Micro Cumulative: UNIT 1

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Micro Cumulative: UNIT 1
2013-05-29 00:26:24

Unit 1...
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  1. What are the groups of microbe organisms:
    • Bacteria
    • Fungi (yeasts/molds)
    • Protozoa
    • Algaea
    • Viruses
    • Helminths
  2. Nomenclature
    Established by Carolus Linnaeus

    Two names: Genus + Speccific eptithet(species--always lowercased)

    ex: Staphylococcus aureus OR Staphylococcus aureus
  3. Bacteria (group)
    --> pro/eukaryotes?
    --> Shapes?
    --> cell walls?
    --> Reproduction?
    --> how do they eat?
    • Unicellular prokaryotes (means DNA is NOT in a nuclear membrane)
    • Either Baccillus (rodlike), coccus (sphere), spiral (corkscrewed)
    • Cell walls: Peptidoglycan (carb + prootein complex)
    • Reproduce by binary fission-divide into two equal cells
    • Some can photosynthesize, while others get food inorganically.
  4. Archaea (group)
    --> what are three groups?
    --> pathogenic?
    • Prokaryotic-No peptidoglycan
    • 3 groups: methanogens, extreme halophilles (salt lovers) and extreme thermophiles (hotsprings)
    • **NOT pathogenic
  5. Fungi (group)

    --> pro/euk?
    --> cell walls?
    --> uni/multi cell?
    --> 2 types and characteristics?
    • Eukayotes
    • Uni or multicellular
    • cell walls: chitin
    • yeast: unicellullar
    • mold: reproduce either sexually or asexually
  6. Protozoa:

    --> Pro/euk?
    --> uni/multi cell?
    --> how do they move?
    --> how do they survive?
    • Unicelluar
    • Eukaryotic
    • Move with: flagella, pseudopods, cillia
    • environments: free living or parasitic
    • Some can photosynthesize (euglena)
  7. Algae:

    --> pro/euk?
    -->Uni/multi cell
    --> cell wall:
    --> most common where?
    --> how do they help envir?
    • Photosyn. Eukaryotes
    • usually unicelluar
    • cell wall: cellulose (carb)
    • Most found: in fresh water, salt water, and soil

    ex: spyrogyra, diatoms,

    **Produce O2 and carbs for other organisms.
  8. Viruses:

    --> Nucleus memb?
    --> euk/pro?
    --> where do they reproduce?
    • Accellular o.0
    • Either only have DNA or RNA in a lipid membrane (neither euk/pro)
    • Reproduce in hosts
  9. Helminths:
    multicellular animal parasites

    Includes: flat and round worms
  10. Three Domains & 4 kingdoms:
    • Bacteria
    • Archaea
    • Eukarya
    • 1.Animalia-Helminths
    • 2. Protista: protozoa & algae
    • 3. Fungi
    • 4. Plants (no microbes)
  11. Gram Positive:
    Bacteria that retain the dye after decolorizing alcohol

    -->thicker peptidoglycan cell wall,dye and iodine enter and form CV-I complex-larger molecule than crystal violet molecules that entered, so it cannot leave==> so alcohol does not wash out the dye.
  12. Gram Negative:
    Bacteria that LOSE the dark violet color after decolorization

    (safranin must be added to stain these pink to counter the original purple stain so called a "counterstain")

    • --> contain layer of lipopolysaccharide as part of cell wall (alcohol wash disrupts this outer layer, and the "CV-I" complex is washed out through the thin layer of petidoglycan)
    • -->must be redyed with safranin. :)
  13. Diphtheria:
    Upper respiratory Bacterial infection caused by Corynebacterium diphtheriae
  14. Diphtheria Symptoms:
    Begins with sore throat and fever, neck swells

    • -often affects throat(pharynx) and larynx (voicebox)
    • -creates a pseudomembrane of fibrin, dead tissue and bacterial cells that clogs throat/air passage
  15. Diphtheria Microbe:
    • Microbe: Corynbacterum diphteriae
    • --> gram positive
    • --> non-endospore-forming rod
    • --> cell arranged: palisades
  16. Diphtheria Vaccines:
    • DTap Vaccine: for children, "D" stands for Diphtheria toxoid (inactivated toxin) that allows body to make antibodies against diphtheria.
    • --> "Toxoid vaccine" based on inactivated exotoxin

    Tdap booster: teens and adults (combined with tetanus shots)
  17. Diphtheria Transmission:
    Droplet transmission; resistant to drying (coughing, sneezing, talking)-also skin contact with humans
  18. Exotoxin:
    • Toxic proteins secreted by bacteria;
    • produces strains that cause disease.
    • Related bacteria are present on skin and are not pathogenic.
  19. Mortality and complications from Diphtheria
    • Suffocation/death-children mostly
    • Heart/peripheral nerve damage
  20. Diphtheria Diagnostic methods & treatments
    Diagnose: throat swab culture; PCR (polymerase chain reaction-method to make many DNA copies) to grown and study

    treatments: Antibiotics & antitoxins (penicillin/erythromycin)
  21. Pertussis:
    Whooping cough; damages cilliated cells in respiratory system

    • -paralyzes the cilliated cells
    • -cause inflammation
    • -impairs immune response
  22. Pertussis Microbe
    • caused by Bacterium "Bordetella pertussis"' obligatory aerobic
    • gram negative
    • coccobacillus
  23. Pertussis Mode of Transportation
    Transportation: respiratory droplets (coughing/sneezing)
  24. The stages of Pertussis:
    First Stage (catarrhal stage) resembles common cold- coughing, sneezing, low fever (100 deg F)

    Second Stage (Paroxysmal stage): severe prolonged coughing fits, may make "whoop" sounds; difficult to cough up phlegm when cilliated cells are destroyed.

    Third stage: coughing eventually become less frequent and less severe (convalescence)
  25. Pertussis Complications:
    • -break ribs
    • -brain damage/death in babies by coughing
    • -pneumonia
  26. Pertussis Diagnosis
    Diagnosis: culturing bacteria (swab and identify)
  27. Pertussis Treatments:
    -Herd immunity
    • 1. First stage: give antibiotics
    • 2. second stage:
    • 3. DTaP: subunit of pertussis (begins at 2 months old, given 3 shots total)
    • 4. Boosters for teens
    • 5. Tdap: adults
    • 5. Vaccine rate: 93% herd immunity (reduced chance of infection of vulnerable individuals if a certain high percentage of individuals in the populations are vaccinated or immune.)
  28. Prokaryotes: distinguishing characteristics
    • 1. Dna has no enclosed membrane
    • 2. lack membrane enclosed organelles
    • 3. cell walls are complex polysacharide peptidoglycan
    • 4. Divide with binary fission
  29. Eukaryotes
    • 1.Has nucleus to sep dna from cytoplasm
    • 2. have many membrane enclosed organeles
    • 3. chemically simple cell walls.
    • 4. cell division: mitosis.
  30. Prokaryote vs Eukaryote Structures (image)
  31. Plasma Membranes: Prokaryote vs. Eukaryote
    BOTH have it!

    similarities: phospholipid bilayer with proteins, separates cells from outside

    Differences: not applicable
  32. Cell Wall: Prokaryote vs. Eukaryote
    • Prokaryote:
    • Bacteria has peptidoglycan;
    • Archea-Pseudopeptidoglycan

    • Eukayotes:
    • Fungi: Chitin
    • Plants&Algae: Cellulose

    Similarities: structural support, resists bursting, made of polysaccharides

    Differences: Chemical composition; some eukaryote do lack cell walls
  33. Chromosome (genetic material)
    Prokaryotes: Circular, only one chromosome in "nucleoid" region

    Eukaryotes: Linear, variable number of chromosomes/associated with histone protiens

    • Similarities: Made of DNA
    • Differences: Different (?) and organization
  34. Nucleus: Prokaryote vs. Eukaryote
    • Prokaryote: NONE
    • Eukaryote: Present :D

  35. Flagellum: Prokaryote vs. Eukaryote
    Prokaryote: Rotational motion in Bacteria

    Eukaryote: whiplike in animals

    • Similarities: Locomotion
    • Differences: Diff type of motion & chem compositon
  36. Ribosomes: Prokaryote vs. Eukaryote
    • Prokaryote: Present
    • Eukaryote: Present, some associated with RER

    • Similarities: Protein synthesis
    • Diffs: prok have smaller ribosomes
  37. Membrane Bound Organelles: Prokaryote vs. Eukaryote
    • Prokaryote: NOT PRESENT,
    • Eukaryote: Rough ER, Mitochondria, Golgi Body, lysosomes, chloroplast

    • Similarities:None.
    • Differences: Prok lack; euk often have several membrane bound organelles
  38. Capsule (pg 70)
    • Firmly attached to cell wall (made of glycolax-gelatinous polymer)
    • -protect pathogenic bacteria from phagocytosis :(
  39. Slime Layer
    • another type of glycolax;
    • Loose, thinner, flexible attached to cell
    • -Helps bacteria attach to surface
  40. Endospores (70. 95-97)
    -purpose and characteristics
    -endospore components
    Resting structures formed by some bacteria, allows for survival during adverse environmental conditions (dry conditions)

    • Characteristics:
    • very little water
    • resistant to heat, uv rays and disinfectants

    • Components: cytoplasm, plasma membrane, ribosomes, peptidoglycan, spore coat (protein) and dipicolinic acid

    Locations: terminal(very end), central and subterminal (almost end)

    ex: clostridium tetani
  41. Sporulation:

    • 1. DNA is replicated
    • 2. Endospore forms when plasma membrane, peptidoglycan layer, and spore coat surround DNA
    • 3. endopsore is related as vegative cell disintegrates

    "germination": return of endospore to it's vegetative state
  42. Practice questions:
    1. How do you get rid of endospores?
    2. How is an endospore diff from a begetative cell?
    3. can bacteria reproduce by using endospores?
    4. what would happen if an endospore got into bloodstream of a patient?
    5. Do we need to strilize our food to get rid of endospores?
    • 1. calibrate by increasing or decreasing temp
    • 4. spermination
    • 5. Pasteurization, canned food: get rid of botchulism endospores
  43. EPS: extracellular polymeric substance
    a glycocalyx that helps cells in biofilm attach to target environment and allow bacteria to survive
  44. Endoplasmic Reticulum (ER) & RER
    • Nuclear envelop attached to Endoplasmic Reticulum (ER)
    • --surface for chem reactions and transport network.
    • --RER: protein synthesis/transport
  45. Golgi complex:
    flattened sacs (cisterns); fuctions in membrane formation & protein secretions
  46. Lysosomes:
    form by golgi complexes; store digestive enzymes
  47. vacuoles:
    memb enclosed cavities; give rigidity to plant cells
  48. Mitochondria
    • primary ATP site production;
    • contain 70S ribosomes & dna.-multiply by binary fission
  49. Peptidoglycan:
    polymer consisting of NAG (N-acetylglucosamine) & NAM (N-acetylmuramic acid) and short amino acid chains; penicillin interferes with this wall

    --in gram positive cell walls; crystal violet combines with peptidoglycan but decolorizer removed the lipid outer memb of gram negative bacteria and washes out crystal violet.

    Gram neg walls: thin peptidoglycan layer and a lipopolysaccharide-lipoprotien-phospholipid layer (-.-)
  50. Gram Negative cells (chemical structure)
    • -MUCH more complex-Thin layer of peptidoglycan
    • -LPS (lipopolysaccaride)
    • -Porins
    • -Periplasms with chemoreceptors: gel like fluid between outer membrane and the plasma membrane
    • -NO teichoic acids;

    • OUTER membrane: contains LPS, lipoprotiens and phospholipids
    • --gives wall strong neg charge
    • --provides barrier to antibiotics, digestive enzymes,and dyes
    • --Porins: channels allow nucleotides, amino acids
  51. Gram Positive Cells (chemical structure)
    • -Many layers of peptidoglycan
    • -Thick ridgid structure
    • -teichoic acids: alcohols (glycerol) and phosphate; gives wall antigenic specificity to allow group into "gram pos" cells
  52. How do Gram stains work?
    -Crystal violet purpose
    -Iodine purpose
    -Alcohol effect to both walls
    - ADD what dye after, what kind of dye is this?
    -Based on differences between cell wall structure (type of differential stain)

    Crystal violet (primary) stain both cells

    Iodine: forms large crystals with dye that are TOO large to escape through wall

    Alcohol: dehydrates peptidoglycan of gram positive cells and make it more impermeable to crytal violet-iodine. BUT on gram negative: the alcohol dissolves the outer membrane of gram negative cells and even leaves small holes in the thin peptidoglycan layer SO THAT crystal-violet-iodiine leaves!

    This is why safranin must be added to stain gram negative cells (turn them red)--contrasting stain
  53. Tetra peptide Side Chain
    • Composed of NAG & NAM
    • -NAG: N-acetylglucosamine
    • -NAM: N-Acetylmuramic acid
  54. Bacterial shapes:
    coccus, spiral, star, pleiomorphic
    • Rod/bacillus: cylinders
    • coccus: sphere
    • spiral: spirillium (w/flagella) or spirochete (axial filaments-rotate)
    • star
    • pleiomorphic: many shapes (corynebacterium diphtheriae-cause diphtheria)
    • coccobacilillus
  55. Bacterial Cell ARRANGEMENTS:
    • the ways cell stick together:
    • 1. strepto: chains of cells
    • 2. tetrad: group of 4 cells
    • 3. stahylo: grape like clusters
    • 4. palisade: picket fence
    • 5. diplococcus: two circle oo
  56. Cytoplasmic bodies
    Nutrient storage
    metachromatic granules
    • a. nutrient storage:
    • --> ex: polysaccharides granules for store starch
    • --> lipid inclusions store lipids
    • -->sulfur bacteria store sulfur as energy source

    • b. metachromatic granules with phosphate (turn red): inorganic phosphate storage
    • --> used to diagnose Corynebacterium diphtheriae

    c. magnetosomes: contains iron compounds, use to orignet to magnetic fields
  57. Pili and Fimbriae
    Pili: straight, hairlike, gene transfering

    Fimbria: straight hairlike for attachment ex: neisseria gonorrheae
  58. Flagellum


    Parts of flagellum?
    long appendages that propel bacteria

    monotrichous: single flagellum at one pole

    Peritrichous: flagella distributed over entire cell

    amphitrichous: flagella at both poles of the cell

    flagellin: protein that is the main component of the filament

    • Main parts of flagella:
    • Basal Body-anchored the whole flagellum to the cell wall and PM
    • Hook: rotates
    • filaments
  59. Biofilms
    -Community of bacteria; form at liquid-solid interfaces; slime layer (extracellular polymeric substance-EPS:helps bacteria attach to surfaces)

    -protected from antibodies and antibiotics; wbc's create inflammation

    -found: teeth, rock in a pond, pet's waterdish

    • advantages of biofilm:
    • prevents dehydration
    • share nutrients
    • protection from host immune system (antibodies or wbc phagocytosis)
  60. Biofilms Review Questions:
    1. Explain how a biofillm protects bacteria from antibiotics
    2. Best way to get rid of biofilms
    • 1. Protective barrier
    • 2. Physically remove them
  61. Quorum Sensing:
    • Bacteria organize into communities using chemical communication to make biofilms,
    • disruption will allow for prevetnion
  62. Dehydration synthesis:
    removes water; convalently link molecules (CONDENSATION)
  63. Hydrolysis:
    ADD water to break apart two covalently linked molecules
  64. Four groups of biological molecules?
    • 1. carbs
    • 2. Lipids
    • 3. Proteins
    • 4. Nucleic acids
  65. Carbohydrates
    Functions: energy source/storage, carbon source and part of cell structure

    • -Composed of C,H,O
    • -Hydrophillic (waterloving)


    -Monosaccharides: hexose, pentose

    -Disaccharides: lactose (glucose+galactose) and sucrose/canesugar (glucose and fructose)

    -Polysaccharides: cellulose (plant/algae cell walls), starch (energy storage), petidoglycan (bacterial cell walls)
  66. Lipids functions and structure::
    1. triglycerides
    2. fatty acids
    3. saturated vs. unsaturated
    4. phosoplipids
    5. sterols
    Fn: energy storage, cell memb components

    Structure: C,O,H and sometimes P & S

    -HydroPHOBIC (dont dissolve)

    Triglycerides: 3 carbon glycerol + 3 Hydroxyl (OH) groups

    Fatty acids: C-H chain + carboxyl group at the end

    saturated fatty acids: only single bonds b/w carbons (fats: butter and shortening)

    Unsaturated: double or triple bonds give it a kink (oils)

    Phosoplipids: two fatty acids + glycerol + phosphate group + "R" group (hydrophillic)

    Sterols: 4 connected carbon rings, not composed of fatty acids, hydrophoics
    FN: cell structure (flagella, cytoskeleton, enzymes, chem signals)

    exotoxins: transporters in cell membranes (botulism toxin)

    • Amino acid: building block of proteins:
    • --> amino group (NH2)
    • --> carboxyl group (COOH)
    • --> R group connected to central carbon

    Peptide bonds: created by dehydration synt. b/w 2 amino acides; spacial type of covalent bond

    Peptide: short chain of amino acids; Polypeptides (structure: primary, secondary, tertiary and quaternary sturcture)
  68. Nucleic Acids:
    DNA: genetic code/template fro protein making

    RNA: helps make proteins

    • Nucleodtide has 3 parts:
    • 1. 5C sugar (ribose/deoxyribose)
    • 2. Phosphate backbone(PO42-)
    • 3. Nitrogenous base (can form H bonds)

    • DNA bases: Adenine, guanine, cytosine, and thymine
    • RNA bases: uracil instead of thyamine

    ATP (adenosine triphosphate): function as energy "currency"; stores and provides chemical energy, made out of ribose, adenine and 3 phosphates linked together.
  69. Growth Condition Factors of Microbes
    • A. Temperature
    • B. Liquid water-with vapor
    • C. pH: most enjoy neutrality; peptones used as buffer salts in mediums
    • D. Nutrients: Carbon (auto/hetero) or Electrons (Chemotrophs)
    • E. Oxygen levels or Lack of it (need a balance)
  70. Temperature Requirements:
    Optimal, Minimal, Maximal
    • Minimum: lowest temp at which species will grow.
    • Optimum: best temperature for growth.
    • Max: highest temp at which growth is possible.
  71. Psychrophile
    • Likes 0-20 deg C
    • 15= optimum

    • -cold-loving microbes
    • -found in oceans/polar regions.
    • -unlikely to spoil food
  72. Psychrotroph
    Grow slowly at low temps but optimum from 20-30

    -Responsible for food spoilage; grow well at refrigerator temps though cold temps slow down reproductive rates.
  73. Mesophile
    Optimum: 20-40 deg temps "middle" (room)

    • -moderate-temperature loving microbes
    • -live in terrestrial/aquatic areas, plants & animals
    • - may cause disease: likes body temp of host
  74. Thermophile
    Optimum: 40 degs Celsius and higher

    • - heat-loving microbes
    • -endospores: fromed by these bacteria; may survive heat treatments given to canned foods.
    • -found: hot spring run offs; compost piles
    • ex: Thermus aquaticus: yellowstone
  75. Hyperthermophile

    • Optimum: Higher than 80 deg C (boiling/acidic water)
    • Domain: Archaea; different from bacteria (don't denature)

    ex: Sulfolobus (yellowstone)
  76. Acidophiles vs. Alkaliphile
    • Bacteria tolerant to acidity
    • -Molds: pH 5; Lactobacillus bacteria
  77. Halophiles:
    -->importance of osmotic pressure?
    --> extreme, obligate and faculative

    --> osmotic pressure: loss of water causes plasmolysis (shrinkage); imp b/c inhibits cell growth and preserve food

    Extreme halophiles/obligate(require) vs. Faculatative halophiles (don't require but won't hurt either)
  78. Chemical requirements:

    Oxygen: obligate aerobes, facultative anaerobes, obligate anaerobes

    Nitrogen :Dna & RNA synthesis; nitrogen fixation by cyanobacteria (anabaena)

    Sulfur: synthesize vitamins-biotin, thiamine

    Phosphorous: ATP synthesis; nucleic acids and phosopholids of cell membranes
  79. Aerobes
    a. Obligate
    b. Microaerophillic
    Use Oxygen; extract more energy from nutrients than anaerobes.

    • a.Obligate/Strict Aerobes: MUST have it.
    • --> disadvantaged b/c not much oxygen in water

    b. Microaerophilic: uses small amounts
  80. Anaerobes:

    a. Obligate
    b. Aerotolerant
    • a. Obligate: bacteria that are unable to use molecular oxygen for energy yielding reactions; require oxygen to live
    • ex: clostridium (known for botulism & tetanus)

    b. Aerotolerant: cant use oxygen for growth, but can tolerate it.

    -ferment carbs to lactic acid. ex: lactobacillus makes pickles/cheese
  81. Anaerobe Jar
    Forms water to remove oxygen
  82. Facultative Anaerobes
    Bacteria that have developed or retained the ability to continue growing WITHOUT oxygen.
  83. Biofilms
    -quorum sensing
    -form where?
    microbe communities; in slime (matrix of polysaccharides with DNA/proteins)

    • -quorum sensing: allows bacteria to coordinate activity and group together
    • ex: plaque, pond rocks

    • -work cooperatively on same task
    • -primitive circulatory systems: incoming nutrients and waste channels
    • -1000x More resistant to microbicides; form on medical devices
    • -protected by antibodies, WBC phagocytosis and antibiotics

    Preventions: block quorum sensing, incorporate antimicrobial into possible biofilm surfaces; must physically remove them
  84. Binary Fission Diagram
    Shows binary fission (bacteria) or mitosis (fungi) reproduction

    • a. Lag Phase: Preping/intense activity; no increase
    • b. Log Phase: exponential increase
    • c. Stationary Phase: equilibrium (deaths balance new cell production)
    • d. Death phase: decreasing population
  85. Nutrional names for organisms
    Phototrophs: use lights a primary energy souce

    chemotrophs: depend on oxidation-reduction reactions of inorganic/inorganic compounds for energy.

    • Autotrophs (self feeders: use CO2)
    • --> litotrophs(rock eaters)

    • Heterotrophs (use organic carbon source)
    • --> organotrophs