Nucleotides of prokaryotes: general information
The structure of the genetic apparatus of prokaryotes has long been the subject of heated debate, the essence of which boils down to whether they have the same nucleus as eukaryotes or not. It has been established that the genetic material of prokaryotic organisms, like eukaryotic ones, is represented by DNA, but there are significant differences in its structural organization. In prokaryotes, DNA is a more or less compact formation that occupies a certain area in the cytoplasm and is not separated from it by a membrane, as is the case in eukaryotes.
To emphasize the structural differences in the genetic apparatus of prokaryotic and eukaryotic cells, it is proposed to call it a nucleoid in the former, in contrast to the nucleus in the latter.
Electron microscopic observation shows that the nucleoid of prokaryotes, despite the absence of a nuclear membrane, is quite clearly demarcated from the cytoplasm, usually occupies the central region in it and is filled with DNA strands with a diameter of about 2 nm. It is possible that the organization of the prokaryotic chromosome revealed in an electron microscope is greatly influenced by the conditions of fixation of the drug. According to available observations, in a living cell the nucleoid occupies more space in the cytoplasm.
All the genetic information of prokaryotes is contained in one DNA molecule, which has the shape of a covalently closed ring and is called the bacterial chromosome. (In a prokaryotic cell, DNA can also be located outside the bacterial chromosome - in plasmids, but the latter are not obligatory cellular components).
The length of an unfolded DNA molecule can be more than 1 mm, i.e. almost 1000 times the length bacterial cell. For a long time it was believed that there was no pattern in the distribution of DNA strands on the bacterial chromosome. However, if we assume that the DNA molecule forms a random tangle, it is difficult to explain the replication process and the subsequent distribution of the resulting chromosomes among daughter cells. Special studies have shown that prokaryotic chromosomes are a highly ordered structure with a sedimentation constant of 1300-2000S for the free form and 3200-7000S for the membrane-bound form. In both cases, part of the DNA in this structure is represented by a system of 20-100 independently supercoiled loops. RNA molecules are involved in ensuring the supercoiled organization of chromosomes.
The chromosomes of most prokaryotes have a molecular weight in the range of (1-3) times 10 to the power of 9 Da. In the group of mycoplasmas, the genetic material is represented by molecules that have the smallest amount of DNA for cellular organisms: (0.4-0.8), multiplied by 10 to the power of 9, and the highest DNA content is found in filamentous cyanobacteria (8.5, multiplied by 10 to the power of 9 degree 9). Although each prokaryotic cell contains 1 chromosome, often in an exponentially growing culture the amount of DNA per cell can reach a mass of 3, 4, 8 or more chromosomes. Often in cells, under the influence of certain factors (temperature, pH of the environment, ionizing radiation, salts of heavy metals, some antibiotics, etc.), the formation of many copies of a chromosome occurs. When the influence of these factors is eliminated, as well as after the transition to the stationary phase, as a rule, one copy of the chromosome is found in cells. Consequently, the terms "nucleoid" and "chromosome" are not always the same. Depending on the conditions, the nucleoid of a prokaryotic cell may consist of one or a certain number of copies of a chromosome
Nucleus: a structure containing the nuclear genome and surrounded by a membrane in eukaryotic organisms.
The nucleus is the largest organelle of a eukaryotic cell, usually ranging from 3 to 10 microns in diameter. The nucleus contains DNA molecules, which store information for the vast majority of features of the cell and the organism as a whole. DNA forms complexes with histone proteins containing large amounts of lysine and arginine. Such complexes - chromosomes - are visible under a light microscope during cell division. In a non-dividing cell, chromosomes are not visible - the DNA strands are elongated and very thin.
The contents of the nucleus are separated from the cytoplasm by the nuclear envelope, consisting of two membranes located close to each other. Each membrane is 8 nm thick, the distance between them is ~30 nm. At certain intervals, both membranes merge with each other, forming holes with a diameter of 70 nm - nuclear pores (Fig. 24). The number of pores is not constant; it depends on the size of the nuclei and their functional activity. For example, in large nuclei of germ cells there can be up to 10#6 pores. Through the pores, various substances are exchanged between the nucleus and the cytoplasm. Molecules of mRNA and tRNA, involved in the synthesis of various proteins, emerge from the nucleus. Proteins pass into the nucleus and interact with DNA molecules. In the nucleus, ribosomes are assembled from ribosomal RNAs formed in the nucleus and ribosomal proteins synthesized in the cytoplasm. The site of ribosome assembly under a microscope looks like a round body with a diameter of about 1 micron. It is called the nucleolus. The nucleus may have one or more nucleoli. Nuclear sap, or karyoplasm (Greek karyon - nut, kernel of a nut), in the form of a structureless mass surrounds the chromosomes and nucleoli. The viscosity of karyoplasm is approximately the same as that of hyaloplasm, and the acidity is higher. Nuclear sap contains proteins and various RNAs. Under an electron microscope, a large number of granules are visible - these are transit ribosomes going from the nucleus to the cytoplasm.
Nucleoid nucleoid
1) DNA-containing zone of the cell prokaryote, not delimited membranes(nucleoplasm). Detected by special staining after removal of RNA from cells (see. Feulgen staining); 2) the bacterial “core,” which in prokaryotes is a DNA strand immersed in the cytoplasm, closed in a ring and not associated with histones. The DNA ring is anchored at one point on the inside of the cell membrane. N.'s division occurs after replication of the DNA strand; the divergence of daughter N. is ensured by the growth of the cell membrane. This formation is also called bacterial chromosome. Functionally, the nucleus is similar to the cell nucleus of eukaryotes. see also prokaryotes.
(Source: “Microbiology: a dictionary of terms”, Firsov N.N., M: Drofa, 2006)
Nucleoid(nuclear zone, chromatin body) - 1) prokaryotic nucleus. The nuclear material of N. consists of one closed double-stranded strand of DNA. The length of the thread is about 1 mm, m.m. is about 3x10 9. It is considered as a solitary bacterium. chromosome or genophore. N. also contains RNA polymerase and basic proteins (but not histones). Bacter. the chromosome is bead-shaped and similar to the DNA chromatin of eukaryotic cells. One end of it is often connected to the mesosome. N. does not have a mitotic apparatus or a nuclear membrane. It can be isolated by mild cell lysis and subsequent centrifugation of the lysate. Bacter. the chromosome is replicated in a semi-conservative way: the complementary DNA strands are separated, and then a complementary strand is assembled on each of them, as on a matrix; 2) genetic apparatus of viruses. Represented by one whole or fragmented molecule of single-stranded or double-stranded RNA or DNA. Some viruses have 2 identical genomes. The NA is often covalently linked to the middle protein. The structure and principle of operation of N. viruses are close to N. bacteria and the nucleus of eukaryotes. In virology it is often replaced by the term “genome”, which is inaccurate in relation to polyploid viruses. (Cm. Genetics of viruses).
(Source: Dictionary of Microbiology Terms)
Synonyms:
See what “nucleoid” is in other dictionaries:
In a prokaryotic cell, Nucleoid (means similar to nucleus, also known as nuclear region) an irregularly shaped compartment within prokaryotic cells, which contains the genetic material. The DNA of the nucleoid is closed... Wikipedia
- (from Latin nucleus nucleus and Greek eidos species), DNA-containing zone of a prokaryotic cell. Usually located in the center of the cell, not delimited by membranes. N. corresponds to one complex circular DNA molecule, not connected to histones and anchored in... ... Biological encyclopedic dictionary
Noun, number of synonyms: 1 ribonucleoprotein (1) ASIS Dictionary of Synonyms. V.N. Trishin. 2013… Synonym dictionary
nucleoid- Circular DNA molecule of prokaryotic cells and autonomous organelles of eukaryotes Biotechnology topics EN nucleoid ... Technical Translator's Guide
Nucleoid, prokaryon nucleoid. An analogue of the nucleus in bacteria, devoid of a DNA membrane and containing a section of a prokaryotic cell (some prokaryotes may have more than one N. per cell), N. division occurs after DNA replication with the participation of the cell... ... Molecular biology and genetics. Dictionary.
- (nucleoidum; nucleo + Greek eidos species; synonym bacterial nucleus) accumulation of nuclear matter. bacterial cell... Big medical dictionary
The first information about the nucleus of bacteria as a completely organized structure was obtained in 1897 thanks to the work of M. Meyer. However, the small size of the bacterial cell and the high content of RNA, which is stained with nuclear dyes in the same way as DNA, made it difficult to clearly identify nuclear structures. Therefore, the question regarding the presence of a nucleus in bacteria, its morphological
structure and physiological functions have been solved for many decades. There was no doubt about the presence of a hereditary apparatus in bacteria. This was confirmed by the fact that cells of one type of bacteria, when multiplied, produce offspring with similar properties, i.e., they produce a culture of the original species. The question of the nucleus in bacteria and its structure received a final solution only with the development of electron microscopy and genetic research. It has now been established that bacteria have structures consisting of DNA that are functionally identical to the cell nuclei of higher organisms. By analogy, they are called bacterial nuclei or nucleoids.
Chemical nature and the organization of bacterial nuclear material were established by the Australian scientist J. Cairns in 1963 using the autoradiographic method. He contributed to nutrient medium tritium-labeled H3-thymidine (the precursor of thymine) and E. coli was grown on this medium. DNA was then extracted from the bacterial cells and placed on photographic film. After appropriate exposure, a radioautograph was obtained on the film. Autoradiography (the result of labeled thymine) confirmed that the substance under study was deoxyribonucleic acid, since DNA is the only substance in the cell that contains thymine.
The autoradiograph (Fig. 3.18) shows that the DNA of E. coli has a filamentous, ring-like structure that replicates as a single unit. Kerns recorded the successive stages of circular DNA replication, showing that both are complementary
These DNA strands are duplicated at the replication point simultaneously.
The length of the E. coli DNA molecule is 1-1.4 mm. In terms of its genetic functions, it is identical to a chromosome.
Thus, the nucleoid of prokaryotes is a circular chromosome, which is a giant DNA molecule with a molecular weight of 1.4-3 x 109 Da. Despite its relatively large sizes The bacterial chromosome is a highly ordered compact structure. Compactness is ensured by the formation of many (20-100) super-twisted loops, which are located in various areas chromosomes. The bacterial chromosome interacts in the cell with polyamine proteins (spermine and spermidine), which perform a function similar to the histones of prokaryotes - they neutralize the negative charges of DNA caused by its chemical structure, namely, the presence of ionized hydroxyl groups in phosphate residues. The bacterial nucleoid differs from the nucleus of eukaryotic cells in the absence of a nuclear membrane, a nucleolus, and a mitotic mode of division. It is in direct contact with the cytoplasm of the cell.
DNA replication. One of the functions of bacterial DNA is replication (self-duplication), or reproduction of a similar structure. Double-stranded circular DNA is characterized by bidirectional replication. In general terms, this process can be represented as follows. There are fixed points on the DNA (chromosome) - loci that determine the beginning and end of replication. These points are designated by the letters “O” (from origin - beginning) and “T” (termination - ending), respectively. Replication always precedes cell division. The chromosome is attached to the cytoplasmic membrane in one or more areas. Initiation of replication occurs at the point “U” and is expressed in the appearance of replication forks. The DNA strands gradually unwind and each of them serves as a template for the formation of a second complementary strand. Replication forks move in opposite directions: one moves clockwise, the other counterclockwise. As they progress, complementary DNA strands are synthesized. Both forks meet at the replication termination point ("T"),
which is located diametrically opposite to point “O” - the beginning of replication. Replication ends with the formation of two identical DNA molecules, or two genetically equivalent chromosomes, carrying the same genetic information, identical to the maternal chromosome (Fig. 3.19). This
provided thanks to a semi-conservative mechanism
replication, in which each of the resulting DNA molecules contains one parent strand and one newly synthesized strand. 
Rice. 3.19. Scheme of bidirectional DNA replication: a - parent molecule; b - intermediate replicative forms; c - daughter molecules; O - point of origin of replication; T - end point of replication
DNA replication is a complex process. Many different proteins take part in it, including enzymes. They provide recognition of the origin of replication, unwinding of the double strand - duplex, stabilization of single strands, formation of the RNA seed strand (primer) to initiate DNA polymerase activity, assembly of intact strands, recognition of the termination site, supercoiling of two new DNA duplexes and formation of the native conformation.
DNA polymerase plays a leading role in DNA replication. It links nucleotides together to form a polynucleotide chain. Moreover, it binds only in the direction from 5" to the 3" end. But
how DNA consists of chains of opposite polarity (5" gt; U
and 3" gt; 5"), then the synthesis of one chain (5" > 3") can occur
continuously in the direction of the advancing replication
forks, and the synthesis of the second, opposite chain (3" gt; 5") should
go to reverse direction. But DNA polymerase is unable to initiate the synthesis of a new DNA strand. To do this, it requires the presence of a “seed” - a polynucleotide chain with a free 3-OH end. Therefore, DNA synthesis begins with the formation of a short piece of RNA (10-60 base pairs), which serves as a “seed” or primer. This process is ensured by the DNA primase enzyme, which caches part of the DNA template strand. DNA polymerase then attaches free nucleotides to the 3-OH end of the primer, forming short stretches of DNA, so-called Okazaki fragments, 1000-2000 nucleotides long. Upon completion of the formation of all fragments, the primer is removed by exonuclease, and the gaps between the fragments are filled by DNA polymerase in accordance with the DNA template sections. Okazaki fragments are cross-linked by ligase, that is, they are sequentially connected by phosphodiester bonds. As a result, two identical double-stranded DNA molecules are formed (Fig. 3.20).
Other replication mechanisms are also known. Thus, the duplication of circular DNA of many viruses, some phages and plasmids is carried out by the rolling ring mechanism. DNA replication in bacteria during conjugation also occurs in a similar way. This is a unidirectional process that works as follows. A break is formed in one of the DNA strands and the synthesis of a new strand begins from the 3" end of this broken parent strand using the second one as a template. This leads to the displacement of the 5" end of the broken strand, which subsequently serves as a template for the synthesis of a new complementary strand.
DNA replication is closely related to cell division. The divergence of the resulting chromosomes occurs as a result of the growth of the cell membrane between the points of chromosome attachment.
The bacterial nucleoid, like the nucleus of plant and animal cells, is a carrier of hereditary information, regulates the direction of protein synthesis, protein specificity, and, in addition, ensures the functioning of all intracellular processes. 
Rice. 3.20. Mechanism of double-stranded DNA replication:
I - replication fork; II - semi-conservative nature of replication; A - old chain; a - newly synthesized chain, b - RNA primer, c - unwinding proteins, d - DNA polymerase, e - Okazaki fragments
Nucleoid is the nuclear apparatus of bacteria. Represented by a DNA molecule corresponding to one chromosome. It is circularly closed, located in a nuclear vacuole, and does not have a membrane limiting it from the cytoplasm and does not have a mitotic apparatus.
A small amount of RNA and RNA polymerase are associated with DNA. DNA is folded around a central core made of RNA and is a highly ordered compact structure. The chromosomes of most prokaryotes have a molecular weight in the range of 1-3x10 9, a sedimentation constant of 1300-2000 S. A DNA molecule includes 1.6x10 7 nucleotide pairs. The differences in the genetic apparatus of prokaryotic and eukaryotic cells are determined by its name: the former have a nucleoid (a structure similar to a nucleus), in contrast to the nucleus in the latter.
The nucleoid of bacteria contains the basic hereditary information, which is realized in the synthesis of specific protein molecules. Systems of replication, repair, transcription and translation are associated with the DNA of a bacterial cell.
The nucleoid in a prokaryotic cell can be identified in stained preparations using a light or phase contrast microscope. To stain nuclear matter, Feulgen dye is used, which specifically stains DNA.
Feulgen DNA staining method
A smear from a bacterial culture is fixed with methyl alcohol for 2-3 minutes and placed in cold 1% HCl for 1 minute.
Subject to hydrolysis at 60 0 C in 1% HCl for 5-10 minutes and rinse with distilled water.
Place the smear in Schiff's reagent for 40-60 minutes, rinse in tap water for 2 minutes.
As a result of the interaction of free aldehyde groups with colorless fuchsinous acid, a violet color characteristic of basic fuchsin appears.
In many bacteria, extrachromosomal genetic elements - plasmids - are found in the cytoplasm. They are double-stranded DNA closed in rings, consisting of 1500-40,000 nucleotide pairs and containing up to 100 genes.
Plasmids can exist in a cell and in an integrated state with the bacterial chromosome, while retaining the ability to transition to autonomy.
12Structure of peptidoglycan in gram-positive and gram-negative bacteria. Its biological properties and significance for bacterial cells.
Cell wall
The cell wall is the outer structure of bacteria, 30-35 nm thick, the main component of which is peptidoglycan (murein). Peptidoglycan is a structural polymer consisting of alternating subunits of α-acetylglucosamine and α-acetylmuramic acid connected by glycosidic bonds (Fig. 2).
Parallel polysaccharide (glycan) chains are connected to each other by cross peptide bridges (Fig. 3).
The polysaccharide framework is easily destroyed by lysozyme, an antibiotic of animal origin. Peptide bonds are targets for penicillin, which inhibits their synthesis and prevents cell wall formation. The quantitative content of peptidoglycan affects the ability of bacteria to Gram stain. Bacteria with a significant thickness of the murein layer (90-95%) are persistently stained blue-violet with gentian violet and are called gram-positive bacteria. Gram-negative bacteria with a thin layer of peptidoglycan (5-10%) in the cell wall lose their gentian violet color after exposure to alcohol and are additionally stained magenta pink. The cell walls of gram-positive and gram-negative prokaryotes differ sharply in both chemical composition (Table 1) and ultrastructure (Fig. 4).
In addition to peptidoglycan, the cell wall of gram-positive bacteria contains teichoic acids (TA), and in smaller quantities lipids, polysaccharides, and proteins.
CYTOPLASMIC MEMBRANE (CPM)
The CPM is 7-10 nm thick, surrounds the cytoplasm of the bacterial cell and consists of a double layer of phospholipids, neutral lipids, glycolipids, etc., the function of which is to maintain the mechanical stability of the CPM and give it hydrophobic properties.
Membrane proteins (integral and peripheral ) are asymmetrically included in the phospholipid bilayer; they are divided into structural and functional (enzymes).
CPM functions:
1) an internal osmotic barrier that regulates selective entry into the cell and release out various substances,
2) transport function;
3) biosynthetic activity;
4) energy and respiratory functions;
5) attachment of chromosome and plasmids.
During invagination of the CPM, intracellular membrane formations - mesosomes:
– lamellar (lamellar),
– tubular (tubular),
– vesicular,
– mixed.
By location in the mesosome cell:
1) peripheral,
2) nuclear (nucleoidosomes),
3) emerging.
INTRACELLULAR STRUCTURES OF BACTERIA
Ribosomes(70 S consists of RNA (60-65%) and protein (35-40%) and is the site of protein synthesis.
Chromatophores in photosynthetic bacteria in the form of tubes, vesicles, double membrane plates - thylakoids.
Chlorosomes – oblong-shaped structures containing bacteriochlorophylls.
Phycobilisomes- hemispherical or rod-shaped granules located on photosynthetic membranes contain water-soluble pigments - phycobiliproteins.
Carboxysomes(or polyhedral bodies) - tetrahedral or hexagonal inclusions contain the enzyme ribulose diphosphate carboxylase.
Gas vacuoles (or aerosomes) consist of gas bubbles and are regulators of the buoyancy of aquatic bacteria.
Magnetosomes ubacteria with magnetotaxis.
INTRACYTOPLASMIC INCLUSIONS OF BACTERIA
Cytoplasm – environment that connects intracellular structures in unified system. Cytosol– semi-liquid colloidal mass of water (70-80%), RNA, enzymes.
Spare substances are formed in the cell as a result of metabolism. Based on their consistency, they are divided into liquid (poly-β-hydroxybutyrate), semi-liquid (sulfur) and solid (glycogen):
1. Nitrogen-free organic reserve substances
2. Granulosa
3. Glycogen
4. Hydrocarbon granules
5. Poly-β-hydroxybutyric acid (poly-β-hydroxybutyrate) is found only in prokaryotes
6. Polyphosphates (volutin, or metachromatic granules)
7. Sulfur inclusions
8. Calcium carbonate inclusions
9. Parasporal inclusions
GENETIC APPARATUS OF BACTERIA
Nucleoid
Features of the genetic apparatus of prokaryotes:
1) the nuclei of bacteria do not have a nuclear membrane and the DNA is in contact with the cytoplasm;
2) there is no division into chromosomes and the DNA strand is called a bacterial chromosome;
3) there is no mitosis and meiosis.
The nuclear apparatus of bacteria is called bacterial nucleus, or nucleoid.
A bacterial chromosome in the form of a closed ring is a giant supercoiled DNA molecule not associated with histones. DNA replication occurs semi-conservatively.
In the cytoplasm - linear or circular molecules of extrachromosomal DNA – plasmids (extrachromosomal determinants), open – relaxed, closed – superspiral.
Basic properties of bacterial plasmids:
– ability for autonomous replication. Plasmids with strict replication control And weakened,
– conjugativeness (transmissibility) – the ability to self-transmit,
– integrability,
– incompatibility,
– superficial exclusion,
– infectiousness,
– phenotypic characteristics that they impart to bacteria: resistance to antibiotics, cations, anions, mutagens, bacteriocins. Cells with plasmids are capable of causing biodegradation of substances, synthesizing bacteriocins, hemolysin, fibrinolysin, toxins, antigens, antibiotics, insecticides, pigments, surface antigens; acquire the ability to conjugate; induce tumors in plants; carry out restriction and modification of DNA.
Plasmids can combine with each other or with phage DNA, forming cointegrates. One cell can contain several types of plasmids. If plasmids cannot coexist in the same cell, they are called incompatible.
By location:
1) autonomous,
2) integrated ones reproduce simultaneously with the bacterial chromosome – episomes.
Plasmids:
1) transmissible (F- and R-plasmids), transmitted during conjugation;
2) non-transmissible.
Functions plasmid:
1. Regulatory ones compensate for metabolic defects by integrating into the damaged genome.
2. Coding ones introduce new genetic information into the cell.
Types of plasmids:
1. F-plasmids control the synthesis of F-pili during conjugation.
2. R-plasmids are a factor of multidrug resistance.
3. Non-conjugative plasmids.
4. Plasmids of bacteriocinogeny - the ability of bacteria to produce specific substances ( colicins or bacteriocins), causing death bacteria of phylogenetically related species.
5. Pathogenicity plasmids control virulence properties.
6. Hidden (cryptic) plasmids.
7. Biodegradation plasmids.
Bacterial plasmids are objects for studying DNA replication and transcription; they are used in genetic engineering and microbial selection.
Migrating genetic elements are individual sections of DNA that carry out their own transfer (transposition) within the genome. Their types:
1. Insertion sequences (IS elements).
2. Transposons (Tn elements).
3. Moderate or defective bacteriophages.
