Primary Structure and Nucleotide Components
The primary structure of nucleic acids represents the strict sequential order of nucleotides within a long polynucleotide chain. Each individual monomer (nucleotide) is a complex chemical entity comprising three basic components:
- Nitrogenous base (adenine, cytosine, guanine, and others).
- Pentose sugar.
- Phosphate group.
Within the nucleotide, atoms are held together by specific bonds. The nitrogenous base is attached to the 1'-carbon of the pentose via an N-glycosidic bond. The phosphate group is attached to the 5'-carbon via a 5'-phosphoester bond.
To form a macromolecule, nucleotides are joined together by a strong 3',5'-phosphodiester bond. This bond forms between the 3'-carbon of the pentose of one nucleotide and the 5'-phosphate of the next in the chain.
A crucial difference between types of nucleic acids lies in the substituent at the 2'-carbon atom of the pentose. If a hydrogen atom (H) is located at this position, the molecule contains deoxyribose (DNA). If a hydroxyl group (OH) is present, it is ribose (RNA).
Notation Rules for Polynucleotide Chains
In biochemistry, strict rules govern the notation of nucleic acid sequences. A convenient single-letter code is traditionally used to designate nucleotides.
- Direction of writing: Always proceeds strictly from left to right.
- Start of the chain (left): The nucleotide bearing a free 5'-phosphate end.
- End of the chain (right): The nucleotide with a free –OH group located at the 3'-position of the pentose.
Special attention should be paid to the use of prime symbols (3', 5'). This labeling is used exclusively for numbering the carbon atoms within the carbohydrate ring (pentose). This approach clearly distinguishes sugar atoms from the atoms making up the rings of the nitrogenous bases.
Secondary Structure of DNA: The Double Helix
The spatial structure of a DNA molecule is a right-handed double helix. It is formed by two separate polynucleotide strands held together by hydrogen bonds.
A key characteristic of the secondary structure is antiparallelism. The two strands run in opposite directions relative to each other. Meanwhile, the nitrogenous bases face inward toward the interior of the molecule. They lie in a single plane, and this plane is oriented almost perpendicular to the main axis of the helix, forming structural "rungs".
Principle of Complementarity and Chargaff's Rules
The two strands of a DNA molecule are not identical copies; they are complementary. This means the nucleotide sequence of one strand strictly and unambiguously dictates the sequence of the other strand. Adenine (A) on one strand always pairs with thymine (T) on the other. Cytosine (C) pairs exclusively with guanine (G). Stable pairs are formed: A = T and G = C.
From this fundamental principle follow quantitative regularities known in biochemistry as Chargaff's rules:
- The total amount of adenine nucleotides in a molecule strictly equals the amount of thymine nucleotides (A = T).
- The total amount of guanine nucleotides equals the amount of cytosine nucleotides (G = C).
Additionally, there is a species-specific ratio, defined as the sum of adenine and thymine divided by the sum of guanine and cytosine: (A + T) / (G + C). This value is completely constant for each specific species of living organisms and serves as its unique chemical characteristic.