taxonomy and cell...
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Taxonomy and Cell Structure/Function
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Microbiology: An Evolving Science © 2009 W. W. Norton & Company, Inc. 2
Evidence of Life
n Stromatolites n Isotope ratios
¨ Limestone depleted of 12CO2
n Microfossils Cyanobacteria
Filamentous Prokaryotes Algae
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Microbiology: An Evolving Science © 2009 W. W. Norton & Company, Inc. 3
Microbial Taxonomy
n Hard to classify microbial species
¨ Asexual reproduction ¨ Horizontal gene transfer
n Some genes can be copied to a recipient bacterium ¨ Not entire genome ¨ Sometimes transfers occur between species
n Example: pathogenicity islands ¨ Large set of genes present in some strains of a species
§ Absent in other strains
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Taxonomic Identification
n Use metabolic, morphologic properties ¨ Reflect genetic background ¨ Growth substrates ¨ Biochemical structure
n Cell envelope—Gram stain
n Rapid pathogen identification ¨ Multiple color tests
n Results scored to give most probable species
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Microbial Divergence
n Mutation naturally occurs at each division
¨ One mistake in a million base pairs n Higher if a mutagen is present
n Very rare mutations are favorable ¨ Allow better survival of cell
n Faster growth, higher reproduction rate
¨ Or allow cell to attack competitors n Antibiotics made by bacteria
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Three Domains of Life
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Carl Woese
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Molecular Clocks
n Assume mutations accumulate steadily
¨ Constant rate per generation n Sequence differences are proportional to
number of generations since divergence n Best to compare conserved sequences
¨ Gene for small subunit rRNA n Adjustments to rate
¨ Conservation of sequences needed for function
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Phylogenetic Trees
n Relate differences between sequences
¨ To time since species divergence n Assume fewest possible changes
¨ “Maximum parsimony”
n Test trees via probability ¨ “Maximum likelihood”
n Tree most likely to give the observed sequences
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Figure 3.47
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Figure 3.52
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Figure 3.53
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Figure 3.23
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The Bacterial Cell
n Cytoplasm surrounded by envelope ¨ Cytoplasm contains DNA in nucleoid
n Envelope has lipid membrane boundary ¨ Plus structural cell wall
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n Made of lipid bilayer
¨ Double layer of phospholipids
n Separate cytoplasm from outside world
n Proteins embedded in membrane ¨ Anchor membranes to envelope ¨ Sense the outside world ¨ Transport materials into cell
Cell Membranes
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n Proton pumps push protons out of cell ¨ Generates proton-motive force (PMF)
n Osmotic force tries to push protons back into cell n Electrical force tries to push protons back into cell
Cell Transport
n PMF is used to create ATP ¨ ATP synthase uses PMF for
energy
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Cell Transport
n Transporters pass material into/out of cell
¨ Passive transport follows gradient of material
n Pumps use energy ¨ ATP or PMF ¨ Move material against their gradient
n Passive diffusion lets small molecules into cell
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The Bacterial Cell Wall
n Sacculus made of peptidoglycan ¨ Sugar chains wrapped in circles around cell
n “glyco” = “sweet”
¨ Sugar chains linked to each other by short polymers of amino acids n amino acid = “peptide”
polysaccharide (sugar) chains
peptide (amino acid) crosslinks
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n Capsule (not all species) ¨ Polysaccharide
n S Layer (not all species) ¨ Made of protein
n Thick cell wall ¨ 9-amino acid crosslinks in
peptidoglycan ¨ Teichoic acids for strength
n Thin periplasm n Plasma membrane
The Gram-Positive Envelope
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n Capsule (not all species) ¨ Polysaccharide
n Outer Membrane ¨ Lipopolysaccharide
n In outer leaflet only
n Thin cell wall ¨ 4-amino acid crosslinks
in peptidoglycan n Thick periplasm n Plasma membrane
The Gram-Negative Envelope
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n Single loop of double-stranded DNA ¨ Single molecule of DNA ¨ ~4x106 bp in many bacteria ¨ Compacted via supercoiling
n Attached to cell envelope ¨ No membrane separates
DNA from cytoplasm
n Replicates once for each cell division
The Bacterial Nucleoid
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Photosynthesis
n Cyanobacteria have thylakoids ¨ Extensively folded inner membrane ¨ Contain chlorophyll ¨ Ancestors of chloroplasts
n Carboxysomes fix carbon ¨ Use energy to make sugar
n Other bacterial photosynthetic pigments ¨ Purple membranes in some ¨ Phycobilisome proteins collect light energy
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Storage Granules n Intracellular deposits of material
¨ Glycogen (sugar) for energy ¨ PHB (fatty acid polymer) for energy ¨ Polyphosphate to store material ¨ Sulfur for disposal
Iridescent sulfur granules
Carboxysomes, lipid energy-storage granules
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Cell Attachment
n Fimbriae and pili attach cells to surfaces ¨ Thin filaments of protein “pilin”
n Secretion Systems attach cells to prey ¨ Six types
n Sex pilus is similar to type IV secretion system
¨ Essential for bacterial pathogenicity
n Stalks attach cells to surfaces ¨ Extension of cell cytoplasm
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Cell Motility
n Flagella ¨ Long, helical protein filaments ¨ Attached at ends, or over whole cell
n Flagella rotate to propel cell ¨ Base resembles type III secretion
system ¨ Proton passage drives rotation
n Clockwise or counterclockwise
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Chemotaxis
n Attractants cause counterclockwise rotation ¨ Flagella bundle together ¨ Push cell forward
n “Run”
n Repellents cause clockwise rotation ¨ Flagella fly apart together
n “Tumble” = change of direction
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Chemotaxis
n Runs + tumbles cause “random walk” ¨ Receptors detect attractant concentrations
n Sugars, amino acids ¨ Attractant concentration increases
and prolongs run n Biases random walk n Net movement of bacteria toward attractants