1. Unit V: Bacteria, Viruses, Protists and Fungi
Chapters 18-20

2. VIRUS

3. Viruses, Viroids, and Prions
are associated with a number of plant, animal, and human diseases;
can only reproduce by using the metabolic machinery of the host cell;
are noncellular;
may have a DNA or RNA genome.
In 1884, Pasteur suspected something smaller than bacteria caused rabies; he chose a Latin term for “poison.”
With the invention of the electron microscope, these infectious agents could be seen for the first time.

4. The classification of viruses is based on:
Viral Structure
A virus is similar in size to a large protein, generally smaller than 200 nm in diameter.
Many viruses can be purified and crystallized, and the crystals stored for long periods of time.
Viral crystals become infectious when the viral particles they contain invade host cells.
The classification of viruses is based on:
their type of nucleic acid, including whether they are single‑stranded or double‑stranded;
their size and shape;
and the presence or absence of an outer envelope.

5. All viruses have at least two parts:
An outer capsid is composed of protein subunits.
An inner core contains either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid), but not both.
The viral genome at most has several hundred genes; a human cell, in comparison, contains thousands of genes.
The viral envelope is usually partly host plasma membrane with viral glycoprotein spikes.
Viral particles have proteins, especially enzymes (e.g., polymerases), to produce viral DNA or RNA.
Not all viruses have an envelope; such viruses are called naked viruses.

6. Parasitic Nature
1. Viruses are obligate intracellular parasites that cannot multiply outside a living cell; they must infect a living cell in order to reproduce.
a. Animal viruses in laboratories are raised in live chick embryos or in cell tissue culture.
b. Viruses infect all sorts of cells, from bacteria to human cells, but they are host specific.
1) The tobacco mosaic virus only infects certain plants.
2) The rabies virus infects only mammals.
3) The AIDS virus, HIV, infects only certain human blood cells.
4) The Hepatitis virus invades only liver tissues.
5) The Polio virus only reproduces in spinal nerve cells.

7. 2. Virus Evolution
a. Some believe that viruses originated from the very cells that they infect.
b. For example, viral nucleic acids originated from the host cell genome.
Therefore, viruses evolved after cells came into existence; new viruses are probably evolving now.

8. 3. Viruses often mutate; therefore, it is correct to say that they evolve.
a. Those that mutate are troublesome; a vaccine effective today may not be effective tomorrow.
b. Influenza (flu) viruses mutate regularly.

9. D. Viral Reproduction
1. Viruses gain entry into and are specific to a particular host cell because portions of the capsid (or spikes of the envelope) adhere to specific receptor sites on the host cell surface.
2. Viral nucleic acid then enters a cell, where viral genome codes for production of protein units in the capsid.
3. A virus relies on host cell enzymes, ribosomes, transfer RNA (tRNA), and ATP for its own replication.

10. E. Reproduction of Bacteriophages
1. Bacteriophages (phages) are viruses that parasitize bacteria.
2. The lytic cycle is a bacteriophage’s “life” cycle consisting of five stages:
a. During attachment, portions of the capsid bind with receptors on the bacterial cell wall.
b. During penetration, a viral enzyme digests part of cell wall; the viral DNA is injected into a bacterial cell.
c. Biosynthesis involves synthesis of viral components
d. During maturation, viral DNA and capsids are assembled to produce several hundred viral particles

11. 3. With the lysogenic cycle, the virus incorporates its DNA into the bacterium but only later is phage produced.
a. Following attachment and penetration, viral DNA becomes integrated into bacterial DNA with no destruction of the host DNA.
b. At this point, the phage is latent and the viral DNA is called a prophage.
c. The prophage is replicated along with host DNA; all subsequent cells (lysogenic cells) carry a copy.
d. Certain environmental factors (e.g., ultraviolet radiation) change the DNA

12. F. Reproduction of Animal Viruses
1. Animal viruses replicate similarly to bacteriophages, but there are modifications.
a. If the virus has an envelope, glycoprotein spikes allow it to adhere to plasma membrane receptors.
b. The virus genome covered by the capsid penetrates the host cell.
c. Once inside, the virus is uncoated as the envelope and capsid are removed.
d. Free of its covering, the viral genome (DNA or RNA) proceeds with biosynthesis.

13. 2. Retroviruses are RNA animal viruses that have a DNA stage.
a. Viral cDNA is integrated into host DNA and is replicated as host DNA replicates.
b. Viral DNA is transcribed; new viruses are produced by biosynthesis and maturation; release is by budding.

14. G. Viral Infections of Special Concern
1. Viruses cause infectious diseases in plants and animals, including humans.
2. Some animal viruses are specific to human cells: papillomavirus, herpes virus, hepatitis virus, and adenoviruses, which can cause specific cancers.
3. Retroviruses include the AIDS viruses (e.g., HIV) and also cause certain forms of cancer.
HIV is an example of an emerging virus: the causative agent of a disease that has only recently arisen and infected people.
In some cases of emerging diseases, the virus is simply transported from one location to another; e.g., West Nile virus and severe acute respiratory syndrome (SARS).
The high mutation rate of viruses also cause infectious viruses to emerge; e.g., AIDS and Ebola fever.
A change in the mode of transmission is yet another way infectious viruses could emerge.

15. H. Viroids and Prions
Viroids are naked strands of RNA, a dozen of which cause crop diseases.
Prions (proteinaceous infectious particles) are newly discovered disease agents that differ from viruses and bacteria.

16. 2. Possible Bird Flu Pandemic of the Future 3. How to Be Prepared
I. Flu Pandemic
1. Flu Viruses
Possible Bird Flu Pandemic of the Future
How to Be Prepared
a. One of the easiest practices to prevent the spread of a flu virus is cleaning hands thoroughly and often using soap and water or alcohol-based sanitizer.
b. Keeping your hands away from your eyes, nose, mouth can help prevent the virus from entering your body.
c. Education will help prepare for a pandemic.
d. For more information, visit

17. BACTERIA

18. A. Prokaryotes include the bacteria and archaea.
The Prokaryotes
A. Prokaryotes include the bacteria and archaea.
1. Bacteria were discovered in the seventeenth century when Antonie van Leeuwenhoek examined scrapings from his teeth.
2. The “little animals” Leeuwenhoek observed were thought by him and others to arise spontaneously from inanimate matter.
3. Around 1850, Pasteur devised an experiment showing that the bacteria present in air contaminated the media (Swan –Neck Flask Experiment).
4. A single spoonful of soil contains 1010 prokaryotes; these are the most numerous life forms.

19. B. Structure of Prokaryotes
1. Prokaryotes range in size from 1–10 µm in length and from 0.7–1.5 µm in width.
2. “Prokaryote” means “before a nucleus”—their cells lack a eukaryotic nucleus.
3. Prokaryotic fossils date back as far as 3.5—3.8 billion years ago.
4. Fossils indicate prokaryotes were alone on earth for 2 billion years; they evolved very diverse metabolic capabilities.
5. Prokaryotes adapted to most environments because they differ in the many ways they acquire and utilize energy.

20. 6. Some prokaryotes move by means of flagella.
7. Many prokaryotes adhere to surfaces by means of fimbriae.
8. Prokaryotic cells lack the membranous organelles of eukaryotic cells.
9. A nucleoid is a dense area in prokaryotes where the chromosome is located; it is a single circular strand of DNA.
10. Plasmids are accessory rings of DNA found in some prokaryotes; they can be extracted and used as vectors to carry foreign DNA into bacteria during genetic engineering procedures.
11. Protein synthesis in prokaryotic cells is carried out by thousands of ribosomes, which are smaller than eukaryotic ribosomes.

21. C. Reproduction in Prokaryotes
Binary fission is the splitting of a parent cell into two daughter cells; it is asexual reproduction in prokaryotes.
A single circular chromosome replicates; the two copies separate as the cell enlarges.
Newly formed plasma membrane and the cell wall separate the cell into two cells.
Prokaryotes are haploid; mutations are therefore immediately subjected to natural selection.

22. 2. In bacteria, genetic recombination can occur in three ways.
Conjugation occurs when a bacterium passes DNA to a second bacterium through a tube (sex pilus) that temporarily joins two cells; this occurs only between bacteria in the same or closely related species.
Transformation involves bacteria taking up free pieces of DNA secreted by live bacteria or released by dead bacteria.
In transduction, bacteriophages transfer portions of bacterial DNA from one cell to another.
Plasmids can carry genes for resistance to antibiotics and transfer them between bacteria by any of these processes.

23. A. Characteristics of Bacterial Cells
The Bacteria
A. Characteristics of Bacterial Cells
1. Bacteria are the more common type of prokaryote
2. Bacterial cell walls are protected by peptidoglycan, a complex of polysaccharides linked by amino acids.
3. The Gram stain procedure (developed in the late s by Hans Christian Gram) differentiates bacteria.
a.Gram‑positive bacteria stain purple, whereas Gram‑negative bacteria stain pink.
b. This difference is dependent on the thick or thin (respectively) peptidoglycan cell wall.
4. Bacteria and archaea have three basic shapes.
a. A spirillum is spiral‑shaped.
b. A bacillus is an elongated or rod‑shaped bacteria.
c. Coccus bacteria are spherical.
Note: Cocci and bacilli tend to form clusters (staph- infections) and chains (strept- infections)of a length typical of the particular species.

24. B. Bacterial Metabolism
1. Bacteria differ in their need for, and tolerance of, oxygen (O2).
a. Obligate anaerobes are unable to grow in the presence of O2; this includes anaerobic bacteria that cause botulism, gas gangrene, and tetanus.
b. Facultative anaerobes are able to grow in either the presence or absence of gaseous O2.
c. Aerobic organisms (including animals and most prokaryotes) require a constant supply of O2 to carry out cellular respiration.

25. 2. Autotrophic Bacteria
a. Photoautotrophs are photosynthetic and use light energy to assemble the organic molecules they require.
b. Chemoautotrophs make organic molecules by using energy derived from the oxidation of inorganic compounds in the environment.
Ex. Deep ocean hydrothermal vents provide H2S to form chemosynthetic bacteria.

26. C. Symbiotic Relationships
Bacteria and archaea form symbiotic relationships, forming relationships with members of other species; forms of symbiosis include mutualistic, commensalistic, and parasitic relationships.
Commensalism occurs when one population modifies the environment in such a way that a second population benefits. Commensalistic bacteria live in or on organisms of other species and cause them no harm.
Mutualistic bacteria that live in the intestines of humans benefit from undigested material and release vitamins K and B12, which we use to produce blood components.
Parasitic bacteria are responsible for a wide variety of infectious plant, animal and human diseases.
Parasitic bacteria that cause disease are called pathogens.

27. D. Cyanobacteria
Cyanobacteria are Gram‑negative bacteria with a number of unusual traits.
They photosynthesize in the same manner as plants.
They were formerly mistaken for eukaryotes and classified with algae.
Cyanobacteria have pigments that mask chlorophyll; they are not only blue‑green but also red, yellow, brown, or black.
They can be unicellular, colonial, or filamentous.
Cyanobacteria are common in fresh water, soil, on moist surfaces, and in harsh habitats (e.g., hot springs).
Some species are symbiotic with other organisms (e.g., liverworts, ferns, and corals).
Lichens are a symbiotic relationship where the cyanobacteria provide organic nutrients to the fungus and the fungus protects and supplies inorganic nutrients.
Cyanobacteria “bloom” when nitrates and phosphates are released as wastes into water; when they die off, decomposing bacteria use up the oxygen and cause fish kills.

28. The Archaea
1. Archaea are prokaryotes with molecular characteristics that distinguish them from bacteria and eukaryotes; their rRNA base sequence is different from that in bacteria.
2. Because archaea and some bacteria are both found in extreme environments (hot springs, thermal vents, salt basins), they may have diverged from a common ancestor.

29. A. Structure of Archaea
1. Archaea have unusual lipids in their plasma membranes that allow them to function at high temperatures: glycerol linked to hydrocarbons rather than fatty acids.
2. Cell walls of archaea do not contain the peptidoglycan found in bacterial cell walls.

30. B. Types of Archaea
1. Methanogens live under anaerobic environments (e.g., marshes) where they produce methane.
2. Halophiles require high salt concentrations (e.g., Great Salt Lake).
3. Thermoacidophiles live under hot, acidic environments (e.g., geysers).

31. PROTISTS

32. General Biology of Protists
A. Protists are classified in the domain Eukarya (they have eukaryotic cells) and the kingdom Protista.
1. The endosymbiotic hypothesis suggests how the eukaryotic cells arose.
2. Although many protists are unicellular, they are highly complex.
3.Most protists are free-living; some are parasitic, some (e.g., slime molds) are saprophytic (feed on decaying plant material), and some are mixotrophic (combining autotrophic and heterotrophic nutrition modes).

33. 4. Some protists are photoautotrophic; some are heterotrophic.
5. Most protists use asexual reproduction, but sexual reproduction occurs in some species.
Formation of spores allows free-living and parasitic protists to survive hostile environments.
A cyst is a dormant cell with a resistant outer covering; the cyst allows a free-living species to overwinter and helps certain parasitic species survive the host’s digestive juices.
6. Some protists are of great medical importance because they cause disease; others are ecologically important.
7. Aquatic plankton serve as food for heterotrophic protists and animals.
8. Photosynthetic plankton produce much of the oxygen in the atmosphere.
9. Many protists enter symbiotic relationships; coral reefs rely on symbiotic photosynthetic protists.

34. B. Evolution and Diversity of Protists
1. Classification of protests has been based on modes of nutrition.
2. Protozoans include photosynthetic, heterotrophic and have some form of locomotion (flagella, pseudopods, cilia).

35. A. Supergroup Archaeplastids
Archaeoplasts include land plants, green and red algae.
Green:
***Contain both chlorophyll a and b.
***They live in the ocean, in fresh water habitats, snowbanks and on moist land.
***The majority of green algae are unicellular, but filamentous (Spirogyra), colonial (Volvox), and multicellular forms exist (Ulva).
***Green algae are not always green; some have pigments that give them an orange, red, or rust color.
***Plants are considered to be most closely related to the green algae.

36. The Red Algae
Red algae are chiefly marine multicellular algae that live in warmer seawater.
Red algae posses a red and a blue pigment in addition to chlorophyll.
They are generally much smaller and more delicate than brown algae.
Some are filamentous, but most are branched, having a feathery, flat, or ribbonlike appearance.
Red algae are economically important.
Mucilaginous material in cell walls of Gelidium and Gracilaria is the source of agar used in drug capsules, dental impressions, and cosmetics.
In the laboratory, agar is a major microbiological media, and when purified, is a gel for electrophoresis.
Agar is used in food preparation to keep baked goods from drying and to set jellies and desserts.
Carrageen, an emulsifying agent extracted from Chondrus crispus, is used in production of chocolate and cosmetics.

37. Life Cycles Among the Algae
Depending on the species and environmental conditions, asexual and sexual reproduction occur in algae.
Asexual Reproduction
a. Asexual reproduction occurs frequently when the environment is favorable to growth.
b. Asexual reproduction only requires one parent.
c. The offspring are genetically identical to parent.
Sexual Reproduction
a. Sexual reproduction occurs when the environment is changing and unfavorable to growth.
b. Genetic recombinations may produce individuals that are more likely to survive environmental extremes such as high or low temperature, acidic or basic pH.

38. Diatoms
Diatoms are stramenopiles that have cell walls consisting of two silica‑impregnated halves or valves.
They are yellow-orange in color because they contain a carotenoid pigment in addition to chlorophyll.
Diatoms are an important part of the phytoplankton, photosynthetic organisms that are a source of food and oxygen for heterotrophs.
The cell wall has an outer layer of silica (glass) with a variety of markings formed by pores.
Diatom remains accumulate on the ocean floor and are mined as diatomaceous earth for use as filters, abrasives, etc.

39. Golden Brown Algae
Golden brown algae derive their color from yellow-brown carotenoid pigments
They are unicellular or colonial protists, with two flagella.
Golden brown algae contribute to freshwater and marine phytoplankton.

40. Euglenids
Euglenids are small (10–500 µm) freshwater unicellular organisms.
One‑third of all genera have chloroplasts; those that lack chloroplasts ingest or absorb their food.
Their chloroplasts are surrounded by three, rather than two, membranes.
Their chloroplasts resemble those of green algae.
They possess two flagella, one of which typically is much longer than the other and projects out of a vase‑shaped invagination; it is called a tinsel flagellum because it has hairs on it.
Near the base of the longer flagellum is a red eyespot that shades a photoreceptor for detecting light.
A contractile vacuole, similar to certain protozoa, eliminates excess water.
Euglenoids reproduce by longitudinal cell division; sexual reproduction is not known to occur.

41. Amoeboids
Amoeboids engulf prey with pseudopods, cytoplasmic extensions formed as cytoplasm streams in one direction.
Amoeba proteus is a commonly studied member.
Amoeboids phagocytize their food; pseudopods surround and engulf prey.
Entamoeba histolytica is an amoebic parasite that invades the human intestinal lining.

42. FUNGI

43. Evolution and Characteristics of Fungi
1. The 80,000 species of the Kingdom Fungi are mostly multicellular eukaryotes that share a common mode of nutrition.
2. Like animals, fungi are heterotrophic and consume preformed organic matter.
3. Animals, however, are heterotrophic by ingestion while fungi are heterotrophic by absorption.
4. Fungal cells secrete digestive enzymes; following breakdown of molecules, the nutrients are absorbed.
5. Most fungi are saprotrophic decomposers, breaking down wastes or remains of plants and animals.

44. Evolution of Fungi
Molecular data shows that animals and fungi share a common ancestor after plants evolved.
The earliest fossil of fungi is dated 450 MYA.

45. Structure of Fungi
1. Fungi can be unicellular (e.g., yeasts).
2. Most fungi are multicellular in structure.
3. Fungal cells lack chloroplasts and have a cell wall made of chitin, not cellulose.
4. The energy reserve of fungi is not starch, but glycogen, as in animals.
5. Except for aquatic chytrids, fungi are nonmotile; their cells lack basal bodies and do not have flagella at any stage in their life.
6. Fungi move to a food source by growing toward it; hyphae can grow up to a kilometer a day.
7. Nonseptate fungi lack septa, or cross walls, in their hyphae; nonseptate hyphae are multinucleated.
8. Septate fungi have cross walls in their hyphae; pores allow cytoplasm and organelles to pass freely.
9. The septa that separate reproductive cells, however, are complete in all fungal groups.

46. 1. In general, fungal sexual reproduction involves the following:
Reproduction of Fungi
1. In general, fungal sexual reproduction involves the following:
haploid hyphae → dikaryotic stage → diploid zygote
2. During sexual reproduction, haploid hyphae from two different mating types fuse.
3. When the nuclei fuse, the resulting zygote undergoes meiotic cell division leading to spore formation.
4. Fungal spores germinate directly into haploid hyphae without embryological development.
Spores are an adaptation to life on land and ensure that the species will be dispersed to new locations.
A spore is a reproductive cell that can grow directly into a new organism.
Fungi produce spores both during sexual and asexual reproduction.
Although nonmotile, the spores are readily dispersed by wind.
5. Asexual reproduction can occur by three mechanisms:
a. Production of spores by a single mycelium is the most common mechanism.
b. Fragmentation is when a portion of a mycelium becomes separated and begins a life of its own.
c. Budding is typical of yeasts; a small cell forms and gets pinched off as it grows to full size.

47. Diversity of Fungi
In 1969, R. H. Whittaker argued for their own kingdom based on their multicellular nature and mode of nutrition.
Not knowing phylogeny, fungal groups are classified according to differences in life cycles and the types of structure that produces spores.

48. Types of Fungi: A. Chytrids B. Zygospore Fungi C. AM Fungi
D. Sac Fungi
E. Deadly Fungi
F. Club Fungi

49. 3 Symbiotic Relationships of Fungi Lichens
1. Lichens are a symbiotic association between a fungus and a cyanobacterium or a green alga.
2. The body of a lichen is composed of three layers:
3. Special fungal hyphae penetrate or envelope the photosynthetic cells and transfer nutrients directly to the rest of the fungus.
4. Lichens can reproduce asexually by releasing fragments that contain hyphae and an algal cell.
5. This association was considered mutualistic, but experimentation suggests a controlled parasitism by the fungus of the alga.
6. Three types of lichens are recognized.
a. Compact crustose lichens are often seen on bare rocks or tree bark.
b. Foliose lichens are leaflike.
c. Fruticose lichens are shrublike.
7. Lichens are efficient at acquiring nutrients; they survive with low moisture, temperature, or poor soil.
8. Lichens may live in extreme environments and on bare rocks; they help form soil.
9. Lichens also take up pollutants and cannot survive where the air is polluted.