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Final

BIOL 240: Final Exam Notes - Topic 16-21

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Department
Biology
Course Code
BIOL 240
Professor
Josh Neufeld

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Topic 16 Methanotrophs Ex. mussel gills – found near hydrocarbon seeps (sources of 4H )  There are different types of compounds that can be used as carbon sources o Some may be favoured over others  Methanotrophs can oxidize compounds that look like methane (ex. ammonium), but they DO NOT get energy from this (they oxide them, but do not use them for growth)  Type I = γ, cystlike body, ribulose monophosphate carbon assimilation pathway  Type II = α, can form exospores, serine carbon assimilation pathway Nitrifiers  Can detect using FISH (fluorescent in situ hybridization) o red = ammonia-oxidizing bacteria o green = nitrite-oxidizing bacteria (nitrobacter) Pseudomonads  found in soil, water, eukaryotic hosts  some can be pathogenic (may infect plants/animals) Rickettsias  coccoid (round) or rod-shaped  obligate intracellular parasites o causes human diseases (Q fever, typhus)  have arthropod vectors  close relative of mitochondria (similar features)  enterics, rickettsias, and pseudomonads do NOT have internal membranes Agrobacterium  gram-negative, aerobic rods  parasitic relationship with plants  mediated by a plasmid  bacteria exchanges DNA with plants (bacteria-eukaryote interaction) Agrobaterium tumefaciens  tumours induced by bacterial infection at the wound site (crown site) of plants  Ti plasmid in A. tumefaciens induce tumour formation  Part of the Ti plasmid (T-DNA) is integrated into the plant’s genome (carries genes for tumour formation and for the production of opines) o Opines provide a source of carbon and nitrogen for the parasitic Agrobacterium cells  To transfer T-DNA to the plant cell, VirA activates VirG by phosphorylation, and VirG activates transcription of other vir genes o 2 component regulatory system: VirA (sensor kinase), VirG (response regulator)  The product of VirD has endonuclease activity and nicks DNA in the Ti plasmid next to T-DNA  VirB (on the bacterial cytoplasmic membrane), mediates transfer of the single strand of T-DNA between the bacterium and plant (this transfer resembles bacterial conjugation) o VirB is similar to a pilus in conjugation  VirE results in DNA binding proteins that bind the single strand of T-DNA and transports it into the plant cell  T-DNA contains oncogenes (genes for tumour formation) and genes for the production of opines o Oncogenes: plant hormone production for tumour formation o Opines: modified amino acids produced by plant cells that are a source of carbon, nitrogen, and phosphate that A. tumefaciens needs Rhizobia  Mutualistic relationship (both rhizobia and plants benefit)  Legumes produce root nodules on root hairs (root nodules fix nitrogen) o Root nodules are formed by infection of legume roots by rhizobia  Because bare unfertilized soils are often nitrogen-deficient, nodulated legumes grow well in areas where other plants grow poorly (if nitrogen is limiting, you will find more nodules)  Root nodules are red (due to leghemoglobin)  Leghemoglobin: maintains microaerobic conditions (needed by rhizobia for N2fixation) 3+ 2+ o “oxygen buffer” = cycles between Fe and Fe to keep free O lo2 Nitrogen Fixation  Expensive = costs lots of ATP  O 2ensitive = nitrogenases are inactivated by O2 Root Nodule Formation 1. Recognition (of both plant and bacterium) and attachment of bacterium to the root hairs a. Cyclic β-1,2-glucan mediated (on exterior of rhizobial cells) 2. Excretion of nod factors by bacterium, causing the root hairs to curl 3. Bacterial invasion of the root hairs (rhizobia penetrate root hairs and multiply) 4. Bacteria in infection travels/grows to the main root via the infection thread a. Infection thread = cellulosic tube made by plants 5. Formation of bacteroids (modified bacterial cells that fix nitrogen) within the plant cell and development of the nitrogen-fixing state a. Bacteroids (swollen, misshapen, branched cells) become surrounded by portions of the plant cytoplasmic membrane to form a structure called the symbiosome 6. Continued plant and bacterial division, forming the mature root nodules Bacteroid Metabolism  Inside the cell, nitrogen gas is being fixed to ammonia (requires a lot of ATP)  Leghemoglobin provides supply of O t2 bacteroids  Sugars provide energy for nitrogen fixation Nodule Formation  Nod genes = bacterial genes that direct the steps in nodulation of a legume  nodD = controls transcription of other nod genes (activated by plant falvonoids) o positive regulatory protein  nodABC = encode proteins that produce oligosaccharides called nod factors o nod factors = induce root hair curling and trigger plant cell division  nodEFLM = modify nod factors  nodIJ = membrane proteins for export of nod factors  NAG chains are the foundation of nod factors  flavonoid molecules can be inducers (luteolin) or inhibitors (genistein) of nod gene expression Topic 18: Proteobacteria II Spirilla  gram-negative  motile (flagellar bundles)  diverse phylogenetically and physiologically o can be really tight coils, long coils, bends, etc. o scattered  vibroid = short spirilla o polar flagella  magnetosomes = magnetic; help bacteria move towards sediments Bdellovibrio bacteriovorus (remember as “BB”)  “bdello” = leech  Small, highly motile (travels at 100 cell lengths per second)  Vibroid shape  Preys on other bacteria (virus-like life cycle)  Polar flagella  When it strikes, it doesn’t stop o Like a drill = it burrows straight through the outer membrane and stops just at the other side (rests in the periplasm) o It then withdraws the nucleotides, proteins, and amino acids from the cytoplasm of the prey and consumes them to grow larger and larger (has hydrolytic enzymes) o It then starts to divide and eventually bursts out of the prey Budding or stalked bacteria  Unequal cell division = daughter cells are distinct from the mother cell (not like binary fission)  Stalks = extension of the cytoplasm and involved in cell division  Appendaged = flat, star-shaped cells, some with gas vesicles  Budding = single hyphae from parent cell Prosthecate bacteria  Live in nutrient-poor (oligotrophic) aquatic habitats  Can use appendages to: o attach to surfaces, plants, microbes o increase S/V ratio (when you extend the surface, you are increasing surface area a lot, but not the volume!) o help cells settle slowly in aquatic environments (fall slowly like a parachute)  MAIN DISTINCTION: inside the “leg-like” extensions contains cytoplasm o Appendages are from stretched out cells, not additional structures like flagella  flagella does NOT contain cytoplasm Budding Bacteria  hyphomicrobium o chemoorganotroph o buds are formed on the tip of the slender hyphae (long extensions of cytoplasm)  hyphae is NOT for attaching to surfaces  DNA of mother cell will pass through into bud to form a new cell  Cell cycle: o Forms hyphae, hyphae lengthens (DNA replication occurs) o bud forms then enlarges, copy of chromosome enters the bud o septum and flagella forms, division (daughter separates from mother cell at septum) o daughter cell loses its flagella, attaches to another surface, makes a hyphae, and starts to bud off offspring o mother cell can continue to produce offspring one after another! Stalked Bacteria  caulobacter o extension of cytoplasm o appendage use to attach to surfaces o found in aquatic environments o can form rosettes o holdfast = goop at the end of the stalk that helps it stick to substrates (doesn’t contain cytoplasm) o motile (flagellated) swarmer cells  cell cycle: o swarmer cells fix to surface, lose their flagella, and form a stalk o after they are attached to a surface by the stalk, they form daughter cells that have a flagella that leave as a swarmer cell and spawn in just the same way  unequal products of cell divis
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