There are three main macromolecules in a living organism: proteins and nucleic acids of two types. Thanks to them, vital activity and the proper functioning of the whole organism are supported. What are nucleic acids? Why are they needed? More on this later in the article.
general information
Nucleic acid is a biopolymer, an organic compound with high molecular weight, which is formed by nucleotide residues. The transfer from generation to generation of all genetic information is the main task that nucleic acids perform. The presentation below will explain this concept in more detail.
Research History
The first nucleotide studied was isolated from the muscles of a bull in 1847 and named "inosinic acid". As a result of studying the chemical structure, it was revealed that it is a riboside-5'-phosphate and stores an N-glycosidic bond. In 1868, a substance called "nuclein" was discovered. It was discovered by the Swiss chemist Friedrich Miescher during the research of some biological substances. The composition of this substance included phosphorus. The compound had acidic properties and was not degraded by proteolytic enzymes.
The substance received the formula C29H49N9O22P3. The assumption of the participation of nuclein in the process of transmission of hereditary information was put forward as a result of the discovery of the similarity of its chemical composition with chromatin. This element is the main component of chromosomes. The term "nucleic acid" was first introduced in 1889 by Richard Altmann. It was he who became the author of a method for obtaining these substances without protein impurities. During the study of alkaline hydrolysis of nucleic acids, Levin and Jacob identified the main components of the products of this process. They were nucleotides and nucleosides. In 1921, Lewin suggested that DNA has a tetranucleotide structure. However, this hypothesis was not confirmed and turned out to be erroneous.
Classification
Nucleic acids are of two types: DNA and RNA. Their presence is found in the cells of all living organisms. DNA is mainly found in the nucleus of the cell. RNA is found in the cytoplasm. In 1935, during the soft fragmentation of DNA, 4 DNA-forming nucleotides were obtained. These components are presented in the state of crystals. In 1953, Watstone and Crick determined that DNA has a double helix.
Extraction methods
Various methods have been developed to obtain compounds from natural sources. The main conditions of these methods are effective separation of nucleic acids and proteins, the least fragmentation of substances obtained during the process. To date, the classical method is widely used. The essence of this method is the destruction of the walls of biological material and their further processing with an anionic detergent. The result is a precipitate of the protein, and the nucleic acids remain in solution. Another method is also used. In this case, nucleic acids can be gelled using ethanol and saline. In doing so, some care must be taken. In particular, ethanol must be added with great care to the saline solution to obtain a gel precipitate. At what concentration the nucleic acid was isolated, what impurities are present in it, can be determined by the spectrophotometric method. Nucleic acids are easily degraded by nuclease, which is a special class of enzymes. With such a release, it is necessary that laboratory equipment undergo mandatory treatment with inhibitors. These include, for example, a DEPC inhibitor, which is used in RNA isolation.
Physical properties
Nucleic acids have good solubility in water, and are almost insoluble in organic compounds. In addition, they are particularly sensitive to temperature and pH levels. High molecular weight nucleic acid molecules can be fragmented by nuclease under the influence of mechanical forces. These include mixing the solution, shaking it.
Nucleic acids. Structure and functions
Polymeric and monomeric forms of the compounds under consideration are found in cells. The polymeric forms are called polynucleotides. In this form, chains of nucleotides are linked by a phosphoric acid residue. Due to the content of two types of heterocyclic molecules called ribose and deoxoriboose, acids, respectively, are ribonucleic and deoxyribonucleic. With their help, the storage, transmission and implementation of hereditary information takes place. Of the monomeric forms of nucleic acids, adenosine triphosphoric acid is the most popular. It is involved in signaling and providing energy reserves in the cell.
DNA
Deoxyribonucleic acid is a macromolecule. With its help, the process of transmission and implementation of genetic information takes place. This information is necessary for the program of development and functioning of a living organism. In animals, plants, fungi, DNA is part of the chromosomes located in the nucleus of the cell, and is also found in mitochondria and plastids. In bacteria and archaea, the deoxyribonucleic acid molecule clings to the cell membrane from the inside. In such organisms, mainly circular DNA molecules are present. They are called "plasmids". According to the chemical structure, deoxyribonucleic acid is a polymer molecule consisting of nucleotides. These components, in turn, are composed of a nitrogenous base, sugar and a phosphate group. It is due to the last two elements that a bond is formed between nucleotides, creating chains. Basically, the DNA macromolecule is presented in the form of a helix of two chains.
RNA
Ribonucleic acid is a long chain of nucleotides. They contain a nitrogenous base, ribose sugar and a phosphate group. Genetic information is encoded using a sequence of nucleotides. RNA is used to program protein synthesis. Ribonucleic acid is created during transcription. This is the process of RNA synthesis on a DNA template. It occurs with the participation of special enzymes. They are called RNA polymerases. After that, matrix ribonucleic acids participate in the translation process. This is how protein synthesis takes place on an RNA template. Ribosomes take an active part in this process. The remaining RNAs undergo chemical transformations at the end of transcription. As a result of the ongoing changes, secondary and tertiary structures of ribonucleic acid are formed. They function depending on the type of RNA.
Nucleic acids are phosphorus-containing irregular heteropolymers. Opened in 1868 by G.F. Misher.
Nucleic acids are found in the cells of all living organisms. Moreover, each type of organism contains its own set of nucleic acids, characteristic only for it. In nature, there are more than 1,200,000 species of living organisms - from bacteria and humans. This means that there are about 10 10 different nucleic acids that are built from only four nitrogenous bases. How can four nitrogenous bases encode 10 10 nucleic acids? Approximately the same as we encode our thoughts on paper. We establish a sequence of letters of the alphabet, grouping them into words, and nature encodes hereditary information, establishing a sequence of many nucleotides.
Nucleotide - a relatively simple monomer, from the molecules of which nucleic acids are built. Each nucleotide consists of: a nitrogenous base, a five-carbon sugar (ribose or deoxyribose) and a phosphoric acid residue. The main part of a nucleotide is the nitrogenous base.
Nitrogenous bases have a cyclic structure, which, along with other atoms (C, O, H), includes nitrogen atoms. Because of this, these compounds are called nitrogenous. The most important properties of nitrogenous bases are also associated with nitrogen atoms, for example, their weakly basic (alkaline) properties. Hence, these compounds are called "bases".
In nature, nucleic acids contain only five of the known nitrogenous bases. They are found in all cell types, from mycoplasmas to human cells.
This is purine nitrogenous bases Adenine (A) and Guanine (G) and pyrimidine Uracil (U), Thymine (T) and Cytosine (C). Purine bases are derivatives of the purine heterocycle, and pyrimidine bases are derivatives of pyrimidine. Uracil is found only in RNA, while thymine is found in DNA. A, G, and C are found in both DNA and DNA.
There are two types of nucleotides in nucleic acids: deoxyribonucleotides - in DNA, ribonucleotides - in RNA. The structure of deoxyribose differs from that of ribose in that there is no hydroxyl group at the second carbon atom of deoxyribose.
As a result of the combination of a nitrogenous base and pentose, nucleoside. Nucleoside linked to a phosphoric acid residue nucleotide:
nitrogenous base + pentose = nucleoside + phosphoric acid residue = nucleotide
The ratio of nitrogenous bases in a DNA molecule is described Chargaff rules:
1. The amount of adenine is equal to the amount of thymine (A = T).
2. The amount of guanine is equal to the amount of cytosine (G = C).
3. The number of purines is equal to the number of pyrimidines (A + G = T + C), i.e. A + G / T + C \u003d 1.
4. The number of bases with six amino groups is equal to the number of bases with six keto groups (A + C = G + T).
5. The ratio of bases A + C / G + T is a constant value, strictly species-specific: man - 0.66; octopus - 0.54; mouse - 0.81; wheat - 0.94; algae - 0.64-1.76; bacteria - 0.45-2.57.
Based on E. Chargaff's data on the ratio of purine and pyrimidine bases and the results of X-ray diffraction analysis obtained by M. Wilkins and R. Franklin in 1953, J. Watson and F. Crick proposed a model of the DNA molecule. For the development of a double-stranded DNA molecule, Watson, Crick and Wilkins in 1962 were awarded the Nobel Prize.
The DNA molecule has two strands parallel to each other but in reverse order. DNA monomers are deoxyribonucleotides: adenyl (A), thymidyl (T), guanyl (G), and cytosyl (C). The chains are held together by hydrogen bonds: between A and T two, between G and C three hydrogen bonds. The double helix of the DNA molecule is twisted in the form of a spiral, and one turn includes 10 pairs of nucleotides. The coils of the helix are held together by hydrogen bonds and hydrophobic interactions. In the deoxyribose molecule, the free hydroxyl groups are in the 3' and 5' positions. At these positions, a diester bond can form between deoxyribose and phosphoric acid, which connects nucleotides to each other. In this case, one end of the DNA carries a 5'-OH group, and the other end carries a 3'-OH group. DNA is the largest organic molecules. Their length ranges from 0.25 nm to 40 mm in humans in bacteria (the length of the largest protein molecule is not more than 200 nm). The mass of a DNA molecule is 6 x 10 -12 g.
DNA postulates
1. Each DNA molecule consists of two antiparallel polynucleotide chains forming a double helix twisted (to the right or left) around the central axis. Antiparallelism is provided by connecting the 5' end of one strand to the 3' end of the other strand and vice versa.
2. 
Each nucleoside (pentose + base) is located in a plane, perpendicular to the axis spirals.
3. Two chains of the helix are held together by hydrogen bonds between the bases A–T (two) and G–C (three).
4. Base pairing is highly specific and occurs according to the principle of complementarity; as a result, only pairs A: T, G: C are possible.
5. The sequence of bases in one chain can vary significantly, but their sequence in another chain is strictly complementary.
DNA has unique properties of replication (the ability to self-doubling) and repair (the ability to self-repair).
DNA replication- the reaction of matrix synthesis, the process of doubling the DNA molecule by reduplication. In 1957, M. Delbrück and G. Stent, based on the results of experiments, proposed three models for doubling the DNA molecule:
To conservative: provides for the preservation of the original double-stranded DNA molecule and the synthesis of a new, also double-stranded molecule;
- semi-conservative: involves the separation of a DNA molecule into monochains as a result of breaking the hydrogen bonds between the nitrogenous bases of the two chains, after which a complementary base is attached to each base that has lost a partner; daughter molecules are obtained as exact copies of the parent molecule;
- dispersed: consists in the breakdown of the original molecule into nucleotide fragments that are replicated. After replication, new and parent fragments are randomly assembled.
In the same year, 1957, M. Meselson and F. Stahl experimentally proved the existence of a semi-conservative model based on Escherichia coli. And 10 years later, in 1967, the Japanese biochemist R. Okazaki deciphered the mechanism of DNA replication in a semi-conservative way.
Replication is carried out under the control of a number of enzymes and proceeds in several stages. The unit of replication is replicon - a section of DNA that in each cell cycle only 1 time comes into an active state. Replicon has starting points and end replication. In eukaryotes, many replicons appear simultaneously in each DNA. The origin of replication moves sequentially along the DNA strand in the same direction or in opposite directions. The moving front of replication is a fork - replicative or replication fork.
As in any matrix synthesis reaction, there are three stages in replication.
Initiation: enzyme attachment helicases (helicases) to the origin of replication. Helicase unwinds short stretches of DNA. After that, a DNA-binding protein (DBP) is attached to each of the separated chains, which prevents the reunion of the chains. Prokaryotes have an additional enzyme DNA gyrase, which helps the helicase unwind DNA.
Elongation: consecutive complementary addition of nucleotides, as a result of which the DNA chain is lengthened.
Synthesis of DNA occurs immediately on both of its chains. Since the DNA polymerase enzyme can only assemble a chain of nucleotides in the direction from 5' to 3', one of the chains replicates continuously (in the direction of the replication fork), and the other replicates discontinuously (with the formation of Okazaki fragments), in the opposite direction to the movement of the replication fork. The first chain is called leading, and the second is lagging behind. DNA synthesis is carried out with the participation of the enzyme DNA polymerase. Similarly, DNA fragments are synthesized on the lagging strand, which are then crosslinked by enzymes - ligases.
Termination: termination of DNA synthesis upon reaching the desired length of the molecule.
DNA repair- the ability of a DNA molecule to “correct” damage that has arisen in its chains. More than 20 enzymes (endonucleases, exonucleases, restriction enzymes, DNA polymerases, ligases) take part in this process. They are:
1) find changed areas;
2) cut and remove them from the chain;
3) restore the correct sequence of nucleotides;
4) the restored DNA fragment is fused with neighboring regions.
DNA performs special functions in the cell, which are determined by its chemical composition, structure and properties: storage, reproduction and implementation of hereditary information between new generations of cells and organisms.
RNAs are common in all living organisms and are represented by molecules of various sizes, structures, and functions. They consist of one polynucleotide chain formed by four types of monomers - ribonucleotides: adenyl (A), uracil (U), guanyl (G) and cytosyl (C). Each ribonucleotide consists of a nitrogenous base, a ribose, and a phosphoric acid residue. All RNA molecules are exact copies of certain sections of DNA (genes).
The structure of RNA is determined by the sequence of ribonucleotides:
- primary– the sequence of ribonucleotides in the RNA chain; it is a kind of record of genetic information; defines the secondary structure;
-secondary- a strand of RNA twisted into a spiral;
- tertiary– spatial arrangement of the entire RNA molecule; the tertiary structure includes the secondary structure and fragments of the primary, which connect one section of the secondary structure to another (transport, ribosomal RNA).
Secondary and tertiary structures are formed by hydrogen bonds and hydrophobic interactions between nitrogenous bases.
Messenger RNA (i-RNA)- programs the synthesis of cell proteins, since each protein is encoded by the corresponding mRNA (i-RNA contains information about the sequence of amino acids in the protein to be synthesized); weight 10 4 -2x10 6; short lived molecule.
Transfer RNA (t-RNA)- 70-90 ribonucleotides, weight 23,000-30,000; when implementing genetic information, it delivers activated amino acids to the site of polypeptide synthesis, “recognizes” the corresponding section of i-RNA; in the cytoplasm it is represented by two forms: t-RNA in free form and t-RNA associated with an amino acid; more than 40 types; ten%.
To nucleic acids include high-polymer compounds that decompose during hydrolysis into purine and pyrimidine bases, pentose and phosphoric acid. Nucleic acids contain carbon, hydrogen, phosphorus, oxygen and nitrogen. There are two classes of nucleic acids: ribonucleic acids (RNA) and deoxyribonucleic acids (DNA).
Structure and functions of DNA
DNA- a polymer whose monomers are deoxyribonucleotides. The model of the spatial structure of the DNA molecule in the form of a double helix was proposed in 1953 by J. Watson and F. Crick (to build this model, they used the work of M. Wilkins, R. Franklin, E. Chargaff).
DNA molecule formed by two polynucleotide chains, spirally twisted around each other and together around an imaginary axis, i.e. is a double helix (exception - some DNA-containing viruses have single-stranded DNA). The diameter of the DNA double helix is 2 nm, the distance between adjacent nucleotides is 0.34 nm, and there are 10 pairs of nucleotides per turn of the helix. The length of the molecule can reach several centimeters. Molecular weight - tens and hundreds of millions. The total length of DNA in the human cell nucleus is about 2 m. In eukaryotic cells, DNA forms complexes with proteins and has a specific spatial conformation.
DNA monomer - nucleotide (deoxyribonucleotide)- consists of residues of three substances: 1) a nitrogenous base, 2) a five-carbon monosaccharide (pentose) and 3) phosphoric acid. The nitrogenous bases of nucleic acids belong to the classes of pyrimidines and purines. Pyrimidine bases of DNA(have one ring in their molecule) - thymine, cytosine. Purine bases(have two rings) - adenine and guanine.
The monosaccharide of the DNA nucleotide is represented by deoxyribose.
The name of the nucleotide is derived from the name of the corresponding base. Nucleotides and nitrogenous bases are indicated by capital letters.
A polynucleotide chain is formed as a result of nucleotide condensation reactions. In this case, between the 3 "-carbon of the deoxyribose residue of one nucleotide and the phosphoric acid residue of the other, phosphoether bond(belongs to the category of strong covalent bonds). One end of the polynucleotide chain ends with a 5 "carbon (it is called the 5" end), the other ends with a 3 "carbon (3" end).
Against one chain of nucleotides is a second chain. The arrangement of nucleotides in these two chains is not random, but strictly defined: thymine is always located opposite the adenine of one chain in the other chain, and cytosine is always located opposite guanine, two hydrogen bonds arise between adenine and thymine, three hydrogen bonds between guanine and cytosine. The pattern according to which the nucleotides of different DNA strands are strictly ordered (adenine - thymine, guanine - cytosine) and selectively connect to each other is called the principle of complementarity. It should be noted that J. Watson and F. Crick came to understand the principle of complementarity after reading the works of E. Chargaff. E. Chargaff, having studied a huge number of tissue and organ samples various organisms, found that in any DNA fragment the content of guanine residues always exactly corresponds to the content of cytosine, and adenine to thymine ( "Chargaff's rule"), but he could not explain this fact.
From the principle of complementarity, it follows that the nucleotide sequence of one chain determines the nucleotide sequence of another.
DNA strands are antiparallel (opposite), i.e. nucleotides of different chains are located in opposite directions, and, therefore, opposite the 3 "end of one chain is the 5" end of the other. The DNA molecule is sometimes compared to spiral staircase. The "railing" of this ladder is the sugar-phosphate backbone (alternating residues of deoxyribose and phosphoric acid); "steps" are complementary nitrogenous bases.
Function of DNA- storage and transmission of hereditary information.
Replication (reduplication) of DNA
- the process of self-doubling, the main property of the DNA molecule. Replication belongs to the category of matrix synthesis reactions and involves enzymes. Under the action of enzymes, the DNA molecule unwinds, and around each strand acting as a template, a new strand is completed according to the principles of complementarity and antiparallelism. Thus, in each daughter DNA, one strand is the parent strand, and the second strand is newly synthesized. This kind of synthesis is called semi-conservative.
The "building material" and source of energy for replication are deoxyribonucleoside triphosphates(ATP, TTP, GTP, CTP) containing three phosphoric acid residues. When deoxyribonucleoside triphosphates are included in the polynucleotide chain, two terminal residues of phosphoric acid are cleaved off, and the released energy is used to form a phosphodiester bond between nucleotides.
The following enzymes are involved in replication:
- helicases ("unwind" DNA);
- destabilizing proteins;
- DNA topoisomerases (cut DNA);
- DNA polymerases (select deoxyribonucleoside triphosphates and complementarily attach them to the DNA template chain);
- RNA primases (form RNA primers, primers);
- DNA ligases (sew DNA fragments together).
With the help of helicases, DNA is untwisted in certain regions, single-stranded DNA regions are bound by destabilizing proteins, and replication fork. With a discrepancy of 10 pairs of nucleotides (one turn of the helix), the DNA molecule must complete a complete revolution around its axis. To prevent this rotation, DNA topoisomerase cuts one DNA strand, allowing it to rotate around the second strand.
DNA polymerase can only attach a nucleotide to the 3" carbon of the deoxyribose of the previous nucleotide, so this enzyme is able to move along template DNA in only one direction: from the 3" end to the 5" end of this template DNA. Since the chains in maternal DNA are antiparallel , then on its different chains the assembly of the daughter polynucleotide chains occurs in different ways and in opposite directions. On the 3 "-5" chain, the synthesis of the daughter polynucleotide chain proceeds without interruption; this daughter chain will be called leading. On the chain 5 "-3" - intermittently, in fragments ( fragments of Okazaki), which, after completion of replication by DNA ligases, are fused into one strand; this child chain will be called lagging (lagging behind).
A feature of DNA polymerase is that it can start its work only with "seeds" (primer). The role of "seeds" is performed by short RNA sequences formed with the participation of the RNA primase enzyme and paired with template DNA. RNA primers are removed after the completion of the assembly of polynucleotide chains.
Replication proceeds similarly in prokaryotes and eukaryotes. The rate of DNA synthesis in prokaryotes is an order of magnitude higher (1000 nucleotides per second) than in eukaryotes (100 nucleotides per second). Replication begins simultaneously in several regions of the DNA molecule. A piece of DNA from one origin of replication to another forms a unit of replication - replicon.
Replication occurs before cell division. Thanks to this ability of DNA, the transfer of hereditary information from the mother cell to the daughter cells is carried out.
Reparation ("repair")
reparations is the process of repairing damage to the nucleotide sequence of DNA. It is carried out by special enzyme systems of the cell ( repair enzymes). The following stages can be distinguished in the process of DNA structure repair: 1) DNA-repairing nucleases recognize and remove the damaged area, resulting in a gap in the DNA chain; 2) DNA polymerase fills this gap by copying information from the second (“good”) strand; 3) DNA ligase “crosslinks” the nucleotides, completing the repair.
Three repair mechanisms have been studied the most: 1) photoreparation, 2) excise or pre-replicative repair, 3) post-replicative repair.
Changes in the structure of DNA occur constantly in the cell under the influence of reactive metabolites, ultraviolet radiation, heavy metals and their salts, etc. Therefore, defects in repair systems increase the rate of mutation processes and cause hereditary diseases (xeroderma pigmentosa, progeria, etc.).
Structure and functions of RNA
is a polymer whose monomers are ribonucleotides. Unlike DNA, RNA is formed not by two, but by one polynucleotide chain (exception - some RNA-containing viruses have double-stranded RNA). RNA nucleotides are capable of forming hydrogen bonds with each other. RNA chains are much shorter than DNA chains.
RNA monomer - nucleotide (ribonucleotide)- consists of residues of three substances: 1) a nitrogenous base, 2) a five-carbon monosaccharide (pentose) and 3) phosphoric acid. The nitrogenous bases of RNA also belong to the classes of pyrimidines and purines.
The pyrimidine bases of RNA are uracil, cytosine, and the purine bases are adenine and guanine. The RNA nucleotide monosaccharide is represented by ribose.
Allocate three types of RNA: 1) informational(matrix) RNA - mRNA (mRNA), 2) transport RNA - tRNA, 3) ribosomal RNA - rRNA.
All types of RNA are unbranched polynucleotides, have a specific spatial conformation and take part in the processes of protein synthesis. Information about the structure of all types of RNA is stored in DNA. The process of RNA synthesis on a DNA template is called transcription.
Transfer RNAs usually contain 76 (from 75 to 95) nucleotides; molecular weight - 25,000-30,000. The share of tRNA accounts for about 10% of the total RNA content in the cell. tRNA functions: 1) transport of amino acids to the site of protein synthesis, to ribosomes, 2) translational mediator. About 40 types of tRNA are found in the cell, each of them has a nucleotide sequence characteristic only for it. However, all tRNAs have several intramolecular complementary regions, due to which tRNAs acquire a conformation that resembles a clover leaf in shape. Any tRNA has a loop for contact with the ribosome (1), an anticodon loop (2), a loop for contact with the enzyme (3), an acceptor stem (4), and an anticodon (5). The amino acid is attached to the 3' end of the acceptor stem. Anticodon- three nucleotides that "recognize" the mRNA codon. It should be emphasized that a particular tRNA can transport a strictly defined amino acid corresponding to its anticodon. The specificity of the connection of amino acids and tRNA is achieved due to the properties of the enzyme aminoacyl-tRNA synthetase.
Ribosomal RNA contain 3000-5000 nucleotides; molecular weight - 1,000,000-1,500,000. rRNA accounts for 80-85% of the total RNA content in the cell. In combination with ribosomal proteins, rRNA forms ribosomes - organelles that carry out protein synthesis. In eukaryotic cells, rRNA synthesis occurs in the nucleolus. rRNA functions: 1) a necessary structural component of ribosomes and, thus, ensuring the functioning of ribosomes; 2) ensuring the interaction of the ribosome and tRNA; 3) initial binding of the ribosome and the mRNA initiator codon and determination of the reading frame, 4) formation of the active center of the ribosome.
Information RNA varied in nucleotide content and molecular weight (from 50,000 to 4,000,000). The share of mRNA accounts for up to 5% of the total RNA content in the cell. Functions of mRNA: 1) transfer of genetic information from DNA to ribosomes, 2) a matrix for the synthesis of a protein molecule, 3) determination of the amino acid sequence of the primary structure of a protein molecule.
The structure and functions of ATP
Adenosine triphosphoric acid (ATP) is a universal source and main accumulator of energy in living cells. ATP is found in all plant and animal cells. The amount of ATP averages 0.04% (of the raw mass of the cell), the largest amount of ATP (0.2-0.5%) is found in skeletal muscles.
ATP consists of residues: 1) a nitrogenous base (adenine), 2) a monosaccharide (ribose), 3) three phosphoric acids. Since ATP contains not one, but three residues of phosphoric acid, it belongs to ribonucleoside triphosphates.
For most types of work occurring in cells, the energy of ATP hydrolysis is used. At the same time, when the terminal residue of phosphoric acid is cleaved, ATP is converted into ADP (adenosine diphosphoric acid), when the second phosphoric acid residue is cleaved, it becomes AMP (adenosine monophosphoric acid). The yield of free energy during the elimination of both the terminal and the second residues of phosphoric acid is 30.6 kJ each. Cleavage of the third phosphate group is accompanied by the release of only 13.8 kJ. The bonds between the terminal and the second, second and first residues of phosphoric acid are called macroergic (high-energy).
ATP reserves are constantly replenished. In the cells of all organisms, ATP synthesis occurs in the process of phosphorylation, i.e. addition of phosphoric acid to ADP. Phosphorylation occurs with different intensity during respiration (mitochondria), glycolysis (cytoplasm), photosynthesis (chloroplasts).
ATP is the main link between processes accompanied by the release and accumulation of energy, and processes that require energy. In addition, ATP, along with other ribonucleoside triphosphates (GTP, CTP, UTP), is a substrate for RNA synthesis.
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1. Composition of nucleic acids
Nucleic acids are biopolymers. Their macromolecules consist of more than once repeating units, which are represented by nucleotides. And they are logically called polynucleotides. One of the main characteristics of nucleic acids is their nucleotide composition. A nucleotide (a structural unit of nucleic acids) consists of three components:
- nitrogenous base. May be pyrimidine or purine. Nucleic acids contain bases of 4 different types: two of them belong to the class of purines and two to the class of pyrimidines. The nitrogen contained in the rings gives the molecules their basic properties.
- phosphoric acid residue. Nucleic acids are acids because their molecules contain phosphoric acid.
- monosaccharide - ribose or 2-deoxyribose. Sugar, which is part of the nucleotide, contains five carbon atoms, i.e. is a pentose. Depending on the type of pentose present in the nucleotide, there are two types of nucleic acids - ribonucleic acids (RNA), which contain ribose, and deoxyribonucleic acids (DNA), which contain deoxyribose.
Nucleotide is essentially the phosphate ester of the nucleoside. The nucleoside consists of two components: a monosaccharide (ribose or deoxyribose) and a nitrogenous base.
At the end of the 1940s and early 1950s, when research methods such as paper chromatography and UV spectroscopy began to appear. Numerous studies of the nucleotide composition of NA have been confirmed (Chargaff, A. N. Belozersky). The data obtained during the research finally destroyed the obsolete and incompetent ideas about nucleic acids as polymers containing repeating tetranucleotide sequences - the tetranucleotide theory of the structure of PC, which dominated in the 30-40s. They also provided grounds for creating modern ideas not only about the primary structure of DNA and RNA, but also about their macromolecular structure and functions.
The method for determining the composition of PC is based on the analysis of hydrolysates formed during their enzymatic or chemical cleavage. Three methods of chemical cleavage of NCs are commonly used. Acid hydrolysis under harsh conditions (70% perchloric acid, 100°C, 1 h or 100% formic acid, 175°C, 2 h), used to analyze both DNA and RNA, breaks all N -glycosidic bonds and the formation of a mixture of purine and pyrimidine bases. In the study of RNA, both mild acid hydrolysis (1 N hydrochloric acid, lOO ° C, 1 h), which results in the formation of purine bases and pyramidal nucleoside-2 "(3") phosphates, and alkaline hydrolysis (0. 3 N potassium hydroxide, 37°C, 20 h), giving a mixture of nucleoside-2" (3")-phosphates.
Since the number of nucleotides of each type in NA is equal to the number of corresponding bases, to establish the nucleotide composition of a given NA, it is sufficient to determine the quantitative ratio of bases. For this purpose, individual compounds are isolated from hydrolysates using paper chromatography or electrophoresis (when nucleotides are obtained as a result of hydrolysis). Each base, whether bound to a carbohydrate moiety or not, has a characteristic UV absorption maximum, the intensity of which depends on the concentration. For this reason, based on the UV spectra of the isolated compounds, it is possible to determine the quantitative ratio of bases and, consequently, the nucleotide composition of the initial NA.
In the quantitative determination of minor nucleotides, especially such unstable ones as dihydrouridylic acid, enzymatic methods of hydrolysis are used (PDE of snake venom and spleen).
Using the analytical techniques described above, it has been shown that PCs of various origins, with rare exceptions, consist of four main nucleotides and that the content of minor nucleotides can vary significantly.
In the study of the nucleotide composition of native DNA of various origins by Chargaff, the following regularities were found.
1. All DNA, regardless of their origin, contains the same number of purine and pyrimidine bases. Therefore, in any DNA, there is one pyrimidine nucleotide for every purine nucleotide.
2. Any DNA always contains equal amounts of adenine and thymine, guanine and cytosine in pairs, which is usually referred to as A=T and G=C. A third pattern follows from these regularities.
3. The number of bases containing amino groups in position 4 of the pyrimidine nucleus and 6 of the purine (cytosine and adenine) is equal to the number of bases containing the oxo group in the same positions (guanine and thymine), i.e. A + C = G + T . These patterns are called the Chargaff rules. Along with this, it was found that for each type of DNA, the total content of guanine and cytosine is not equal to the total content of adenine and thymine, i.e., that (G + C) / (A + T), as a rule, differs from unity (maybe both more and less). On this basis, two main types of DNA are distinguished: A T-type with a predominant content of adenine and thymine and G C-type with a predominant content of guanine and cytosine.
The value of the ratio of the content of the sum of guanine and cytosine to the sum of the content of adenine and thymine, which characterizes the nucleotide composition of a given type of DNA, is commonly called the specificity coefficient. Each DNA has a characteristic coefficient of specificity, which can vary from 0.3 to 2.8. When calculating the coefficient of specificity, the content of minor Bases is taken into account, as well as the replacement of the main bases by their derivatives. For example, when calculating the specificity coefficient for EDNA of wheat germ, which contains 6% 5-methylcytosine, the latter is included in the sum of the content of guanine (22.7%) and cytosine (16.8%). The meaning of Chargaff's rules for DNA became clear after the establishment of its spatial structure.
The first information about the nucleotide composition of RNA referred to preparations that are mixtures of cellular RNA (ribosomal, informational, and transport) and are usually called the total RNA fraction. Chargaff's rules are not observed in this case, although there is still a certain correspondence between the content of guanine and cytosine, as well as adenine and uracil.
Data received in last years when analyzing individual RNAs, they show that Chargaff's rules do not apply to them either. However, the differences in the content of adenine and uracil, as well as guanine and cytosine for most RNAs, are small and, consequently, a tendency to fulfill these rules is still observed. This fact is explained by the peculiarities of the RNA macrostructure.
The characteristic structural elements of some RNAs are minor bases. The nucleotide residues corresponding to them are usually present in transport and some other RNAs in very small amounts; therefore, determining the complete nucleotide composition of such RNAs is sometimes a very difficult task.
2. Macromolecular structure of DNA
In 1953, Watson and Crick, relying on known data on the conformation of nucleoside residues, on the nature of the internucleotide bond in DNA, and on the regularities of the nucleotide composition of DNA (Chargaff's rules), deciphered the X-ray patterns of the paracrystalline form of DNA [the so-called B-form, formed at a humidity above 80 % and at a high concentration of counterions (Li+) in the sample]. According to their model, the DNA molecule is a regular helix formed by two polydeoxyribonucleotide chains twisted relative to each other and around a common axis. The diameter of the spiral is practically constant along its entire length and is equal to 1.8 nm (18 A).
Macromolecular structure of DNA.
(a) Watson-Crick model;
(6) - parameters of helices of B-, C- and T-forms of DNA (projections perpendicular to the axis of the helix);
(c) cross section of the DNA helix in B-shape (hatched rectangles represent base pairs);
(d) parameters of the DNA helix in A-form;
(e) cross section of the DNA helix in A-shape.
The length of the helix turn, which corresponds to its identity period, is 3.37 nm (33.7 A). There are 10 base residues in one chain per turn of the helix. The distance between the planes of the bases is thus approximately 0.34 nm (3.4 A). The planes of the rests of the bases are perpendicular to the long axis of the helix. The planes of carbohydrate residues deviate somewhat from this axis (originally, Watson and Crick suggested that they are parallel to it).
It can be seen from the figure that the carbohydrate-phosphate backbone of the molecule is turned outward. The spiral is twisted in such a way that two grooves of different sizes can be distinguished on its surface (they are often also called grooves) - a large one, about 2.2 nm wide (22 A), and a small one, about 1.2 nm wide (12 A). The spiral is dextrorotatory. The polydeoxyribonucleotide chains in it are antiparallel: this means that if we move along the long axis of the helix from one end to the other, then in one chain we will pass phosphodiester bonds in the direction 3 "a 5", and in the other - in the direction 5 " a 3". In other words, at each end of a linear DNA molecule are located the 5' end of one and the 3' end of the other strand.
The regularity of the helix requires that, opposite a purine base residue in one chain, there is a pyrimidine base residue in the other chain. As already emphasized, this requirement is realized in the form of the principle of the formation of complementary base pairs, i.e., adenine and guanine residues in one chain correspond to thymine and cytosine residues in the other chain (and vice versa).
Thus, the sequence of nucleotides in one strand of the DNA molecule predetermines the nucleotide sequence of the other strand.
This principle is a major corollary of Watson and Crick's model, as it explains, in remarkably simple chemical terms, DNA's primary function as the repository of genetic information.
Finishing the consideration of the Watson and Crick model, it remains to add that neighboring pairs of base residues in DNA in the B-form are rotated relative to each other by 36° (the angle between the straight lines connecting C 1 " atoms in neighboring complementary pairs).
3. Isolation of deoxyribonucleic acids
Living cells, with the exception of spermatozoa, normally contain significantly more ribonucleic acid than deoxyribonucleic acid. Methods for the isolation of deoxyribonucleic acids were greatly influenced by the fact that, while ribonucleoproteins and ribonucleic acids are soluble in a dilute (0.15 M) solution of sodium chloride, deoxyribonucleoprotein complexes are in fact insoluble in it. Therefore, the homogenized organ or organism is thoroughly washed with a dilute saline solution, deoxyribonucleic acid is extracted from the residue with a strong saline solution, which is then precipitated by the addition of ethanol. On the other hand, eluting the same residue with water gives a solution from which the deoxyribonucleoprotein precipitates when the salt is added. Cleavage of the nucleoprotein, which is basically a salt-like complex between polybasic and polyacid electrolytes, is easily achieved by dissolution in a strong saline solution or by treatment with potassium thiocyanate. Most of the protein can be removed either by the addition of ethanol or by emulsification with chloroform and amyl or octyl alcohol (the protein forms a gel with chloroform). Detergent treatment was also widely used. Later, deoxyribonucleic acids were isolated by extraction with aqueous n-aminosalicylate - phenolic solutions. Using this method, preparations of deoxyribonucleic acid were obtained, of which some contained residual protein, while others were virtually free of protein, indicating that the nature of the protein-nucleic acid bond is different in different tissues. A convenient modification is to homogenize the animal tissue in a 0.15 M phenolphthalein diphosphate solution followed by the addition of phenol to precipitate DNA (RNA free) in good yield.
Deoxyribonucleic acids, no matter how they are isolated, are mixtures of polymers of various molecular weights, with the exception of samples obtained from some types of bacteriophages.
FRACTIONATION
An early separation method consisted of fractional dissociation of deoxyribonucleoprotein (eg, nucleohistone) gels by extraction with increasing molarity aqueous sodium chloride solutions. In this way, preparations of deoxyribonucleic acid were divided into a number of fractions characterized by different ratios of the content of adenine with thymine to the amount of guanine with cytosine, and the fractions enriched in guanine and cytosine were more easily isolated. Similar results were obtained in the chromatographic separation of deoxyribonucleic acid from histone adsorbed on diatomaceous earth using gradient elution with sodium chloride solutions. In an improved version of this method, purified histone fractions were combined with n-aminobenzylcellulose to form diazo bridges from the tyrosine and histidine groups of the protein. Fractionation of nucleic acids on methylated serum albumin (with diatomaceous earth as carrier) has also been described. The rate of elution from the column with salt solutions of increasing concentration depends on the molecular weight, composition (nucleic acids with a high content of guanine with cytosine are eluted more easily) and secondary structure (denatured DNA is more firmly retained by the column than native). In this way, a natural component, polydeoxyadenylic-thymidylic acid, was isolated from the DNA of the sea crab Cancer borealis. Fractionation of deoxyribonucleic acids was also carried out by gradient elution from a column filled with calcium phosphate.
4. Isolation of ribonucleic acids
The methods used to extract ribonucleic acids depend in part on the nature of the organ or organism. In one of the early methods used by Levin, alkali was added to a thick yeast dough, the mixture was stirred with picric acid, filtered, and the nucleic acid was precipitated from the filtrate by adding of hydrochloric acid. This rather harsh processing resulted in the resulting nucleic acid differing significantly from the "native" ribonucleic acid. In order to isolate ribonucleic acids approaching in structure to the nucleic acids of a living cell, it is necessary to avoid the use of harsh conditions (pH, temperature), at the same time, it is necessary to slow down the enzymatic degradation as much as possible. The extraction of ribonucleoproteins with an isotonic sodium chloride solution was widely used. Proteins can be cleaved from nucleic acids by various methods, such as treatment with mixtures of chloroform with octyl alcohol, sodium dodecyl sulfate, strontium nitrate, or alcohol, as well as digestion of the protein fraction with trypsin. Again, the effectiveness of each method is determined by the nature of the ribonucleoprotein. The use of guanidine hydrochloride (a denaturing agent) is useful for inactivating enzymes during the extraction process; to isolate ribonucleic acids and native ribonucleoproteins from yeast, a method was used that uses the adsorption of ribonucleases on bentonite after pretreatment with zinc ions.
Of particular advantage is the isolation of ribonucleic acids from tissue homogenates of mammals, microorganisms and viruses by extraction with phenol and water at room temperature, since in this case proteins and deoxyribonucleic acids precipitate, the activity of ribonuclease is suppressed and high-polymer products can be obtained with good exits. Direct extraction of yeast with an aqueous solution of phenol was used for the preparative preparation of transfer RNAs.
FRACTIONATION
In addition to a number of viral nucleic acids, most of the isolated polyribonucleotides undoubtedly represent complex mixtures containing polymers with different chain lengths, nucleotide sequences, and base compositions (presence or absence of “minor” bases). There are a number of techniques for partial fractionation, however, until satisfactory methods of characterization are developed, it is difficult to determine the degree of purity or homogeneity of ribonucleic acids. The assessment of the purity of transport RNAs, these relatively low molecular weight polyribonucleotides, can be based on their enzymatic reaction with amino acids (through aminoacyladenylates), which, of course, allows one to evaluate their biochemical homogeneity.
Fractionation methods include neutral salt precipitation, electrophoresis, calcium phosphate chromatography, and dihydrostreptomycin precipitation. Recently, fractional dissociation of nucleic acid-histone complexes, previously applied to deoxynucleic acids, has been used to fractionate ribonucleic acids. In all fractions, the ratio of 6-amino- to 6-ketonucleosides was close to unity. Some fractionation occurs during phenol extraction, possibly as a result of differential binding of nucleic acids to proteins. Anion-exchange celluloses, such as ECTEOLA and DEAE, are currently widely used for the fractionation of not only ribonucleic acids, including amino acid-specific transfer RNAs, but also ribonucleoproteins and even viral preparations. For elution, solutions of neutral or near-neutral salts are usually used. A striking feature of the method is the ability of these ion exchangers to separate very a wide range substances ranging from isomers of mononucleotides and oligonucleotides of various chain lengths or compositions to extremely high molecular weight polynucleotides. A report has been published on the separation on DEAE-dextran columns of valine labeled RNA from unlabeled acceptor RNA. For the fractionation of ribonucleic acids, modified ion-exchange celluloses have also been used, in which nucleosides (instead of triethanolamine), especially adenosine and guanosine, are attached to cellulose using epichlorohydrin. Similar use of ECTEOL-cellulose for fractionation or isolation of messenger RNA bound in this moment with DNA, based on the ability to specifically form hydrogen bonds: ECTEOL binds the denatured DNA of a given organism (elution of DNA requires a solvent of extremely high ionic strength), and messenger RNA is eluted with solutions of decreasing ionic strength. By chromatography on tert-aminoalkylated starch, the transport ribonucleic acid was fractionated based on the increased affinity for tyrosine and leucine. Chromatography on hydroxyapatite gives a good separation of valine and phenylalanine specific ribonucleic acids.
Another method of considerable potential value uses cross-linked polydiazostyrene obtained from the reaction of polyaminostyrene with nitrous acid; the method is based on the observation that diazonium compounds readily react with certain amino acids to form covalently bonded derivatives. Within the pH range of 7 to 8.5, only tyrosine and histidine react rapidly. Transfer RNA preparations fully esterified with amino acids were shaken with insoluble polydiazostyrene, which reacted only with nucleic acids labeled with tyrosine and histidine.
Further purification was achieved by re-esterification with tyrosine using purified tyrosine-activating enzyme and re-treatment with polydiazostyrene. The non-esterified histidine-specific ribonucleic acid did not react and remained in solution while the tyrosine-specific nucleic acid was released, as before, by treatment with alkali under mild conditions. Both fractions were obtained almost pure in terms of their amino acid acceptor specificity. Preliminary observations have shown that valine-specific ribonucleic acid is likely to be esterified with the dipeptide tyrosylvaline.
5. Nature of internucleotide bonds
Work on determining the method of connecting nucleotides in NA polymer molecules was successfully completed in the early 1950s immediately after the structure of nucleotides was established and some properties of their derivatives (mainly esters) were studied. By the same time, methods for isolating and purifying DNA and RNA had been developed, so that the nature of intermonomer bonds was studied using pure, albeit highly degraded, NA preparations.
The first information about the type of intermonomeric, or, as it is commonly called, internucleotide bond, was obtained using potentiometric titration. These data indicated the presence of only one gpdroxy group in each phosphate group (pKa ~ 1) in both RNA and DNA. Based on this, it was concluded that NA contains a structural unit of disubstituted phosphoric acid.
It was natural to assume that phosphate residues “crosslink” nucleosides due to their two hydroxyls, while one remains free. It remained to find out which parts of the nucleoside fragments are involved in the formation of bonds with phosphate groups.
Since NA can be deaminated by the action of nitrous acid, it is obvious that the amino groups of pyrimidine and purine bases do not take part in the formation of internucleotide bonds. In addition, potentiometric titration indicated that the oxo(oxy) groups of guanine and uracil residues included in the composition of NA are also free. Based on these data, it was concluded that the internucleotide bonds are formed by the phosphate group and hydroxyl groups of carbohydrate residues (i.e., that they are phosphodiester), which, therefore, are responsible for the formation of the polymer chain (NA). Thus, what is usually called an internucleotide bond is essentially a knot that includes a system of bonds:
(where C is the primary or secondary carbon atom of the carbohydrate residue). During the hydrolysis of DNA and RNA, depending on the reaction conditions, nucleotides are formed with different positions of the phosphate residue:
If we assume that all internucleotide bonds in NA are identical, then it is obvious that, in addition to the phosphate residue, they can include only the 3'-hydroxyl group of one nucleoside unit and the 5'-hydroxyl group of another nucleoside unit (3'-Y-bond). in the case of their unequal value, three types of bonds could simultaneously exist in the DNA polymer chain: 3"-5", 3"-3" and 5"-5". there should have been more.
It was possible to establish the true nature of internucleotide bonds in native DNA and RNA as a result of targeted cleavage of biopolymers using chemical and enzymatic hydrolysis and subsequent isolation and identification of the resulting fragments.
Chemical hydrolysis of DNA as a method of polymer degradation with the aim of establishing the nature of the internucleotide bond turned out to be practically unsuitable. DNA is not cleaved at alkaline pH values, which is in good agreement with the assumption of the phosphodiester nature of the internucleotide bond (the stability of dialkyl phosphates in an alkaline medium was discussed in the section). When treated with acid, even under mild conditions, DNA is cleaved at both phosphodiester and N-glycosidic bonds formed by purine bases. As a result, the cleavage of the polymer proceeds ambiguously, but it was still possible to isolate di-phosphates of pyrimidine deoxynucleosides from the products of acidic DNA hydrolysis, which turned out to be identical to synthetic 3,5'-diphosphates of deoxycytidine and deoxythymidine:
It is also important to note here that the presence of these compounds in the products of DNA degradation indicates the participation of both hydroxyl groups, at least of the pyrimidine monomeric components, in the formation of the internucleotide bond.
Enzymatic cleavage of DNA turned out to be more specific. When DNA preparations are treated with phosphodiesterase (PDE) of snake venom, the polymer is almost completely hydrolyzed to deoxin-nucleoside-5'-phosphates, the structure of which was stopped by comparison with the corresponding nucleotides obtained by counter synthesis.
These data indicate the participation of the 5'-hydroxyl groups of all four deoxynucleosides that make up DNA in the formation of internucleotide bonds. Similarly, but to 3'-phosphates of deoxynucleosides, DNA is cleaved in the presence of PDE isolated from Micrococci or from the spleen.
From the data of DNA hydrolysis by phosphodiesterases of various specificities, it becomes obvious that the bonding of nucleoside residues in DNA is carried out by a phosphate group, which simultaneously esterifies the hydroxyl group at the secondary carbon atom (position 3") of one nucleoside unit and the hydroxyl group at the primary carbon atom (position 5") - another nucleotide unit.
Thus, it was convincingly proved that in DNA the internucleotide bond is carried out due to the phosphate group, as well as 3 "- and 5"-hydroxyl groups of nucleoside residues [(a) and (b) - the direction of cleavage of the DNA polynucleotide chain by phosphodiesterases, respectively, of snake venom and spleen or micrococci]:
The assumption about the possibility of a different structure of the polymer with regularly alternating bonds of nucleoside residues of the 3'-3' and 5'-5' type was rejected, since it did not satisfy all the experimental data. Thus, a polymer of this type should not be completely hydrolyzed (to monomers) in the presence of snake venom PDE, which selectively cleaves only alkyl esters of nucleoside-5 "phosphates. The same can be said about PDE of the spleen, which selectively hydrolyzes alkyl esters of nucleoside-3" - phosphates.
The question of the nature of the internucleotide bond in RNA turned out to be the most obscure and complex. Already at the initial stages, when studying the structure of RNA, it was found that they are extremely unstable during alkaline hydrolysis. The main products of alkaline hydrolysis of RNA are ribonucleoside-2"- and ribonucleoside-3"-phosphates, which are formed in almost equal amounts.
Ribonucleoside-5 "-phosphates are not formed in this case. These data did not fit into the concept of the phosphodiester nature of the internucleotide bond in RNA and required a comprehensive study. A very important role in such a study, which was performed in the early 50s by Todd and co-workers, was played by synthetic alkyl esters of ribonucleotides, which were obtained specifically to model one or another type of phosphodiester bond.
The studies of the Todd school provided data on the mechanisms of the conversion of alkyl esters of ribonucleotides in an alkaline environment, suggesting that in RNA, as well as in DNA, the internucleotide bond is carried out by a phosphate group and 3 "- and 5"-hydroxyl groups of carbohydrate residues. Such a bond in RNA should be very easy to cleave in an alkaline environment, since the neighboring 2 "-hydroxyl group should catalyze this process at pH> 10, when the ionization of the ribose hydroxyl groups begins. It is very important to emphasize that all four should be intermediates during alkaline cleavage ribonucleoside-2",3"-cyclophosphate, and the final ones are ribonucleoside-3"-phosphates and ribonucleoside-2"-phosphates formed during their hydrolysis (four pairs of isomers).
Alkaline hydrolysis data limited the number of possible types of internucleotide bonds for RNA, but did not clarify the question of how this polymer is built.
The most accurate information about the type of internucleotide bond in RNA, as in the case of DNA, was obtained using enzymatic hydrolysis.
The hydrolysis of RNA using the PDE of snake venom, proceeding to ribonucleoside-5'-phosphates, already directly confirmed the assumption of the participation of 5'-hydroxyl groups in the formation of a phosphodiester bond between monomeric units.
Subsequently, data were obtained on the basis of which it can be argued that this is indeed the case (as a result of the discovery of RNA phosphorolysis in the presence of the enzyme polynucleotide phosphorylase (PNPase), leading to the formation of ribonucleoside-5 "-pyrophosphates):
It was only necessary to elucidate the nature of the second hydroxyl group involved in the formation of the internucleotide bond. Another enzyme that was used for targeted RNA cleavage, pyrimidyl ribonuclease (RNase), helped to partially solve this problem.
Previously it was shown that this enzyme cleaves only alkyl esters of pyrimidine ribonucleoside-3'-phosphates to ribonucleoside-3'-phosphates (via the intermediate ribonucleoside-2,3'-cyclophosphate). It turned out that this enzyme acts in a similar way on RNA. In experiments with any purified RNA samples, it was found that the amount of phosphoric acid that is formed when the polymer is sequentially treated with pyrimidyl RNase and phosphomonoesterase (PME), as well as the amount of iodic acid spent on subsequent oxidation, is equivalent to the amount of pyrimidine residues in a given RNA sample. This spoke in favor of the fact that at least pyrimidine nucleotides in RNA are connected to neighboring nucleotides only through a 3'-5'-internucleotide bond. This conclusion is confirmed by the data of alkaline treatment of enzymatic RNA hydrolysates obtained after the action of RNase on it: in an alkaline medium, the migration of the phosphate residue in ribonucleoside-3"- and -2"-phosphates is impossible, and the presence in the corresponding hydrolysates of only pyrimidine ribonucleoside-3"-phosphates makes obvious the 3"-5" type of internucleotide bond for pyrimidine nucleotides.
6. Nucleic acids, their significance
The value of nucleic acids is very high. Some features in the chemical structure provide the possibility of injury, transfer to the cytoplasm and transmission by inheritance to daughter cells of information about the structure of protein molecules that are synthesized in each cell. Proteins determine most of the properties and characteristics of cells. It is therefore clear that the stability of the structure of nucleic acids - essential condition normal functioning of cells and the organism as a whole. Any changes in the structure of nucleic acids entail changes in the structure of cells or the activity of physiological processes in them, thus affecting viability.
There are two types of nucleic acids: DNA and RNA. DNA (deoxyribonucleic acid) is a biological polymer consisting of two polynucleotide chains connected to each other. The monomers that make up each of the DNA chains are complex organic compounds that include one of four nitrogenous bases: adenine (A) or thymine (T), cytosine (C) or guanine (G); the five-atom sugar pentose - deoxyribose, after which DNA itself was named, as well as a residue of phosphoric acid. These compounds are called nucleotides. In each strand, the nucleotides are joined by the formation of covalent bonds between the deoxyribose of one and the phosphoric acid residue of the next nucleotide. Two chains are combined into one molecule using hydrogen bonds that occur between nitrogenous bases that are part of the nucleotides that form different chains. The number of such bonds between different nitrogenous bases is not the same and, as a result, they can only be connected in pairs: the nitrogenous base A of one chain of polynucleotides is always connected by two hydrogen bonds with the T of the other chain, and G - by three hydrogen bonds with the nitrogenous base C of the opposite polynucleotide chain. This ability to selectively combine nucleotides is called complementarity. The complementary interaction of nucleotides leads to the formation of pairs of nucleotides. In a polynucleotide chain, adjacent nucleotides are linked together through a sugar and a phosphoric acid residue.
RNA (ribonucleic acid), like DNA, is a polymer whose monomers are nucleotides. The nitrogenous bases are the same as those that make up DNA (adenine, guanine, cetosine); the fourth - uracil - is present in the RNA molecule instead of thymine. RNA nucleotides contain another pentose, ribose, instead of deoxyribose. In an RNA chain, nucleotides are joined by the formation of covalent bonds between the ribose of one nucleotide and the phosphoric acid residue of another.
Double- and single-stranded molecules of ribonucleic acid are known. Double-stranded RNAs serve to store and reproduce hereditary information in some viruses, i.e. perform the functions of chromosomes. Single-stranded RNAs carry out the transfer of information about the sequence of amino acids in proteins from the chromosome to the place of their synthesis and participate in the synthesis processes.
There are several types of single-stranded RNA. Their names are due to their function or location in the cell. The main part of the cytoplasmic RNA (80-90%) is ribosomal RNA (rRNA). It is contained in the cell organelles that synthesize proteins - ribosomes. The size of rRNA molecules is relatively small, they contain from 3 to 5 thousand nucleotides. Another type of RNA is informational RNA (mRNA), which carries information from chromosomes to ribosomes about the sequence of amino acids in proteins that must be synthesized. Transfer RNAs (rRNAs) are 76-85 nucleotides long and perform several functions. They deliver amino acids to the site of protein synthesis, “recognize” (according to the principle of complementarity) the mRNA section corresponding to the transferred amino acid, and carry out amino acids on the ribosome.
7. References
- N. Green, W. Stout, D. Taylor - Biology.
- BEHIND. Shabarova and A.A. Bogdanov - Chemistry of nucleic acids and their polymers.
- A.P. Pekhov - Biology and general gynetics.
- 2. A. Mickelson - Chemistry of nucleosides and nucleotides.
- Z. Hauptman, J. Grefe, H. Remane – Organic chemistry.
Nucleic acids- These are high-molecular organic compounds of paramount biological importance. They were first discovered in the nucleus of cells (at the end XIX c.), hence the corresponding name (nucleus - nucleus). Nucleic acids store and transmit hereditary information.
There are two types of nucleic acids: deoxyribonucleic(DNA)-and ribonucleic acid (RNA). The main location of DNA is the nucleus of the cell. DNA has also been found in some organelles (plastids, mitochondria, centrioles). RNAs are found in the nucleolus, ribosomes, and cytoplasm cells.
The DNA molecule consists of two helical strands twisted next to each other. Its monomers are nucleotides. Each nucleotide is a chemical compound consisting of three substances: a nitrogenous base, a five-atom sugar deoxyribose, and a phosphoric acid residue. There are four types of nitrogenous bases: adenine (A), thymine (T), guanine (G) and cytosine (C), which form four types of nucleotides in the DNA molecule: adenyl, thymidyl, guanyl and cytidyl.
Diagram of the nucleotide structure
The nitrogenous bases in the DNA molecule are interconnected by an unequal number of hydrogen bonds. Adenine - thymine correspond to each other in spatial configuration and form two hydrogen bonds. In the same way, the molecules of guanine and cytosine correspond in their configuration; they are connected by three hydrogen bonds. The ability for selective interaction of adenine with thymine, and guanine with cytosine, based on the spatial arrangement of the atoms of these molecules, is called complementarity (additionality). In a polynucleotide chain, adjacent nucleotides are linked together through a sugar (deoxyribose) and a phosphoric acid residue. Many thousands of nucleotides are connected in series in a DNA molecule. The molecular weight of this compound reaches tens and hundreds of millions.
DNA is called the substance of heredity. Biological hereditary information is encrypted (encoded) in DNA molecules using a chemical code. The cells of all living beings have the same code. It is based on the sequence of connection in the DNA strands of four nitrogenous bases: A, T, G, C. Various combinations of three adjacent nucleotides form triplets called codons. The sequence of codons in the DNA strand, in turn, determines (encodes) the sequence of amino acids in the polypeptide protein chain. For each of the 20 amino acids, from which cells build all the proteins of a given organism, without exception, there is its own specific codon, and neighboring triplets do not overlap: in the process of reading information from a DNA molecule, the nitrogenous bases of one codon are never included in another - a triple of those nucleotides is read and in the order in which they appear in that particular codon. Each triplet corresponds to one of the 20 amino acids.
Of the four nitrogenous bases (G, C, A, T) each triplet includes only three in various combinations:
G-A-T, C-G-A, A-C-T, G-C-G, T-C-T, etc. There can be 4x4x4 = 64 such non-repeating combinations, and the number of amino acids is 20.
As a result, some amino acids are coded for by multiple triplets. This redundancy code is of great importance for increasing the reliability of the transmission of genetic information. For example, the amino acid arginine corresponds to the triplets HCA, HCH, HCT, HCC. It is clear that a random replacement of the third nucleotide in these triplets will not affect the structure of the synthesized protein in any way. The diagram below schematically shows the sequence of five codon triplets in a small section of a DNA strand. The alternation of individual nucleotides in one strand of DNA can vary as you like, but their sequence in another strand must be complementary to it, for example:
1st thread GAT____ CGA____ATST____GCG____TCT, etc.
2nd thread CTA____GCT____TGA____CGTs____ AGA, etc.
The cell has the necessary mechanism of self-doubling (self-reproduction) genetic code. The process of self-doubling proceeds in stages: first, with the help of enzymes, hydrogen bonds between nitrogenous bases are broken. As a result of this, one strand of DNA departs from the other, then each of them synthesizes a new one by attaching complementary nucleotides located in the cytoplasm. Since each of the bases in the nucleotides can attach another base only complementary to itself, then an exact copy of the "mother" DNA molecule is reproduced. In other words, each strand of DNA serves as a template, and its doubling is called matrix synthesis. Matrix synthesis resembles casting on a matrix of coins, medals, typographic type, etc., in which the hardened casting must be an exact copy of the original form. Therefore, in living cells, as a result of duplication, new DNA molecules have the same structure as the original ones: one strand was the original one, and the second was reassembled.
Since the new DNA molecules have the same structure as the original ones, the same hereditary information is preserved in the daughter cells. However, in the event of a rearrangement or replacement of nucleotides with others, or their complete loss in any DNA region, the resulting distortion will be exactly copied in the daughter DNA molecules. . This is what molecular mechanism of variability: any distortion of hereditary information on a DNA section in the process of self-copying will be transmitted from cell to cell, from generation to generation
Another important property of DNA molecules is the ability to synthesize ribonucleic acids in separate sections of disconnected strands. For this, enzymes (RNA polymerase) are used and are required for
Waste of energy. DNA transfers its sequence of nucleotides to the RNA strand according to the principle of matrix synthesis. This process is called transcription RNA is a single-stranded molecule, it is much shorter than DNA. Each nucleotide in it consists of a five-atom ribose sugar, phosphoric acid residues and a nitrogenous base. There are also four of them here: adenine, guanine, cytosine, but instead of thymine there is uracil (U), which is close to it in structure, complementary to adenine.
Diagram of the structure of a ribonucleotide
Isolate RNA informational(mRNA), transport(tRNA) and ribosomal(rRNA). At the same time, mRNA removes information from a portion of the DNA molecule and then migrates to ribosomes located in the cytoplasm of the cell, while tRNA delivers amino acid residues to ribosomes. The tRNA strand is short and consists of only 70-80 nucleotides. One of the tRNA sections contains a triplet, to which one of the 20 amino acids is attached. Each amino acid has its own tRNA. Amino acid attachment is activated by a specific enzyme, due to which tRNA "recognizes" one or another amino acid. The second region of tRNA has a triplet complementary to one of the mRNA triplets; this triplet on tRNA is called anticodon. Ultimately, the amino acid takes its place in the polypeptide chain in accordance with the information on the mRNA, which is recognized due to the complementarity of the tRNA anticodon to the mRNA codon.
rRNA is part of ribosomes, forming ribosomal bodies with proteins, which are the site of protein synthesis. It also binds with mRNA, and this complex carries out protein synthesis.
Comparative characteristics of DNA and RNA(T.L. Bogdanova. Biology. Assignments and exercises. A guide for applicants to universities. M., 1991)
|
signs |
||
|
Location in the cell |
Nucleus, mitochondria, chloroplasts |
Nucleus, ribosomes, cytoplasm, mitochondria, chloroplasts |
|
Location in the core |
Chromosomes |
|
|
The structure of the macromolecule |
Double unbranched linear polymer coiled in a right-handed helix |
Single polynucleotide chain |
|
Monomers |
Deoxyribonucleotides |
Ribonucleotides |
|
The composition of the nucleotide |
Nitrogenous base (purine - adenine, guanine, pyrimidine - thymine, cytosine); deoxyribose (carbohydrate); phosphoric acid residue |
Nitrogenous base (purine - adenine, guanine, pyrimidine - uracil, cytosine); ribose (carbohydrate); phosphoric acid residue |
|
Nucleo-tnd types |
Adenyl (A), guanyl (G), thymidyl (T), cytidyl (C) |
Adenyl (A), guanyl (G), uridyl (U), cytidyl (C) |
|
Properties |
Capable of self-doubling according to the principle of complementarity (reduplication): A=T, T=A, G=C, C=G Stable |
Not capable of self-doubling. Labile |
|
The chemical basis of the chromosomal genetic material (gene); DNA synthesis; RNA synthesis; information about the structure of proteins |
Informational(mRNA) - transmits the code of hereditary information about the primary structure of the protein molecule; ribosomal(rRNA) - is part of the ribosome; transport(tRNA) - carries amino acids to ribosomes; mitochondrial and plastid RNA - are part of the ribosomes of these organelles |
