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Microbiology tonic

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Microbiology tonic

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The study of small living things - germ, virus, bacteria, fungus, parasite
     The study of wide and diverse group of microscopic organisms that are
parasitic, saprophytic (saprobic) or free living and that exists as single cells,
cell clusters or multi-cellular organisms
Microscopic - seen only with a microscope
Parasitic - depends totally on living organisms (host) for its survival
Saprophytic - decomposes, live off death and decaying matter (fungi)
Free living - live entirely on its own
      2 types
         solitary - single celled organisms (ameoba, bacteria)
         colonial - clusters of cells share a common space (algae)
Multi-cellular - parasitic insects, arthropods, worms

  Bacteriology - bacteria (highest reproductive rate)
  Virology - viruses
  Mycology - fungus
  Phycology - algae
  Parasitology - parasites
  Helminthology - parasitic worms
  Protozoology - animal like, single celled

Focus of General Microbiology Course
  Procaryotes - no nucleus or membranous organelles
  Microscopic Eucaryotes - True nucleus and many organelles

Example of the significance of Microbiology as a Natural Science
- Anthrax is a disease caused by the organism Bacillus anthracis (bacterium)
       - DISEASE - results in damage or harm to the body
       - Infectious diseases – diseases caused by organisms that invade and
       spread throughout the body causing damage
- “Etiological agent” of a disease = causative agent
       - Bacillus anthracis (a bacterium) is the etiological agent of Anthrax
       disease. It is a rod-shaped bacterium capable of producing endospores
              -Bacillus - rod shape organisms
              -Bacillus - genus name
- AIDS – disease; HIV – a virus that is the etiological agent of the disease
    -resistant to chemical disinfectants, antiseptics, antibiotics, freezing,
    dessication, radiation
   - capable of germinating to re-establish vegetative cell
   - inc. in environmental glucose is major initiator of sporogenesis
      - can be destroyed only with sterilization procedure (121 degrees C,
      under 15# pressure/square inch for 15 – 20 minutes)
      - formaldehyde, gluteraldehyde, ethylene dioxide gas are chemical

Moist Heat (boiling) for as little as 15 seconds at 42 degrees C or higher
KILLS most growing, vegetative cells

Louis Pasteur first described conditions required for steam sterilization that
ensures destruction of bacteria endospores.
  Can not sterilize a room; Can disinfect a room

Bacillus anthracis
    -1st organism found to be the specific cause of a specific infectious
    -1st identified in cattle
     - manifests in three ways - depends on portal of entry
       1) pulmonary anthrax - lungs 90% fatal if not treated
       2) cutaneous - skin - easier to treat
       3) gastrointestinal - diarrhea, nausea and vomiting

PROCARYOTE                   versus              EUCARYOTE

1) No true nucleus                               True nucleus
    Nucleoid                                       has DNA, genetic material
     No membrane                                   contained in a membrane
      Region of "naked" DNA                        bound space

     DNA has NO histones;                        DNA has histones;
     One Big DNA circular                        Chromosomes are linear,
     E.coli DNA is 1400 um                       in pairs
     in (1.4 mm)

Central Dogma of Molecular Genetics in All CELLULAR organisms:
     Replication           Transcription     translation & protein
                                             Synethesis (on ribosomes)

2) Reproduction by Binary fission               Reproduction by mitosis
   - NO mitosis,meiosis; essentially do:        and/or meiosis:
      - G1 - part interphase (growth)            mitosis-nuclear division
      - S - DNA Replicates, and                  meiosis-prod. gametes
      - Cytokinesis
      -considered haploid                         Most are diploid

3) Highest reproductive and                  Slower reproductive and
   metabolic rates known:                    metabolic rate:
   -average GT =17-20 minute                 - humans GT = 15 - 20 years
    (GT = generation time)                    - ameoba 3 - 5 hours
     1 cell (10-9 oz.) in 24 to 48 hours =
        2144 (80 tons)

4) NO membraneous organelles                      numerous membraneous
                                                  organelles: mitochondria,
  only organelle is the Ribosome                  (makes ATP) golgi,ER,
                                                    Highly specialized
    70s                         s = svedburg units                80s
                        determine density of small cell parts
                                                tRNA molecules attach
                         large subunit           carry amino acids

                                                   mRNA codones feed

              small subunit
                                                    Protein synthesis =
                                                    proteins are made

  Total Density 70s (50s and 30s)          Total Density 80s (60s and 40s)
              (Different density when together than when apart)

Many ANTIBIOTICS will INHIBIT protein synthesis on 70s ribosomes but
will have NO effect on 80s = SELECTIVE TOXCITY: TOXIC to
prokaryotes; NOT eucaryotes
      - IMPORTANT because - humans are eucaryotes
             - Antibiotics Effective on Procaryotes
      -Chloramphicol, tetracycline,erythomycin,streptomycin inhibit protein
      synthesis on 70s but not 80s ribosomes

5) procaryotic flagellum                             euk. Flagellum is a
   is a single fiber of protein                      9 + 2 arrangement of
   subunits called flagellin                         protein fibers

6) HIGHLY susceptible to drugs,                        Resistant
    antiseptics, disinfectants
      70s ribosome density SELECTIVE TOXICITY 80s ribosome density
    Microbes CAN become resistant
    KNOW the difference
                 Mass = Density (size + weight)
7) Size 1 to 5 micrometers                   >10 mm average 150-180 mm
                          1 mm = 1,000 micrometers
                  1 micrometer = 1,000 nanometers (used to measure viruses
          1 million nanometers = 1 millimeters

In light of some of the above differences in pro- and eukaryotes, you should
also know:
Procaryotes and Eucaryote are ALIKE in a few ways:
   1) both have ribosomes (although they differ)
   2) cell membranes are essentially phospholipids bilayers
   3) DNA AND RNA are present
   4) cytoplasm/protoplasm (A cell solution is present)

Mitochondria and chloroplasts are membranous organelles in eukaryotes that
are believed to have evolved from prokaryotes.
Q: Is there any evidence in the scientific literature to support this theory?


All cells have ribosomes for protein synthesis. All cells then have proteins.
Q: Why is protein synthesis, and therefore the presence of proteins, so
important in cells?

A: Think in terms of what you know about groups of proteins that are
identified based on their functions in developing your answr.
       Marker -
       Structure -
       Enzyme -
       Transport -
       Immune -

The Diversity of Life: Taxonomy and Classification

3 Domains in the living world:



       1) Eukarya         {1 is eucaryotic}
       2) Archea
       3) Bacteria        {2,3 are Procaryotic, unicellular}
      Eukarya contains 4 Kingdoms differentiated based on cellular
      organization and structure, means of reproduction, motility, nutritional
           1) Protista - unicellular, algae, protozoa
           2) Myceteae - fungi, uni or multicellular, have cell walls
           3) Plantae - plants, multicellular, have cell walls
           4) Animalia - animals, multicellular, do NOT have cell walls

Classification: Diversity In Living World
3 Domains:

Eukarya                          Archaea                        Bacteria

6 Kingdoms:
1. Animalia                      Archaeabacteria                Eubacteria
2. Plantae                       ancient bacteria               Common,
3. Mycota-(mold,yeast            3.6 billion yrs old            true,bacteria
Mildew,smuts,rusts)              Inhabit harsh environ.         E.coli
4. Protisa-algae,protoza         Hot: >0-250 degrees            Staph
                                 Acidic: pH = 1-2               Strep
                                 Salty: 30 – 40% NaCl           Salmonella

Q: Which Domain; Which Kingdom? Consider:
    -Acellular, obligate intracellular parasites
    -Protein and a nucleic acid (RNA or DNA, never both)
         -Active - only when within their host cell
         -Inactive - outside the host - INFECTIOUS STATE

Classification: Carolus LINNAEUS 1700's
       "Binomial        Nomenclature         System"
        (2 name)         (naming of)
species/scientific name/scientific binomial = Genus + specific epithet

Currently, there are 8 Taxa of Classification:
Q: What is a Taxon (sing. Form of Taxa)?
The 8 Taxa:
              GENERA (GENUS)
Bergy's Manual of Systematic Bacteriology = BMSB
4 volume group of books that identifies nearly 4800 species of Bacteria:

Procaryotes:     4 DIVISIONS of Bacteria          7 CLASSES of Bacteria

4 Divisions (1st 3 are Eubacteria; 4th is Archaebacteria
1. Gracilicutes    2. Firmicutes     3. Tenericutes    4. Mendosicutes
Gracilis = thin    firmi = thick     teneri = soft     mendosi=false
Thin skin bacteria thick skin        soft skin         false skin
Thin cell wall     thick cell wall   NO cell wall      cell walls of
1layer of PDG      multi layers PDG                    unique chemical
                                                       composition that
                                                       may or may not
                                                       have PDG
7 Classes distributed among the 4 divisions:
D1. Gracilicutes
      C1: Oxygenicphotobacteria - produce O2 - use photosynthesis l
      C2: Anoxygenicphotobacteria - does NOT produce oxygen as a by-
      product of photosynthesis.
      C3: **Scotobacteria - gram negative bacteria of medical importance
D2: Firmicutes
      C4: **Firmibacteria - gram positive bacteria
      C5: **Thallobacteria - gram positive filamentous bacteria
D3: Tenericutes
      C6: **Mollicutes - mycoplasma - gram negative - walking pnemonia
D4: Mendosicutes
      C7: Archaeabacteria

** Contain the majority of pathogenic and potentially pathogenic
Species name = genus name + specific epithet
  Genus name is Capitalized and underlined
   Specific epithet is not capitalized
      i.e. Bacillus anthracis

Q: Are you able to classify completely:
Borrelia burgdorferi
Chlamydia trachomatis
Rickettsia rickettsii
Mycoplasma pneumoniae

Gonorrhea one of oldest known diseases - symptomatic in males - painful
Known about infectious diseases for 1,000's of years
1500 - 1600's: 3 questions sparked new interest in natural sciences
  1) Does spontaneous generation occur?
     ? life arise from non-living matter
     (abiogenesis = a - without bio - life genesis – beginning)
  2) What is the Nature of contagious diseases
  3)? Prevent, control and treat contagious diseases

1547: Fracastoro, while peeling an onion - felt that his body's response
must be from invisible particles or seeds
   1st hypothesis proposed there may be infectious diseases caused by
   invisible particles or seeds
   2nd: Fomite - inaminate object – may be a source of transmission of
   disease from person to person

1500 - 1600 until mid 1800's
Few advances due to wars, focus on controlling pain; loss of focus on
infectious diseases
1664     Hooke
   coined the term "CELL"
   With hand-held magnifying lenses observed (among others) cork tissue -
looked like cubes in the monastery that were called cells
    Led to "cell theory" - all living things are cellular and all living cells
                          come from living cells.
1668      REDI
   did not believe in spontaneous generation
   did experiments to show it doesn't occur, rotten meat covered and
     uncovered with growth of maggots, larvae found on covering
      -suggested life comes from existing life
1668     NEEDHAM
   challenged Redi, controversy between the two.
   Needham provided evidence to support spont. Gen.
Later was discovered that Needham’s technique was poor and results
probably due to contamination.

1684         LEEUWENHOOK              "FATHER OF BACTERIOLOGY"
Made and used over 300 hundred different microscopes, son of a glassmaker
Discoverer of microbial world
1) described in detail microscopic organisms, cell types
2) described the 3 major morphological classes of Bacteria (based on shape
or form)
   bacilli - rod shape (longer than wide, and cylindrical)
   cocci - round shape (spherical, ball shape)
   spirilla - curved rods (bent)

1790      Hunter
Dedicated physician. Interested in gonorrhea symptoms, stages,
development and course of the disease.
Inoculated himself with an inoculum from patient with gonorrhea NOT
knowing patient also had syphillis. He died from syphillis.
    Major contribution to understanding infectious diseases

1847        Oliver Wendall Holmes & Semmelweis
Both concerned with childbed fever (puerperal fever) in post partum wards
after childbirth. 90% new mother's were dying after giving birth. Doctor's at
that time did their own autopsies and before going home they would go back
after doing autopsies and check the new recently delivered mothers. Did so
WITHOUT changing clothes or washing up between the two activities.
Semmelweis and Holmes found puerperal fever to be transmitted by
“cadaveric particles”
They instituted handwashing between these activities AND changing of
clothes and found immediate results in reduction of deaths due to instigation
of aseptic techniques.

1854       Snow
Specific etiology of specific disease. He found direct link between well
water contaminated with Vibrio cholerae and cholera epidemic.
1857           Pasteur                      "Father of Microbiology"
Published his 1st paper on Anthrax in cattle
His work started the "Golden Age" of Microbiology
Duplicated work of Redi and developed more technical experiments to test
spontaneous generation.
Classic “swan-neck flasks” experiments supported Redi's abandonment of
the theory.
1) refuted abiogenesis
2) discovered anaerobic respiration
        Was asked by wine industry to help figure out why wine turning to
        vinegar found wine was contaminated
3) developed "Pasteurization" to purify the wine; for foods and beverages,
moderate heat for 30 minutes, cool rapidly
       -keeps alcohol from boiling away and destroys contaminants
       - kills pathogens, does NOT sterilize, purifies or decontaminates
       without destroying good qualities of food/beverage.
4) was asked to help figure out why cattle were dying; indentified
Bacillus anthracis in cattle, boiling and pasteurizing didn't destroy the
pathogen. Independently, concurrently with Ferdinand Kohn:
     -Found and described endospores in bacteria that caused anthrax in
5) described steam sterilization procedure to destroy endospores
           121 C, 15 lbs pressure /sq inch for 15 to 20 minutes
     6) developed and discovered First vaccine for RABIES
     7) Proposed "Germ Theory" of disease
       microorganisms may cause disease in animals; microbes could be a
       result of a disease rather than the cause.

1865 Robert KOCH "FATHER of Modern Day BACTERIOLOGY"
Involved in understanding of Anthrax.
1) PROVED Pasteur’s germ theory
2) Proposed of a set of criteria that must be met in order to prove that a
particular microbe causes a particular disease. Criteria became known as:

KOCH'S POSTULATES - to prove germ theory
     If you suspect a certain microbe causes a certain disease:
1) the suspected microbe MUST be found in EVERY case of the disease in
2) the suspected microbe must be isolated in axenic/pure culture (one
organism growing by itself) in the lab.
 3) inoculate the microbe into a healthy and susceptible host and that host
 MUST develop ALL the signs and symptoms of the disease.
 4) re-isolate the microbe in pure culture in the lab.

If all criteria are met, it has been proven that the suspected microbe causes
the suspected disease. Prior to this disease etiologies were unknown.

Koch also developed new procedures for producing and using biological
media and new techniques for growing and maintaining microbes in pure lab

1884      Hans Christian GRAM
  Gram stain
1887      PETRI
  petri plate, petri dish
1892      Ivanovski
  Russian scientist, first described VIRUSes
1910      Ehrlich
  magic bullet for syphillus
  substance - salvarsan (arsenic derivitive)
1796 Jenner
   SmallPox vaccine
   cover surgical wounds with phenol (carbolic acid)
1929 Fleming
   discovered Penicillin, FIRST true antibiotic
1935 Domagk
    sulfa drugs, (husband & wife team)

Procaryotic Morphology and Structure
Leewenhook, Father of Bacteriology, described 3 morphological classes
Bacilli - bacillus

  rod shape - 1-5 micrometers length, 0.1 - 0.5 micrometers in diameter

Cocci - coccus
  spherical - 1 - 5 micrometers in diameter
Spirilla - spirillum

    curved rods - 1-5 micrometers length-0.1-0.5 micrometers diameter
     spirochetes up to 30 micrometers

   Square shape

    star shape


  Diplococcus             bean, kidney shape Nieisseria menengitis

  Tetrad     Gaffkya sp.

  Cuboidal packet with 4 behind it, Sarcina sp., Sporosarcina sp.

  Chains         "Strepto" Streptococcus sp.

  Clusters       "Staphylo"     Staphylococcus sp., Micrococcus lutea

  Solitary                    E. coli, pseudomonas sp.

   Diplococcus          pair

   Streptobacillus       chain

   Pleomorphic         many varible shape and arrangements
   Palisade       picket fence    Corynebacterium diptheriae

   Filamentous      branch in cluster branch

Vibros     comma shape         Vibrio cholerae

TRUEspirilla@least 2 CURVES Spirillum undula,Rhodospirillum

Spirochetes   coiled springs     tightly coiled

Binomial Classification - Lannieus
  8 Taxa
Domain       Bacteria             Bacteria       Bacteria      Bacteria
Kingdom Eubacteria                Eubacteria     Eubacteria    Eubacteria
Division     Gracilicutes         Gracilicutes   Gracilicutes  Tenericutes
Class        Scotobacteria        Scotobacteria Scotobacteria  Mollicutes
Order        Spirochaetales       Rickettsiales  Chlamydiales  Mycoplasmatales
Family       Spirochaetaceae      Rickettsiaceae Chlamydiaceae Mycoplasmataceae
Genus        Borrelia             Rickettsia     Chlamydia     Mycoplasma
Species      Borrelia burgdorferi Rickettsia sp. Chlamydia sp. Mycoplasma sp.
(Lower) Bacteria - most primitive, smaller, simplier Chlamydia - smallest
cellular organism known to live
             Cell Membrane


                       70% water 30% solutes
      Cell Wall
                                              enfoldings of
                                              cell membrane
                                                                  Plasmids or Episomes
                  Ribosomes 70S
                                                                  extra DNA

 Glycocalyx capsule               Flagellum
 slime layer                                                        Fimbriae

The typical bacteria cell is HYPERtonic to its environment
Environment is HYPOtonic to the cell (water moves into the cell)
4 invariant bacterial cell structure
 1) cell membrane - delemyting barrier, semi-permeable
 2) nucleoid/DNA - blueprint of a cell, directs protein synthesis,
    transcription of RNA -protein enzymes
 3) ribosomes - 70 s
 4) protoplasm - chemical of metabolism reactions only occur in water
the rest of the cell is variant - find in some not in others
GLYCOCALYX pages 94,95
 Layer of polysaccarhides or polypeptides or both found outside of a cell
     membrane or cell wall
 Capsule - firmly held to cell with a smooth appearance
 Slime layer - loosely held, irregular
    Virulance-degree of pathogenesis, to what degree it can cause disease
 ENCAPSULATED (more virulant) bacteria have a glycocalyx
 Non-ENCAPSULATED bacteria have NO glycocalyx (less virulent=
    avirulent -doesn't make us sick)
  Storage area for food depository, for waste depository
   Survival value to bacterium
      allows resistance to phagocytosis (antiphagocytic)
      covers receptor sites-markers are not presented to WBC's
 avirulant can become virulant human tissue can be transformed (viruses)
  Transformation = absorb naked (loose) DNA from environment of dead
    encapsulated cell (heated bacterium to kill it, mixed with
    nonencapsulated, inoculated the mice and mice died)
  Antibodies produced in response to antigens of the capsule of the
       encapsulated bacteria (opsonins)[evolution for host]
  tie up polysaccrahides or polypeptides [antigenic-humoral response-
       production of antibodies]
  (K antigen)of capsule [evolution for the bacteria]
  capsule disintegrates and falls off the cell. [leaves macrophage able to
       identify for phagocytosis].
  Antibodies in the elderly, children, and immuno-compromised can't
       keep up with the reproduction of the bacteria.
 Antigenic - advantage for the host
 Antiphagocytic - advantage for the bacteria
    Encapsulated -wastewater-activated sludge forms
     Eubacteria EXCEPT Tenericutes
MOST important cell structure
Consists of peptidoglycan (PDG)
     proteins-polypeptides and
     complex chains of complex sugars

PDG - glycan polymers (big chain)
      are held together thru peptide linkages (bridges).
  Glycan polymer = 2 types of amino sugars
       NAG N-acetylgluseanine
       NAM N-acetylmuramic acid

  NAM           NAG          NAM
     B1,4 glycoside Bonds

                             Peptide Bridge
                             only between NAMS

   NAG         NAM          NAG

What is the significance of NAM, what makes it unique to the bacteria cell
wall?? It is only found here in the bacteria cell wall.

Glycocalyx - capsule, slime layer
             K-antigen - polysaccharides
             Encapsulated - Bacillus anthracis
  Psuedomonias - inhabits a wide range of environments = ubiquity
                   Indwelling catheters
   Transformed - naked DNA absorbed from cells in environment
   Virulent - degree of pathogenic causing
      Capsulated - non capsulated absorbs capsulated

   Tenericutes - NO cell wall
   Gracilicutes - thin cell wall
   Firmicutes - thick cell wall
 1) Peptide bridges (alternating NAMS)
 2) Glycanpolymers - NAG & NAM (amino sugars) Beta 1,4 linkages
1 and 2 form framework of the cell wall
Differences in CELL WALL
Gram negative
   8 amino acids in peptide bridge
   NO transpeptidation
   NO interbridge of 5 glycines

  NAM            NAG           NAM
     B1,4 glycoside Bonds
                               Peptide Bridge
                               only between NAMS

   NAG          NAM          NAG

Gram positive
13 amino acids in peptide bridge
   NAM                   NAG                  NAM
         B1,4 glycoside Bonds

                                              Peptide Bridge
                                              only between NAMS

     NAG                 NAM              NAG
                         4            5"Glycines"

  H              R

         N       C       C    O           H
  H              H
                                 R2       DEHYDRATION
 H           R       H
                             N   C        C      O    H
     N       C       C
 H           H

Last step in synthesis involves transpeptidation shifting of amino group to
form peptide bond interbridge.

Gram Negative Peptide Bridge 1 specific amino acid
    DAP (diaminopemelic acid) found only in Gram Negative peptide
     linkage in cell wall.

"L" form amino acid common in Nature (bends light to the left)
"D" form amino acid RARE in Nature (bends light to the right)

NAM is unique to bacteria cell wall

Penicillin (Beta Lactum antibiotic) inhibits transpeptidation (last step in
       forming peptide bridge)
      Penicillin works ONLY on young GROWING Gram positive cells

PROTOPLAST - Bacteria cell with NO cell wall
    Rupture very easily in hypotonic environments
Bacteria cells are typically hypertonic to their environment (leaves the
    environment hypotonic)
Bacteria Cells - 70% water and 30% solute

Major function - prevent premature osmotic lysis under hypotonic conditions
       Hypotonic cell ruptures in hypotonic environment by osmosis into
            the cell - cell ruptures
Mature cell NOT effected because Peptide bridges are already formed

DAP - significance is found only in peptide bridge of Gram Negative
  Bacteria, STOP DAP = NO peptide bridge, cell wall falls off = protoplast
 CONTROLS the growth of the bacteria
Gram Negative bacteria MORE resistant to antibiotics (E.coli, psuedemonas,
     salmonella, typhoid)
Gram positive cell wall is 90% PDG 10% Teichoic acid
 XXXX                           XXXX
 XXXX                           XXXX
 XXXX                           XXXX
 XXXX                           XXXX
           GRAM POSITIVE        XXXX
 XXXX                           XXXX
 XXXX                           XXXX
 XXXX         X=PDG             XXXX
 XXXX                           XXXX
 XXXX                           XXXX
 XXXX           = Teichoic Acid XXXX
 XXXX                           XXXX
 XXXX                           XXXX

Firmicutes "Thick skin"
Page 99
Gram negative cell wall is 15-20% PDG, 80-85% outer membrane material

            X GRAM Negative         X
            X                X=PDG  X
            X      lipoproteins     X
            X                       x
            X              Porins   X      Outer
Periplasmic X lipopolysaccaride
                                    X      Membrane
space       X    polysaccaride tail X
            X    lipo head
            X                       X

Gracilicutes- Thin Skin
Outer membrane - contains
phospholipids and proteins
lipopolysaccarides (LPS) lipo head and polysaccaride tail
lipoproteins (LP)
porins - transport proteins
Periplasmic space - has enzymes
ins - transport proteins
Periplasmic space - has enzymes

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