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5 Kingdoms
Prokaryotae, Protista, Plantae, Fungi, Anamalia
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3 Domains
Bacteria, Archaea, Eukarya
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Archaea: Cell wall - peptidomuran
membrane lipids - ether bonds tween hydrocarbons & glycerol
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Archaea - 2 Phylums
Crenarchaeota & Euryarchaeota
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Crenarchaeota -
anaerobic, thermophillic, acidophillic, oxidize S or H
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Euryarchaeota - Methanogens (reduce CO2 ->CH4)
live in rumen/intestines of animals, anaerobic, halophiles (require high [ ] NaCl, pump KCl into cell, Thermophillic-thermoacidophiles (high temp low pH), reduce S to H2S
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Domain: Bacteria
- most primitive
- Aquifex - microaerophillic chemolithoautotroph
- Thermotogas - anaerovic chemoorganohererotroph
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Deinococci
- spherical or tetrads
- aerobic
- Gram + (no techoic acid or outer membrane)
- resistant to drying & radiation (1.5 million rads)
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Photosynthetic - Phylum: Chloroflexi
- photosynthetic green nonsulfur bacteria & heterotrophic members
- bacteriochlorophyll
- anoxygenic
- thermophillic
- organic molecules as e- source
- filamentous (gliding motility)
- Chloroflex
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Phylum: Chlorobi
- green sulfur bacteria
- bacteriochlorophyll
- anaerobic
- anoxygenic
- H2S as e- source
- deposit S outside cell
- rods, cocci, or vibrios
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Phylum: Cyanobacteria
- largest/most diverse photosynthetic bacteria
- oxygenic
- chlorophyll a
- phycobilins in phycobilisomes
- 2 photosystems
- single cells (filaments)
- some fix N (heterocytes)
- some gliding motility
- Oscillatoria, Nostoc, Anabaena, Chroococcus
- Prochloron - (proposed ancestor of chloroplasts) chlorophyll a & b, DNA doesn't support hypothesis
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Phylum: Chlamydiae
- chlamydias
- obligate intracelllular parasite of mammals & birds
- small < 1um
- small genome
- no peptidoclycan wall (penicillin resistant)
- cannot catabolize carbs or synth ATP (energy parasites)
- Chlamydia trachomatis - eye & urogenital infection
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Phylum: Spirochaetes
- Spirochetes
- Gram -
- helical
- flixible
- 5-18 um long
- modified flagella in bundle (axial filament, outside cell inside outer sheath, swim corkscrew motion)
- Habitat - soil, water, animal pathogen
- Treponema pallidum - syphilis
- Borrelia burgdorferii - lyme disease
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Phylum: Bacteroidetes
- Bacteroides
- Gram -
- anaerobic rods
- mixed acid fermentation
- rumen/intestine/mouth of animals
- cellulose digestion
- 30% of population of human feces
- few pathogens
- Sphingobacteria - non-photosynthetic, non-fruiting, gliding, Gram -, sphingolipids in cell walls, not motile in suspension, degrade (cellulose, chitin, pectin, keratin, & agar), Cytophaga & Spirocytophaga
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Proteobacteria
- largest & most diverse
- variety of morphology, metabolism, and reproduction
- common 16S rRNA
- 5 Groups - a, b, y, s, e
- purple photosynthetic bacteria
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Class a-Proteobacteria
photoautotroph, chemolithotroph, organoheterotroph
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Purple nonsulfur
- Anaerobic - photoorganoheterotroph, bacteriochlorophyll, organic molecules as e- & C source
- Aerobic w/ no light - no bacteriochlorophyll, chemoheterotrophic, anaerobic muds, Rhodospirillum & Rhodopseudomonas
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Order Rickettsiales
- rods, cocci, pleimorphic (variable shapes)
- Gram -
- small < 1um
- obligate parasite in vertebrae cells
- Arthropod vectors - ticks, mites, fleas, cannot synth CoA or NAD from host, no glycolysis, oxidize organic acids in Krebs, can take up ATP from host
- Rickettsia rickettsii - Rocky Mountain spotted fever
- R. prowazekii, R. typhi - typhus
- Coxiella burnettii - Q fever
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Other a-Proteobacteria
- Rhizobiaceae - aerobic N fixers
- Rhizobium
- Agrobacterium (plant tumor causing)
- Nitritying bacteria (Nitrobacteriaceae) - oxidize NH4+ or NO2- ->NO3-, Nitrobacter & Nitromonas
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Order: Pseudomonadales
- Gram -
- aerobic rods & cocci
- Pseudomonas (degrade wide variety of molecules)
- Azotobacter (free living N fixer)
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Order: Vibrionales
- Facultative anaerobic
- Gram - curved rods
- Pathogens (Vibrio cholerae)
- bioluminescent bacteria (Photobacterium)
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Order: Enterobacteriales
- Family: Enterobacteriaceae
- largest group (35 genera)
- facultative anaerobic
- Enteric bacteria (live in animal intestines)
- most are mixed acid fermentation
- Eschericia, Salmonella, Proteus, Klebsiella, Enterobacter, Shigella, Serratia
- some are pathogens
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Order: Pasteurellales
- small non-motile parasites of vertebrates
- Pasteurella & Haemophilis
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Class: S-Proteobacteria
- chemoorganoheterotroph
- Order: Deslufovibrionales - anaerobic, dissimillatory S reducers, Use S or SO4 2- as e- acceptor, important in S cycle
- Bdellovibrio - bacteriovorous bacterium, chemoorganoheterotrophs
- Order: Myxobacteria - gliding - fruiting bacteria, chemoorgaoheterotroph, spores in fruiting body
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Class: B-Proteobacteria
- chemoheterotroph, chemolithotroph, photoautotroph
- Order: Neisseriales - Gram -, non motile, aerobic, chemoorganoheterotrophic cocci
- Neisseria gonorrhoeae & N. meningitidis
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Order: Burkholderiales
- aerobic
- Alcaligenes, Bordetella (whooping cough)
- Some sheathed bacteria - sheath attach cell to surfaces (Fe, Mn), aquatic & sewage treatment, Leptothrix
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Order: Nitrosomonadales
- chemolithotroph
- Nitrifying bacteria - oxidize NH4+ or NO2- -> NO3-
- Nitrosomonas & Nitrosococcus
- colorless sulfur bacteria - oxidize H2S, deposit S inside or outside cell, Thiobacillus
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Class Y-Proteobacteria
- largest group w/ some best know bacteria
- wide variety of metabolism - photosynthetic, many important chemoorganoheterotrophs
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Purple Sulfur Bacteria
- photosynthetic
- anaerobic
- oxidize H2S to S deposit in cell
- Chromatium
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Other Thiotrichales - non fruiting gliding bacteria
- S oxidizing
- Beggiotoa
- Thiothrix
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Class: E-Proteobacteria
- smalles group
- curved or straight rod
- Campylobacter - gastroenteritis
- Helicobacter - stomach ulcers
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Class: Mollicutes - Mycoplasmas
- no cell wall (penicillin resistant)
- very small < 0.9 um
- once thought to be virus
- smalles genome 580kb, 482 genes
- Genome sequence in 1995 in project to see what smallest genome to live would be
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Mycoplasmas
- Habitat - soil, water, pathogens of plants & animals
- Mycoplasma pneumoniae - atypical pheumonia
- M. Urealytica - STD in humans
- Plant diseases - lethal yellowing of coconut palms
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Class: Clostridia
- Clostridium - gram +, anaerobic, spore forming rod
- C. botulinum - boulism
- C. perfringens - gas gangrene & food poisoning
- C. tetani - tetanus
- C. difficile - diarrhea
- Epulopiscium - giant bacterium
- Veillonella - anaerobes in mouth & digestive tract of humans/mammals
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Class: Bacilli
- Order: Bacillales - gram + endospore forming rods, aerobic or facultative anaerobic, motile
- Bacillus: B. anthracis - anthrax
- B. cereus - food poison
- B. thuringiensis - insect protein toxin
- some make antibiotics
- Staphylococcus
- some human pathogens
- S. aureus - food poison & skin infection
- Order: Lactobacillales - large genus, non motile, non sporing, rods or coccobacilli, lactic acid fermentation, Milk - spoilage & cheese production
- Leuconostoc & Streptococcus
- S. pyogenes - strep throat & other infections
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Patterns of Cocci
- Single
- Diplococci (pair)
- Tetrads (4's)
- Sarcinia (4's layered like cube)
- Streptococci (chains)
- Staphylococci (grape like clusters)
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Actinomycetes
- Strptomyces - large genus, aerobes, antibiotics (Amphotericin B, Chloramphenicol, Erythromycin, Neomycin, Nystatin, Streptomycin, Tetrcycline), decompose (lignin, chitin, wax, keratin), smell of moist earth (geosmin)
- Micrococcus - cocci (tetrads), pigmented (yellow, orange, red), normal flora of human skin
- Corynebacteria - Norcardia, opportunistic infections of lungs, CNS & other organs human/animals, Mycobacterium - acid fast, high wax cell walls, M. leprae - leprosy, M. tuberculosis - tuberculosis, Corynebacterium diphtheriae - diphtheria, club shaped cells, Paisade
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Eukaryotic microorganisms
- Fungi
- Slime molds
- Protozoa
- Algae
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Fungi
Eurkaryotic, chemoorganoheterotroph, Saprotrophic - nutrients from non living organic matter, Pathogenic - nutrition from living organism, chitin cell wall (polymer of N-acetylglucoseamine), usually for hyphae (cylindrical cells, tip growth), Mass of hyphae (mycelium), reproduce by spores (sexual & asexual), often dimorphic
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Yeasts
- single celled fungi
- lost or alternate to hypal stage
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Fungal Classification - Kingdom: Fungi
- Division Chytridlomycota
- Division Zygomycota
- Division Ascomycota
- Division Basidiomycota
- Division Glomeromycota
- Division Microsporidia
- classification based on spore type & DNA sequence
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Division Chytridiomycota
chitin cell wall, asexual zoospores (single flagellum), Rhizophydium sphaerotheca, Thallus, divides to produce zoospores, some chytirds have sexual stage (flagellated gametes, Allomyces)
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Division Zygomycota
parasites & saprotrophs, haploid non-septate hyphae, coenocytic, chitin cell wall, asexual spores in sporangium, sexual spore - zygospore
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Division Ascomycota
- sac fungi, asexual spores (conidia), sexual spores (ascospores in ascus), saprotrophic, many plant parasites, many hyphal forms (some yeasts), septate hyphae, 1n hyphae w/ dif mating types (+)(-) fuse, dikaryon (cell w/ 2 haploid nuclei), fertilization, zygote, meiosis (4 haploid spores, 2(+)2(-), mitosis, 8 spores in ascus)
- Saccharomyces - Baker's yeast - unicellular ascomycete, sexual & asexual spores
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Division Basidiomycota
club fungi, sexual spores (basidiospores on basidium), mushrooms, dikaryotic hyphae
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Division Glomeromycota
- Mycorrhizal symbionts w/ plants
- fungus provides nutrients for plant & plant provides carbs to fungus
- only asexual reproduction
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Division Microsporidia
long confused taxonomy, formerly classified as protist, obligate intracellular parasite of animals, lack mitochondria (peroxisomes), Polar tube (penetrates host plasma membrane to infect cell)
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Division Deuteromycota
no longer considered a division, imperfect fungi, no sexual stages, Asexual spores (conidia), DNA allos classification - most Ascomycetes (Penicillium & Aspergillus) & Basidiomycetes
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Water Molds
- Division: Oomycota
- Kingdom: Chromista or Stramenopiles
- hyphae
- cellulose cell walls
- coenocytic (no septa)
- habitat - soil & water
- flagellated zoospores
- Saprolegnia - opportunistic animal pathogen
- Phytophtora infestans - Irish potato famine/blight of potato
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Slime Molds
- Division: Acrasiomycota - cellular slime molds, free living soil amoebae, pseudoplasmodium formed by aggregation of amoebae (some cells become stalk, some spores)
- Dictyostellum discoidium
- Division: Myxomycota - plasmodial slime molds, free living haploid soil amoebo-flagellate, two amoebo-flagellates fuse to make zygote, zygote nucleus divides (no cytokinesis), plasmodium (giant cell w/ millions of nuclei), migrates, spores
- Physarum polycephalum
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Viruses
- obligate intracellular parasites
- no cellular structure or metabolism
- many can pass thru membrane filter
- small - some <10nm
- Composition - nucleic acid, protein, some w/ layers of lipid or carbs
- can be crystallized
- cannot replicate w/o host cell
- not considered alive
- specific for host
- Viruses infect each domain
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Virus Structure
- usually cannot be seen in light microscope need EM
- Capsid - protein coat
- Capsid symmetry - Helical (helix of protein), Icosahedra (20 sides), Enveloped, Complex
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Enveloped Virus
- membrane derived from host cell
- around helical or icosahedral capsid
- virus proteins in envelope (spikes) allow virus to enter cell
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Complex Virus
- Pox virus
- Bacteriophage - combined helical & icosahedral
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Nucleic acids
- RNA
- DNA
- single or double stranded DNA/RNA
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Viruses of Bacteria & Archaea
- Bacteriophage - infect bacteria
- most are DNA viruses
- icosahedral, helical, complex, a few enveloped
- Phage attach to host by binding to flagella, pili, or cell wall
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Bacteriophage T4
- infects E. coli
- lytic cycle
- Complex capsid - elongated icosahedral head, helical tail, base plate & tail fibers
- DNA injected
- E. coli DNA degraded (2 min)
- Phage mRNA made
- Phage DNA replicated (5 min)
- Phage proteins made
- Virus particles assembled
- Lysis
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Animal viruses classification
- Capsid morphology
- Nucleic acid content
- Genetic relatedness
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Entry of virus into cell
- attachment to receptor
- fusion of viral and cell membranes
- endocytosis
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Release of Enveloped viruses
- pick up some host cell membrane
- budding
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Viruses & Cancer
- Oncogenes - gene that transform norm cell into tumor
- 7 types of human cancer caused -
- Epstein-Barr virus - Burkitt's lymphoma & nasopharyngal carcinoma
- Hepatits B & C - liver cancer
- Human Papilloma - cervical cancer
- HTLV - leukemia
- KS Herpes - Kaposi's sarcoma
- Merkel Cell Polyoma - Merkle cell sarcoma
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Latent infections
- viral DNA incorporated into host chromosomes
- remain latent for years
- can be activated & cause symptoms (Herpes & HIV)
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Plant Viruses
- wide variety infect plants - DNA or RNA, helical/icosahedral, enveloped & non enveloped
- many transmitted by insects
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Tobacco Mosaic Virus
- helical ss-RNA virus
- replicates in cells
- causes yellow lesions by inhibiting chlorophyll synthesis
- crystalline mass
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Fungal & Algal Viruses
- Fungal - viruses infecting Penicillium & Aspergillus (dsDNA), latent
- Algal - most know from EM
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Insect Viruses
- Iridiovirdae - icosahedral head, dsDNA, infects insect larvae, virus crystals cause iridescence
- possible biological control
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Viroids
infectious ssRNA, plant diseases, circular RNA 250-370 nucleotides, found in nucleus, potato spindle tuber disease
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Prions
- infectious proteins (no nucleic acid), cause degenerative neurological disorders
- animals diseases - scrapie (sheep/goats), bovine spongiform (BSE) mad cow disease
- named after Stanley Pruisner (nobel prize)
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Human Prion Disease
- Kuru (New Guinea)
- CJD - Creutzfeld-Jacob Disease
- Gerstmann-Straussler-Scheinker Syndrome (GSS)
- Fatal Familial Insomnia (FFI)
- infections progress slowly
- Symptoms - dementia, insomnia, uncontrolled laughing, lack of motor control
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Prion Chemistry
- Prion Protein (PrP) coded for by nuclear gene
- Membrane protein of neurons
- mutated gene has less a-helix more b-pleated sheet
- second conformation more stable
- converts norm to other form
- resists heat & acid
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