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Survey of the Microbial World
Unit 3: 5 days
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February 24th and 25th: Prokaryotes
• Important manuals divide bacteria based on several criteria:– Gram stain reaction– Cellular morphology– Oxygen requirements– Nutritional properties
• Many rRNA discoveries are helping to classify bacteria better
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Classification
• Three major domains:
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Archaea
• Highly diverse with respect to morphology, reproduction, physiology, and ecology
• Grow in extreme habitats– Anaerobic– Hypersaline– High temps
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Archaea
• Cell walls do not contain peptidoglycan• Differ from bacterial cell walls in structure• Membrane lipids have branched chain
hydrocarbons connected to glycerol by ether links– Bacteria and eukaryotes
have glycerol connected to fatty acids through ester bonds
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Archaea
• Some can synthesize methane• Have unique glucose catabolism and pathways
for CO2 fixation• Have distinguishable tRNA, ribosomes,
elongation factors, and RNA polymerases
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Archaea
• Five major types:– Methanogenic archaea– Sulfate reducers– Extreme halophiles– Cell wall-less archaea– Extreme thermophiles
• Two official phyla:– Crenarchaeota– Euryarchaeota
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Crenarchaeota
• Extremely thermophilic• Sulfur metabolizers• Frequently acidophiles• S may be used as an electron
acceptor in anaerobic respiration, or as an electron donor for lithotrophs
• Most are strict anaerobes• Found in geothermally
heated soil and water that is rich in sulfur
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Euryarchaeota
• Contains 5 major groups:– Methanogens– Halobacteria– Thermoplasms– Extreme thermophilic S metabolizers– Sulfate reducers
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Methanogens
• Strict anaerobes• Obtain energy through
synthesis of methane• Several unusual cofactors
involved in methanogenesis
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Halobacteria
• Aerobic chemoheterotrophs• Require at least 1.5 M NaCl for growth• Found in salt urns, salt lakes, and salted fish
• Halobacterium salinarium can carry out photosynthesis without chlorophyll (uses a different pigment)
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Thermoplasma
• Thermophilic• Grows in hot, acid coal refuse piles• Survives even without a cell wall
• Picrophilus can grow at pH 0
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Thermococci
• Extremely thermophilic organisms• Can reduce sulfur to sulfide
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Sulfate Reducers
• Many extreme thermophiles• Some use a variety of electron donors to
reduce sulfate
These archaea are being used to clean heavy metal waste from nuclear reactors
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Bacteria
• Four major divisions:– The Deinococci and Nonproteobacteria Gram
Negatives– The Proteobacteria– The Low G and C Gram Positives– The High G and C Gram Positives
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Deinococci and Nonproteobacteria Gram Negatives
• Order Deinococcales:– Aerobic– Gram positive– Cocci and rods– Unusually high resistance
to desiccation and radiation
Deinococcus radiodurans
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Deinococci and Nonproteobacteria Gram Negatives
• Photosynthetic bacteria:– Cyanobacteria carryout oxygenic photosynthesis• Very similar mechanism to the eukaryotic process
– Purple and green bacteria use anoxygenic photosynthesis• Bacteriochlorophyll pigments allow them to live in
deeper, anaerobic zones of aquatic habitats
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Cyanobacteria and Purple Bacteria
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Deinococci and Nonproteobacteria Gram Negatives
• Phylum Planctomycetes:– Lack peptidogylcan in their cell walls
• Phylum Chlamydiae:– Nonmotile– Coccoid– Reproduce within the cytoplasmic vacuoles of
their host cells– Energy parasites
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Deinococci and Nonproteobacteria Gram Negatives
• Phylum Spirochaetes:– Slender, long, helical bacteria– Motile due to axial filament
• Phylum Bacteriodetes:– Obligate aerobes– Chemoheterotrophic– Nonsporing– Variable shapes
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Proteobacteria
• General characteristics:– Largest and most diverse group– Gram negative– Often called the purple bacteria– No obvious overall pattern of morphology or
metabolism– Divided into 5 classes
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Proteobacteria
• Class Alphaproteobacteria:– Purple nonsulfur bacteria can grow anaerobically
as photoorganoheterotrophs– Also aerobically as chemoorganoheterotrophs– Rickettsias are obligate
intracellular parasites– Rhizobium carries out
nitrogen fixation• Oxidize either ammonia
or nitrite to nitrate
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Proteobacteria
• Class Betaproteobacteria:– Neisseria contains nonmotile, aerobic cocci that
usually occur in pairs• Colonize mucous membranes
– Buckholderia are aerobic rods• Almost always have a polar flagella
– Some have sheaths– Some are chemolithotrophic
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Proteobacteria
• Class Gammaproteobacteria:– Largest subgroup– Some grow in long filaments or trichomes– Have gliding motility– Some use methane as their carbon source– Contains:• Pseudomonas – soil bacteria, pneumonia• Vibrionaceae – cholera, in raw shellfish• Enterobacteriaceae – human pathogen• Pasteurellaceae – domestic animal pathogens
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Proteobacteria
• Class Deltaproteobacteria:– Anaerobic– Can use sulfur as electron acceptots– Bdellovibrio is a bacteria parasite• Grows in their periplasmic space
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Proteobacteria
• Class Epsilonproteobacteria:– Smallest of the proteobacteria classes– Contain two important pathogenic genera:• Campylobacter• Helicobacter
– Microaerophilic – Motile– Helical of vibroid
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Low G and C Gram Positives
• Phylum Firmicutes:– Class Clostridia– Class Mollicutes– Class Bacilli
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Low G and C Gram Positives
• Class Clostridia:– Anaerobic– Rods– Form endospores– Responsible for
botulism, food spoilage, and putrefaction
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Low G and C Gram Positives
• Class Mollicutes:– Mycoplasmas are actually Gram negative– Grow on agar to resemble fried eggs– Smallest bacteria capable of self-reproduction– Lack cell walls
• Why are they located in this section rather than with the other gram negative bacteria?
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Low G and C Gram Positives
• Class Bacilli:– Divided into 2 orders• Bacillales and Lactobacillales
– Several important genera • Bacillus – food poisoning and anthrax• Thermoactinomyces – alergic reactions that lead to
Farmer’s Lung• Lactobacillus – carries out lactic acid fermentation• Leuconostoc – used in cheese and buttermilk
production
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High G and C Gram Positives
• General characteristics:– Form branching usually non-fragmenting hyphae– Asexual spores• Called conidiospores
– Several distinctively different cell wall types
• Phylum is Actinomycetes
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High G and C Gram Positives
• Suborder Actinomycineae:– Irregular in shape– Nonsporing– Rods– Cause disease in cattle an humans
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High G and C Gram Positives
• Suborder Corynebacterineae:– Mycobacterium form rods or filaments that readily
fragment– Cell walls have a high lipid content and mycolic
acids– Acid-fast– Contain several important human pathogens– Some form aerial mycelia with spores
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High G and C Gram Positives
• Suborder Propionibacterineae:– Common skin and intestinal inhabitants– Important in cheese making– Causative agents of acne vulgaris
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High G and C Gram Positives
• Suborder Streptomycineae:– Important decomposers of complex organic
material– Produce useful antibiotics– Some are pathogenic to plants and animals
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High G and C Gram Positives
• Suborder Bifidobacteriales:– Irregular rod– Anaerobic– One of the first colonizers of the intestinal tract of
babies
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February 27th: Fungi
• Widespread in the environment• Major limitation to growth are often water
and temperature range• Secrete enzymes outside of their body and
then absorb the digested food molecules• Eukaryotic, spore bearing, absorptive nutrition• No chlorophyll• Cell walls usually contain chitin
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Importance
• Important decomposers• All heterotrophic• Play a role in many industrial processes• Used as research tools
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Structure
• The body, or vegetative structure, of a fungus is called a thallus
• Fungi are grouped into molds or yeasts based on the development of the thallus
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Structure
• Yeast:– Unicellular fungi that have a single nucleus– Asexual or budding reproduction– Sexual spore formation
• Mold:– Consist of long branched filaments of cells, called
hyphae, which form a tangled mass called a mycelium
– Mycelium can produce reproductive structures
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Structure
• Some fungi alternate between mold and yeast forms in their lifecycle
• This is called being dimorphic
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Fungi Structure
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Nutrition
• Most are saprophytes• Grow best in moist dark habitats• Chemoorganoheterotrophic• Usually aerobic
• Some yeasts are fermentive
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Reproduction
• Asexual reproduction often occurs in the fungi by production of spores that are easily dispersed
• Sexual reproduction is initiated by the fusion of hyphae of different mating strains– In some fungi the nucleus of the two conjoined
hyphae immediately fuse to form a zygote– In others the two nuclei stay separate, but divide
synchronously, and may fuse later
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Fungi Lifecycle
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Fungal Divisions
• Zygomycetes:– Coenocytic (multinucleate cells)– Saprophytic (decomposer)– Includes bread mold, Rhizopus stolonifer– Conjugation involves + and – strains
• Basidiomycetes:– Called the club fungi
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Fungal Divisions
• Ascomycetes:– Called the sac fungi– Sac-shaped reproductive structure called an ascus
• Deuteromycetes:– Also called ‘fungi imperfecta’– They have no know sexual phase• Therefore imperfect
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Slime Molds and Water Molds
• The plasmodial (acellular) slime molds move about as a multinucleate plasmodium
• When food or water is scarce, they form sporangia from which spores are produced
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Slime Molds and Water Molds
• The cellular slime molds consist of a vegetative stage called a myxamoeba
• These feed until their nutrients are exhausted, then the cells come together to form a moldlike multicellular structure called a sorocarp
• The sorocarp produces haploid cells that germinate when conditions are favorable
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Slime Mold Pictures
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Slime Molds and Water Molds
• The chytrids are a group of terrestrial and aquatic fungi that produce motile zoospores – These have a single, posterior, whiplash flagella
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Slime Molds and Water Molds
• The oomycota (water molds) are characterized by the production of motile spores and production of resistant sexual spores
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Additional Fungi Pictures
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Fungal Diseases
• Systemic mycoses – infections within the body, typically begin in the lungs from inhalation of spores
• Subcutaneous mycoses – under the skin infections, spores enter through puncture wounds
• Yeast infections are common in the urinary tract and vaginal canal
• Most are opportunistic
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Fungal Infection
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March 5th: Algae, Protozoa, and Multicellular Parasites
• Algae – eukaryotic photoautotrophs
• Protozoa – unicellular, eukaryotic, chemoheterotrophs
• Helminths – parasitic worms of the phyla Platyhelminthes and Nemartoda
• Arthropods – (as vectors) animals from the phylum Arthropoda
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Algae
• Most live in aquatic ecosystems• Reproduce asexually by cell division and
fragmentation• Many algae are sexual as well• Produce oxygen• Classified by structures and pigments
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Algae Anatomy
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Types of Algae
• Red algae grow deep in the ocean, can absorb blue light
• Green algae have chlorophyll a and b, store starch
• Multicellular algae include: Brown, Red, and Green
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Types of Algae• Diatoms are unicellular and have silica in their
cell walls– Some produce a neurotoxin
• Dinoflagellates produce a neurotoxin that can cause paralytic shellfish poisoning and ciguatera
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Types of Algae
• Euglenoids have a semi-rigid cell membrane and one flagellum– They are unicellular
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Importance
• Algae produce most of the world’s oxygen
• Responsible for petroleum reserves
• Often symbiotic
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Protozoa
• Unicellular• Chemoheterotrophic• Found in soil and water• Also as normal microbiota in animals
» Giardia lamblia
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Types of Protozoa
• Entamoeba, Naegleria, and Acanthamoeba are parasitic amoeboflagellates that use pseudopods for motility
• Parasitic amoeboflagellates that use flagella include:– Giardia lamblia – intestinal infection– Trichomonas vaginalis – urogenital infections – Trypanosomes – blood transmitted by insect
vectors
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Types of Protozoa
• Only one ciliate is parasitic to humans– Balantidium coli – form of dysentery
• Plasmodium causes malaria– Asexual reproduction occurs in red blood cells and
the liver of humans– Sexual reproduction takes place in the intestines
of the female mosquito
• Lots of others cause lots of diarrhea
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Helminths
• Multicellular animals• A few are parasites in humans• The anatomy and lifecycle of a helminth is
modified for parasitism– The adult stage is found in the definitive host– Each larva stage requires an intermediate host
• Can be monoecious or dioecious
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Platyhelminths
• Flatworms• Dorsoventrally flattened• Some may lack a digestive system• Some have a sucker which allows them to
attach to a host• Eggs often hatch into free swimmers• These enter an intermediate host
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Platyhelminths
• Typically the flatworm bores out of its intermediate host
• They are then eaten by a definitive host
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Tapeworm Anatomy
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Circle of Life
• Beef tapeworm– Cattle are intermediate hosts– Humans are definitive hosts
• Pork tapeworm– Humans can be definitive or intermediate host
• Echinococcus granulosus– Humans are intermediate hosts– Dogs, wolves, and foxes are the definitive host
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Nematodes
• Roundworms• Have a complex digestive system• Infect humans with their eggs:– Pinworms– Ascaris lumbricoides
• Infect humans with their larvae:– Hookworms– Trichinella spiralis– Anisakis worms
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Pinworms
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Ascaris lumbricoides
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Hookworms
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Trichinella spiralis
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Anisakis worms
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Arthropods
• Joint legged animals• Include ticks and insects• Often vectors for parasites
• Elimination of vector borne diseases is best accomplished by control or eradication of the vectors
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March 11th: Viruses
• Either:– Exceptionally complex aggregations of nonliving
chemicals– Exceptionally simple living microbes
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Viruses
• Contain: – A single type of nucleic acid– Protein coat– Sometimes a lipid, protein, and carbohydrate
envelope
• Obligatory intracellular parasites• Must use the cells synthesizing machinery to
replicate
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Viruses
• Host range – refers to the spectrum of cells in which a virus can multiply
• Most viruses only infect one type of cell in one species
• Determined by the specific attachment site on the cell’s surface and the availability of host cellular factors
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Viruses
• Viral size is determined by electron microscopy
• They range from 20 to 14,000 nm in length
• Viruses must be grown in living cells• The easiest viruses to grow are
bacteriophages
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Viral Structure
• A virion is a complete, fully developed, viral particle – Composed of nucleic acid surrounded by a protein
coat
• The nucleic acid to protein relation is anywhere from 1% to 50%
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Viral Structure
• The protein coat surrounding the nucleic acid is called the capsid
• Composed of subunits called capsomeres– Can be a single type of protein or many
• Some capsids are enclosed by envelopes – Made from protein, lipids, and carbohydrates
• Some envelopes are covered with carbohydrate-protein complexes called spikes
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Viral Structure
• Helical viruses resemble long rods, and their capsids are long cylinders surrounding the nucleic acid– Ebola
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Viral Structure
• Polyhedral viruses are many sided, usually the capsid is an icosahedron– adenovirus
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• Enveloped viruses are covered by an envelope and are roughly spherical– Highly pleomorphic– Some are helical (influenza)– Some are polyhedral
(herpes simplex)
• Complex viruses have complex structures– E.g. many bacteriophages have a polyhedral
capsid, with a helical tail attached
Viral Structure
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Taxonomy of Viruses
• Classification is based on:– Type of nucleic acid– Replication strategy– Morphology
• Family names end in –viridae• Genus names end in virus• Species names have not been assigned
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Identification
• Serological tests are used most often to identify viruses
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Viral Multiplication
• Viruses do not contain enzymes for energy production or protein synthesis
• To multiply a virus must invade a host cell and direct the cell’s metabolic machinery
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Multiplication of Bacteriophages
• During a lytic cycle a phage causes the death and lysis of a host cell
• Some viruses can insert their nucleic acid into the nucleic acid of the host cell– This is called lysogeny
• During the attachment phase of the lytic cycle, sites on the phage’s tail fibers attach to complimentary receptor sites on the bacterial cell
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Multiplication of Bacteriophages
• In penetration, phage lysozyme opens a portion of the bacterial cell wall, the tail sheath contracts to force the tail core through the cell wall, and the phage DNA enters the bacterial cell
• The capsid is discarded outside
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Multiplication of Bacteriophages
• In biosynthesis, transcription of phage DNA produces mRNA coding for necessary proteins
• Phage DNA is replicated, and capsid proteins are produced
• During the eclipse period, separate phage DNA and protein can be found
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Multiplication of Bacteriophages
• During maturation, phage DNA and capsids are assembled into complex viruses
• During release, phage lysozyme breaks down the bacterial cell wall, and the phages are released
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Multiplication of Bacteriophages
• The time from absorption to release is called burst time – 20 to 40 mins
• Burst size is the number of newly formed phages that are released from a single cell – 50 to 200
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Multiplication of Bacteriophages
• During the lysogenic cycle, the phage DNA is integrated into the bacterial DNA, and each subsequent cell division includes a replication of the bacteriophage DNA
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Multiplication of Animal Viruses
• Attach to the plasma membrane• Penetration occurs by endocytosis or fusion• DNA is put into the nucleus, where
transcription occurs• Capsid and other proteins are produced in the
cytoplasm
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DNA Animal Viruses
• Adenoviridae (Kennel Cough)• Poxviridae • Herpesviridae • Papovaviridae (HPV)• Hepadnaviridae (Hep B)
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RNA Viruses
• Multiplication of RNA viruses occurs in the cytoplasm
• Retroviridae uses reverse transcriptase to transcribe DNA from RNA
• Some are released through budding of the host cell plasma membrane
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Viruses and Cancer
• Some viruses have been linked to cancers in humans
• HPV is the most well known
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Latent Viruses
• A viral infection that stays in the host for long periods of time without causing symptoms
• E.g. herpes and shingles
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Exceptions to the Rule
• Viroids– Common in plants– Potato spindle tuber viroid disease
• Prions– CJD– Mad cow– Kuru