15.04.2015 13.10.2015
Features of the structure and functionality of the "double helix"
It is difficult to imagine a person without genetic habits, characteristics, hereditary changes in the body of a newborn. It turns out that all information is encoded in the notorious genes that are carriers of the genetic chain of nucleotides.
The history of the discovery of DNA
The structure of the DNA molecule became known to the world for the first time in 1869. I.F. Misher derived the well-known designation for DNA, which consists of cells, or rather, molecules responsible for the transmission of the genetic code for the development of living organisms. At first, this substance was called nuclein, for a long time no one could determine the number of chains of the structure, their modes of functioning.
Today, scientists have finally deduced the composition of DNA, which includes 4 types of nucleotides, which, in turn, contain:
· Residues of phosphorus Н3РО4;
Peptoses C5H10O4;
· Nitrogenous base.
All these elements are in the cell and are part of the DNA and combine into a double helix, which was deduced by F. Crick, D. Watson in 1953. Their research made a breakthrough in the world of science and medicine, the work became the basis for many scientific research, opened the gates for the knowledge of the genetic inheritance of each person.
Connection structure
The DNA molecule resides in the nucleus with many different functions. Despite the fact that the main role of a substance is the storage of gene information, compounds are responsible for the following types of work:
· Encode an amino acid;
· Control the work of body cells;
· Produce protein for the external manifestation of genes.
Each part of the joint forms helical filaments, the so-called chromatids. The structural units of the helix are nucleotides, which are in the middle of the chain and allow DNA to double. It works like this:
1. Thanks to special enzymes in the cell of the body, the unweaving of the spiral is produced.
2. Hydrogen bonds diverge, releasing the enzyme - polymerases.
3. The parent DNA molecule combines with a single-stranded fragment of 30 nucleotides.
4. Two molecules are formed, in which one thread is maternal, the other is synthetic.
Why are the nucleotide chains still wrapped around the thread? The fact is that the number of enzymes is very large, and thus, they are easily placed on one axis. This phenomenon is called spiralization, the threads are shortened several times, sometimes up to 30 units.
Molecular genetic methods of using DNA in medicine
The DNA molecule has made it possible for mankind to use the structure of nucleotide compounds in various directions. Primarily for the diagnosis of hereditary diseases. For monogenic diseases as a result of coupling inheritance. When identifying a history of infectious, oncological excesses. And also in forensic medicine for personal identification.
There are a lot of possibilities for using DNA; today there is a list of monogenic diseases that have left the list of fatal ones, thanks to the concept of the development of the structures of compounds and diagnostics of the molecular biofield. In the future, we can talk about the "genetic document of the newborn", which will contain the entire list of common diseases of an individual nature.
All molecular genetic processes have not yet been studied; this is a rather complex and laborious mechanism. Perhaps, many genetic diseases will be able to prevent in the near future by changing the structure of the incipient human life!
What else is planned in the future based on this substance?
Computer programs based on nucleotide strands have bright prospects for creating ultra-intelligent computing robots. The founder of this idea is L. Adleman.
The idea of the invention is as follows: for each strand, a sequence of molecular bases is synthesized, which mix with each other and form various RNA variants. Such a computer will be able to execute data with an accuracy of 99.8%. According to optimistic scientists, this trend will soon cease to be exotic, and in 10 years it will become a visible reality.
DNA computers will be brought to life in living cells, executing digital programs that will interact with the biochemical processes of the body. The first schemes of such molecules have already been invented, which means that their serial production will begin soon.
Amazing and extraordinary DNA facts
An interesting historical fact indicates that many years ago, "Homo sapiens" interbred with Neanderthals. The information was confirmed in the medical center of Italy, where the mitochondrial DNA of the found person, which was supposedly 40,000 years old, was determined. She inherited it from a generation of mutant people who disappeared from planet Earth many years ago.
Another fact tells about the composition of DNA. There are cases when pregnancies are conceived as twins, but one of the embryos 
"Pulls in" the other. This means that there will be 2 DNA in the newborn's body. This phenomenon is known to many of the pictures of the history of Greek mythology, when organisms possessed several body parts of different animals. Today, many people live and do not know that they are carriers of two structural compounds. Even genetic studies cannot always confirm these findings.
Attention: there are amazing creatures in the world, whose DNA is eternal, and persons are immortal. Is it so? The theory of aging is very complex. In simple terms, with each division, the cell loses its strength. However, if you have a constant structural thread, you can live forever. Some lobsters, turtles, under special conditions, can live for a very long time. But nobody canceled the disease, it becomes the cause of many deaths of long-lived animals.
DNA gives hope for improving the life of every living organism, helping to diagnose serious ailments, to become more developed, perfect personalities.
DNA is one of two types of nucleic acids - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). These biopolymers are made up of monomers called nucleotides. Monomers-nucleotides of DNA and RNA are similar in basic structural features. Each nucleotide consists of three components linked by strong chemical bonds
The nucleotides that make up DNA contain a five-carbon sugar - deoxyribose, one of four nitrogenous bases: adenine, guanine, cytosine, thymine (A, G, C, T) and a phosphoric acid residue.
In the composition of nucleotides, a nitrogenous base is attached to the ribose (or deoxyribose) molecule on one side, and a phosphoric acid residue on the other. The nucleotides are linked together in long chains. The backbone of such a chain is formed by regularly alternating residues of sugar and organic phosphates, and the side groups of this chain are four types of irregularly alternating nitrogenous bases.
A DNA molecule is a structure consisting of two strands that are hydrogen bonded to each other along their entire length. This structure, inherent only to DNA molecules, is called a double helix. A feature of the DNA structure is that against one nitrogenous base in one chain there is a strictly defined nitrogenous base in the other chain - these base pairs are called complementary bases (complementary to each other): A = T; G C
A set of proteins (enzymes, hormones, etc.) determines the properties of a cell and an organism. DNA molecules store information about these properties and pass them on to generations of descendants.
DNA was discovered by Johann Friedrich Miescher in 1869. At first, the new substance was named nuclein, and later, when Miescher determined that this substance has acidic properties, the substance was named nucleic acid ... The biological function of the newly discovered substance was unclear, and for a long time DNA was considered a storehouse of phosphorus in the body. Moreover, even at the beginning of the 20th century, many biologists believed that DNA had nothing to do with the transmission of information, since the structure of the molecule, in their opinion, was too monotonous and could not contain encoded information.
Gradually, it was proved that it is DNA, and not proteins, as it was believed before, that is the carrier of genetic information. One of the first decisive evidence came from the experiments of O. Avery, Colin McLeod and McLean McCarthy (1944) on the transformation of bacteria. They managed to show that DNA isolated from pneumococci is responsible for the so-called transformation (the acquisition of disease-causing properties by a harmless culture as a result of the addition of dead disease-causing bacteria to it). The experiment of American scientists Alfred Hershey and Martha Chase (The Hershey-Chase Experiment, 1952) with radioactively labeled proteins and bacteriophage DNA showed that only phage nucleic acid is transferred into an infected cell, and the new generation of phage contains the same proteins and nucleic acid, as the original phage.
Until the 50s of the XX century, the exact structure of DNA, as well as the way of transmitting hereditary information, remained unknown. Although it was known for certain that DNA is made up of several strands of nucleotides, no one knew exactly how many of these strands and how they were connected.
The structure of the DNA double helix was proposed by Francis Crick and James Watson in 1953 on the basis of X-ray diffraction data obtained by Maurice Wilkins and Rosalind Franklin, and the Chargaff rules, according to which strict ratios are observed in each DNA molecule linking the number of nitrogenous bases of different types ... Later, the model of the structure of DNA proposed by Watson and Crick was proven, and their work was awarded the Nobel Prize in Physiology or Medicine. 1962 Rosalind Franklin, who had died by that time, was not among the laureates, since the prize is not awarded posthumously
On the right is the largest spiral of human DNA, built of people on the beach in Varna (Bulgaria), entered the Guinness Book of Records on April 23, 2016
Deoxyribonucleic acid. General information
DNA (deoxyribonucleic acid) is a kind of blueprint for life, a complex code that contains data on hereditary information. This complex macromolecule is capable of storing and transmitting hereditary genetic information from generation to generation. DNA determines such properties of any living organism as heredity and variability. The information encoded in it sets the entire program for the development of any living organism. Genetically inherent factors predetermine the entire course of life of both a person and any other organism. Artificial or natural effects of the external environment can only slightly affect the overall severity of individual genetic traits or affect the development of programmed processes.
Deoxyribonucleic acid(DNA) is a macromolecule (one of the three main ones, the other two are RNA and proteins), which provides storage, transmission from generation to generation and the implementation of the genetic program for the development and functioning of living organisms. DNA contains information about the structure of various types of RNA and proteins.
In eukaryotic cells (animals, plants and fungi), DNA is found in the nucleus of the cell as part of chromosomes, as well as in some cellular organelles (mitochondria and plastids). In the cells of prokaryotic organisms (bacteria and archaea), a circular or linear DNA molecule, the so-called nucleoid, is attached from the inside to the cell membrane. They and lower eukaryotes (for example, yeast) also have small, autonomous, predominantly circular DNA molecules called plasmids.
From a chemical point of view, DNA is a long polymer molecule made up of repeating blocks - nucleotides. Each nucleotide is composed of a nitrogenous base, a sugar (deoxyribose), and a phosphate group. The bonds between the nucleotides in the chain are formed due to deoxyribose ( WITH) and phosphate ( F) groups (phosphodiester bonds).
Rice. 2. Nuclertide consists of a nitrogenous base, sugar (deoxyribose) and a phosphate group
In the overwhelming majority of cases (except for some viruses containing single-stranded DNA), a DNA macromolecule consists of two chains oriented by nitrogenous bases to each other. This double-stranded molecule is twisted in a helical line.
There are four types of nitrogenous bases in DNA (adenine, guanine, thymine and cytosine). The nitrogenous bases of one of the chains are connected with the nitrogenous bases of the other chain by hydrogen bonds according to the principle of complementarity: adenine is connected only with thymine ( AT), guanine - only with cytosine ( G-C). It is these pairs that make up the “crossbars” of the spiral “staircase” of DNA (see: Fig. 2, 3 and 4).
Rice. 2. Nitrogenous bases
The sequence of nucleotides allows you to "encode" information about various types of RNA, the most important of which are informational, or messenger (mRNA), ribosomal (rRNA) and transport (tRNA). All these types of RNA are synthesized on the DNA template by copying the DNA sequence into the RNA sequence synthesized during the transcription process, and take part in the biosynthesis of proteins (translation process). In addition to coding sequences, cell DNA contains sequences that perform regulatory and structural functions.
Rice. 3. DNA replication
The location of the basic combinations of chemical DNA compounds and the quantitative relationships between these combinations ensure the coding of hereditary information.
Education new DNA (replication)
- Replication process: unwinding of the DNA double helix - synthesis of complementary strands by DNA polymerase - formation of two DNA molecules from one.
- The double helix "unfastens" into two branches when enzymes break the bond between the base pairs of chemical compounds.
- Each branch is an element of new DNA. New base pairs are connected in the same sequence as in the parent branch.
Upon completion of duplication, two independent helices are formed, created from chemical compounds of the parental DNA and having the same genetic code with it. In this way, DNA is able to digest information from cell to cell.
More detailed information:
STRUCTURE OF NUCLEIC ACIDS
Rice. 4 . Nitrogen bases: adenine, guanine, cytosine, thymine
Deoxyribonucleic acid(DNA) refers to nucleic acids. Nucleic acids is a class of irregular biopolymers, the monomers of which are nucleotides.
NUCLEOTIDES consist of nitrogenous base combined with a five-carbon carbohydrate (pentose) - deoxyribose(in the case of DNA) or ribose(in the case of RNA), which combines with the phosphoric acid residue (H 2 PO 3 -).
Nitrogenous bases there are two types: pyrimidine bases - uracil (only in RNA), cytosine and thymine, purine bases - adenine and guanine.
Rice. 5. The structure of nucleotides (left), the location of the nucleotide in DNA (bottom) and types of nitrogenous bases (right): pyrimidine and purine
The carbon atoms in the pentose molecule are numbered from 1 to 5. Phosphate combines with the third and fifth carbon atoms. This is how the nucleotides combine to form a nucleic acid chain. Thus, we can isolate the 3 'and 5' ends of the DNA strand:
Rice. 6. Isolation of 3 'and 5' ends of the DNA strand
Two DNA strands form double helix... These chains in a spiral are oriented in opposite directions. In different DNA strands, nitrogenous bases are interconnected by hydrogen bonds... Adenine always combines with thymine, and cytosine with guanine. It is called rule of complementarity(cm. principle of complementarity).
Complementarity rule:
| A-T G-C |
For example, if we are given a DNA strand with the sequence
3'- ATGTCCTAGCTGCTCG - 5 ',
then the second chain will be complementary to it and directed in the opposite direction - from the 5'-end to the 3'-end:
5'-TACAGGATCGACGAGC-3 '.
Rice. 7. Direction of the chains of the DNA molecule and the connection of nitrogenous bases using hydrogen bonds
DNA REPLICATION
DNA replication is the process of doubling a DNA molecule by means of matrix synthesis. In most cases of natural DNA replicationprimerfor DNA synthesis is short snippet (re-created). Such a ribonucleotide primer is created by the enzyme primase (DNA primase in prokaryotes, DNA polymerase in eukaryotes), and is subsequently replaced by deoxyribonucleotides polymerase, which normally performs repair functions (correcting chemical damage and breaks in the DNA molecule).
Replication occurs by a semi-conservative mechanism. This means that the double helix of DNA unwinds and a new strand is completed on each of its strands according to the principle of complementarity. The daughter DNA molecule, therefore, contains one chain from the parent molecule and one newly synthesized one. Replication occurs in the direction from the 3 'to the 5' end of the parent chain.
Rice. 8. Replication (doubling) of the DNA molecule
DNA synthesis- this is not such a complicated process as it might seem at first glance. If you think about it, then first you need to figure out what synthesis is. It is the process of bringing something together. The formation of a new DNA molecule takes place in several stages:
1) DNA topoisomerase, located in front of the replication fork, cuts DNA in order to facilitate its unwinding and unwinding.
2) DNA helicase, following topoisomerase, influences the process of “untwisting” of the DNA helix.
3) DNA-binding proteins carry out the binding of DNA strands, and also carry out their stabilization, preventing them from sticking to each other.
4) DNA polymerase δ(delta) , coordinated with the speed of movement of the replicative fork, carries out the synthesisleadingchains subsidiary DNA in the 5 "→ 3" direction on the template maternal DNA strand in the direction from its 3 "-end to 5" -end (speed up to 100 base pairs per second). These events on this maternal DNA strands are limited.
Rice. 9. Schematic representation of the DNA replication process: (1) Lagging strand (lagging strand), (2) Leading strand (leading strand), (3) DNA polymerase α (Polα), (4) DNA ligase, (5) RNA -primer, (6) Primase, (7) Okazaki fragment, (8) DNA polymerase δ (Polδ), (9) Helicase, (10) Single-stranded DNA-binding proteins, (11) Topoisomerase.
The following describes the synthesis of the lagging strand of daughter DNA (see. Scheme replication fork and replication enzyme function)
For a more visual explanation of DNA replication, see
5) Immediately after the unwinding and stabilization of another thread of the parent molecule,DNA polymerase α(alpha)and in the 5 "→ 3" direction synthesizes a primer (RNA primer) - an RNA sequence on a DNA template 10 to 200 nucleotides in length. After that, the enzymeis removed from the DNA strand.
Instead of DNA polymeraseα
attaches to the 3 "end of the primer DNA polymeraseε
.
6)
DNA polymeraseε
(epsilon) as if it continues to lengthen the primer, but as a substrate it embedsdeoxyribonucleotides(in the amount of 150-200 nucleotides). As a result, a solid thread is formed from two parts -RNA(i.e. primer) and DNA.
DNA polymerase εworks until it meets the previous primerfragment of Okazaki(synthesized a little earlier). This enzyme is then removed from the chain.
7) DNA polymerase β(beta) gets up insteadDNA polymerase ε,moves in the same direction (5 "→ 3") and removes the primer ribonucleotides, while inserting deoxyribonucleotides in their place. The enzyme works until the complete removal of the primer, i.e. until a deoxyribonucleotide (even earlier synthesizedDNA polymerase ε). The enzyme is not able to connect the result of its work and the DNA in front of it, so it leaves the chain.
As a result, a fragment of daughter DNA "lies" on the matrix of the mother thread. It is calledfragment of Okazaki.
8) DNA ligase stitches two adjacent fragments of Okazaki , i.e. 5 "-end of the segment synthesizedDNA polymerase ε,and 3 "-end of the circuit, built-inDNA polymeraseβ .
RNA STRUCTURE
Ribonucleic acid(RNA) is one of the three main macromolecules (the other two are DNA and proteins) that are found in the cells of all living organisms.
Just like DNA, RNA is made up of a long chain in which each link is called nucleotide... Each nucleotide is composed of a nitrogenous base, a ribose sugar, and a phosphate group. However, unlike DNA, RNA usually has not two strands, but one. Pentose in RNA is represented by ribose, not deoxyribose (ribose has an additional hydroxyl group on the second carbohydrate atom). Finally, DNA differs from RNA in the composition of nitrogenous bases: instead of thymine ( T) uracil ( U) which is also complementary to adenine.
The sequence of nucleotides allows RNA to encode genetic information. All cellular organisms use RNA (mRNA) to program protein synthesis.
Cellular RNAs are produced by a process called transcription , that is, the synthesis of RNA on the DNA matrix, carried out by special enzymes - RNA polymerases.
Then messenger RNAs (mRNAs) take part in a process called broadcast, those. protein synthesis on the mRNA matrix with the participation of ribosomes. Other RNAs, after transcription, undergo chemical modifications, and after the formation of secondary and tertiary structures, they perform functions depending on the type of RNA.
Rice. 10. The difference between DNA and RNA at the nitrogenous base: instead of thymine (T), RNA contains uracil (U), which is also complementary to adenine.
TRANSCRIPTION
It is the process of RNA synthesis on a DNA template. DNA unwinds at one of the sites. One of the strands contains information that needs to be copied onto an RNA molecule - this strand is called a coding strand. The second DNA strand, complementary to the coding one, is called the template. In the process of transcription on the template strand in the direction 3 '- 5' (along the DNA strand), a complementary RNA strand is synthesized. Thus, an RNA copy of the coding strand is created.
Rice. 11. Schematic representation of transcription
For example, if we are given the sequence of the coding strand
3'- ATGTCCTAGCTGCTCG - 5 ',
then, according to the rule of complementarity, the matrix chain will carry the sequence
5'- TACAGGATCGACGAGC- 3 ',
and the RNA synthesized from it is the sequence
Broadcast
Consider the mechanism protein synthesis on the RNA matrix, as well as the genetic code and its properties. Also, for clarity, using the link below, we recommend watching a short video about the processes of transcription and translation that take place in a living cell:
Rice. 12. Protein synthesis process: DNA encodes RNA, RNA encodes protein
GENETIC CODE
Genetic code- a method of encoding the amino acid sequence of proteins using a nucleotide sequence. Each amino acid is encoded by a sequence of three nucleotides - a codon or a triplet.
Genetic code common to most pro- and eukaryotes. The table lists all 64 codons and indicates the corresponding amino acids. The base order is from the 5 "to the 3" end of the mRNA.
Table 1. Standard genetic code
|
1st nie |
2nd base |
3rd nie |
|||||||
|
U |
C |
A |
G |
||||||
|
U |
U U U |
(Phe / F) |
U C U |
(Ser / S) |
U A U |
(Tyr / Y) |
U G U |
(Cys / C) |
U |
|
U U C |
U C C |
U A C |
U G C |
C |
|||||
|
U U A |
(Leu / L) |
U C A |
U A A |
Stop codon ** |
U G A |
Stop codon ** |
A |
||
|
U U G |
U C G |
U A G |
Stop codon ** |
U G G |
(Trp / W) |
G |
|||
|
C |
C U U |
C C U |
(Pro / P) |
C A U |
(His / H) |
C G U |
(Arg / R) |
U |
|
|
C U C |
C C C |
C A C |
C G C |
C |
|||||
|
C U A |
C C A |
C A A |
(Gln / Q) |
C GA |
A |
||||
|
C U G |
C C G |
C A G |
C G G |
G |
|||||
|
A |
A U U |
(Ile / I) |
A C U |
(Thr / T) |
A A U |
(Asn / N) |
A G U |
(Ser / S) |
U |
|
A U C |
A C C |
A A C |
A G C |
C |
|||||
|
A U A |
A C A |
A A A |
(Lys / K) |
A G A |
A |
||||
|
A U G |
(Met / M) |
A C G |
A A G |
A G G |
G |
||||
|
G |
G U U |
(Val / V) |
G C U |
(Ala / A) |
G A U |
(Asp / D) |
G G U |
(Gly / G) |
U |
|
G U C |
G C C |
G A C |
G G C |
C |
|||||
|
G U A |
G C A |
G A A |
(Glu / E) |
G G A |
A |
||||
|
G U G |
G C G |
G A G |
G G G |
G |
|||||
Among the triplets, there are 4 special sequences that function as "punctuation marks":
- *Triplet AUG, also encoding methionine, is called start codon... The synthesis of a protein molecule begins from this codon. Thus, during protein synthesis, the first amino acid in the sequence will always be methionine.
- ** Triplets UAA, UAG and UGA are called stop codons and do not encode a single amino acid. At these sequences, protein synthesis stops.
Properties of the genetic code
1. Triplet... Each amino acid is encoded by a sequence of three nucleotides - a triplet or a codon.
2. Continuity... There are no additional nucleotides between the triplets, the information is read continuously.
3. Non-overlap... One nucleotide cannot enter simultaneously into two triplets.
4. Unambiguity... One codon can encode only one amino acid.
5. Degeneracy... One amino acid can be encoded by several different codons.
6. Versatility... The genetic code is the same for all living organisms.
Example. We are given the sequence of the coding chain:
3’- CCGATTGCACGTCGATCGTATA- 5’.
The matrix chain will have the sequence:
5’- GGCTAACGTGCAGCTAGCATAT- 3’.
Now we "synthesize" informational RNA from this chain:
3’- CCGAUUGCACGUCGAUCGUAUA- 5’.
Protein synthesis goes in the 5 '→ 3' direction, therefore, we need to flip the sequence to "read" the genetic code:
5’- AUAUGCUAGCUGCACGUUAGCC- 3’.
Now let's find the AUG start codon:
5’- AU AUG CUAGCUGCACGUUAGCC- 3’.
Let's divide the sequence into triplets:
sounds like this: information from DNA is transferred to RNA (transcription), from RNA - to protein (translation). DNA can also be duplicated by replication, and the reverse transcription process is also possible, when DNA is synthesized from the RNA template, but this process is mainly typical for viruses.
Rice. 13. Central dogma of molecular biology
GENOME: GENES and CHROMOSOMES
(general concepts)
Genome - the totality of all genes of an organism; its complete chromosome set.
The term "genome" was proposed by G. Winkler in 1920 to describe a set of genes contained in a haploid set of chromosomes of organisms of one biological species. The original meaning of this term indicated that the concept of the genome, in contrast to the genotype, is a genetic characteristic of the species as a whole, and not of an individual individual. With the development of molecular genetics, the meaning of this term has changed. It is known that DNA, which is the carrier of genetic information in most organisms and, therefore, forms the basis of the genome, includes not only genes in the modern sense of the word. Most of the DNA of eukaryotic cells is represented by non-coding ("redundant") nucleotide sequences that do not contain information about proteins and nucleic acids. Thus, the main part of the genome of any organism is the entire DNA of its haploid set of chromosomes.
Genes are sections of DNA molecules that encode polypeptides and RNA molecules
Over the past century, our understanding of genes has changed significantly. Previously, the genome was called a section of the chromosome that encodes or determines one trait or phenotypic a (visible) property, such as eye color.
In 1940, George Beadle and Edward Tatem proposed a molecular definition of the gene. Scientists treated fungal spores Neurospora crassa X-rays and other agents that cause changes in the DNA sequence ( mutations), and found mutant strains of the fungus that had lost some specific enzymes, which in some cases led to disruption of the entire metabolic pathway. Beadle and Tatem concluded that a gene is a piece of genetic material that defines or encodes a single enzyme. This is how the hypothesis appeared "One gene - one enzyme"... This concept was later expanded to define "One gene - one polypeptide", since many genes encode proteins that are not enzymes, and the polypeptide may be a subunit of a complex protein complex.
In fig. 14 is a diagram of how triplets of nucleotides in DNA determine the polypeptide, the amino acid sequence of a protein, mediated by mRNA. One of the DNA strands plays the role of a template for the synthesis of mRNA, the nucleotide triplets (codons) of which are complementary to the DNA triplets. In some bacteria and many eukaryotes, coding sequences are interrupted by non-coding regions (the so-called introns).
Modern biochemical gene definition even more specifically. Genes are all sections of DNA that encode the primary sequence of final products, which include polypeptides or RNA that have structural or catalytic function.
Along with genes, DNA also contains other sequences that perform exclusively a regulatory function. Regulatory sequences can denote the beginning or end of genes, affect transcription, or indicate the site of initiation of replication or recombination. Some genes can be expressed in different ways, with the same piece of DNA serving as a template for the formation of different products.
We can roughly calculate minimum gene size coding for a medium protein. Each amino acid in the polypeptide chain is encoded as a sequence of three nucleotides; the sequences of these triplets (codons) correspond to the amino acid chain in the polypeptide encoded by the given gene. A polypeptide chain of 350 amino acid residues (medium chain) corresponds to a sequence of 1050 bp. ( base pairs). However, many genes of eukaryotes and some genes of prokaryotes are interrupted by DNA segments that do not carry information about the protein, and therefore turn out to be much longer than a simple calculation shows.
How many genes are on one chromosome?
Rice. 15. View of chromosomes in procarytic (left) and eukaryotic cells. Histones are a broad class of nuclear proteins that perform two main functions: they are involved in the packaging of DNA strands in the nucleus and in the epigenetic regulation of nuclear processes such as transcription, replication and repair.
DNA of prokaryotes is more simple: their cells do not have a nucleus, therefore DNA is located directly in the cytoplasm in the form of a nucleoid.
As you know, bacterial cells have a chromosome in the form of a DNA strand, packed into a compact structure - a nucleoid. Chromosome of a prokaryote Escherichia coli, whose genome has been completely decoded, is a circular DNA molecule (in fact, it is not a regular circle, but rather a loop without beginning and end), consisting of 4 639 675 bp. This sequence contains approximately 4300 genes for proteins and 157 genes for stable RNA molecules. V human genome approximately 3.1 billion base pairs, corresponding to nearly 29,000 genes located on 24 different chromosomes.
Prokaryotes (Bacteria).
Bacterium E. coli has one double-stranded circular DNA molecule. It consists of 4 639 675 bp. and reaches a length of about 1.7 mm, which exceeds the length of the cell itself E. coli approximately 850 times. In addition to the large circular chromosome in the nucleoid, many bacteria contain one or more small circular DNA molecules that are freely located in the cytosol. Such extrachromosomal elements are called plasmids(fig. 16).
Most plasmids consist of only a few thousand base pairs, some contain more than 10,000 bp. They carry genetic information and replicate with the formation of daughter plasmids, which enter the daughter cells during the division of the parent cell. Plasmids are found not only in bacteria, but also in yeast and other fungi. In many cases, plasmids do not provide any advantage to host cells, and their only task is to reproduce independently. However, some plasmids carry genes useful to the host. For example, genes contained in plasmids can confer resistance to antibacterial agents to bacterial cells. Plasmids carrying the β-lactamase gene confer resistance to β-lactam antibiotics such as penicillin and amoxicillin. Plasmids can migrate from antibiotic-resistant cells to other cells of the same or a different species of bacteria, causing these cells to become resistant as well. The intensive use of antibiotics is a powerful selective factor contributing to the spread of plasmids encoding antibiotic resistance (as well as transposons encoding similar genes) among pathogenic bacteria, and leads to the emergence of bacterial strains with resistance to several antibiotics. Doctors are beginning to understand the dangers of widespread use of antibiotics and only prescribe them when urgently needed. For similar reasons, the widespread use of antibiotics for the treatment of farm animals is limited.
See also: Ravin N.V., Shestakov S.V. The genome of prokaryotes // Vavilov Journal of Genetics and Selection, 2013. V. 17. No. 4/2. S. 972-984.
Eukaryotes.
Table 2. DNA, genes and chromosomes of some organisms
|
Shared DNA, p.n. |
Chromosome number * |
Approximate number of genes |
|
|
Escherichia coli(bacterium) |
4 639 675 |
4 435 |
|
|
Saccharomyces cerevisiae(yeast) |
12 080 000 |
16** |
5 860 |
|
Caenorhabditis elegans(nematode) |
90 269 800 |
12*** |
23 000 |
|
Arabidopsis thaliana(plant) |
119 186 200 |
33 000 |
|
|
Drosophila melanogaster(fruit fly) |
120 367 260 |
20 000 |
|
|
Oryza sativa(rice) |
480 000 000 |
57 000 |
|
|
Mus musculus(mouse) |
2 634 266 500 |
27 000 |
|
|
Homo sapiens(Human) |
3 070 128 600 |
29 000 |
Note. Information is constantly updated; for more up-to-date information, refer to the sites dedicated to individual genomic projects
* For all eukaryotes, except for yeast, a diploid set of chromosomes is given. Diploid kit chromosomes (from the Greek diploos- double and eidos- species) - double set of chromosomes(2n), each of which has a homologous one.
** Haploid set. Wild yeast strains usually have eight (octaploid) or more sets of such chromosomes.
*** For females with two X chromosomes. Males have an X chromosome, but no Y, that is, there are only 11 chromosomes.
A yeast cell, one of the smallest eukaryotes, has 2.6 times more DNA than a cell E. coli(Table 2). Fruit fly cells Drosophila, a classical object of genetic research, contain 35 times more DNA, and human cells - about 700 times more DNA than cells E. coli. Many plants and amphibians contain even more DNA. The genetic material of eukaryotic cells is organized in the form of chromosomes. Diploid set of chromosomes (2 n) depends on the type of organism (Table 2).
For example, in a human somatic cell there are 46 chromosomes ( rice. 17). Each chromosome of a eukaryotic cell, as shown in Fig. 17, a, contains one very large double-stranded DNA molecule. Twenty-four human chromosomes (22 paired chromosomes and two sex chromosomes X and Y) differ in length by more than 25 times. Each eukaryotic chromosome contains a specific set of genes.
Rice. 17. Eukaryotic chromosomes.a- a pair of linked and condensed sister chromatids from the human chromosome. In this form, eukaryotic chromosomes remain after replication and in metaphase during mitosis. b- a complete set of chromosomes from the leukocyte of one of the authors of the book. Each normal human somatic cell contains 46 chromosomes.
The size and function of DNA as a matrix for storing and transmitting hereditary material explains the presence of special structural elements in the organization of this molecule. In higher organisms, DNA is distributed between chromosomes.
The collection of DNA (chromosomes) of an organism is called the genome. Chromosomes are found in the cell nucleus and form a structure called chromatin. Chromatin is a complex of DNA and basic proteins (histones) in a 1: 1 ratio. DNA length is usually measured by the number of complementary nucleotide pairs (bp). For example, the 3rd chromosome is humancentury is a DNA molecule with a size of 160 million bp. The isolated linearized DNA with a size of 3 * 10 6 bp. has a length of about 1 mm, therefore, the linearized molecule of the 3rd human chromosome would be 5 mm in length, and the DNA of all 23 chromosomes (~ 3 * 10 9 bp, MR = 1.8 * 10 12) of the haploid cell - ovum or sperm - in linearized form would be 1 m. With the exception of germ cells, all cells of the human body (there are about 1013) contain a double set of chromosomes. During cell division, all 46 DNA molecules are replicated and re-organized into 46 chromosomes.
If you connect the DNA molecules of the human genome (22 chromosomes and chromosomes X and Y or X and X), you get a sequence about one meter long. Note: All mammals and other organisms with a heterogametic male sex, females have two X chromosomes (XX), and males have one X chromosome and one Y chromosome (XY).
Most human cells, therefore, the total length of the DNA of such cells is about 2m. An adult has approximately 10 14 cells, so the total length of all DNA molecules is 2 ・ 10 11 km. For comparison, the circumference of the Earth is 4 ・ 10 4 km, and the distance from the Earth to the Sun is 1.5 ・ 10 8 km. This is how surprisingly compactly packed DNA is in our cells!
In eukaryotic cells, there are other organelles containing DNA - mitochondria and chloroplasts. Many hypotheses have been put forward regarding the origin of mitochondrial and chloroplast DNA. The generally accepted point of view today is that they are the rudiments of the chromosomes of ancient bacteria that entered the cytoplasm of host cells and became the precursors of these organelles. Mitochondrial DNA codes for mitochondrial tRNA and rRNA, as well as several mitochondrial proteins. More than 95% of mitochondrial proteins are encoded by nuclear DNA.
STRUCTURE OF GENES
Consider the structure of the gene in prokaryotes and eukaryotes, their similarities and differences. Despite the fact that a gene is a piece of DNA that encodes only one protein or RNA, in addition to the directly coding part, it also includes regulatory and other structural elements that have a different structure in prokaryotes and eukaryotes.
Coding sequence- the main structural and functional unit of the gene, it is in it that the triplets of nucleotides encodingamino acid sequence. It starts with a start codon and ends with a stop codon.
Before and after the coding sequence are untranslated 5'- and 3'-sequences... They perform regulatory and auxiliary functions, for example, they ensure the landing of the ribosome on m-RNA.
Untranslated and coding sequences constitute a transcription unit - a transcribed DNA section, that is, a DNA section from which m-RNA synthesis occurs.
Terminator- non-transcribed DNA region at the end of the gene, where RNA synthesis stops.
At the beginning of the gene is regulatory area including promoter and operator.
Promoter- the sequence to which the polymerase binds during the initiation of transcription. Operator is a region that special proteins can bind to - repressors, which can reduce the activity of RNA synthesis from this gene - in other words, reduce it expression.
Gene structure in prokaryotes
The general structure of genes in prokaryotes and eukaryotes does not differ - they both contain a regulatory region with a promoter and operator, a transcription unit with coding and untranslated sequences, and a terminator. However, the organization of genes in prokaryotes and eukaryotes is different.
Rice. 18. Scheme of the structure of the gene in prokaryotes (bacteria) -the image is enlarged
At the beginning and at the end of the operon, there are common regulatory regions for several structural genes. One mRNA molecule is read from the transcribed region of the operon, which contains several coding sequences, each of which has its own start and stop codon. From each of these sites withone protein is interrupted. In this way, several protein molecules are synthesized from one i-RNA molecule.
For prokaryotes, it is characteristic to combine several genes into a single functional unit - operon... The work of the operon can be regulated by other genes that can be noticeably distant from the operon itself - regulators... The protein translated from this gene is called repressor... It binds to the operator of the operon, regulating the expression of all genes contained in it at once.
The phenomenon is also characteristic of prokaryotes pairing transcription and translation.
Rice. 19 The phenomenon of conjugation of transcription and translation in prokaryotes - the image is enlarged
Such conjugation does not occur in eukaryotes due to the presence of a nuclear envelope that separates the cytoplasm, where translation takes place, from the genetic material on which transcription takes place. In prokaryotes, during the synthesis of RNA on the DNA template, the ribosome can immediately bind to the synthesized RNA molecule. Thus, the translation begins even before the completion of the transcription. Moreover, several ribosomes can simultaneously bind to one RNA molecule, synthesizing several molecules of one protein at once.
Gene structure in eukaryotes
The genes and chromosomes of eukaryotes are very complexly organized
Many species of bacteria have only one chromosome, and in almost all cases, there is one copy of each gene on each chromosome. Only a few genes, such as rRNA genes, are contained in multiple copies. Genes and regulatory sequences make up virtually the entire genome of prokaryotes. Moreover, almost every gene strictly corresponds to the amino acid sequence (or RNA sequence) that it encodes (Fig. 14).
The structural and functional organization of eukaryotic genes is much more complex. The study of eukaryotic chromosomes, and later sequencing of complete sequences of eukaryotic genomes, brought many surprises. Many, if not most, eukaryotic genes have an interesting feature: their nucleotide sequences contain one or more DNA regions in which the amino acid sequence of the polypeptide product is not encoded. Such untranslated insertions break the direct correspondence between the nucleotide sequence of the gene and the amino acid sequence of the encoded polypeptide. These untranslated segments of genes are called introns, or embedded sequences and the coding segments are exons... In prokaryotes, only a few genes contain introns.
So, in eukaryotes, there is practically no combination of genes into operons, and the coding sequence of the eukaryotic gene is most often divided into translated regions - exons, and untranslated sections - introns.
In most cases, the function of the introns has not been established. In general, only about 1.5% of human DNA are "coding", that is, they carry information about proteins or RNA. However, taking into account large introns, it turns out that 30% of human DNA consists of genes. Since genes make up a relatively small proportion of the human genome, a significant portion of DNA remains unaccounted for.
Rice. 16. Scheme of the structure of the gene in eukaryotes - the image is enlarged
From each gene, immature, or pre-RNA is first synthesized, which contains both introns and exons.
After this, a splicing process takes place, as a result of which the intron regions are excised, and a mature mRNA is formed, from which the protein can be synthesized.
Rice. 20. Process of alternative splicing - the image is enlarged
Such organization of genes makes it possible, for example, to realize when different forms of a protein can be synthesized from one gene, due to the fact that in the process of splicing exons can be stitched in different sequences.
Rice. 21. Differences in the structure of genes of prokaryotes and eukaryotes - the image is enlarged
MUTATIONS AND MUTAGENESIS
Mutation called a persistent change in genotype, that is, a change in the nucleotide sequence.
The process that leads to the occurrence of mutations is called mutagenesis, and the organism, all whose cells carry the same mutation - mutant.
Mutation theory was first formulated by Hugo de Vries in 1903. Its modern version includes the following provisions:
1. Mutations appear suddenly, in leaps and bounds.
2. Mutations are passed from generation to generation.
3. Mutations can be beneficial, harmful or neutral, dominant or recessive.
4. The probability of detecting mutations depends on the number of individuals examined.
5. Similar mutations can occur repeatedly.
6. Mutations are not targeted.
Mutations can occur due to various factors. Distinguish between mutations that have arisen under the influence mutagenic impacts: physical (for example, ultraviolet or radiation), chemical (for example, colchicine or reactive oxygen species) and biological (for example, viruses). Also mutations can be caused by replication errors.
Depending on the conditions of appearance, mutations are subdivided into spontaneous- that is, mutations that have arisen under normal conditions, and induced- that is, mutations that have arisen under special conditions.
Mutations can occur not only in nuclear DNA, but also, for example, in the DNA of mitochondria or plastids. Accordingly, we can distinguish nuclear and cytoplasmic mutations.
As a result of mutations, new alleles can often appear. If the mutant allele suppresses the action of the normal one, the mutation is called dominant... If a normal allele suppresses a mutant one, such a mutation is called recessive... Most of the mutations leading to the emergence of new alleles are recessive.
By effect, mutations are distinguished adaptive leading to an increase in the body's adaptation to the environment, neutral that do not affect survival, harmful that reduce the adaptability of organisms to environmental conditions and lethal leading to the death of the organism in the early stages of development.
According to the consequences, mutations are distinguished, leading to loss of protein function, mutations leading to the emergence the protein has a new function, as well as mutations that change the dose of the gene, and, accordingly, the dose of protein synthesized from it.
A mutation can occur to any cell in the body. If a mutation occurs in the germ cell, it is called germinal(germinal, or generative). Such mutations do not appear in the organism in which they appeared, but lead to the appearance of mutants in the offspring and are inherited, therefore they are important for genetics and evolution. If a mutation occurs in any other cell, it is called somatic... Such a mutation can, to one degree or another, manifest itself in the organism in which it arose, for example, lead to the formation of cancerous tumors. However, this mutation is not inherited and does not affect offspring.
Mutations can affect regions of the genome of different sizes. Allocate gene, chromosomal and genomic mutations.
Gene mutations
Mutations that occur on a scale of less than one gene are called genetic, or point (point)... Such mutations lead to a change in one or more nucleotides in the sequence. Among gene mutations, there arereplacements leading to the replacement of one nucleotide with another,deletions leading to the loss of one of the nucleotides,insertions leading to the addition of an extra nucleotide to the sequence.
Rice. 23. Gene (point) mutations
According to the mechanism of action on protein, gene mutations are divided into:synonymous, which (as a result of the degeneracy of the genetic code) do not lead to a change in the amino acid composition of the protein product,missense mutations, which lead to the substitution of one amino acid for another and can affect the structure of the synthesized protein, although they often turn out to be insignificant,nonsense mutations leading to the replacement of the coding codon with a stop codon,mutations leading to splicing disorder:
Rice. 24. Schemes of mutations
Also, according to the mechanism of action on the protein, mutations are isolated, leading to frame shift readouts for example, insertions and deletions. Such mutations, like nonsense mutations, although they occur at one point in a gene, often affect the entire structure of a protein, which can lead to a complete change in its structure.
when the chromosome section is rotated 180 degrees, Rice. 28. Translocation
Rice. 29. Chromosome before and after duplication
Genomic mutations
Finally, genomic mutations affect the entire genome as a whole, that is, the number of chromosomes changes. Allocate polyploidy - an increase in cell ploidy, and aneuploidy, that is, a change in the number of chromosomes, for example, trisomy (the presence of an additional homologue in one of the chromosomes) and monosomy (the absence of a homologue in a chromosome).
DNA Videos
DNA REPLICATION, RNA CODING, PROTEIN SYNTHESIS
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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 packed 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 got their name.
Deoxyribonucleic acid structure
Nucleic acids have a primary, secondary and tertiary structure.
Primary DNA structure
The primary structure of DNA is called a linear polynucleotide chain, in which mononucleotides are linked by 3 ", 5" -phosphodiester bonds. The starting material for the assembly of the nucleic acid chain in the cell is the nucleoside 5 "-triphosphate, 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 covalently binds to the 5" carbon atom of the other deoxyribose via one phosphoric acid residue and forms a linear polynucleotide nucleic acid chain. Hence the name: 3 ", 5" -phosphodiester bonds. Nitrogenous bases do not take part in the combination of nucleotides of one chain (Fig. 1.).
Such a connection, between the remainder of the phosphoric acid molecule 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 one by one on the side. Their sequence of arrangement in the chains of nucleic acid molecules is strictly specific for cells of different organisms, i.e. is of a specific nature (Chargaff's rule).
A linear DNA chain, the length of which depends on the number of nucleotides included in the chain, has two ends: one is called the 3 "end and contains a free hydroxyl, and the other, the 5" end, contains a phosphoric acid residue. The chain is polarized and can have a direction of 5 "-> 3" and 3 "-> 5". An exception is circular DNA.
The genetic "text" of DNA is made up of code "words" - triplets of nucleotides called codons. The regions of DNA that contain information about the primary structure of all types of RNA are called structural genes.
Polynucleodite DNA chains reach gigantic sizes, so they are packed in a certain way in the cell.
Studying the composition of DNA, Chargaff (1949) established important laws regarding the content of individual DNA bases. They helped uncover the secondary structure of DNA. These patterns are called Chargaff rules. Chargaff rules
These rules indicate that when building DNA, a fairly strict correspondence (pairing) should not be observed between purine and pyrimidine bases in general, but specifically thymine with adenine and cytosine with guanine. Based on these rules, including, 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 the creation of a DNA model
Initial analyzes gave the impression that DNA of any origin contains all four nucleotides in equal molar amounts. However, in the 1940s, E. Chargaff and his collaborators, as a result of the analysis of DNA isolated from various organisms, clearly showed that nitrogenous bases are contained in them in various quantitative ratios. Chargaff found that although these ratios are the same for DNA from all cells of the same type 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 analysis results, a certain pattern emerged: in all samples the total amount of purines was equal to the total amount of pyrimidines (A + G = T + C), the amount of adenine was equal to the amount of thymine (A = T), and the amount of guanine - the amount of cytosine (G = C). DNA isolated from mammalian cells was generally richer in adenine and thymine and relatively poorer in guanine and cytosine, while in bacteria DNA 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 a model of the structure of Watson-Crick DNA was later built.
Another important indirect indication of the possible structure of DNA was the data of L. Pauling 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 of the common configurations of the peptide chain, the α-helix, is a regular helical structure. With such a structure, the formation of hydrogen bonds between amino acids located on adjacent turns of the chain is possible. Pauling described the α-helical configuration of the polypeptide chain in 1950 and suggested that DNA molecules, too, probably have a helical structure, fixed by hydrogen bonds.
However, the most valuable information about the structure of the DNA molecule was provided by the results of X-ray structural analysis. X-rays, passing through a DNA crystal, undergo diffraction, that is, they are deflected in certain directions. The degree and nature of the deflection of the rays depend on the structure of the molecules themselves. The X-ray diffraction pattern (Fig. 3) gives the experienced eye a number of indirect indications regarding the structure of the molecules of the investigated substance. Analysis of X-ray diffraction patterns of DNA led to the conclusion that the nitrogenous bases (having a flat shape) are stacked 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, the X-ray diffraction patterns obtained by Wilkins and the research of chemists who provided information about the exact distances between atoms in a molecule, about the angles between the bonds of a given atom and the size of the atoms, Watson and Crick began to build physical models of individual constituent parts of the DNA molecule on a certain scale. and "fit" them to each other in such a way that the resulting system would correspond to different experimental data [show] .
It was known even earlier that adjacent nucleotides in the DNA chain are connected by phosphodiester bridges linking the 5'-carbon atom of deoxyribose of one nucleotide with the 3'-carbon atom of deoxyribose of the next nucleotide. Watson and Crick had no doubt that the 0.34 nm period corresponds to the distance between consecutive nucleotides in the DNA chain. Further, it could be assumed that the period of 2 nm corresponds to the chain thickness. And in order to explain which real structure corresponds to the period of 3.4 nm, Watson and Crick, just like 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 the word is obtained when the turns form a conical rather than a cylindrical surface in space). Then the period of 3.4 nm will correspond to the distance between successive turns of this spiral. Such a spiral can be very dense or somewhat stretched, that is, its turns can be gentle or steep. Since the period of 3.4 nm is exactly 10 times the distance between consecutive nucleotides (0.34 nm), it is clear that each complete turn of the helix contains 10 nucleotides. From these data, Watson and Crick were able to calculate the density of a polynucleotide chain twisted into a helix 2 nm in diameter with a distance between the turns equal to 3.4 nm. It turned out that the density of such a chain would be half the actual density of DNA, which was already known. I had to assume that the DNA molecule consists of two strands - that it is a double helix of nucleotides.
The next task was, of course, to clarify the spatial relationship between the two circuits forming a double helix. After testing a number of chain layouts on their physical model, Watson and Crick found that all available data best fit with a variant in which two polynucleotide helices run in opposite directions; in this case, chains consisting of sugar and phosphate residues form the surface of a double helix, and purines and pyrimidines are located inside. The bases located opposite each other, belonging to two chains, are connected in pairs by hydrogen bonds; it is these hydrogen bonds that hold the chains together, thus fixing the overall configuration of the molecule.
The double helix of DNA can be imagined as a spiral-shaped rope ladder so that its rungs remain in a horizontal position. Then two longitudinal ropes will correspond to chains of sugar and phosphate residues, and the crossbars will correspond to pairs of nitrogenous bases connected by hydrogen bonds.
As a result of further study of possible models, Watson and Crick concluded that each "bar" should be composed of one purine and one pyrimidine; with a period of 2 nm (which corresponds to the diameter of the double helix), there would not be enough room for the two purines, and the two pyrimidines would not be close enough to each other to form proper hydrogen bonds. An in-depth study of a detailed model showed that adenine and cytosine, making up a suitable combination in size, still could not be located in such a way as to form hydrogen bonds between them. Similar reports forced the exclusion of the guanine-thymine combination, while the adenine-thymine and guanine-cytosine combinations were quite acceptable. The nature of hydrogen bonds is such that adenine forms a pair with thymine, and guanine with cytosine. This concept of specific base pairing made it possible to explain the "Chargaff rule", according to which in any DNA molecule the amount of adenine is always equal to the content of thymine, and the amount of guanine is equal to the amount of cytosine. Two hydrogen bonds are formed between adenine and thymine, and three hydrogen bonds are formed between guanine and cytosine. Due to this specificity in the formation of hydrogen bonds against each adenine in one chain, thymine is found in the other; likewise, against every guanine, only cytosine can be found. 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, a DNA molecule consists of two complementary polynucleotide chains. Each DNA strand is a polynucleotide of several tens of thousands of nucleotides. In it, adjacent nucleotides form a regular pentose-phosphate backbone due to the connection of the phosphoric acid residue and deoxyribose with a strong covalent bond. In this case, the nitrogenous bases of one polynucleotide chain are arranged in a strictly defined order against the nitrogenous bases of the other. The alternation of nitrogenous bases in the polynucleotide chain is irregular.
The location of nitrogenous bases in the DNA chain is complementary (from the Greek "complement" - addition), i.e. against adenine (A) there is always thymine (T), and against guanine (G) only cytosine (C). This is due to the fact that A and T, as well as G and C strictly correspond to each other, i.e. complement each other. This correspondence is given by the chemical structure of the bases, which allows the formation of hydrogen bonds in the pair of purine and pyrimidine. There are two connections between A and T, three between G and C. These bonds provide partial stabilization of the DNA molecule in space. In this case, the stability of the double helix is directly proportional to the number of G≡C bonds, which are more stable in comparison with the A = T bonds.
The known sequence of the arrangement of nucleotides in one DNA strand makes it possible, according to the principle of complementarity, to establish the nucleotides of the other strand.
In addition, it was found that nitrogenous bases with 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 located 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 interaction between the planes of the bases in the polynucleotide chain due to van der Waals forces (vertically) provides the DNA molecule with additional stabilization in space.
The sugar-phosphate backbones of both chains are facing outward, and the bases inward, towards each other. The direction of the chains in DNA is antiparallel (one of them has the direction 5 "-> 3", the other - 3 "-> 5", ie the 3 "end of one chain is 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 coil is 3.4 nm, the height of each nucleotide is 0.34 nm, and the diameter of the helix is 2.0 nm. As a result of rotation of one strand around the other, a large groove (about 20 Å in diameter) and a small groove (about 12 Å) 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.
DNA functions
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 the genetic code, the ability to self-reproduce and transfer genetic information, provided by the replication process, and the implementation of genetic information. in the form of proteins, as well as any other compounds formed with the help of enzyme proteins.
Basic functions of DNA.
- DNA is the carrier of genetic information, which is ensured by the fact of the existence of the genetic code.
- Reproduction and transmission of genetic information in generations of cells and organisms. This functionality is provided by the replication process.
- Realization of genetic information in the form of proteins, as well as any other compounds formed with the help of protein-enzymes. This function is provided by the transcription and translation processes.
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 water in the nucleic acid molecule. In studies of DNA fibers using X-ray structural analysis, it was shown that the X-ray diffraction pattern radically depends on at what relative humidity, at what degree of water saturation of this fiber, the experiment takes place. If the fiber was sufficiently saturated with water, then one X-ray was obtained. On drying, a completely different X-ray pattern emerged, very different from the X-ray pattern of the 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 is the Watson-Crick model). The helix pitch of such a molecule is 3.4 nm. There are 10 complementary pairs per turn in the form of twisted stacks of "coins" - nitrogenous bases. The stacks are held by hydrogen bonds between two opposing "coins" of the stack, and are "wrapped" in two ribbons of phosphodiester skeleton twisted into a right-hand spiral. The planes of nitrogenous bases are perpendicular to the axis of the spiral. Adjacent complementary pairs are rotated relative to each other by 36 °. The diameter of the helix is 20 Å, with the purine nucleotide being 12 Å, and the pyrimidine nucleotide 8 Å.
The DNA molecule of lower humidity is called the A-form... The A-form is formed under conditions of less high hydration and with a higher content of Na + or K + ions. This broader right-handed conformation has 11 base pairs per turn. The planes of nitrogenous bases have a stronger inclination to the spiral axis; they are deflected from the normal to the spiral axis by 20 °. Hence, the presence of an internal void with a diameter of 5 Å follows. The distance between adjacent nucleotides is 0.23 nm, the coil length is 2.5 nm, and the helix diameter is 2.3 nm.
Originally, the A-form of DNA was thought to be less important. However, later it became clear that the A-form of DNA, as well as the B-form, has enormous biological significance. An RNA-DNA helix in the template-primer complex has an A-form, as well as an RNA-RNA helix and RNA hairpin structures (the 2'-hydroxyl group of ribose does not allow RNA molecules to form a B-form). The A-form of DNA has been found in controversy. It was found 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 be observed only in special experiments, and, apparently, they do not exist in vivo. C-form DNA has a structure similar to B-DNA. The number of base pairs per turn is 9.33, the length of the helix is 3.1 nm. The base pairs are tilted at an angle of 8 degrees relative to the perpendicular position to the axis. The grooves are similar in size to the B-DNA grooves. In this case, the main groove is somewhat shallower, and the minor groove is deeper. Natural and synthetic DNA polynucleotides can pass into the C-form.
| Table 1. Characteristics of some types of DNA structures | |||
| Spiral type | A | B | Z |
| Spiral step | 0.32 nm | 3.38 nm | 4.46 nm |
| Spiral twist | Right | Right | Left |
| Base pairs per turn | 11 | 10 | 12 |
| Distance between base planes | 0.256 nm | 0.338 nm | 0.371 nm |
| Glycosidic bond conformation | anti | anti | anti-C syn-g |
| Furanose cycle conformation | C3 "-endo | C2 "-endo | C3 "-endo-G C2 "-endo-c |
| Groove width small / large | 1.11 / 0.22 nm | 0.57 / 1.17 nm | 0.2 / 0.88 nm |
| Groove depth, small / large | 0.26 / 1.30 nm | 0.82 / 0.85 nm | 1.38 / 0.37 nm |
| Spiral diameter | 2.3 nm | 2.0 nm | 1.8 nm |
Structural elements of DNA
(non-canonical DNA structures)
The structural elements of DNA include unusual structures, limited by some special sequences:
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Z-shape DNA was discovered in 1979 while studying hexanucleotide d (CG) 3 -. It was discovered by MIT professor Alexander Rich and his colleagues. The Z-form became one of the most important structural elements of DNA due to the fact that its formation was observed in DNA regions where purines alternate with pyrimidines (for example, 5'-HCGCH-3 '), or in repeats of 5'-CHCH-3' containing methylated cytosine. An essential condition for the formation and stabilization of Z-DNA was the presence of purine nucleotides in the syn-conformation, alternating with pyrimidine bases in the anti-conformation.
Natural DNA molecules generally exist in the right B-form if they do not contain sequences of the type (CH) n. However, if such sequences are included in DNA, then these regions, when the ionic strength of the solution or cations neutralizing the negative charge on the phosphodiester backbone changes, can transform into the Z-form, while other DNA regions in the chain remain in the classical B-form. The possibility of such a transition indicates that the two chains in the DNA double helix are in a dynamic state and can unwind relative to each other, passing from the right form to the left one and vice versa. The biological consequences of such lability, which allows conformational transformations of the DNA structure, are not yet fully understood. It is believed that the Z-DNA regions play a role in the regulation of the expression of some genes and are involved in genetic recombination.
The Z-form of DNA is a left-handed double helix, in which the phosphodiester backbone is located in a zigzag manner along the axis of the molecule. Hence the name of the molecule (zigzag) -DHK. Z-DNA is the least twisted (12 base pairs per turn) and the thinnest known in nature. The distance between adjacent nucleotides is 0.38 nm, the coil length is 4.56 nm, and the Z-DNA diameter is 1.8 nm. 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. Currently, antibodies have been obtained that can distinguish the Z-form from the B-form of DNA. These antibodies bind to specific regions of the giant chromosomes of the cells of the salivary glands of Drosophila (Dr. melanogaster). The binding reaction is easy to follow due to the unusual structure of these chromosomes, in which denser regions (discs) contrast with less dense regions (interdiscs). The Z-DNA regions are located in the interbands. 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.
(shifters) are the most well-known and frequently found base sequences in DNA. A palindrome is a word or phrase that reads from left to right and vice versa in the same way. Examples of such words or phrases are: SHALASH, KAZAK, POTOP, AND ROSE FALLED ON AZOR'S Paw. When applied to DNA regions, 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 having second-order symmetry with respect to two DNA strands. Such sequences, for a completely understandable reason, are self-complementary and tend to form hairpin or cruciform structures (Fig.). The hairpins help regulatory proteins to recognize the place where the genetic text of the chromosome DNA is written off.
In cases where an inverted repeat is present on the same DNA strand, this sequence is called a mirror repeat. Mirror repeats do not possess the properties of self-complementarity and, therefore, are not capable of forming hairpin or cruciform structures. Sequences of this type are found in virtually all large DNA molecules and can range from just a few base pairs to several thousand base pairs.
The presence of palindromes in the form of cruciform structures in eukaryotic cells has not been proven, although a number of cruciform structures have been found in vivo in E. coli cells. The presence of self-complementary sequences in RNA or single-stranded DNA is the main reason for the folding of a nucleic 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 - the DNA triple helix. It is a complex of the Watson-Crick double helix with the third single-stranded DNA strand, which fits into its large groove, with the formation of the so-called Hoogsteen pair.
The formation of such a triplex occurs as a result of the folding of the 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 disconnected. In this case, one of the disconnected spirals forms a new structure with the first half of the double spiral - a triple spiral, and the second turns out to be unstructured, in the form of a single-strand section. A feature of this structural transition is a sharp dependence on the pH of the medium, the protons of which stabilize the new structure. Due to this feature, the new structure was named the H-form of DNA, the formation of which was found in supercoiled plasmids containing homopurine-homopyrimidine regions, which are a mirror repeat.
In further studies, the possibility of 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 the canonical triads isomorphic to CGC + and TAT. Stabilization of the triplex requires protonation of the CGC + triad; therefore, these triplexes depend on the pH of the solution.
- one homopyrimidine and two homopurine strands ( Py-Pu-Pu triplex) [reverse Hoogsteen interaction].
The constituent blocks of the Py-Pu-Pu triplex are canonical isomorphic to the 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: the direct and reverse Hoogsteen interaction is explained by the symmetry of 1-methylthymine: a 180 ° rotation leads to the fact that the O4 atom is replaced by the O2 atom, while the system of hydrogen bonds is preserved.
There are two types of triple spirals:
- 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-stranded DNA. Such a structure is formed if there are four guanines, which form the so-called G-quadruplex - a round dance of four guanines.
The first hints of the possibility of the formation of such structures were 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 - guanosic acid - forms gels at high concentrations, while other components of DNA do not have this property.
In 1962, using the X-ray diffraction method, it was possible to establish the cell structure of this gel. It turned out to be composed of four guanine residues, linking each other in a circle and forming a characteristic square. In the center, the bond is supported by a metal ion (Na, K, Mg). The same structures can 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 intertwined into four-stranded complexes, but this is rather an exception. More often, a single strand of nucleic acid is simply tied into a knot, forming characteristic thickenings (for example, at the ends of chromosomes), or double-stranded DNA forms a local quadruplex in some guanine-rich region.
The most studied is the existence of quadruplexes at the ends of chromosomes - on telomeres and in oncopromotors. However, until now, a complete understanding of the localization of such DNA in human chromosomes is not known.
All these unusual structures of DNA in a linear form are unstable compared to the B-form of DNA. However, DNA often exists in a circular form of topological stress 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 - it is noted when it is isolated 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 supercoil (takes the form of a figure of eight).
- The relaxed state of DNA is observed with a single break (breaking of one strand). In this case, the supercoils disappear and the DNA takes the form of a closed ring.
- Linear form of DNA - observed when two strands of a double helix are broken.
DNA tertiary structure
DNA tertiary structure is formed as a result of additional twisting in space of a double-stranded molecule - its supercoiling. Supercoiling of the DNA molecule in eukaryotic cells, in contrast to prokaryotes, is carried out in the form of complexes with proteins.
Almost all eukaryotic DNA is found in the chromosomes of nuclei, only a small amount of it is contained in mitochondria, and in plants and in plastids. The main substance of the chromosomes of eukaryotic cells (including human chromosomes) is chromatin, consisting of double-stranded DNA, histone and non-histone proteins.
Chromatin histone proteins
Histones are simple proteins that make up up to 50% of chromatin. In all studied cells of animals and plants, five main classes of histones were found: H1, H2A, H2B, H3, H4, differing in size, amino acid composition, and charge value (always positive).
Mammalian histone H1 consists of a single polypeptide chain of about 215 amino acids; the sizes of other histones vary from 100 to 135 amino acids. All of them are spiralized and twisted into a globule with a diameter of about 2.5 nm, contain an unusually large amount of positively charged amino acids lysine and arginine. Histones can be acetylated, methylated, phosphorylated, poly (ADP) -ribosylated, and histones H2A and H2B are covalently linked to ubiquitin. What is the role of such modifications in the formation of the structure and the performance of functions by histones has not yet been fully elucidated. It is assumed that this is their ability to interact with DNA and provide one of the mechanisms for regulating the action of genes.
Histones interact with DNA mainly through ionic bonds (salt bridges) formed between the negatively charged phosphate groups of DNA and the positively charged lysine and arginine residues of histones.
Non-histone chromatin proteins
Unlike histones, non-histone proteins are very diverse. Up to 590 different fractions of DNA-binding non-histone proteins have been isolated. They are also called acidic proteins, since acidic amino acids predominate in their structure (they are polyanions). Specific regulation of chromatin activity is associated with a variety of non-histone proteins. For example, enzymes required for DNA replication and expression can bind to chromatin temporarily. Other proteins, for example, participating in various regulatory processes, bind to DNA only in specific tissues or at certain stages of differentiation. Each protein is complementary to a specific DNA nucleotide sequence (DNA site). This group includes:
- a family of site-specific zinc finger proteins. Each zinc finger recognizes a specific site consisting of 5 nucleotide pairs.
- family of site-specific proteins - homodimers. A 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 are highly mobile during polyacrylamide gel electrophoresis.
- enzymes of replication, transcription and repair.
With the participation of structural, regulatory proteins and enzymes involved in the synthesis of DNA and RNA, the nucleosome strand is converted into a highly condensed complex of proteins and DNA. The resulting structure is 10,000 times shorter than the original DNA molecule.
Chromatin
Chromatin is a complex of proteins with nuclear DNA and inorganic substances. Most of the chromatin is inactive. It contains tightly packed, condensed DNA. It is heterochromatin. Distinguish between constitutive, genetically inactive chromatin (satellite DNA), consisting of unexpressed regions, and optional - inactive in a number of generations, but under certain circumstances capable of expressing.
Active chromatin (euchromatin) is non-condensed, i.e. packed less tightly. In different cells, its content ranges from 2 to 11%. In the cells of the brain, it is most of all - 10-11%, in the cells of the liver - 3-4 and kidneys - 2-3%. Active transcription of euchromatin is noted. At the same time, its structural organization allows one and the same DNA genetic information inherent in a given type of organism to be used in different ways in specialized cells.
In an electron microscope, the image of chromatin resembles a bead: spherical thickenings about 10 nm in size, separated by threadlike bridges. These globular thickenings are called nucleosomes. The nucleosome is a structural unit of chromatin. Each nucleosome contains a supercoiled segment of DNA with a length of 146 base pairs, wound with the formation of 1.75 left turns on the nucleosome core. The nucleosomal core is a histone octamer consisting of histones H2A, H2B, H3, and H4, two molecules of each type (Fig. 9), which looks like a disc 11 nm in diameter and 5.7 nm thick. The fifth histone, H1, is not part of the nucleosomal core and is not involved in the process of DNA winding on the histone octamer. It contacts DNA where the double helix enters and exits the nucleosomal core. These are intercortical (linker) DNA regions, the length of which varies depending on the cell type from 40 to 50 base pairs. As a result, the length of the DNA fragment included in the nucleosome also varies (from 186 to 196 nucleotide pairs).
The nucleosome contains about 90% of the DNA, the rest of it is the linker. 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 is how the dependence of the function on the structure is clearly manifested. It can be assumed that the more chromatin is in the composition of globular nucleosomes, the less active it is. Obviously, in different cells, the unequal proportion of resting chromatin is associated with the number of such nucleosomes.
On electron microscopic photographs, depending on the isolation conditions and the degree of stretching, chromatin may 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 a helix of six nucleosomes per turn with the formation of 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 above-described interactions of DNA with histones, a segment of the DNA double helix of 186 base pairs with an average diameter of 2 nm and a length of 57 nm transforms into a helix with a diameter of 10 nm and a length of 5 nm. With the subsequent compression of this spiral to a fiber with a diameter of 30 nm, the degree of condensation increases by a factor of six.
Ultimately, packaging a DNA duplex with five histones results in a 50-fold DNA condensation. However, even such a high degree of condensation cannot explain the almost 50,000 - 100,000-fold densification of DNA in the metaphase chromosome. Unfortunately, the details of further chromatin packing up to the metaphase chromosome are not yet known; therefore, only general features of this process can be considered.
DNA compaction levels in chromosomes
Each DNA molecule is packed 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 the chromosomes of a cell is 1.74 m, but the diameter of the nucleus in which the chromosomes are packed is millions of times smaller. Such a compact packing of DNA in chromosomes and chromosomes in the cell nucleus is provided by a variety of histone and non-histone proteins that interact in a specific sequence with DNA (see above). Compaction of DNA in chromosomes makes it possible to reduce its linear dimensions by about 10,000 times - conventionally 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.
- nucleosomal level- chromatin looks in an electron microscope as a chain of "beads" - nucleosomes - "on a string". 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 provided by special proteins - histones. Eight positively charged histone domains form the core (core) of the nucleosome around which the negatively charged DNA molecule is wound. This results in a 7-fold shortening, while the diameter increases from 2 to 11 nm.
- solenoid level
The solenoid level of chromosome organization is characterized by the twisting of the nucleosomal filament and the formation of thicker fibrils 20-35 nm in diameter from it - solenoids or superbids. The pitch of the solenoid is 11 nm; there are about 6-10 nucleosomes per turn. Solenoid packing is considered more likely than superbid, 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 the 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 provides gene expression, i. E. the loop is not only a structural, but also a functional formation. The shortening at this level occurs 20-30 times. The diameter increases to 300 nm. Loop-like structures of the "lamp-brush" type in amphibian oocytes can be seen on cytological preparations. These loops are apparently supercoiled and represent DNA domains, which probably correspond to the units of chromatin transcription and replication. Specific proteins fix the bases of the loops and, possibly, some of their inner regions. The loop-shaped 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 been insufficiently studied. At this level, the formation of loop domains is noted - structures of threads (fibrils) with a thickness of 25-30 nm, which contain 60% protein, 35% DNA and 5% RNA, are practically invisible in all phases of the cell cycle with the exception of mitosis and are somewhat randomly distributed over cell nucleus. Loop-like structures of the "lamp-brush" type in amphibian oocytes can be seen on cytological preparations.
Loop domains attach their bases to the intranuclear protein matrix at the so-called embedded 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, which are characterized by a high content (> 65%) A / T base pairs. Each domain appears to have a single origin of replication and functions as a self-contained supercoiled unit. Any looped domain contains many transcription units, the functioning of which is probably coordinated - the entire domain is either in an active or inactive state.
At the domain level, as a result of the sequential packing of chromatin, the linear dimensions of DNA decrease by about 200 times (700 nm).
- chromosomal level
At the chromosomal level, the condensation of the prophase chromosome into the metaphase one occurs with the compaction of looped 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 tightly packed solenoid loops coiled into a tight spiral. A typical human chromosome can contain up to 2600 loops. The thickness of such a structure reaches 1400 nm (two chromatids), while the DNA molecule is shortened 104 times, i.e. with 5 cm of stretched DNA to 5 μm.
Chromosome functions
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-doubling of genetic material
- transfer of genetic material from the mother cell to the daughter.
There is evidence that when the chromatin region is activated, i.e. during transcription, histone H1 is reversibly removed from it first, and then the histone octet. This causes chromatin decondensation, the sequential transition of a 30-nanometer chromatin fibril into a 10-nanometer filament and its further unfolding into regions of free DNA, i.e. loss of nucleosomal structure.
After the discovery of the principle of molecular organization of such a substance as DNA in 1953, molecular biology began to develop. Further, in the process of research, scientists found out how DNA recombines, its composition and how our human genome works.
The most complex processes take place at the molecular level every day. How is a DNA molecule structured, what does it consist of? And what role do DNA molecules play in the cell? Let's talk in detail about all the processes taking place inside the double chain.
What is hereditary information?
So where did it all start? Back in 1868, they were found in the nuclei of bacteria. And in 1928 N. Koltsov put forward the theory that it is in DNA that all genetic information about a living organism is encrypted. Then J. Watson and F. Crick found a model of the now known DNA helix in 1953, for which they deservedly received recognition and an award - the Nobel Prize.
What is DNA anyway? This substance consists of 2 united filaments, more precisely, spirals. A section of such a chain with certain information is called a gene.
DNA stores all the information about which proteins will be formed and in what order. The DNA macromolecule is a material carrier of incredibly voluminous information, which is recorded by a strict sequence of individual building blocks - nucleotides. There are 4 nucleotides in total, they complement each other chemically and geometrically. This principle of complementarity, or complementarity, in science will be described later. This rule plays a key role in the encoding and decoding of genetic information.
Since the DNA strand is incredibly long, there are no repetitions in this sequence. Every living thing has its own unique DNA strand.
DNA functions
The functions include the storage of hereditary information and its transmission to offspring. Without this function, the genome of the species could not be preserved and developed for millennia. Organisms that have undergone major gene mutations are more likely to not survive or lose the ability to produce offspring. This is how the natural protection from the degeneration of the species occurs.
Another essential function is the implementation of stored information. The cell cannot make a single vital protein without the instructions that are stored in a double chain.
Nucleic acid composition
Now it is already reliably known what the nucleotides themselves - the building blocks of DNA - consist of. They are composed of 3 substances:
- Orthophosphoric acid.
- Nitrous base. Pyrimidine bases - which have only one ring. These include thymine and cytosine. Purine bases, which contain 2 rings. These are guanine and adenine.
- Sucrose. As part of DNA - deoxyribose, In RNA - ribose.
The number of nucleotides is always equal to the number of nitrogenous bases. In special laboratories, a nucleotide is cleaved and a nitrogenous base is isolated from it. This is how the individual properties of these nucleotides and possible mutations in them are studied.
Levels of organization of hereditary information
There are 3 levels of organization: gene, chromosomal and genomic. All the information required for the synthesis of a new protein is contained in a small section of the chain - the gene. That is, the gene is considered the lowest and simplest level of information encoding.
Genes, in turn, are assembled into chromosomes. Thanks to this organization of the carrier of hereditary material, groups of characters alternate according to certain laws and are transmitted from one generation to another. It should be noted that there are incredibly many genes in the body, but information is not lost even when it is recombined many times.
There are several types of genes:
- according to their functional purpose, there are 2 types: structural and regulatory sequences;
- according to the influence on the processes occurring in the cell, they are distinguished: supervital, lethal, conditionally lethal genes, as well as mutator and antimutator genes.
Genes are located along the chromosome in a linear order. In chromosomes, information is not randomly focused, there is a certain order. There is even a map showing the positions, or loci of genes. For example, it is known that chromosome number 18 encodes data on the color of a child's eyes.
What is a genome? This is the name for the entire set of nucleotide sequences in the cell of the body. The genome characterizes the whole species, not an individual.
What is the human genetic code?
The fact is that the entire enormous potential of human development is already laid down in the period of conception. All hereditary information that is necessary for the development of the zygote and the growth of the child after birth is encoded in the genes. Parts of DNA are the most basic carriers of hereditary information.
A person has 46 chromosomes, or 22 somatic pairs, plus one sex-determining chromosome from each parent. This diploid set of chromosomes encodes the entire physical appearance of a person, his mental and physical abilities, and a predisposition to disease. Somatic chromosomes are outwardly indistinguishable, but they carry different information, since one of them is from the father, the other from the mother.
The male code differs from the female code in the last pair of chromosomes - XY. The female diploid set is the last pair, XX. Men get one X chromosome from their biological mother, and then it is passed on to their daughters. The sex Y chromosome is passed on to sons.
Human chromosomes vary considerably in size. For example, the smallest pair of chromosomes is # 17. And the biggest pair is 1 and 3.
The diameter of a double helix in humans is only 2 nm. The DNA is twisted so tightly that it fits into the small nucleus of the cell, although its length will reach 2 meters if it is unwound. The length of the helix is hundreds of millions of nucleotides.
How is the genetic code transmitted?
So, what role do DNA molecules play in the cell during division? Genes - carriers of hereditary information - are found inside every cell of the body. To pass on their code to a daughter organism, many creatures divide their DNA into 2 identical spirals. This is called replication. In the process of replication, DNA is unwound and special "machines" complement each strand. After the genetic spiral is bifurcated, the nucleus and all organelles begin to divide, and then the entire cell.
But a person has a different process of gene transfer - sexual. The signs of the father and mother are intermingled, the new genetic code contains information from both parents.
The storage and transmission of hereditary information is possible due to the complex organization of the DNA helix. After all, as we said, the structure of proteins is encoded in genes. Once created at the time of conception, this code will copy itself throughout its life. The karyotype (personal set of chromosomes) does not change during organ cell renewal. The transfer of information is carried out with the help of sexual gametes - male and female.
Only viruses containing one RNA strand are not capable of transmitting their information to their offspring. Therefore, in order to reproduce, they need human or animal cells.
Realization of hereditary information
Important processes are constantly taking place in the cell nucleus. All information recorded in chromosomes is used to build proteins from amino acids. But the DNA strand never leaves the nucleus, so the help of another important compound = RNA is needed here. It is RNA that is able to penetrate the nuclear membrane and interact with the DNA strand.
Through the interaction of DNA and 3 types of RNA, all encoded information is realized. At what level is the implementation of hereditary information? All interactions take place at the nucleotide level. Messenger RNA copies a section of the DNA strand and brings this copy to the ribosome. This is where the synthesis of a new molecule from nucleotides begins.
In order for the mRNA to copy the required part of the strand, the helix is unfolded, and then, upon completion of the recoding process, is restored again. Moreover, this process can occur simultaneously on 2 sides of 1 chromosome.
The principle of complementarity
They consist of 4 nucleotides - adenine (A), guanine (G), cytosine (C), thymine (T). They are connected by hydrogen bonds according to the complementarity rule. The works of E. Chargaff helped to establish this rule, as the scientist noticed some patterns in the behavior of these substances. E. Chargaff discovered that the molar ratio of adenine to thymine is equal to one. And in the same way, the ratio of guanine to cytosine is always equal to one.
On the basis of his work, genetics have formed a rule for the interaction of nucleotides. The rule of complementarity states that adenine combines only with thymine, and guanine with cytosine. During the decoding of the helix and the synthesis of a new protein in the ribosome, this rotation rule helps to quickly find the required amino acid, which is attached to the transport RNA.
RNA and its types
What is hereditary information? nucleotides in a double strand of DNA. What is RNA? What is her job? RNA, or ribonucleic acid, helps to extract information from DNA, decode it and, based on the principle of complementarity, create proteins necessary for cells.
In total, 3 types of RNA are isolated. Each of them strictly fulfills its function.
- Informational (mRNA), or else it is called matrix. It goes straight into the center of the cell, into the nucleus. Finds in one of the chromosomes the necessary genetic material for the construction of a protein and copies one of the sides of the double chain. Copying occurs again according to the principle of complementarity.
- Transport Is a small molecule with decoders on one side and amino acids on the other side. The task of tRNA is to deliver it to the "workshop", that is, to the ribosome, where it synthesizes the necessary amino acid.
- rRNA - ribosomal. It controls the amount of protein that is produced. Consists of 2 parts - amino acid and peptide site.
The only difference in decoding is that RNA does not have thymine. Instead of thymine, there is uracil. But then, in the process of protein synthesis, with tRNA, it still correctly sets all the amino acids. If there are any failures in decoding information, then a mutation occurs.
Repair of damaged DNA molecule
The process of repairing a damaged double strand is called repair. During the repair process, damaged genes are removed.
Then the required sequence of elements is reproduced exactly and cut back into the same place on the chain from where it was extracted. All this happens thanks to special chemicals - enzymes.
Why do mutations occur?
Why do some genes begin to mutate and stop performing their function - storing vital hereditary information? This is due to a decoding error. For example, if adenine is accidentally replaced with thymine.
There are also chromosomal and genomic mutations. Chromosomal mutations occur when sections of hereditary information are lost, duplicated, or even transferred and integrated into another chromosome.
Genomic mutations are the most serious. Their cause is a change in the number of chromosomes. That is, when, instead of a pair - a diploid set, a triploid set is present in the karyotype.
The most famous example of a triploid mutation is Down's syndrome, in which a personal set of chromosomes is 47. In such children, 3 chromosomes are formed in place of the 21st pair.
A mutation such as polyploidy is also known. But polyploidy is found only in plants.