BMSC 210 Lec 1-5

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BMSC 210 Lec 1-5
2014-01-27 18:55:37
BMSC 210 Lec

BMSC 210 Lec 1-5
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  1. Microbial Life
    • -about 5x1030 cells on earth 
    • -most in oceanic and terrestrial subsurfaces
    • -microbial biomass are key reservoirs of essential nutrients (C, P, N)
  2. 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
  3. Robert Hooke
    • -first to describe microbes
    • -saw fruiting structures of molds
  4. Antoni Van Leeuwenhoek
    -first to describe bacteria
  5. Ferdinand Cohn
    • -founded the field of bacterial classification
    • -discovered bacterial endospores
  6. 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
  7. 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
  8. 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
  9. Martinus Beijerinck
    • -developed enrichment culture technique 
    • -microbes were isolated from natural samples
  10. Sergei Winogradsky
    • -showed specific bacteria and linked to specific biochemical transformations
    • -proposed chemolithotrophy (oxidation of inorganic compounds)
  11. 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
  12. Gram Positive appear?
    • -appear purple
    • -cyanobacteria
  13. Gram Negative appear?
    • -red/pink
    • -proteobacteria
  14. Phase Contrast
    • -Frits Zernike
    • -allows visualization of live cells
    • -dark cells on light background
  15. Dark Field
    • -light comes in from sides
    • -image appears light on dark background
    • -good for observing motility
  16. Fluorescence Microscopy
    • -can be microbes that autofluorescence or can be stained 
    • -used in microbial ecology
  17. Differential Interference Contrast (DIC)
    • -use polarizer to create 2 beams of polarized light 
    • -gives 3 dimensional appearance to endospores, vacuoles and granules
  18. Atomic Force Microscopy
    • -tiny stylus placed close to specimen, this measures weak repulsive forces between it and specimen 
    • -computer generates image based on this
  19. 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
  20. Transmission Electron Microscope
    • -electromagnets as lenses 
    • -done in vacuum
    • -.2nm resolution
    • -specimens must be thin and stained
    • -see the inside
  21. Scanning Electron Microscope
    • -specimen coated with thin layer of heavy metal (gold)
    • -electron beam scans it
    • -see the surface
  22. Genome
    -cells full complement of genes
  23. Plasmids
    -small amounts of "extra" chromosomal DNA found in prokaryotes that confer special properties like antibiotic resistance
  24. 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
  25. Phylogeny
    • -the evolutionary relationships between organisms
    • -rRNA good for this
  26. 3 Domains of Cellular Lineage
    • -bacteria->prokaryotic
    • -archaea->prokaryotic
    • -eukarya->eukaryotic
    • -archaea and bacteria NOT closely related 
    • -archaea closer to eukarya than bacteria
  27. Endosymbiosis
    -the way mitochondria and chloroplasts took up residence in eukarya millions of years ago and still contain their own genomes
  28. LUCA
    -last common ancestor between 3 domains of cell lineages (archaea, bacteria and eukarya)
  29. Chemoorganotrophs
    • -oxidation of organic molecules (glucose, acetate)
    • -aerobes use oxygen to obtain energy
    • -anaerobes obtain energy in the absence of oxygen
  30. Chemolithotrophs
    • -oxidation of inorganic molecules (H2, H2S, Fe2+, NH4+)
    • -only in prokaryotes
  31. Phototrophs
    • -contain pigments allowing light as energy source 
    • -can produce O2->oxygenic
    • -anoxygenic-> doesnt produce O2
  32. Autotrophs
    • -use CO2 as primary C source 
    • -primary producers
  33. Heterotrophs
    • -obtain one or more organic molecules for C source
    • -feed directly on autotrophs, or live off products produced from autotrophs
  34. Extremophiles
    • -inhabit extreme environments
    • -hot springs, glaciers, high pH or salinity
  35. All known pathogenic prokaryotes are what?
  36. Proteobacteria
    • -largest phylum of bacteria
    • -gram negative (red)
  37. Deinococcus
    -extremely resistant to radioactivity
  38. Green sulfur bacteria and green nonsulfur bacteria are what?
  39. Chlamydia is what?
    -an obligate intracellular parasite
  40. 2 Phyla of Archaea
    • -Euryarchaeota(methanogens, extreme halophiles, thermoacidophiles)
    • -crenarchaeota(hyperthermophiles)
  41. Euryarchaeota
    • -methanogens-degrade organic matter anaerobically, produce methane
    • -extreme halophiles-require high salinity 
    • -thermoacidophiles-moderately high temps and low pH environments
  42. Crenarchaeota
    -hyperthermophiles(can be marine, freshwater or soil system)
  43. Eukarya include what?
    -algae, fungi, protozoa and slime molds
  44. Fungi are?
  45. Protists include______, which are _____ and _____ which are______
    -protists include algae, which are phototrophic and protozoa which are NOT phototrophic
  46. Algae and fungi have what that protozoa and slime molds do not?
    -cell walls
  47. Lichens are made up of what?
    -fungi and cyanobacteria
  48. Coccus
    -spherical or oval
  49. Rod
    -cylindrical shape
  50. Spirillum
    -spiral shape
  51. What 2 ions stabilize the cytoplasmic membrane?
    • Mg2+ and Ca2+
    • also stabilized by hydrogen bonds and hydrophobic interactions
  52. Cytoplasmic membrane strengthening agents of eukaryotes
    -sterols: rigid, planar lipids in eukaryotes strengthen and stabilize the membranes
  53. Cytoplasmic membrane strengthening agents of bacteria
    -hopanoids: structurally similar to sterols
  54. Archaeal membranes have _____ linkages, bacteria and eukarya have _____ linkages
    • archea->ether
    • bactera and eukarya->ester
  55. Archaeal Membranes
    • -ether linkages 
    • -no FA have isoprenes instead 
    • -major lipids are glycerol diethers and tetraethers 
    • -can be monolayers, bilayers or mixture
  56. 3 functions of cytoplasmic membrane
    • -permeability barrier
    • -protein anchor
    • -energy conservation (creation)
  57. 3 transport systems in prokaryotes
    • -simple transport
    • -group translocation
    • -ABC system
    • -all require some form of energy
  58. Simple transport
    • -energy from proton motive force
    • -Lac permease of E coli
  59. Lac Permease
    • -for E. Coli
    • -lactose brought into E coli by simple symporter, lac permease
    • -energy driven through proton gradient
  60. 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)
  61. 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)
  62. 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
  63. Gram Positive Cells Walls
    • -bacteria
    • -common to have teichoic acids embedded in cell walls
  64. Lipoteichoic Acids
    • -teichoic acids covalently bound to membrane lipids
    • -found in gram positive cell walls
  65. 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
  66. Endotixin
    -toxic component of LPS (outer membrane portion of outer membrane in gram negative bacteria)
  67. Periplasm
    • -space located between cytoplasmic and outer membranes in gram negative bacteria 
    • -gel like
    • -many proteins
  68. Metabolism
    -sum of all chemical reactions that occur in a cell
  69. Carbon
    Heterotrophs use?
    Autotrophs use?
    • -typical bacterial cell is 50% carbon dry weight
    • -heterotrophs->organic C
    • -autotrophs-> inorganic C
  70. Nitrogen
    • -typically 12% dry weight
    • -key uses in proteins, nucleic acid
  71. Phosphorous
    • -macronutrient
    • -nucleic acids and phospholipids
  72. Sulfur
    • -macronutrient 
    • -used in cysteine and methionine 
    • -vitamins=thiamine, biotin, lipoic acid
    • -coenzyme A
  73. Potassium
    • -macronutrient
    • -used as compatible solute by bacteria
    • -enzyme activity
  74. Magnesium
    • -macronutrient
    • -stabilizes ribosomes, membranes and nucleic acids
    • -enzyme activity
  75. Calcium
    • -macronutrient 
    • -stabilize cell walls
    • -heat stability of endospores
  76. Sodium
    • -macronutrient
    • -needed in marine microbes
  77. Iron
    • -used in cytochromes and FeS proteins in electron transport
    • -no oxygen=ferrous form Fe2+, soluble
    • -with oxygen=ferric Fe3+, insoluble mineral
  78. Siderophores
    -iron binding agents produced by cells to obtain iron from insoluble mineral form(ferric Fe3+)
  79. 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
  80. Growth Factors
    • -requires in small amount by certain organisms
    • -vitamins, AA, purines, pyrimidines
  81. Vitamins
    • -most commonly required as growth factors
    • -many function as coenzymes
  82. Defined Media
    • -used to grow microbes in the lab
    • -precise chemical composition is known
  83. Complex Media
    • -for growing microbes in the lab
    • -composed of digests of chemically undefined substances (yeast, meat extracts)
  84. Pure Culture
    -culture containing only a single kind of microbe
  85. Contaminants
    -unwanted organisms in a culture
  86. Exergonic reactions have what value of deltaG?
    • -negative value, release energy (exergonic)
    • -positive value, require energy (endergonic)
  87. Enzymes
    • -typically proteins, sometimes RNA
    • -high specificity 
    • -larger than substrate 
    • -rely on weak bonds(H bonds, van der waals, hydrophobic interactions)
  88. Prosthetic Group
    • -bind tightly to enzymes
    • -bind covalently and permanently
  89. Coenzymes
    • -loosely bound to enzymes 
    • -usually derivatives of vitamins (NADH)
  90. Electron donor is?
    Electron acceptor is?
    • -donor is oxidized
    • -acceptor is reduced
  91. Reduction Potential
    -the more negative value donate to the less negative value
  92. Energy Storing Molecules
    • -ATP
    • -phosphoenolpyruvate
    • -Glucose-6-phosphate
    • -coenzyme A