Viruses

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Viruses

• Viruses are nucleic acids (DNA/RNA) wrapped in
  protein
• Typically the protein coat, or capsid, of an
  individual virus particle, or virion, is composed
  of multiple copies of one or several types of
  protein subunits, or capsomeres. Some viruses
  contain enzymes, and some have an outer
  membranous envelope. Many viruses have striking
  geometrically regular shapes

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Virus Shapes

• 3 main shapes
• Icosohedron/polyhedron 20 triangular sections
  (HIV)
• Spiral RNA surrounded by capsomere proteins
• Bacteriophage spaceship
• Others (ebola)

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Types of Viruses

• Viruses depend on the host cells that they infect
  to reproduce. When found outside of host cells,
  viruses exist as a protein coat or capsid,
  sometimes enclosed within a membrane. The capsid
  encloses either DNA or RNA which codes for the
  virus elements.

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Sizes of Viruses
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Nucleic Acid

• Plus/Minus strand designation mRNA polarity
• mRNA 5 GAC UCG AGC 3
• DNA 5 GAC TCG AGC 3
• -DNA 5 CTG AGC TCG 3
• RNA 5 GAC UCG AGC 3 (operates like mRNA)
• -RNA 5 CUG AGC UCG 3 (euk. cells dont have
  enz)
• ssDNA()?-DNA?mRNA
• Retrovirus RNA?dsDNA using reverse transcriptase

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Reverse transcription of retroviruses Reverse
Transcriptase 2 Classification of Viruses
(reference)
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Exceptions

• Viroids? circular ssRNA material, infectious to
  plants, escaped introns???
• Prions? proteinaceous infectious particles, no
  n.a. Against dogma of molecular biology
• Scrapie (sheep), kuru (Papau New Guinea), bovine
  spongiform encephalitis (Mad Cow Disease), and
  Creutzfeldt-Jakob disease.

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Harmful Viruses

• Viruses are notorious for the plethora of
  diseases they cause, including influenza, rabies,
  AIDS, polio, herpes, ebola, measles, mumps,
  chicken pox, warts, small pox --gt

Warts
herpes
Lewandowsky-Lutz/ 2 Epidermodysplasia
verruciformis,
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Helpful Viruses

• Viruses carry out natural "genetic engineering"
  by incorporating genetic material into its host
• This is known as transduction, and in some cases
  it may serve as a means of evolutionary change
• Certain varieties of flowers have been developed
  using viruses to alter the genetic code.
• Dr Patrick Lee uses reovirus to kill brain cancer
  cells transplanted into laboratory mice, while
  sparing normal, healthy cells. Clinical trials
  involving reovirus in people are now underway.
• Virus Rap

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Helpful Viruses

• A good virus
• Most of us go out of our way to avoid viruses.
  But Dr Patrick Lee - formerly of the University
  of Calgary and now at Dalhousie University -
  spends a lot of time in the company of a very
  common virus known as a reovirus. Normally this
  bug causes nothing more serious than a mild
  infection. But Dr Lees team discovered that the
  reovirus has the ability to kill brain cancer
  cells transplanted into laboratory mice, while
  sparing normal, healthy cells. Clinical trials
  involving reovirus in people are now underway.

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How do they get in?

• Lambda phage Replication
• Replication of a Positive () Sense Strand of
  Lytic RNA Phage
• T4 Replication
• Entry into Animal Cell
• Release of Enveloped Viruses
• Replication of Retrovirus
• Influenza

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Essential knowledge 3.C.3 Viral replication
results in genetic variation, and viral infection
can introduce genetic variation into the hosts.

• b. The reproductive cycles of viruses facilitate
  transfer of genetic information.
• 1. Viruses transmit DNA or RNA when they infect a
  host cell.
• Transduction in bacteria (Specialized
  Transduction)
• Transposons present in incoming DNA
• 2. Some viruses are able to integrate into the
  host DNA and establish a latent (lysogenic)
  infection. These latent viral genomes can result
  in new properties for the host such as increased
  pathogenicity in bacteria.
• LO 3.29 The student is able to construct an
  explanation of how viruses introduce genetic
  variation in host organisms.

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Lysogenic Cycle

• When it comes into contact with a host cell, a
  virus can insert its genetic material into its
  host, literally taking over the host's functions.
  An infected cell produces more viral protein and
  genetic material instead of its usual products.
  Some viruses may remain dormant inside host cells
  for long periods, causing no obvious change in
  their host cells (a stage known as the lysogenic
  phase).

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Lytic Cycle

• when a dormant virus is stimulated, it enters the
  lytic phase new viruses are formed,
  self-assemble, and burst out of the host cell,
  killing the cell and going on to infect other
  cells
• Attachment?entry?replication?assembly?lysis
  release
• 1, 2, 3

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Essential knowledge 3.C.3 Viral replication
results in genetic variation, and viral infection
can introduce genetic variation into the hosts.

• a. Viral replication differs from other
  reproductive strategies and generates genetic
  variation via various mechanisms.
• 1. Viruses have highly efficient replicative
  capabilities that allow for rapid evolution and
  acquisition of new phenotypes. Viral
  Recombination , 1918 Spanish Flu, 2, 3
• 2. Viruses replicate via a component assembly
  model allowing one virus to produce many progeny
  simultaneously via the lytic cycle.
• 3. Virus replication allows for mutations to
  occur through usual host pathways.
• 4. RNA viruses lack replication error-checking
  mechanisms, and thus have higher rates of
  mutation.
• 5. Related viruses can combine/recombine
  information if they infect the same host cell.
  (Antigenic Shift)
• 6. HIV is a well-studied system where the rapid
  evolution of a virus within the host contributes
  to the pathogenicity of viral infection.
• LO 3.30 The student is able to use
  representations and appropriate models to
  describe how viral replication introduces genetic
  variation in the viral population.

Life Cycle of HIV HIV Life Cycle 2 HIV
Replication Future of HIV
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Vaccines

• Constructing a Vaccine
• Engineering the Avian Flu
• 1918 Flu
• Malarial Vaccine
• Virus Rap

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Lysogenic Cycle vs Lytic Cycle

• Attachment?entry?replication?assembly?lysis
  release

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Eubacteria true bacteria

• Typical monerans found where humans live
• Evolution of the 3 Domains

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Archaea archaic/oldextremophiles

• Methanogens
• Thermophiles
• Acidophiles
• Halophiles
• Alkaliphiles
• Psychrophiles
• Xerophiles
• Barophiles
• Archae vs Bacteria

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Bacteria Characteristics

• Bacteria are distinguished from other living
  things because of their cell structure
• All bacterial cells have a cell wall surrounding
  a cell membrane, inside of which lies the unbound
  nuclear matter and other material.

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• Bacteria have extra genomic DNA that is round and
  called a plasmid
• Plasmid Cloning

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Bacteria Classified by Shape

• There are three types of bacterial cells, based
  on shape spherical (coccus), rodlike (bacillus),
  and spiral (spirillum).

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• Some bacteria have flagella for locomotion and
  some have pili to transfer DNA (conjugation) and
  to stick to substrates of host cells

Bacterial Chemotaxis
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Harmful Bacteria

• A number of bacteria cause disease, these are
  called pathogenic bacteria.
• They can cause diseases of plants, animals,
  fungi, protists and other bacteria
• E. coli infection
• Salmonella infection

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• Some bacterial diseases include strep throat,
  scarlet fever, toxic shock syndrome, pneumonia,
  ear infections, gonorrhea, syphilis, Tuberculosis
• Bacteria can also be used by some countries to
  harm other countries in an act called bioterrorism

Eczema w/ 2o infection
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Helpful Bacteria

• actinomycetes, produce antibiotics such as
  streptomycin and nocardicin
• live symbiotically in the guts of animals
• put the tang in yogurt and the sour in sourdough
  bread, cheese spoiled milk

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• break down dead (and living) organic matter
• Bioremediation
• used in genetic engineering
• Nitrogen Fixation? roots of certain plants,
  converting nitrogen into a usable form (nitrate).
  

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Producers in Geothermal Vents
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Reproduction

• Bacteria reproduce asexually by binary fission
• Bacterial Conjugation (lateral/horizontal gene
  exchange)
• Bacterial Transformation (lateral/horizontal gene
  exchange)
• Bacteria life cycle

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BB Checkpoint

• BB1?SB1a. Explain the role of cell organelles
  for both prokaryotic and eukaryotic cells,
  including the cell membrane, in maintaining
  homeostasis and cell reproduction.
• BB8 ? SB2e. Compare the advantages of sexual
  reproduction and asexual reproduction in
  different situations
• BB10 ? SB3b. Compare how structures and function
  vary between the six groups (archaebacteria,
  eubacteria, protists, fungi, plants, and
  animals).

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Kingdom Protista

• All protists are eukaryotes. This means that
  their cells contain a nucleus, a membrane-bounded
  structure that encloses the cell's genetic
  material.
• Some protists are autotrophs like plants, others
  are consumers like animals. Unlike plants and
  animals, however, protists do not have cells
  organized into specialized tissues.

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Protista Classified by Nutrition

• The first detailed descriptions of protists were
  made in 1676 by the inventor of the microscope,
  Dutch naturalist Leewenhoek.
• The classification is currently based on the
  structure and organization of the cell, the
  presence of organelles, and the pattern of
  reproduction or life cycles. The five-kingdom
  system divides the Protista into 27 phyla.
  However, classifications based on DNA sequences
  suggest that many protist phyla may be
  sufficiently large and diverse to be classified
  as kingdoms.
• Gallimaufry, cornucopia, hodge-podge, potpourri
  

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• Auto trophic Protists are called Algae.
  Scientists believe they gave rise to the kingdome
  Plantae
• Ingestive Heterotrophic protists are called
  Proto zoa. Scientists believe they gave rise to
  the kingdom Animalia
• Absorptive heterotrophic protists are called
  Slimemolds. Scientists believe they gave rise
  to the kingdom Fungi
• Protist Rap

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Harmful Protists

• Produce a nerve poison in shellfish that kills
  humans and fish in red tide
• Cause diseases Chagas disease, Malaria, 2, Lyme
  disease, diarrhea, toxoplasmosis, dysentary,
  Trypanosomaisis, 2, Leishmaniasis, 2, Toxoplasma,
  Cryptospiridium, Leishmaniasis, Brain Amoeba
• Cause mold and mildew which can spoil food and
  cause allergic reactions
• Cause algal blooms which can result in
  eutrophication

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Beneficial Protists

• Used as insect pathogens
• Used in ice cream, soups, nori (seaweed in
  sushi), jello, agar, vitamin supplements, or
  eaten as a sea vegetable
• Ancient dinoflagellates formed oil deposits
• Bioluminescent
• Diatoms mined for fine abrasives in silver polish
  and toothpaste and as packing in air and water
  filters
• Marine phytoplankton make up 70 of the oxygen
  on the planet
• Forensic uses Diatom Detectives
• Algae for Biofuel

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BB Checkpoint

• BB9?SB3a. Explain the cycling of energy through
  the processes of photosynthesis and respiration.
• BB10 ? SB3b. Compare how structures and function
  vary between the six groups (archaebacteria,
  eubacteria, protists, fungi, plants, and
  animals).

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Fungi Multicellular absorptive heterotrophs

• Though they grow in soil like plants, they are
  not autotrophic.
• The have cell walls made of the polysaccharide
  chitin
• What are the cell walls of plants made of?
  Bacteria?

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Fungi Anatomy

• Hyphae? basic structural unit of a fungus made up
  of branching filaments
• Mycelium? tangled network of fibers
• Fruiting body? reproductive structure. In Phylum
  Basidiomycota it is the mushroom itself

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Fungi Classified by Reproduction

• Division Zygomycota? form zygospores i.e.
  Rhizopus (bread mold)
• Division Ascomycota? form ascospores i.e. yeast,
  morels, ergot, Dutch elm disease
• Division Basidiomycota? Most commonly known,
  forms basidiospores i.e. shelf fungi, mushrooms
• Division Deuteromycota/ Imperfecti? sexual
  reproduction unknown i.e. Penicillium,
  Aspergillus

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Fungi Life Cycle
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Harmful Fungi

• Many fungi are parasitic and cause diseases like
  ringworm, athletes foot,
• Can rot and contaminate foods
• Can destroy almost every type of product or food
  aside from some plastics
• Black Mold in Buildings
• Building a House Recipe for Disaster
• Lungus Fungus

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Beneficial Fungi

• People eat mushrooms, truffles and other fungi,
  citric acid in Coke
• Fungi are decomposers like bacteria and help to
  recycle organic matter to inorganic saprophytic
• Yeasts are used in making bread, wine, beer,
  solvents, cheese.
• Drugs made from fungi cure diseases and stop the
  rejection of transplanted hearts and other
  organs.
• Fungi are also grown in large vats to produce
  flavorings for cooking, vitamins and enzymes for
  removing stains.
• Beneficial Protists Fungi

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Fungi Engage in Symbiosis

• Parasitic /- Mind control
• Mutualistic / Lichens, a pioneer organism, a
  fungus and algae living together
• The mycorrhizal fungi live as partners with
  plants, helping them absorb nutrients
• Predatory /- Arthrobotrys, a deuteromycete

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BB Checkpoint

• BB9?SB3a. Explain the cycling of energy through
  the processes of photosynthesis and respiration.
• BB10 ? SB3b. Compare how structures and function
  vary between the six groups (archaebacteria,
  eubacteria, protists, fungi, plants, and
  animals).

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Resources

• Virus Links
• Virus Pictures
• Virus Review
• Exploring Life
• Big Picture Book of Viruses
• AIDS Online
• Replication of Herpes Animation
• Influenza Entry Animation
• Antigenic Shift Animation
• Immuno- biology Animations
• Biological Diversity
• Protists
• Protist Kingdom
• Phylogenetic Tree
• Protozoa Bio 4 Kids
• Microbe Zoo, Dirtland

• Bacteria Links
• Bioterrorism
• Bacterial Cell Walls
• 10 Ways a World Will End Monster Plague
• Discovery of the Germ Theory
• Antibiotics Tutorial
• Anti-antibiotics/Efflux Pump
• Immunology Primer
• When Worlds Collide, Macro vs. Micro
• Immuno- biology Animations
• Fungi Links
• Fungi Chapter 30
• Tom Volks Fungi

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Virus Links
Virus Pictures Virus Review Exploring Life
Big Picture Book of Viruses AIDS Online
Replication of Herpes Animation Influenza
Entry Animation Antigenic Shift Animation
Immuno- biology Animations Chapter 6
Viruses Introduction to Plasmids
Viruses Bozeman Viral Replication Super Flu
Antigenic shift in influenza