Molecular architecture and helical parameters
The basis of the DNA molecule is two polynucleotide chains twisted into a classic right-handed helix. The molecular framework (sugar-phosphate backbone) is formed by deoxyribose molecules and phosphoric acid residues connected by strong covalent bonds. This backbone is located on the outside of the helix.
Inside the structure are nitrogenous bases. They have a flat shape and lie strictly perpendicular to the axis of the macromolecule. The three-dimensional model proposed on the basis of X-ray diffraction analysis (B-form) has strict geometric parameters:
- A complete turn or pitch of the helix (360°) is 3.4 nm.
- There are 10 base pairs per turn.
- The distance between adjacent "steps" is 0.34 nm, and the rotation angle of each successive pair is 36°.
- Two distinct grooves form on the surface of the helix: a minor groove (about 1.62 nm wide) and a major groove (about 2.2 nm).
The polynucleotide chains are antiparallel: they are oriented in opposite directions. Where one chain has a 5'-end (bearing a phosphoric acid residue), the complementary chain has a 3'-end (with a free OH group). The thermodynamic stability of this entire structure is provided by the free energy of multiple hydrogen bonds.
Fundamental structural principles
The organization of DNA chains obeys strict molecular laws that make the copying of genetic information possible.
- Complementarity. The nitrogenous bases of the two chains spatially correspond to each other, forming hydrogen bonds. Adenine (A) always binds to thymine (T) with two bonds, and guanine (G) connects to cytosine (C) with three. Because of this, the sequence of one chain strictly predetermines the composition of the other.
- Chargaff's rules (discovered in 1949). In any DNA molecule, the amount of purines (A + G) is always equal to the amount of pyrimidines (T + C). Accordingly, the amount of adenine equals thymine, and guanine equals cytosine. At the same time, the (A + T) / (C + G) ratio is species-specific and varies among different organisms.
Modern science views DNA not as a single rigid structure, but as a family of structures (DNA polymorphism). Alternative forms differ in the number of nucleotides per turn and the distance between repeating elements.
Cellular localization
The location and shape of the molecule depend on the cell type and the stage of its lifecycle.
In eukaryotic cells, the bulk of DNA is securely hidden in the nucleus. There, it binds to special proteins, forming a complex spatial conformation (conformatio). During nuclear division, these complexes maximally coil into linear chromosomes. During the resting phase (interphase), they uncoil and can be observed under a microscope as stained bodies — chromatin. Outside the nucleus, circular forms of DNA are present in mitochondria and plastids.
Prokaryotes lack a distinct nucleus. Their genetic material is represented by a single giant circular molecule in the nucleoid region, as well as small plasmids located directly in the cytoplasm.
Key properties and biological role
DNA is a dynamic macromolecule possessing three vital properties that ensure cell life:
- Replication (self-duplication). Occurs in a semi-conservative manner during the synthetic phase of the cell cycle. Enzymes create an exact copy of the molecule for transmission to daughter cells.
- Repair (self-restoration). The unique ability of DNA to "fix" damage in its chains, restoring the correct initial nucleotide sequence.
- Mutations. The process of changing the number or order of nucleotides under the influence of external factors during replication.
The main biological function of DNA lies in the reliable storage of genetic information, its error-free transmission to subsequent generations of cells, and its implementation during ontogenesis.
Briefly: answers to topical questions
Which enzymes ensure the DNA replication process?
The DNA replication process is ensured by an enzymatic apparatus. It includes:
- DNA helicases — carry out unwinding.
- DNA polymerases — are responsible for DNA synthesis; 7 types are known in eukaryotes, and 5 types in E. coli.
- RNA primases.
- DNA ligases — ensure sealing (joining).
- DNA topoisomerases.
- Destabilizing proteins.
What specific proteins bind to DNA in the eukaryotic nucleus to form chromatin?
In the eukaryotic nucleus, the DNA molecule binds to two main groups of proteins to form chromatin:
- Histone proteins — small positively charged molecules rich in arginine and lysine. Include 5 types: H1, H2A, H2B, H3, H4. An octamer of histones H2A, H2B, H3, and H4 forms the nucleosome core around which DNA is wrapped, and histone H1 attaches to linker regions.
- Non-histone proteins — perform functions in the processes of compaction, replication, transcription, and repair.
What are the main mechanisms (types) of DNA repair?
The sources indicate the following types and mechanisms of DNA repair:
- Light repair (photoreactivation).
- Prereplicative repair (excision).
- Base excision repair (BER): DNA glycosylase recognizes and removes the damaged base with the formation of an AP site, AP endonuclease cuts the sugar-phosphate backbone, DNA polymerase β fills the gap with the correct nucleotide, and DNA ligase seals the break.
- SOS repair: activated when DNA replication is necessary and there is damage not eliminated by other repair systems; allows building daughter DNA opposite defective segments of the template chain, but leads to a large number of errors.
- Direct repair: insertase attaches a nitrogenous base directly to the AP site.
What types of DNA mutations are distinguished in medical genetics?
In medical genetics, mutations are classified according to several main criteria. By the level of organization of genetic material, the following are distinguished:
- Gene mutations — point changes in gene structure (base substitution, frameshift, inversion, splicing and "dynamic" mutations, insertion).
- Chromosomal mutations (aberrations) — disruption of chromosome structure (intrachromosomal: deletion, duplication, inversion; interchromosomal: translocation).
- Genomic mutations — a change in the number of genomes or individual chromosomes (haploidy, polyploidy, aneuploidy).
Additionally, mutations are subdivided by cell type (somatic and germline), by cause of occurrence (spontaneous and induced), and by localization (nuclear and cytoplasmic).
To remember the principle of complementarity, use a simple association: "Apple in the Plate, Goose in the Cylinder" (Adenine pairs with Thymine, and Guanine pairs with Cytosine).
Class and exam questions
What is the difference between the 5'- and 3'-ends of the molecule?
DNA chains are polar and antiparallel. At the 5'-end (five-prime) of the polynucleotide chain lies a phosphoric acid residue, and at the 3'-end (three-prime) is a free hydroxyl (OH) group.
What bonds maintain the DNA structure?
The sugar-phosphate framework (backbone) of the molecule is held together by strong covalent bonds. And the two parallel chains are connected to each other by hydrogen bonds arising inside the helix between pairs of complementary nitrogenous bases.
What is DNA polymorphism?
This is a modern concept according to which DNA can exist in the form of multiple different conformations (a family of structures) rather than just the classic B-form. They differ in helix pitch and the number of nucleotides per turn.
What else to study on this topic
- Mechanisms and enzymes of semi-conservative DNA replication
- Types of DNA damage and molecular DNA repair systems
- Levels of chromatin compaction in a eukaryotic cell
- Structural and inheritance features of mitochondrial DNA
- Molecular mechanisms of mutation during replication
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