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Chapter 2

Biology 2EE3 - chapter 2 - Bacteria.docx

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Turlough Finan

Chapter 2 - Bacteria - some bacteria are very rich in iron because of membrane enclosed magnetite particles (magnetosomes) - these bacteria use the Earth's magnetic field in order to orient themselves and travel - magnetotactic bacteria prefer environments with little or no oxygen - bacteria use this ability to direct themselves towards areas which are anoxic - this process is magnetic-aerotaxis by which they find the desired oxygen concentration by moving a long a magnetic field 2.1 Morphology of bacterial cells - shape of bacterial cell caused by organization of cell wall - coccus is spherical; bacillus is rod, vibrio is curved rod, spirillum is spiral - ecoli is rod shaped; vibrio cholerae is vibrio; staphylococcus aureus is spherical; treponema pallidum is spirrilium - morphology itself is not enough to classify bacteria - ecoli are individual cells; other bacteria like bacillus anthracis or streptococcus pyogenes form long chains and physically connected after division - staphylococci usually produce irregular clumps rather than chains - some bacteria do not create regular shapes but create variable shapes called pleiopmorphic - mycoplasma genus are all pleiomorphic because they do not produce a cell wall - some bacteria can form hyphae which are branching filaments and can also produce mycelia which are 3-d networks penetrating out or into the soil surfaces; similar to fungi - cyanobacteria form trichomes are smooth unbranched chains of cells; sometimes have polysaccharide sheet coating - between the cells in both trichomes and hyphae have intercellular connections for nutrient/signalling molecules - most bacteria are 0.5 to 5 micrometers in length - some large bacteria have been found, largest is spherical thiomargarita namibiensis - epulopiscium fiehelsoni have multiple genomes found in cytoplasm and replicate within themselves - all bacteria limited in shortest size by the rna genome as that is usually 0.5 micrometers itself 2.2 Cytoplasm - cytoplasm is the aqueous environment inside bacteria and contains diverse components - nucleoid is the largest entity and contains a mass of DNA (ususally single, circular chromosome) coated with proteins and rna - gas vesicles are also found in bacteria for buoyancy; inclusion bodies for storage of polymers - no membrane surrounding the nucleoid - cations shield the negative charge of the sugar phosphate backbone which allows it to pack more tightly - topoisomerases are enzymes that allow the dna to coil upon itself (supercoiling) - other proteins like dna/rna polymerases exist in the nucleoid and proteins that control gene expression - most enzyme catalyzed metabolic reactions occur in the cytoplasm - depending on conditions some bacteria have includion bodies which allow them to store extra carbon, nitrogen and phosphorous - no membrane surrounds this body, ex. PHB is a lipid polymer used to store carbons - PHB can be 50% of dry weight (polyhydroxylalkanoates), used for plastic industry substitute - sulfur globules are stores of sulfur to be used as energy when oxidizing sulfur compounds - gas vesicles regulate buoyancy in a cell based on cell positions in water column in response to light/nutrients - photosynthetic bacteria also have carboxysomes which help convert inorganic carbon to organic carbon - magnetosomes are a membrane enclosed organelle which have magnetite; these may provide clues to bacterial evolution 2.3 The bacterial cytoskeleton - cytoskeleton provides internal framework for cell and interact with plasma/cell wall - the FtsZ protein forms the Z ring which is needed for bacterial division - this protein is related to tubulin which is building block for microtubules in eukarya - ftsz monomers polymerize to filaments that bundle to form z ring which form on the inner face of plasma membrane - z ring contracts by releasing subunits which ends up causing cell envelope to go inward until cell division is done - zring is missing but will reform from elements in the cytoplasm for the next division - MreB protein is another important cytoskeleton element - mreb is related to actin and form long helical bands underlying the plasma membrane - mreb is universal in non spherical bacteria and help to guide cell wall formation/cell elonglation -parM protein forms actin like filaments; found on certain plasmids - role of parM is to ensure that during seperation there will be one copy of the plasmid on each side of the cell Perspective 2.1 - Marvelous Magnetosomes - magnetoaxis is used to direct movement based on the earths magnetic field - magnetosomes are used to achieve this and are filled with magnetite (Fe3O4) - formed by the plasma membrane; and acts as a compass needle, organized in chains - they are organized into a chain through the mamk protein which creates actin like filaments - discovered through using gfp to fluoresce the molecule - mamj faciliates interaction between magnetosomes and the actin like filaments 2.4 The cell envelope - all the layers as a membrane in total are called the cell envelope The plasma membrane - plasma membrane is bilayer composed of amphipathic phospholipids - also called cytoplasmic membrane or cell membrane - bacterial membranes lack sterol lipids like cholesterol, but form sterol like compounds like hopanoids - hopanoids are planar molecules and thought to stabilize the plasma membrane - these molecules are abundant in soils and sediments - membranes are not fluid depends on temperature, lipid type, other molecules - membranes are not pure lipids, half composed of protein - functions of membrane are transport. energy production, sensing Permeability of the Plasma membrane to water - has differential permeability, uncharged molecules like O2/CO2 flow through freely - larger compounds that are polar or charged cross less easily - water usually is small enough to pass through even though it is polar, might use aquaporins - hypotonic if cytoplasm has higher solute concentration than external - these changes can cause cell to swell/prune but cell wall helps prevent this Nutirent transport - there are facilitated diffusion systems which allow molecules (abundant in environment) to cross without energy - active transport systems require energy and drive against a gradient - one way this is done is through symport; which occurs when one molecule travels down a gradient and takes along a molecule not travelling along its gradient, energy is released which allows the other molecule to move - antiport involves the ejection of one molecule releasing energy to allow another one in - ABC transporters (ATP binding cassette) have a nucleotide binding domain where ATP is hydrolyzed to give energy for transport - ABC transporters are made of 4 subunits, 2 hydrophobic in the membrane and 2 hydrophilic in the cytoplasm - also has a high-affinity solute binding protein which binds to substrates and brings them to the complex which increases the affinity Energy capture - cytochromes and membrane soluble electron carriers exist in the membrane which allows for the production of ATP through respiratory electron transport system and photosynthetic systems - ejection of electrons create proton gradient to create proton motile force Sensory sytems - plasma membrane sense environment around bacteria to signal cytoplasm response systems - links to gene expression to ensure proper protein production - ex. transporter system only expressed when substrate is sensed in environment Protein secretion - general secretory pathway allows for proteins to move out of the cell, identified by a signal peptide made up of hydrophobic amino acids at the amino terminal end of a protein - secB protein binds to the polypeptide which stops it from folding inside the cytoplasm - next secA takes it to the sexYEG channel and helps it move through to the periplasm where a signal peptidase removes the signal peptide and folding occurs outside the cell The bacterial cell wall - cell wall is made up of highly linked poly saccharide called peptidoglycan - helps prevent damage from osmotic pressure, mechanical forces, and shearing - cell wall also gives shape to the bacteria ; however mycoplasmas survive without cell wall - mycoplasma live inside hosts for protection, however - peptidoglycan is made up of NAM and NAG (N-acetylglucosamine and N-acetylmurmamic acid) - these sugars are linked by beta (1,4) glycosidic linkages, NAM is also attached to a short peptide chain to cross link peptidoglycan strands - peptide chains differ between bacteria and the cross linking differs as well - some bacteria have direct cross links between short peptide chains, others have a interlink peptide chain to connect the short peptide chains connected to NAM - some of the amino acids found in these chains are rarely found in proteins, some d isomers when only l isomers are used with ribosomes - peptidoglycan production starts in cytoplasm, where enzymes link NAM and UDP to a pentapeptide complex - then this complex is attached to bactoprenol, a cytoplasmic lipid carrier - NAG then attaches to NAM, then bactoprenol flips and the complex is in the periplasm now - it then links to other sugar complexes - some organisms produce lysozyme that can degrade peptidoglycan by hydrolyzing the beta 1,4 glycosidic linkage between NAM and NAG - if isotonic, bacteria can exist as protoplast, fragile form of bacteria without cell wall - if hypotonic then water may enter when it is a protoplast causing it to burst - gram negative have an extra layer which shields cell wall from lysozyme - lysozyme are found in mucus and tears for humans to control bacterial populations - lysostaphin is an enzyme found in staphlococcus simulans which degrades the intercross linking bridge (pentaglycine bridge) in s aereus - this gene has been engineered into cattle to stop aereus infection - therefore lysozyme degrades the glycosidic linkage and lysostaphin degrades the pentaglycine linkage - some antibiotics deactivate the peptidase enzymes that cross link peptidoglycan - for example, beta-lactam mimics an amino acid to trick the petidase enzyme - however, when enzymes attach trying to catalyze a peptide bond reaction, the active side is permanently bounded to and destroys the enzyme - this antibiotic works well only with growing cells as this can only affect those with growing peptidoglycan strands - lysozyme can work on any cell as it just tears apart the linkages - beta-lactamases destory these beta-lactams by hydrolyzing the C-N bond in the ring which is necessary for the substrate to bind to the enzyme - modified antibiotics were made to challenge this resistance, but bacteria evolved as well - in response, products like c
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