Nucleic Acid Structure
High-Yield Summary
- Watson & Crick built the double helix model from X-ray diffraction data ("Photo 51") produced in Rosalind Franklin's lab — shown to Watson without her knowledge; she died in 1958, before the 1962 Nobel Prize went to Watson, Crick, and Wilkins.
- Four defining features of the double helix: (1) two strands spiral around a shared axis, (2) strands are antiparallel (5'→3' / 3'→5'), (3) sugar-phosphate backbone on the outside, (4) bases point inward.
- Base pairing: A-T via 2 H-bonds, G-C via 3 H-bonds (G-C regions bind tighter, harder to separate). Chargaff's rules: %A = %T, %G = %C, so purines (A+G) = pyrimidines (C+T).
- Base stacking (van der Waals between stacked aromatic bases) adds stability alongside H-bonding.
- B-DNA (right-handed, ~10 bp/turn, 3.4 nm/turn) is the standard cellular form, with major/minor grooves for protein access. Z-DNA (left-handed, ~12 bp/turn, ~4.6 nm/turn) appears under high-GC/unusual supercoiling.
- Denaturation = H-bonds break (heat/pH/chemicals) → single strands. Reannealing = H-bonds re-form → double strand. This cycle is the conceptual basis of PCR.
Key Terms
- Antiparallel
- The two DNA strands run in opposite directions — one 5'→3', the other 3'→5'.
- Chargaff's rules
- In double-stranded DNA, %A=%T and %G=%C, so total purines equal total pyrimidines.
- Base stacking
- Van der Waals interactions between stacked aromatic bases inside the helix; adds stability.
- Major/minor groove
- Spaces between the backbone strands in B-DNA where proteins access the bases.
- Denaturation
- Breaking of hydrogen bonds between base pairs (heat, pH, chemicals), separating DNA strands.
- Reannealing
- Re-formation of hydrogen bonds between complementary single strands, restoring double-stranded DNA.
B-DNA vs. Z-DNA
| Feature | B-DNA vs. Z-DNA |
|---|---|
| Handedness | Right-handed / Left-handed |
| Shape | Smooth spiral / Extended, zigzag |
| Base pairs per turn | ~10 / ~12 |
| Length per turn | 3.4 nm / ~4.6 nm |
| Typical occurrence | Standard cellular form / High GC-content or unusual supercoiling |
Denaturation → Reannealing Cycle (Basis of PCR)
- 1Heat, pH change, or chemical agent breaks hydrogen bonds between base pairs.
- 2Denaturation: double-stranded DNA separates into two single strands.
- 3Single-stranded DNA is now accessible to enzymes (DNA polymerase, RNA polymerase) or, in PCR, to primers.
- 4Conditions reverse (e.g. cooling) — reannealing: complementary bases re-form hydrogen bonds.
- 5Double-stranded structure is restored (or, in PCR, primers anneal and are extended before the next heat cycle).
Common MCAT Trap
- G-C pairs form 3 hydrogen bonds vs. A-T's 2 — GC-rich DNA denatures at a higher temperature. This detail resurfaces for telomeres/centromeres (also GC-rich, for stability).
- Chargaff's rules give %A=%T and %G=%C — NOT %A=%G. Don't conflate base pairing partners with base pairing amounts across all four bases.
- B-DNA is the default/standard form tested — Z-DNA is a recognizable exception (left-handed, high-GC/supercoiled context), not the norm.
Quick Recall
How many hydrogen bonds hold a G-C pair together vs. an A-T pair?
What do Chargaff's rules state?
What distinguishes Z-DNA from B-DNA structurally?
What two processes, applied cyclically, form the conceptual basis of PCR?