The principles of DNA repair are similar in different organisms. A cell removes a number of damages from DNA by direct reactivation. Thus, alkylated nitrogenous bases are corrected. The removal of thymine dimers in the light also belongs to the same type of repair. Other types of repair of ultraviolet DNA damage are called dark repair, to distinguish from direct photoreactivation.

If direct reactivation is not possible, the mechanisms excision repair that remove damaged regions from DNA. With this type of repair, special endonucleases cut one strand of DNA near the site of damage. Next, exonucleases remove the damaged area. The resulting gap is filled by DNA polymerase, and the remaining gap is crosslinked by DNA ligase. It can be seen that excision repair always uses the same principle: the damaged DNA region is removed and then restored on the template of the undamaged complementary DNA strand.

induced repair. Under conditions that increase the amount of DNA damage, additional reparative resources of the cell are induced. In bacteria, induced repair is used only when there is so much damage in the DNA that it begins to threaten the cell with death. Therefore, the induced repair system is called SOS reparation. The degree of induction of the SOS system is determined by the amount of damage. The degree of induction of the SOS system in a certain sense reflects the "well-being" of the cell and its chances of survival. Therefore, some temperate bacteriophages use the induction of the SOS system as a signal to multiply and destroy the host cell.

Duplication of information in two complementary strands of DNA does not allow correcting all types of damage without error. The described repair mechanisms cannot cope with such damage to the DNA structure, such as covalent interstrand crosslinks, which can occur under the action of a number of mutagens, or DNA double-strand breaks. Such damage can be repaired only in the presence of a homologous intact DNA molecule, i.e. through recombination.

The high stability of DNA is ensured not only by the conservatism of its structure and high replication accuracy, but also by the presence of special systems in the cells of all living organisms. reparations that remove damage from DNA.

The action of various chemical substances, ionizing radiation and ultraviolet radiation can cause the following damage to the DNA structure:

Damage to single bases (deamination leading to the conversion of cytosine to uracil, adenine to hypoxanthine; base alkylation; inclusion of base analogues, insertions and deletions of nucleotides);

base pair damage (formation of thymine dimers);

chain breaks (single and double);

the formation of cross-links between bases, as well as DNA-protein cross-links.

Some of these violations may also occur spontaneously, i.e. without the involvement of any damaging factors.

Any type of damage leads to a violation of the secondary structure of DNA, which is the cause of partial or complete blocking of replication. Such conformational disturbances serve as a target for repair systems. The process of restoring the DNA structure is based on the fact that genetic information is represented in DNA by two copies - one in each of the chains of the double helix. Due to this, damage in one of the chains can be removed by the repair enzyme, and this section of the chain is resynthesized in its normal form due to the information contained in the undamaged chain.

Currently, three main mechanisms of DNA repair have been identified: photoreactivation, excision, and post-replication repair. The last two types are also called dark reparation.

Photoreactivation is broken down by an enzyme photolyase, activated by visible light, thymine dimers that occur in DNA under the action of ultraviolet radiation.

excisional repair consists in recognition of DNA damage, excision of the damaged area, resynthesis of DNA according to the template of the intact chain with restoration of DNA chain continuity. This method is also called reparation by the type of splitting - substitution, or more figuratively, the "cut - patch" mechanism. Excisional repair is a multi-stage process and consists of:

1) "recognition" of damage;

2) incision of one DNA strand near the damage (incision);

3) removal of the damaged area (excision);

4) DNA resynthesis at the site of the removed site;

5) restoration of the continuity of the repaired chain due to the formation of phosphodiester bonds between nucleotides
(Figure 6.2)

Rice. 6.2 Excision repair scheme

Reparation begins with joining DNA-N-glycosylase to the damaged base. There are many DNA-N-glycosylases specific to various modified bases. Enzymes hydrolytically cleave the N-glycosidic bond between the altered base and deoxyribose, which leads to the formation of an AP (apurinic-apyrimidine) site in the DNA chain (first step). AP site repair can only occur with the participation of DNA insertases, which adds a base to deoxyribose in accordance with the rule of complementarity. In this case, there is no need to cut the DNA strand, cut out the wrong nucleotide and repair the break. With more complex damage to the DNA structure, the participation of the entire complex of enzymes involved in repair is necessary (Fig. 6.2.): AP-endonuclease recognizes the AP site and cuts the DNA chain near it (stage II). As soon as a break occurs in the circuit, the work comes into play AP exonuclease, which removes a DNA fragment containing an error (stage III). DNA polymerase b builds up the gap that has arisen according to the principle of complementarity (stage IV). DNA ligase connects the 3¢-end of the newly synthesized fragment with the main chain and completes the damage repair (stage V).

Postreplicative repair is switched on in those cases when the excisional one cannot cope with the elimination of all DNA damage before its replication. In this case, the reproduction of damaged molecules leads to the appearance of DNA with single-strand gaps, and the native structure is restored during recombination.

Congenital defects in the repair system are the cause of such hereditary diseases as xeroderma pigmentosum, ataxia-telangiectasia, trichothiodystrophy, and progeria.

DNA synthesis occurs by a semi-conservative mechanism: each strand of DNA is copied. Synthesis occurs in sections. There is a system that eliminates errors in DNA reduplication (photoreparation, pre-reproductive and post-reproductive repair). The reparation process is very long: up to 20 hours, and complex. Enzymes - restriction enzymes cut out an inappropriate section of DNA and complete it again. Repairs never proceed with 100% efficiency, if it did, evolutionary variability would not exist. The repair mechanism is based on the presence of two complementary chains in the DNA molecule. The distortion of the nucleotide sequence in one of them is detected by specific enzymes. Then the corresponding site is removed and replaced by a new one, synthesized on the second complementary DNA strand. This reparation is called excisional, those. with cutout. It is carried out before the next replication cycle, so it is also called pre-replicative. In the event that the excision repair system does not correct a change that has arisen in one DNA strand, this change is fixed during replication and it becomes the property of both DNA strands. This leads to the replacement of one pair of complementary nucleotides with another or to the appearance of breaks in the newly synthesized chain against the changed sites. Restoration of the normal DNA structure can also occur after replication. Post-reply reparation is carried out by recombination between two newly formed double strands of DNA. During pre-replicative and post-replicative repair, most of the damaged DNA structure is restored. If in the cell, despite the ongoing repair, the amount of damage remains high, the processes of DNA replication are blocked in it. Such a cell does not divide.

19. Gene, its properties. Genetic code, its properties. Structure and types of RNA. Processing, splicing. The role of RNA in the process of realization of hereditary information.

Gene - a section of a DNA molecule that carries information about the structure of a polypeptide chain or macromolecule. The genes of one chromosome are arranged linearly, forming a linkage group. DNA in the chromosome performs different functions. There are different sequences of genes, there are sequences of genes that control gene expression, replication, etc. There are genes that contain information about the structure of the polypeptide chain, ultimately structural proteins. Such sequences of nucleotides one gene long are called structural genes. Genes that determine the place, time, duration of the inclusion of structural genes are regulatory genes.

Genes are small in size, although they consist of thousands of base pairs. The presence of a gene is established by the manifestation of the trait of the gene (final product). The general scheme of the structure of the genetic apparatus and its work was proposed in 1961 by Jacob, Monod. They proposed that there is a section of the DNA molecule with a group of structural genes. Adjacent to this group is a 200 bp site, the promoter (the site of adjunction of DNA-dependent RNA polymerase). The operator gene adjoins this site. The name of the whole system is operon. Regulation is carried out by a regulatory gene. As a result, the repressor protein interacts with the operator gene, and the operon begins to work. The substrate interacts with the gene regulators, the operon is blocked. Feedback principle. The expression of the operon is turned on as a whole.

In eukaryotes, gene expression has not been studied. The reason is serious obstacles:

Organization of genetic material in the form of chromosomes

In multicellular organisms, cells are specialized and therefore some of the genes are turned off.

The presence of histone proteins, while prokaryotes have “naked” DNA.

DNA is a macromolecule; it cannot enter the cytoplasm from the nucleus and transmit information. Protein synthesis is possible due to mRNA. In a eukaryotic cell, transcription occurs at a tremendous rate. First, pro-i-RNA or pre-i-RNA appears. This is explained by the fact that in eukaryotes, mRNA is formed as a result of processing (maturation). The gene has a discontinuous structure. The coding regions are exons and the non-coding regions are introns. The gene in eukaryotic organisms has an exon-intron structure. The intron is longer than the exon. In the process of processing, introns are "cut out" - splicing. After the formation of a mature mRNA, after interacting with a special protein, it passes into a system - the informosome, which carries information to the cytoplasm. Now exon-intron systems are well studied (for example, oncogene - P-53). Sometimes the introns of one gene are exons of another, then splicing is not possible. Processing and splicing are able to combine structures that are distant from each other into one gene, so they are of great evolutionary importance. Such processes simplify speciation. Proteins have a block structure. For example, the enzyme is DNA polymerase. It is a continuous polypeptide chain. It consists of its own DNA polymerase and endonuclease, which cleaves the DNA molecule from the end. The enzyme consists of 2 domains that form 2 independent compact particles linked by a polypeptide bridge. There is an intron at the border between two enzyme genes. Once the domains were separate genes, and then they got closer. Violations of such a gene structure leads to gene diseases. Violation of the structure of the intron is phenotypically imperceptible, a violation in the exon sequence leads to mutation (mutation of globin genes).

10-15% of RNA in a cell is transfer RNA. There are complementary regions. There is a special triplet - an anticodon, a triplet that does not have complementary nucleotides - GHC. The interaction of 2 subunits of the ribosome and mRNA leads to initiation. There are 2 sites - pectidyl and aminoacyl. They correspond to amino acids. Synthesis of the polypeptide occurs step by step. Elongation - the process of building a polypeptide chain continues until it reaches a meaningless codon, then termination occurs. The synthesis of the polypeptide ends, which then enters the ER channels. The subunits separate. Different amounts of protein are synthesized in a cell.

Discovery history

Single-strand and double-strand DNA damage

The study of repair was initiated by the work of A. Kellner (USA), who discovered the phenomenon of photoreactivation (PR) - a decrease in damage to biological objects caused by ultraviolet (UV) rays, with subsequent exposure to bright visible light ( light repair).

Excision repair

Post-replicative repair has been discovered in cells E.Coli unable to cleave thymine dimers. This is single type repair that does not have a stage of damage recognition.

Notes

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See what "DNA repair" is in other dictionaries:

Repair of defects in DNA resulting from mutation or recombination. It is carried out by a system of reparative enzymes, some of which establish the site of damage, others “cut it out”, others synthesize damaged areas, fourth ... ... Dictionary of microbiology

dna repair- - correction of "mistakes" in the primary structure of DNA as a result of the action of special reparative enzymes ... Concise Dictionary of Biochemical Terms

DNA repair- — Biotechnology topics EN DNA repair … Technical Translator's Handbook

DNA repair- DNR reparacija statusas T sritis augalininkystė apibrėžtis DNR struktūros atsikūrimas po pažeidimo. atitikmenys: engl. DNA repair DNA repair... Žemės ūkio augalų selekcijos ir sėklininkystės terminų žodynas

DNA REPAIR- Restoration of the original structure in the DNA molecule, i.e. correct sequence of nucleotides... Terms and definitions used in breeding, genetics and reproduction of farm animals

DNA repair- * DNA repair * DNA repair Enzymatic error correction in the nucleotide sequence of the DNA molecule. Mechanisms of DNA r. protect genetic information body from damage caused by environmental mutagens (e.g. ultraviolet, ... ...

DNA-dependent DNA polymerase DNA polymerase- DNA dependent DNA polymerase, DNA polymerase * DNA dependent DNA polymerase, DNA polymerase * DNA dependent DNA polymerase or DNA polymerase enzyme that catalyzes the polymerization (see) of deoxyribonucleoside triphosphates into a polymer ... ... Genetics. encyclopedic Dictionary

- (from late Latin reparatio restoration), characteristic of all cells of living organisms, restoration of the original (native) DNA structure in case of its violation. Damage to the DNA structure can lead to blocking of DNA replication (lethal ... ... Chemical Encyclopedia

Repair: DNA repair is the ability of cells to repair chemical damage and breaks in DNA molecules. Reparations are a form of material liability of a subject of international law for damage caused as a result of an international act committed by him ... ... Wikipedia

A system for detecting and repairing insertions, gaps and mismatches of nucleotides that occur during DNA replication and recombination, as well as as a result of some types of DNA damage The very fact of mismatch does not allow ... ... Wikipedia

Books

• DNA methylation in plants. Mechanisms and biological role, BF Vanyushin. This reading by one of the pioneers and famous world leaders in the study of DNA methylation in various organisms details the current state of the general biological problem, ...

12. Enzymes, definition. Features of enzymatic catalysis. The specificity of the action of enzymes, types.

13. Classification and nomenclature of enzymes, examples.

1. Oxydoreductives

2.Transfers

V. The mechanism of action of enzymes

1. Formation of the enzyme-substrate complex

3. Role of the active site in enzymatic catalysis

1. Acid-base catalysis

2. Covalent catalysis

15. Kinetics of enzymatic reactions. Dependence of the rate of enzymatic reactions on temperature, pH of the medium, concentration of the enzyme and substrate. Michaelis-Menten equation, Km.

16. Enzyme cofactors: metal ions and their role in enzymatic catalysis. Coenzymes as derivatives of vitamins. Coenzyme functions of vitamins B6, pp and B2 on the example of transaminases and dehydrogenases.

1. The role of metals in substrate attachment to the active site of the enzyme

2. The role of metals in the stabilization of the tertiary and quaternary structure of the enzyme

3. Role of metals in enzymatic catalysis

4. The role of metals in the regulation of enzyme activity

1. Ping pong mechanism

2. Sequential mechanism

17. Enzyme inhibition: reversible and irreversible; competitive and non-competitive. Drugs as enzyme inhibitors.

1. Competitive inhibition

2. Noncompetitive inhibition

1. Specific and non-specific inhibitors

2. Irreversible enzyme inhibitors as drugs

19. Regulation of the catalytic activity of enzymes by covalent modification by phosphorylation and dephosphorylation (on the example of enzymes for the synthesis and breakdown of glycogen).

20. Association and dissociation of protomers on the example of protein kinase a and limited proteolysis upon activation of proteolytic enzymes as ways to regulate the catalytic activity of enzymes.

21. Isoenzymes, their origin, biological significance, give examples. Determination of enzymes and isoenzyme spectrum of blood plasma for the purpose of diagnosing diseases.

22. Enzymopathies hereditary (phenylketonuria) and acquired (scurvy). The use of enzymes in the treatment of diseases.

23. General scheme for the synthesis and decay of pyrimidine nucleotides. Regulation. Orotaciduria.

24. General scheme for the synthesis and decay of purine nucleotides. Regulation. Gout.

27. Nitrogenous bases included in the structure of nucleic acids - purine and pyrimidine. Nucleotides containing ribose and deoxyribose. Structure. Nomenclature.

27. Hybridization of nucleic acids. DNA denaturation and regeneration. Hybridization (dna-dna, dna-rna). Methods of laboratory diagnostics based on the hybridization of nucleic acids. (PCR)

29. Replication. Principles of DNA replication. stages of replication. Initiation. Proteins and enzymes involved in the formation of the replication fork.

30. Elongation and termination of replication. Enzymes. Asymmetric DNA synthesis. Fragments of the Okazaki. The role of DNA ligase in the formation of a continuous and lagging chain.

31. DNA damage and repair. Types of damage. Reparation methods. Defects in repair systems and hereditary diseases.

32. Transcription Characterization of the components of the RNA synthesis system. The structure of DNA-dependent RNA polymerase: the role of subunits (α2ββ'δ). Process initiation. elongation, termination of transcription.

33. Primary transcript and its processing. Ribozymes as an example of the catalytic activity of nucleic acids. Biorol.

35. Assembly of the polypeptide chain on the ribosome. Formation of an initiatory complex. Elongation: formation of a peptide bond (transpeptidation reaction). Translocation. Translocase. Termination.

1. Initiation

2. Elongation

3. Termination

36. Features of the synthesis and processing of secreted proteins (on the example of collagen and insulin).

37. Biochemistry of nutrition. The main components of human food, their biorole, daily need for them. Essential components of food.

38. Protein nutrition. The biological value of proteins. nitrogen balance. Completeness of protein nutrition, protein norms in nutrition, protein deficiency.

39. Protein digestion: gastrointestinal proteases, their activation and specificity, pH optimum and the result of action. Formation and role of hydrochloric acid in the stomach. Protection of cells from the action of proteases.

1. Formation and role of hydrochloric acid

2. Pepsin activation mechanism

3. Age features of protein digestion in the stomach

1. Activation of pancreatic enzymes

2. Specificity of action of proteases

41. Vitamins. Classification, nomenclature. Provitamins. Hypo-, hyper- and beriberi, causes. Vitamin-dependent and vitamin-resistant states.

42. Mineral substances of food, macro- and microelements, biological role. Regional pathologies associated with a lack of trace elements.

3. Fluidity of membranes

1. Structure and properties of membrane lipids

45. Mechanisms for the transfer of substances across membranes: simple diffusion, passive symport and antiport, active transport, regulated channels. membrane receptors.

1. Primary active transport

2. Secondary active transport

Membrane receptors

3. Endergonic and exergonic reactions

4. Coupling of exergonic and endergonic processes in the body

2. Structure of ATP synthase and ATP synthesis

3. Oxidative phosphorylation coefficient

4.Respiratory control

50. Formation of reactive oxygen species (singlet oxygen, hydrogen peroxide, hydroxyl radical, peroxynitrile). Place of formation, reaction schemes, their physiological role.

51. . The mechanism of the damaging effect of reactive oxygen species on cells (sex, oxidation of proteins and nucleic acids). Examples of reactions.

1) Initiation: formation of a free radical (l)

2) Chain development:

3) Destruction of the structure of lipids

1. Structure of the pyruvate dehydrogenase complex

3. Relationship between the oxidative decarboxylation of pyruvate and cpe

53. Citric acid cycle: sequence of reactions and characteristics of enzymes. The role of the cycle in metabolism.

1. The sequence of reactions of the citrate cycle

54. Citric acid cycle, process diagram. Communication cycle for the purpose of transfer of electrons and protons. Regulation of the citric acid cycle. Anabolic and anaplerotic functions of the citrate cycle.

55. Basic animal carbohydrates, biological role. Carbohydrates food, digestion of carbohydrates. Absorption of products of digestion.

Methods for determining blood glucose

57. Aerobic glycolysis. Sequence of reactions until pyruvate is formed (aerobic glycolysis). Physiological significance of aerobic glycolysis. The use of glucose for fat synthesis.

1. Stages of aerobic glycolysis

58. Anaerobic glycolysis. Glycolytic oxidoreduction reaction; substrate phosphorylation. Distribution and physiological significance of anaerobic breakdown of glucose.

1. Reactions of anaerobic glycolysis

59. Glycogen, biological significance. Biosynthesis and mobilization of glycogen. Regulation of the synthesis and breakdown of glycogen.

61. Hereditary disorders of monosaccharide and disaccharide metabolism: galactosemia, fructose and disaccharide intolerance. Glycogenoses and aglycogenoses.

2. Aglycogenoses

62. Lipids. General characteristics. biological role. Classification of lipids. Higher fatty acids, structural features. polyene fatty acids. Triacylglycerols..

64. Deposition and mobilization of fats in adipose tissue, the physiological role of these processes. The role of insulin, adrenaline and glucagon in the regulation of fat metabolism.

66. The breakdown of fatty acids in the cell. Activation and transport of fatty acids into mitochondria. Β-oxidation of fatty acids, energy effect.

67. Biosynthesis of fatty acids. The main stages of the process. regulation of fatty acid metabolism.

2. Regulation of fatty acid synthesis

69. Cholesterol. Routes of entry, use and excretion from the body. Serum cholesterol level. Biosynthesis of cholesterol, its stages. regulation of synthesis.

Fund of cholesterol in the body, ways of its use and excretion.

1. Reaction mechanism

2. Organ-specific aminotransferases ant and act

3. Biological significance of transamination

4. Diagnostic value of determination of aminotransferases in clinical practice

1. Oxidative deamination

74. Indirect deamination of amino acids. Process scheme, substrates, enzymes, cofactors.

3. Non-oxidative deamidation

76. Orinitin cycle of urea formation. Chemistry, place of the process. Energy effect of the process, its regulation. Quantitative determination of blood serum urea, clinical significance.

2. Formation of spermidine and spermine, their biological role

78. Exchange of phenylalanine and tyrosine. Features of tyrosine metabolism in different tissues.

79. Endocrine, paracrine and autocrine systems of intercellular communication. The role of hormones in the metabolic regulation system. Feedback regulation of hormone synthesis.

80. Classification of hormones by chemical structure and biological function.

1. Classification of hormones by chemical structure

2. Classification of hormones according to biological functions

1. General characteristics of receptors

2. Regulation of the number and activity of receptors

82. Cyclic amp and hmp as second mediators. Activation of protein kinases and phosphorylation of proteins responsible for the manifestation of the hormonal effect.

3. Signaling through receptors coupled to ion channels

85. Hormones of the hypothalamus and anterior pituitary gland, chemical nature and biological role.

2. Corticoliberin

3. GnRH

4. Somatoliberin

5. Somatostatin

1. Growth hormone, prolactin

2. Thyrotropin, luteinizing hormone and follicle stimulating hormone

3. A group of hormones derived from proopiomelanocortin

4. Posterior pituitary hormones

86. Regulation of water-salt metabolism. Structure, mechanism of action and functions of aldosterone and vasopressin. The role of the renin-angiotensin-aldosterone system. atrial natriuretic factor.

1. Synthesis and secretion of antidiuretic hormone

2. Mechanism of action

3. Diabetes insipidus

1. Mechanism of action of aldosterone

2. The role of the renin-angiotensin-aldosterone system in the regulation of water-salt metabolism

3. Restoration of blood volume during dehydration

4. Hyperaldosterontm

87. Regulation of the exchange of calcium and phosphate ions. Structure, biosynthesis and mechanism of action of parathyroid hormone, calcitonin and calcitriol. Causes and manifestations of rickets, hypo- and hyperparathyroidism.

1. Synthesis and secretion of PTH

2. The role of parathyroid hormone in the regulation of calcium and phosphate metabolism

3. Hyperparathyroidism

4. Hypoparathyroidism

1. Structure and synthesis of calcitriol

2. Mechanism of action of calcitriol

3. Rickets

2. Biological functions of insulin

3. Mechanism of action of insulin

1. Insulin-dependent diabetes mellitus

2. Non-insulin dependent diabetes mellitus

1. Symptoms of diabetes

2. Acute complications of diabetes. Mechanisms of development of diabetic coma

3. Late complications of diabetes

1. Biosynthesis of iodothyronines

2. Regulation of synthesis and secretion of iodothyronines

3. Mechanism of action and biological functions of iodothyronines

4. Diseases of the thyroid gland

90. Hormones of the adrenal cortex (corticosteroids). Their influence on cell metabolism. Metabolic changes in hypo- and hyperfunction of the adrenal cortex.

3. Metabolic changes in hypo- and hyperfunction of the adrenal cortex

91. Hormones of the adrenal medulla. secretion of catecholamines. Mechanism of action and biological functions of catecholamines. Pathology of the adrenal medulla.

1. Synthesis and secretion of catecholamines

2. Mechanism of action and biological functions of catecholamines

3. Pathology of the adrenal medulla

1. Main enzymes of microsomal electron transport chains

2. Functioning of cytochrome p450

3. Properties of the microsomal oxidation system

93. Heme decay. Scheme of the process, place of flow. "Direct" and "indirect" bilirubin, its neutralization in the liver. Diagnostic value of the determination of bilirubin in the blood and urine.

94. . Heme catabolism disorders. Jaundice: hemolytic, neonatal jaundice, hepatocellular, mechanical, hereditary (impaired synthesis of udf-glucuronyltransferase).

31. DNA damage and repair. Types of damage. Reparation methods. Defects in repair systems and hereditary diseases.

The process that allows living organisms to repair damage that occurs in DNA is called repair. All repair mechanisms are based on the fact that DNA is a double-stranded molecule; There are 2 copies of genetic information in a cell. If the nucleotide sequence of one of the two strands is damaged (changed), the information can be restored, since the second (complementary) strand is preserved.

The recovery process takes place in several stages. At the first stage, a violation of the complementarity of DNA chains is detected. During the second stage, the non-complementary nucleotide or only the base is eliminated; at the third and fourth stages, the integrity of the chain is restored according to the principle of complementarity. However, depending on the type of damage, the number of stages and enzymes involved in its elimination may be different.

Very rarely, damage occurs that affects both strands of DNA, i.e. violations of the structure of nucleotides of the complementary pair. Such damage in germ cells is not repaired, since complex repair involving homologous recombination requires the presence of a diploid set of chromosomes.

A. Spontaneous injury

Violations of complementarity of DNA strands can occur spontaneously, i.e. without the participation of any damaging factors, for example, as a result of replication errors, deamination of nucleotides, depurination.

Replication errors

The accuracy of DNA replication is very high, but about once per 10 5 -10 6 nucleotide residues pairing errors occur, and then instead of a pair nucleotides A-T, G-C, nucleotides that are not complementary to the nucleotides of the template chain are included in the daughter DNA chain. However, DNA polymerases δ, ε are able, after adding the next nucleotide to the growing DNA chain, to take a step back (in the direction from the 3" to the 5" end) and cut out the last nucleotide if it is not complementary to the nucleotide in the template DNA chain. This process of correcting mating errors (or correction) sometimes does not work, and then non-complementary pairs remain in the DNA at the end of replication, especially since DNA polymerase a lacks a correcting mechanism and “mistakes” more often than other polymerases.

In case of incorrect pairing, unusual bases do not appear in the primary structure of the daughter DNA strand, only complementarity is violated. The system of repair of non-complementary pairs should occur only on the daughter strand and replace non-complementary bases only in it. Enzymes involved in the removal of the wrong base pair recognize the template strand by the presence of methylated adenine residues in the sequences -GATC-. As long as the bases of the nucleotide residues in the daughter chain are unmethylated, the enzymes must have time to detect the replication error and eliminate it.

Recognition and removal (first stage) of a non-complementary nucleotide occurs with the participation of special proteins mut S, mut L, mut H. Each of the proteins performs its specific function. Mut S finds the wrong pair and links to this fragment. Mut H attaches to the methylated (adenine) site -GATC- located near the non-complementary pair. The link between mut S and mut H is the mut L protein, its attachment completes the formation of the active enzyme. The formation of the mut S, mut L, mut H complex at the site containing the error contributes to the manifestation of endonuclease activity in the mut H protein. The enzymatic complex hydrolyzes the phosphoester bond in the unmethylated chain.

An exonuclease is attached to the free ends of the chain (second stage). Cleaving one nucleotide in the direction from the 3 "to the 5" end of the daughter chain, it eliminates the site containing the non-complementary pair. The gap is built up by DNA polymerase β (third stage), the connection of the main and newly synthesized sections of the chain is catalyzed by the enzyme DNA ligase (fourth stage). Successful functioning of exonuclease, DNA polymerase p, and DNA ligase requires participation in the repair of helicase and SSB proteins.

Depurination (apurinization)

The DNA of each human cell loses about 5,000 purine residues per day due to the breaking of the N-glycosidic bond between purine and deoxyribose.

Then in the DNA molecule, in place of these bases, a site devoid of nitrogenous bases is formed, called the AP site (AP-site, or apurine site). The term "AP site" is also used when pyrimidine bases drop out of DNA and apyrimidine sites are formed (from English, apurinic-apyrimidinic site).

This type of damage is repaired by an enzyme DNA insertase(from English, insert- insert), which can attach a base to deoxyribose in accordance with the rule of complementarity. In this case, there is no need to cut the DNA strand, cut out the wrong nucleotide and repair the break.

Deamination

Cytosine deamination reactions and its transformation into uracil, adenine into hypoxanthine, guanine into xanthine occur much less frequently than depurination, and amount to 10 reactions per genome per day.

Correction of this type of spontaneous damage occurs in 5 stages (Fig. 4-24). Participates in reparation DNA-N-glycosylase, hydrolyzing the bonds between the abnormal base and deoxyribose (first stage), resulting in the formation of an AP site that recognizes the enzyme AP-endonuclease(second phase). As soon as a break occurs in the DNA chain, another enzyme, AP-exonuclease, comes into play, which cleaves off base-free deoxyribose from the chain (third stage). A single nucleotide gap appears in the DNA chain. The next enzyme, DNA polymerase b, adds a nucleotide to the 3 "end of the broken chain according to the principle of complementarity (fourth stage). To connect two free ends (3"-end of the built-in nucleotide and 5"-end of the main chain), one more enzyme is required - DNA -ligase (fifth stage).

Deamination of methylated cytosine is unrepairable and therefore dangerous. The product of its spontaneous deamination is thymine,

B. Inducible damage

Inducible damage occurs in DNA as a result of exposure to various mutagenic factors of both radiation and chemical nature.

Formation of dimers of pyrimidine bases

Under the action of ultraviolet radiation, the double bond between C 5 and C 6 carbon atoms in the composition of pyrimidine bases (thymine and cytosine) can be broken. The carbon atoms remain connected by a single bond. The distance between the parallel planes of the bases of the polynucleotide chain in which the break occurred is approximately 3.4. This distance allows the released valences between the C-C atoms of the pyrimidine bases located sequentially in the DNA chain to form a cyclobutane ring. Depending on which bases are connected in a dimer, they are called thymine, cytosine, or thymine-cytosine dimers.

The removal of pyrimidine dimers occurs under the action of photolyases The enzyme cleaves newly formed bonds between adjacent pyrimidine bases and restores the native structure. There is a site in photolyase that either itself absorbs photons (in the blue part of the spectrum) or binds to cofactors that adsorb light. Thus, light activates photolyase, which recognizes dimers in irradiated DNA, attaches to them, and breaks the bonds that have arisen between the pyrimidine rings. The enzyme is then separated from the DNA.

Damage to DNA bases by chemical mutagens

Nitrogenous bases in DNA can undergo a variety of damages: alkylation, oxidation, reduction, or base binding to formamide groups. Repair begins with the attachment of DNA-N-glycosylase to the damaged base. There are many DNA-M-glycosylases specific to various modified bases. Enzymes hydrolytically cleave the N-glycosidic bond between the modified base and deoxyribose, which leads to the formation of an AP site in the DNA chain (first step). Repair of the AP site can occur either only with the participation of DNA insertase, which adds a base to deoxyribose in accordance with the rule of complementarity, or with the participation of the entire complex of enzymes involved in repair: AP endonuclease, AP exonuclease, DNA polymerase β and DNA -ligases.

B. Defects in repair systems and hereditary diseases

Repair is necessary to maintain the native structure of the genetic material throughout the life of the organism. A decrease in the activity of enzymes of repair systems leads to the accumulation of damage (mutations) in DNA.

The cause of many human hereditary diseases is the violation of certain stages of the repair process.

Pigmented xeroderma

In patients in the repair system, the activity of enzymes responsible for the removal of incorrect bases, the “building up” of the gap, and other functions is reduced. The defect in the repair system manifests itself in hypersensitivity to UV light, which leads to the appearance of red spots on the skin, turning into non-healing scabs and often into skin cancer.

Trichothiodystrophy

The disease is associated with increased photosensitivity of DNA caused by a decrease in the activity of an enzyme involved in the removal of thymine dimers. Symptoms of the disease: brittle hair due to lack of sulfur in the proteins of the hair and their follicles; often mental and physical retardation; anomalies of the skin and teeth.

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