Lecture Outline - Chapter 28

28.1. Viruses (p. 540)

1. Are noncellular and therefore not included in classification table. (Appendix B)
2. Traits of Viruses
   • a. Generally smaller than 200 nm in diameter; comparable to large protein macromolecule.
   • b. Many can be purified, crystallized, and stored as chemicals, different from living cells.
3. Virus Structure
   • a. Outer capsid is composed of protein subunits; often surrounded by outer membranous envelope which is piece of host plasma membrane.
   • b. Inner core contains nucleic acid (DNA or RNA); contains at most several hundred genes.
   • c. May also contain enzymes for nucleic acid replication.
4. Classification is based on: (Fig. 28.1)
   • a. Type of genome (DNA or RNA) and whether single or double stranded.
   • b. Viral size and shape.
   • c. Presence or absence of outer envelope.
5. Viruses Are Parasites
   • a. Are obligate intracellular parasites (only activated within living cells).
   • b. Animal viruses are replicated by injecting them into live chick embryos or tissue culture cell lines.
   • c. Types include:
     • i. Bacteriophages infect bacteria.
     • ii. Plant viruses such as tobacco mosaic virus infect only plants.
     • iii. Animal viruses include rabies virus that infects only mammals.
     • iv. Some infect only very specific tissues (HIV in T-cells; polio virus in nerve cells; hepatitis virus in liver cells).
     • v. Likely that viruses derived from host cells; therefore viruses evolved after cells.
   • d. Viruses can mutate; antibodies effective against one strain of flu may not recognize new mutated strain.
   • e. Viruses Replicate
     • i. Viruses are specific to host cell because portions of capsid bind in lock-and-key manner with host cell plasma membrane.
     • ii. When viral nucleic acid is inside host cell, it takes over metabolic machinery of host cell.
6. Bacteriophages Have Two Cycles (Fig. 28.2)
   • a. Bacteriophages (or phages) are viruses that parasitize bacteria.
   • b. In lytic cycle, host cell breaks open to release viruses.
   • c. In lysogenic cycle, viral replication is deferred to future.
7. Lytic Cycle
   • a. During attachment stage, portion of capsid of virus attaches to receptor site on bacterial cell in lock- and-key manner.
   • b. During penetration stage, viral enzyme digests away part of bacterial cell wall and viral DNA injects into bacterial cell.
   • c. Biosynthesis begins after virus inactivates host genes; takes over machinery of cell to make multiple copies of DNA and capsid protein subunits.
   • d. During maturation, viral DNA and capsids are assembled.
   • e. At release stage, lysozyme is synthesized by virus to disrupt cell wall; phage particles are released.
8. Lysogenic Cycle
   • a. Following attachment and penetration, viral DNA becomes integrated into bacterial DNA but with no destruction of host DNA.
   • b. Virus is latent, not actively replicating; termed a prophage.
   • c. Prophage is replicated along with host DNA; all subsequent cells are lysogenic cells with prophage copy.
   • d. Factors such as ultraviolet radiation, can induce prophage to enter lytic cycle, completing biosynthesis, maturation, and release.
9. Animal Viruses Also Cycle (p. 542)
   • a. Animal virus stages differ from bacteriophages because:
     • i. Entire animal virus penetrates host cell by endocytosis.
     • ii. Once inside, virus is uncoated to remove the envelope and capsid; exposes either DNA or RNA viral genome.
     • iii. Viral release occurs by budding if virus has envelope composed of cell membrane of host cell plus some glycoproteins coded by viral genes.
   • b. Common animal viruses include: papillomavirus, herpes viruses, hepatitis viruses, adenoviruses.
   • c. Cancerous cells may result from viruses that bring in oncogenes or viruses that alter host genes to become cancerous.
10. Retroviruses Have RNA Genes (p. 542)
    • a. Retroviruses are RNA viruses with a DNA stage. (Fig. 28.3)
    • b. Contains reverse transcriptase (carries out RNA --> DNA transcription).
    • c. The resulting double-stranded DNA (cDNA) is copy of viral genome.
    • d. cDNA is integrated into host genome, replicated with host genes.
    • e. New viruses are produced when DNA is transcribed; released by budding.
    • f. Retroviruses cause AIDS (HIV) and certain cancers.

1. Contains the different types of bacteria. (Fig. 28.4)
2. As prokaryotes, cells lack nucleus found in eukaryotic cells.
3. Structure of Bacteria
   • a. Very small size; 1 - 10 um in length, 0.2 - 0.3 um width.
   • b. Lack cytoplasmic organelles of eukaryotes, except for ribosomes.
   • c. Chromosome contained in nucleoid rather than within nuclear membrane.
   • d. Accessory rings of DNA called plasmids; used as vectors in genetic engineering.
   • e. Respiratory enzymes supplying ATP are on plasma membrane projections called mesosomes.
   • f. Eubacteria ("true bacteria") have a cell wall with unique amino acids cross-linked by peptide chains; may be surrounded by a capsule.
   • g. Some move by flagella; some adhere to surfaces by hairlike fimbriae.
4. Metabolism of Bacteria (p. 544)
   • a. Obligate anaerobes are unable to grow in presence of oxygen; these bacteria include tetanus and botulism bacteria.
   • b. Facultative anaerobes are able to grow in presence or absence of oxygen.
   • c. Most bacteria are aerobic, requiring constant oxygen supply for cell respiration.
5. Bacterial Nutrition
   • a. Use all modes except heterotrophism by ingestion.
   • b. Saprotrophic bacteria carry out external digestion of organic matter and absorb released nutrients.
   • c. Bacteria are called decomposers in an ecosystem because they break down organic matter; have role in digesting sewage and oil, production of alcohol, vitamins, antibiotics, and (by gene splicing) human insulin and growth hormone.
6. Symbiotic Bacteria
   • a. Live in association with other organisms.
   • b. Mutualist nitrogen-fixing bacteria live in nodules of legumes (both benefit).
   • c. Commensalistic bacteria live on human skin without harming us.
   • d. Parasitic bacteria harm host, cause plant and animal diseases.
7. How to Classify Bacteria (p. 545)
   • a. Bergey's Manual has kept standard classification since 1920s; categorizes highly diverse bacteria; we focus on two subkingdoms here.
   • b. Archaebacteria Came First
     • i. Earliest prokaryotes with different cell wall, plasma membrane, and ribosome composition than eubacteria.
     • ii. Live in extreme environments representing primitive earth habitats.
     • iii. Methanogens are anaerobes in swamps and marshes.
     • iv. Halophiles live in salty environments such as Great Salt Lake in Utah.
     • v. Thermacidophiles live in hot and acid sulfur springs; obtain energy by oxidizing sulfur.
8. Eubacteria Are Prevalent
   • a. Also adapted to most habitats; exhibit autotrophic and heterotrophic nutrition.
   • b. Classification
     • i. Gram stain procedure developed by Hans Christian Gram.
     • ii. Gram-positive bacteria stain purple due to thick layer of peptidoglycan in cell wall; Staphylococcus aureus is example.
     • iii. Gram-negative bacteria stain red due to thin layer of peptidoglycan in cell wall; syphilis agent Treponema pallidum is example.
     • iv. Three basic shapes of eubacteria: (Fig. 28.5)
       - coccus is round or spherical.
       - bacillus is rod-shaped.
       - spirillum or spirochete is spiral-shaped.
9. Cyanobacteria
   • a. Are gram-negative rods with unusual traits.
   • b. Carry on photosynthesis similar to plants; believed responsible for first introducing oxygen into primitive atmosphere.
   • c. Formerly were called blue-green algae; were classified with eukaryotic algae but now known to be prokaryotes.
   • d. Other pigments can mask chlorophyll producing red, yellow, brown, and black.
   • e. Cells are larger, from 1 um to 50 um in width.
   • f. May be unicellular, filamentous, or colonial.
   • g. Some have heterocysts to fix atmospheric nitrogen; combined with photosynthesis, nutritional requirements are minimal.
   • h. Common in fresh water, soil, and even hot springs.
   • i. Form symbiotic relationships with liverworts, ferns, corals.
   • j. In association with fungi, they form lichens; may have been first to colonize land.
   • k. High concentrations ("blooms") result when lakes and ponds receive heavy loads of wastes, phosphates and nitrates; when water becomes thick and light cannot penetrate, cyanobacteria die off and decomposing bacteria use up oxygen, killing fish.
10. Reproduction of Bacteria (p. 547)
    • a. Asexually by means of binary fission. (Fig. 28.7)
      • i. Single circular chromosome duplicates.
      • ii. Two resulting chromosomes each attach to inside of plasma membrane.
      • iii. Cell elongates and separates the two strands.
      • iv. Cell membrane grows inward; cell wall forms separating two daughter cells, each with chromosome.
    • b. Sexual exchange of DNA occurs in three ways:
      • i. Conjugation: male cell passes DNA to female cell by a sex pilus.
      • ii. Transformation: bacterium takes up DNA released into medium by dead bacteria.
      • iii. Transduction: bacteriophages carry DNA from one cell to another.
    • c. Under unfavorable environmental conditions, some bacteria form endospores. (Fig. 28.8)
      • i. Portion of cytoplasm plus chromosome dehydrate; encased by three protective spore coats.
      • ii. Rest of bacterial cell deteriorates; endospore released.
      • iii. Highly resistant to high temperature, drying out, and harsh chemicals.
      • iv. In good conditions, spore absorbs water and returns to typical cell form.

1. Protists are eukaryotes; therefore they have a nucleus and organelles.
2. Most are unicellular; multicellular forms lack tissue differentiation.
3. They are grouped, according to their mode of nutrition and other features, into three typical groups: algae, protozoa, and slime molds.
4. Algae: Live in Water and Photosynthesize (p. 549)
   • a. Autotrophic by photosynthesis, similar to plants, and also aquatic.
   • b. Major source of food supporting aquatic food chains.
   • c. Organisms named according to biochemical differences and their pigmentation: green, golden brown, brown, and red algae.
5. Green Algae Are Most Plantlike (p. 550)
   • a. About 7,000 species in phylum Chlorophyta.
   • b. May be closest related to ancestral green plants since:
     • i. They have cell walls made up of cellulose.
     • ii. They possess chlorophylls a and b.
     • iii. They store starch; other algae store food outside chloroplast.
6. Green Algae That Have Flagella
   • a. Chlamydomonas is single-celled algae.
   • b. Two flagella that move cell toward light; red-pigmented eyespot is sensitive to light.
   • c. Structures include definite cell wall and single large cup-shaped chloroplast with pyrenoid body where starch is synthesized.
   • d. When conditions are favorable, uses asexual reproduction where adult divides and forms zoospores, flagellated spores similar to parent cells.
   • e. When conditions are unfavorable, reproduces sexually using haplontic life cycle. (Fig. 28.9a)
   • f. In haplontic life cycle, gametes of two different strains join to form a zygote, which results in a resistant zygospore.
7. Green Algae That are Colonial (p. 550)
   • a. Volvox is flagellated green algae that forms a hollow sphere.
   • b. Individual cells resembling Chlamydomonas cooperate for flagellar movement.
   • c. Asexual reproduction forms daughter colonies. (Fig. 28.11)
   • d. Sexual reproduction involves heterogametes, large nonmotile eggs and small flagellated sperm.
8. Green Algae That Are Filamentous
   • a. Spirogyra has band of chloroplasts arranged in a spiral within cell. (Fig. 28.12)
   • b. Filaments are long chains of cells resulting from end-to-end cell division.
   • c. In conjugation, cell contents of one filament move across to cells of other filament, forming diploid zygotes that survive winter in ponds and streams.
   • d. After winter, filaments undergo meiosis to produce haploid filaments.
9. Green Algae That Are Multicellular
   • a. Ulva, or sea lettuce, is multicellular with leafy appearance. (Fig. 28.13)
   • b. Has alternation of generations. (Fig. 28.9b)
     • i. However, both generations look exactly alike.
     • ii. Spores are identical isogametes.
     • iii. Spores are flagellated.
10. Brown and Golden Brown Algae
    • a. Have chlorophylls a and c in chloroplasts plus fucoxanthin carotenoid pigment that gives color.
    • b. Brown Algae
      • i. In phylum Phaeophyta with about 1,500 species.
      • ii. Size varies from small filaments to large blades of seaweed 50 - 100 m length. (Fig. 28.14)
      • iii. Often grow along rocky shoreline in temperate zones; anchored by holdfasts to rocks and buoyed by air bladders.
      • iv. Fucus has a diplontic life cycle; most exhibit alternation of generations.
      • v. Harvested for human food, fertilizer, and algin (smoothing agent for ice cream, etc.).
    • c. Diatoms are type of golden brown algae.
      • i. In phylum Chrysophyta with about 11,000 species.
      • ii. Has two box-like halves composed of silica and forming beautiful patterns; each "lid" reproduces new half to fit. (Fig. 28.15)
      • iii. Most numerous of unicellular algae in ocean; used as important source of food for other organisms, and major source of earth's oxygen.
      • iv. Their remains form diatomaceous earth that is mined for filtering agents, scouring powders, etc.
11. Dinoflagellates (p. 552)
    • a. In phylum Dinoflagella with 1,000 species.
    • b. Bounded by protective cellulose plates. (Fig. 28.15b)
    • c. Most have two flagella, one in transverse groove that cause cells to spin.
    • d. Can cause "red tide" in ocean; waste toxins kill fish and can paralyze humans who eat shellfish that feed on dinoflagellates.
    • e. Are important source of food for small animals in ocean.
    • f. Also are symbionts in some invertebrates; increase growth of corals, etc.
12. Euglenoids
    • a. In phylum Euglenophyta, 1,000 species.
    • b. One-third of euglenoids have chloroplasts; rest do not.
    • c. Euglenoids grown without light can lose chloroplasts and become heterotrophic.
    • d. Structures
      • i. Two flagella, one usually much longer, project from anterior invagination. (Fig. 28.16)
      • ii. Near base of flagellum is photoreceptor eyespot.
      • iii. In freshwater, contractile vacuole rids body of excess water.
      • iv. Reproduce by longitudinal cell division; sexual reproduction unknown.
13. Red Algae Are Source of Agar
    • a. In phylum Rhodophyta with 4,000 species.
    • b. Multicellular algae found mostly in both shallow and deep warmer seawater.
    • c. Some are filamentous, most are branched or feathery. (Fig. 28.17)
    • d. Coralline algae cell walls have calcium carbonate; add to growth of coral reefs.
    • e. Cell walls contain sticky source of agar for bacterial culture media, cosmetics, drug capsules, etc.and to make jellies and desserts set rapidly.
14. Protozoa Are Animal-like
    • a. Are heterotrophic, motile and unicellular.
    • b. Not animals (animals are multicellular and undergo embryonic development).
    • c. Live in water, moist soil, inside other organisms.
    • d. Nutrition
      • i. Some engulf whole food; termed holozoic.
      • ii. Some are saprophytic, absorbing nutrients across plasma membrane.
      • iii. Some are parasitic, causing serious human infections.
    • e. Food digested inside food vacuoles.
    • f. Contractile vacuoles eliminate excess water in freshwater species.
    • g. Use binary fission and mitosis for asexual reproduction; many also reproduce sexually.
    • h. Classified in four groups according to locomotor organelle.
15. Amoeboids Move by Pseudopods
    • a. In phylum Sarcodina with 40,000 species.
    • b. Pseudopod
      • i. Term means "false foot."
      • ii. Used to move by extending fluid "arms"; therefore no definite shape.
      • iii. Feeds by surrounding and engulfing prey (algae, bacteria, other protozoa).
    • c. Amoeba proteus is common freshwater species. (Fig. 28.18a)
    • d. Food vacuoles form from phagocytosis.
    • e. Contractile vacuoles release excess water through temporary opening in plasma membrane.
    • f. Entamoeba histolytica lives in human intestine, causes amoebic dysentery.
    • g. Foraminifera
      • i. Mostly marine.
      • ii. Secrete calcium carbonate shell; pseudopods extend through holes in shell.
      • iii. Huge numbers live in sediment of ocean floor.
      • iv. Deposits over millions of years formed White Cliffs of Dover, limestone of Egyptian pyramids.
16. Ciliates Move by Cilia (p. 555)
    • a. In phylum Ciliophora with 8,000 species.
    • b. Paramecium caudatum represent most complex protozoa. (Fig. 28.19)
    • c. Hundreds of cilia beat in coordination for locomotion.
    • d. Cilia extend through holes in semirigid covering called pellicle.
    • e. Long, barbed trichocysts are discharged for defense or to capture prey.
    • f. Food moves down gullet, formed into food vacuoles; wastes exit at anal pore.
    • g. Asexual reproduction involves transverse binary fission.
    • h. Ciliates have two types of nuclei: macronucleus controls metabolism and micronuclei are exchanged in sexual reproduction.
17. Zooflagellates Move by Flagella
    • a. In phylum Zoomastigophora.
    • b. Many enter symbiotic relationships with their host.
    • c. Trichonympha collaris lives in gut of termites; contains bacterium that digests wood and converts cellulose to soluble carbohydrates for termite.
    • d. Giardia lamblia is in contaminated water; causes severe diarrhea.
    • e. Trichomonas vaginalis infects vagina and urethra of women, prostate, seminal vesicles and urethra of men.
    • f. Trypanosoma brucei, transmitted by tsetse flies, causes African sleeping sickness. (Fig. 28.20)
18. Sporozoa Form Spores (p. 556)
    • a. In phylum Sporozoa with 3,600 species.
    • b. Are parasitic and lack locomotor organelles.
    • c. Form spores at some point in life cycle.
    • d. Plasmodium vivax causes one type of malaria.
      • i. Transmitted to humans in saliva of infected female Anopheles mosquito.
      • ii. Malarial cells invade red blood cells; chills and fever result when infected RBCs burst and release toxic substances into blood. (Fig. 28.21)
      • iii. Resistant malarial strains remain major killer of humans.
    • e. Pneumocystis carinii causes pneumonia seen primarily in AIDS patients.
    • f. Toxoplasma gondii causes toxoplasmosis in cats; parasite poses risk to human fetus during pregnancy, also causes brain damage in AIDS patients.
19. Slime Molds and Water Molds Are Funguslike (p. 556)
    • a. Slime Molds
      • i. In phylum Gymnomycota with 560 species.
      • ii. Appear to be molds but vegetative state is amoeboid, while fungi are filamentous.
      • iii. Are heterotrophic by ingestion while fungi are saprotrophic.
      • iv. Produce spores resistant to environmental extremes, similar to fungi.
      • v. Cellular slime molds exist as individual amoeboid cells; each feeds alone but aggregate by chemical communication when food runs out; produce spores in sporangia.
      • vi. Acellular, multinucleated plasmodia creep along as diploid, cytoplasmic mass, phagocytizing decayed plant material; forms fruiting bodies that produce windblown spores. (Fig. 28.22)
    • b. Water Molds
      • i. In phylum Oomycota with 580 species.
      • ii. May live in water; common species parasitizes fish forming furry growths on gills.
      • iii. Land species includes mold responsible for Irish potato famine in 1840s.
      • iv. Most are saprophytic similar to true fungi.
      • v. Sexual life cycle is diplontic, fungi have haplontic cycle. (Fig. 28.9a, c)

1. Multicellular eukaryotes.
2. Heterotrophic by absorption.
   • a. Secrete digestive enzymes into environment.
   • b. Absorb nutrient molecules.
3. Many are saprotrophic decomposers of dead plant and animal remains, similar to bacteria.
4. Fungal human parasites include ringworm, athlete's foot, yeast infections.
5. Structure
   • a. Body of fungus is mycelium network of filaments called hyphae (except in unicellular yeast).
   • b. Cells differ from plant cells by lacking chloroplasts.
   • c. Cell wall contains chitin rather than cellulose found in plant cell walls.
   • d. Produce windblown nonflagellate spores for both sexual and asexual reproduction.
6. Zygospore Fungi Form Zygospores
   • a. In phylum Zygomycota with 600 species.
   • b. Includes fungi of soil, bakery goods, and some parasites.
   • c. Rhizopus stolonifer forms common black bread mold.
     • i. Stolons are horizontal hyphae on surface of bread.
     • ii. Rhizoids grown down into bread.
     • iii. Sporangiophores are upright stalks that bear sporangia that form sporangiospores.
     • iv. In asexual reproduction, all structures are haploid.
     • v. During sexual reproduction, hyphae from two mating types (+ and -) merge and nuclei fuse to form a diploid zygote; a thick wall forms around this zygospore; a haplontic life cycle. (Fig. 28.9a)
7. Sac Fungi Form Ascospores (p. 559)
   • a. In phylum Ascomycota with 30,000 species.
   • b. Examples:
     • i. Red bread molds (Neurospora spp.).
     • ii. Cup fungi. (Fig. 28.24a)
     • iii. Morels and truffles, highly valued gourmet fungi.
     • iv. Plant parasites including: powdery mildews, leaf curl, chestnut blight, and Dutch elm disease.
     • v. Ergot of rye and other grains.
   • c. Most sac fungi produce an ascus, a fingerlike sac formed when hyphae from two mating strains merge.
   • d. In an ascus, diploid nucleus formed undergoes meiosis to produce eight haploid nuclei that become eight ascospores.
   • e. In asexual reproduction, ascomycetes produce conidiospores. (Fig. 28.26)
8. Yeasts Are Single Cells
   • a. Yeasts are unicellular sac fungi that reproduce asexually either by mitosis or by budding.
   • b. When actively fermenting, yeasts produce ethanol and carbon dioxide.
   • c. Commercial Uses
     • i. Wild grapes carried natural yeast populations that produced early wines.
     • ii. Select yeasts used today to ferment grape juice into wine.
     • iii. Special yeasts also added to grain preparations to make beer.
     • iv. Both ethanol and carbon dioxide used for beer and sparkling wine; carbon dioxide bubbles off in still wines.
     • v. Yeasts in baking provides carbon dioxide expansion of bread.
     • vi. Yeasts are important genetic engineering eukaryote.
9. Club Fungi Have Basidiospores
   • a. In phylum Basidiomycota with 16,000 species.
   • b. Includes many mushrooms, bracket fungi, puffballs, stinkhorns. (Fig. 28.25)
   • c. Above structures are fruiting bodies containing club-shaped basidia.
   • d. Sexual reproduction occurs by merging of two mating types that fuse to become dikaryotic (n + n) mycelium.
   • e. Fruiting Bodies
     • i. Are tightly packed hyphae that form club-shaped basidia.
     • ii. In basidia, nuclear fusion and meiosis produce spores.
     • iii. Each basidium has four projections through which cytoplasm and haploid nucleus enter to form basidiospores.
10. Imperfect Fungi Reproduce Asexually Only
    • a. In phylum Deuteromycota with 25,000 species
    • b. No sexual portion of their life cycle has yet been observed, and may not exist; therefore are called "imperfect" fungi.
    • c. Always reproduce asexually using conidiospores. (Fig. 28.26)
    • d. Species of direct use to humans include:
      • i. Penicillium, some are original source of antibiotic penicillin.
      • ii. Other species give flavor to Roquefort and Camembert cheese; blue streaks in blue cheese are conidiospores.
      • iii. Cyclosporine used to suppress immune system following organ transplants is from soil fungus.
    • e. Disease-causing fungi in this group include: respiratory infections from inhaling spores, ringworm, athletes foot, and the yeast Candida albicans, which can cause thrush and vaginal infection in females on birth control pill.
11. Fungi Form Relationships
    • a. Lichens
      • i. Symbiotic relationship between fungus and cyanobacteria or green algae.
      • ii. Are identified according to the fungal partner.
      • iii. Fungus forms thin, protective, tough upper layer and loose lower layer.
      • iv. Algae shielded in middle layer. (Fig. 28.27a)
      • v. Previously assumed both benefit; algae provide food and are sheltered from desiccation by fungus (mutualism).
      • vi. Recent experiments show algae grow faster when separate from lichen; lichen fungus may be a parasite unable to live alone.
      • vii. Varieties of lichens:
        - crustose lichens are often on rocks and tree bark. (Fig. 28.27b)
        - foliose lichens are leaflike.
        - fruticose lichens are shrublike.

        viii. Lichens survive harsh conditions; are important soil formers.

        ix. Arctic reindeer "moss" are important source of food for animals.
    • b. Mycorrhizae
      • i. Term means "fungus roots."
      • ii. Form symbiotic relationships between soil fungi and roots of most plants.
      • iii. Fungus provides plants with inorganic nutrients.
      • iv. Plant provides fungus with organic nutrients.
      • v. Plants with roots infected with mycorrhizae grow better in poor soils deficient in phosphates.
      • vi. Fungus may enter cortex of roots but does not enter plant cells.