1. 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

2. Virus Shapes 3 main shapes: Icosohedron/polyhedron: 20 triangular sections (HIV) Spiral: RNA surrounded by capsomere proteins Bacteriophage: spaceship Others (ebola)

3. 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.

4. Sizes of Viruses

5. Nucleic Acid Plus/Minus strand designation mRNA = +polarity mRNA5’ GAC UCG AGC 3’ +DNA5’ GAC TCG AGC 3’ -DNA5’ CTG AGC TCG 3’ +RNA5’ GAC UCG AGC 3’ (operates like mRNA) -RNA5’ CUG AGC UCG 3’ (euk. cells don’t have enz) ssDNA(+)  -DNA  +mRNA Retrovirus= RNA  dsDNA using reverse transcriptase

6. Reverse transcription of retroviruses Reverse Transcriptase 2 Classification of Viruses (reference)

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

10. 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 --> influenza Lewandowsky-LutzLewandowsky-Lutz/ 2 2 Epidermodysplasia verruciformis, herpes Warts

11. 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.Clinical trials Virus Rap

12. 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 Lee’s 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.Clinical trials

13. How do they get in? Lambda phage Replication Replication of a Positive (+) Sense Strand of Lytic RNA PhageReplication of a Positive (+) Sense Strand of Lytic RNA Phage T4 Replication Entry into Animal Cell Release of Enveloped Viruses Replication of Retrovirus Influenza

14. 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)Transduction Specialized Transposons present in incoming DNATransposons 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.

15. 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). lysogenic

16. 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, 3123

17. 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, 3Viral Recombination 1918 Spanish Flu23 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)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 Life Cycle of HIV HIV Life Cycle 2HIV Life Cycle 2 HIV ReplicationHIV Replication Future of HIVFuture of HIV

18. Vaccines Constructing a Vaccine Engineering the Avian Flu 1918 Flu Malarial Vaccine Virus Rap

19. Lysogenic Lysogenic Cycle vs Lytic CycleLytic Cycle Attachment  entry  replication  assembly  lysis & release

20. Eubacteria Eubacteria “true bacteria” Typical “monerans” found where humans live Evolution of the 3 Domains

21. Archaea “archaic/old” extremophiles Methanogens Thermophiles Acidophiles Halophiles Alkaliphiles Psychrophiles Xerophiles Barophiles Archae vs Bacteria

22. 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.

23. Bacteria have extra genomic DNA that is round and called a “plasmid” Plasmid CloningPlasmid Cloning

24. Bacteria: Classified by Shape There are three types of bacterial cells, based on shape: spherical (coccus), rodlike (bacillus), and spiral (spirillum).

25. Some bacteria have flagella for locomotion and some have pili to transfer DNA (conjugation) and to stick to substrates of host cellsconjugation Bacterial Chemotaxis

26. 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 infectionE. coli infection Salmonella infectionSalmonella infection

27. Some bacterial diseases include: strep throat, scarlet fever, toxic shock syndrome, pneumonia, ear infections, gonorrhea, syphilis, Tuberculosis syphilisTuberculosis Bacteria can also be used by some countries to harm other countries in an act called bioterrorism Eczema w/ 2 o infection

28. 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

29. 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).

30. Producers in Geothermal Vents

31. Reproduction Bacteria reproduce asexually by binary fissionbinary fission Bacterial Conjugation (lateral/horizontal gene exchange)Bacterial Conjugation Bacterial Transformation (lateral/horizontal gene exchange)Bacterial Transformation Bacteria life cycle

32. BB Checkpoint BB#1  SB1a. Explain the role of cell organelles for both prokaryotic and eukaryotic cells, including the cell membrane, in maintaining homeostasis and cell reproduction. BB#8  SB2e. Compare the advantages of sexual reproduction and asexual reproduction in different situations BB#10  SB3b. Compare how structures and function vary between the six groups (archaebacteria, eubacteria, protists, fungi, plants, and animals).

33. Kingdom ProtistaProtista 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.

34. 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

35. 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

36. Harmful Protists Produce a nerve poison in shellfish that kills humans and fish in red tidered tide Cause diseases: Chaga’s disease, Malaria, 2, Lyme disease, diarrhea, toxoplasmosis, dysentary, Trypanosomaisis, 2, Leishmaniasis, 2, Toxoplasma, Cryptospiridium, Leishmaniasis, Brain AmoebaChaga’s disease Malaria2Trypanosomaisis2 Leishmaniasis2Toxoplasma CryptospiridiumLeishmaniasis Brain Amoeba Cause mold and mildew which can spoil food and cause allergic reactions Cause algal blooms which can result in eutrophicationeutrophication

37. Beneficial Protists Used as insect pathogens Used in ice cream, soups, nori (seaweed in sushi), jello, agar, vitamin supplements, or eaten as a sea vegetablesea 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 DetectivesDiatom Detectives Algae for Biofuel

38. BB Checkpoint BB#9  SB3a. Explain the cycling of energy through the processes of photosynthesis and respiration. BB#10  SB3b. Compare how structures and function vary between the six groups (archaebacteria, eubacteria, protists, fungi, plants, and animals).

39. FungiFungi: 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?

40. Fungi AnatomyAnatomy 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

41. 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, AspergillusPenicillium

42. Fungi Life Cycle

43. 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

44. 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

45. Fungi Engage in Symbiosis Parasitic +/-: Mind control Mind control Mutualistic +/+: Lichens, a pioneer organism, a fungus and algae living together Lichens The mycorrhizal fungi live as partners with plants, helping them absorb nutrientsmycorrhizal Predatory +/-: Arthrobotrys, a deuteromycete Arthrobotrys

46. BB Checkpoint BB#9  SB3a. Explain the cycling of energy through the processes of photosynthesis and respiration. BB#10  SB3b. Compare how structures and function vary between the six groups (archaebacteria, eubacteria, protists, fungi, plants, and animals).

47. Resources Virus Links Virus Pictures:Virus Pictures Virus Review:Virus Review Exploring Life:Exploring Life Big Picture Book of Viruses:Big Picture Book of Viruses AIDS Online:AIDS Online Replication of Herpes Animation:Replication of Herpes Animation Influenza Entry Animation:Influenza Entry Animation Antigenic Shift Animation Immuno- biology Animations Biological Diversity Protists Protist Kingdom:Protist Kingdom Phylogenetic Tree:Phylogenetic Tree Protozoa Bio 4 Kids:Protozoa Bio 4 Kids Microbe Zoo, Dirtland:Microbe Zoo, Dirtland Bacteria Links Bioterrorism: Bacterial Cell Walls: 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 Volk’s Fungi

48. Virus Links Virus PicturesVirus Pictures: Virus ReviewVirus Review: Exploring LifeExploring Life: Big Picture Book of VirusesBig Picture Book of Viruses: AIDS OnlineAIDS Online: Replication of Herpes AnimationReplication of Herpes Animation: Influenza Entry AnimationInfluenza Entry Animation: Antigenic Shift Animation Immuno- biology Animations Chapter 6 Viruses Introduction to Plasmids & Viruses Bozeman Viral Replication Super Flu: Antigenic shift in influenza