Chapter 20 Biology Notes.docx

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Biological Sciences
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Bebhinn Treanor

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Chapter 20: Bacteria and Archaea Antigen- Substances that stimulate antibody production by the immune system 20.1 The Full Extent of the Diversity of Bacteria and Archaea is Unknown  Everything known about bacteria and archaea is based on tiny fraction of total number of speices  Only isolated and identified 6000 species, what is as low as 1% of total number  Know nothing of prokaryotes in oceans  In past, we identified and classified bacteria and archaea based on external features (cell wall structure) and physiological differences which meant that we had to grow the organism in culture  Most prokaryotic organisms cannot be grown in culture because they require extreme physiochemical conditions so not much have been learnt about these organisms.  Molecular techniques have been developed that isolate and clone DNA from an environment and analyze gene sequences  Thus identifying and characterizing bacteria and archaea with having to culture them  Approach known as metagenomics now enables us to investigate the diversity of prokaryotic organisms  However, some environments are remote and are difficult/costly to sample organisms from there. 20.1a Prokaryotic Organisms Make up Two of the Three Domains of Life  Two of three domains of living organisms, archaea and bacteria consist of prokaryotic organisms  Bacteria is known to us as some are responsible for diseases and others are relied for production of cheese yogurt and other foods.  Archaea are not well known, as they were only discovered 40 years ago  Archaea share some features with bacteria and some with eukaryotes and some are completely unique  Many archaea live under very extreme conditions that no other organism can survive. 20.2 Prokaryotic Structure and Function  Generally, prokaryotic organisms are the smallest in world  Few species are more than 1-2 um long  500-600 could fit on the dot in this “i”  Despite small size, the dominate life on Earth; billions of species and collective mass (biomass) exceeds that of animals and may be greater than all of plant life  Colonize every survivable area off Earth, even deep in the curst  Also colonize other organisms by inhibiting the surfaces of health human bodies including the skin mouth, naval passages and large intestine  Bacteria in and on your body outnumber other cells in body  Diversity if greater because they have been on planet for 3 billion years, before eukaryotes appeared 20.2a Prokaryotic Cells Appear simple in Structure Compared to Eukaryotic Cells  Three cell shapes are common among prokaryotes: spiral, spherical (coccoid =berry) and cylindrical (rods), and but some archaea even have square cells.  Prokaryotic cell seems simpler than eukaryotic cell; images tkane with standard electron microscopy typical reveals little more than a cell wall and plasma membrane surrounding cytoplasm with DNA concentrated in one region and ribosomes scattered throughout.  The chromosome is not contained in a membrane-bound nucleus but is packed into an area of the cell called the nucleoid.  Prokaryotic cells have no cytoplasmic organelles equivalent to the endoplasmic reticulum or Golgi complex of eukaryotic cells.  Usually, the reaction carried out by organelles in eukaryotes are distributed between the plasma membrane and the cytoplasmic solution of prokaryotic cells  This means that macro molecules such as proteins are very concentrated in the cytoplasm of these cells, making the cytoplasm quite viscous.  Because prokaryotic cells were seen as simple, people disregarded them as featureless and disorganized.  Apparent simplicity is misleading  Prokaryotic cells do have a cytoskeleton- not homologous to that of a eukaryote but serving the same functions (thus more sophisticated organization)  Recent research has identified a prokaryotic organelle  Bacteria that obtain energy by oxidizing ammonia have an internal membrane-bound compartment where ammonia oxidation occurs.  Hypothesized that as ammonia oxidation proceeds inside the compartment, a proton motive force could be generated across the membrane, generating ATP.  Research found that the membrane around this compartment does contain ATP synthase, supporting the above hypothesis.  Therefore, some prokaryotic cells have organelles with specialized funtions. Internal Structures:  Genome of most prokaryotic cells consist of single, circular DNA molecules, although some have a linear chromosome  Many prokaryotic cells also contain small circles of DNA called plasmids, which generally contain genes for nonessential but beneficial function such as antibiotic resistance  Plasmids replicate independently of the cell’s chromosome and can be transferred from one cell to another  This means that the genes for antibiotic resistance are readily shared among prokaryotic cell, even among cells of different species  Horizontal gene transfer allows antibiotic resistance and other traits to spread very quickly in bacterial populations  Horizontal gene transfer also occurs when bacteria cells take up DNA from their environment (form other cells that have lysed) or when viruses transfer DNA from one bacterium to another  Prokaryotic cells contain ribosomes like eukaryotic cells  Bacterial ribosomes smaller than eukaryotic ribosome but carry out protein synthesis by essentially the same mechanisms.  Archael ribosome resemble those of bacteria in size but differ in structure  Protein synthesis in Archae is combination of bacterial and eukaryotic processes with some unique features  Antibiotics that stop bacterial infections by targeting ribosome activity do not interfere with archael protein synthesis. Prokaryotic Cell Walls  Most prokaryotic cells have a cell wall that lies outside their plasma membrane and protects the cell from lysing if subjected to hypnotic conditions or exposed to membrane-disputing compounds such as detergents.  Peptidoglycan is the primary component of bacterial cell walls, which is a polymer of sugars and amino acids that forms linear chains.  Peptide cross linkages between the chains give the cell wall great strength and rigidity  Antibiotic penicillin prevents the formation of these cross linkages resulting in a weak cell wall that is easily ruptured, killing the cell.  Bacteria can be divided into two main groups: gram positive and gram negative cells, based on their reaction to the gram stain procedure (first step in identifying an unknown bacterium)  Cells are first stained with crystal-violet and then treated with iodine which forms a complex with crystal violet  Cells are then rinsed with ethanol and counterstained with safranin  Some cells retain the crystal violet iodine complex and thus appear purple when viewed under the microscope; these are termed Gram-positive cells  In other bacteria, ethanol washes the crystal- violet iodine complex out of the cells which are colourless until counterstained with safranin; these are gram-negative cells and appear pink.  Different response to staining related to differences in cell wall structure  Gram positive bacteria have cell walls composed almost entirely of a single relatively thick layer of peptidoglycan, a complex polymer of sugars and amino acids.  The thick peptidoglycan layer retain the crystal violet-iodine complex inside the cell.  Gram-negative cells have only a think peptidoglycan layer in their walls, and the crystal-violet iodine complex is washed out  In contrast, the cell wall of Gram-negative bacteria has two distinct layers; a thin peptidoglycan later and an outer membrane external (outside plasma membrane) to the peptidoglycan layer.  Outer layer contains lipopolysaccharides and thus is very different from the plasma membrane.  Outer membrane protects gram-negative bacteria from potentially harmful substances in the environment (ex; inhibits entry of penicillin)  Gram-negative cells are less sensitive to penicillin than Gram-positive cells.  Cell wall of some Archaea are made form a molecule related to peptidoglycan but with different molecular components and bonding structure.  Others have walls made fomr proteins or polysaccharides instead of peptidoglycan.  Archaea have a variable response to the Gram stain, so this procedure is not useful in identifying archaea.  Cell wall of many prokaryotic cells is surrounded by a layer of polysaccharides known as a capsule.  Capsules are sticky and play important roles in protecting cells in different environments  Cells with capsules are protected from extreme temperatures, desiccation, viruses and harmful molecules  In many pathogenic bacteria, the presence or absence of the capsule makes a difference of an infective from noninfective form.  Capsulated and virulent bacteria causes server harm in humans and animals where as non capsulated bacteria can easily be eliminated by the body’s immune system. Flagella and Pilli:  Many prokaryotic cells can move through liquids and even through films of liquid on a surface, usually through the flagella which extends from the cell wall  Prokaryotic flagella is very different from eukaryotic flagella both in structure in movement  Prokaryotic flagella are made of rigid helical proteins, some which act like a motor which rotates the flagellum much like a propeller of a boat  Archael flagella are similar to bacterial flagella and carry out the same function but the two flagella contain different components, develop differently and are coded for by different genes.  Some prokaryotic cells have rigid shafts of protein called pili extending from their cell walls which allows them to adhere to or move along a surface.  One type called sex pilus not only allows bacteria cells to adhere to each other, but acts as a conduit for the transfer of plasmids from one cell to another.  Other pili enable bacteria to bind to animal cells  Pilli of some bacteria conduct electricity; nanowires transfer electrons out of the cell into mineral such as iron oxides in their environment.  Such electricity generation bacteria hold promise for development of microbial fuel cells as alternative energy source.  Prokaryotic cells are much simpler and less diverse structurally but are more diverse metabolically. 20.2b Prokaryotic Organisms Have the Greatest Metabolic Diversity of All Organisms  Organisms grouped into four modes of nutrition based on sources of energy and carbon.  Focus on carbon, instead of other nutrients because carbon is backbone to all organic molecules synthesized by an organism  Autotrophs are organisms like plants that synthesize organic carbon molecules using inorganic carbon (Co2)  Heterotrophs obtain carbon from organic molecules either from living hosts or from organic molecules in the products, waste or remains of dead organisms.  Organisms are also divided according to the source of energy they use to drive biological activities.  Chemotrophs obtain energy by oxidizing inorganic or organic substances, whereas phototrophs obtain energy from light.  Combining carbon and energy sources groups organisms into 4 categories.  Prokaryotic organisms show the greatest diversity in their modes of securing carbon and energy; only represent two of the categories (chemoautotrophs, and photoheterotrophs)  Photoheterotrophs use light as an energy source and obtain carbon from organic molecules rather than from Co2.  Chemoautotrophs are known as lithotrophs  Chemoautotrophs obtain energy by oxidizing inorganic substances such as hydrogen, iron, sulfur, ammonia and nitrites and use Co2 as their carbon source.  Chemolithotrophs thrive in habitats such as deep sea vents where reduced inorganic compounds are abundant; their ability to harness energy from these compounds make them the foundation which the rest of the vent community depends on  Similar to how terrestrial organisms rely on plants to capture light energy  Some prokaryotic organisms use oxygen as a final electron acceptors; like humans these are aerobic organisms also knowns as aerobes  Aerobes may be obligate, that is they cannot survive without oxygen  Some prokaryotic organisms breathe metals using metal as the final electron acceptor for electrons; obtain energy via anaerobic respiration  Anaerobic respiration can involve other inorganic molecules (nitrate, sulfate) as final electron acceptors.  Only prokaryotic organisms are capable of this type of respiration  Obligate anaerobes are poisoned by oxygen and survive either by fementation, in which organic molecules are the final electron acceptors, or by anaerobic respiration.  Facultative anaerobes use O2 when it is present, but under anaerobic condition, they live by fermentation or anaerobic respiration. 20.2c Bacteria and Archaea Play Key Roles in Biogeochemical Cycles  Prokaryotes can metabolize a wide range of substances which makes them key players in the life sustaining recycling of elements such as carbon, oxygen and nitrogen.  Biogeochemical cycle is the pathway by which a chemical element moves through an ecosystem.  As elements flow from through its cycle, it is transformed from one form to another, prokaryotic organisms are crucial in many of these transformations.  Nitrogen cycle will used as an example of the key role prokaryotic organisms play in biogeochemical cycles.  Nitrogen is component of proteins and nucleotides and so is of vital importance for all organisms  Atmosphere contains 80% nitrogen  Most organisms can’t use this nitrogen because they cannot break the strong triple bond between the two nitrogen atoms.  Some bacteria and archaea can, using the enzyme nitrogenase and convert N2 into forms that can be used by other organisms.  In conversion process known as nitrogen fixation, N2 is reduced to ammonia (Nh3) and ammonia is quickly ionized to ammonium (Nh4+)  Prokaryotic cells then use this to produce nitrogen containing molecules such as amino acids and nucleic acids.  Nitrogen fixation is the only way of replenishing the nitrogen sources used by most organisms (meaning that all organism rely on nitrogen fixed by bacteria, including cynabacteria)  Other prokaryotic organisms carry out nitrification, the oxidation of ammonium (Nh4+) to nitrate (No3-).  The oxidation is carried out in two steps by two types of nitrifiers, ammonia oxidizers and nitrate oxidizers, present in soil and water  Ammonia oxidizers convert ammonium intro nitrite (No2-) whereas nitire oxidizers convert nitrite to nitrate.  Nitrate is then taken up by plants and fungi and incorporated into their organic molecules  Animals obtain nitrogen in organic form by eating other organism.  Nitrification makes nitrogen available to many other organisms including plants, animals and bacteria that cannot metabolize ammonia.  Metabolic versatility of bacteria and archaea is one factor that accounts for their abundance and persistence on the planet; another factor is reproductive capacity 20.2d Asexual Reproduction Can Result in Rapid Population Growth  In prokaryotic organisms asexual reproduction is the normal mode of reproduction.  A parent cell divides my binary fission into two daughter cells that are exact genetic copies of the parents.  Reproducing by binary fission means that under favourable conditions, populations of prokaryotic organisms can have very rapid exponential growth.  Some prokaryotic cells can produce double their population in 20 minutes and will even begin a second round of cell division before the first is complete.  Thus one cell can produce millions in only a few hours.  Short generation times and small genomes means that prokaryotic organism have higher mutation rates than eukaryotic organisms.  1000 times more mutations per gene, per unit time, per individual  The basis for their dibersity is the genetic variability and it dertives largely from mutation and to a lesser degree from horizontal gene transfer.  Large population of prokaryotic organisms compared with eukaryotes contribute to the much greater genetic variability in bacteria and archaea.  Prokaryotic organisms have an enormous capacity to adapt which is a reason for their evolutionary success.  Success of bacteria is beneficial to humans in many ways, but can also be determintal when detailing with pathogenic bacteria. 20.2e Pathogenic Bacteria Causes Diseases by Different Mechanisms  Some bacteria produce exotoxins, toxic proteins that leak from or are secreted from the bacterium.  For example, botulism food poisioning is caused by the exotoxin of the Gram-positive bacterium Clostridium botulinum which grows in poorly preserved foods.  Just a few nanograms of botulin can cause sever illness because it produces muscle paralysis that can be fatal if that muscles that are controlling breathing are affected.  Exotoxins produced by certain strain of Stretoccus pyogens have superantigen properties that cause necrotizing fasciitis (flesh eating disease)  Other bacteria cause disease through endotoxins. 
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