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Chapter Outline
20.1 Viruses, Viroids, and Prions
1. are associated with a number of ________________ , animal, and ________________diseases;
2. can only ________________by using the metabolic machinery of the host ________________;
3. are ________________;
4. may have a ________________or RNA genome.
5. In 1884, Pasteur suspected something smaller than bacteria caused ________________; he chose a Latin
term for “________________.”
6. In 1892, Russian biologist Dimitri Ivanowsky, working with the ________________mosaic virus,
confirmed Pasteur’s hypothesis that an infectious agent smaller than a ________________existed.
7. With the invention of the ________________microscope, these infectious agents could be seen for the first
A. Viral Structure
1. A virus is ________________in size to a large ________________, generally smaller than 200 nm in
2. Many viruses can be purified and crystallized, and the crystals ________________for long
periods of time.
3. Viral crystals become ________________when the viral particles they contain
________________host cells.
4. All viruses have at least ________________parts:
a. An outer ________________is composed of protein subunits.
b. An inner core contains either ________________ (deoxyribonucleic acid) or
________________ (ribonucleic acid), but not both.
1) The viral genome at most has several hundred ________________; a human cell, in
comparison, contains ________________of genes.
2) The viral ________________is usually partly host plasma membrane with viral
glycoprotein ________________.
3) Viral particles have proteins, especially enzymes (e.g., ________________), to
produce viral ________________or RNA.
4) Not all viruses have an envelope; such viruses are called naked viruses.
5. The classification of viruses is based on
a. their type of ________________, including whether they are single-stranded or
b. their ________________and shape; and
c. the presence or ________________of an outer envelope.
B. Parasitic Nature
1. Viruses are obligate intracellular parasites that cannot ________________outside a living
a. Animal viruses in laboratories are raised in ________________chick embryos or in cell
tissue culture.
b. Viruses infect all sorts of cells, from bacteria to human cells, but they are
1) The tobacco mosaic virus only infects certain ________________.
2) The ________________virus infects only mammals.
3) The AIDS virus, ________________, infects only certain human blood cells.
4) The ________________virus invades only liver tissues.
5) The Polio virus only reproduces in spinal ________________cells.
Virus Evolution
a. Some believe that viruses originated from the very cells that they ________________.
b. For example, viral nucleic acids originated from the ________________cell genome.
c. Therefore, viruses evolved ________________cells came into existence; new viruses are
probably evolving now.
d. Others suggest that viruses arose ________________the three domains.
3. Viruses often mutate; therefore, it is correct to say that they ________________.
a. Those that mutate are troublesome; a vaccine ________________today may not be
effective ________________.
b. Influenza (flu) viruses ________________regularly.
C. Viral Reproduction
1. Viruses gain entry into and are specific to a ________________host cell because portions of
the ________________ (or spikes of the envelope) adhere to specific receptor
________________on the host ________________surface.
2. Viral nucleic acid then enters a cell, where viral genome ________________for production of
protein units in the ________________.
3. A virus may have genes for a few special ________________needed for the virus to
reproduce and exit from a ________________cell.
4. A virus relies on host cell enzymes, ________________, transfer RNA (tRNA), and ATP for
its own ________________.
D. Reproduction of Bacteriophages
1. Bacteriophages (phages) are ________________that parasitize ________________.
2. The lytic cycle is a bacteriophage’s “life” cycle consisting of five stages:
a. During ________________, portions of the capsid bind with receptors on the bacterial
cell wall.
b. During ________________, a viral enzyme digests part of cell wall; the viral DNA is
injected into a bacterial cell.
c. ________________involves synthesis of viral components and begins after the virus
brings about inactivation of host genes not necessary to viral replication.
d. During ________________, viral DNA and capsids are assembled to produce several
hundred viral particles and lysozyme, coded by the virus, is produced.
e. When lysozyme disrupts the cell wall, ________________of the viral particles occurs
and the bacterial cell ________________.
3. With the lysogenic cycle, the virus ________________its DNA into the bacterium but only
later is phage produced.
a. Following attachment and ________________, viral DNA becomes
________________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 ________________.
c. The prophage is ________________along with host DNA; all subsequent cells (lysogenic
cells) carry a ________________.
d. Certain ________________factors (e.g., ultraviolet radiation) induce prophage to enter
the biosynthesis stage of the lytic cycle, followed by ________________and release.
E. Reproduction of Animal Viruses
1. Animal viruses replicate ________________to bacteriophages, but there are modifications.
a. If the virus has an ________________, glycoprotein spikes allow it to adhere to plasma
membrane ________________.
b. The virus genome covered by the ________________penetrates the host cell.
c. Once inside, the virus is uncoated as the envelope and ________________are removed.
Free of its covering, the ________________genome (DNA or RNA) proceeds with
e. Newly ________________viral particles are released by budding.
f. Components of viral envelopes (i.e., lipids, proteins, and carbohydrates) are
________________from the plasma or nuclear membrane of the host cell as the viruses
2. Retroviruses are ________________animal viruses that have a DNA stage.
a. Retroviruses contain the ________________reverse transcriptase that uses RNA as a
template to produce cDNA; cDNA is a ________________of the viral genome.
b. Viral cDNA is ________________into host DNA and is replicated as host DNA
c. Viral DNA is ________________; new viruses are produced by biosynthesis and
maturation; release is by budding.
F. Viral Infections of Special Concern
1. Viruses cause ________________diseases in plants and animals, including humans.
2. Some animal viruses are ________________to human cells: papillomavirus, herpes virus,
hepatitis virus, and adenoviruses, which can cause specific ________________.
3. Retroviruses include the ________________viruses (e.g., HIV) and also cause certain forms
of ________________.
4. Emerging Viruses
5. HIV is an example of an emerging virus: the causative agent of a disease that has only
________________arisen and ________________people.
7. In some cases of ________________diseases, the virus is simply transported from one
location to another; e.g., West Nile virus and severe acute ________________syndrome
8. The high ________________rate of viruses also cause infectious viruses to
________________; e.g., AIDS and Ebola fever.
9. A change in the ________________of transmission is yet another way infectious
________________could emerge.
G. Viroids and Prions
1. ________________are naked strands of RNA, a dozen of which cause ________________diseases.
2. Like viruses, ________________direct the cell to produce more viroids.
3. ________________ (proteinaceous infectious particles) are newly discovered disease agents that differ
from viruses and bacteria.
a. ________________are rogue proteins with a wrongly-shaped tertiary structure that cause other
proteins to distort.
b. Creutzfeldt-Jakob disease in humans and scrapie and ________________ ________________
(BSE) in cattle are due to ________________.
20.2 The Prokaryotes
Prokaryotes include the bacteria and archaea.
1. Bacteria were ________________ 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
________________ spontaneously from inanimate matter.
3. Around 1850, Pasteur devised an experiment showing that the ________________ present in
air contaminated the media.
4. A single ________________ of soil contains 1010 prokaryotes; these are the most numerous
________________ forms.
A. Structure of Prokaryotes
1. Prokaryotes ________________ in size from 1–10 µm in length and from 0.7–1.5 µm in
2. “Prokaryote” means “________________ a nucleus”—their cells lack a eukaryotic nucleus.
3. Prokaryotic ________________ date back as far as 3.5—3.8 billion years ago.
4. Fossils indicate ________________ were alone on earth for 2 billion years; they evolved
very diverse metabolic capabilities.
5. Prokaryotes adapted to most ________________ because they differ in the many ways they
acquire and utilize energy.
6. Outside the plasma membrane of most cells is a ________________ cell wall that keeps the
cell from bursting or collapsing due to osmotic changes by peptidoglycan, a complex molecule
containing a unique ________________ disaccharide and peptide fragments.
a. The ________________ may be surrounded by an organized capsule called a glycocalyx
and/or by a loose gelatinous sheath called a ________________ layer.
b. In parasitic forms, these outer ________________ protect the cell from host defenses.
7. Some prokaryotes move by means of ________________.
a. The flagellum has a ________________ composed of three strands of the protein
flagellin wound in a helix and inserted into a hook that is anchored by a basal body.
b. The flagellum is capable of ________________ rotation which causes the cell to spin and
move forward.
8. Many prokaryotes ________________ to surfaces by means of fimbriae.
a. Fimbriae are short ________________ filaments extending from the surface.
b. The fimbriae of Neisseria gonorrhoeae allow it to attach to host cells and cause gonorrhea.
9. ________________ cells lack the membranous organelles of eukaryotic cells.
10. Various ________________ pathways are located on the plasma membrane.
11. A ________________ is a dense area in prokaryotes where the chromosome is located; it is a
single circular strand of DNA.
12. ________________ 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
13. Protein synthesis in prokaryotic cells is carried out by thousands of ________________,
which are smaller than eukaryotic ________________.
B. Reproduction in Prokaryotes
1. Binary fission is the ________________ of a parent cell into two daughter cells; it is
asexual reproduction in prokaryotes.
a. A ________________ circular chromosome replicates; the two copies separate as the
cell enlarges.
b. Newly formed plasma membrane and the cell wall ________________ the cell into two
c. ________________, which involves formation of a spindle apparatus, does not occur in
d. Because prokaryotes have a short generation time, ________________ are generated
and distributed through a population more rapidly.
e. Prokaryotes are ________________; mutations are therefore immediately subjected to
natural selection.
2. In bacteria, genetic recombination can occur in three ways.
a. ________________ occurs when a bacterium passes DNA to a second bacterium
through a tube (sex pilus) that temporarily joins ________________ cells; this occurs
only between bacteria in the same or closely ________________ species.
b. ________________ involves bacteria taking up free pieces of DNA secreted by live
bacteria or released by ________________ bacteria.
In transduction, bacteriophages ________________ portions of bacterial DNA from
one cell to another.
d. Plasmids can carry genes for ________________ to antibiotics and transfer them
________________ bacteria by any of these processes.
3. Some bacteria form resistant endospores in response to ________________ environmental
a. Some cytoplasm and the chromosome ________________ and are encased by three
heavy, protective spore coats.
b. The rest of the bacterial cell deteriorates and the ________________ is released.
c. Endospores ________________ in the harshest of environments: desert heat and
dehydration, ________________ temperatures, polar ice, and extreme ultraviolet
d. ________________ also survive very long periods of time; anthrax spores 1,300 years
old can cause disease.
e. When environmental conditions are again suitable, the ________________ absorbs
water and grows out of its spore coat.
In a few hours, newly emerged cells become typical bacteria capable of
________________ by binary fission.
g. Endospore formation is not ________________ --it is a means of survival and dispersal
to new locations.
C. Prokaryotic Nutrition
1. Bacteria differ in their need for, and tolerance of, ________________ (O2).
a. Obligate anaerobes are ________________ to grow in the presence of
________________; this includes anaerobic bacteria that cause botulism, gas gangrene,
and tetanus.
b. Facultative anaerobes are able to grow in either the presence or ________________ of
gaseous O2.
c. Aerobic organisms (including ________________ and most prokaryotes) require a
constant supply of ________________ to carry out cellular respiration.
2. Autotrophic Prokaryotes
a. Photoautotrophs are ________________ and use light energy to assemble the organic
molecules they require.
1) Primitive photosynthesizing bacteria (e.g., green sulfur bacteria and
________________ sulfur bacteria) use only photosystem I that contains
bacteriochlorophyll; they do not give off O2 because hydrogen sulfide (H2S) is used as an
electron and H+ donor instead of________________.
2) Advanced photosynthesizing ________________ (e.g., cyanobacteria) use both
photosystem I and II that contain the same types of ________________ found in
plants; they do give off ________________ because H2O is used as an electron and
H+ donor.
b. Chemoautotrophs make ________________ molecules by using energy derived from
the oxidation of inorganic ________________ in the environment.
1) ________________ ocean hydrothermal vents provide H2S to form chemosynthetic
2) The methanogens are chemosynthetic ________________ that produce methane
(CH4) from hydrogen gas and CO2; ________________ synthesis and CO2
reduction are linked to this reaction and methanogens can decompose animal wastes to
produce electricity as an ecological ________________ energy source.
3) Nitrifying bacteria ________________ ammonia (NH3) to nitrites (NO2) and nitrites
to nitrates (NO3).
Heterotrophic Prokaryotes
a. Most free-living ________________ are chemoheterotrophs that take in pre-formed
organic ________________.
b. As aerobic saprotrophs, there is probably no ________________ organic molecule that
cannot be ________________ down by some prokaryotic species.
c. Detritivores (saprophytic ________________) are critical in
________________ materials in the ecosystem; they decompose dead organic matter
and make it ________________ to photosynthesizers.
d. Prokaryotes produce chemicals including ethyl alcohol, acetic acid, butyl alcohol, and
e. Prokaryotic action produces butter, cheese, sauerkraut, ________________, cotton, silk,
coffee and cocoa.
________________ are produced by some bacteria.
4. Some chemoheterotrophs are ________________, forming relationships with members of
other species; forms of symbiosis include ________________, commensalistic, and parasitic
a. ________________ nitrogen-fixing Rhizobium bacteria live in nodules on roots of
soybean, clover, and alfalfa where they reduce N2 to ammonia for their host; bacteria use some of
a plant’s photosynthetically produced organic molecules.
b. ________________ bacteria that live in the intestines of humans benefit from
undigested material and release vitamins K and B 12, which we use to produce blood components.
c. In the stomachs of cows and goats, ________________ prokaryotes digest cellulose.
d. ________________ bacteria live in or on organisms of other species and cause them no
e. ________________ bacteria are responsible for a wide variety of infectious plant,
animal and human diseases.
5. Bacterial Diseases in Humans
a. Microbes that cause disease are called ________________.
b. ________________ may be able to produce a toxin, and or adhere to surfaces and
sometimes invade organs or cells.
1) ________________ are small organic molecules, or small pieces of protein or parts
of the bacterial cell wall, that are released when bacteria die.
2) In almost all cases, the growth of the bacteria does not cause disease but instead the toxins
they ________________ cause the disease. Example: Clostridium tetani, the
causative agent of ________________.
c. Adhesion factors allow a ________________ to bind to certain cells, which determines
which tissue in the body will be the ________________. Example: Shigella dysentariae
releases a ________________ and also sticks to the intestinal wall, making it a lifethreatening form of ________________.
d. ________________ compounds either inhibit cell wall synthesis or protein biosynthesis;
increasingly, many pathogenic bacteria are becoming ________________ to bacteria.
20.3 The Bacteria
The Gram stain ________________ (developed in the late 1880s by Hans Christian Gram)
differentiates bacteria.
a. ________________ bacteria stain purple, whereas Gram-negative bacteria stain pink.
b. This difference is dependent on the thick or ________________ (respectively)
peptidoglycan cell wall.
Bacteria and ________________ have three basic shapes.
a. A ________________ is spiral-shaped.
A ________________ is an elongated or rod-shaped bacteria.
________________ bacteria are spherical.
Cocci and bacilli tend to form clusters and ________________ of a length typical of the
particular species.
3. Other criteria for ________________ of bacteria are the presence of
________________, metabolism, growth and nutritional characteristics, and other
physiological ________________.
A. Cyanobacteria
1. Cyanobacteria are ________________ bacteria with a number of unusual traits.
2. They ________________ in the same manner as plants, and thus are responsible for
introducing O2 into the primitive atmosphere.
3. They were ________________ mistaken for eukaryotes and classified with algae.
4. Cyanobacteria have ________________ that mask chlorophyll; they are not only blue-green
but also red, yellow, brown, or black.
5. They are relatively ________________ (1–50 µm in width).
6. They can be ________________, colonial, or filamentous.
7. Some move by ________________ or oscillating.
8. Some possess ________________, thick-walled cells without a nucleoid, where nitrogen
fixation occurs.
9. Cyanobacteria are ________________ in fresh water, soil, on moist surfaces, and in harsh
habitats (e.g., hot springs).
10. Some species are ________________ with other organisms (e.g., liverworts, ferns, and
11. Lichens are a symbiotic ________________ where the cyanobacteria provide organic
nutrients to the fungus and the fungus protects and supplies inorganic nutrients.
12. Cyanobacteria were probably the ________________ colonizers of land during evolution.
13. Cyanobacteria “________________” when nitrates and phosphates are released as wastes into
water; when they ________________ off, decomposing bacteria use up the oxygen and
cause fish kills.
20.4 The Archaea
A. Relationship to Domain Bacteria and Domain Eukarya
1. Archaea are ________________ with molecular characteristics that distinguish them from
bacteria and eukaryotes; their rRNA base sequence is ________________ from that in
2. Because archaea and some ________________ are both found in extreme environments (hot
springs, thermal vents, salt basins), they may have diverged from a common
3. Later, the eukarya split from the archaea; archaea and ________________ share some
ribosomal ________________ not found in bacteria; initiate transcription in the same
manner, and have similar types of ________________.
B. Structure and Function
1. Archaea have unusual ________________ in their plasma membranes that allow them to
function at high ________________: glycerol linked to hydrocarbons rather than fatty acids.
2. Cell walls of archaea do not contain the peptidoglycan found in ________________ cell
3. Only some ________________ have the ability to form methane.
4. Most are ________________; none are photosynthetic; this suggests chemoautotrophy
evolved first.
5. Some are ________________ or commensalistic but none are parasitic—none are known to
cause disease.
C. Types of Archaea
1. Methanogens live under ________________ environments (e.g., marshes) where they
produce methane.
a. Methane is produced from ________________ gas and carbon dioxide and is coupled to
formation of ATP.
b. Methane released to the ________________ contributes to the greenhouse effect.
c. About 65% of the ________________ found in our atmosphere is produced by
methanogenic archaea.
2. Halophiles require high ________________ concentrations (e.g., Great Salt Lake).
a. Their proteins have unique chloride pumps that use halorhodopsin to synthesize ATP in the
presence of ________________.
b. They usually require 12–15% salt concentrations; the ________________ is only 3.5%
3. Thermoacidophiles live under ________________, acidic environments (e.g., geysers).
a. They survive best at ________________ above 80oC; some survive above boiling
b. Metabolism of ________________ forms acidic sulfates; these bacteria grow best at pH of 1
to 2.