Introduction
A. Viruses and bacteria differ significantly.
1. Viruses
a. are noncellular;
b. cannot metabolize;
c. cannot respond to stimuli;
d. can only multiply within living cells by parasitizing the synthetic machinery of the infected cell; and
e. can evolve as a result of mutation and natural selection
2. Bacteria
a. are unicellular;
b. can metabolize;
c. can respond to stimuli;
d. can reproduce independently; and
e. can evolve as a result of mutation and natural selection
29.1. Viruses Are Particles
A. Viruses are nonliving with varied appearance.
1. All viruses are infectious.
2. Louis Pasteur suspected something smaller than bacteria caused rabies; he chose Latin term for "poison."
3. In 1892, Russian biologist Dimitri Ivanowsky, working with tobacco mosaic virus, confirmed Pasteur's hypothesis that an infectious agent smaller than a bacterium existed.
4. With the invention of the electron microscope, these infectious agents smaller than bacteria could be seen.
B. Viruses Are Noncellular
1. A virus is similar in size to a large protein macromolecule; it is generally smaller than 200 nm in diameter.
2. Many viruses can be purified and crystallized, and the crystals stored for long periods of time.
3. Viral crystals become infectious when the viral particles they contain are given opportunity to invade host cells.
4. All viruses have at least two parts:
a. An outer capsid is composed of protein subunits.
b. An inner core contains either DNA (deoxyribonucleic acid) or RNA (ribonucleic acid), but not both.
1) The viral genome at most has several hundred genes; a human cell contains thousands of genes.
2) A viral particle may also contain various proteins, especially enzymes (e.g., polymerases), needed to produce viral DNA or RNA.
5. The classification of viruses is based on
a. their type of nucleic acid, including whether it is single-stranded or double-stranded;
b. their size and shape; and
c. the presence or absence of an outer envelope.
C. Viruses Are Parasites
1. Viruses are obligate intracellular parasites that can be maintained only inside living cells; they cannot multiply outside a living cell; can only replicate inside of a specific host.
a. Animal viruses in laboratories are raised in live chick embryos or propagated in cell tissue culture.
b. Viruses infect all sorts of cells, from bacteria to human cells, but are very specific.
1) 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) Hepatitis virus invades only liver tissues.
5) Polio virus only reproduces in spinal nerve cells.
2. Virus evolution
a. Viruses are likely to have originated from the very cells that they infect.
b. Therefore, the nucleic acids originated from the host cell genome.
c. Therefore, viruses evolved after cells came into existence, and new viruses are probably evolving now.
3. Viruses often mutate; therefore, it is correct to say that they evolve.
a. Those that mutate often are troublesome because a vaccine effective today may not be effective tomorrow.
b. Influenza (flu) viruses mutate regularly.
c. Although viruses reproduce and evolve, they lack other traits of independent life and are not considered living.
D. Viruses Replicate
1. Viruses gain entry and are specific to a particular host cell because portions of the capsid (or spikes of the envelope) adhere to specific receptor sites on host cell plasma membrane.
2. Their nucleic acid then enters the cell, where viral genome codes for production of protein units in the capsid.
3. Virus may have genes for a few special enzymes needed for the virus to reproduce and exit from the host cell.
4. Virus relies on host enzymes, ribosomes, transfer RNA (tRNA), and ATP for its own replication.
5. A virus takes over the metabolic machinery of the host cell when it reproduces.
E. Bacteriophages Have Two Cycles
1. Bacteriophages (phages) are viruses that parasitize a bacterial cell as its host.
2. The lytic cycle is one of the bacteriophage "life" cycles in which the virus takes over operation of the bacterium immediately upon entering it and subsequently destroys the bacterium.
a. During attachment, portions of the capsid bind with receptors on the bacterial cell wall.
b. During penetration, a viral enzyme digests away part of cell wall, and viral DNA is injected into the bacterial cell.
c. Biosynthesis involves synthesis of viral components and begins after the virus brings about inactivation of host genes not necessary to viral replication.
d. During maturation, viral DNA and capsids are assembled to produce several hundred viral particles and lysozyme is produced.
e. When lysozyme disrupts the cells wall resulting in the lysis of the cell, release of the viral particles cells into the external environment occurs; the bacterial cell dies.
3. The lysogenic cycle is a bacteriophage life cycle in which the virus incorporates its DNA into that of the bacterium but only later does it produce phage.
a. Following attachment and penetration, viral DNA becomes integrated into bacterial DNA with no destruction of host DNA; at this point the phage is latent, and the viral DNA is called a prophage.
b. Prophage is replicated along with host DNA; all subsequent cells (lysogenic cells) carry a copy of prophage.
c. Certain environmental factors (e.g., ultraviolet radiation) can induce the prophage to enter the biosynthesis stage of the lytic cycle, followed by maturation and release.
F. Animal Viruses Also Cycle
1. Animal viruses replicate similarly to bacteriophages but there are modifications
a. If the virus has an envelope, glycoprotein spikes first adhere to plasma membrane receptors.
b. The entire virus (not just the viral nucleic acid) is taken into the host cell by endocytosis.
c. Once inside, the virus is uncoated as the envelope and capsid are removed.
d. Once free of its covering, the viral genome (DNA or RNA) proceeds with biosynthesis.
e. Newly assembled viral particles are released by budding, during which viral particles pick up their envelopes.
f. Components of viral envelopes (i.e., lipids, proteins, and carbohydrates) are obtained from the plasma membrane as the viruses leave the cell.
g. Budding does not necessarily result in the death of the host cell.
2. Some animal viruses are specific to human cells: papillomavirus, herpes virus, hepatitis virus, and adenoviruses, which can cause specific cancers.
a. These viruses undergo a period of latency and alter the genotype so the cell becomes cancerous.
b. Some viruses are cancer-producing because they bring with them oncogenes, normal genes transformed so that they can cause the cell to undergo repeated cell divisions.
3. Retrovirus is an RNA animal virus with a DNA stage.
a. Retroviruses contain the enzyme reverse transcriptase that carries out reverse transcription, thereby producing cDNA.
b. Viral cDNA is integrated into host DNA, remains in the genome, and is replicated as host DNA replicates.
c. If viral DNA is transcribed, new viruses are produced by biosynthesis, maturation, and release by budding.
d. Retroviruses include the AIDS viruses (e.g., HIV) and also cause certain forms of cancer.
G. Viruses Cause Infections
1. Viruses cause infectious diseases in plants and animals, including humans.
2. In plants, infectious diseases can be controlled only by burning those plants that show symptoms of disease.
3. In humans, viral diseases are controlled by preventing transmission, administering vaccines, and only recently by the administration of antiviral drugs.
a. Frequent hand washing and condom use help prevent transmission.
b. Vaccines that stimulate an immune response without causing illness; common virus vaccines include polio, measles, and mumps.
c. Antibiotics do not cure viral infections because viruses use host cell enzymes, not their own enzymes.
Bacteria Are Cellular
A. The kingdom Monera includes the bacteria.
1. Bacteria were not discovered until the seventeenth century, when Dutch naturalist Antonie van Leeuwenhoek examined all sorts of specimens, including scrapings from his own teeth.
2. Organisms that Leeuwenhoek observed were thought to arise spontaneously from inanimate matter.
3. Around 1850, Pasteur devised an experiment showing that bacteria present in air contaminate suitable growth media.
4. Today, we know a single spoonful of soil can contain 1010 bacteria; these are the most numerous life form.
B. Bacterial Structure Is Simple
1. Bacteria range in size from 1-10 µm in length and from 0.7-1.5 µm in width.
2. Bacterial cells lack a eukaryotic nucleus.
3. There are prokaryotic fossils dated as long ago as 3.5 billion years.
4. The fossil record indicates that the prokaryotes were alone on earth for at least 2 billion years, during which time they became extremely diverse in metabolic capabilities.
5. Bacteria adapted to most environments because bacteria differ in ways they acquire and utilize energy.
6. Outside the plasma membrane of most bacterial cells is a rigid cell wall that keeps the cell from bursting or collapsing due to osmotic changes.
a. The cell wall is composed of peptidoglycan, a molecule that contains chains of a unique amino disaccharide joined by peptide chains.
b. The cell wall may be surrounded by an attached capsule and/or by a loose gelatinous sheath (slime layer).
c. In parasitic forms, these outer coverings protect the cell from host defenses.
7. Some bacteria move by means of flagella.
a. The flagellum is a filament 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 360° rotation, which causes the bacterium to spin and move forward.
8. Many bacteria adhere to surfaces by means of fimbriae.
a. Fimbriae are short hairlike filaments extending from the surface.
b. The fimbriae of Neisseria gonorrhoeae allow it to attach to host cells and cause gonorrhea.
9. Bacterial cells lack the membranous organelles of eukaryotic cells.
10. Various metabolic pathways are located on the plasma membrane.
11. The nucleoid is a dense area in bacteria where the bacterial chromosome is located; it is a single circular strand of DNA.
12. Plasmids are accessory rings of DNA found in some bacteria; they can be extracted and used as vectors to carry foreign DNA into bacteria during genetic engineering procedures.
13. Protein synthesis in bacterial cells is carried out by thousands of ribosomes, which are smaller than eukaryotic ribosomes.
C. Bacteria Reproduce Asexually
1. Binary fission is a splitting of a parent cell into two daughter cells; it is asexual reproduction in bacteria.
a. The single circular chromosome replicates, and then the two copies separate as the cell enlarges.
b. Newly formed plasma membrane and cell wall separate the cell into two cells.
c. Mitosis, which involves formation of a spindle apparatus, does not occur in prokaryotes.
2. Sources of genetic variation
a. In bacteria, genetic recombination can occur in three ways.
1) Conjugation occurs when one bacterium passes DNA to a second bacterium through a tube (sex pilus) that temporarily joins two cells; takes place only between bacteria in same or closely related species.
2) Transformation involves a bacterium taking up, from the medium, free pieces of DNA secreted by live bacteria or released by dead bacteria.
3) In transduction, bacteriophage transfer portions of bacterial DNA from one cell to another.
b. Plasmids, which sometimes carry genes for resistance to antibiotics, can be transferred between bacteria by any of these processes.
c. Because genetic recombination does not occur routinely, mutation is the most important source of genetic variation for evolutionary change.
d. Because of typically short generation times (under favorable conditions), mutations are generated and distributed throughout bacterial populations more quickly than in eukaryotes.
e. Prokaryotes are haploid; therefore, mutations are immediately subjected to natural selection, which assesses any possible benefit.
D. Endospore Formation
1. Endospores are resistant forms of certain bacteria that form in response to unfavorable environmental conditions (e.g., unavailability of nutrients, desiccation, and high temperature).
2. A portion of cytoplasm and a copy of the chromosome dehydrate and are encased by three heavy, protective spore coats.
3. The rest of the bacterial cell deteriorates and the endospore is released.
4. Endospores survive in the harshest of environments (e.g., desert heat and dehydration, boiling temperatures, polar ice, and extreme ultraviolet radiation).
5. They also survive for very long periods of time; anthrax spores 1,300 years old can cause disease.
6. When environmental conditions are again suitable, endospore absorbs water and grows out of spore coat.
7. In a few hours, newly emerged cells become typical bacteria capable of reproducing by binary fission.
8. Endospore formation is not a form of reproduction, but a means of survival and dispersal to new locations.
E. Bacterial Nutrition Is Diverse
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 O2.
c. Aerobic organisms (including animals and most bacteria) require a constant supply of O2 to carry out cellular respiration.
2. Every type of nutrition, except for ingestion of whole food, is found in bacteria.
3. Autotrophic Bacteria
a. Most autotrophic bacteria are photosynthetic and use light as a source of energy to assemble the organic molecules they require.
1) More primitive photosynthesizing bacteria (e.g., green sulfur bacteria and purple sulfur bacteria) use only photosystem I that contains bacteriochlorophyll, and they do not give off O2 because hydrogen sulfide (H2S) is used as an electron and H+ donor instead of H2O.
2) More advanced photosynthesizing bacteria (e.g., cyanobacteria) use both photosystem I and II that contain the same types of chlorophylls found in plants, and they do give off O2 because H2O is used as an electron and H+ donor.
b. Some autotrophic bacteria carry out chemosynthesis, making organic molecules by using energy derived from the oxidation of inorganic compounds in the environment.
1) In deep ocean hydrothermal vents, hot minerals spew forth, providing H2S to a form of chemosynthetic bacteria, which live both freely and within the tissues of giant tube worms.
2) The methanogens are chemosynthetic bacteria that produce methane (CH4) from hydrogen gas and CO2; ATP synthesis and CO2 reduction are linked to this reaction and methanogens can decompose animal wastes to produce electricity as an ecological friendly energy source.
3) Nitrifying bacteria, chemosynthesizing bacteria that cycle nitrogen within ecosystems, oxidize ammonia (NH3) to nitrites (NO2-) and nitrites to nitrates (NO3-).
4. Heterotrophic Bacteria
a. Most free-living bacteria are saprotrophs, organisms that secrete digestive enzymes into their immediate environment and absorb the resulting nutrients back across their plasma membranes.
b. These decomposers break down virtually all large organic molecules into elements that can be recycled in the ecosystem; responsible for decomposing dead organic matter.
5. Commercial Uses
a. Bacteria produce essential chemicals including ethyl alcohol, acetic acid, butyl alcohol, and acetones.
b. Bacterial action helps produce butter, cheese, sauerkraut, rubber, cotton, silk, coffee and cocoa.
c. Antibiotics are produced by some bacteria.
6. Some heterotrophs are symbiotic, forming intimate, long-term relationships with members of other species; includes mutualistic, commensalistic, and parasitic relationships.
a. Mutualistic nitrogen-fixing bacteria such as Rhizobium live in nodules on the roots of soybean, clover, and alfalfa plants, where they reduce N2 to ammonia to the benefit of their host; bacteria benefit by using some of a plant'sphotosynthetically produced organic molecules. (Fig. 29.8)
b. Mutualistic bacteria that live in the intestines of humans benefit from the undigested material and release vitamins K and B12, which we use to help produce blood components.
c. In the stomachs of ruminants (e.g., cows and goats), special mutualistic bacteria digest cellulose, producing sugars that nourish the host.
d. Commensalistic bacteria live in or on organisms of other species, and cause them no harm.
e. Parasitic bacteria are responsible for a wide variety of infectious plant and animal diseases.
29.3. How Bacteria Are Classified
A. Gram Stain and Shape
1. The Gram stain procedure (developed 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.
2. Bacteria have three basic shapes.
a. A spirillum is a rigid spiral-shaped bacterium.
b. A bacillus is an elongated or rod-shaped bacteria
c. Coccus bacteria are spherical.
d. Cocci and bacilli tend to form clusters and chains of a length typical of the particular species.
3. Types of Bacteria
Twelve groups are now recognized based on bacterial 165 ribosomal RNA sequences.
A. Cyanobacteria
1. Cyanobacteria are Gram-negative bacteria with a number of unusual traits.
2. They photosynthesize in the same manner as plants and are thought to be responsible for first introducing O2 into the primitive atmosphere.
3. They were formerly mistaken for eukaryotes and classified with algae.
4. They have many pigments that mask the color of chlorophyll; they are not only blue-green but also red, yellow, brown, or black.
5. They are relatively large (1-50 µm in width).
6. They can be unicellular, colonial, or filamentous
7. Some can move by gliding or oscillating.
8. Some possess heterocysts, thick-walled cells without a nucleoid, where nitrogen fixation occurs.
9. Cyanobacteria are common in fresh water, in soil, and on moist surfaces; they can also be found in harsh habitats (e.g., hot springs).
10. Some species are symbiotic with other organisms (e.g., liverworts, ferns, and corals).
11. Lichens are a symbiotic relationship where the cyanobacteria provide organic nutrients to the fungus and the fungus protects and supplies inorganic nutrients.
12. Cyanobacteria are presumed to have been the first colonizers of land during evolution.
13. These organisms "bloom" when nitrates and phosphates are released as wastes; when they die off, decomposing bacteria use up the oxygen and cause fish kills.
. Archaea Compared to Bacteria
A. Archaea are Prokaryotes
1. Archaea are prokaryotes with molecular characteristics that distinguish them from both bacteria and eukaryotes.
2. Because archaea and bacteria are both found in extreme environments (hot springs, thermal vents, salt basins). They may have diverged from a common ancestor.
3. Later, the eukarya split from the archaea.
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).