNA replication.

Process of DNA Replication

Initiation

  • Pre-replication complex binds to the origin, opening DNA and forming replication forks.
  • Helicase unwinds strands, with gyrase relieving torsional strain.
  • Single-strand binding proteins stabilize the DNA.

Elongation

  • Primase adds RNA primer.
  • DNA Polymerase III synthesizes new DNA, adding nucleotides to the 3’ end towards the parent strand’s 5’ end.
  • Occurs continuously on the leading strand and semidiscontinuously on the lagging strand, where Okazaki fragments are formed.

Termination

  • Prokaryotes: Termination occurs when DNA polymerase III reaches the origin.
  • Eukaryotes: More complex due to telomeres.
    • Telomeres: Repeat sequences at chromosome ends, unique to Eukaryotes.
    • Telomerase: Enzyme that maintains telomere length, related to aging and cancer.

DNA Repair Mechanisms

  • Despite high fidelity, DNA replication has mistakes that need repair.
  • Repair mechanisms include:
    • Proofreading: DNA polymerase recognizes mismatched pairs.
    • Mismatch repair: Scans newly replicated DNA, correcting errors found.
    • Excision repair: Damaged bases are excised, replaced by DNA polymerase I.