Viruses

1. Viruses Living or non-living? This is debatable! Living Thing? Viruses can reproduce. Non-living thing? Viruses can only show characteristics of a living thing (reproduce) inside a host cell Viruses are infectious particles made only of a strand of DNA or RNA surrounded by protein coat. Viruses are small or very small (50-200 nm) and cannot be seen with a light microscope (you need an electron microscope). Some scientists consider viruses as complex chemicals

2. Common Viral Diseases Common cold Influenza (flu), such as H1N1 (swine flu) SARS Chicken pox Ebola Measles Mumps Polio Mad-cow disease HIV West Nile HPV (Human papillomavirus) Herpes Rabies Hepatitis

4. Viral Infections • 2 types: • Lytic infection – host cell bursts and releases new viruses that infect more host cells • Lysogenic infection – virus combines it’s DNA into the host cell’s DNA but does not produce viruses (dormancy stage) but eventually viruses are porduced.

5. Questions 1-2, p 551 • Name and describe the main parts of a typical virus. • capsid: protein shell • genetic material: single-stranded or double-stranded DNA or RNA • Some viruses have a lipid envelope covering the capsid • What are the differences between a lytic infection and a lysogenic infection? Include the effects of each type of infection on the cells of the host organism in your answer. • Lytic infection: virus replicates many times, producing many offspring • Lysogenic Infection: virus integrates into the host cell’s DNA, with viral genes passed to the host cell’s daughter cells during mitosis. Lytic infection destroys the host cell after viral replication and release of offspring, whereas lysogenic infection generally causes no initial harm to the cell, though it can alter some of the cell’s traits.

6. Questions 3-4, p551 • Researchers studying infection can often grow bacteria more easily than they can grow viruses. What conditions must scientists provide for viruses to multiply? • In order to replicate, viruses need living cells they can infect • A wart is caused by a virus that may lie dormant for years before any symptoms appear. Does this resemble a lytic or lysogenic infection? Explain. • Lysogenic. It is characterized by a virus that lies dormant.

7. Question 5, p551 • If the virus is a foreign invader, how is it possible for the proteins of its capsid to match the receptors on the host cell’s surface? Consider natural selection in your answer. • Over time, viruses that happened to have the right protein “key” would survive and pass on these traits to their viral offspring. Viruses without the right proteins would not be able to successfully infect the host and would probably become extinct.

8. Questions 1-3, p554 • Name and describe two infectious viruses and a body’s first defense against infection. • Common cold, flu, SARS, HIV, chicken pox. • The skin is the body’s first defense against infection. • Briefly describe how a vaccine can prevent some viral infections. - A vaccine is made from a weakened pathogen or parts of a virus. When given, it stimulates the host’s own immune system, preparing it for future infections by the real virus.

9. Questions 3 – 4, p554 • If a vaccine is in short supply, why is it often recommended that older adults and children get vaccinated first? • The immune system of older adults and children are often weaker than those of the rest of the population, so they are more likely to become infected than a healthy person who is not very young or very old. • Why might getting a flu vaccination sometimes cause you to get a mild case of the flu? • because you may be getting a weakened strain of live virus in order to build up your immune system.

10. Question 5, p554 • People infected with HIV (the virus that causes AIDS) can become unable to fight off infections by organisms that normally do not harm people. Why is this so? - HIV affects the immune system of an infected person, making him or her susceptible to organisms that are normally harmless.

11. Prokaryotes (Bacteria & Archaea) • Both groups are prokaryotic (lack a nucleus and organelles) • Divided up based on need for oxygen (O2): • obligate anaerobes • cannot live in presence of O2 • Some produce methane gas • Live in marshes, lake bottoms, or digestive tracts of herbivores like cows, deer and sheep • obligate aerobes • Need O2 or will die • Many common pathogens like tuberculosis and leprosy • Facultative aerobe - Can survive with or without O2

12. Bacteria and archaea are similar structurally but differ in genetics and biochemistry • Both groups are small single-celled organisms with a cell wall and cell membrane • Archaea have many shapes, bacteria have 3: • Bacilli – (rod-shaped) • Spirochetes - (spirilla or spiral-shaped) • Cocci - (round or spherical)

13. Archaea and bacteria move by gliding or using flagella (whip-like tail used for locomotion) or pili (smaller locomotive structures) • Typical prokaryote structure:

14. Archaea and bacteria differ their cell wall, flagella and plasma membrane composition • 4 main groups of Archaea: • Methanogens – produce methane • Psychrophiles – live in cold temperatures • Halophiles – live in salty environments • Thermophiles – live in extremely warm/hot temperatures • Bacteria – two main groups: • Gram Positive – stain purple with a Gram stain • Gram Negative – stain red in a Gram Stain

15. Gram Positive / Negative Bacteria

16. Bacteria – benefits to humans • Bacteria help humans and other animals in their digestive tract: • Cattle (and other ruminants) use bacteria to breakdown their food • Human use bacteria in their intestinal track to produce vitamins and other substances • Many foods produced by fermentation by bacteria: • yogurt, cheese • pickles • sauerkraut • vinegar, soy sauce

17. Cyanobacteria – produce huge amounts of oxygen Nitrifying bacteria (in the soil) fix nitrogen from the atmosphere into usable form for plants Bioremediation – uses microbes and other living things to break down or destroy pollutants. Bacteria are a key organism is biological decay (biodegradation)

18. Bacterial Diseases acne tuberculosis anthrax Lyme disease tetanus gangrene botulism (as well as other forms of food poisoning, such as salmonella) tooth decay strep throat, ear infections, flesh-eating disease bacterial pneumonia STI – syphilis, Chlamydia, etc…

19. Questions 1-3 page 558 • What are the three most common shapes of bacteria? • rod, spiral and sphere • Why are bacteria and archaea classified into different domains? • Archaea are biochemically and genetically different from bacteria • Prokaryotes will take up foreign DNA. How is this characteristic used in genetic engineering? • Pieces of genes can be inserted into the genetic material of prokaryotes so that they will make the protein products encoded in the genes or copies of the genes themselves.

20. Question 4-5, p558 • Scientists estimate that only 1 percent of prokaryotes can be grown in the lab. What does this suggest about our knowledge of bacteria and archaea? • We do not know much about prokaryotes. Our understanding of prokaryotes will likely change as scientists learn more about prokaryotes that have not been able to be cultured, or grown, in the lab. • Prokaryotes multiply by binary fission, which simply divides a cell in two. Why are mutations and conjugation important for natural selection in prokaryotes? • Binary fission produces no variation, but mutations and conjugation do. Natural selection requires variation in a population.

21. Question 6 • Bacteria in your mouth convert foods containing sugar and starch into acids that can then cause cavities in your teeth. These bacteria will be present even if you brush your teeth, floss, or use mouthwash. So why are these hygiene habits so important? • Brushing teeth is important to keep the population of these bacteria down and to remove the food that the bacteria convert into acid.

22. Questions 1-3, p561 • Describe two ways bacteria provide nutrients to humans. - Bacteria in our bodies make vitamins that we absorb, and some bacteria are needed to make foods that we eat, such as soy and dairy products. • What are two roles prokaryotes play in the cycling of elements in an ecosystem? • producing oxygen through photosynthesis, fixing nitrogen, decomposing other organisms • Think of an example in which the use of bioremediation either has improved the environment or has the potential to do so. • Cleaning up industrial accidents, sewage and other waste.

23. Questions 4, p561 • How do prokaryotes lend to stability to an ecosystem? - Prokaryotes lend stability to an ecosystem through their role as decomposers. Other organisms rely on prokaryotes for nitrogen and other compounds that are broken down through prokaryote metabolic activity. Some prokaryotes also help the stability of an ecosystem by releasing oxygen into the environment during photosynthesis.

24. Question 5, p561 • Prokaryotes in cow intestines produce more methane if the cow is fed a diet high in grains rather than grass. Some scientists propose that overfeeding grain to cows contributes to global warming. How did these scientists arrive at this hypothesis, and how could it be tested? • Students can infer that the amount of methane produced by the intestines of a grain-fed cow can be compared to that produced by a grass-fed cow, perhaps by measuring concentrations of methane in closed environments after cows have fed and lived inside them for some time. The effect of methane concentration on the heat retention of the atmosphere can also presumably be tested in a small, enclosed space that is open to sunlight.

25. Domain Eukarya • all are eukaryotic (possess a nucleus and organelles) • 4 kingdoms: • Kingdom Protista • Kingdom Fungi • Kingdom Plantae • Kingdom Animalia

26. Kingdom Protista • Eukaryotic (cells have a nucleus and organelles) • Mostly unicellular, some are colonial • Most are microscopic, some are huge (slime molds)! • Divided into three informal categories, based on their food-gathering method: • Animal-like protists: eat (ingests) their food (heterotrophic) • Plant-like protists: make their own food by photosynthesis (autotrophic) • Fungal-like protists: absorb their food (heterotrophic)

27. Animal-like Protists • Sometimes called “zooplankton” or “protozoa” • 4 phyla: • Zooflagellates (Phylum Zoomastigophora) • Have flagella to move around (whip-like structures) • Trypanosoma causes African Sleeping Sickness, which is transmitted by tsetse fly • Sarcodines (Phylum Rhizopoda) • Have pseudopods (“false feet”) to move around • Engulfs food by surrounding it with their pseudopods • amoebas, foraminiferans

28. Animal-like Protists - continued • Ciliates (Phylum Ciliaphora) • Move by cilia (hair-like projections) • Paramecium – common genus • Sporozoans (Phylum Apicomplexa) • Parasitic, reproduce using spores • Plasmodium – genus causes Malaria • Malaria passed on by Anopheles mosquitoes • Malaria kills millions of people annually

29. Questions 1-2, page 576 • Name the three main groups within the kingdom Protista. What characteristics distinguish each group from the other two? • Protozoa (animal-like) - heterotrophic consumers • Algae (plant-like) - autotrophic producers • slime molds (fungal-like) - heterotrophic decomposers • Give two reasons why protists are difficult to classify. • Answers should include two of the following: Some protist phyla are very distantly related, and some are more closely related to members of other kingdoms than they are to other protists. The definition of protists is based on the absence of traits that characterize the other kingdoms.

30. Questions 3 & 4, p576 • What observable traits might green algae and plants share that support the molecular evidence that these two groups are closely related? • Both are green, have chloroplasts, are eukaryotic, and are (sometimes) multicellular • At one time, scientists grouped all single-celled organisms together. What are the main differences between single celled protists and bacteria or archaea? • Protists are eukaryotic, meaning they are made up of cells that have a nucleus and membrane-bound organelles; bacteria and archaea are prokaryotic, meaning their cells do not have a nucleus or organelles.

31. Question 5, p 576 • Organisms that get their food by ingesting it called heterotrophs, while those that make their own food are called autotrophs. Categorize animal-like, plant-like, and fungus-like protists using these two terms. • Animal-like protists and fungus-like are heterotrophs. Plant-like protists are autotrophs.

32. Questions 1-2, p580 • Name and describe the three basic means of movement used by animal-like protists. • flagella: tail-like extensions of cytoplasm that are used in a whip like motion to propel the organism forward • Pseudopods: the plasma membrane and cytoplasm extend to form a bulge that anchors to the surface and pulls the rest of the organism along; cilia: short hair like structures on the surface of the organism that wave. • Describe how the parasite Plasmodium causes disease in humans. • The bite of a mosquito carrying Plasmodium transmits sporozoites into a human‘s bloodstream. The sporozoites enter the liver, where they develop and then move to red blood cells. They reproduce asexually until the red blood cells burst open, releasing Plasmodium cells that can then be ingested by mosquitoes that bite the infected host. Symptoms include severe fever, vomiting, and possibly liver and kidney problems.

33. Questions 3-4, p 580 • In what ways are cilia and flagella similar? How are they different? • Cilia and flagella are both used for movement in protists. Both are formed from the cell membrane and are permanent structures. However, cilia are shorter and more hair like and can be in rows or clusters that cover parts of a cell or the entire cell. Flagella are longer, and there are usually only one or two per cell. • Why do amoebas form pseudopods only when they need them? • because pseudopod formation requires energy

34. Question 5, p580 • The flagella of eukaryotes and prokaryotes serve the same function, but they are structurally very different. What does this suggest about the evolution of flagella? • The flagella of eukaryotes and prokaryotes arose separately and are an example of convergent evolution

35. Plant-like Protists (Algae) • Was classified in the plant kingdom in the past, are not any more because they lack roots, stems, leaves or specialized tissues • Can be single-celled or multicellular • along with photosynthetic bacteria are sometimes called phytoplankton (photosynthesis) • Provide about half of the earth’s oxygen supply! • Base of aquatic food chains as the producers • Most are autotrophic (make their own food by photosynthesis

36. Plant-like Protists – 6 phyla • Euglenoids (phylum Euglenophyta) • Swim by flagella, yet they photosynthesize! • Mostly freshwater species, some marine • Commonly green in colour • Euglena • Most are autotrophic, some are heterotrophic • Dinoflagellates (phylum Dinoflagellata) • Most species are marine (90%) • Have two flagella • Some species produce toxins (cause “red tide”) – kill large numbers of fish, can contaminate shellfish (can kill people!)

37. Diatoms (phylum Bacillariophyta) • Covered by delicate glass-like shells • Freshwater or marine species, unicellular • Release huge amounts of the earth’s atmospheric oxygen • Diatomaceous earth – used in many things like tooth paste, swimming pool filters, insulation materials • Green Algae (phylum Chlorophyta) • Most species are aquatic, some live on land in moist environments • Some unicellular, some colonial, some multicellular • Ancestor to land plants

38. Brown Algae (phylum Phaeophyta) • Kelps that form underwater forests • multicellular • Mostly marine species • Red Algae (phylum Rhodophyta) • Mostly marine, some freshwater • Multicellular • Carrageenan - thickening agent from red algae used dairy product like milkshakes and ice cream • Agar – used in bacterial culture plates

39. Fungal-like Protists • Slime Molds (phylum Myxomycota / Acrasiomycota) • eukaryotic, can move around • Water Molds (phylum Oomycota) • Many are decomposers, some are parasites on plants and fish • One species caused the Irish potato famine – killed millions of people in Ireland “Great Potato Famine”