What is DNA made of. Nucleotide - what is it? Composition, structure, number and sequence of nucleotides in the DNA chain DNA double helix is stabilized by ions
Nucleic acids are macromolecular substances consisting of mononucleotides, which are connected to each other in a polymer chain using 3",5" - phosphodiester bonds and packed in cells in a certain way.
Nucleic acids are biopolymers of two varieties: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Each biopolymer consists of nucleotides that differ in carbohydrate residue (ribose, deoxyribose) and one of the nitrogenous bases (uracil, thymine). Accordingly, nucleic acids got their name.
Structure of deoxyribonucleic acid
Nucleic acids have primary, secondary and tertiary structures.
Primary structure of DNA
The primary structure of DNA is a linear polynucleotide chain in which the mononucleotides are connected by 3", 5" phosphodiester bonds. The starting material for assembling a nucleic acid chain in a cell is the nucleoside 5'-triphosphate, which, as a result of the removal of β and γ residues of phosphoric acid, is able to attach the 3'-carbon atom of another nucleoside. Thus, the 3" carbon atom of one deoxyribose covalently binds to the 5" carbon atom of another deoxyribose via one phosphoric acid residue and forms a linear polynucleotide chain of nucleic acid. Hence the name: 3", 5"-phosphodiester bonds. Nitrogenous bases do not take part in the connection of nucleotides of one chain (Fig. 1.).
Such a connection, between the phosphoric acid molecule of one nucleotide and the carbohydrate of another, leads to the formation of a pentose-phosphate backbone of the polynucleotide molecule, on which nitrogenous bases are added one after the other from the side. Their sequence in the chains of nucleic acid molecules is strictly specific for cells of different organisms, i.e. has a specific character (Chargaff's rule).
A linear DNA chain, the length of which depends on the number of nucleotides included in the chain, has two ends: one is called the 3 "end and contains a free hydroxyl, and the other, the 5" end, contains a phosphoric acid residue. The circuit is polar and can be 5"->3" and 3"->5". An exception is circular DNA.
The genetic "text" of DNA is made up of code "words" - triplets of nucleotides called codons. DNA segments containing information about the primary structure of all types of RNA are called structural genes.
Polynucleoditic DNA chains reach gigantic sizes, so they are packed in a certain way in the cell.
Studying the composition of DNA, Chargaff (1949) established important regularities concerning the content of individual DNA bases. They helped uncover the secondary structure of DNA. These patterns are called Chargaff's rules. Chargaff rules
These rules say that when building DNA, a rather strict correspondence (pairing) must be observed not for purine and pyrimidine bases in general, but specifically for thymine with adenine and cytosine with guanine. Based on these rules, among other things, in 1953 Watson and Crick proposed a model of the secondary structure of DNA, called the double helix (Fig.). |
Secondary structure of DNA
The secondary structure of DNA is a double helix, the model of which was proposed by D. Watson and F. Crick in 1953.
Prerequisites for creating a DNA model
As a result of initial analyzes, the idea was that DNA of any origin contains all four nucleotides in equal molar amounts. However, in the 1940s, E. Chargaff and his colleagues, as a result of the analysis of DNA isolated from various organisms, clearly showed that nitrogenous bases are contained in them in various quantitative ratios. Chargaff found that, although these ratios are the same for DNA from all cells of the same species of organisms, DNA from different species can differ markedly in the content of certain nucleotides. This suggested that the differences in the ratio of nitrogenous bases might be related to some biological code. Although the ratio of individual purine and pyrimidine bases in different DNA samples was not the same, when comparing the results of the analyzes, a certain pattern was revealed: in all samples, the total amount of purines was equal to the total amount of pyrimidines (A + G = T + C), the amount of adenine was equal to the amount of thymine (A = T), and the amount of guanine was equal to the amount of cytosine (G = C). DNA isolated from mammalian cells was generally richer in adenine and thymine and relatively poorer in guanine and cytosine, while DNA from bacteria was richer in guanine and cytosine and relatively poorer in adenine and thymine. These data formed an important part of the factual material, on the basis of which the Watson-Crick DNA structure model was later built.
Another important indirect indication of the possible structure of DNA was L. Pauling's data on the structure of protein molecules. Pauling showed that several different stable configurations of the amino acid chain are possible in a protein molecule. One of the common configurations of the peptide chain - α-helix - is a regular helical structure. With such a structure, the formation of hydrogen bonds between amino acids located on adjacent turns of the chain is possible. Pauling described the α-helical configuration of the polypeptide chain in 1950 and suggested that DNA molecules also probably have a helical structure fixed by hydrogen bonds.
However, the most valuable information about the structure of the DNA molecule was provided by the results of X-ray diffraction analysis. X-rays, passing through a DNA crystal, undergo diffraction, that is, they are deflected in certain directions. The degree and nature of the deflection of the rays depend on the structure of the molecules themselves. The X-ray diffraction pattern (Fig. 3) gives the experienced eye a number of indirect indications regarding the structure of the molecules of the substance under study. Analysis of DNA X-ray diffraction patterns led to the conclusion that the nitrogenous bases (having a flat shape) are stacked like a stack of plates. X-ray patterns made it possible to identify three main periods in the structure of crystalline DNA: 0.34, 2, and 3.4 nm.
Watson-Crick DNA Model
Starting from Chargaff's analytical data, Wilkins' x-rays, and chemist's research, which provided information about the exact distances between atoms in a molecule, about the angles between the bonds of a given atom, and about the size of atoms, Watson and Crick began to build physical models of the individual components of the DNA molecule on a certain scale and "fit" them to each other so that the resulting system corresponded to various experimental data. [show] .
Even earlier, it was known that adjacent nucleotides in a DNA chain are connected by phosphodiester bridges that link the 5'-carbon atom of deoxyribose of one nucleotide to the 3'-carbon atom of deoxyribose of the next nucleotide. Watson and Crick had no doubt that a period of 0.34 nm corresponds to the distance between successive nucleotides in a DNA strand. Further, it could be assumed that the period of 2 nm corresponds to the thickness of the chain. And in order to explain what real structure corresponds to a period of 3.4 nm, Watson and Crick, just like Pauling earlier, assumed that the chain is twisted in the form of a spiral (or, more precisely, forms a helix, since a spiral in the strict sense of the word is obtained when the turns form a conical rather than a cylindrical surface in space). Then the period of 3.4 nm will correspond to the distance between successive turns of this spiral. Such a spiral can be very dense or somewhat stretched, i.e., its turns can be flat or steep. Since the period of 3.4 nm is exactly 10 times the distance between consecutive nucleotides (0.34 nm), it is clear that each complete turn of the helix contains 10 nucleotides. From these data, Watson and Crick were able to calculate the density of a polynucleotide chain twisted into a helix with a diameter of 2 nm, with a distance between turns equal to 3.4 nm. It turned out that such a strand would have a density half that of the actual density of DNA, which was already known. I had to assume that the DNA molecule consists of two chains - that it is a double helix of nucleotides.
The next task was, of course, to elucidate the spatial relationship between the two strands forming the double helix. Having tried a number of variants of the arrangement of chains on their physical model, Watson and Crick found that the best fit for all available data is one in which two polynucleotide helices go in opposite directions; in this case, chains consisting of sugar and phosphate residues form the surface of a double helix, and purines and pyrimidines are located inside. The bases located opposite each other, belonging to two chains, are connected in pairs by hydrogen bonds; it is these hydrogen bonds that hold the chains together, thus fixing the overall configuration of the molecule.
The DNA double helix can be thought of as a helical rope ladder, with the rungs remaining horizontal. Then two longitudinal ropes will correspond to chains of sugar and phosphate residues, and the crossbars will correspond to pairs of nitrogenous bases connected by hydrogen bonds.
As a result of further study of possible models, Watson and Crick came to the conclusion that each "crossbar" should consist of one purine and one pyrimidine; at a period of 2 nm (corresponding to the diameter of the double helix), there would not be enough space for two purines, and the two pyrimidines could not be close enough together to form proper hydrogen bonds. An in-depth study of the detailed model showed that adenine and cytosine, making up a combination of the right size, still could not be arranged in such a way that hydrogen bonds formed between them. Similar reports also forced the guanine-thymine combination to be excluded, while the combinations adenine-thymine and guanine-cytosine were found to be quite acceptable. The nature of hydrogen bonds is such that adenine pairs with thymine, and guanine pairs with cytosine. This concept of specific base pairing made it possible to explain the "Chargaff rule", according to which in any DNA molecule the amount of adenine is always equal to the content of thymine, and the amount of guanine is always equal to the amount of cytosine. Two hydrogen bonds form between adenine and thymine, and three between guanine and cytosine. Due to this specificity in the formation of hydrogen bonds against each adenine in one chain, thymine is in the other; in the same way, only cytosine can be placed against each guanine. Thus, the chains are complementary to each other, that is, the sequence of nucleotides in one chain uniquely determines their sequence in the other. The two chains run in opposite directions and their phosphate end groups are at opposite ends of the double helix.
As a result of their research, in 1953 Watson and Crick proposed a model for the structure of the DNA molecule (Fig. 3), which remains relevant to the present. According to the model, a DNA molecule consists of two complementary polynucleotide chains. Each DNA strand is a polynucleotide consisting of several tens of thousands of nucleotides. In it, neighboring nucleotides form a regular pentose-phosphate backbone due to the combination of a phosphoric acid residue and deoxyribose by a strong covalent bond. The nitrogenous bases of one polynucleotide chain are arranged in a strictly defined order against the nitrogenous bases of the other. The alternation of nitrogenous bases in the polynucleotide chain is irregular.
The arrangement of nitrogenous bases in the DNA chain is complementary (from the Greek "complement" - addition), i.e. against adenine (A) is always thymine (T), and against guanine (G) - only cytosine (C). This is explained by the fact that A and T, as well as G and C, strictly correspond to each other, i.e. complement each other. This correspondence is given by the chemical structure of the bases, which allows the formation of hydrogen bonds in a pair of purine and pyrimidine. Between A and T there are two bonds, between G and C - three. These bonds provide partial stabilization of the DNA molecule in space. The stability of the double helix is directly proportional to the number of G≡C bonds, which are more stable than the A=T bonds.
The known sequence of nucleotides in one strand of DNA makes it possible, by the principle of complementarity, to establish the nucleotides of another strand.
In addition, it was found that nitrogenous bases having an aromatic structure, in aqueous solution are arranged one above the other, forming, as it were, a stack of coins. This process of forming stacks of organic molecules called stacking. The polynucleotide chains of the DNA molecule of the considered Watson-Crick model have a similar physicochemical state, their nitrogenous bases are arranged in the form of a stack of coins, between the planes of which van der Waals interactions (stacking interactions) occur.
Hydrogen bonds between complementary bases (horizontally) and stacking interaction between base planes in a polynucleotide chain due to van der Waals forces (vertically) provide the DNA molecule with additional stabilization in space.
The sugar-phosphate backbones of both chains are turned outward, and the bases are inward, towards each other. The direction of the strands in DNA is antiparallel (one of them has the direction 5"->3", the other - 3"->5", i.e. the 3"-end of one strand is located opposite the 5"-end of the other.). The chains form right helixes with a common axis. One turn of the helix is 10 nucleotides, the size of the turn is 3.4 nm, the height of each nucleotide is 0.34 nm, the diameter of the helix is 2.0 nm. As a result of the rotation of one strand around the other, a major groove (about 20 Å in diameter) and a minor groove (about 12 Å) are formed in the DNA double helix. This form of the Watson-Crick double helix was later called the B-form. In cells, DNA usually exists in the B form, which is the most stable.
Functions of DNA
The proposed model explained many biological properties of deoxyribonucleic acid, including the storage of genetic information and the diversity of genes provided by a wide variety of consecutive combinations of 4 nucleotides and the fact of the existence of a genetic code, the ability to self-reproduce and transfer genetic information provided by the replication process, and the implementation of genetic information in the form of proteins, as well as any other compounds formed with the help of enzyme proteins.
Basic functions of DNA.
- DNA is the carrier of genetic information, which is ensured by the fact of the existence of the genetic code.
- Reproduction and transmitted genetic information in generations of cells and organisms. This function is provided by the replication process.
- Implementation of genetic information in the form of proteins, as well as any other compounds formed with the help of enzyme proteins. This function is provided by the processes of transcription and translation.
Forms of organization of double-stranded DNA
DNA can form several types of double helixes (Fig. 4). Currently, six forms are already known (from A to E and Z-form).
Structural forms of DNA, as established by Rosalind Franklin, depend on the saturation of the nucleic acid molecule with water. In studies of DNA fibers using X-ray diffraction analysis, it was shown that the X-ray diffraction pattern radically depends on at what relative humidity, at what degree of water saturation of this fiber the experiment takes place. If the fiber was sufficiently saturated with water, then one radiograph was obtained. When dried, a completely different X-ray pattern appeared, very different from the X-ray pattern of a high-moisture fiber.
Molecule of high humidity DNA is called B-shape. Under physiological conditions (low salt concentration, high degree of hydration), the dominant structural type of DNA is the B-form (the main form of double-stranded DNA is the Watson-Crick model). The helix pitch of such a molecule is 3.4 nm. There are 10 complementary pairs per turn in the form of twisted stacks of "coins" - nitrogenous bases. The stacks are held together by hydrogen bonds between two opposite "coins" of the stacks, and are "coiled" with two ribbons of the phosphodiester backbone twisted into a right-handed helix. The planes of the nitrogenous bases are perpendicular to the axis of the helix. Neighboring complementary pairs are rotated relative to each other by 36°. The helix diameter is 20Å, with the purine nucleotide occupying 12Å and the pyrimidine nucleotide occupying 8Å.
DNA molecule of lower moisture is called A-form. The A-form is formed under conditions of less high hydration and at a higher content of Na + or K + ions. This wider right-handed conformation has 11 base pairs per turn. The planes of nitrogenous bases have a stronger inclination to the axis of the helix, they deviate from the normal to the axis of the helix by 20°. This implies the presence of an internal void with a diameter of 5 Å. The distance between adjacent nucleotides is 0.23 nm, the length of the coil is 2.5 nm, and the diameter of the helix is 2.3 nm.
Initially, the A-form of DNA was thought to be less important. However, later it turned out that the A-form of DNA, as well as the B-form, is of great biological importance. The RNA-DNA helix in the template-seed complex has the A-form, as well as the RNA-RNA helix and RNA hairpin structures (the 2'-hydroxyl group of ribose does not allow RNA molecules to form the B-form). The A-form of DNA is found in spores. It has been established that the A-form of DNA is 10 times more resistant to UV rays than the B-form.
A-form and B-form are called canonical forms DNA.
Forms C-E also right-handed, their formation can only be observed in special experiments, and, apparently, they do not exist in vivo. The C-form of DNA has a structure similar to B-DNA. The number of base pairs per turn is 9.33, and the length of the helix is 3.1 nm. The base pairs are inclined at an angle of 8 degrees relative to the perpendicular position to the axis. The grooves are close in size to the grooves of B-DNA. In this case, the main groove is somewhat smaller, and the minor groove is deeper. Natural and synthetic DNA polynucleotides can pass into the C-form.
| Table 1. Characteristics of some types of DNA structures | |||
| Spiral type | A | B | Z |
| Spiral pitch | 0.32 nm | 3.38 nm | 4.46 nm |
| Spiral twist | Right | Right | Left |
| Number of base pairs per turn | 11 | 10 | 12 |
| Distance between base planes | 0.256 nm | 0.338 nm | 0.371 nm |
| Glycosidic bond conformation | anti | anti | anti-C syn-G |
| Furanose ring conformation | C3 "-endo | C2 "-endo | C3 "-endo-G C2 "-endo-C |
| Groove width, small/large | 1.11/0.22 nm | 0.57/1.17 nm | 0.2/0.88 nm |
| Groove depth, small/large | 0.26/1.30 nm | 0.82/0.85 nm | 1.38/0.37 nm |
| Spiral diameter | 2.3 nm | 2.0 nm | 1.8 nm |
Structural elements of DNA
(non-canonical DNA structures)
Structural elements of DNA include unusual structures limited by some special sequences:
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Z-form of DNA was discovered in 1979 while studying the hexanucleotide d(CG)3 - . It was opened by MIT professor Alexander Rich and his staff. The Z-form has become one of the most important structural elements of DNA due to the fact that its formation was observed in DNA regions where purines alternate with pyrimidines (for example, 5'-HCHCHC-3'), or in 5'-CHCHCH-3' repeats containing methylated cytosine. An essential condition for the formation and stabilization of Z-DNA was the presence in it of purine nucleotides in the syn-conformation, alternating with pyrimidine bases in the anti-conformation.
Natural DNA molecules mostly exist in the right B form unless they contain sequences like (CG)n. However, if such sequences are part of DNA, then these regions, when the ionic strength of the solution or cations that neutralize the negative charge on the phosphodiester backbone, can change into the Z-form, while other DNA regions in the chain remain in the classical B-form. The possibility of such a transition indicates that the two strands in the DNA double helix are in a dynamic state and can unwind relative to each other, passing from the right form to the left one and vice versa. The biological consequences of this lability, which allows conformational transformations of the DNA structure, are not yet fully understood. It is believed that Z-DNA regions play a role in the regulation of the expression of certain genes and take part in genetic recombination.
The Z-form of DNA is a left-handed double helix, in which the phosphodiester backbone is zigzag along the axis of the molecule. Hence the name of the molecule (zigzag)-DNA. Z-DNA is the least twisted (12 base pairs per turn) and thinnest known in nature. The distance between adjacent nucleotides is 0.38 nm, the coil length is 4.56 nm, and the Z-DNA diameter is 1.8 nm. Besides, appearance This DNA molecule is distinguished by the presence of a single groove.
The Z-form of DNA has been found in prokaryotic and eukaryotic cells. To date, antibodies have been obtained that can distinguish between the Z-form and the B-form of DNA. These antibodies bind to specific regions of the giant chromosomes of Drosophila (Dr. melanogaster) salivary gland cells. The binding reaction is easy to follow due to the unusual structure of these chromosomes, in which denser regions (disks) contrast with less dense regions (interdisks). Z-DNA regions are located in the interdiscs. It follows from this that the Z-form actually exists in natural conditions, although the sizes of the individual sections of the Z-form are not yet known.
(shifters) - the most famous and frequently occurring base sequences in DNA. A palindrome is a word or phrase that reads from left to right and vice versa in the same way. Examples of such words or phrases are: HUT, COSSACK, FLOOD, AND A ROSE FALLED ON AZOR'S PAWS. When applied to sections of DNA, this term (palindrome) means the same alternation of nucleotides along the chain from right to left and from left to right (like the letters in the word "hut", etc.).
A palindrome is characterized by the presence of inverted repeats of base sequences having a second-order symmetry with respect to two DNA strands. Such sequences, for obvious reasons, are self-complementary and tend to form hairpin or cruciform structures (Fig.). Hairpins help regulatory proteins to recognize the place where the genetic text of chromosome DNA is copied.
In cases where an inverted repeat is present in the same DNA strand, such a sequence is called a mirror repeat. Mirror repeats do not have self-complementary properties and therefore are not capable of forming hairpin or cruciform structures. Sequences of this type are found in almost all large DNA molecules and can range from just a few base pairs to several thousand base pairs.
The presence of palindromes in the form of cruciform structures in eukaryotic cells has not been proven, although a number of cruciform structures have been found in vivo in E. coli cells. The presence of self-complementary sequences in RNA or single-stranded DNA is the main reason for the folding of the nucleic chain in solutions into a certain spatial structure, characterized by the formation of many "hairpins".
H-form of DNA- this is a helix that is formed by three strands of DNA - the triple helix of DNA. It is a complex of the Watson-Crick double helix with the third single-stranded DNA strand, which fits into its large groove, with the formation of the so-called Hoogsteen pair.
The formation of such a triplex occurs as a result of the addition of the DNA double helix in such a way that half of its section remains in the form of a double helix, and the second half is disconnected. In this case, one of the disconnected spirals forms a new structure with the first half of the double helix - a triple helix, and the second turns out to be unstructured, in the form of a single-filament section. A feature of this structural transition is a sharp dependence on the pH of the medium, the protons of which stabilize the new structure. Due to this feature, the new structure was called the H-form of DNA, the formation of which was found in supercoiled plasmids containing homopurine-homopyrimidine regions, which are a mirror repeat.
In further studies, the possibility of structural transition of some homopurine-homopyrimidine double-stranded polynucleotides was established with the formation of a three-stranded structure containing:
- one homopurine and two homopyrimidine strands ( Py-Pu-Py triplex) [Hoogsteen interaction].
The constituent blocks of the Py-Pu-Py triplex are canonical isomorphic CGC+ and TAT triads. Stabilization of the triplex requires protonation of the CGC+ triad, so these triplexes are dependent on the pH of the solution.
- one homopyrimidine and two homopurine strands ( Py-Pu-Pu triplex) [inverse Hoogsteen interaction].
The constituent blocks of the Py-Pu-Pu triplex are the canonical isomorphic CGG and TAA triads. An essential property of Py-Pu-Pu triplexes is the dependence of their stability on the presence of doubly charged ions, and different ions are needed to stabilize triplexes of different sequences. Since the formation of Py-Pu-Pu triplexes does not require protonation of their constituent nucleotides, such triplexes can exist at neutral pH.
Note: the direct and reverse Hoogsteen interaction is explained by the symmetry of 1-methylthymine: a 180 ° rotation leads to the fact that the place of the O4 atom is occupied by the O2 atom, while the system of hydrogen bonds is preserved.
There are two types of triple helixes:
- parallel triple helixes in which the polarity of the third strand is the same as that of the homopurine chain of the Watson-Crick duplex
- antiparallel triple helixes, in which the polarities of the third and homopurine chains are opposite.
G-quadruplex- 4-stranded DNA. Such a structure is formed if there are four guanines, which form the so-called G-quadruplex - a round dance of four guanines.
The first hints of the possibility of the formation of such structures were obtained long before the breakthrough work of Watson and Crick - as early as 1910. Then the German chemist Ivar Bang discovered that one of the components of DNA - guanosic acid - forms gels at high concentrations, while other components of DNA do not have this property.
In 1962, using the X-ray diffraction method, it was possible to establish the cell structure of this gel. It turned out to be composed of four guanine residues, linking each other in a circle and forming a characteristic square. In the center, the bond is supported by a metal ion (Na, K, Mg). The same structures can be formed in DNA if it contains a lot of guanine. These flat squares (G-quartets) are stacked to form fairly stable, dense structures (G-quadruplexes).
Four separate strands of DNA can be woven into four-stranded complexes, but this is rather an exception. More often, a single strand of nucleic acid is simply tied into a knot, forming characteristic thickenings (for example, at the ends of chromosomes), or double-stranded DNA forms a local quadruplex at some guanine-rich site.
The most studied is the existence of quadruplexes at the ends of chromosomes - on telomeres and in oncopromoters. However, a complete understanding of the localization of such DNA in human chromosomes is still not known.
All these unusual structures of DNA in the linear form are unstable compared to the B-form of DNA. However, DNA often exists in a ring form of topological tension when it has what is known as supercoiling. Under these conditions, non-canonical DNA structures are easily formed: Z-forms, "crosses" and "hairpins", H-forms, guanine quadruplexes, and the i-motif.
- Supercoiled form - noted when released from the cell nucleus without damage to the pentose-phosphate backbone. It has the form of supertwisted closed rings. In the supertwisted state, the DNA double helix is "twisted on itself" at least once, i.e. it contains at least one supercoil (takes the shape of a figure eight).
- Relaxed state of DNA - observed with a single break (break of one strand). In this case, the supercoils disappear and the DNA takes the form of a closed ring.
- The linear form of DNA is observed when two strands of the double helix are broken.
Tertiary structure of DNA
Tertiary structure of DNA is formed as a result of additional twisting in space of a double-stranded molecule - its supercoiling. Supercoiling of the DNA molecule in eukaryotic cells, in contrast to prokaryotes, is carried out in the form of complexes with proteins.
Almost all eukaryotic DNA is located in the chromosomes of the nuclei, only a small amount of it is found in mitochondria, and in plants and in plastids. The main substance of the chromosomes of eukaryotic cells (including human chromosomes) is chromatin, consisting of double-stranded DNA, histone and non-histone proteins.
Histone proteins of chromatin
Histones are simple proteins that make up up to 50% of chromatin. In all the studied cells of animals and plants, five main classes of histones were found: H1, H2A, H2B, H3, H4, differing in size, amino acid composition and charge (always positive).
Mammalian histone H1 consists of a single polypeptide chain containing approximately 215 amino acids; the sizes of other histones vary from 100 to 135 amino acids. All of them are spiralized and twisted into a globule with a diameter of about 2.5 nm, contain an unusually large amount of positively charged amino acids lysine and arginine. Histones can be acetylated, methylated, phosphorylated, poly(ADP)-ribosylated, and histones H2A and H2B can be covalently linked to ubiquitin. What is the role of such modifications in the formation of the structure and performance of functions by histones has not yet been fully elucidated. It is assumed that this is their ability to interact with DNA and provide one of the mechanisms for regulating the action of genes.
Histones interact with DNA mainly through ionic bonds (salt bridges) formed between the negatively charged phosphate groups of DNA and the positively charged lysine and arginine residues of histones.
Non-histone proteins of chromatin
Non-histone proteins, unlike histones, are very diverse. Up to 590 different fractions of DNA-binding nonhistone proteins have been isolated. They are also called acidic proteins, since acidic amino acids predominate in their structure (they are polyanions). The specific regulation of chromatin activity is associated with a variety of non-histone proteins. For example, enzymes essential for DNA replication and expression can bind to chromatin transiently. Other proteins, say those involved in various regulatory processes, bind to DNA only in specific tissues or at certain stages of differentiation. Each protein is complementary to a specific sequence of DNA nucleotides (DNA site). This group includes:
- a family of site-specific zinc finger proteins. Each "zinc finger" recognizes a specific site consisting of 5 nucleotide pairs.
- a family of site-specific proteins - homodimers. A fragment of such a protein in contact with DNA has a "helix-turn-helix" structure.
- high mobility proteins (HMG proteins - from English, high mobility gel proteins) are a group of structural and regulatory proteins that are constantly associated with chromatin. They have a molecular weight of less than 30 kD and are characterized by a high content of charged amino acids. Due to their low molecular weight, HMG proteins are highly mobile during polyacrylamide gel electrophoresis.
- enzymes of replication, transcription and repair.
With the participation of structural, regulatory proteins and enzymes involved in the synthesis of DNA and RNA, the nucleosome thread is converted into a highly condensed complex of proteins and DNA. The resulting structure is 10,000 times shorter than the original DNA molecule.
Chromatin
Chromatin is a complex of proteins with nuclear DNA and inorganic substances. Most of the chromatin is inactive. It contains densely packed, condensed DNA. This is heterochromatin. There are constitutive, genetically inactive chromatin (satellite DNA) consisting of non-expressed regions, and facultative - inactive in a number of generations, but under certain circumstances capable of expressing.
Active chromatin (euchromatin) is uncondensed, i.e. packed less tightly. In different cells, its content ranges from 2 to 11%. In the cells of the brain, it is the most - 10-11%, in the cells of the liver - 3-4 and kidneys - 2-3%. There is an active transcription of euchromatin. At the same time, its structural organization makes it possible to use the same DNA genetic information inherent in a given type of organism in different ways in specialized cells.
In an electron microscope, the image of chromatin resembles beads: spherical thickenings about 10 nm in size, separated by filamentous bridges. These spherical thickenings are called nucleosomes. The nucleosome is the structural unit of chromatin. Each nucleosome contains a 146 bp long supercoiled DNA segment wound to form 1.75 left turns per nucleosome core. The nucleosomal core is a histone octamer consisting of histones H2A, H2B, H3 and H4, two molecules of each type (Fig. 9), which looks like a disk with a diameter of 11 nm and a thickness of 5.7 nm. The fifth histone, H1, is not part of the nucleosomal core and is not involved in the process of DNA winding around the histone octamer. It contacts DNA at the points where the double helix enters and exits the nucleosomal core. These are intercore (linker) sections of DNA, the length of which varies depending on the type of cell from 40 to 50 nucleotide pairs. As a result, the length of the DNA fragment that is part of the nucleosomes also varies (from 186 to 196 nucleotide pairs).
The nucleosome contains about 90% of DNA, the rest of it is the linker. It is believed that nucleosomes are fragments of "silent" chromatin, while the linker is active. However, nucleosomes can unfold and become linear. Unfolded nucleosomes are already active chromatin. This clearly shows the dependence of the function on the structure. It can be assumed that the more chromatin is in the composition of globular nucleosomes, the less active it is. Obviously, in different cells the unequal proportion of resting chromatin is associated with the number of such nucleosomes.
On electron microscopic photographs, depending on the conditions of isolation and the degree of stretching, chromatin can look not only as a long thread with thickenings - “beads” of nucleosomes, but also as a shorter and denser fibril (fiber) with a diameter of 30 nm, the formation of which is observed during the interaction of histone H1 associated with the linker region of DNA and histone H3, which leads to additional twisting of the helix of six nucleosomes per turn to form a solenoid with a diameter of 30 nm. In this case, the histone protein can interfere with the transcription of a number of genes and thus regulate their activity.
As a result of the interactions of DNA with histones described above, a segment of the DNA double helix of 186 base pairs with an average diameter of 2 nm and a length of 57 nm turns into a helix with a diameter of 10 nm and a length of 5 nm. With the subsequent compression of this helix to a fiber with a diameter of 30 nm, the degree of condensation increases by another six times.
Ultimately, the packaging of the DNA duplex with five histones results in a 50-fold DNA condensation. However, even such a high degree of condensation cannot explain the almost 50,000-100,000-fold DNA compaction in the metaphase chromosome. Unfortunately, the details of the further packing of chromatin up to the metaphase chromosome are not yet known; therefore, only general features of this process can be considered.
Levels of DNA compaction in chromosomes
Each DNA molecule is packaged into a separate chromosome. Diploid human cells contain 46 chromosomes, which are located in the cell nucleus. The total length of the DNA of all the chromosomes of a cell is 1.74 m, but the diameter of the nucleus in which the chromosomes are packed is millions of times smaller. Such compact packing of DNA in chromosomes and chromosomes in the cell nucleus is provided by a variety of histone and non-histone proteins interacting in a certain sequence with DNA (see above). Compaction of DNA in chromosomes makes it possible to reduce its linear dimensions by about 10,000 times - conditionally from 5 cm to 5 microns. There are several levels of compactization (Fig. 10).
- DNA double helix is a negatively charged molecule with a diameter of 2 nm and a length of several cm.
- nucleosomal level- chromatin looks in an electron microscope as a chain of "beads" - nucleosomes - "on a thread". The nucleosome is a universal structural unit that is found both in euchromatin and heterochromatin, in the interphase nucleus and metaphase chromosomes.
The nucleosomal level of compaction is provided by special proteins - histones. Eight positively charged histone domains form the core (core) of the nucleosome around which the negatively charged DNA molecule is wound. This gives a shortening by a factor of 7, while the diameter increases from 2 to 11 nm.
- solenoid level
The solenoid level of chromosome organization is characterized by the twisting of the nucleosomal filament and the formation of thicker fibrils 20-35 nm in diameter from it - solenoids or superbids. The solenoid pitch is 11 nm, there are about 6-10 nucleosomes per turn. Solenoid packing is considered more probable than superbid packing, according to which a chromatin fibril with a diameter of 20–35 nm is a chain of granules, or superbids, each of which consists of eight nucleosomes. At the solenoid level, the linear size of DNA is reduced by 6-10 times, the diameter increases to 30 nm.
- loop level
The loop level is provided by non-histone site-specific DNA-binding proteins that recognize and bind to specific DNA sequences, forming loops of approximately 30-300 kb. The loop ensures gene expression, i.e. the loop is not only a structural, but also a functional formation. Shortening at this level occurs by 20-30 times. The diameter increases to 300 nm. Loop-like "lampbrush" structures in amphibian oocytes can be seen on cytological preparations. These loops appear to be supercoiled and represent DNA domains, probably corresponding to units of chromatin transcription and replication. Specific proteins fix the bases of the loops and, possibly, some of their internal regions. The loop-like domain organization facilitates the folding of chromatin in metaphase chromosomes into helical structures of higher orders.
- domain level
The domain level of chromosome organization has not been studied enough. At this level, the formation of loop domains is noted - structures of filaments (fibrils) 25-30 nm thick, which contain 60% protein, 35% DNA and 5% RNA, are practically invisible in all phases of the cell cycle with the exception of mitosis and are somewhat randomly distributed over the cell nucleus. Loop-like "lampbrush" structures in amphibian oocytes can be seen on cytological preparations.
Loop domains are attached with their base to the intranuclear protein matrix in the so-called built-in attachment sites, often referred to as MAR / SAR sequences (MAR, from the English matrix associated region; SAR, from the English scaffold attachment regions) - DNA fragments several hundred base pairs long, which are characterized by a high content (> 65%) of A / T nucleotide pairs. Each domain appears to have a single origin of replication and functions as an autonomous supercoiled unit. Any loop domain contains many transcription units, the functioning of which is likely to be coordinated - the entire domain is either in an active or inactive state.
At the domain level, as a result of sequential packing of chromatin, the linear dimensions of DNA decrease by about 200 times (700 nm).
- chromosome level
On chromosome level the condensation of the prophase chromosome into the metaphase chromosome occurs with the compaction of loop domains around the axial framework of non-histone proteins. This supercoiling is accompanied by phosphorylation of all H1 molecules in the cell. As a result, the metaphase chromosome can be depicted as densely packed solenoid loops coiled into a tight spiral. A typical human chromosome can contain up to 2600 loops. The thickness of such a structure reaches 1400 nm (two chromatids), while the DNA molecule is shortened by 104 times, i.e. from 5 cm stretched DNA to 5 µm.
Functions of chromosomes
In interaction with extrachromosomal mechanisms, chromosomes provide
- storage of hereditary information
- using this information to create and maintain cellular organization
- regulation of reading hereditary information
- self-duplication of genetic material
- the transfer of genetic material from a mother cell to daughter cells.
There is evidence that upon activation of a chromatin region, i.e. during transcription, histone H1 is reversibly removed from it first, and then the histone octet. This causes decondensation of chromatin, the successive transition of a 30-nm chromatin fibril into a 10-nm filament and its further unfolding into free DNA regions, i.e. loss of nucleosomal structure.
We all know that the appearance of a person, some habits and even diseases are inherited. All this information about a living being is encoded in the genes. So what do these notorious genes look like, how do they function, and where are they located?
So, the carrier of all genes of any person or animal is DNA. This compound was discovered in 1869 by Johann Friedrich Miescher. Chemically, DNA is deoxyribonucleic acid. What does this mean? How does this acid carry the genetic code of all life on our planet?
Let's start by looking at where DNA is located. There are many organelles in the human cell that perform various functions. DNA is located in the nucleus. The nucleus is a small organelle that is surrounded by a special membrane that stores all the genetic material - DNA.
What is the structure of a DNA molecule?
First, let's look at what DNA is. DNA is a very long molecule consisting of structural elements - nucleotides. There are 4 types of nucleotides - adenine (A), thymine (T), guanine (G) and cytosine (C). The chain of nucleotides schematically looks like this: GGAATTSTAAG.... This sequence of nucleotides is the DNA chain.The structure of DNA was first deciphered in 1953 by James Watson and Francis Crick.
In one DNA molecule, there are two chains of nucleotides that are helically twisted around each other. How do these nucleotide chains stick together and twist into a spiral? This phenomenon is due to the property of complementarity. Complementarity means that only certain nucleotides (complementary) can be opposite each other in two chains. So, opposite adenine is always thymine, and opposite guanine is always only cytosine. Thus, guanine is complementary with cytosine, and adenine with thymine. Such pairs of nucleotides opposite each other in different chains are also called complementary.
It can be schematically represented as follows:
G - C
T - A
T - A
C - G
These complementary pairs A - T and G - C form chemical bond between the nucleotides of the pair, and the bond between G and C is stronger than between A and T. The bond is formed strictly between complementary bases, that is, the formation of a bond between non-complementary G and A is impossible.
The "packaging" of DNA, how does a strand of DNA become a chromosome?
Why do these nucleotide chains of DNA also twist around each other? Why is this needed? The fact is that the number of nucleotides is huge and you need a lot of space to accommodate such long chains. For this reason, there is a spiral twisting of two strands of DNA around the other. This phenomenon is called spiralization. As a result of spiralization, DNA chains are shortened by 5-6 times.Some DNA molecules are actively used by the body, while others are rarely used. Such rarely used DNA molecules, in addition to helicalization, undergo even more compact “packaging”. Such a compact package is called supercoiling and shortens the DNA strand by 25-30 times!
How is DNA helix packaged?
For supercoiling, histone proteins are used, which have the appearance and structure of a rod or spool of thread. Spiralized strands of DNA are wound onto these "coils" - histone proteins. In this way, the long filament becomes very compactly packed and takes up very little space. If it is necessary to use one or another DNA molecule, the process of “unwinding” occurs, that is, the DNA thread is “unwound” from the “coil” - the histone protein (if it was wound on it) and unwinds from the helix into two parallel chains. And when the DNA molecule is in such a untwisted state, then the necessary genetic information can be read from it. Moreover, the reading of genetic information occurs only from untwisted DNA strands!
A set of supercoiled chromosomes is called heterochromatin, and the chromosomes available for reading information - euchromatin.
What are genes, what is their relationship with DNA?
Now let's look at what genes are. It is known that there are genes that determine the blood group, the color of the eyes, hair, skin and many other properties of our body. A gene is a strictly defined section of DNA, consisting of a certain number of nucleotides arranged in a strictly defined combination. Location in a strictly defined section of DNA means that a particular gene has its place, and it is impossible to change this place. It is appropriate to make such a comparison: a person lives on a certain street, in a certain house and apartment, and a person cannot arbitrarily move to another house, apartment or to another street. A certain number of nucleotides in a gene means that each gene has a specific number of nucleotides and cannot become more or less. For example, the gene encoding insulin production is 60 base pairs long; the gene encoding the production of the hormone oxytocin is 370 bp. A strict nucleotide sequence is unique for each gene and strictly defined. For example, the AATTAATA sequence is a fragment of a gene that codes for insulin production. In order to obtain insulin, just such a sequence is used; to obtain, for example, adrenaline, a different combination of nucleotides is used. It is important to understand that only a certain combination of nucleotides encodes a certain "product" (adrenaline, insulin, etc.). Such a unique combination of a certain number of nucleotides, standing in "its place" - this is gene.
In addition to genes, the so-called "non-coding sequences" are located in the DNA chain. Such non-coding nucleotide sequences regulate the functioning of genes, help chromosome spiralization, and mark the start and end points of a gene. However, to date, the role of most non-coding sequences remains unclear.
What is a chromosome? sex chromosomes
The totality of an individual's genes is called the genome. Naturally, the entire genome cannot be packed into a single DNA. The genome is divided into 46 pairs of DNA molecules. One pair of DNA molecules is called a chromosome. So it is precisely these chromosomes that a person has 46 pieces. Each chromosome carries a strictly defined set of genes, for example, the 18th chromosome contains genes encoding eye color, etc. Chromosomes differ from each other in length and shape. The most common forms are in the form of X or Y, but there are also others. A person has two chromosomes of the same shape, which are called paired (pairs). In connection with such differences, all paired chromosomes are numbered - there are 23 pairs. This means that there is a pair of chromosomes #1, pair #2, #3, and so on. Each gene responsible for a particular trait is located on the same chromosome. In modern manuals for specialists, the localization of the gene may be indicated, for example, as follows: chromosome 22, long arm.What are the differences between chromosomes?
How else do chromosomes differ from each other? What does the term long arm mean? Let's take X-shaped chromosomes. The crossing of DNA strands can occur strictly in the middle (X), or it can occur not centrally. When such an intersection of DNA strands does not occur centrally, then relative to the point of intersection, some ends are longer, others, respectively, are shorter. Such long ends are commonly called the long arm of the chromosome, and short ends, respectively, the short arm. Y-shaped chromosomes are mostly occupied by long arms, and short ones are very small (they are not even indicated on the schematic image). The size of the chromosomes fluctuates: the largest are the chromosomes of pairs No. 1 and No. 3, the smallest chromosomes of pairs No. 17, No. 19.
In addition to shapes and sizes, chromosomes differ in their functions. Out of 23 pairs, 22 pairs are somatic and 1 pair is sexual. What does it mean? Somatic chromosomes determine all the external signs of an individual, his features behavioral responses, hereditary psychotype, that is, all the features and characteristics of each individual person. A pair of sex chromosomes determines the sex of a person: male or female. There are two types of human sex chromosomes - X (X) and Y (Y). If they are combined as XX (X - X) - this is a woman, and if XY (X - Y) - we have a man in front of us.
Hereditary diseases and chromosome damage
However, there are "breakdowns" of the genome, then genetic diseases are detected in people. For example, when there are three chromosomes in 21 pairs of chromosomes instead of two, a person is born with Down syndrome.There are many smaller "breakdowns" of the genetic material that do not lead to the onset of the disease, but, on the contrary, give good properties. All "breakdowns" of the genetic material are called mutations. Mutations that lead to disease or deterioration of the properties of the organism are considered negative, and mutations that lead to the formation of new beneficial properties are considered positive.
However, in relation to most of the diseases that people suffer today, it is not a disease that is inherited, but only a predisposition. For example, in the father of a child, sugar is absorbed slowly. This does not mean that the child will be born with diabetes, but the child will have a predisposition. This means that if a child abuses sweets and flour products, then he will develop diabetes.
Today, the so-called predicative medicine. As part of this medical practice, predispositions are identified in a person (based on the identification of the corresponding genes), and then recommendations are given to him - what diet to follow, how to properly alternate the regime of work and rest so as not to get sick.
How to read the information encoded in DNA?
But how can you read the information contained in DNA? How does her own body use it? DNA itself is a kind of matrix, but not simple, but encoded. To read information from the DNA matrix, it is first transferred to a special carrier - RNA. RNA is chemically ribonucleic acid. It differs from DNA in that it can pass through the nuclear membrane into the cell, while DNA lacks this ability (it can only be found in the nucleus). The encoded information is used in the cell itself. So, RNA is a carrier of coded information from the nucleus to the cell.How does RNA synthesis occur, how is protein synthesized with the help of RNA?
The DNA strands from which information must be “read” are untwisted, a special enzyme, the “builder”, approaches them and synthesizes a complementary RNA chain in parallel with the DNA strand. The RNA molecule also consists of 4 types of nucleotides - adenine (A), uracil (U), guanine (G) and cytosine (C). In this case, the following pairs are complementary: adenine - uracil, guanine - cytosine. As you can see, unlike DNA, RNA uses uracil instead of thymine. That is, the “builder” enzyme works as follows: if it sees A in the DNA strand, then it attaches Y to the RNA strand, if G, then it attaches C, etc. Thus, a template is formed from each active gene during transcription - a copy of RNA that can pass through the nuclear membrane. How is the synthesis of a protein encoded by a particular gene?
After leaving the nucleus, RNA enters the cytoplasm. Already in the cytoplasm, RNA can be, as a matrix, built into special enzyme systems (ribosomes), which can synthesize, guided by the information of RNA, the corresponding amino acid sequence of the protein. As you know, a protein molecule is made up of amino acids. How does the ribosome manage to know which amino acid to attach to the growing protein chain? This is done on the basis of a triplet code. The triplet code means that the sequence of three nucleotides of the RNA chain ( triplet, for example, GGU) code for one amino acid (in this case, glycine). Each amino acid is encoded by a specific triplet. And so, the ribosome “reads” the triplet, determines which amino acid should be added next as information is read into the RNA. When a chain of amino acids is formed, it takes a certain spatial form and becomes a protein capable of carrying out enzymatic, building, hormonal and other functions assigned to it.Protein for any living organism is a gene product. It is proteins that determine all the various properties, qualities and external manifestations of genes.
On the right is the largest human DNA helix built from people on the beach in Varna (Bulgaria), which was included in the Guinness Book of Records on April 23, 2016
Deoxyribonucleic acid. General information
DNA (deoxyribonucleic acid) is a kind of blueprint of life, a complex code that contains data on hereditary information. This complex macromolecule is capable of storing and transmitting hereditary genetic information from generation to generation. DNA determines such properties of any living organism as heredity and variability. The information encoded in it determines the entire development program of any living organism. Genetically embedded factors predetermine the entire course of life of both a person and any other organism. Artificial or natural influence of the external environment can only slightly affect the overall severity of individual genetic traits or affect the development of programmed processes.
Deoxyribonucleic acid(DNA) is a macromolecule (one of the three main ones, the other two are RNA and proteins), which provides storage, transmission from generation to generation and implementation of the genetic program for the development and functioning of living organisms. DNA contains information about the structure of various types of RNA and proteins.
In eukaryotic cells (animals, plants, and fungi), DNA is found in the cell nucleus as part of chromosomes, as well as in some cell organelles (mitochondria and plastids). In the cells of prokaryotic organisms (bacteria and archaea), a circular or linear DNA molecule, the so-called nucleoid, is attached from the inside to the cell membrane. They and lower eukaryotes (for example, yeast) also have small autonomous, mostly circular DNA molecules called plasmids.
From a chemical point of view, DNA is a long polymeric molecule consisting of repeating blocks - nucleotides. Each nucleotide is made up of a nitrogenous base, a sugar (deoxyribose), and a phosphate group. The bonds between nucleotides in a chain are formed by deoxyribose ( WITH) and phosphate ( F) groups (phosphodiester bonds).
Rice. 2. Nuclertide consists of a nitrogenous base, sugar (deoxyribose) and a phosphate group
In the overwhelming majority of cases (except for some viruses containing single-stranded DNA), the DNA macromolecule consists of two chains oriented by nitrogenous bases to each other. This double-stranded molecule is twisted in a helix.
There are four types of nitrogenous bases found in DNA (adenine, guanine, thymine, and cytosine). The nitrogenous bases of one of the chains are connected to the nitrogenous bases of the other chain by hydrogen bonds according to the principle of complementarity: adenine combines only with thymine ( A-T), guanine - only with cytosine ( G-C). It is these pairs that make up the "rungs" of the helical "ladder" of DNA (see: Fig. 2, 3 and 4).
Rice. 2. Nitrogenous bases
The sequence of nucleotides allows you to "encode" information about various types of RNA, the most important of which are informational or template (mRNA), ribosomal (rRNA) and transport (tRNA). All these types of RNA are synthesized on the DNA template by copying the DNA sequence into the RNA sequence synthesized during transcription and take part in protein biosynthesis (translation process). In addition to coding sequences, cell DNA contains sequences that perform regulatory and structural functions.
Rice. 3. DNA replication
The location of the basic combinations of DNA chemical compounds and the quantitative ratios between these combinations provide encoding of hereditary information.
Education new DNA (replication)
- The process of replication: the unwinding of the DNA double helix - the synthesis of complementary strands by DNA polymerase - the formation of two DNA molecules from one.
- The double helix "unzips" into two branches when enzymes break the bond between the base pairs of chemical compounds.
- Each branch is a new DNA element. New base pairs are connected in the same sequence as in the parent branch.
Upon completion of the duplication, two independent helices are formed, created from the chemical compounds of the parent DNA and having the same genetic code with it. In this way, DNA is able to rip through information from cell to cell.
More detailed information:
STRUCTURE OF NUCLEIC ACIDS
Rice. 4 . Nitrogenous bases: adenine, guanine, cytosine, thymine
Deoxyribonucleic acid(DNA) refers to nucleic acids. Nucleic acids is a class of irregular biopolymers whose monomers are nucleotides.
NUCLEOTIDES consist of nitrogenous base, connected to a five-carbon carbohydrate (pentose) - deoxyribose(in the case of DNA) or ribose(in the case of RNA), which combines with a phosphoric acid residue (H 2 PO 3 -).
Nitrogenous bases There are two types: pyrimidine bases - uracil (only in RNA), cytosine and thymine, purine bases - adenine and guanine.
Rice. Fig. 5. The structure of nucleotides (left), the location of the nucleotide in DNA (bottom) and the types of nitrogenous bases (right): pyrimidine and purine
The carbon atoms in a pentose molecule are numbered from 1 to 5. Phosphate combines with the third and fifth carbon atoms. This is how nucleic acids are linked together to form a chain of nucleic acids. Thus, we can isolate the 3' and 5' ends of the DNA strand:
Rice. 6. Isolation of the 3' and 5' ends of the DNA strand
Two strands of DNA form double helix. These chains in a spiral are oriented in opposite directions. In different strands of DNA, nitrogenous bases are connected to each other by means of hydrogen bonds. Adenine always combines with thymine, and cytosine always combines with guanine. It is called complementarity rule(cm. principle of complementarity).
Complementarity rule:
| A-T G-C |
For example, if we are given a DNA strand that has the sequence
3'-ATGTCCTAGCTGCTCG - 5',
then the second chain will be complementary to it and directed in the opposite direction - from the 5'-end to the 3'-end:
5'- TACAGGATCGACGAGC- 3'.
Rice. 7. The direction of the chains of the DNA molecule and the connection of nitrogenous bases using hydrogen bonds
DNA REPLICATION
DNA replication is the process of doubling a DNA molecule by template synthesis. In most cases of natural DNA replicationprimerfor DNA synthesis is short snippet (created again). Such a ribonucleotide primer is created by the enzyme primase (DNA primase in prokaryotes, DNA polymerase in eukaryotes), and is subsequently replaced by deoxyribonucleotide polymerase, which normally performs repair functions (correcting chemical damage and breaks in the DNA molecule).
Replication occurs in a semi-conservative manner. This means that the double helix of DNA unwinds and a new chain is completed on each of its chains according to the principle of complementarity. The daughter DNA molecule thus contains one strand from the parent molecule and one newly synthesized. Replication occurs in the 3' to 5' direction of the parent strand.
Rice. 8. Replication (doubling) of the DNA molecule
DNA synthesis- this is not such a complicated process as it might seem at first glance. If you think about it, then first you need to figure out what synthesis is. It is the process of bringing something together. The formation of a new DNA molecule takes place in several stages:
1) DNA topoisomerase, located in front of the replication fork, cuts the DNA in order to facilitate its unwinding and unwinding.
2) DNA helicase, following topoisomerase, affects the process of "unwinding" the DNA helix.
3) DNA-binding proteins carry out the binding of DNA strands, and also carry out their stabilization, preventing them from sticking to each other.
4) DNA polymerase δ(delta) , coordinated with the speed of movement of the replication fork, performs the synthesisleadingchains subsidiary DNA in the direction 5" → 3" on the matrix maternal strands of DNA in the direction from its 3" end to the 5" end (speed up to 100 base pairs per second). These events on this maternal strands of DNA are limited.
Rice. 9. Schematic representation of the DNA replication process: (1) Lagging strand (lag strand), (2) Leading strand (leading strand), (3) DNA polymerase α (Polα), (4) DNA ligase, (5) RNA -primer, (6) Primase, (7) Okazaki fragment, (8) DNA polymerase δ (Polδ ), (9) Helicase, (10) Single-stranded DNA-binding proteins, (11) Topoisomerase.
The synthesis of the lagging daughter DNA strand is described below (see below). scheme replication fork and functions of replication enzymes)
For more information on DNA replication, see
5) Immediately after the unwinding and stabilization of another strand of the parent molecule, it joinsDNA polymerase α(alpha)and in the direction 5 "→3" synthesizes a primer (RNA primer) - an RNA sequence on a DNA template with a length of 10 to 200 nucleotides. After that, the enzymeremoved from the DNA strand.
Instead of DNA polymeraseα
attached to the 3" end of the primer DNA polymeraseε
.
6)
DNA polymeraseε
(epsilon) as if continues to lengthen the primer, but as a substrate embedsdeoxyribonucleotides(in the amount of 150-200 nucleotides). The result is a solid thread of two parts -RNA(i.e. primer) and DNA.
DNA polymerase εworks until it encounters the primer of the previousfragment Okazaki(synthesized a little earlier). This enzyme is then removed from the chain.
7) DNA polymerase β(beta) stands in place ofDNA polymerases ε,moves in the same direction (5" → 3") and removes primer ribonucleotides while inserting deoxyribonucleotides in their place. The enzyme works until the complete removal of the primer, i.e. until a deoxyribonucleotide (even more previously synthesizedDNA polymerase ε). The enzyme is not able to link the result of its work and the DNA in front, so it leaves the chain.
As a result, a fragment of the daughter DNA "lies" on the matrix of the mother thread. It is calledfragment of Okazaki.
8) DNA ligase ligates two adjacent fragments Okazaki , i.e. 5 "-end of the segment, synthesizedDNA polymerase ε,and 3" chain end built-inDNA polymeraseβ .
STRUCTURE OF RNA
Ribonucleic acid(RNA) is one of the three main macromolecules (the other two are DNA and proteins) that are found in the cells of all living organisms.
Just like DNA, RNA is made up of a long chain in which each link is called nucleotide. Each nucleotide is made up of a nitrogenous base, a ribose sugar, and a phosphate group. However, unlike DNA, RNA usually has one rather than two strands. Pentose in RNA is represented by ribose, not deoxyribose (ribose has an additional hydroxyl group on the second carbohydrate atom). Finally, DNA differs from RNA in the composition of nitrogenous bases: instead of thymine ( T) uracil is present in RNA ( U) , which is also complementary to adenine.
The sequence of nucleotides allows RNA to encode genetic information. All cellular organisms use RNA (mRNA) to program protein synthesis.
Cellular RNAs are formed in a process called transcription , that is, the synthesis of RNA on a DNA template, carried out by special enzymes - RNA polymerases.
Messenger RNAs (mRNAs) then take part in a process called broadcast, those. protein synthesis on the mRNA template with the participation of ribosomes. Other RNAs undergo chemical modifications after transcription, and after the formation of secondary and tertiary structures, they perform functions that depend on the type of RNA.
Rice. 10. The difference between DNA and RNA in terms of the nitrogenous base: instead of thymine (T), RNA contains uracil (U), which is also complementary to adenine.
TRANSCRIPTION
This is the process of RNA synthesis on a DNA template. DNA unwinds at one of the sites. One of the chains contains information that needs to be copied onto the RNA molecule - this chain is called coding. The second strand of DNA, which is complementary to the coding strand, is called the template strand. In the process of transcription on the template chain in the 3'-5' direction (along the DNA chain), an RNA chain complementary to it is synthesized. Thus, an RNA copy of the coding strand is created.
Rice. 11. Schematic representation of transcription
For example, if we are given the sequence of the coding strand
3'-ATGTCCTAGCTGCTCG - 5',
then, according to the rule of complementarity, the matrix chain will carry the sequence
5'- TACAGGATCGACGAGC- 3',
and the RNA synthesized from it is the sequence
BROADCAST
Consider the mechanism protein synthesis on the RNA matrix, as well as the genetic code and its properties. Also, for clarity, at the link below, we recommend watching a short video about the processes of transcription and translation occurring in a living cell:
Rice. 12. Process of protein synthesis: DNA codes for RNA, RNA codes for protein
GENETIC CODE
Genetic code- a method of encoding the amino acid sequence of proteins using a sequence of nucleotides. Each amino acid is encoded by a sequence of three nucleotides - a codon or a triplet.
Genetic code common to most pro- and eukaryotes. The table lists all 64 codons and lists the corresponding amino acids. The base order is from the 5" to the 3" end of the mRNA.
Table 1. Standard genetic code
|
1st nie |
2nd base |
3rd nie |
|||||||
|
U |
C |
A |
G |
||||||
|
U |
U U U |
(Phe/F) |
U C U |
(Ser/S) |
U A U |
(Tyr/Y) |
U G U |
(Cys/C) |
U |
|
U U C |
U C C |
U A C |
U G C |
C |
|||||
|
U U A |
(Leu/L) |
U C A |
U A A |
Stop codon** |
U G A |
Stop codon** |
A |
||
|
U U G |
U C G |
U A G |
Stop codon** |
U G G |
(Trp/W) |
G |
|||
|
C |
C U U |
C C U |
(Pro/P) |
C A U |
(His/H) |
C G U |
(Arg/R) |
U |
|
|
C U C |
C C C |
C A C |
C G C |
C |
|||||
|
C U A |
C C A |
C A A |
(Gln/Q) |
CGA |
A |
||||
|
C U G |
C C G |
C A G |
C G G |
G |
|||||
|
A |
A U U |
(Ile/I) |
A C U |
(Thr/T) |
A A U |
(Asn/N) |
A G U |
(Ser/S) |
U |
|
A U C |
A C C |
A A C |
A G C |
C |
|||||
|
A U A |
A C A |
A A A |
(Lys/K) |
A G A |
A |
||||
|
A U G |
(Met/M) |
A C G |
A A G |
A G G |
G |
||||
|
G |
G U U |
(Val/V) |
G C U |
(Ala/A) |
G A U |
(Asp/D) |
G G U |
(Gly/G) |
U |
|
G U C |
G C C |
G A C |
G G C |
C |
|||||
|
G U A |
G C A |
G A A |
(Glu/E) |
G G A |
A |
||||
|
G U G |
G C G |
G A G |
G G G |
G |
|||||
Among the triplets, there are 4 special sequences that act as "punctuation marks":
- *Triplet AUG, also encoding methionine, is called start codon. This codon begins the synthesis of a protein molecule. Thus, during protein synthesis, the first amino acid in the sequence will always be methionine.
- **Triplets UAA, UAG And UGA called stop codons and do not code for any amino acids. At these sequences, protein synthesis stops.
Properties of the genetic code
1. Tripletity. Each amino acid is encoded by a sequence of three nucleotides - a triplet or codon.
2. Continuity. There are no additional nucleotides between the triplets, information is read continuously.
3. Non-overlapping. One nucleotide cannot be part of two triplets at the same time.
4. Uniqueness. One codon can code for only one amino acid.
5. Degeneracy. One amino acid can be encoded by several different codons.
6. Versatility. The genetic code is the same for all living organisms.
Example. We are given the sequence of the coding strand:
3’- CCGATTGCACGTCGATCGTATA- 5’.
The matrix chain will have the sequence:
5’- GGCTAACGTGCAGCTAGCATAT- 3’.
Now we “synthesize” informational RNA from this chain:
3’- CCGAUUGCACGUCGAUCGUAUA- 5’.
Protein synthesis goes in the direction 5' → 3', therefore, we need to flip the sequence in order to "read" the genetic code:
5’- AUAUGCUAGCUGCACGUUAGCC- 3’.
Now find the start codon AUG:
5’- AU AUG CUAGCUGCACGUUAGCC- 3’.
Divide the sequence into triplets:
sounds like this: information from DNA is transferred to RNA (transcription), from RNA to protein (translation). DNA can also be duplicated by replication, and the process of reverse transcription is also possible, when DNA is synthesized from an RNA template, but such a process is mainly characteristic of viruses.
Rice. 13. Central Dogma molecular biology
GENOM: GENES AND CHROMOSOMES
(general concepts)
Genome - the totality of all the genes of an organism; its complete chromosome set.
The term "genome" was proposed by G. Winkler in 1920 to describe the totality of genes contained in the haploid set of chromosomes of organisms of the same biological species. The original meaning of this term indicated that the concept of the genome, in contrast to the genotype, is a genetic characteristic of the species as a whole, and not of an individual. With the development of molecular genetics, the meaning of this term has changed. It is known that DNA, which is the carrier of genetic information in most organisms and, therefore, forms the basis of the genome, includes not only genes in the modern sense of the word. Most of The DNA of eukaryotic cells is represented by non-coding (“redundant”) nucleotide sequences that do not contain information about proteins and nucleic acids. Thus, the main part of the genome of any organism is the entire DNA of its haploid set of chromosomes.
Genes are segments of DNA molecules that code for polypeptides and RNA molecules.
Over the past century, our understanding of genes has changed significantly. Previously, a genome was a region of a chromosome that encodes or determines one trait or phenotypic(visible) property, such as eye color.
In 1940, George Beadle and Edward Tatham proposed a molecular definition of a gene. Scientists processed fungus spores Neurospora crassa X-rays and other agents that cause changes in the DNA sequence ( mutations), and found mutant strains of the fungus that lost some specific enzymes, which in some cases led to disruption of the entire metabolic pathway. Beadle and Tatham came to the conclusion that a gene is a section of genetic material that defines or codes for a single enzyme. This is how the hypothesis "one gene, one enzyme". This concept was later extended to the definition "one gene - one polypeptide", since many genes encode proteins that are not enzymes, and a polypeptide can be a subunit of a complex protein complex.
On fig. 14 shows a diagram of how DNA triplets determine a polypeptide, the amino acid sequence of a protein, mediated by mRNA. One of the DNA strands plays the role of a template for the synthesis of mRNA, the nucleotide triplets (codons) of which are complementary to the DNA triplets. In some bacteria and many eukaryotes, coding sequences are interrupted by non-coding regions (called introns).
Modern biochemical definition of a gene even more specifically. Genes are all sections of DNA that encode the primary sequence of end products, which include polypeptides or RNA that have a structural or catalytic function.
Along with genes, DNA also contains other sequences that perform an exclusively regulatory function. Regulatory sequences may mark the beginning or end of genes, affect transcription, or indicate the site of initiation of replication or recombination. Some genes can be expressed in different ways, with the same piece of DNA serving as a template for the formation of different products.
We can roughly calculate minimum gene size coding for the intermediate protein. Each amino acid in a polypeptide chain is encoded by a sequence of three nucleotides; the sequences of these triplets (codons) correspond to the chain of amino acids in the polypeptide encoded by the given gene. A polypeptide chain of 350 amino acid residues (medium length chain) corresponds to a sequence of 1050 bp. ( bp). However, many eukaryotic genes and some prokaryotic genes are interrupted by DNA segments that do not carriers of information about the protein, and therefore turn out to be much longer than a simple calculation shows.
How many genes are on one chromosome?
Rice. 15. View of chromosomes in prokaryotic (left) and eukaryotic cells. Histones are a broad class of nuclear proteins that perform two main functions: they are involved in the packaging of DNA strands in the nucleus and in the epigenetic regulation of nuclear processes such as transcription, replication, and repair.
The DNA of prokaryotes is more simple: their cells do not have a nucleus, so the DNA is located directly in the cytoplasm in the form of a nucleoid.
As you know, bacterial cells have a chromosome in the form of a DNA strand, packed into a compact structure - a nucleoid. prokaryotic chromosome Escherichia coli, whose genome is completely decoded, is a circular DNA molecule (in fact, it is not right circle, but rather a loop without beginning or end), consisting of 4,639,675 b.p. This sequence contains approximately 4300 protein genes and another 157 genes for stable RNA molecules. IN human genome approximately 3.1 billion base pairs corresponding to almost 29,000 genes located on 24 different chromosomes.
Prokaryotes (Bacteria).
Bacterium E. coli has one double-stranded circular DNA molecule. It consists of 4,639,675 b.p. and reaches a length of approximately 1.7 mm, which exceeds the length of the cell itself E. coli about 850 times. In addition to the large circular chromosome as part of the nucleoid, many bacteria contain one or more small circular DNA molecules that are freely located in the cytosol. These extrachromosomal elements are called plasmids(Fig. 16).
Most plasmids consist of only a few thousand base pairs, some contain more than 10,000 bp. They carry genetic information and replicate to form daughter plasmids, which enter the daughter cells during the division of the parent cell. Plasmids are found not only in bacteria, but also in yeast and other fungi. In many cases, plasmids offer no advantage to the host cells and their only job is to reproduce independently. However, some plasmids carry genes useful to the host. For example, genes contained in plasmids can confer resistance to antibacterial agents in bacterial cells. Plasmids carrying the β-lactamase gene confer resistance to β-lactam antibiotics such as penicillin and amoxicillin. Plasmids can pass from antibiotic-resistant cells to other cells of the same or different bacterial species, causing those cells to also become resistant. Intensive use of antibiotics is a powerful selective factor that promotes the spread of plasmids encoding antibiotic resistance (as well as transposons that encode similar genes) among pathogenic bacteria, and leads to the emergence of bacterial strains with resistance to several antibiotics. Doctors are beginning to understand the dangers of widespread use of antibiotics and prescribe them only when absolutely necessary. For similar reasons, the widespread use of antibiotics for the treatment of farm animals is limited.
See also: Ravin N.V., Shestakov S.V. Genome of prokaryotes // Vavilov Journal of Genetics and Breeding, 2013. V. 17. No. 4/2. pp. 972-984.
Eukaryotes.
Table 2. DNA, genes and chromosomes of some organisms
|
shared DNA, b.s. |
Number of chromosomes* |
Approximate number of genes |
|
|
Escherichia coli(bacterium) |
4 639 675 |
4 435 |
|
|
Saccharomyces cerevisiae(yeast) |
12 080 000 |
16** |
5 860 |
|
Caenorhabditis elegans(nematode) |
90 269 800 |
12*** |
23 000 |
|
Arabidopsis thaliana(plant) |
119 186 200 |
33 000 |
|
|
Drosophila melanogaster(fruit fly) |
120 367 260 |
20 000 |
|
|
Oryza sativa(rice) |
480 000 000 |
57 000 |
|
|
Mus muscle(mouse) |
2 634 266 500 |
27 000 |
|
|
Homo sapiens(Human) |
3 070 128 600 |
29 000 |
Note. Information is constantly updated; For more up-to-date information, refer to individual genomic project websites.
* For all eukaryotes, except yeast, the diploid set of chromosomes is given. diploid kit chromosomes (from Greek diploos - double and eidos - view) - double set of chromosomes(2n), each of which has a homology to itself.
**Haploid set. Wild strains of yeast typically have eight (octaploid) or more sets of these chromosomes.
***For females with two X chromosomes. Males have an X chromosome, but no Y, i.e. only 11 chromosomes.
A yeast cell, one of the smallest eukaryotes, has 2.6 times more DNA than a cell E. coli(Table 2). fruit fly cells Drosophila, a classic object of genetic research, contains 35 times more DNA, and human cells contain about 700 times more DNA than cells E. coli. Many plants and amphibians contain even more DNA. The genetic material of eukaryotic cells is organized in the form of chromosomes. Diploid set of chromosomes (2 n) depends on the type of organism (Table 2).
For example, in a human somatic cell there are 46 chromosomes ( rice. 17). Each chromosome in a eukaryotic cell, as shown in Fig. 17, A, contains one very large double-stranded DNA molecule. Twenty-four human chromosomes (22 paired chromosomes and two sex chromosomes X and Y) differ in length by more than 25 times. Each eukaryotic chromosome contains a specific set of genes.
Rice. 17. eukaryotic chromosomes.A- a pair of connected and condensed sister chromatids from the human chromosome. In this form, eukaryotic chromosomes remain after replication and in metaphase during mitosis. b- a complete set of chromosomes from a leukocyte of one of the authors of the book. Each normal human somatic cell contains 46 chromosomes.
The size and function of DNA as a matrix for storing and transmitting hereditary material explains the presence of special structural elements in the organization of this molecule. In higher organisms, DNA is distributed between chromosomes.
The set of DNA (chromosomes) of an organism is called the genome. Chromosomes are located in the cell nucleus and form a structure called chromatin. Chromatin is a complex of DNA and basic proteins (histones) in a 1:1 ratio. The length of DNA is usually measured by the number of pairs of complementary nucleotides (bp). For example, the 3rd human chromosomecentury is a DNA molecule with a size of 160 million bp. has a length of approximately 1 mm, therefore, a linearized molecule of the 3rd human chromosome would be 5 mm in length, and the DNA of all 23 chromosomes (~ 3 * 10 9 bp, MR = 1.8 * 10 12) of a haploid cell - an egg or a sperm cell - would be 1 m in linearized form. With the exception of germ cells, all cells of the human body (there are about 1013 of them) contain a double set chromosomes. During cell division, all 46 DNA molecules replicate and reorganize into 46 chromosomes.
If you connect the DNA molecules of the human genome (22 chromosomes and chromosomes X and Y or X and X) to each other, you get a sequence about one meter long. Note: In all mammals and other heterogametic male organisms, females have two X chromosomes (XX) and males have one X chromosome and one Y chromosome (XY).
Most human cells, so the total DNA length of such cells is about 2m. An adult human has about 10 14 cells, so the total length of all DNA molecules is 2・10 11 km. For comparison, the circumference of the Earth is 4・10 4 km, and the distance from the Earth to the Sun is 1.5・10 8 km. That's how amazingly compactly packaged DNA is in our cells!
In eukaryotic cells, there are other organelles containing DNA - these are mitochondria and chloroplasts. Many hypotheses have been put forward regarding the origin of mitochondrial and chloroplast DNA. The generally accepted point of view today is that they are the rudiments of the chromosomes of ancient bacteria that penetrated into the cytoplasm of the host cells and became the precursors of these organelles. Mitochondrial DNA codes for mitochondrial tRNA and rRNA, as well as several mitochondrial proteins. More than 95% of mitochondrial proteins are encoded by nuclear DNA.
STRUCTURE OF GENES
Consider the structure of the gene in prokaryotes and eukaryotes, their similarities and differences. Despite the fact that a gene is a section of DNA encoding only one protein or RNA, in addition to the direct coding part, it also includes regulatory and other structural elements that have a different structure in prokaryotes and eukaryotes.
coding sequence- the main structural and functional unit of the gene, it is in it that the triplets of nucleotides encodingamino acid sequence. It starts with a start codon and ends with a stop codon.
Before and after the coding sequence are untranslated 5' and 3' sequences. They perform regulatory and auxiliary functions, for example, ensure the landing of the ribosome on mRNA.
Untranslated and coding sequences make up the unit of transcription - the transcribed DNA region, that is, the DNA region from which mRNA is synthesized.
Terminator A non-transcribed region of DNA at the end of a gene where RNA synthesis stops.
At the beginning of the gene is regulatory area, which includes promoter And operator.
promoter- the sequence with which the polymerase binds during transcription initiation. Operator- this is the area to which special proteins can bind - repressors, which can reduce the activity of RNA synthesis from this gene - in other words, reduce it expression.
The structure of genes in prokaryotes
The general plan for the structure of genes in prokaryotes and eukaryotes does not differ - both contain a regulatory region with a promoter and operator, a transcription unit with coding and non-translated sequences, and a terminator. However, the organization of genes in prokaryotes and eukaryotes is different.
Rice. 18. Scheme of the structure of the gene in prokaryotes (bacteria) -the image is enlarged
At the beginning and at the end of the operon, there are common regulatory regions for several structural genes. From the transcribed region of the operon, one mRNA molecule is read, which contains several coding sequences, each of which has its own start and stop codon. From each of these areasone protein is synthesized. Thus, Several protein molecules are synthesized from one i-RNA molecule.
Prokaryotes are characterized by the combination of several genes into a single functional unit - operon. The work of the operon can be regulated by other genes, which can be noticeably removed from the operon itself - regulators. The protein translated from this gene is called repressor. It binds to the operator of the operon, regulating the expression of all the genes contained in it at once.
Prokaryotes are also characterized by the phenomenon transcription and translation conjugations.
Rice. 19 The phenomenon of conjugation of transcription and translation in prokaryotes - the image is enlarged
This pairing does not occur in eukaryotes due to the presence of a nuclear membrane that separates the cytoplasm, where translation occurs, from the genetic material, on which transcription occurs. In prokaryotes, during the synthesis of RNA on a DNA template, a ribosome can immediately bind to the synthesized RNA molecule. Thus, translation begins even before transcription is complete. Moreover, several ribosomes can simultaneously bind to one RNA molecule, synthesizing several molecules of one protein at once.
The structure of genes in eukaryotes
The genes and chromosomes of eukaryotes are very complexly organized.
Bacteria of many species have only one chromosome, and in almost all cases there is one copy of each gene on each chromosome. Only a few genes, such as rRNA genes, are contained in multiple copies. Genes and regulatory sequences make up almost the entire genome of prokaryotes. Moreover, almost every gene strictly corresponds to the amino acid sequence (or RNA sequence) that it encodes (Fig. 14).
The structural and functional organization of eukaryotic genes is much more complex. The study of eukaryotic chromosomes, and later the sequencing of complete eukaryotic genome sequences, has brought many surprises. Many, if not most, eukaryotic genes have an interesting feature: their nucleotide sequences contain one or more DNA regions that do not encode the amino acid sequence of the polypeptide product. Such non-translated inserts disrupt the direct correspondence between the nucleotide sequence of the gene and the amino acid sequence of the encoded polypeptide. These untranslated segments in the genes are called introns, or built-in sequences, and the coding segments exons. In prokaryotes, only a few genes contain introns.
So, in eukaryotes, there is practically no combination of genes into operons, and the coding sequence of a eukaryotic gene is most often divided into translated regions. - exons, and untranslated sections - introns.
In most cases, the function of introns has not been established. In general, only about 1.5% of human DNA is "coding", that is, it carries information about proteins or RNA. However, taking into account large introns, it turns out that 30% of human DNA consists of genes. Since genes make up a relatively small proportion of the human genome, a significant amount of DNA remains unaccounted for.
Rice. 16. Scheme of the structure of the gene in eukaryotes - the image is enlarged
From each gene, an immature, or pre-RNA, is first synthesized, which contains both introns and exons.
After that, the splicing process takes place, as a result of which the intron regions are excised, and a mature mRNA is formed, from which a protein can be synthesized.
Rice. 20. Alternative splicing process - the image is enlarged
Such an organization of genes allows, for example, when different forms of a protein can be synthesized from one gene, due to the fact that exons can be fused in different sequences during splicing.
Rice. 21. Differences in the structure of genes of prokaryotes and eukaryotes - the image is enlarged
MUTATIONS AND MUTAGENESIS
mutation called a persistent change in the genotype, that is, a change in the nucleotide sequence.
The process that leads to mutation is called mutagenesis, and the organism All whose cells carry the same mutation mutant.
mutation theory was first formulated by Hugh de Vries in 1903. Its modern version includes the following provisions:
1. Mutations occur suddenly, abruptly.
2. Mutations are passed down from generation to generation.
3. Mutations can be beneficial, deleterious or neutral, dominant or recessive.
4. The probability of detecting mutations depends on the number of individuals studied.
5. Similar mutations can occur repeatedly.
6. Mutations are not directed.
Mutations can occur under the influence of various factors. Distinguish between mutations caused by mutagenic impacts: physical (eg ultraviolet or radiation), chemical (eg colchicine or reactive oxygen species) and biological (eg viruses). Mutations can also be caused replication errors.
Depending on the conditions for the appearance of mutations are divided into spontaneous- that is, mutations that have arisen under normal conditions, and induced- that is, mutations that arose under special conditions.
Mutations can occur not only in nuclear DNA, but also, for example, in the DNA of mitochondria or plastids. Accordingly, we can distinguish nuclear And cytoplasmic mutations.
As a result of the occurrence of mutations, new alleles can often appear. If the mutant allele overrides the normal allele, the mutation is called dominant. If the normal allele suppresses the mutated one, the mutation is called recessive. Most mutations that give rise to new alleles are recessive.
Mutations are distinguished by effect adaptive, leading to an increase in the adaptability of the organism to the environment, neutral that do not affect survival harmful that reduce the adaptability of organisms to environmental conditions and lethal leading to the death of the organism in the early stages of development.
According to the consequences, mutations are distinguished, leading to loss of protein function, mutations leading to emergence the protein has a new function, as well as mutations that change the dose of a gene, and, accordingly, the dose of protein synthesized from it.
A mutation can occur in any cell of the body. If a mutation occurs in a germ cell, it is called germinal(germinal, or generative). Such mutations do not appear in the organism in which they appeared, but lead to the appearance of mutants in the offspring and are inherited, so they are important for genetics and evolution. If the mutation occurs in any other cell, it is called somatic. Such a mutation can manifest itself to some extent in the organism in which it arose, for example, lead to the formation of cancerous tumors. However, such a mutation is not inherited and does not affect offspring.
Mutations can affect parts of the genome of different sizes. Allocate genetic, chromosomal And genomic mutations.
Gene mutations
Mutations that occur on a scale smaller than one gene are called genetic, or dotted (dotted). Such mutations lead to a change in one or more nucleotides in the sequence. Gene mutations includesubstitutions, leading to the replacement of one nucleotide by another,deletions leading to the loss of one of the nucleotides,insertions, leading to the addition of an extra nucleotide to the sequence.
Rice. 23. Gene (point) mutations
According to the mechanism of action on the protein, gene mutations are divided into:synonymous, which (as a result of the degeneracy of the genetic code) do not lead to a change in the amino acid composition of the protein product,missense mutations, which lead to the replacement of one amino acid by another and can affect the structure of the synthesized protein, although often they are insignificant,nonsense mutations, leading to the replacement of the coding codon with a stop codon,mutations leading to splicing disorder:
Rice. 24. Mutation schemes
Also, according to the mechanism of action on the protein, mutations are isolated, leading to frame shift readings such as insertions and deletions. Such mutations, like nonsense mutations, although they occur at one point in the gene, often affect the entire structure of the protein, which can lead to complete change its structures.
when a segment of a chromosome rotates 180 degrees Rice. 28. Translocation
Rice. 29. Chromosome before and after duplication
Genomic mutations
Finally, genomic mutations affect the entire genome, that is, the number of chromosomes changes. Polyploidy is distinguished - an increase in the ploidy of the cell, and aneuploidy, that is, a change in the number of chromosomes, for example, trisomy (the presence of an additional homologue in one of the chromosomes) and monosomy (the absence of a homolog in the chromosome).
Video related to DNA
DNA REPLICATION, RNA CODING, PROTEIN SYNTHESIS
(If the video is not displayed, it is available on
According to the chemical structure of DNA ( Deoxyribonucleic acid) is biopolymer, whose monomers are nucleotides. That is, DNA is polynucleotide. Moreover, a DNA molecule usually consists of two chains twisted relative to each other along a helical line (often called “spiral twisted”) and interconnected by hydrogen bonds.
Chains can be twisted both to the left and to the right (most often) side.
Some viruses have single strand DNA.
Each DNA nucleotide consists of 1) a nitrogenous base, 2) deoxyribose, 3) a phosphoric acid residue.
Double right-handed DNA helix
The DNA contains the following: adenine, guanine, thymine And cytosine. Adenine and guanine are purines, and thymine and cytosine - to pyrimidines. Sometimes DNA contains uracil, which is usually characteristic of RNA, where it replaces thymine.
The nitrogenous bases of one chain of a DNA molecule are connected to the nitrogenous bases of another strictly according to the principle of complementarity: adenine only with thymine (they form two hydrogen bonds between themselves), and guanine only with cytosine (three bonds).
The nitrogenous base in the nucleotide itself is connected to the first carbon atom of the cyclic form deoxyribose, which is a pentose (carbohydrate with five carbon atoms). The bond is covalent, glycosidic (C-N). Unlike ribose, deoxyribose lacks one of its hydroxyl groups. The ring of deoxyribose is formed by four carbon atoms and one oxygen atom. The fifth carbon atom is outside the ring and is connected through an oxygen atom to a phosphoric acid residue. Also, through the oxygen atom at the third carbon atom, the phosphoric acid residue of the neighboring nucleotide is attached.
Thus, in one strand of DNA, adjacent nucleotides are interconnected covalent bonds between deoxyribose and phosphoric acid (phosphodiester bond). A phosphate-deoxyribose backbone is formed. Perpendicular to it, towards another strand of DNA, nitrogenous bases are directed, which are connected to the bases of the second strand by hydrogen bonds.
The structure of DNA is such that the backbones of chains connected by hydrogen bonds are directed in different directions (they say “multidirectional”, “antiparallel”). On the side where one ends with phosphoric acid connected to the fifth carbon atom of deoxyribose, the other ends with a "free" third carbon atom. That is, the skeleton of one chain is turned upside down, as it were, relative to the other. Thus, in the structure of DNA chains, 5 "ends and 3" ends are distinguished.
When replicating (doubling) DNA, the synthesis of new chains always proceeds from their 5th end to the third, since new nucleotides can only be attached to the free third end.
Ultimately (indirectly via RNA), each consecutive three nucleotides in the DNA chain code for one amino acid of the protein.
The discovery of the structure of the DNA molecule occurred in 1953 thanks to the work of F. Crick and D. Watson (which was also facilitated by the early work of other scientists). Although how Chemical substance DNA has been known since the 19th century. In the 1940s, it became clear that DNA is the carrier of genetic information.
The double helix is considered the secondary structure of the DNA molecule. In eukaryotic cells, the vast majority of DNA is located in the chromosomes, where it is associated with proteins and other substances, and also undergoes denser packaging.
Deoxyribonucleic acid or DNA is the carrier of genetic information. Most of the DNA in cells is located in the nucleus. It is the main component of chromosomes. In eukaryotes, DNA is also found in mitochondria and plastids. DNA consists of mononucleotides covalently linked to each other, representing a long unbranched polymer. The mononucleotides that make up DNA consist of deoxyribose, one of the 4 nitrogenous bases (adenine, guanine, cytosine and thymine), and a phosphoric acid residue. The number of these mononucleotides is very large. For example, in prokaryotic cells containing one single chromosome, DNA is a single macromolecule with a molecular weight of more than 2 x 10 9 .
Mononucleotides of one strand of DNA are connected in series with each other due to the formation covalent phosphodiester bonds between the deoxyribose OH group of one mononucleotide and the phosphoric acid residue of another. On one side of the formed backbone of one strand of DNA are nitrogenous bases. They can be compared with four different beads put on one thread, because. they are, as it were, strung on a sugar-phosphate chain.
The question arises, how can this long polynucleotide chain encode the program for the development of a cell or even an entire organism? The answer to this question can be obtained by understanding how the spatial structure of DNA is formed. The structure of this molecule was deciphered and described by J. Watson and F. Crick in 1953.
DNA molecules are two strands that are parallel to each other and form right-handed helix
. The width of this spiral is about 2 nm, but its length can reach hundreds of thousands of nanometers. Watson and Crick proposed a model of DNA, according to which all DNA bases are located inside the helix, the sugar-phosphate backbone is outside. Thus, the bases of one chain are as close as possible to the bases of the other,
so hydrogen bonds form between them. The structure of the DNA helix is such that the polynucleotide chains that make up it can only be separated after it is unwound.
Due to the maximum proximity of the two strands of DNA, its composition contains the same amount of nitrogenous bases of one type (adenine and guanine) and nitrogenous bases of another type (thymine and cytosine), i.e., the formula is valid: A+G=T+C. This is due to the size of the nitrogenous bases, namely, the length of the structures that are formed due to the occurrence of a hydrogen bond between adenine-thymine and guanine-cytosine pairs is approximately 1.1 nm. The total dimensions of these pairs correspond to the dimensions of the inner part of the DNA helix. To form a spiral couple C-T would be too small couple A-G, on the contrary, is too large. That is, the nitrogenous base of the first strand of DNA, specifies the base that is located in the same place of the other strand of DNA. The strict correspondence of nucleotides located in a DNA molecule in paired chains parallel to each other is called complementarity (optional). exact reproduction or replication genetic information is possible precisely because of this feature of the DNA molecule.
In DNA, biological information is recorded in such a way that it can be exactly copied and transmitted to descendant cells. Before cell division, replication (self-doubling ) DNA. Since each chain contains a nucleotide sequence that is complementary to the sequence of the partner chain, they actually carry the same genetic information. If you separate the strands and use each of them as a template (matrix) to build a second strand, you will get two new identical DNA strands. This is how DNA is duplicated in a cell.
