romikgosai/squad_modified huggingface dataset:
In most bacteria, a cell wall is present on the outside of the cell membrane. The cell membrane and cell wall comprise the cell envelope. A common bacterial cell wall material is peptidoglycan (called "murein" in older sources), which is made from polysaccharide chains cross-linked by peptides containing D-amino acids. Bacterial cell walls are different from the cell walls of plants and fungi, which are made of cellulose and chitin, respectively. The cell wall of bacteria is also distinct from that of Archaea, which do not contain peptidoglycan. The cell wall is essential to the survival of many bacteria, and the antibiotic penicillin is able to kill bacteria by inhibiting a step in the synthesis of peptidoglycan.

Questions and answers:
['
Q: What composes the cell envelope?
A: cell membrane and cell wall', '
Q: What is most common cell wall material?
A: peptidoglycan', '
Q: Are cell walls of bacteria similar to cell walls of plants and fungi?
A: Bacterial cell walls are different', '
Q: How can antibiotic penicillin destroy bacteria?
A: by inhibiting a step in the synthesis of peptidoglycan', '
Q: What are the main materials of cell walls of plants and fungi?
A: cellulose and chitin']
Gram-positive bacteria possess a thick cell wall containing many layers of peptidoglycan and teichoic acids. In contrast, gram-negative bacteria have a relatively thin cell wall consisting of a few layers of peptidoglycan surrounded by a second lipid membrane containing lipopolysaccharides and lipoproteins. Lipopolysaccharides, also called endotoxins, are composed of polysaccharides and lipid A that is responsible for much of the toxicity of gram-negative bacteria. Most bacteria have the gram-negative cell wall, and only the Firmicutes and Actinobacteria have the alternative gram-positive arrangement. These two groups were previously known as the low G+C and high G+C Gram-positive bacteria, respectively. These differences in structure can produce differences in antibiotic susceptibility; for instance, vancomycin can kill only gram-positive bacteria and is ineffective against gram-negative pathogens, such as Haemophilus influenzae or Pseudomonas aeruginosa. If the bacterial cell wall is entirely removed, it is called a protoplast, whereas if it is partially removed, it is called a spheroplast. β-Lactam antibiotics, such as penicillin, inhibit the formation of peptidoglycan cross-links in the bacterial cell wall. The enzyme lysozyme, found in human tears, also digests the cell wall of bacteria and is the body's main defense against eye infections.

Questions and answers:
['
Q: What does gram-positive bacteria have?
A: thick cell wall containing many layers of peptidoglycan and teichoic acids', '
Q: Why gram-negative cell bacteria is more toxic than gram-positive bacteria?
A: polysaccharides and lipid A', '
Q: What can be endotoxins called?
A: Lipopolysaccharides', '
Q: What can different structure of the cell walls of bacteria effect?
A: differences in antibiotic susceptibility', '
Q: What is the main defense of human body against eye infections?
A: enzyme lysozyme, found in human tears']
Acid-fast bacteria, such as Mycobacteria, are resistant to decolorization by acids during staining procedures. The high mycolic acid content of Mycobacteria, is responsible for the staining pattern of poor absorption followed by high retention. The most common staining technique used to identify acid-fast bacteria is the Ziehl-Neelsen stain or acid-fast stain, in which the acid-fast bacilli are stained bright-red and stand out clearly against a blue background. L-form bacteria are strains of bacteria that lack cell walls. The main pathogenic bacteria in this class is Mycoplasma (not to be confused with Mycobacteria).

Questions and answers:
['
Q: What is the most typical staining technique used to identify acid-fast bacteria?
A: Ziehl-Neelsen stain', '
Q: What is mycolic acid is responsible for in Mycobacteria?
A: staining pattern of poor absorption followed by high retention.', '
Q: What helps Mycobacteria be resistant to decolorization?
A: high mycolic acid content', '
Q: What is the main pathogenic bacteria in L-form class ?
A: Mycoplasma']
Fimbriae (sometimes called "attachment pili") are fine filaments of protein, usually 2–10 nanometres in diameter and up to several micrometers in length. They are distributed over the surface of the cell, and resemble fine hairs when seen under the electron microscope. Fimbriae are believed to be involved in attachment to solid surfaces or to other cells, and are essential for the virulence of some bacterial pathogens. Pili (sing. pilus) are cellular appendages, slightly larger than fimbriae, that can transfer genetic material between bacterial cells in a process called conjugation where they are called conjugation pili or "sex pili" (see bacterial genetics, below). They can also generate movement where they are called type IV pili (see movement, below).

Questions and answers:
['
Q: What are fimbriae?
A: fine filaments of protein', '
Q: What are fimbriae liable for?
A: involved in attachment to solid surfaces or to other cells', '
Q: What is the diameter of fimbriae?
A: 2–10 nanometres', '
Q: What are pili?
A: cellular appendages']
Certain genera of Gram-positive bacteria, such as Bacillus, Clostridium, Sporohalobacter, Anaerobacter, and Heliobacterium, can form highly resistant, dormant structures called endospores. In almost all cases, one endospore is formed and this is not a reproductive process, although Anaerobacter can make up to seven endospores in a single cell. Endospores have a central core of cytoplasm containing DNA and ribosomes surrounded by a cortex layer and protected by an impermeable and rigid coat. Dipicolinic acid is a chemical compound that composes 5% to 15% of the dry weight of bacterial spores. It is implicated as responsible for the heat resistance of the endospore.

Questions and answers:
['
Q: What are highly resistant dormant structures of certain gram-positive bacteria called?
A: endospores', '
Q: Is creating endospore a reproductive process?
A: is not a reproductive process', '
Q: What are ribosomes in endospores are enclosed in?
A: cortex layer', '
Q: What chemical compound comprises 5% to 15% of the dry weight of bacterial spores?
A: Dipicolinic acid']
Endospores show no detectable metabolism and can survive extreme physical and chemical stresses, such as high levels of UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure, and desiccation. In this dormant state, these organisms may remain viable for millions of years, and endospores even allow bacteria to survive exposure to the vacuum and radiation in space. According to scientist Dr. Steinn Sigurdsson, "There are viable bacterial spores that have been found that are 40 million years old on Earth — and we know they're very hardened to radiation." Endospore-forming bacteria can also cause disease: for example, anthrax can be contracted by the inhalation of Bacillus anthracis endospores, and contamination of deep puncture wounds with Clostridium tetani endospores causes tetanus.

Questions and answers:
['
Q: Is there a metabolism in endospores?
A: show no detectable metabolism', '
Q: What extreme physical and chemical stresses can endospores endure?
A: UV light, gamma radiation, detergents, disinfectants, heat, freezing, pressure', '
Q: How long can endospores of bacteria stay alive in dormant state?
A: for millions of years', '
Q: What endospore-forming bacteria can cause tetanus disease?
A: Clostridium tetani']
Bacteria exhibit an extremely wide variety of metabolic types. The distribution of metabolic traits within a group of bacteria has traditionally been used to define their taxonomy, but these traits often do not correspond with modern genetic classifications. Bacterial metabolism is classified into nutritional groups on the basis of three major criteria: the kind of energy used for growth, the source of carbon, and the electron donors used for growth. An additional criterion of respiratory microorganisms are the electron acceptors used for aerobic or anaerobic respiration.

Questions and answers:
['
Q: What is commonly used to determine taxonomy of bacteria?
A: The distribution of metabolic traits', '
Q: How is bacterial metabolism determined?
A: nutritional groups', '
Q: What are electron acceptors accountable for?
A: aerobic or anaerobic respiration', '
Q: What are three main criterias of bacterial metabolism?
A: the kind of energy used for growth, the source of carbon, and the electron donors']
Carbon metabolism in bacteria is either heterotrophic, where organic carbon compounds are used as carbon sources, or autotrophic, meaning that cellular carbon is obtained by fixing carbon dioxide. Heterotrophic bacteria include parasitic types. Typical autotrophic bacteria are phototrophic cyanobacteria, green sulfur-bacteria and some purple bacteria, but also many chemolithotrophic species, such as nitrifying or sulfur-oxidising bacteria. Energy metabolism of bacteria is either based on phototrophy, the use of light through photosynthesis, or based on chemotrophy, the use of chemical substances for energy, which are mostly oxidised at the expense of oxygen or alternative electron acceptors (aerobic/anaerobic respiration).

Questions and answers:
['
Q: How does heterotrophic carbon metabolism occur?
A: organic carbon compounds are used as carbon sources', '
Q: When carbon metabolism is called autotrophic?
A: cellular carbon is obtained by fixing carbon dioxide', '
Q: What category do parasitic bacteria fall into?
A: Heterotrophic bacteria', '
Q: Green sulfur-bacteria is typical representative of what type of bacteria?
A: autotrophic bacteria', '
Q: What is chemotrophy ?
A: the use of chemical substances for energy']
Bacteria are further divided into lithotrophs that use inorganic electron donors and organotrophs that use organic compounds as electron donors. Chemotrophic organisms use the respective electron donors for energy conservation (by aerobic/anaerobic respiration or fermentation) and biosynthetic reactions (e.g., carbon dioxide fixation), whereas phototrophic organisms use them only for biosynthetic purposes. Respiratory organisms use chemical compounds as a source of energy by taking electrons from the reduced substrate and transferring them to a terminal electron acceptor in a redox reaction. This reaction releases energy that can be used to synthesise ATP and drive metabolism. In aerobic organisms, oxygen is used as the electron acceptor. In anaerobic organisms other inorganic compounds, such as nitrate, sulfate or carbon dioxide are used as electron acceptors. This leads to the ecologically important processes of denitrification, sulfate reduction, and acetogenesis, respectively.

Questions and answers:
['
Q: What do lithotrophs use ?
A: inorganic electron donors', '
Q: What type of electron donors organotrophs use?
A: organic compounds', '
Q: In what organisms is oxygen used as eelectron acceptor?
A: anaerobic organisms', '
Q: What do respiratory organisms use as electron donors?
A: chemical compounds']
These processes are also important in biological responses to pollution; for example, sulfate-reducing bacteria are largely responsible for the production of the highly toxic forms of mercury (methyl- and dimethylmercury) in the environment. Non-respiratory anaerobes use fermentation to generate energy and reducing power, secreting metabolic by-products (such as ethanol in brewing) as waste. Facultative anaerobes can switch between fermentation and different terminal electron acceptors depending on the environmental conditions in which they find themselves.

Questions and answers:
['
Q: What is sulfate-reducing bacteria accountable for?
A: the production of the highly toxic forms of mercury', '
Q: What is the by-product of non-repiratory anaerobes?
A: ethanol', '
Q: How can anaerobes adjust to the surrounding environment?
A: can switch between fermentation and different terminal electron acceptors']
Lithotrophic bacteria can use inorganic compounds as a source of energy. Common inorganic electron donors are hydrogen, carbon monoxide, ammonia (leading to nitrification), ferrous iron and other reduced metal ions, and several reduced sulfur compounds. In unusual circumstances, the gas methane can be used by methanotrophic bacteria as both a source of electrons and a substrate for carbon anabolism. In both aerobic phototrophy and chemolithotrophy, oxygen is used as a terminal electron acceptor, whereas under anaerobic conditions inorganic compounds are used instead. Most lithotrophic organisms are autotrophic, whereas organotrophic organisms are heterotrophic.

Questions and answers:
['
Q: What are hydrogen and carbon monoxide for Lithotrophic bacteria?
A: Common inorganic electron donors', '
Q: How can gas methane be used in exceptional set of conditions by methanotrophic bacteria?
A: both a source of electrons and a substrate for carbon anabolism', '
Q: What is the main element for aerobic photorophy?
A: oxygen']
Regardless of the type of metabolic process they employ, the majority of bacteria are able to take in raw materials only in the form of relatively small molecules, which enter the cell by diffusion or through molecular channels in cell membranes. The Planctomycetes are the exception (as they are in possessing membranes around their nuclear material). It has recently been shown that Gemmata obscuriglobus is able to take in large molecules via a process that in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external items.

Questions and answers:
['
Q: What chemical process  helps bacteria to absorb raw materials?
A: diffusion', '
Q: How can bacteria obtain raw materials from the environment?
A: in the form of relatively small molecules', '
Q: What process is used by eukaryotic cells to absorb external items?
A: endocytosis', '
Q: What part of bacteria cell is used during diffusion?
A: molecular channels in cell membranes']
Unlike in multicellular organisms, increases in cell size (cell growth) and reproduction by cell division are tightly linked in unicellular organisms. Bacteria grow to a fixed size and then reproduce through binary fission, a form of asexual reproduction. Under optimal conditions, bacteria can grow and divide extremely rapidly, and bacterial populations can double as quickly as every 9.8 minutes. In cell division, two identical clone daughter cells are produced. Some bacteria, while still reproducing asexually, form more complex reproductive structures that help disperse the newly formed daughter cells. Examples include fruiting body formation by Myxobacteria and aerial hyphae formation by Streptomyces, or budding. Budding involves a cell forming a protrusion that breaks away and produces a daughter cell.

Questions and answers:
['
Q: How size and reproduction are linked in bacteria?
A: Bacteria grow to a fixed size and then reproduce', '
Q: How does bacteria reproduce?
A: through binary fission', '
Q: If the conditions are right how long does it take for bacteria to reproduce?
A: divide extremely rapidly', '
Q: What are produced in cell division?
A: two identical clone daughter cells']
In the laboratory, bacteria are usually grown using solid or liquid media. Solid growth media, such as agar plates, are used to isolate pure cultures of a bacterial strain. However, liquid growth media are used when measurement of growth or large volumes of cells are required. Growth in stirred liquid media occurs as an even cell suspension, making the cultures easy to divide and transfer, although isolating single bacteria from liquid media is difficult. The use of selective media (media with specific nutrients added or deficient, or with antibiotics added) can help identify specific organisms.

Questions and answers:
['
Q: In what environment are bacteria being cultivated in labs?
A: solid or liquid media', '
Q: What is typical solid setting?
A: agar plates', '
Q: What can help to indentify specific bacteria?
A: The use of selective media', '
Q: Which environment is better to isolate a single example of bacteria strain?
A: agar plates', '
Q: Which media is preffered to grow larger volumes of bacteria?
A: liquid growth media']
Most laboratory techniques for growing bacteria use high levels of nutrients to produce large amounts of cells cheaply and quickly. However, in natural environments, nutrients are limited, meaning that bacteria cannot continue to reproduce indefinitely. This nutrient limitation has led the evolution of different growth strategies (see r/K selection theory). Some organisms can grow extremely rapidly when nutrients become available, such as the formation of algal (and cyanobacterial) blooms that often occur in lakes during the summer. Other organisms have adaptations to harsh environments, such as the production of multiple antibiotics by Streptomyces that inhibit the growth of competing microorganisms. In nature, many organisms live in communities (e.g., biofilms) that may allow for increased supply of nutrients and protection from environmental stresses. These relationships can be essential for growth of a particular organism or group of organisms (syntrophy).

Questions and answers:
['
Q: What is the simple way of producing large volume of bacteria cells?
A: high levels of nutrients', '
Q: What caused the evolution of different growth strategies in bacteria?
A: nutrients are limited', '
Q: What can create a subsequent increase of nutrients in natural environment?
A: biofilms', '
Q: What do algal bacteria if nutrients are available?
A: grow extremely rapidly']
Bacterial growth follows four phases. When a population of bacteria first enter a high-nutrient environment that allows growth, the cells need to adapt to their new environment. The first phase of growth is the lag phase, a period of slow growth when the cells are adapting to the high-nutrient environment and preparing for fast growth. The lag phase has high biosynthesis rates, as proteins necessary for rapid growth are produced. The second phase of growth is the log phase, also known as the logarithmic or exponential phase. The log phase is marked by rapid exponential growth. The rate at which cells grow during this phase is known as the growth rate (k), and the time it takes the cells to double is known as the generation time (g). During log phase, nutrients are metabolised at maximum speed until one of the nutrients is depleted and starts limiting growth. The third phase of growth is the stationary phase and is caused by depleted nutrients. The cells reduce their metabolic activity and consume non-essential cellular proteins. The stationary phase is a transition from rapid growth to a stress response state and there is increased expression of genes involved in DNA repair, antioxidant metabolism and nutrient transport. The final phase is the death phase where the bacteria run out of nutrients and die.

Questions and answers:
['
Q: What is the first stage of bacteria adaptation?
A: lag phase', '
Q: What is the second phase of bacteria growth known for?
A: rapid exponential growth', '
Q: The absence of what causes the last stage of bacteria growth?
A: nutrients', '
Q: What is called the third statge of growth of bacteria?
A: stationary phase', '
Q: How many phase are in the growth of bacteria?
A: four phases']
Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii, to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum. Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome. The genes in bacterial genomes are usually a single continuous stretch of DNA and although several different types of introns do exist in bacteria, these are much rarer than in eukaryotes.

Questions and answers:
['
Q: What shape is chromosome of bacteria?
A: circular chromosome', '
Q: What bacteria is an exception to single circular chromosome rule?
A: Spirochaetes of the genus Borrelia', '
Q: What bacteria is responsible for Lyme disease?
A: Borrelia burgdorferi', '
Q: How does chromosome of Borrelia burgdoferi look like?
A: single linear chromosome']
Bacteria, as asexual organisms, inherit identical copies of their parent's genes (i.e., they are clonal). However, all bacteria can evolve by selection on changes to their genetic material DNA caused by genetic recombination or mutations. Mutations come from errors made during the replication of DNA or from exposure to mutagens. Mutation rates vary widely among different species of bacteria and even among different clones of a single species of bacteria. Genetic changes in bacterial genomes come from either random mutation during replication or "stress-directed mutation", where genes involved in a particular growth-limiting process have an increased mutation rate.

Questions and answers:
["
Q: What makes bacteria an asexual organism?
A: inherit identical copies of their parent's genes", '
Q: What can cause mutation in bacteria?
A: changes to their genetic material DNA', '
Q: What are two ways changes to DNA of bacteria can occur?
A: random mutation during replication or "stress-directed mutation"']
Transduction of bacterial genes by bacteriophage appears to be a consequence of infrequent errors during intracellular assembly of virus particles, rather than a bacterial adaptation. Conjugation, in the much-studied E. coli system is determined by plasmid genes, and is an adaptation for transferring copies of the plasmid from one bacterial host to another. It is seldom that a conjugative plasmid integrates into the host bacterial chromosome, and subsequently transfers part of the host bacterial DNA to another bacterium. Plasmid-mediated transfer of host bacterial DNA also appears to be an accidental process rather than a bacterial adaptation.

Questions and answers:
['
Q: What is the aftermath of infrequent errors during intracellular assembly of virus particles?
A: Transduction of bacterial genes', '
Q: What is the result of bacterial adaptation of E.coli bacteria host and plasmid of another bacteria?
A: Conjugation', '
Q: How does conjugation take place?
A: conjugative plasmid integrates into the host bacterial chromosome', '
Q: Is conjugation a common bacterial adaptation?
A: It is seldom']
Transformation, unlike transduction or conjugation, depends on numerous bacterial gene products that specifically interact to perform this complex process, and thus transformation is clearly a bacterial adaptation for DNA transfer. In order for a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state termed competence (see Natural competence). In Bacillus subtilis, about 40 genes are required for the development of competence. The length of DNA transferred during B. subtilis transformation can be between a third of a chromosome up to the whole chromosome. Transformation appears to be common among bacterial species, and thus far at least 60 species are known to have the natural ability to become competent for transformation. The development of competence in nature is usually associated with stressful environmental conditions, and seems to be an adaptation for facilitating repair of DNA damage in recipient cells.

Questions and answers:
['
Q: What does transformation of bacteria depends on?
A: numerous bacterial gene products', '
Q: How simple is the process of transformation?
A: this complex process', "
Q: What is the first requirement in order for bacteria to bind and recombine with other bacteria's DNA
A: enter a special physiological state termed competence", '
Q: How big can be the transformation level?
A: between a third of a chromosome up to the whole chromosome', '
Q: How rare is the transformation among bacteria organisms?
A: common']