DNA structure

1. Nucleotide Structure and Nucleic Acids Polymerization

• Nucleotide components:

• Phosphate group

• Sugar: Deoxyribose in DNA, ribose in RNA

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

• Polymerization:

• Nucleotides are linked by phosphodiester bonds between the 5’ phosphate group of one nucleotide and the 3’ hydroxyl group of another.

• This creates the sugar-phosphate backbone of nucleic acids.

2. Purines vs. Pyrimidines

• Purines: Double-ring structure (Adenine and Guanine).

• Pyrimidines: Single-ring structure (Cytosine, Thymine in DNA, Uracil in RNA).

Tip: Remember “CUT the pie” for pyrimidines (C, U, T).

3. Base Pairing Basics

• Complementary base pairing:

• A pairs with T (or U in RNA)

• G pairs with C

• Base pairs are held together by hydrogen bonds.

4. A-T vs. G-C Bonds

• A-T (or A-U): 2 hydrogen bonds.

• G-C: 3 hydrogen bonds → Makes G-C pairs stronger and more stable.

• This matters in DNA stability and melting temperature (higher G-C content = higher stability).

5. Nucleic Acid Directionality and Antiparallel Nature

• 5’ end: Has a phosphate group.

• 3’ end: Has a hydroxyl (-OH) group.

• DNA strands run antiparallel: One strand runs 5’ → 3’, the other 3’ → 5’.

Why it matters: Directionality is crucial for replication and transcription.

6. Major and Minor Grooves of DNA

• DNA’s double helix has major and minor grooves created by the twisting of the helix.

• Major groove: Larger, allows more access for protein binding.

• Minor groove: Smaller, limited protein interaction.

7. Differences Between DNA and RNA

Feature DNA RNA

Sugar Deoxyribose Ribose

Bases A, T, G, C A, U, G, C

Strands Double-stranded Single-stranded

Stability More stable (no OH on 2’) Less stable

8. Why DNA Doesn’t Have Uracil

• Cytosine can spontaneously deaminate to form uracil.

• If DNA had uracil, it would be hard for the cell to distinguish this mutation from real uracil.

• Thymine ensures integrity in DNA.

9. DNA Organization and Compaction

• Histones: Proteins that DNA wraps around to form nucleosomes.

• Nucleosome: DNA-histone complex, ~147 base pairs wrap around an octamer of histones.

• 30-nm fiber: Further coiling of nucleosomes.

• Radial loop domains: Loops anchored to a protein scaffold.

• Chromatin: DNA-protein complex in chromosomes:

• Euchromatin: Loosely packed, transcriptionally active.

• Heterochromatin: Tightly packed, transcriptionally inactive.