DNA Structure: Nucleotides and Chargaff’s Rules

DNA and Chromosome Structure

Nucleotide Structure

Nucleotides are the basic building blocks of nucleic acids such as DNA and RNA. Each nucleotide consists of three distinct components:

• Phosphate Group: A negatively charged group attached to the 5' carbon of the sugar. It forms the backbone of the DNA or RNA strand by linking to the next nucleotide.

• Pentose Sugar: In DNA, the sugar is deoxyribose; in RNA, it is ribose. The sugar has numbered carbons (1' to 5'). The 3' hydroxyl (OH) group is crucial for chain elongation during DNA/RNA synthesis.

• Nitrogenous Base: This is either a purine (adenine, guanine) or pyrimidine (cytosine, thymine in DNA; uracil in RNA). The base is attached to the 1' carbon of the sugar.

Key Features:

• The 3' hydroxyl group (–OH) on the sugar is essential for forming phosphodiester bonds during DNA/RNA synthesis.

• The 5' carbon is where the phosphate group attaches, forming the start of the nucleotide chain.

• The presence of deoxyribose (lacking a 2' OH group) indicates the nucleotide is from DNA; ribose (with a 2' OH group) is found in RNA.

Example: The diagram shows a nucleotide with a deoxyribose sugar, a phosphate group, and a purine base (adenine). The 3' OH group is labeled, and the 5' carbon attached to the phosphate is highlighted.

Additional info: The absence of a 2' hydroxyl group in the sugar confirms this is a DNA nucleotide.

DNA and Chromosome Structure

Chargaff’s Rules and Base Composition

Erwin Chargaff discovered fundamental relationships between the amounts of nucleotide bases in DNA, which are now known as Chargaff’s rules. These rules are crucial for understanding the double-helical structure of DNA.

• Chargaff’s Key Insight: In any double-stranded DNA molecule, the amount of adenine (A) equals the amount of thymine (T), and the amount of guanine (G) equals the amount of cytosine (C).

• Mathematical Representation: $[A] = [T]$ and $[G] = [C]$

• Relation to DNA Structure: This equality is due to base pairing: A pairs with T via two hydrogen bonds, and G pairs with C via three hydrogen bonds, stabilizing the double helix.

Example Calculation:

• If a DNA molecule is 30% adenine (A), then it must also be 30% thymine (T).

• The remaining 40% is divided equally between guanine (G) and cytosine (C): 20% G and 20% C.

Base	Percentage
Adenine (A)	30%
Thymine (T)	30%
Guanine (G)	20%
Cytosine (C)	20%

Application: Chargaff’s rules are used to predict base composition and to verify the integrity of DNA samples in molecular biology.

Additional info: In single-stranded DNA or RNA, these ratios may not hold, as base pairing is not enforced.