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?????A hook departs from the basal body, passing into a filament, which ends with a "cap". The filament is a rigid cylinder formed by the flagellin protein. In the cell membrane there are rings M and S, which are often considered as a single whole. The MS ring is surrounded by several motor proteins that transmit torque to the filament. Gram-negative bacteria, in addition to the M and S rings, have two more rings: P, which lies in the peptidoglycan layer, and L, which is located in the outer membrane. A rigid rod passes through all the rings, transmitting the torque to the filament. The movement of the cell occurs due to the rotation of the flagellum clockwise or counterclockwise. In monotrichs, the cell slowly rotates in the direction opposite to the rotation of the flagellum. If the flagellum rotates clockwise, then the cell moves forward with the flagellum, and if against, then the cell is pushed forward with the flagellum (that is, it moves backward with the flagellum). Some bacteria that have a single flagellum rotate it only clockwise, and in order to change the direction of movement, they need to stop and reorient themselves. In peritrichs, the flagella rotate counterclockwise, and if you need to change the direction of movement, the cell stops and makes a somersault. ????? 30. Pili (also known as fimbriae or villi) are filamentous protein structures located on the cell surface of many bacteria. The size of the pili varies from fractions of microns to more than 20 microns in length and 2-11 nm in diameter. Pili are involved in the transfer of genetic material between bacterial cells (conjugation), the attachment of bacteria to the substrate and other cells, are responsible for the adaptation of organisms, serve as attachment sites for many bacteriophages. Structurally, the saws can be from thin filamentous formations to thick rod-shaped structures with axial holes. Peels consist of one or more types of spirally stacked protein molecules, which are called pilin. ????? 32. How does the replication machinery know where to start? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. E. coli has a single origin of replication on its one chromosome, as do most prokaryotes. The origin of replication is approximately 245 base pairs long and is rich in AT sequences. This sequence of base pairs is recognized by certain proteins that bind to this site. An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process because it requires energy. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks are formed at the origin of replication and these get extended bi-directionally as replication proceeds. ????? 33. Two replication forks are formed at the origin of replication and these get extended bi-directionally as replication proceeds. Single-strand binding proteins (Figure 2) coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. The next important enzyme is DNA polymerase III, also known as DNA pol III, which adds nucleotides one by one to the growing DNA chain (Figure 2). The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them. ATP structurally is an adenine nucleotide which has three phosphate groups attached; breaking off the third phosphate releases energy. In addition to ATP, there are also TTP, CTP, and GTP. Each of these is made up of the corresponding nucleotide with three phosphates attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the existing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. DNA pol III is the enzyme required for DNA synthesis; DNA pol I is used later in the process and DNA pol II is used primarily required for repair (this is another irritating example of naming that was done based on the order of discovery rather than an order that makes sense). DNA polymerase is able to add nucleotides only in the 5? to 3? direction (a new DNA strand can be only extended in this direction). It requires a free 3?-OH group (located on the sugar) to which it can add the next nucleotide by forming a phosphodiester bond between the 3?-OH end and the 5? phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3?-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3?-OH end. Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. RNA primase does not require a free 3?-OH group. Because this sequence primes the DNA synthesis, it is appropriately called the primer. DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand. The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5? to 3? direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5? to 3? direction and the other is oriented in the 3? to 5? direction. One strand, which is complementary to the 3? to 5? parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. The other strand, complementary to the 5? to 3? parental DNA, is extended away from the replication fork, in small fragments known as Okazaki fragments, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the lagging strand. The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3? to 5?, and that of the leading strand 5? to 3?. A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA pol I, which breaks down the RNA and fills the gaps with DNA nucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA ligase that catalyzes the formation of phosphodiester linkage between the 3?-OH end of one nucleotide and the 5? phosphate end of the other fragment. ????? 34. ????? I think this process is almost impossible to visualize from reading text. I strongly recommend that you watch a couple of animations / videos like the one available here. ????? 35. DNA unwinds at the origin of replication. Helicase opens up the DNA-forming replication forks; these are extended in both directions. Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling (over-winding). Primase synthesizes RNA primers complementary to the DNA strand. DNA polymerase III starts adding nucleotides to the 3?-OH (sugar) end of the primer. Elongation of both the lagging and the leading strand continues. RNA primers are removed and gaps are filled with DNA by DNA pol I.
The gaps between the DNA fragments are sealed by DNA ligase. ????? 36. Unlike multicellular organisms, in unicellular organisms, including bacteria, cell size increase and reproduction by cell division are closely related. Bacterial cells reach a certain size and then divide by binary division. Under optimal conditions, the bacteria grow and divide very quickly, an example of the marine Pseudomonas aeruginosa is described, the population of which can double every 9.8 minutes. In binary division, two daughter cells are formed, identical to the mother. Some bacteria are capable of budding when the daughter cell forms growths on the mother cell, which subsequently separates and goes on to independent life. In the laboratory, bacteria are grown on solid or liquid media. Solid media, such as agar, are used to isolate pure cultures of bacterial strains. Liquid media are used when it is necessary to measure the growth rate or to obtain a large number of cells. When growing bacteria in a liquid medium with mixing, homogeneous cell cultures are obtained, but it is difficult to notice contamination by other bacteria. To identify individual bacteria, selective media containing antibiotics, specific nutrients, or, conversely, devoid of any compounds are used. Most laboratory methods of growing bacteria require large amounts of nutrients to ensure that large volumes of cells are produced quickly. However, in natural conditions, nutrients are limited, and bacteria cannot multiply indefinitely. Due to the limited amount of nutrients, various growth strategies have evolved. Some species grow extremely fast when nutrients are available, for example, cyanobacteria often cause blooming of organic-rich reservoirs. Other organisms are adapted to harsh environmental conditions, for example, bacteria of the genus Streptomyces secrete antibiotics that inhibit the growth of competing bacteria. In nature, many bacterial species live in communities (for example, in the form of biofilms), which provide each cell with the necessary nutrition and protect it from adverse conditions. Some organisms and groups of organisms grow only as part of communities and cannot be isolated into a pure culture. ????? 37. Biofilm -- a set (conglomerate) of microorganisms located on a surface, the cells of which are attached to each other. Usually, the cells are immersed in the extracellular polymer substance (extracellular matrix) secreted by them -- mucus. Biofilm development, and sometimes the biofilm itself, is also called biofouling. The term "biofilm" is defined in different ways, but in general, we can say that a biofilm is a community (colony) of microorganisms located on the interface of media and immersed in an extracellular polymer matrix with a spatial and metabolic structure.There is no single "natural" (phylogenetic) classification of them, reflecting the kinship relationships between individual groups of bacteria, the evolutionary development of individual species. Bacterial classification systems are essentially artificial, and bacteria are grouped into specific groups based on their similarity in a complex of morphological, physiological, and biochemical features (in particular, in the composition of DNA). As of 2020, about 7,000 species of the bacterium and about 600 species of archaea have been described. It is known that most bacteria and archaea (more than 99%) do not grow on laboratory culture media and, therefore, cannot be studied. Pace and several other scientists proposed extracting, cloning, sequencing, and comparing ribosomal RNAs directly from the environment, which allowed for accurate counting and identification of microorganisms without the need for isolation and cultivation. This is especially important for the completely accurate identification of pathogens of infectious diseases and food poisoning. ????? 5
Systematics (taxonomy) of organisms consists in the distribution (classification) of them into certain groups, each of which has a name: class, order, family, genus, species. The species is the main taxonomic unit. In microbiology, the term "strain" is often used.Large and medium-sized straight or slightly curved rods, capable of forming endospores resistant to adverse effects (extreme temperatures, drying, ionizing radiation, chemical agents), most species are mobile and have flagella arranged peritrichially, Bacillus anthracis forms capsules.Those that remain attached can be classified based on cellular arrangement:
Diplococci are pairs of cocci
Streptococci are chains of cocci
Staphylococci are irregular (grape-like) clusters of cocci
Tetrads are clusters of four cocci arranged within the same plane
Sarcina is a genus of bacteria that are found in cuboidal arrangements of eight cocci

?????The giant ring DNA of prokaryotes, the nucleode (a), using RNA and proteins, is repeatedly folded to form numerous spiral loops protruding from the dense central region (b), resulting in a significant nucleoid compaction.The cell membrane maintains the osmotic balance of the cell, carries out various types of transport, including the secretion of proteins, is involved in the formation of the cell wall and the biosynthesis of extracellular polymers, and also receives regulatory signals from the external environment.The cytoplasm occupies the main volume of the bacterial cell and consists of soluble proteins, ribonucleic acids, inclusions and numerous small granules-ribosomes responsible for the synthesis (translation) of proteins.Spiral bacteria, bacteria spiral (helical) shape, form the third major morphological category prokaryotes along with the rod-shaped bacilli and round cocci.[1][2] Spiral bacteria can be subclassified by the number of twists per cell, cell thickness, cell flexibility, and motility.Termination The newly formed protein, which consists of protranslated amino acids, is disconnected.Maturation-II.Elongation.?????????????????8.?????9.?????10.?????11.?????12.13.?????14.?????15.?????16.?????17.?????18.?????19.?????20.?????21.?????22.?????23.?????24.?????25.26.?????27.?????28.?????29.?????38.


النص الأصلي

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Currently, most microbiologists adhere to the division of cellular organisms into three domains –- Bacteria, Archaea, Eucarya. He first proposed the concept of archaebacteria, then called archaea by him. The main difference between this scheme and the previous and subsequent systems is that the organisms of all three lines of evolution appeared from a common ancestor simultaneously or almost simultaneously. This system is built as a result of molecular biological research. Bacteria and archaea are prokaryotes, all the others are eukaryotes (eukaryotes).
The taxonomy of bacteria is a complex problem. There is no single "natural" (phylogenetic) classification of them, reflecting the kinship relationships between individual groups of bacteria, the evolutionary development of individual species.
Bacterial classification systems are essentially artificial, and bacteria are grouped into specific groups based on their similarity in a complex of morphological, physiological, and biochemical features (in particular, in the composition of DNA).
As of 2020, about 7,000 species of the bacterium and about 600 species of archaea have been described. It is known that most bacteria and archaea (more than 99%) do not grow on laboratory culture media and, therefore, cannot be studied. Pace and several other scientists proposed extracting, cloning, sequencing, and comparing ribosomal RNAs directly from the environment, which allowed for accurate counting and identification of microorganisms without the need for isolation and cultivation. This is especially important for the completely accurate identification of pathogens of infectious diseases and food poisoning.


Слайд 5
Systematics (taxonomy) of organisms consists in the distribution (classification) of them into certain groups, each of which has a name: class, order, family, genus, species. The species is the main taxonomic unit.
In microbiology, the term "strain“ is often used. This is a narrower concept than a view. Strains are pure cultures of microorganisms of the same species, isolated from different media (substrates).


Слайд 6 - 7. Таблица
Слайд 8.
Bacteria are the domain of prokaryotic microorganisms.
Bacteria are one of the first forms of life on Earth and are found in almost all terrestrial habitats. They inhabit the soil, fresh and marine reservoirs, acidic hot springs, radioactive waste and deep layers of the earth's crust. Bacteria are often symbionts and parasites of plants and animals. Most of the bacteria have not yet been described, and only half of the bacterial types can be grown in the laboratory.
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The ancestors of modern bacteria were single-celled microorganisms that became one of the first forms of life on Earth, appearing about 4 billion years ago. For almost three billion years, all life on Earth was microscopic. Although fossils (for example, stromatolites) are known for bacteria, their morphology is very uniform, which makes it impossible to identify individual species. However, gene sequences can be used to reconstruct the phylogeny of bacteria, and it was with their help that it was shown that bacteria separated earlier than archaea and eukaryotes. The closest common ancestor of bacteria and archaea was most likely a hyperthermophile that lived 3-2. 5 billion years ago.


Слайд 10.
Cocci – A bacterium that is spherical or ovoid is called a coccus (Plural, cocci). e.g. Streptococcus, Staphylococcus.
Bacilli – A bacterium with cylindrical shape called rod or a bacillus (Plural, bacilli).
Spiral bacteria – Some rods twist into spiral shapes and are called spirilla (singular, spirillum).
Vibrio – comma-shaped
The archaeon Haloquadratum has flat square-shaped cells.


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Depending on their shape, bacteria are classified into: spherical (cocci), rod (bacilli), spiral (spirilla), comma (vibrios).


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A coccus (plural cocci) is any bacterium or archaeon that has a spherical, ovoid, or generally round shape. Coccus refers to the shape of the bacteria, and can contain multiple genera, such as staphylococci or streptococci. Cocci can grow in pairs, chains, or clusters, depending on their orientation and attachment during cell division. Contrast to many bacilli-shaped bacteria, most cocci bacteria do not have flagella and are non-motile.
Cocci may occur as single cells or remain attached following cell division. Those that remain attached can be classified based on cellular arrangement:
Diplococci are pairs of cocci
Streptococci are chains of cocci
Staphylococci are irregular (grape-like) clusters of cocci
Tetrads are clusters of four cocci arranged within the same plane
Sarcina is a genus of bacteria that are found in cuboidal arrangements of eight cocci


Слайд 13.
Bacillus (Latin: Bacillus) — extensive (about 217 species) a genus of rod-shaped bacteria that form intracellular spores. Most bacilli are soil reducers. Some bacilli cause diseases of animals and humans, such as anthrax, toxicoinfections (Bacillus cereus).
Large and medium-sized straight or slightly curved rods, capable of forming endospores resistant to adverse effects (extreme temperatures, drying, ionizing radiation, chemical agents), most species are mobile and have flagella arranged peritrichially, Bacillus anthracis forms capsules.


Слайд 14.
Spiral bacteria, bacteria spiral (helical) shape, form the third major morphological category prokaryotes along with the rod-shaped bacilli and round cocci.[1][2] Spiral bacteria can be subclassified by the number of twists per cell, cell thickness, cell flexibility, and motility. The two types of spiral cells are spirillum and spirochete, with spirillum being rigid with external flagella, and spirochetes being flexible with internal flagella.


Слайд 15.
Vibrio-genus Gram-negative bacteria, possessing a curved-rod (comma) shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in salt water, Vibrio species are facultative anaerobes that test positive for oxidase and do not form spores.. All members of the genus are motile. They are able to have polar or lateral flagellum with or without sheaths. Vibrio species typically possess two chromosomes, which is unusual for bacteria. Each chromosome has a distinct and independent origin of replication, and are conserved together over time in the genus. Recent phylogenies have been constructed based on a suite of genes (multilocus sequence analysis).


Слайд 16.
As a rule, the size of the bacterial cells is in the range from 0.2 to 10 microns. There are, however, bacteria that are visible to the naked eye.
Bacteria whose cells are less than 0.5 microns in diameter are called nanobacteria, or ultramicrobacteria, and they are even able to pass through membrane filters. Many ultramicrobacteria are parasitic, including Mycoplasma, chlamydia, and rickettsia.


Слайд 17.
Depending on the type of structure of the cell wall, the bacteria are divided into gram-positive and gram-negative (the names of the groups were given due to their different staining by the Gram method). Most bacterial cells are surrounded by a rigid cell wall made up of the polymer peptidoglycan, also known as murein. Peptidoglycan consists of polysaccharide chains held together by short peptide cross-links.
Gram-positive bacteria have a peptidoglycan shell (from 20 to 50 nm) with a thickness of up to 40 molecular layers on top of the membrane. Their positive Gram staining is due to the fact that their thick peptidoglycan cell wall strongly binds the crystal violet dye complex to iodine, which is not washed out. Therefore, on the preparations, Gram-positive bacteria look purple.


Слайд 18.
In gram-negative bacteria, a layer of peptidoglycan also lies on top of the cell membrane, but it is significantly (almost 40 times thinner) than in Gram-positive bacteria, and is covered from above by a second membrane. The cell and outer membranes differ in their chemical composition. The space between the cell and outer membranes is called the periplasmic space (periplasm).


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The cell wall of bacteria is often covered with mucus. The mucosal layer can be thin, barely discernible, but it can also be significant, it can form a micro-and macro-capsule. The size of the capsule is often much larger than the bacterial cell. The slime of the cell walls is sometimes so strong that the capsules of individual cells merge into the mucous masses (zooglia), which are interspersed with bacterial cells. The mucous substances formed by some bacteria are not retained as a compact mass around the cell wall, but diffuse into the environment. When rapidly multiplying in liquid substrates, mucus-forming bacteria can turn them into a solid mucus mass.
The capsule has useful properties. It protects the cell from mechanical damage and drying, creates an additional osmotic barrier, serves as an obstacle to the penetration of phages, antibodies, and sometimes is a source of spare nutrients. Mucus protects cells from adverse conditions – many bacteria in such conditions increase mucus formation.


Слайд 20.
Like any living cell, the bacterial cell is surrounded by a membrane, which is a lipid bilayer (also called the cytoplasmic membrane). The cell membrane maintains the osmotic balance of the cell, carries out various types of transport, including the secretion of proteins, is involved in the formation of the cell wall and the biosynthesis of extracellular polymers, and also receives regulatory signals from the external environment. In many cases, the cell membrane can participate in the synthesis of ATP due to the transmembrane electrochemical gradient (proton-motive force). The bacterial cell membrane is involved in the replication and separation of daughter bacterial chromosomes during cell division, as well as in the transmission of DNA by transduction or conjugation.
In addition to lipids, bacterial membranes contain various proteins. The chemical composition of bacterial cell membranes is much more diverse than that of eukaryotic cells. Unlike eukaryotes, which change the properties of the lipid base of the membrane by changing the ratio between phospholipids and cholesterol, bacteria change the properties of the membrane by varying the fatty acids that make up the lipids. Steroids are found in bacterial membranes extremely rarely, and instead of steroids, the membranes contain hopanoids, which are pentacyclic hydrocarbons. Hopanoids are actively involved in the regulation of the physical properties of bacterial cell membranes.
With excessive growth (compared to the growth of the cell wall), the cytoplasmic membrane forms invaginates — vypyachivaniya in the form of complex twisted membrane structures, called mesosomes. The less complex structures are called intracytoplasmic membranes. The role of mesosomes and intracytoplasmic membranes is not fully understood. It is even assumed that they are an artifact that occurs after the preparation (fixation) of the preparation for electron microscopy. Nevertheless, it is believed that the derivatives of the cytoplasmic membrane participate in cell division, providing energy for the synthesis of the cell wall, participate in the secretion of substances, spore formation, i.e. in processes with a high energy consumption. The cytoplasm occupies the main volume of the bacterial cell and consists of soluble proteins, ribonucleic acids, inclusions and numerous small granules-ribosomes responsible for the synthesis (translation) of proteins.


Слайд 21.
Bacterial ribosomes have a size of about 20 nm and a sedimentation coefficient of 70S, in contrast to the 80S ribosomes characteristic of eukaryotic cells. Therefore, some antibiotics, binding to the ribosomes of bacteria, inhibit the synthesis of bacterial protein a, without affecting the protein synthesis of eukaryotic cells.


Слайд 22.
The process of protein synthesis has the following cycle:
initiation;
elongation;
termination.
Initiation begins with the fact that a matrix RNA is attached to a small subunit of the ribosome. If the ribosomal macromolecule recognizes the three-letter oh code that is on the mRNA, then the anti-codon of the tRNA is attached.
Elongation. The addition of amino acids brought by tRNA and the promotion of the ribosome along the matrix with the release of the tRNA molecule. The movement along the mRNA is carried out until it reaches the stop codon, which is present in all matrices.
Termination The newly formed protein, which consists of protranslated amino acids, is disconnected. In some cases, the completion of the translation of the newly formed protein is accompanied by the disintegration (dissociation) of the ribosome.
Most free-living bacteria are able to synthesize all the amino acids they need. Theoretically, all 20 essential amino acids can be found in the environment and be available for disposal. In addition, bacteria are able to obtain amino acids from protein molecules by splitting them with bacterial proteases and peptidases. The resulting oligopeptides and amino acids are transported to the cell, where they are included in the biosynthetic pathways or are broken down into low-molecular products. Parasitic bacteria consume ready-made amino acids from the host body. Bacteria cultivated on nutrient media containing only inorganic nitrogen sources or a limited number of amino acids have to synthesize some (or even all) of them from available nitrogen-containing compounds.
At the same time, nitrogen-containing substances, in addition to raw materials for plastic metabolism, can be included in energy metabolism (for example, in anaerobes, some amino acids can form redox systems). The most accessible mineral sources of nitrogen in nature are the ammonium ion (NH4+) and ammonia (NH3), which easily penetrate into cells and simply transform into amino and imine groups.
A bacterial cell is capable of synthesizing several thousand different proteins, each of which contains an average of 200 amino acid residues. The information directing the synthesis of these proteins is encoded in the sequence of DNA nucleotides. The synthesis of the polypeptide chain occurs in the cytoplasm of the cell on ribosomes in combination with an mRNA or informational RNA molecule, which is synthesized on the DNA matrix during transcription.


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Prokaryotes are highly organized cells, they are simpler compared to eukaryotes, but their structure is not primitive. They have no membrane-enclosed nucleus, one ring-shaped DNA molecule forms a nucleoid or nucleoplasm. Prokaryotic DNA contains up to 5×10^6 pairs of nitrogenous bases, and is up to several mm long. For example, the human E. coli symbiote has a giant cyclic DNA molecule about 1.6 mm long. The smallest ringed DNA, 0.25 mm long, is found in mycoplasma cells. There are no internal membranes, but specific prokaryotic proteins are confined to certain subcellular areas.


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The giant ring DNA of prokaryotes, the nucleode (a), using RNA and proteins, is repeatedly folded to form numerous spiral loops protruding from the dense central region (b), resulting in a significant nucleoid compaction. One such loop, or domain, contains up to 10–15 μm of DNA. The number of loops can reach 100–120. It should be noted that part of the nucleoid DNA is associated with a small number of special basic proteins that differ from eukaryote histones. The DNA ring molecule represents one unit of replication, a replicon. The rate of replication is about 30 μm per minute. The average time between bacterial cell divisions is 20–40 minutes.


Слайд 25.
A distinctive feature of prokaryotes' nuclear structures is that RNA synthesis and protein synthesis can occur in them simultaneously: ribosomes bind to the not yet fully synthesized molecules of mRNA and perform protein synthesis on them. Thus, a triple synthetic complex emerges: DNA – the synthesizing RNA chain – ribosomes with the synthesized polypeptide chain. Consequently, transcription and translation processes are not separated territorially in prokaryotes


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Unlike eukaryotic cells, bacteria usually lack large membrane organelles, such as the nucleus, mitochondria, and chloroplasts. However, some bacteria have organelles with a protein shell, in which certain metabolic processes take place, for example, carboxysomes.
Carboxysomes (polyhedral bodies) are micro — compartments in bacterial cells containing carbon-fixing enzymes. They are polyhedral single-layer protein bodies of polyhedral shape from 80 to 140 nanometers in diameter. They are the main part of the mechanism of CO2 concentration, which helps to overcome the inefficiency of ribulose diphosphate carboxylase (Rubisco), the main enzyme that limits the rate of carbon fixation in the Calvin cycle. These organelles are found in all cyanobacteria and many chemotrophic CO2-fixing bacteria.


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Magnetosomes are a single crystal of chemically pure magnetite (Fe3O4) or greigite (Fe3S4) surrounded by a membrane. Bacteria with magnetosomes are capable of magnetotaxis, a movement associated with the reaction of a cell to a magnetic field (they are called magnetotactic bacteria). The magnetosome membrane is a phospholipid bilayer, and some of its proteins are not found anywhere else. As a rule, magnetosomes form a longitudinal chain, less often they are assembled into 2 or 3 parallel or intersecting chains. Some bacteria have single magnetosomes. Bacteria with magnetosomes live in sea, river and lake bottom silts, on sandy beaches, rice fields and in flooded soils.


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Many aquatic bacteria, especially cyanobacteria, have gas vesicles that serve to regulate buoyancy. The membrane that restricts the gas vesicle has a protein nature, and atmospheric air is located inside the gas vesicle. Gas vesicles are located singly in the cytoplasm or form sieve-like clusters, which are sometimes incorrectly called gas vacuoles. Gas vesicles are hollow cylinders with conical ends with a diameter of 50-200 nm and a length of 100-1200 nm. The wall has a thickness of about 2 nm and is a single-layer protein membrane consisting of two homologous hydrophobic proteins.


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Most bacteria are mobile, and their mobility is provided by one or more flagella, which are surface protein structures. The location of the flagella on the cell can be different. Monotrichs have only one flagellum, lofotrichs have a bundle of flagella at one of the poles of the cell, amphitrichs have one flagellum at the opposite poles of the cell, and peritrichs have numerous flagella scattered over the entire surface of the cell. The length of the flagellum varies, but the diameter is usually 20 nm.
The base of the bacterial flagellum is represented by a basal body consisting of two (in gram-positive) or four (in gram-negative bacteria) protein rings, a rod and motor proteins. A hook departs from the basal body, passing into a filament, which ends with a "cap". The filament is a rigid cylinder formed by the flagellin protein. In the cell membrane there are rings M and S, which are often considered as a single whole. The MS ring is surrounded by several motor proteins that transmit torque to the filament. Gram-negative bacteria, in addition to the M and S rings, have two more rings: P, which lies in the peptidoglycan layer, and L, which is located in the outer membrane. A rigid rod passes through all the rings, transmitting the torque to the filament.
The movement of the cell occurs due to the rotation of the flagellum clockwise or counterclockwise. In monotrichs, the cell slowly rotates in the direction opposite to the rotation of the flagellum. If the flagellum rotates clockwise, then the cell moves forward with the flagellum, and if against, then the cell is pushed forward with the flagellum (that is, it moves backward with the flagellum). Some bacteria that have a single flagellum rotate it only clockwise, and in order to change the direction of movement, they need to stop and reorient themselves. In peritrichs, the flagella rotate counterclockwise, and if you need to change the direction of movement, the cell stops and makes a somersault.


Слайд 30.
Pili (also known as fimbriae or villi) are filamentous protein structures located on the cell surface of many bacteria. The size of the pili varies from fractions of microns to more than 20 microns in length and 2-11 nm in diameter. Pili are involved in the transfer of genetic material between bacterial cells (conjugation), the attachment of bacteria to the substrate and other cells, are responsible for the adaptation of organisms, serve as attachment sites for many bacteriophages. Structurally, the saws can be from thin filamentous formations to thick rod-shaped structures with axial holes. Peels consist of one or more types of spirally stacked protein molecules, which are called pilin.


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How does the replication machinery know where to start? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. E. coli has a single origin of replication on its one chromosome, as do most prokaryotes. The origin of replication is approximately 245 base pairs long and is rich in AT sequences. This sequence of base pairs is recognized by certain proteins that bind to this site. An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process because it requires energy. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks are formed at the origin of replication and these get extended bi-directionally as replication proceeds.
Слайд 33.
Two replication forks are formed at the origin of replication and these get extended bi-directionally as replication proceeds. Single-strand binding proteins (Figure 2) coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix.
The next important enzyme is DNA polymerase III, also known as DNA pol III, which adds nucleotides one by one to the growing DNA chain (Figure 2). The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them. ATP structurally is an adenine nucleotide which has three phosphate groups attached; breaking off the third phosphate releases energy. In addition to ATP, there are also TTP, CTP, and GTP. Each of these is made up of the corresponding nucleotide with three phosphates attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the existing chain.
In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. DNA pol III is the enzyme required for DNA synthesis; DNA pol I is used later in the process and DNA pol II is used primarily required for repair (this is another irritating example of naming that was done based on the order of discovery rather than an order that makes sense).
DNA polymerase is able to add nucleotides only in the 5′ to 3′ direction (a new DNA strand can be only extended in this direction). It requires a free 3′-OH group (located on the sugar) to which it can add the next nucleotide by forming a phosphodiester bond between the 3′-OH end and the 5′ phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3′-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3′-OH end. Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. RNA primase does not require a free 3′-OH group. Because this sequence primes the DNA synthesis, it is appropriately called the primer. DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand.
The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5′ to 3′ direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5′ to 3′ direction and the other is oriented in the 3′ to 5′ direction. One strand, which is complementary to the 3′ to 5′ parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. The other strand, complementary to the 5′ to 3′ parental DNA, is extended away from the replication fork, in small fragments known as Okazaki fragments, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the lagging strand.
The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3′ to 5′, and that of the leading strand 5′ to 3′. A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA pol I, which breaks down the RNA and fills the gaps with DNA nucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA ligase that catalyzes the formation of phosphodiester linkage between the 3′-OH end of one nucleotide and the 5′ phosphate end of the other fragment.


Слайд 34. Видео
I think this process is almost impossible to visualize from reading text. I strongly recommend that you watch a couple of animations / videos like the one available here.


Слайд 35.
DNA unwinds at the origin of replication.
Helicase opens up the DNA-forming replication forks; these are extended in both directions.
Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA.
Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling (over-winding).
Primase synthesizes RNA primers complementary to the DNA strand.
DNA polymerase III starts adding nucleotides to the 3′-OH (sugar) end of the primer.
Elongation of both the lagging and the leading strand continues.
RNA primers are removed and gaps are filled with DNA by DNA pol I.
The gaps between the DNA fragments are sealed by DNA ligase.


Слайд 36.
Unlike multicellular organisms, in unicellular organisms, including bacteria, cell size increase and reproduction by cell division are closely related. Bacterial cells reach a certain size and then divide by binary division. Under optimal conditions, the bacteria grow and divide very quickly, an example of the marine Pseudomonas aeruginosa is described, the population of which can double every 9.8 minutes. In binary division, two daughter cells are formed, identical to the mother. Some bacteria are capable of budding when the daughter cell forms growths on the mother cell, which subsequently separates and goes on to independent life.
In the laboratory, bacteria are grown on solid or liquid media. Solid media, such as agar, are used to isolate pure cultures of bacterial strains. Liquid media are used when it is necessary to measure the growth rate or to obtain a large number of cells. When growing bacteria in a liquid medium with mixing, homogeneous cell cultures are obtained, but it is difficult to notice contamination by other bacteria. To identify individual bacteria, selective media containing antibiotics, specific nutrients, or, conversely, devoid of any compounds are used.
Most laboratory methods of growing bacteria require large amounts of nutrients to ensure that large volumes of cells are produced quickly. However, in natural conditions, nutrients are limited, and bacteria cannot multiply indefinitely. Due to the limited amount of nutrients, various growth strategies have evolved. Some species grow extremely fast when nutrients are available, for example, cyanobacteria often cause blooming of organic-rich reservoirs. Other organisms are adapted to harsh environmental conditions, for example, bacteria of the genus Streptomyces secrete antibiotics that inhibit the growth of competing bacteria. In nature, many bacterial species live in communities (for example, in the form of biofilms), which provide each cell with the necessary nutrition and protect it from adverse conditions. Some organisms and groups of organisms grow only as part of communities and cannot be isolated into a pure culture.


Слайд 37.
Biofilm — a set (conglomerate) of microorganisms located on a surface, the cells of which are attached to each other. Usually, the cells are immersed in the extracellular polymer substance (extracellular matrix) secreted by them — mucus.
Biofilm development, and sometimes the biofilm itself, is also called biofouling. The term "biofilm" is defined in different ways, but in general, we can say that a biofilm is a community (colony) of microorganisms located on the interface of media and immersed in an extracellular polymer matrix with a spatial and metabolic structure.
Usually biofilms are formed in contact with liquids in the presence of substances necessary for growth. The surface to which the biofilm is attached can be either inanimate (stones) or the surface of a living organism (intestinal walls, teeth). It is believed that 95-99% of all microorganisms in the natural environment exist in the form of biofilm.


Слайд 38.
There are five stages of biofilm development:
First, the primary attachment of microorganisms to the surface (adhesion, sorption) from the environment (usually liquid) occurs. This stage is reversible.
Final (irreversible) attachment, otherwise called fixation. At this stage, the microbes secrete extracellular polymers that provide strong adhesion.
Maturation -I. Cells attached to the surface facilitate the attachment of subsequent cells, the extracellular matrix holds the entire colony together. Nutrients accumulate, and cells begin to divide.
Maturation-II. A mature biofilm has been formed, and now it is changing its size and shape. The extracellular matrix protects cells from external threats.
Dispersion (release of bacteria): as a result of division, individual cells periodically break off from the biofilm, which are able to attach to the surface after a while and form a new colony


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