1: DNA structure/replication

Section 1: Molecular Genetics - 1: DNA Structure & Replication

DNA Structure: The Blueprint Molecule

Deoxyribonucleic acid (DNA) is the hereditary material encoding the instructions for life. Its structure, famously deduced by Watson, Crick, Franklin, and Wilkins, is a double helix. Each strand is a polymer composed of nucleotides. Each nucleotide consists of:

1. A deoxyribose sugar molecule.
2. A phosphate group.
3. One of four nitrogenous bases: Adenine (A), Thymine (T), Guanine (G), or Cytosine (C).

Nucleotides link via phosphodiester bonds, forming a sugar-phosphate backbone with bases projecting inward. The two strands run antiparallel (one $5'$ to $3'$, the other $3'$ to $5'$). They are held together by specific complementary base pairing: A pairs with T via two hydrogen bonds, and G pairs with C via three hydrogen bonds. This pairing ensures the strands are complementary – the sequence of one dictates the sequence of the other. The helix is stabilized by hydrogen bonding between bases and hydrophobic interactions between stacked base pairs. Key features include major and minor grooves, which provide binding sites for proteins regulating gene expression.

DNA Replication: Faithful Duplication

DNA replication is semi-conservative (demonstrated by the Meselson-Stahl experiment). Each original (parental) strand serves as a template for the synthesis of a new complementary strand, resulting in two double helices, each containing one original and one new strand. This process occurs during the S phase of the cell cycle and is highly accurate, crucial for genetic inheritance.

Replication begins at specific origins of replication. Key enzymes and proteins orchestrate the process:

1. Helicase: Unwinds the double helix, separating the strands and creating the replication fork.
2. Single-Stranded DNA Binding Proteins (SSBs): Stabilize the unwound single strands, preventing re-annealing.
3. Topoisomerase (e.g., DNA gyrase): Relieves torsional stress (supercoiling) ahead of the fork by cutting and rejoining DNA strands.
4. Primase: Synthesizes short RNA primers on each template strand, providing a free $3'$-OH group for DNA polymerase to begin synthesis.
5. DNA Polymerase III (Prokaryotes) / DNA Polymerase δ and ε (Eukaryotes): The primary replication enzymes. They add nucleotides to the growing DNA chain only in the $5'$ to $3'$ direction, using the parental strand as a template and obeying base-pairing rules (A-T, G-C). They also possess proofreading ($3'$ to $5'$ exonuclease) activity to correct errors.
6. DNA Polymerase I (Prokaryotes): Removes RNA primers and replaces them with DNA nucleotides.
7. DNA Ligase: Joins the Okazaki fragments (short, discontinuous segments synthesized on the lagging strand) by catalyzing phosphodiester bonds, creating a continuous strand.

Due to the antiparallel nature of DNA and the $5'$ to $3'$ synthesis constraint, replication is continuous on the leading strand (synthesized toward the fork) and discontinuous on the lagging strand (synthesized away from the fork in Okazaki fragments). The replication fork is asymmetrical, requiring coordinated action of multiple polymerases and accessory proteins. Telomerase solves the end-replication problem at chromosome termini in eukaryotes.