EUKARYA - EUKARYOTES - TRUE NUCLEUS ANIMALS PLANTS PROTISTS – ALGAE & PROTOZOA FUNGI -MOLDS & YEASTS; SOME RESEMBLE PLANTS MORE CLOSELY RELATED TO ANIMALS ABSORB FOOD REQUIRE ORGANIC CARBON IN THE DIET BACTERIA -EUBACTERIA; TRUE BACTERIA PROKARYOTES; NO NUCLEUS - NUCLEOID SINGLE CELLS CONTAIN BOTH RNA & DNA ARCHEA -UNUSUAL BACTERIA - ARCHEOBACTERIA UNUSUAL ENVIRONMENTS HOT SPRINGS HIGH SALT CONCENTRATIONS VERY ACIDIC ENVIRONMENTS UNUSUAL CELL WALL COMPOSITION REPLICATION, TRANSCRIPTION; RIBOSOMES SIMILAR TO THOSE OF EUKARYOTES KINGDOMS - CELLULAR LINEAGES INTRO 1

INTRO 2 EUKARYOTES ARCHEOBACTERIA EUBACTERIA COMMON ANCESTOR [PROKARYOTIC]

INTRO 3 BACTERIAL CLASSIFICATION DIVISION, SECTION, FAMILY, GENUS, SPECIES DIVISION 1 -GRAM NEGATIVE BACTERIA STAIN RED WITH GRAM STAIN DIVISION 2 -GRAM POSITIVE BACTERIA STAIN BLUE WITH GRAM STAIN DIVISION 3 -BACTERIA WITHOUT CELL WALLS DIVISION 4 -BACTERIA WITH UNUSUAL CELL WALLS [ARCHEOBACTERIA] OTHER CHARACTERISTICS CELL MORPHOLOGY - SHAPE, SIZE MOTILE OR NON-MOTILE - [FLAGELLUM] COLONY COLOR, SHAPE, SIZE PATHOGENICITY [OR NON-PATHOGENICITY] BIOCHEMICAL PROPERTIES, SUCH AS PRODUCTION OF A CERTAIN ENZYME

INTRO 4 EXAMPLES DIVISION 1 - GRAM NEGATIVE BACTERIA SECTION 1 - SPIROCHETES - SPIRAL SHAPE, FLEXIBLE Treponema pallidum SYPHILIS DIVISION 2 - GRAM POSITIVE BACTERIA SECTION 16 - MYCOBACTERIA - RODS, THICK WAXY CELL WALLS, RESISTANT TO DRYING Mycobacterium tuberculosis TUBERCULOSIS SECTION 12 - SPHERES [COCCI, COCCUS] FAMILY 1 MICROCOCCACEAE GRAM POSITIVE SPHERES, GROW IN: IRREGULAR CLUMPS, or PACKETS OF FOUR, or PACKETS OF EIGHT GENUS - Staphylococcus - GRAM POSITIVE SPHERES, IRREGULAR CLUMPS

INTRO 5 GENUS & SPECIES Staphylococcus aureus - YELLOW COLONIES, PATHOGEN [BOILS, PIMPLES, BLOOD INFECTIONS, PNEUMONIA] Staphylococcus epidermidis - WHITE COLONIES, GENERALLY NON-PATHOGENIC Streptococcus pyrogenes - IMPORTANT PATHOGEN, GRAM POSITIVE, SPHERES, GROW IN CHAINS [NOT A MEMBER OF ANY FAMILY] “PYOGENES” - PRODUCING PUS STREP THROAT - RHEUMATIC FEVER, HEART VALVE DAMAGE TOXIC SHOCK SYNDROME SOME STRAINS CAUSE NECROTIZING FASCITIS [FLESH - EATING BACTERIA] “-ITIS” - INDICATION INFLAMMATION “FASCIA” - CONNECTIVE TISSUE BETWEEN SKIN AND MUSCLE OR BETWEEN MUSCLES “NECROTIZING” - KILLING

Phylogeny Based on Nucleotide Sequence of the Gene for the 16S Ribosomal RNA PHYLOGENY BASED ON DNA SEQUENCE HOMOLOGY (OR DEGREE OF SIMILARITY) From a common ancestor, mutations occurred within genomes, evolution occurred, and biodiversity is the end result. During evolution, the number of mutations within a chromosome (or within a given gene) increases with time. Therefore, relatedness of two organisms can be determined by measuring the degree of nucleotide sequence similarity within their genomes (or within a specific gene). That is, if two organisms share a great degree of homology within their genome, they are closely related and they evolved from a common ancestor relatively recently. There has not been much time for many different mutations to occur. On the other hand, if two organisms have a very low degree of homology within their genome, they are not closely related and they evolved from a common ancestor long ago. Over that long time, many mutations occurred. One of the gene sequences used to measure homology is the gene for the 16S ribosomal RNA (or 18S RNA in eukaryotes). This gene is advantageous because it is universally conserved (that is, present in all organisms), was likely to be present even in the most ancient organisms, and is neither too short nor too long. INTRO 6

Aquifex: Most ancient Hyperthermophile Chemolithotrophic Spirochetes: Flexible coils Treponema pallidum Borrelia burgdorferi Green Sulfur: Anoxygenic photosynthesis H 2 S S 0 SO 4 Chlamydia: Obligate intracellular bacteria Chlamydia trachomatis Cyanobacteria: Blue green bacteria Oxygenic photosynthesis; First O 2 - evolving creatures on earth Atmosphere converted from anoxic to oxic (Synechococcus) Gram positive: Staphylococcus Bacillus Proteobacteria: Gram negative rods and cocci Most common in medicine, agriculture, industry Phenotypes diverse e.g.Enteric Pseudomonas, N 2 -fixing Azotobacter INTRO 7

INTRO 8 COMPOSITION OF MEDIA ENRICHED / COMPLEX MEDIA EXTRACT OF BEEF MUSCLE, HEART, BRAIN EXTRACT OF YEAST CELLS [EXTRACT = EVERYTHING DISSOLVING IN WATER] MILK PROTEIN HYDROLYSATE [HYDROLYSATE = MACROMOLECULES BROKEN DOWN INTO LOW MOLECULAR WEIGHT, SOLUBLE COMPONENTS, SUCH AS AMINO ACIDS] DEFINED - EXACTLY KNOWN COMPOSITION GLUCOSE - CARBON / ENERGY SOURCE NITROGEN - NH 4 Cl SULFUR - MgSO 4 PHOSPHOROUS - Na 2 HPO 4 COMMON MINERALS Mg ++ K + Na + Cl - TRACE MINERALS Fe +++ Ca ++ WATER

MEDIA CAN BE LIQUID OR SOLID [SEMI-SOLID] LIQUID SOLUTIONS SEMI-SOLID - ADD A GELLING AGENT - AGAR AGAR: MELTS AT 100ºC [WHEN THE MEDIUM IS HEATED FOR STERILIZATION] SOLIDIFIES AGAIN AT 41ºC [WHEN THE MEDIUM COOLS] PETRI PLATE INTRO 9

DRY HEAT ºC, 2 HOURS MOIST HEAT -AUTOCLAVE 121ºC, 15 POUNDS/SQUARE INCH, 15 MINUTES FILTRATION -STERILE FILTER 0.45 MICRON DIAMETER PORES IN FILTER BACTERIA = 1 X 3 MICRONS INCINERATION -FLAME INOCULATING WIRE POISON GAS - ETHYLENE OXIDE, PLASTICWARE RADIATION -GAMMA RAYS, X-RAYS PLASTICWARE STERILIZATION INTRO 10

INTRO 11 STREAK PLATE TECHNIQUE FOR PURE CULTURES 1. SWAB 2. STERILE LOOP 3. STERILIZE LOOP, STREAK AGAIN PETRI PLATE AFTER INOCULATION PETRI PLATE AFTER INCUBATION COLONY, PURE KOCH

INTRO 12 STAINS SIMPLEFIX CELLS ON SLIDE ADD DYE [CRYSTAL VIOLET] ALL CELLS TAKE UP DYE WASH AWAY EXCESS DYE NEGATIVE STAINCOLORS BACKGROUND, CELLS APPEAR WHITE GRAM STAINFIX CELLS CRYSTAL VIOLET PLUS IODINE [ALL CELLS STAIN VIOLET] WASH WITH ALCOHOL [ALCOHOL REMOVES DYE FROM GRAM NEGATIVE CELLS] ADD SAFRANIN - COUNTER STAIN TO STAIN GRAM NEGATIVE CELLS RED ACID FASTFIX CELLS DYE WITH HEAT DECOLORIZE WITH HEAT AND ALCOHOL MOST CELLS ARE NOW COLORLESS; MYCOBACTERIA RETAIN RED DYE