Main types of genetic material damage
Every day, the genome structure is subjected to attacks by external and internal factors, including radiation, chemical agents, and ultraviolet (UV) irradiation. This leads to various defects that are normally repaired by specific enzymes.
The following types of molecular lesions are distinguished:
- Base deamination: spontaneous loss of an amino group. Cytosine most commonly converts to uracil. Adenine may convert to hypoxanthine, and guanine to xanthine.
- Loss of nitrogenous bases: hydrolytic process of depurination or depyrimidination, where the base is cleaved off, leaving an empty deoxyribose residue.
- Pyrimidine dimers: covalent cross-linking of adjacent bases in a single strand under the influence of UV radiation.
- Nucleotide strand breaks and replication errors.
- Covalent cross-links: between two complementary DNA strands or between DNA and histone proteins.
- DNA alkylation: attachment of alkyl groups under the influence of chemicals (e.g., formation of 3-methyladenine, 6-methylguanine, or 7-methylguanine).
How the strand is restored upon base loss
When hydrolytic cleavage of a purine or pyrimidine base occurs, a specific defect forms in the strand. The cell can use two main pathways to resolve it.
The first pathway is the direct action of DNA insertase. This enzyme is capable of independently attaching the missing nitrogenous base to the empty deoxyribose, strictly adhering to the rule of complementarity.
The second pathway is more complex and is called excision repair. In this case, the enzyme AP endonuclease (apurinic/apyrimidinic) acts. It detects the site with a deoxyribose lacking a base and performs hydrolysis of the 3', 5'-phosphodiester bond, making a nick in the sugar-phosphate backbone for the subsequent work of the entire repair complex.
Stages of DNA excision repair
Elimination of damaged regions (excision) in eukaryotes requires a coordinated and strict sequence of actions by the enzyme complex.
Sometimes the initial step is performed by DNA-N-glycosylase, which recognizes the chemically modified base and hydrolyzes the N-glycosidic bond, leaving a so-called AP site (apurinic/apyrimidinic site). The further process of eliminating the "gap" follows a clear scenario:
- Identification of the damage site: the endonuclease finds the defect and hydrolyzes the phosphodiester bond, nicking the damaged strand.
- Excision (removal): the exonuclease finds the break site and carefully excises the defective nucleotides from the strand.
- Synthesis (fill-in): DNA polymerase $\beta$ attaches to the 3'-end of the formed gap. Using deoxynucleoside triphosphates (dNTPs) and strictly guided by the undamaged complementary template strand, it synthesizes the missing fragment. During this reaction, inorganic pyrophosphate ($PP_i$) is released.
- Ligation: the enzyme DNA ligase finally seals the newly synthesized fragment with the main undamaged region. This process requires energy expenditure, so an ATP molecule is cleaved into AMP and $PP_i$.
Biological basis of reliability
The main principle ensuring the possibility of error correction is the presence of two strands in the DNA molecule, which represents two copies of genetic information. The second strand always serves as a reliable template for restoring the defect.
However, critical situations occur when both nucleotides in a complementary pair are damaged simultaneously. In this case, the outcome depends on the cell type:
- In haploid cells, repair of such damage becomes impossible because there is no backup copy of the information for correct synthesis.
- In diploid cells, the repair system is able to restore the structure using the identical undamaged gene located in the homologous chromosome.
Briefly: answers to topical questions
What hereditary diseases occur due to genetic defects in DNA repair enzymes?
Genetic defects in repair enzymes and genes lead to the accumulation of mutations in the genome, resulting in malignant cell transformation and a number of pathologies.
The following associated hereditary diseases occur:
- Xeroderma pigmentosum (Xeroderma pigmentosum) — caused by a defect in excision repair enzymes (most commonly endonucleases). It manifests upon exposure to ultraviolet light, characterized by photosensitivity, skin atrophy, and a dramatically increased risk of skin cancer.
- Hereditary nonpolyposis colorectal cancer — a disease associated with a decrease in antineoplastic defense.
- Bloom syndrome — a hereditary pathology associated with impaired DNA repair.
- Fanconi anemia — a disease associated with a defect in DNA structure restoration.
- Ataxia-telangiectasia — a hereditary disease from the group of repair gene defects.
For quick memorization of the order of eukaryotic excision repair enzymes: Endo (cuts) → Exo (excises) → Polymerase (builds) → Ligase (seals).
Class and exam questions
Which nitrogenous bases should not be found in normal DNA?
Normally, DNA lacks uracil, hypoxanthine, and xanthine. They appear only as a result of spontaneous deamination of cytosine, adenine, and guanine, respectively, after which they are removed by repair enzymes.
What chemical bond does the enzyme DNA-N-glycosylase break?
The enzyme hydrolyzes the N-glycosidic bond between the damaged nitrogenous base and the deoxyribose residue, forming a base-free site (AP site).
Where does the energy for DNA ligase action come from at the final stage?
To seal the break in the sugar-phosphate backbone, the enzyme uses the energy of an ATP molecule, cleaving it during the process into AMP and pyrophosphate.
What else to study on this topic
- Chemical modification by alkylating agents (formation of 6-methylguanine and 3-methyladenine)
- Mechanisms of pyrimidine dimer formation under UV irradiation
- Differences in the repair of simultaneous nucleotide pair damage in haploid and diploid cells
- The role of DNA-N-glycosylases in the formation of AP sites during BER repair
Master the entire topic in the "Biochemistry" course
This is a summary. The course covers everything tested in classes and exams.
- Complete study guide on "DNA Repair" and 3,616 more pages of the subject
- Assignments and quizzes after every topic — just like in a colloquium
- AI tutor answers questions on the topic anytime
- 115 video lessons on the subject
Other topics in the section "Template Biosyntheses"
Free video lessons: biochemistryShort lessons with study notes — no registration required.
Prepared by WhiteCoat Pro faculty in accordance with the medical school curriculum. For educational purposes only.