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Microbial Life
- -about 5x1030 cells on earth
- -most in oceanic and terrestrial subsurfaces
- -microbial biomass are key reservoirs of essential nutrients (C, P, N)
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Positive Impact of Microorganisms in Agriculture
- -nitrogen fixing bacteria
- -cellulose degrading microbes in the rumen
- -regeneration of nutrients in soil and water
- -negative impacts are diseases
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Robert Hooke
- -first to describe microbes
- -saw fruiting structures of molds
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Antoni Van Leeuwenhoek
-first to describe bacteria
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Ferdinand Cohn
- -founded the field of bacterial classification
- -discovered bacterial endospores
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Louis Pasteur
- -discovered living organisms discriminate between optical isomers
- -discovered that alcoholic fermentation was a biologically mediated process (originally thought purely chemical)
- -disproved spontaneous generation
- -developed vaccines for anthrax, fowl cholera and rabies
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Robert Koch
- -link between microbes and infectious diseases
- -came up with Koch's postulates
- -developed techniques for obtaining pure cultures of microbes
- -nobel prize for physiology and medicine in 1905
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Koch's Postulates
- 1. suspected pathogen must be present in all cases of the disease and never in healthy subjects
- 2. suspected pathogen must be grown in pure culture
- 3. grown pathogen must cause disease in healthy animal
- 4. pathogen must be re-isolated from diseases animal and shown to be the same as original
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Martinus Beijerinck
- -developed enrichment culture technique
- -microbes were isolated from natural samples
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Sergei Winogradsky
- -showed specific bacteria and linked to specific biochemical transformations
- -proposed chemolithotrophy (oxidation of inorganic compounds)
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Resolution
- -ability to distinguish two adjacent objects as separate and distinct
- -determined by wavelength of light used
- -limits for light microscope is about .2 um
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Gram Positive appear?
- -appear purple
- -cyanobacteria
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Phase Contrast
- -Frits Zernike
- -allows visualization of live cells
- -dark cells on light background
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Dark Field
- -light comes in from sides
- -image appears light on dark background
- -good for observing motility
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Fluorescence Microscopy
- -can be microbes that autofluorescence or can be stained
- -used in microbial ecology
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Differential Interference Contrast (DIC)
- -use polarizer to create 2 beams of polarized light
- -gives 3 dimensional appearance to endospores, vacuoles and granules
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Atomic Force Microscopy
- -tiny stylus placed close to specimen, this measures weak repulsive forces between it and specimen
- -computer generates image based on this
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Confocal Scanning Laser
- -3d image based on computerized microscope and laser
- -focuses in layers which can be combined to make 3d image
- -resolution of .1um
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Transmission Electron Microscope
- -electromagnets as lenses
- -done in vacuum
- -.2nm resolution
- -specimens must be thin and stained
- -see the inside
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Scanning Electron Microscope
- -specimen coated with thin layer of heavy metal (gold)
- -electron beam scans it
- -see the surface
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Genome
-cells full complement of genes
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Plasmids
-small amounts of "extra" chromosomal DNA found in prokaryotes that confer special properties like antibiotic resistance
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E. Coli vs Human
- -4.64 million BP
- -4,300 genes
- -1,900 proteins
- -2.4 million protein molecules
- --humans have 100 more DNA per cell
- --7 more genes in humans
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Phylogeny
- -the evolutionary relationships between organisms
- -rRNA good for this
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3 Domains of Cellular Lineage
- -bacteria->prokaryotic
- -archaea->prokaryotic
- -eukarya->eukaryotic
- -archaea and bacteria NOT closely related
- -archaea closer to eukarya than bacteria
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Endosymbiosis
-the way mitochondria and chloroplasts took up residence in eukarya millions of years ago and still contain their own genomes
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LUCA
-last common ancestor between 3 domains of cell lineages (archaea, bacteria and eukarya)
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Chemoorganotrophs
- -oxidation of organic molecules (glucose, acetate)
- -aerobes use oxygen to obtain energy
- -anaerobes obtain energy in the absence of oxygen
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Chemolithotrophs
- -oxidation of inorganic molecules (H2, H2S, Fe2+, NH4+)
- -only in prokaryotes
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Phototrophs
- -contain pigments allowing light as energy source
- -can produce O2->oxygenic
- -anoxygenic-> doesnt produce O2
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Autotrophs
- -use CO2 as primary C source
- -primary producers
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Heterotrophs
- -obtain one or more organic molecules for C source
- -feed directly on autotrophs, or live off products produced from autotrophs
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Extremophiles
- -inhabit extreme environments
- -hot springs, glaciers, high pH or salinity
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All known pathogenic prokaryotes are what?
-bacteria
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Proteobacteria
- -largest phylum of bacteria
- -gram negative (red)
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Deinococcus
-extremely resistant to radioactivity
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Green sulfur bacteria and green nonsulfur bacteria are what?
-photosynthetic
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Chlamydia is what?
-an obligate intracellular parasite
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2 Phyla of Archaea
- -Euryarchaeota(methanogens, extreme halophiles, thermoacidophiles)
- -crenarchaeota(hyperthermophiles)
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Euryarchaeota
- -methanogens-degrade organic matter anaerobically, produce methane
- -extreme halophiles-require high salinity
- -thermoacidophiles-moderately high temps and low pH environments
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Crenarchaeota
-hyperthermophiles(can be marine, freshwater or soil system)
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Eukarya include what?
-algae, fungi, protozoa and slime molds
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Protists include______, which are _____ and _____ which are______
-protists include algae, which are phototrophic and protozoa which are NOT phototrophic
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Algae and fungi have what that protozoa and slime molds do not?
-cell walls
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Lichens are made up of what?
-fungi and cyanobacteria
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Coccus
-spherical or oval
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What 2 ions stabilize the cytoplasmic membrane?
- Mg2+ and Ca2+
- also stabilized by hydrogen bonds and hydrophobic interactions
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Cytoplasmic membrane strengthening agents of eukaryotes
-sterols: rigid, planar lipids in eukaryotes strengthen and stabilize the membranes
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Cytoplasmic membrane strengthening agents of bacteria
-hopanoids: structurally similar to sterols
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Archaeal membranes have _____ linkages, bacteria and eukarya have _____ linkages
- archea->ether
- bactera and eukarya->ester
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Archaeal Membranes
- -ether linkages
- -no FA have isoprenes instead
- -major lipids are glycerol diethers and tetraethers
- -can be monolayers, bilayers or mixture
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3 functions of cytoplasmic membrane
- -permeability barrier
- -protein anchor
- -energy conservation (creation)
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3 transport systems in prokaryotes
- -simple transport
- -group translocation
- -ABC system
- -all require some form of energy
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Simple transport
- -energy from proton motive force
- -Lac permease of E coli
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Lac Permease
- -for E. Coli
- -lactose brought into E coli by simple symporter, lac permease
- -energy driven through proton gradient
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Phosophotransferase system in E coli
- -group translocation
- -transported substance is chemically modified during transport across the membrane
- -moves glucose, fructose and mannose
- -5 proteins required
- -energy from phosphoenolpyruvate
- -sugar ends up with an added phosphate molecule (ex. G6P)
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ABC transport Systems
- -ATP-Binding Cassette system
- -over 200 identified in prokaryotes
- -can uptake organic compounds (sugars, AA), inorganic nutrients (sulfate, phosphate) and trace metals
- -high substrate specificity
- -periplasmic binding proteins(act as receptors to mediate transport in the periplasm)
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Peptidoglycan
- -rigid, provides strength to bacterial cell wall
- -made of N-acetylglucosamine and N-acetylmuramic acid, AA, diaminopimelic acid
- -cross linked differently in gram positive and gram negative bacteria
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Gram Positive Cells Walls
- -bacteria
- -common to have teichoic acids embedded in cell walls
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Lipoteichoic Acids
- -teichoic acids covalently bound to membrane lipids
- -found in gram positive cell walls
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Outer Membrane in bacteria
- -gram negative only
- -composes most of cell surface barrier
- -lipopolysaccharide layer (LPS)
- -LPS consists of core polysaccharide and O-polysaccharide
- -LPS replaces most of the phospholipids in outer half of membrane
- -contain porins for some movement
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Endotixin
-toxic component of LPS (outer membrane portion of outer membrane in gram negative bacteria)
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Periplasm
- -space located between cytoplasmic and outer membranes in gram negative bacteria
- -gel like
- -many proteins
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Metabolism
-sum of all chemical reactions that occur in a cell
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Carbon
Heterotrophs use?
Autotrophs use?
- -typical bacterial cell is 50% carbon dry weight
- -heterotrophs->organic C
- -autotrophs-> inorganic C
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Nitrogen
- -typically 12% dry weight
- -key uses in proteins, nucleic acid
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Phosphorous
- -macronutrient
- -nucleic acids and phospholipids
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Sulfur
- -macronutrient
- -used in cysteine and methionine
- -vitamins=thiamine, biotin, lipoic acid
- -coenzyme A
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Potassium
- -macronutrient
- -used as compatible solute by bacteria
- -enzyme activity
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Magnesium
- -macronutrient
- -stabilizes ribosomes, membranes and nucleic acids
- -enzyme activity
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Calcium
- -macronutrient
- -stabilize cell walls
- -heat stability of endospores
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Sodium
- -macronutrient
- -needed in marine microbes
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Iron
- -used in cytochromes and FeS proteins in electron transport
- -no oxygen=ferrous form Fe2+, soluble
- -with oxygen=ferric Fe3+, insoluble mineral
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Siderophores
-iron binding agents produced by cells to obtain iron from insoluble mineral form(ferric Fe3+)
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What molecule is used to convert ferric to ferrous iron?
- -hydroxamate which reduces ferric to ferrous iron as it moves across the cell membrane
- -type of siderophore
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Growth Factors
- -requires in small amount by certain organisms
- -vitamins, AA, purines, pyrimidines
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Vitamins
- -most commonly required as growth factors
- -many function as coenzymes
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Defined Media
- -used to grow microbes in the lab
- -precise chemical composition is known
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Complex Media
- -for growing microbes in the lab
- -composed of digests of chemically undefined substances (yeast, meat extracts)
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Pure Culture
-culture containing only a single kind of microbe
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Contaminants
-unwanted organisms in a culture
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Exergonic reactions have what value of deltaG?
endergonic?
- -negative value, release energy (exergonic)
- -positive value, require energy (endergonic)
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Enzymes
- -typically proteins, sometimes RNA
- -high specificity
- -larger than substrate
- -rely on weak bonds(H bonds, van der waals, hydrophobic interactions)
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Prosthetic Group
- -bind tightly to enzymes
- -bind covalently and permanently
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Coenzymes
- -loosely bound to enzymes
- -usually derivatives of vitamins (NADH)
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Electron donor is?
Electron acceptor is?
- -donor is oxidized
- -acceptor is reduced
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Reduction Potential
-the more negative value donate to the less negative value
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Energy Storing Molecules
- -ATP
- -phosphoenolpyruvate
- -Glucose-6-phosphate
- -coenzyme A
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