DNA Structure and Replication

Foundations of Heredity and Nucleic Acids

• Chromosomes and Genes:

  • Chromosomes are tightly coiled strands of DNA and histones (e.g., humans possess $23$ pairs / $46$ total chromosomes; dogs possess $37$ pairs / $74$ total chromosomes).

  • Genes are specific segments of DNA located along chromosomes that carry instructions for protein synthesis.

• Nucleic Acid Composition:

  • Nucleic acids (DNA and RNA) are macromolecules that store genetic information.

  • Monomer units are nucleotides, each comprising three components:

  • A $5$-carbon sugar (deoxyribose in DNA; ribose in RNA)

  • A phosphate group

  • A nitrogen base: Adenine (A), Guanine (G), Cytosine (C), Thymine (T, DNA only), or Uracil (U, RNA only)

DNA Molecular Structure

• Double Helix Discovery:

  • Proposed in $1953$ by James Watson and Francis Crick, utilizing chemical data from Erwin Chargaff and X-ray diffraction patterns produced by Rosalind Franklin and Maurice Wilkins.

• Structural Framework:

  • Sugar-phosphate backbone is linked along the outside by strong covalent bonds.

  • Complementary nitrogen base pairs meet in the interior, linked by weak hydrogen bonds.

• Base-Pairing (Chargaff's Rules):

  • Purines ($2$ rings: Adenine, Guanine) pair exclusively with Pyrimidines ($1$ ring: Cytosine, Thymine).

  • Adenine forms $2$ hydrogen bonds with Thymine ($\text{A} = \text{T}$).

  • Cytosine forms $3$ hydrogen bonds with Guanine ($\text{C} \equiv \text{G}$).

• Antiparallel Strands:

  • Strands run in opposite orientations: one strand runs $5' \rightarrow 3'$ while the opposite strand runs $3' \rightarrow 5'$.

  • The $5'$ end terminates at a phosphate group, and the $3'$ end terminates at the deoxyribose sugar.

DNA Replication Process and Machinery

• Timing and Mechanism:

  • Occurs inside the nucleus during the S Phase (Synthesis) of Interphase.

  • Operates via semi-conservative replication: each newly synthesized double helix retains one original parent strand and one newly assembled complementary strand.

• Key Replication Enzymes:

  • Helicase: Unwinds and unzips the double helix by cleaving hydrogen bonds at origins of replication.

  • Primase: Synthesizes short RNA primers required to initiate strand extension.

  • DNA Polymerase: Adds complementary nucleotides exclusively to the free $3'$ end of the template, synthesizing new DNA strictly in the $5' \rightarrow 3'$ direction; replaces RNA primers with DNA; proofreads the newly constructed strand.

  • DNA Ligase: Connects discontinuous DNA segments by forming phosphodiester bonds, sealing gaps in the sugar-phosphate backbone.

• Strand Elongation Dynamics:

  • Leading Strand: Synthesized continuously toward the replication fork ($5' \rightarrow 3'$); requires only $1$ RNA primer.

  • Lagging Strand: Synthesized discontinuously away from the replication fork; produces Okazaki fragments; requires multiple RNA primers; fragments are joined together by DNA ligase.

Foundations of Heredity & Nucleic Acids

• Chromosomes & Genes:

  • Chromosomes: Tightly coiled strands of DNA and histone proteins ($23$ pairs / $46$ total in humans).

  • Genes: Segments of DNA located on chromosomes that code for specific proteins.

• Nucleotide Structure:

  • The monomer unit of nucleic acids, consisting of:

  • A $5$-carbon sugar (deoxyribose in DNA; ribose in RNA)

  • A phosphate group

  • A nitrogen base (A, T, C, G in DNA; A, U, C, G in RNA)

DNA Molecular Structure

• Double Helix:

  • Proposed in $1953$ by Watson and Crick (aided by Rosalind Franklin, Maurice Wilkins, and Erwin Chargaff).

  • Sugar-Phosphate Backbone: External support held by strong covalent bonds.

  • Internal Rungs: Complementary base pairs joined by weak hydrogen bonds.

• Base-Pairing Rules (Chargaff's Rules):

  • Purines ($2$ rings): Adenine (A), Guanine (G)

  • Pyrimidines ($1$ ring): Cytosine (C), Thymine (T)

  • Adenine binds Thymine ($A = T$ via $2$ hydrogen bonds)

  • Cytosine binds Guanine ($C \equiv G$ via $3$ hydrogen bonds)

• Antiparallel Orientation:

  • Strands run in opposite directions: $5' \rightarrow 3'$ and $3' \rightarrow 5'$.

  • $5'$ end terminates at a phosphate group; $3'$ end terminates at a deoxyribose sugar.

DNA Replication

• Overview:

  • Occurs during the S Phase (Synthesis) of Interphase inside the nucleus.

  • Semi-Conservative: Each resulting DNA molecule contains one original (template) strand and one newly synthesized strand.

• Key Enzymes:

  • Helicase: Unzips the double helix at origins of replication.

  • Primase: Synthesizes short RNA primers to initiate synthesis.

  • DNA Polymerase: Adds complementary nucleotides in the $5' \rightarrow 3'$ direction only, replaces RNA primers with DNA, and proofreads.

  • DNA Ligase: Connects DNA segments and Okazaki fragments by sealing phosphodiester bonds.

• Replication Strands:

  • Leading Strand: Synthesized continuously toward the replication fork (needs only $1$ primer).

  • Lagging Strand: Synthesized discontinuously away from the replication fork in short chunks called Okazaki fragments (needs multiple primers).