Topic 9 – Nucleic Acids & DNA Replication

Key Elements & Acronym

• Remember: CHONP – Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus are the constituent atoms of nucleic acids.

Components of Nucleic Acids

• Nucleic acids (DNA & RNA) are polymers of nucleotides.
• Each nucleotide (monomer) consists of:
  • A 5-carbon (pentose) sugar.
  • A phosphate (PO₄³⁻) group – identical in DNA & RNA.
  • A nitrogenous base (one per nucleotide).
• Generalized structural formula:
  \text{Base}-\text{C}1'\text{(Sugar)}-\text{C}5'\text{—PO}_4^{3-}

DNA Nucleotides

• Sugar: Deoxyribose (formula C5H{10}O_4).
• Phosphate group.
• Four bases: Adenine (A), Guanine (G), Cytosine (C), Thymine (T).

RNA Nucleotides

• Sugar: Ribose (formula C5H{10}O_5).
• Phosphate group (same as DNA).
• Four bases: Adenine (A), Guanine (G), Cytosine (C), Uracil (U) (replaces thymine).
• Difference between the two sugars = one extra oxygen at the 2' carbon (–OH in ribose vs –H in deoxyribose).

Nitrogenous Bases: Classes & Structures

• Purines (double-ring): Adenine, Guanine.
  • Memory: "Pure As Gold" (Pu = purine, A & G).
• Pyrimidines (single-ring): Cytosine, Thymine, Uracil.
  • Memory: "CUT the PY (pie)" (C, U, T = pyrimidine).
• Structural distinction relevant to replication & drug targeting (e.g., anti-viral nucleoside analogs often mimic a specific ring size).

Complementary Base-Pairing Rules

• DNA: A \leftrightarrow T ; G \leftrightarrow C.
• RNA: A \leftrightarrow U ; G \leftrightarrow C.
• Binding forces: hydrogen bonds.
  • A–T (or A–U) = 2 H-bonds.
  • G–C = 3 H-bonds.
  • Consequence: G–C regions are more thermostable; require more energy to denature.
• Bases in a given strand dictate the complementary sequence—foundation for semi-conservative replication & accurate transcription/translation.

DNA Double-Helix Architecture

• Discovered via:
  • Rosalind Franklin (1952) – X-ray diffraction photo.
  • Watson & Crick (1953) – built 3-D model using Franklin’s data.
• Structural features:
  • Two antiparallel strands (one 5' \to 3', the other 3' \to 5').
  • Sugar-phosphate backbone on exterior; bases form internal "rungs".
  • Major & minor grooves—binding sites for regulatory proteins.
• Functional implications:
  • Stability for information storage.
  • Accessibility via grooves for gene regulation.

Directionality & "Language" of DNA

• 5' end: Free phosphate on carbon 5'.
• 3' end: Free hydroxyl on carbon 3'.
• DNA/RNA polymerases can only add nucleotides to the 3'-OH, thus synthesis always proceeds 5' \to 3' on the new strand.

DNA vs RNA – Three Core Differences

1. Sugar: Ribose vs deoxyribose (extra O).
2. Base: Uracil replaces thymine in RNA.
3. Backbone: RNA is single-stranded (though intra-strand base-pairing can create secondary structures).

• Functional result: RNA serves as a versatile "middleman"—mRNA, tRNA, rRNA, etc.—facilitating protein synthesis, regulation, catalysis.

Biological Roles

• DNA = Blueprint:
  • Encodes hereditary info in unique nucleotide sequences ("recipes" for proteins).
  • Stability & double-helix allow faithful replication with low mutation rates.
  • Mutations (base changes) may become permanent if they do not disrupt overall structure—basis for evolution & genetic disease.
• RNA = Translator & Worker:
  • Converts DNA information into proteins (transcription → translation).
  • Multiple RNA species orchestrate the process (detailed Ch. 10).

Overview of DNA Replication (Semi-Conservative)

• Each original strand serves as a template; new complementary strands built adjacent → two identical daughter molecules.
• Essential during all cell divisions (binary fission, mitosis, meiosis).
• Human genome size ≈ 3 \times 10^9 base pairs → high fidelity imperative.

Key Enzymes

1. Helicase – Unwinds double helix, breaks H-bonds at replication fork.
2. DNA Polymerase – Adds nucleotides to 3' end; also possesses proofreading exonuclease activity.
3. Ligase – Seals nicks in sugar-phosphate backbone, especially between Okazaki fragments on lagging strand.
4. (Mentioned) Primase – Synthesizes short RNA primer on lagging strand.

Step 1: Unwinding

• Begins at origins of replication (multiple in eukaryotes).
• Forms replication bubbles; two forks proceed bidirectionally.

Step 2: Reconstruction / Elongation

• Leading Strand: Continuous synthesis toward replication fork.
• Lagging Strand: Discontinuous; primase lays primers → DNA Pol builds Okazaki fragments away from fork; RNA primers replaced; fragments joined by ligase.

Proofreading & Fidelity

• DNA Pol error rate ≈ 1/10^{9} bases.
• Mismatch repair pathways further reduce mutations; however, residual changes underpin genetic variation.

Practice Example (Complementary Sequence)

• Given 5'\ \text{ATAACGTCGG}\ 3' → complementary = 3'\ \text{TATTGCAGCC}\ 5' (antiparallel orientation).

Prokaryotic vs Eukaryotic Replication

• Prokaryotes (bacteria):
  • Single, circular chromosome (supercoiled).
  • One origin; replication proceeds in both directions around the loop → two identical circles.
• Eukaryotes:
  • Multiple linear chromosomes within nucleus.
  • Numerous origins per chromosome; bubbles expand bidirectionally until meeting.

Bacterial Supercoiling & Relaxation

• DNA exists in a highly twisted supercoiled state.
• Topoisomerase & DNA gyrase relieve tension by cutting, swiveling, re-ligating DNA—essential before replication machinery can operate.

Sample Quiz/Recall Points

• Which nucleotide component is unchanged between DNA & RNA? → Phosphate group.
• Adenine is a purine (double ring).
• Base not in DNA? → Uracil.
• Guanine pairs with? → Cytosine, via 3 hydrogen bonds.
• Energy to break G–C vs A–T/U? → G–C requires more energy (extra H-bond).

Ethical & Practical Notes

• Understanding replication enzymes enables development of antibiotics (e.g., quinolones target bacterial gyrase) and chemotherapy (nucleoside analogs).
• Mutation rates & repair efficiency influence cancer risk, antibiotic resistance, and biotechnological applications (PCR fidelity).