Molecular genetics – a branch of genetics that deals with the study of heredity at the molecular level.
Nucleic acids. DNA replication. Template synthesis reactions
Nucleic acids (DNA, RNA) were discovered in 1868 by the Swiss biochemist I.F. Misher. Nucleic acids are linear biopolymers consisting of monomers - nucleotides.
DNA - structure and functions
The chemical structure of DNA was deciphered in 1953 by the American biochemist J. Watson and the English physicist F. Crick.
General structure of DNA. The DNA molecule consists of 2 chains that are twisted into a spiral (Fig. 11) one around the other and around a common axis. DNA molecules can contain from 200 to 2x10 8 nucleotide pairs. Along the DNA helix, neighboring nucleotides are located at a distance of 0.34 nm from each other. A full turn of the helix includes 10 base pairs. Its length is 3.4 nm.
Rice. 11 . DNA structure diagram (double helix)
Polymerity of the DNA molecule. The DNA molecule - bioploimer consists of complex compounds - nucleotides.
Structure of a DNA nucleotide. A DNA nucleotide consists of 3 units: one of the nitrogenous bases (adenine, guanine, cytosine, thymine); deoxyribose (monosaccharide); phosphoric acid residue (Fig. 12).
There are 2 groups of nitrogenous bases:
purines - adenine (A), guanine (G), containing two benzene rings;
pyrimidine - thymine (T), cytosine (C), containing one benzene ring.
DNA contains the following types of nucleotides: adenine (A); guanine (G); cytosine (C); thymine (T). The names of nucleotides correspond to the names of the nitrogenous bases that make up them: adenine nucleotide - the nitrogenous base adenine; guanine nucleotide nitrogenous base guanine; cytosine nucleotide nitrogenous base cytosine; thymine nucleotide nitrogenous base thymine.
Combining two strands of DNA into one molecule
Nucleotides A, G, C and T of one chain are connected, respectively, to nucleotides T, C, G and A of the other chain hydrogen bonds. Two hydrogen bonds are formed between A and T, and three hydrogen bonds are formed between G and C (A=T, G≡C).
Pairs of bases (nucleotides) A – T and G – C are called complementary, i.e. mutually corresponding. Complementarity- this is the chemical and morphological correspondence of nucleotides to each other in paired DNA chains.
5 ’ 3 ’
1 2 3
3’ 5’
Rice. 12 Section of the DNA double helix. The structure of the nucleotide (1 – phosphoric acid residue; 2 – deoxyribose; 3 – nitrogenous base). Connecting nucleotides using hydrogen bonds.
Chains in a DNA molecule antiparallel, that is, they are directed in opposite directions, so that the 3' end of one chain is located opposite the 5' end of the other chain. Genetic information in DNA is written in the direction from the 5' end to the 3' end. This strand is called sense DNA,
because this is where the genes are located. The second thread – 3’–5’ serves as a standard for storing genetic information.
The relationship between the number of different bases in DNA was established by E. Chargaff in 1949. Chargaff found that in DNA of various species the amount of adenine is equal to the amount of thymine, and the amount of guanine is equal to the amount of cytosine.
E. Chargaff's rule:
in a DNA molecule, the number of A (adenine) nucleotides is always equal to the number of T (thymine) nucleotides or the ratio of ∑ A to ∑ T = 1. The sum of G (guanine) nucleotides is equal to the sum of C (cytosine) nucleotides or the ratio of ∑ G to ∑ C = 1;
the sum of purine bases (A+G) is equal to the sum of pyrimidine bases (T+C) or the ratio of ∑ (A+G) to ∑ (T+C)=1;
Method of DNA synthesis - replication. Replication is the process of self-duplication of a DNA molecule, carried out in the nucleus under the control of enzymes. Self-satisfaction of the DNA molecule occurs based on complementarity– strict correspondence of nucleotides to each other in paired DNA chains. At the beginning of the replication process, the DNA molecule unwinds (despirals) in a certain area (Fig. 13), and hydrogen bonds are released. On each of the chains formed after the rupture of hydrogen bonds, with the participation of the enzyme DNA polymerases the daughter strand of DNA is synthesized. The material for synthesis is free nucleotides contained in the cytoplasm of cells. These nucleotides are aligned complementary to the nucleotides of the two mother DNA strands. DNA polymerase enzyme attaches complementary nucleotides to the DNA template strand. For example, to a nucleotide A polymerase adds a nucleotide to the template strand T and, accordingly, to nucleotide G - nucleotide C (Fig. 14). Crosslinking of complementary nucleotides occurs with the help of an enzyme DNA ligases. Thus, two daughter strands of DNA are synthesized by self-duplication.
The resulting two DNA molecules from one DNA molecule are semi-conservative model, since they consist of an old mother and a new daughter chain and are an exact copy of the mother molecule (Fig. 14). The biological meaning of replication lies in the accurate transfer of hereditary information from the mother molecule to the daughter molecule.
Rice. 13 . Unspiralization of a DNA molecule using an enzyme
1
Rice. 14 . Replication is the formation of two DNA molecules from one DNA molecule: 1 – daughter DNA molecule; 2 – maternal (parental) DNA molecule.
The DNA polymerase enzyme can only move along the DNA strand in the 3’ –> 5’ direction. Since the complementary chains in a DNA molecule are directed in opposite directions, and the DNA polymerase enzyme can move along the DNA chain only in the 3’–>5’ direction, the synthesis of new chains proceeds antiparallel ( according to the principle of antiparallelism).
DNA localization site. DNA is found in the cell nucleus and in the matrix of mitochondria and chloroplasts.
The amount of DNA in a cell is constant and amounts to 6.6x10 -12 g.
Functions of DNA:
Storage and transmission of genetic information over generations to molecules and - RNA;
Structural. DNA is the structural basis of chromosomes (a chromosome is 40% DNA).
Species specificity of DNA. The nucleotide composition of DNA serves as a species criterion.
RNA, structure and functions.
General structure.
RNA is a linear biopolymer consisting of one polynucleotide chain. There are primary and secondary structures of RNA. The primary structure of RNA is a single-stranded molecule, and the secondary structure has the shape of a cross and is characteristic of t-RNA.
Polymerity of the RNA molecule. An RNA molecule can contain from 70 nucleotides to 30,000 nucleotides. The nucleotides that make up RNA are the following: adenyl (A), guanyl (G), cytidyl (C), uracil (U). In RNA, the thymine nucleotide is replaced by uracil (U).
Structure of RNA nucleotide.
The RNA nucleotide includes 3 units:
nitrogenous base (adenine, guanine, cytosine, uracil);
monosaccharide - ribose (ribose contains oxygen at each carbon atom);
phosphoric acid residue.
Method of RNA synthesis - transcription. Transcription, like replication, is a reaction of template synthesis. The matrix is the DNA molecule. The reaction proceeds according to the principle of complementarity on one of the DNA strands (Fig. 15). The transcription process begins with despiralization of the DNA molecule at a specific site. The transcribed DNA strand contains promoter – a group of DNA nucleotides from which the synthesis of an RNA molecule begins. An enzyme attaches to the promoter RNA polymerase. The enzyme activates the transcription process. According to the principle of complementarity, nucleotides coming from the cell cytoplasm to the transcribed DNA chain are completed. RNA polymerase activates the alignment of nucleotides into one chain and the formation of an RNA molecule.
There are four stages in the transcription process: 1) binding of RNA polymerase to the promoter; 2) the beginning of synthesis (initiation); 3) elongation – growth of the RNA chain, i.e. nucleotides are sequentially added to each other; 4) termination – completion of mRNA synthesis.
Rice. 15 . Transcription scheme
1 – DNA molecule (double strand); 2 – RNA molecule; 3-codons; 4– promoter.
In 1972, American scientists - virologist H.M. Temin and molecular biologist D. Baltimore discovered reverse transcription using viruses in tumor cells. Reverse transcription– rewriting genetic information from RNA to DNA. The process occurs with the help of an enzyme reverse transcriptase.
Types of RNA by function
Messenger RNA (i-RNA or m-RNA) transfers genetic information from the DNA molecule to the site of protein synthesis - the ribosome. It is synthesized in the nucleus with the participation of the enzyme RNA polymerase. It makes up 5% of all types of RNA in a cell. mRNA contains from 300 nucleotides to 30,000 nucleotides (the longest chain among RNAs).
Transfer RNA (tRNA) transports amino acids to the site of protein synthesis, the ribosome. It has the shape of a cross (Fig. 16) and consists of 70–85 nucleotides. Its amount in the cell is 10-15% of the cell's RNA.
Rice. 16. Scheme of the structure of t-RNA: A–G – pairs of nucleotides connected by hydrogen bonds; D – place of amino acid attachment (acceptor site); E – anticodon.
3. Ribosomal RNA (r-RNA) is synthesized in the nucleolus and is part of ribosomes. Includes approximately 3000 nucleotides. Makes up 85% of the cell's RNA. This type of RNA is found in the nucleus, in ribosomes, on the endoplasmic reticulum, in chromosomes, in the mitochondrial matrix, and also in plastids.
Basics of cytology. Solving typical problems
Problem 1
How many thymine and adenine nucleotides are contained in DNA if 50 cytosine nucleotides are found in it, which is 10% of all nucleotides.
Solution. According to the rule of complementarity in the double strand of DNA, cytosine is always complementary to guanine. 50 cytosine nucleotides make up 10%, therefore, according to Chargaff’s rule, 50 guanine nucleotides also make up 10%, or (if ∑C = 10%, then ∑G = 10%).
The sum of the C + G nucleotide pair is 20%
Sum of nucleotide pair T + A = 100% – 20% (C + G) = 80%
In order to find out how many thymine and adenine nucleotides are contained in DNA, you need to make the following proportion:
50 cytosine nucleotides → 10%
X (T + A) →80%
X = 50x80:10=400 pieces
According to Chargaff's rule, ∑A= ∑T, therefore ∑A=200 and ∑T=200.
Answer: the number of thymine and adenine nucleotides in DNA is 200.
Problem 2
Thymine nucleotides in DNA make up 18% of the total number of nucleotides. Determine the percentage of other types of nucleotides contained in DNA.
Solution.∑Т=18%. According to Chargaff's rule ∑T=∑A, therefore the share of adenine nucleotides also accounts for 18% (∑A=18%).
The sum of the T+A nucleotide pair is 36% (18% + 18% = 36%). Per pair of GiC nucleotides there are: G+C = 100% –36% = 64%. Since guanine is always complementary to cytosine, their content in DNA will be equal,
i.e. ∑ Г= ∑Ц=32%.
Answer: guanine content, like cytosine, is 32%.
Problem 3
The 20 cytosine nucleotides of DNA make up 10% of the total number of nucleotides. How many adenine nucleotides are there in a DNA molecule?
Solution. In a double strand of DNA, the amount of cytosine is equal to the amount of guanine, therefore, their sum is: C + G = 40 nucleotides. Find the total number of nucleotides:
20 cytosine nucleotides → 10%
X (total number of nucleotides) →100%
X=20x100:10=200 pieces
A+T=200 – 40=160 pieces
Since adenine is complementary to thymine, their content will be equal,
i.e. 160 pieces: 2=80 pieces, or ∑A=∑T=80.
Answer: There are 80 adenine nucleotides in a DNA molecule.
Problem 4
Add the nucleotides of the right chain of DNA if the nucleotides of its left chain are known: AGA – TAT – GTG – TCT
Solution. The construction of the right strand of DNA along a given left strand is carried out according to the principle of complementarity - strict correspondence of nucleotides to each other: adenony - thymine (A-T), guanine - cytosine (G-C). Therefore, the nucleotides of the right strand of DNA should be as follows: TCT - ATA - CAC - AGA.
Answer: nucleotides of the right strand of DNA: TCT – ATA – TsAC – AGA.
Problem 5
Write down the transcription if the transcribed DNA chain has the following nucleotide order: AGA - TAT - TGT - TCT.
Solution. The mRNA molecule is synthesized according to the principle of complementarity on one of the chains of the DNA molecule. We know the order of nucleotides in the transcribed DNA chain. Therefore, it is necessary to build a complementary chain of mRNA. It should be remembered that instead of thymine, the RNA molecule contains uracil. Hence:
DNA chain: AGA – TAT – TGT – TCT
mRNA chain: UCU – AUA – ACA – AGA.
Answer: the nucleotide sequence of i-RNA is as follows: UCU – AUA – ACA – AGA.
Problem 6
Write down the reverse transcription, i.e., construct a fragment of a double-stranded DNA molecule based on the proposed fragment of i-RNA, if the i-RNA chain has the following nucleotide sequence:
GCG – ACA – UUU – UCG – TsGU – AGU – AGA
Solution. Reverse transcription is the synthesis of a DNA molecule based on the genetic code of mRNA. The mRNA encoding the DNA molecule has the following nucleotide order: GCH - ACA - UUU - UCG - TsGU - AGU - AGA. The DNA chain complementary to it is: CGC – TGT – AAA – AGC – GCA – TCA – TCT. Second DNA strand: HCH–ACA–TTT–TCG–CHT–AGT–AGA.
Answer: as a result of reverse transcription, two chains of the DNA molecule were synthesized: CGC - TTG - AAA - AGC - GCA - TCA and GCH - ACA - TTT - TCG - CGT - AGT - AGA.
Genetic code. Protein biosynthesis.
Gene– a section of a DNA molecule containing genetic information about the primary structure of one specific protein.
Exon-intron structure of the geneeukaryotes
promoter– a section of DNA (up to 100 nucleotides long) to which the enzyme attaches RNA polymerase, necessary for transcription;
2) regulatory zone– zone affecting gene activity;
3) structural part of a gene– genetic information about the primary structure of the protein.
A sequence of DNA nucleotides that carries genetic information about the primary structure of a protein - exon. They are also part of mRNA. A sequence of DNA nucleotides that does not carry genetic information about the primary structure of a protein – intron. They are not part of mRNA. During transcription, with the help of special enzymes, copies of introns are cut out from i-RNA and copies of exons are stitched together to form an i-RNA molecule (Fig. 20). This process is called splicing.
Rice. 20 . Splicing pattern (formation of mature mRNA in eukaryotes)
Genetic code - a system of nucleotide sequences in a DNA, or RNA, molecule that corresponds to the sequence of amino acids in a polypeptide chain.
Properties of the genetic code:
Triplety(ACA – GTG – GCH…)
The genetic code is triplet, since each of the 20 amino acids is encoded by a sequence of three nucleotides ( triplet, codon).
There are 64 types of nucleotide triplets (4 3 =64).
Uniqueness (specificity)
The genetic code is unambiguous because each individual nucleotide triplet (codon) codes for only one amino acid, or one codon always corresponds to one amino acid (Table 3).
Multiplicity (redundancy, or degeneracy)
The same amino acid can be encoded by several triplets (from 2 to 6), since there are 20 protein-forming amino acids and 64 triplets.
Continuity
Reading of genetic information occurs in one direction, from left to right. If one nucleotide is lost, then when read, its place will be taken by the nearest nucleotide from the neighboring triplet, which will lead to a change in genetic information.
Versatility
The genetic code is common to all living organisms, and the same triplets code for the same amino acid in all living organisms.
Has start and terminal triplets(starting triplet - AUG, terminal triplets UAA, UGA, UAG). These types of triplets do not code for amino acids.
Non-overlapping (discreteness)
The genetic code is non-overlapping, since the same nucleotide cannot simultaneously be part of two neighboring triplets. Nucleotides can belong to only one triplet, and if they are rearranged into another triplet, the genetic information will change.
Table 3 – Genetic code table
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Codon bases |
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Note: abbreviated names of amino acids are given in accordance with international terminology.
Protein biosynthesis
Protein biosynthesis – type of plastic exchange substances in the cell that occur in living organisms under the action of enzymes. Protein biosynthesis is preceded by matrix synthesis reactions (replication - DNA synthesis; transcription - RNA synthesis; translation - assembly of protein molecules on ribosomes). There are 2 stages in the process of protein biosynthesis:
transcription
broadcast
During transcription, the genetic information contained in the DNA located in the chromosomes of the nucleus is transferred to an RNA molecule. Upon completion of the transcription process, mRNA enters the cell cytoplasm through pores in the nuclear membrane, is located between the 2 ribosomal subunits and participates in protein biosynthesis.
Translation is the process of translating the genetic code into a sequence of amino acids. Translation occurs in the cytoplasm of the cell on ribosomes, which are located on the surface of the ER (endoplasmic reticulum). Ribosomes are spherical granules with an average diameter of 20 nm, consisting of large and small subunits. The mRNA molecule is located between two ribosomal subunits. The translation process involves amino acids, ATP, mRNA, t-RNA, and the enzyme amino-acyl t-RNA synthetase.
Codon- a section of a DNA molecule, or mRNA, consisting of three sequentially located nucleotides, encoding one amino acid.
Anticodon– a section of a t-RNA molecule, consisting of three consecutive nucleotides and complementary to the codon of the i-RNA molecule. The codons are complementary to the corresponding anticodons and are connected to them using hydrogen bonds (Fig. 21).
Protein synthesis begins with start codon AUG. From it the ribosome
moves along the mRNA molecule, triplet by triplet. Amino acids are supplied according to the genetic code. Their integration into the polypeptide chain on the ribosome occurs with the help of t-RNA. The primary structure of t-RNA (chain) transforms into a secondary structure that resembles a cross in shape, and at the same time the complementarity of the nucleotides is maintained in it. At the bottom of the tRNA there is an acceptor site to which an amino acid is attached (Fig. 16). Activation of amino acids is carried out using an enzyme aminoacyl tRNA synthetase. The essence of this process is that this enzyme interacts with amino acid and ATP. In this case, a ternary complex is formed, represented by this enzyme, an amino acid and ATP. The amino acid is enriched with energy, activated, and acquires the ability to form peptide bonds with a neighboring amino acid. Without the process of amino acid activation, a polypeptide chain from amino acids cannot be formed.
The opposite, upper part of the tRNA molecule contains a triplet of nucleotides anticodon, with the help of which tRNA is attached to its complementary codon (Fig. 22).
The first t-RNA molecule, with an activated amino acid attached to it, attaches its anticodon to the i-RNA codon, and one amino acid ends up in the ribosome. Then the second tRNA is attached with its anticodon to the corresponding codon of the mRNA. In this case, the ribosome already contains 2 amino acids, between which a peptide bond is formed. The first tRNA leaves the ribosome as soon as it donates an amino acid to the polypeptide chain on the ribosome. Then the 3rd amino acid is added to the dipeptide, it is brought by the third tRNA, etc. Protein synthesis stops at one of the terminal codons - UAA, UAG, UGA (Fig. 23).
1 – mRNA codon; codonsUCGUCG; CUACUA; CGU -Central State University;
2– tRNA anticodon; anticodon GAT - GAT
Rice. 21 . Translation phase: the mRNA codon is attracted to the tRNA anticodon by the corresponding complementary nucleotides (bases)
Nucleic acids are high-molecular substances consisting of mononucleotides, which are connected to each other in a polymer chain using 3", 5" phosphodiester bonds and are packaged in cells in a certain way.
Nucleic acids are biopolymers of two types: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Each biopolymer consists of nucleotides that differ in the carbohydrate residue (ribose, deoxyribose) and one of the nitrogenous bases (uracil, thymine). According to these differences, nucleic acids received their name.
Structure of deoxyribonucleic acid
Nucleic acids have a primary, secondary and tertiary structure.
Primary structure of DNA
The primary structure of DNA is a linear polynucleotide chain in which mononucleotides are connected by 3", 5" phosphodiester bonds. The starting material for the assembly of a nucleic acid chain in a cell is the 5"-triphosphate nucleoside, which, as a result of the removal of β and γ phosphoric acid residues, is capable of attaching the 3" carbon atom of another nucleoside. Thus, the 3" carbon atom of one deoxyribose is covalently linked to the 5" carbon atom of another deoxyribose through a single phosphoric acid residue and forms a linear polynucleotide chain of nucleic acid. Hence the name: 3", 5" phosphodiester bonds. Nitrogen bases do not take part in connecting nucleotides of one chain (Fig. 1.).
Such a connection, between the phosphoric acid molecule residue of one nucleotide and the carbohydrate of another, leads to the formation of a pentose-phosphate skeleton of the polynucleotide molecule, on which nitrogenous bases are attached to the side one after another. Their sequence of arrangement in the chains of nucleic acid molecules is strictly specific for the 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 is called the 5" end and contains a phosphoric acid residue. The circuit is polar and can have a direction of 5"->3" and 3"->5". The exception is circular DNA.
The genetic "text" of DNA is composed of code "words" - triplets of nucleotides called codons. Sections of DNA containing information about the primary structure of all types of RNA are called structural genes.
Polynucleotide DNA chains reach gigantic sizes, so they are packaged in a certain way in the cell.
While studying the composition of DNA, Chargaff (1949) established important patterns regarding the content of individual DNA bases. They helped reveal the secondary structure of DNA. These patterns are called Chargaff's rules. Chargaff rules
These rules indicate that when constructing DNA, a fairly strict correspondence (pairing) must be observed not of purine and pyrimidine bases in general, but specifically of thymine with adenine and cytosine with guanine. Based on these rules, 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, it was believed that DNA of any origin contains all four nucleotides in equal molar quantities. However, in the 1940s, E. Chargaff and his colleagues, as a result of analyzing DNA isolated from a variety of organisms, clearly showed that they contained nitrogenous bases in different quantitative ratios. Chargaff found that although these ratios are the same for DNA from all cells of the same species of organism, DNA from different species can differ markedly in the content of certain nucleotides. This suggested that the differences in the ratio of nitrogenous bases may be associated with some kind of biological code. Although the ratio of individual purine and pyrimidine bases in different DNA samples turned out to be different, when comparing the test results, a certain pattern emerged: in all samples, the total number of purines was equal to the total number of pyrimidines (A + G = T + C), the amount of adenine was equal to the amount of thymine (A = T), and the amount of guanine is 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, whereas 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 model of DNA structure was later built.
Another important indirect indication of the possible structure of DNA was provided by L. Pauling’s data on the structure of protein molecules. Pauling showed that several different stable configurations of the amino acid chain in a protein molecule are possible. One common peptide chain configuration, the α-helix, is a regular helical structure. With this 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 probably have a helical structure held in place 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. An 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 X-ray diffraction patterns of DNA led to the conclusion that the nitrogenous bases (which have a flat shape) are arranged like a stack of plates. X-ray diffraction patterns revealed three main periods in the structure of crystalline DNA: 0.34, 2 and 3.4 nm.
Watson-Crick DNA model
Based on Chargaff's analytical data, Wilkins' X-ray patterns, and the research of chemists who provided information about the precise distances between atoms in a molecule, the angles between the bonds of a given atom, and the size of the atoms, Watson and Crick began to build physical models of the individual components of the DNA molecule at a certain scale and “adjust” them to each other in such a way that the resulting system corresponds to various experimental data [show] .
It was known even earlier that neighboring nucleotides in a DNA chain are connected by phosphodiester bridges, linking the 5"-carbon deoxyribose atom of one nucleotide with the 3"-carbon deoxyribose atom of the next nucleotide. Watson and Crick had no doubt that the period of 0.34 nm corresponds to the distance between successive nucleotides in the DNA chain. 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 the period of 3.4 nm corresponds to, Watson and Crick, as well as Pauling earlier, suggested that the chain is twisted in the form of a spiral (or, more precisely, forms a helical line, since a spiral in the strict sense of this words are obtained when the coils form a conical rather than cylindrical surface in space). Then a period of 3.4 nm will correspond to the distance between successive turns of this helix. Such a spiral can be very dense or somewhat stretched, that is, its turns can be flat or steep. Since the period of 3.4 nm is exactly 10 times the distance between successive 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 of 3.4 nm. It turned out that such a chain would have a density that was 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 clarify the spatial relationships between the two chains forming the double helix. Having tried a number of options for the arrangement of chains on their physical model, Watson and Crick found that all the available data was best matched by the option in which two polynucleotide helices go in opposite directions; in this case, chains consisting of sugar and phosphate residues form the surface of the 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 double helix of DNA can be imagined as a rope ladder that is twisted in a helical manner, so that its rungs remain horizontal. Then the 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 concluded 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 to each other to form proper hydrogen bonds. An in-depth study of the detailed model showed that adenine and cytosine, while forming a combination of a suitable size, could still not be positioned in such a way that hydrogen bonds would form between them. Similar reports forced the exclusion of the combination guanine - thymine, while the combinations adenine - thymine and guanine - cytosine turned out to be quite acceptable. The nature of hydrogen bonds is such that adenine forms a pair with thymine, and guanine with cytosine. This idea 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 are formed between adenine and thymine, and three between guanine and cytosine. Due to this specificity, the formation of hydrogen bonds against each adenine in one chain causes thymine to form on the other; in the same way, only cytosine can be opposite 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 terminal phosphate groups are at opposite ends of the double helix.
As a result of their research, in 1953 Watson and Crick proposed a model of the structure of the DNA molecule (Fig. 3), which remains relevant to the present day. According to the model, the 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 connection 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 opposite the nitrogenous bases of the other. The alternation of nitrogenous bases in a polynucleotide chain is irregular.
The arrangement of nitrogenous bases in the DNA chain is complementary (from the Greek “complement” - addition), i.e. Thymine (T) is always against adenine (A), and only cytosine (C) is against guanine (G). 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 determined by the chemical structure of the bases, which allows the formation of hydrogen bonds in the purine and pyrimidine pair. There are two connections between A and T, and three between G and C. 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 compared to A=T bonds.
The known sequence of arrangement of nucleotides in one DNA chain makes it possible, according to the principle of complementarity, to establish the nucleotides of another chain.
In addition, it has been established that nitrogenous bases having an aromatic structure in an aqueous solution are located one above the other, forming, as it were, a stack of coins. This process of forming stacks of organic molecules is called stacking. The polynucleotide chains of the DNA molecule of the Watson-Crick model under consideration 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) arise.
Hydrogen bonds between complementary bases (horizontally) and stacking interactions between planes of bases 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 face outward, and the bases face inward, towards each other. The direction of the chains in DNA is antiparallel (one of them has a direction of 5"->3", the other - 3"->5", i.e. the 3" end of one chain is located opposite the 5" end of the other.). The chains form right-handed spirals 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 another, a major groove (about 20 Å in diameter) and a minor groove (about 12 Å in diameter) of the DNA double helix are formed. 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 sequential combinations of 4 nucleotides and the fact of the existence of a genetic code, the ability to self-reproduce and transmit 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 a genetic code.
- Reproduction and transmission of genetic information across generations of cells and organisms. This functionality 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 helices (Fig. 4). Currently, six forms are already known (from A to E and Z-form).
The structural forms of DNA, as Rosalind Franklin established, 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 pattern radically depends on the 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 high-moisture fiber.
High humidity DNA molecule is called B-form. 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 - 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 opposing “coins” of the stacks, and are “wound” by two ribbons of phosphodiester backbone twisted into a right-handed helix. The planes of the nitrogenous bases are perpendicular to the axis of the helix. Adjacent complementary pairs are rotated relative to each other by 36°. The diameter of the helix is 20Å, with the purine nucleotide occupying 12Å and the pyrimidine nucleotide 8Å.
The lower humidity DNA molecule 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 broader right-handed helical conformation has 11 base pairs per turn. The planes of the nitrogenous bases have a stronger inclination to the helix axis; they are deviated from the normal to the helix axis by 20°. This implies the presence of an internal void with a diameter of 5Å. The distance between adjacent nucleotides is 0.23 nm, the length of the turn is 2.5 nm, and the diameter of the helix is 2.3 nm.
The A form of DNA was initially thought to be less important. However, it later became clear that the A-form of DNA, like the B-form, has enormous biological significance. The RNA-DNA helix in the template-primer complex has the A-form, as well as the RNA-RNA helix and RNA hairpin structures (the 2'-hydroxyl group of ribose prevents RNA molecules from forming 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.
The A-form and B-form are called the canonical forms of 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, the length of the helix turn 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 similar in size to the grooves of B-DNA. In this case, the main groove is somewhat shallower, and the minor groove is deeper. Natural and synthetic DNA polynucleotides can transform 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 sin-G |
| Conformation of the furanose ring | 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)
The structural elements of DNA include unusual structures limited by some special sequences:
|
Z-shape DNA was discovered in 1979 while studying the hexanucleotide d(CG)3 -. It was discovered by MIT professor Alexander Rich and his colleagues. The Z-form has become one of the most important structural elements of DNA due to the fact that its formation has been observed in DNA regions where purines alternate with pyrimidines (for example, 5'-GCGCGC-3'), or in repeats 5'-CGCGCG-3' containing methylated cytosine. An essential condition for the formation and stabilization of Z-DNA was the presence of purine nucleotides in it in the syn conformation, alternating with pyrimidine bases in the anti conformation.
Natural DNA molecules mainly exist in the right-handed B-form unless they contain sequences like (CG)n. However, if such sequences are part of DNA, then these sections, when the ionic strength of the solution or cations that neutralize the negative charge on the phosphodiester framework changes, these sections can transform into the Z-form, while other sections of DNA 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, moving from the right-handed form to the left-handed one and vice versa. The biological consequences of such lability, which allows conformational transformations of the DNA structure, are not yet fully understood. It is believed that sections of Z-DNA play a certain role in regulating 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 located in a zigzag pattern along the axis of the molecule. Hence the name of the molecule (zigzag)-DNK. Z-DNA is the least twisted (12 base pairs per turn) and thinnest DNA known in nature. The distance between adjacent nucleotides is 0.38 nm, the length of the turn is 4.56 nm, and the diameter of Z-DNA is 1.8 nm. In addition, the appearance of 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. Antibodies have now been obtained that can distinguish the Z-form from the B-form of DNA. These antibodies bind to certain regions of the giant chromosomes of the salivary gland cells of Drosophila (Dr. melanogaster). The binding reaction is easy to monitor 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 interdisks. It follows from this that the Z-form actually exists in natural conditions, although the sizes of individual sections of the Z-form are still unknown.
(inverters) are the most famous and frequently occurring base sequences in DNA. A palindrome is a word or phrase that reads the same from left to right and vice versa. Examples of such words or phrases are: HUT, COSSACK, FLOOD, AND THE ROSE FALLED ON AZOR'S PAW. When applied to DNA sections, this term (palindrome) means the same alternation of nucleotides along the chain from right to left and left to right (like the letters in the word “hut”, etc.).
A palindrome is characterized by the presence of inverted repeats of base sequences that have second-order symmetry relative 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 recognize where the genetic text of chromosome DNA is copied.
When an inverted repeat is present on the same DNA strand, the sequence is called a mirror repeat. Mirror repeats do not have self-complementarity 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 certain number of cruciform structures have been detected 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 acid chain in solutions into a certain spatial structure, characterized by the formation of many “hairpins”.
H-form DNA is a helix formed by three DNA strands - a DNA triple helix. It is a complex of a Watson-Crick double helix with a third single-stranded DNA strand, which fits into its major groove, forming a so-called Hoogsteen pair.
The formation of such a triplex occurs as a result of the folding of a DNA double helix in such a way that half of its section remains in the form of a double helix, and the other half is separated. In this case, one of the disconnected helices 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-stranded section. A feature of this structural transition is its 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 discovered in supercoiled plasmids containing homopurine-homopyrimidine regions, which are a mirror repeat.
In further studies, it was established that it is possible to carry out a structural transition of some homopurine-homopyrimidine double-stranded polynucleotides 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 depend 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 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 required 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: direct and reverse Hoogsteen interactions are explained by the symmetry of 1-methylthymine: a rotation of 180° results in the O2 atom taking the place of the O4 atom, while the system of hydrogen bonds is preserved.
Two types of triple helices are known:
- parallel triple helices in which the polarity of the third strand coincides with the polarity of the homopurine chain of the Watson-Crick duplex
- antiparallel triple helices, in which the polarities of the third and homopurine chains are opposite.
G-quadruplex- 4-strand DNA. This 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 received long before the breakthrough work of Watson and Crick - back in 1910. Then the German chemist Ivar Bang discovered that one of the components of DNA - guanosinic 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, connecting 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 form 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 at some guanine-rich region forms a local quadruplex.
The existence of quadruplexes at the ends of chromosomes - at telomeres and in tumor promoters - has been most studied. However, a complete picture of the localization of such DNA in human chromosomes is still not known.
All of these unusual DNA structures in linear form are unstable compared to B-form DNA. However, DNA often exists in a circular form of topological tension when it has what is called supercoiling. Under these conditions, non-canonical DNA structures are easily formed: Z-forms, “crosses” and “hairpins”, H-forms, guanine quadruplexes and i-motif.
- Supercoiled form - noted when released from the cell nucleus without damaging the pentose phosphate backbone. It has the shape of super-twisted closed rings. In the supercoiled state, the DNA double helix is “twisted onto itself” at least once, that is, it contains at least one superturn (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 a 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-helical molecule - its supercoiling. Supercoiling of the DNA molecule in eukaryotic cells, unlike prokaryotes, occurs in the form of complexes with proteins.
Almost all of the DNA of eukaryotes is found in the chromosomes of the nuclei; only a small amount is contained in mitochondria, and in plants, 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 chromatin proteins
Histones are simple proteins that make up up to 50% of chromatin. In all studied animal and plant cells, 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, and 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 are covalently linked to ubiquitin. 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 gene action.
Histones interact with DNA primarily 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 chromatin proteins
Non-histone proteins, unlike histones, are very diverse. Up to 590 different fractions of DNA-binding non-histone proteins have been isolated. They are also called acidic proteins, since their structure is dominated by acidic amino acids (they are polyanions). The diversity of non-histone proteins is associated with specific regulation of chromatin activity. For example, enzymes required for DNA replication and expression may 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:
- family of site-specific zinc finger proteins. Each “zinc finger” recognizes a specific site consisting of 5 nucleotide pairs.
- family of site-specific proteins - homodimers. The fragment of such a protein in contact with DNA has a helix-turn-helix structure.
- high mobility gel proteins (HMG proteins) are a group of structural and regulatory proteins that are constantly associated with chromatin. They have a molecular weight of less than 30 kDa and are characterized by a high content of charged amino acids. Due to their low molecular weight, HMG proteins have high mobility during polyacrylamide gel electrophoresis.
- replication, transcription and repair enzymes.
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. The bulk of the chromatin is inactive. It contains tightly 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 expression.
Active chromatin (euchromatin) is uncondensed, i.e. packed less tightly. In different cells its content ranges from 2 to 11%. In brain cells it is most abundant - 10-11%, in liver cells - 3-4 and kidney cells - 2-3%. Active transcription of euchromatin is noted. Moreover, its structural organization allows the same genetic DNA information inherent in a given type of organism to be used differently in specialized cells.
In an electron microscope, the image of chromatin resembles beads: spherical thickenings about 10 nm in size, separated by thread-like bridges. These spherical thickenings are called nucleosomes. The nucleosome is a structural unit of chromatin. Each nucleosome contains a 146-bp supercoiled DNA segment wound to form 1.75 left turns per nucleosomal 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 winding DNA onto the histone octamer. It contacts DNA at the sites where the double helix enters and exits the nucleosomal core. These are intercore (linker) DNA sections, the length of which varies depending on the cell type from 40 to 50 nucleotide pairs. As a result, the length of the DNA fragment included in the nucleosomes also varies (from 186 to 196 nucleotide pairs).
Nucleosomes contain approximately 90% DNA, the rest being linkers. It is believed that nucleosomes are fragments of “silent” chromatin, and the linker is active. However, nucleosomes can unfold and become linear. Unfolded nucleosomes are already active chromatin. This clearly demonstrates the dependence of function on structure. It can be assumed that the more chromatin is contained in 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.
In 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 interaction histone H1 bound to 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 a DNA double helix of 186 base pairs with an average diameter of 2 nm and a length of 57 nm is converted into a helix with a diameter of 10 nm and a length of 5 nm. When this helix is subsequently compressed to a fiber with a diameter of 30 nm, the degree of condensation increases another sixfold.
Ultimately, the packaging of a DNA duplex with five histones results in 50-fold condensation of DNA. However, even such a high degree of condensation cannot explain the almost 50,000 - 100,000-fold compaction of DNA in the metaphase chromosome. Unfortunately, the details of further chromatin packaging up to the metaphase chromosome are not yet known, so we can only consider the general features of this process.
Levels of DNA compaction in chromosomes
Each DNA molecule is packaged into a separate chromosome. Human diploid cells contain 46 chromosomes, which are located in the cell nucleus. The total length of the DNA of all chromosomes in a cell is 1.74 m, but the diameter of the nucleus in which the chromosomes are packaged is millions of times smaller. Such compact packaging of DNA in chromosomes and chromosomes in the cell nucleus is ensured by a variety of histone and non-histone proteins that interact in a certain sequence with DNA (see above). Compacting DNA in chromosomes makes it possible to reduce its linear dimensions by approximately 10,000 times - roughly from 5 cm to 5 microns. There are several levels of compaction (Fig. 10).
- DNA double helix is a negatively charged molecule with a diameter of 2 nm and a length of several cm.
- nucleosome 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 in both euchromatin and heterochromatin, in the interphase nucleus and metaphase chromosomes.
The nucleosomal level of compaction is ensured by special proteins - histones. Eight positively charged histone domains form the core of the nucleosome around which a negatively charged DNA molecule is wound. This gives a shortening of 7 times, while the diameter increases from 2 to 11 nm.
- solenoid level
The solenoid level of chromosome organization is characterized by twisting of the nucleosome filament and the formation of thicker fibrils 20-35 nm in diameter - solenoids or superbids. The solenoid pitch is 11 nm; there are about 6-10 nucleosomes per turn. Solenoid packing is considered more likely 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 20-30 times. The diameter increases to 300 nm. Loop-shaped structures such as “lamp brushes” in amphibian oocytes can be seen in cytological preparations. These loops appear to be supercoiled and represent DNA domains, probably corresponding to units of transcription and chromatin replication. Specific proteins fix the bases of the loops and, possibly, some of their internal sections. The loop-like domain organization promotes 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 threads (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 throughout cell nucleus. Loop-shaped structures such as “lamp brushes” in amphibian oocytes can be seen in cytological preparations.
Loop domains are attached at 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 in length base pairs that 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 superhelical unit. Any loop domain contains many transcription units, the functioning of which is likely coordinated - the entire domain is either in an active or inactive state.
At the domain level, as a result of sequential chromatin packaging, a decrease in the linear dimensions of DNA occurs by approximately 200 times (700 nm).
- chromosomal level
At the chromosomal level, condensation of the prophase chromosome into a metaphase chromosome occurs with 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 2,600 loops. The thickness of such a structure reaches 1400 nm (two chromatids), and 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
- transfer of genetic material from the mother cell to the daughter cells.
There is evidence that when a region of chromatin is activated, i.e. during transcription, first histone H1 and then the histone octet are reversibly removed from it. This causes chromatin decondensation, the sequential transition of a 30-nm chromatin fibril into a 10-nm fibril and its further unfolding into sections of free DNA, i.e. loss of nucleosome structure.
We all know that a person’s appearance, some habits and even diseases are inherited. All this information about a living being is encoded in 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. A human cell contains many organelles that perform various functions. DNA is located in the nucleus. The nucleus is a small organelle, which is surrounded by a special membrane, and in which all the genetic material - DNA - is stored.
What is the structure of a DNA molecule?
First of all, 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: GGAATTCTAAG... 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 stay together and twist into a spiral? This phenomenon is due to the property of complementarity. Complementarity means that only certain nucleotides (complementary) can be found opposite each other in two chains. Thus, opposite adenine there is always thymine, and opposite guanine there is always only cytosine. Thus, guanine is complementary to cytosine, and adenine is complementary to thymine. Such pairs of nucleotides opposite each other in different chains are also called complementary.
It can be shown schematically as follows:
G - C
T - A
T - A
C - G
These complementary pairs A - T and G - C form a 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.
"Packaging" of DNA, how does a DNA strand become a chromosome?
Why do these DNA nucleotide chains also twist around each other? Why is this necessary? The fact is that the number of nucleotides is huge and a lot of space is needed to accommodate such long chains. For this reason, two strands of DNA twist around each other in a helical manner. 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. In addition to spiralization, such rarely used DNA molecules undergo even more compact “packaging.” This compact packaging is called supercoiling and shortens the DNA strand by 25-30 times!
How do DNA helices pack?
Supercoiling uses histone proteins, which have the appearance and structure of a rod or spool of thread. Spiralized strands of DNA are wound onto these “coils” - histone proteins. Thus, the long thread becomes very compactly packaged 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 strand is “unwound” from the “spool” - the histone protein (if it was wound onto it) and unwinds from the spiral into two parallel chains. And when the DNA molecule is in such an untwisted state, then the necessary genetic information can be read from it. Moreover, genetic information is read only from untwisted DNA strands!
A set of supercoiled chromosomes is called heterochromatin, and the chromosomes available for reading information are euchromatin.
What are genes, what is their connection with DNA?
Now let's look at what genes are. It is known that there are genes that determine blood type, eye color, 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 DNA section means that a specific gene is assigned its place, and it is impossible to change this place. It is appropriate to make the following comparison: a person lives on a certain street, in a certain house and apartment, and a person cannot voluntarily 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 they cannot become more or less. For example, the gene encoding insulin production consists of 60 nucleotide pairs; the gene encoding the production of the hormone oxytocin - of 370 nucleotide pairs. The strict nucleotide sequence is unique for each gene and strictly defined. For example, the sequence AATTAATA is a fragment of a gene that codes for insulin production. In order to obtain insulin, exactly this 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 DNA chain contains so-called “non-coding sequences”. Such non-coding nucleotide sequences regulate the functioning of genes, help in the spiralization of chromosomes, and mark the starting and ending point of a gene. However, to date, the role of most non-coding sequences remains unclear.
What is a chromosome? Sex chromosomes
The collection of genes of an individual is called the genome. Naturally, the entire genome cannot be contained in one DNA. The genome is divided into 46 pairs of DNA molecules. One pair of DNA molecules is called a chromosome. So, humans have 46 of these chromosomes. Each chromosome carries a strictly defined set of genes, for example, chromosome 18 contains genes encoding eye color, etc. Chromosomes differ from each other in length and shape. The most common shapes are X or Y, but there are others as well. Humans have two chromosomes of the same shape, which are called pairs. Due to such differences, all paired chromosomes are numbered - there are 23 pairs. This means that there is chromosome pair No. 1, pair No. 2, No. 3, etc. Each gene responsible for a specific trait is located on the same chromosome. Modern guidelines for specialists may indicate the location of the gene, 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 shoulder mean? Let's take chromosomes of the form X. The intersection 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, shorter. Such long ends are usually called the long arm of the chromosome, and short ends are called the short arm. In chromosomes of the Y shape, most of the arms are occupied by long arms, and the short ones are very small (they are not even indicated in the schematic image). The size of the chromosomes varies: the largest are chromosomes of pairs No. 1 and No. 3, the smallest chromosomes are pairs No. 17, No. 19.
In addition to their shape and size, chromosomes differ in the functions they perform. Of the 23 pairs, 22 pairs are somatic and 1 pair is sexual. What does it mean? Somatic chromosomes determine all the external characteristics of an individual, the characteristics of his behavioral reactions, hereditary psychotype, that is, all the traits and characteristics of each individual person. A pair of sex chromosomes determines a person’s gender: 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.
Hereditary diseases and chromosome damage
However, “breakdowns” of the genome occur, and then genetic diseases are detected in people. For example, when there are three chromosomes in the 21st pair of chromosomes instead of two, a person is born with Down syndrome.There are many smaller “breakdowns” of genetic material that do not lead to disease, but on the contrary, impart good properties. All “breakdowns” of genetic material are called mutations. Mutations leading to diseases or deterioration of the body's properties are considered negative, and mutations leading to the formation of new beneficial properties are considered positive.
However, with most of the diseases that people suffer from today, it is not the disease that is inherited, but only a predisposition. For example, the father of a child absorbs sugar 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, he will develop diabetes.
Today, the so-called predicative medicine. As part of this medical practice, a person’s predispositions are identified (based on the identification of the corresponding genes), and then he is given recommendations - what diet to follow, how to properly alternate between work and rest so as not to get sick.
How to read the information encoded in DNA?
How can you read the information contained in DNA? How does its 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 encoded information from the nucleus to the cell.How does RNA synthesis occur, how is protein synthesized using RNA?
The DNA strands from which information needs to be “read” unwind, a special “builder” enzyme approaches them and synthesizes a complementary RNA chain parallel to 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 does the synthesis of a protein encoded by a specific gene occur?
After leaving the nucleus, RNA enters the cytoplasm. Already in the cytoplasm, RNA can be embedded as a matrix into special enzyme systems (ribosomes), which can synthesize, guided by RNA information, the corresponding sequence of protein amino acids. As you know, a protein molecule consists of amino acids. How does the ribosome know which amino acid to add to the growing protein chain? This is done based on the triplet code. The triplet code means that the sequence of three nucleotides of the RNA chain ( triplet, for example, GGU) code for a single 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 it reads the information in the RNA. When a chain of amino acids is formed, it takes on a certain spatial shape and becomes a protein capable of performing the enzymatic, construction, hormonal and other functions assigned to it.Protein for any living organism is the product of a gene. It is proteins that determine all the various properties, qualities and external manifestations of genes.
The abbreviation cellular DNA is familiar to many from a school biology course, but few can easily answer what it is. Only a vague idea of heredity and genetics remains in memory immediately after graduation. Knowing what DNA is and what impact it has on our lives can sometimes be very necessary.
DNA molecule
Biochemists distinguish three types of macromolecules: DNA, RNA and proteins. Deoxyribonucleic acid is a biopolymer that is responsible for transmitting data about the hereditary traits, characteristics and development of a species from generation to generation. Its monomer is a nucleotide. What are DNA molecules? It is the main component of chromosomes and contains the genetic code.
DNA structure
Previously, scientists imagined that the DNA structure model was periodic, where identical groups of nucleotides (combinations of phosphate and sugar molecules) were repeated. A certain combination of nucleotide sequences provides the ability to “encode” information. Thanks to research, it has become clear that the structure differs in different organisms.
American scientists Alexander Rich, David Davis and Gary Felsenfeld are especially famous in studying the question of what DNA is. They presented a description of a three-helix nucleic acid in 1957. 28 years later, scientist Maxim Davidovich Frank-Kamenitsky demonstrated how deoxyribonucleic acid, which consists of two helices, folds into an H-shape of 3 strands.
The structure of deoxyribonucleic acid is double-stranded. In it, nucleotides are connected in pairs to form long polynucleotide chains. These chains make possible the formation of a double helix using hydrogen bonds. The exception is viruses that have a single-stranded genome. There are linear DNA (some viruses, bacteria) and circular (mitochondria, chloroplasts).
DNA composition
Without knowledge of what DNA is made of, there would be no medical advances. Each nucleotide is made up of three parts: a pentose sugar residue, a nitrogenous base, and a phosphoric acid residue. Based on the characteristics of the compound, acids can be called deoxyribonucleic or ribonucleic. DNA contains a huge number of mononucleotides of two bases: cytosine and thymine. In addition, it contains pyrimidine derivatives, adenine and guanine.
There is a definition in biology called DNA - junk DNA. Its functions are still unknown. An alternative version of the name is “non-coding”, which is not correct, because it contains coding proteins and transposons, but their purpose is also a mystery. One of the working hypotheses suggests that a certain amount of this macromolecule contributes to the structural stabilization of the genome with respect to mutations.
Where is
The location inside the cell depends on the characteristics of the species. In single-celled organisms, DNA is located in the membrane. In other living beings it is located in the nucleus, plastids and mitochondria. If we talk about human DNA, it is called a chromosome. True, this is not entirely true, because chromosomes are a complex of chromatin and deoxyribonucleic acid.
Role in the cage
The main role of DNA in cells is the transmission of hereditary genes and the survival of the future generation. Not only the external data of the future individual, but also its character and health depend on it. Deoxyribonucleic acid is in a supercoiled state, but for a high-quality life process it must be untwisted. Enzymes help her with this - topoisomerases and helicases.
Topoisomerases are nucleases and are capable of changing the degree of torsion. Another of their functions is participation in transcription and replication (cell division). Helicases break hydrogen bonds between bases. There are ligase enzymes, which “cross-link” broken bonds, and polymerases, which are involved in the synthesis of new polynucleotide chains.
How DNA is deciphered
This abbreviation for biology is familiar. The full name of DNA is deoxyribonucleic acid. Not everyone can say this the first time, so DNA decoding is often omitted in speech. There is also the concept of RNA - ribonucleic acid, which consists of amino acid sequences in proteins. They are directly related, and RNA is the second most important macromolecule.
Human DNA
Human chromosomes are separated within the nucleus, making human DNA the most stable, complete carrier of information. During genetic recombination, the helices are separated, sections are exchanged, and then the connection is restored. Due to DNA damage, new combinations and patterns are formed. The whole mechanism promotes natural selection. It is still unknown how long it has been responsible for genome transmission and what its metabolic evolution has been.
Who opened
The first discovery of the structure of DNA is attributed to the English biologists James Watson and Francis Crick, who in 1953 revealed the structural features of the molecule. It was found by the Swiss doctor Friedrich Miescher in 1869. He studied the chemical composition of animal cells using leukocytes, which accumulate en masse in purulent lesions.
Miescher was studying methods for washing white blood cells, isolated proteins when he discovered that there was something else besides them. A sediment of flakes formed at the bottom of the dish during processing. Having examined these deposits under a microscope, the young doctor discovered nuclei that remained after treatment with hydrochloric acid. It contained a compound that Friedrich called nuclein (from the Latin nucleus - nucleus).
The DNA molecule consists of two strands forming a double helix. Its structure was first deciphered by Francis Crick and James Watson in 1953.
At first, the DNA molecule, consisting of a pair of nucleotide chains twisted around each other, gave rise to questions about why it had this particular shape. Scientists call this phenomenon complementarity, which means that only certain nucleotides can be found opposite each other in its strands. For example, adenine is always opposite thymine, and guanine is always opposite cytosine. These nucleotides of the DNA molecule are called complementary.
Schematically it is depicted like this:
T - A
C - G
These pairs form a chemical nucleotide bond, which determines the order of amino acids. In the first case it is a little weaker. The connection between C and G is stronger. Non-complementary nucleotides do not form pairs with each other.
About the building
So, the structure of the DNA molecule is special. It has this shape for a reason: the fact is that the number of nucleotides is very large, and a lot of space is needed to accommodate long chains. It is for this reason that the chains are characterized by a spiral twist. This phenomenon is called spiralization, it allows the threads to shorten by about five to six times.
The body uses some molecules of this type very actively, others rarely. The latter, in addition to spiralization, also undergo such “compact packaging” as superspiralization. And then the length of the DNA molecule decreases by 25-30 times.
What is the “packaging” of a molecule?
The process of supercoiling involves histone proteins. They have the structure and appearance of a spool of thread or a rod. Spiralized threads are wound onto them, which immediately become “compactly packaged” and take up little space. When the need arises to use one or another thread, it is unwound from a spool, for example, a histone protein, and the helix unwinds into two parallel chains. When the DNA molecule is in this state, the necessary genetic data can be read from it. However, there is one condition. Obtaining information is possible only if the structure of the DNA molecule has an untwisted form. Chromosomes that are accessible for reading are called euchromatins, and if they are supercoiled, then they are already heterochromatins.
Nucleic acids
Nucleic acids, like proteins, are biopolymers. The main function is the storage, implementation and transmission of hereditary (genetic information). They come in two types: DNA and RNA (deoxyribonucleic and ribonucleic). The monomers in them are nucleotides, each of which contains a phosphoric acid residue, a five-carbon sugar (deoxyribose/ribose) and a nitrogenous base. The DNA code includes 4 types of nucleotides - adenine (A) / guanine (G) / cytosine (C) / thymine (T). They differ in the nitrogenous base they contain.
In a DNA molecule, the number of nucleotides can be huge - from several thousand to tens and hundreds of millions. Such giant molecules can be examined through an electron microscope. In this case, you will be able to see a double chain of polynucleotide strands, which are connected to each other by hydrogen bonds of the nitrogenous bases of the nucleotides.
Research
During the course of research, scientists discovered that the types of DNA molecules differ in different living organisms. It was also found that guanine of one chain can only bind to cytosine, and thymine to adenine. The arrangement of nucleotides in one chain strictly corresponds to the parallel one. Thanks to this complementarity of polynucleotides, the DNA molecule is capable of doubling and self-reproduction. But first, the complementary chains, under the influence of special enzymes that destroy paired nucleotides, diverge, and then in each of them the synthesis of the missing chain begins. This occurs due to the free nucleotides present in large quantities in each cell. As a result of this, instead of the “mother molecule”, two “daughter” ones are formed, identical in composition and structure, and the DNA code becomes the original one. This process is a precursor to cell division. It ensures the transmission of all hereditary data from mother cells to daughter cells, as well as to all subsequent generations.
How is the gene code read?
Today, not only the mass of a DNA molecule is calculated - it is also possible to find out more complex data that was previously inaccessible to scientists. For example, you can read information about how an organism uses its own cell. Of course, at first this information is in encoded form and has the form of a certain matrix, and therefore it must be transported to a special carrier, which is RNA. Ribonucleic acid is able to penetrate into the cell through the nuclear membrane and read the encoded information inside. Thus, RNA is a carrier of hidden data from the nucleus to the cell, and it differs from DNA in that it contains ribose instead of deoxyribose, and uracil instead of thymine. In addition, RNA is single-stranded.
RNA synthesis
In-depth analysis of DNA has shown that after RNA leaves the nucleus, it enters the cytoplasm, where it can be integrated as a matrix into ribosomes (special enzyme systems). Guided by the information received, they can synthesize the appropriate sequence of protein amino acids. The ribosome learns from the triplet code which type of organic compound needs to be attached to the forming protein chain. Each amino acid has its own specific triplet, which encodes it.
After the formation of the chain is completed, it acquires a specific spatial form and turns into a protein capable of performing its hormonal, construction, enzymatic and other functions. For any organism it is a gene product. It is from it that all kinds of qualities, properties and manifestations of genes are determined.
Genes
Sequencing processes were primarily developed to obtain information about how many genes a DNA molecule has in its structure. And, although research has allowed scientists to make great progress in this matter, it is not yet possible to know their exact number.
Just a few years ago it was assumed that DNA molecules contain approximately 100 thousand genes. A little later, the figure decreased to 80 thousand, and in 1998, geneticists stated that only 50 thousand genes are present in one DNA, which are only 3% of the total DNA length. But the latest conclusions of geneticists were striking. Now they claim that the genome includes 25-40 thousand of these units. It turns out that only 1.5% of chromosomal DNA is responsible for coding proteins.
The research did not stop there. A parallel team of genetic engineering specialists found that the number of genes in one molecule is exactly 32 thousand. As you can see, it is still impossible to get a definitive answer. There are too many contradictions. All researchers rely only on their results.
Was there evolution?
Despite the fact that there is no evidence of the evolution of the molecule (since the structure of the DNA molecule is fragile and small in size), scientists still made one assumption. Based on laboratory data, they voiced the following version: at the initial stage of its appearance, the molecule had the form of a simple self-replicating peptide, which included up to 32 amino acids found in the ancient oceans.
After self-replication, thanks to the forces of natural selection, molecules acquired the ability to protect themselves from external elements. They began to live longer and reproduce in larger quantities. Molecules that found themselves in the lipid bubble had every chance to reproduce themselves. As a result of a series of successive cycles, lipid bubbles acquired the form of cell membranes, and then - the well-known particles. It should be noted that today any section of a DNA molecule is a complex and clearly functioning structure, all the features of which scientists have not yet fully studied.
Modern world
Recently, scientists from Israel have developed a computer that can perform trillions of operations per second. Today it is the fastest car on Earth. The whole secret is that the innovative device is powered by DNA. Professors say that in the near future, such computers will even be able to generate energy.
A year ago, specialists from the Weizmann Institute in Rehovot (Israel) announced the creation of a programmable molecular computing machine consisting of molecules and enzymes. They replaced silicon microchips with them. To date, the team has made further progress. Now just one DNA molecule can provide a computer with the necessary data and the necessary fuel.
Biochemical “nanocomputers” are not a fiction; they already exist in nature and are manifested in every living creature. But often they are not managed by people. A person cannot yet operate on the genome of any plant in order to calculate, say, the number “Pi”.
The idea of using DNA for storing/processing data first came to the minds of scientists in 1994. It was then that a molecule was used to solve a simple mathematical problem. Since then, a number of research groups have proposed various projects related to DNA computers. But here all attempts were based only on the energy molecule. You cannot see such a computer with the naked eye; it looks like a transparent solution of water in a test tube. There are no mechanical parts in it, but only trillions of biomolecular devices - and this is just in one drop of liquid!
Human DNA
People became aware of the type of human DNA in 1953, when scientists were first able to demonstrate to the world a double-stranded DNA model. For this, Kirk and Watson received the Nobel Prize, since this discovery became fundamental in the 20th century.
Over time, of course, they proved that a structured human molecule can look not only like in the proposed version. After conducting a more detailed DNA analysis, they discovered the A-, B- and left-handed form Z-. Form A- is often an exception, since it is formed only if there is a lack of moisture. But this is only possible in laboratory studies; for the natural environment this is anomalous; such a process cannot occur in a living cell.
The B- shape is classic and is known as a double right-handed chain, but the Z- shape is not only twisted in the opposite direction to the left, but also has a more zigzag appearance. Scientists have also identified the G-quadruplex form. Its structure has not 2, but 4 threads. According to geneticists, this form occurs in areas where there is an excess amount of guanine.
Artificial DNA
Today there is already artificial DNA, which is an identical copy of the real one; it perfectly follows the structure of the natural double helix. But, unlike the original polynucleotide, the artificial one has only two additional nucleotides.
Since the dubbing was created based on information obtained from various studies of real DNA, it can also be copied, self-replicating and evolving. Experts have been working on the creation of such an artificial molecule for about 20 years. The result is an amazing invention that can use the genetic code in the same way as natural DNA.
To the four existing nitrogenous bases, geneticists added two additional ones, which were created by chemical modification of natural bases. Unlike natural DNA, artificial DNA turned out to be quite short. It contains only 81 base pairs. However, it also reproduces and evolves.
Replication of a molecule obtained artificially takes place thanks to the polymerase chain reaction, but so far this does not happen independently, but through the intervention of scientists. They independently add the necessary enzymes to the said DNA, placing it in a specially prepared liquid medium.
Final result
The process and final outcome of DNA development can be influenced by various factors, such as mutations. This makes it necessary to study samples of matter so that the analysis result is reliable and reliable. An example is a paternity test. But we can’t help but rejoice that incidents such as mutation are rare. Nevertheless, samples of matter are always rechecked in order to obtain more accurate information based on the analysis.
Plant DNA
Thanks to high sequencing technologies (HTS), a revolution has been made in the field of genomics - DNA extraction from plants is also possible. Of course, obtaining high-quality molecular weight DNA from plant material poses some difficulties due to the large number of copies of mitochondria and chloroplast DNA, as well as the high level of polysaccharides and phenolic compounds. To isolate the structure we are considering in this case, a variety of methods are used.
Hydrogen bond in DNA
The hydrogen bond in the DNA molecule is responsible for the electromagnetic attraction created between a positively charged hydrogen atom that is attached to an electronegative atom. This dipole interaction does not meet the criterion of a chemical bond. But it can occur intermolecularly or in different parts of the molecule, i.e. intramolecularly.
A hydrogen atom attaches to the electronegative atom that is the donor of the bond. An electronegative atom can be nitrogen, fluorine, or oxygen. It - through decentralization - attracts the electron cloud from the hydrogen nucleus to itself and makes the hydrogen atom (partially) positively charged. Since the size of H is small compared to other molecules and atoms, the charge is also small.
DNA decoding
Before deciphering a DNA molecule, scientists first take a huge number of cells. For the most accurate and successful work, about a million of them are needed. The results obtained during the study are constantly compared and recorded. Today, genome decoding is no longer a rarity, but an accessible procedure.
Of course, deciphering the genome of a single cell is an impractical exercise. The data obtained during such studies are of no interest to scientists. But it is important to understand that all currently existing decoding methods, despite their complexity, are not effective enough. They will only allow reading 40-70% of the DNA.
However, Harvard professors recently announced a method through which 90% of the genome can be deciphered. The technique is based on adding primer molecules to isolated cells, with the help of which DNA replication begins. But even this method cannot be considered successful; it still needs to be refined before it can be openly used in science.