Primary structure and nucleotide components
The primary structure of nucleic acids is the precise sequential order of nucleotides in 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 (carbohydrate component — sugar).
- Phosphate group.
Within the nucleotide itself, 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 through a 5'-phosphoester bond.
To form a macromolecule, nucleotides are joined together by a strong 3',5'-phosphodiester bond. It 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 instead, it is ribose (RNA).
Rules for polynucleotide chain notation
In biochemistry, strict rules are adopted for writing nucleic acid sequences. A convenient single-letter code is traditionally used to denote nucleotides.
- Direction of notation: is always strictly from left to right.
- Beginning of the chain (left): this is the nucleotide possessing a free 5'-phosphate end.
- End of the chain (right): this is the nucleotide with a free –OH group located at the 3'-position of the pentose.
Particular attention should be paid to the use of primes (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 nitrogenous bases.
DNA secondary structure: 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 secondary structure is antiparallelism. The two chains run in opposite directions relative to each other, with the nitrogenous bases oriented toward the interior of the molecule. They lie in the same plane, which is positioned nearly perpendicular to the main axis of the helix, forming step-like structures.
Principle of complementarity and Chargaff's rules
The two strands of a DNA molecule are not identical copies; they are complementary. This means that the nucleotide sequence of one strand strictly and unambiguously dictates the sequence in the other strand. Adenine (A) of one chain always forms a bond with thymine (T) of the other. Cytosine (C) binds only with guanine (G). Stable pairs are formed: A = T and G = C.
From this fundamental principle follow quantitative patterns known in biochemistry as Chargaff's rules:
- The total amount of adenylic nucleotides in the molecule is strictly equal to the amount of thymidylic nucleotides (A = T).
- The total amount of guanylic nucleotides is equal to the amount of cytidylic nucleotides (G = C).
There is also a species-specific coefficient. This is the ratio of the sum of adenine and thymine to the sum of guanine and cytosine: (A + T) / (G + C). This value is absolutely constant for each specific species of living organisms and serves as its unique chemical characteristic.
Briefly: answers to topical questions
Which nitrogenous bases are classified as purines and which as pyrimidines?
Nitrogenous bases include purine and pyrimidine derivatives that are part of nucleotides along with a pentose and a phosphoric acid residue.
- Purine bases — adenine and guanine (common to both DNA and RNA molecules).
- Pyrimidine bases — cytosine (common to both nucleic acids), thymine (found only in DNA), and uracil (found only in RNA).
How many hydrogen bonds are formed between the A–T and G–C pairs?
A varying number of hydrogen bonds is formed between complementary nitrogenous bases of antiparallel DNA strands.
- A–T pair (Adenine — Thymine) — held together by two hydrogen bonds.
- G–C pair (Guanine — Cytosine) — held together by three hydrogen bonds.
These hydrogen bonds between paired bases ensure the thermodynamic stability of the spatial structure of the molecule's double helix.
What are the main types of RNA and what are their functions?
The cited sources mention mRNA, tRNA, and rRNA.
- mRNA — contains codons (triplets) according to which the polypeptide chain is synthesized on ribosomes.
- tRNA — has an acceptor site at the 3'-end with a CCA sequence, which serves for amino acid attachment; its anticodon interacts complementarily with the mRNA codon.
- rRNA — sources indicate that nuclear DNA encodes 4 types of rRNA; the specific function of rRNA is not disclosed in the cited sources.
Remember the prime rule: numbers with a prime sign (3', 5') always refer to the carbons of the sugar (pentose). This is specifically done to avoid confusing them with atom numbering within the nitrogenous base itself.
Class and exam questions
How does DNA chemically differ from RNA?
The main difference lies in the substituent at the 2'-carbon atom of the sugar (pentose). In DNA, it is hydrogen (deoxyribose), while in RNA, it is a hydroxyl group (ribose).
What does "DNA strands are antiparallel" mean?
This means that the two polynucleotide strands in the double helix run in opposite directions. Opposite the 5'-end of one chain is always the 3'-end of the other chain.
What bonds hold the two DNA strands together?
The two chains are held together by hydrogen bonds. These form between nitrogenous bases directed toward the interior of the helix, strictly according to the principle of complementarity (A=T, G=C).
What else to study on this topic
- Detailed chemical structure of nitrogenous bases
- Mechanism of 3',5'-phosphodiester bond formation
- Nucleosome formation and DNA packaging
- Biological significance of the species-specific coefficient
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