Part IV Diversity of Life
The First Forms of Life
Chapter
17
Outline
	17.1	The Viruses
	•	All viruses have an outer capsid composed of protein and an inner core of nucleic acid. Some animal viruses have an outer membranous envelope.266
	•	Viruses reproduce in human cells much the same way as they do in bacteria.268
	•	Emerging viral diseases, including those caused by retroviruses, are of special concern today.269
	17.2	Viroids and Prions
	•	Viroids that attack crops, and prions that attack animals are less complex than viruses.270
	17.3	The Prokaryotes
	•	Prokaryotes—the bacteria and archaea—lack a nucleus and most of the other cytoplasmic organelles found in eukaryotic cells.270
	•	Prokaryotes reproduce asexually by binary fission.272
	•	Most bacteria are free-living heterotrophs that play important roles in the environment, food science, and biotechnology. Some bacteria are disease-causing parasites.273–74
	•	Biochemical characteristics distinguish archaea from bacteria and eukaryotes.275
	•	The archaea are quite specialized and are well known for living in extreme habitats.275
	17.4	The Protists
	•	Endosymbiosis may have played a role in the origin of the eukaryotic cell.276
	•	The protists are largely unicellular, but are quite varied in structure and life cycle.276–77
	•	This text groups the protists according to their modes of nutrition.276–79
AIDS, polio, tuberculosis, gonorrhea, SARS, leprosy, malaria. Microbes, named for their microscopic size, cause these diseases. Disease-causing microbes, discussed in this chapter, include tiny viruses, some bacteria, and certain protists. Although microscopic size unifies the microbes, their structures differ. Viruses are noncellular, bacteria are prokaryotes, and protists are eukaryotes. Viruses always cause disease, but only some bacteria and a few protists do. Among the protists, algae rarely cause disease because they usually make their own food. The parasitic way of life allows the disease-causing bacteria and protozoans (protists) to get their food and reproduce. Viruses don’t need food—after entering a cell, they cause the cell to make hundreds of viruses at one time. 
We didn’t always know that microbes cause disease. The germ theory of disease didn’t take hold until the twentieth century. After that, rapid progress was made in identifying which microbes cause which diseases and how they are transmitted. For example, we now know that AIDS and gonorrhea are sexually transmitted, tuberculosis and SARS are contracted by way of the respiratory tract, and the Anopheles mosquito spreads malaria. Each microbe lives in a different part of the body: HIV replicates in just certain types of white blood cells, tuberculosis usually centers in the lungs, and the protozoan that causes malaria reproduces in red blood cells. 
This chapter provides basic information about microbes and the various ways they reproduce. Such knowledge enables us not only to fight the diseases microbes sometimes cause, but also to take advantage of the many benefits they provide. 
17.1		The Viruses 
The study of viruses has contributed much to our understanding of disease, genetics, and even the characteristics of living things. Their contribution is surprising because viruses are not included in the classification of organisms. They are noncellular, while organisms are always cellular. Also, they are amazingly small; at 0.2 microns, a virus is only about one-fifth the size of a bacterium.
Each type of virus always has at least two parts: an outer capsid, composed of protein subunits, and an inner core of nucleic acid—either DNA or RNA. The adenovirus shown in Figure 17.1 also has spikes (formed from a glycoprotein) that are involved in attaching the virus to the host cell. In some animal viruses, the capsid is surrounded by an outer membranous envelope with glycoprotein spikes. The envelope is actually a piece of the host’s plasma membrane that also contains proteins produced by the virus. The interior of a virus can contain various enzymes such as the polymerases, which are needed to produce viral DNA and/or RNA. The viral genome has at most several hundred genes; by contrast, a human cell contains thousands of genes. 
Should viruses be considered living? Both scientific and philosophical debates have raged with regard to this question. Viruses are obligate intracellular parasites because they can only reproduce inside a living cell. Outside a living cell, viruses can be stored as chemicals or even synthesized in the laboratory from chemicals. Still, viruses do have a genome that mutates and functions to direct their reproduction when inside a cell.
Viral Reproduction
Viruses are specific to a particular host cell because a portion of the capsid (often a spike) adheres in a lock-and-key manner to a specific molecule (called a receptor) on the host cell’s outer surface. Once inside, the viral genome takes over the metabolic machinery of the host cell. In large measure, the virus uses the host’s enzymes, ribosomes, transfer RNA (tRNA), and ATP for its reproduction. 
Reproduction of Bacteriophages
A bacteriophage, or simply phage, is a virus that reproduces in a bacterium. Bacteriophages are named in different ways; the one shown in Figure 17.2 is called lambda (). When phage  reproduces, it can undergo the lytic cycle or the lysogenic cycle (Fig. 17.3). The lytic cycle may be divided into five stages: attachment, penetration, biosynthesis, maturation, and release. During attachment, the capsid combines with a receptor in the bacterial cell wall. During penetration, a viral enzyme digests away part of the cell wall, and viral DNA is injected into the bacterial cell. Biosynthesis of viral components begins after the virus inactivates host genes not necessary to viral replication. The machinery of the host cell then carries out (1) viral DNA replication and (2) production of multiple copies of the capsid protein subunits. During maturation, viral DNA and capsids assemble to produce several hundred viral particles. Lysozyme, an enzyme coded for by a viral gene, disrupts the cell wall, and the release of phage particles occurs. The bacterial cell dies as a result.
In the lysogenic cycle, the infected bacterium does not immediately produce phage, but may do so sometime in the future. In the meantime, the phage is latent—not actively reproducing. Following attachment and penetration, integration occurs: Viral DNA becomes incorporated into bacterial DNA with no destruction of host DNA. While latent, the viral DNA is called a prophage. The prophage is replicated along with the host DNA, and all subsequent cells, called lysogenic cells, carry a copy of the prophage. Certain environmental factors, such as ultraviolet radiation, can induce the prophage to enter the lytic stage of biosynthesis, followed by maturation and release.
The herpesviruses, which cause cold sores, genital herpes, and chickenpox in humans, are examples of infections that remain latent much of the time. Herpesviruses linger in spinal ganglia until stress, excessive sunlight, or some other stimulus causes them to undergo the lytic cycle. HIV (human immu-nodeficiency virus), the cause of AIDS, remains relatively latent in lymphocytes, slowly releasing new viruses.
Plant Viruses 
Crops and garden plants are also subject to viral infections. Plant viruses tend to enter through damaged tissues and then move about the plant through plasmodesmata, cytoplasmic strands that extend between plant cell walls. The best-studied plant virus is tobacco mosaic virus, a long, rod-shaped virus with only one type of protein subunit in its capsid (Fig. 17.4). Not all viruses are deadly, but over time, they often debilitate a plant. 
Viruses are passed from one plant to another by insects, and by gardening tools, which move sap from one plant to another. Viral particles are also transmitted by way of seeds and pollen. Unfortunately, no chemical can control viral diseases. Until recently, the only way to control viral diseases was to destroy symptomatic plants and to control the insect vector, if there is one. Now that bioengineering is routine, it is possible to transfer genes conferring disease resistance between plants. One of the most successful examples to date is the creation of papaya plants resistant to papaya ring spot virus (PRSV) in Hawaii. One transgenic line is now completely resistant to PRSV. 
Animal Viruses 
Viruses that cause diseases in animals, including humans, reproduce in a manner similar to that of -bacteriophages. However, there are modifications. In particular, some, but not all, animal viruses have an outer membranous envelope beyond their capsid. After attachment to a receptor in the plasma membrane, viruses with an envelope either fuse with the plasma membrane or enter by endocytosis. After an enveloped virus enters, uncoating follows—that is, the capsid is removed. Once the viral genome, either DNA or RNA, is free of its covering, biosynthesis plus the other steps then proceed, as described in Figure 17.5. While a naked animal virus exits the host cell in the same manner as does a bacteriophage, those with an envelope bud from the cell. During budding, the virus picks up its envelope, consisting mainly of lipids and proteins, from the host plasma membrane. Spikes, those portions of the envelope that allow the virus to enter a host cell, are coded for by -viral genes. 
Retroviruses
Retroviruses are RNA animal viruses that have a DNA stage. Figure 17.5 illustrates the reproduction of HIV, the retrovirus that causes AIDS. A retrovirus contains a special enzyme called reverse transcriptase, which carries out transcription of RNA to cDNA. The DNA is called cDNA because it is a DNA copy of the viral genome. Following replication of the single strand, the resulting -double-stranded DNA is integrated into the host genome. The viral DNA remains in the host genome and is replicated when host DNA is replicated. When and if this DNA is transcribed, new viruses are produced by the steps we have already cited: biosynthesis, maturation, and release. Being an animal virus with an envelope, HIV buds from the cell.
Emerging Viruses
HIV is an emerging virus, the causative agent of a disease that only recently has arisen and infected people. Other examples of emerging viruses are West Nile virus, SARS virus, hantavirus, Ebola virus, and avian influenza (bird flu) virus (Fig. 17.6). 
Infectious diseases emerge in several different ways. In some cases, the virus is simply transported from one location to another. The West Nile virus is making headlines because it changed its range: It was transported into the United States and is taking hold in bird and mosquito populations. Severe acute respiratory syndrome (SARS) was clearly transported from Asia to Toronto, Canada. A world in which you can begin your day in Bangkok and end it in Los Angeles is a world in which disease can spread at an unprecedented rate. 
Other factors can also cause infectious viruses to emerge. Viruses are well known for their high mutation rates. Some of these mutations affect the structure of the spikes, so a virus that previously could only infect a particular animal species can now also infect the human species. For example, the diseases AIDS and Ebola fever are caused by viruses that at one time infected only monkeys and apes. SARS is another example of a mutant virus that most likely jumped species. A related virus was isolated from the palm civet, a catlike carnivore sold for food in China. Wild ducks are resistant to avian influenza viruses that can spread from them to chickens, which increases the likelihood the disease, often called bird flu, will spread to humans. Another possible way a virus could emerge is by a change in the mode of transmission. What would happen if a little-known virus were suddenly able to be transmitted like the common cold? 
Drug Control of Human Viral Diseases 
Because viruses reproduce using the metabolic machinery of the cell, it has been difficult to develop antiviral drugs. If a patient has not been vaccinated against the agent, he or she is usually told to simply let the virus run its course. However, some antiviral drugs are available. Most antiviral compounds, such as ribavirin and acyclovir, are structurally similar to nucleotides, and therefore they interfere with viral genome synthesis. Compounds related to acyclovir are commonly used to suppress herpes outbreaks. HIV is treated with antiviral compounds specific to a retrovirus. The well-publicized drug AZT and others block  reverse transcriptase. And HIV protease inhibitors block enzymes required for the maturation of viral proteins. 
17.2		Viroids and Prions
About a dozen crop diseases have been attributed not to viruses but to viroids, which are naked strands of RNA (not covered by a capsid). Like viruses, though, viroids direct the cell to produce more viroids.
Some diseases in humans have been attributed to prions, a term coined for proteinaceous infectious particles. The discovery of prions began when it was observed that members of a primitive tribe in the highlands of Papua New Guinea died from a disease called kuru (meaning trembling with fear) after participating in the cannibalistic practice of eating a deceased person’s brain (Fig. 17.7). The causative agent was smaller than a virus—it was a rogue protein. It appears that a normal protein changes shape so that its polypeptide chain is in a different configuration. The result is a fatal prion and a neuro-degenerative disorder. 
It is believed that a prion can interact with normal proteins to turn them over to the “dark side,” but the mechanism is unclear. The process has been best studied in a disease called scrapie, which attacks sheep. Other prion diseases include the popularized mad cow disease, human maladies such as Creutzfeldt-Jakob syndrome (CJD), and a variety of chronic wasting syndromes in animals.
17.3		The Prokaryotes
What was the first cellular life on Earth like? What features in modern organisms are the most primitive? The answers to these questions will probably come from a study of prokaryotes. These cells harbor no nucleus to contain their genome. They have no sealed compartments and no membrane-bounded organelles to perform specific functions. Yet these structurally simple, unicellular organisms are endowed with far greater metabolic capabilities than more structurally complex organisms; some of them need neither air nor organic matter to survive. The two types of prokaryotes are the bacteria and the archaea. 
Bacteria
Bacteria are the most diverse and prevalent organisms on Earth. Billions of bacteria exist in nearly every square meter of soil, water, and air. They also make a home on your skin and in your intestines. Although tens of thousands of different bacteria have been identified, this is likely only a very small fraction of living bacteria. Less than 1% of bacteria in the soil can be grown on agar plates in the laboratory. Molecular genetic techniques are now being used to discover the extent of bacterial diversity. 
General Biology of Bacteria
Bacterial StructureBacteria have a number of different shapes; however, most bacteria are spheres, called cocci, or rods, called bacilli, or spirals, called spirilla (Fig. 17.8). Intermediate forms between a sphere and rod are coccobacilli. A spirillum can be slightly curved (called a vibrio) or highly coiled (called a spirochete). Many bacteria grow as single cells, but some form doublets (the diplococci and diplobacilli). Others form filaments (chains) as do the streptococci, the cause of strep throat. A third growth habit resembles a bunch of grapes, as in the staphylococci, a cause of food poisoning. 
Figure 4.4 on page 51 reviews the structure of a bacterium. A bacterium, being a prokaryote, has no nucleus. A single, closed circle of double-stranded DNA constitutes the chromosome, which occurs in a limited area of the cell called the nucleoid. In some cases, extrachromosomal DNA molecules called plasmids are also found in bacteria. 
Bacteria have ribosomes but not membrane-bounded organelles such as mitochondria and chloroplasts. Those that are photosynthetic have thylakoid membranes, but these are not enclosed by another membrane. Motile bacteria generally use flagella for locomotion, but never cilia. The bacterial flagellum is not structured like a eukaryotic flagellum (Fig. 17.9). It has a filament composed of three strands of the protein flagellin wound in a helix. The filament is inserted into a hook that is anchored by a basal body. The 360° rotation causes the bacterium to spin as it moves forward and backward. 
Bacteria have an outer cell wall strengthened not by cellulose, but by peptidoglycan, a complex molecule containing a unique amino disaccharide and peptide fragments. The cell wall prevents bacteria from bursting or collapsing due to osmotic changes. Parasitic bacteria are further protected from host defenses by a polysaccharide capsule that surrounds the cell wall.
Bacterial ReproductionBacteria (and Archaea) reproduce asexually by means of binary fission. The single, circular chromosome replicates, and then the two copies separate as the cell enlarges. The newly formed plasma membrane and cell wall partition the two new cells, with a chromosome in each one (Fig. 17.10a,b). -Mitosis, which requires the formation of a spindle apparatus, does not occur in prokaryotes. Binary fission turns one cell into two cells, two cells into four cells, four cells into eight cells, and continuing on until billions of cells have been produced. 
In eukaryotes, genetic recombination occurs as a result of sexual reproduction. Sexual reproduction does not occur among prokaryotes, but three means of genetic recombination have been observed in bacteria. Conjugation occurs between bacteria when a donor cell passes DNA to a recipient cell by way of tubes, called sex pili, which temporarily join the two cells. Conjugation takes place only between bacteria in the same or closely related species. Transformation occurs when a bacterium picks up (from the surroundings) free pieces of DNA secreted by live prokaryotes or released by dead prokaryotes. During transduction, bacteriophages carry portions of bacterial DNA from one cell to another. Plasmids, which sometimes carry genes for resistance to antibiotics, can be transferred between infectious bacteria by any of these means.
When faced with unfavorable environmental conditions, some bacteria form endospores (Fig. 17.10c). A portion of the cytoplasm and a copy of the chromosome dehydrate and are then encased by three heavy, protective spore coats. The rest of the bacterial cell deteriorates, and the endospore is released. Spores survive in the harshest of environments—desert heat and desiccation, boiling temperatures, polar ice, and extreme ultraviolet radiation. They also survive for very long periods. When anthrax spores 1,300 years old germinate, they can still cause a severe infection (usually seen in cattle and sheep). Humans also fear a deadly but uncommon type of food poisoning called botulism, which is caused by the germination of endospores inside cans of food. Spore formation is not a means of reproduction, but it does allow survival and dispersal of bacteria to new places.
Bacterial NutritionEukaryotes are limited in their metabolic capabilities. For example, plants are photoautotrophs (many times called autotrophs or photosynthesizers) that can only perform oxygenic photosynthesis: They depend on solar energy to split water and energize electrons for the reduction of carbon dioxide. Among bacteria, the cyanobacteria are also photoautotrophs and do the same. The cyanobacteria may well represent the oldest lineage of oxygenic organisms (Fig. 17.11a). Some fossil cyanobacteria have been dated at 3.7 billion years old. Many cyanobacteria are capable of fixing atmospheric nitrogen and reducing it to an organic form. Therefore, they need only minerals, air, sunlight, and water for growth. 
Other bacterial photosynthesizers don’t release oxygen because they take electrons from a source other than water; some split hydrogen sulfide (H2S) and release sulfur (S) in marshes where they live anaerobically.
The chemoautotrophs (many times called chemosynthesizers) don’t use solar energy at all. They reduce carbon dioxide using energetic electrons derived from inorganic molecules such as ammonia or hydrogen gas. Electrons can also be extracted from certain minerals, such as iron. Some chemoautotrophs oxidize sulfur compounds spewing from deep-sea vents 2.5 kilometers below sea level. The organic compounds they produce support the growth of communities of organisms found at vents, where only darkness prevails (Fig. 17.11b).
Most bacteria are chemoheterotrophs (often referred to as simply heterotrophs) and, like animals, take in organic nutrients that they use as a source of energy and building blocks to synthesize macromolecules. Unlike animals, they are saprotrophs that -send enzymes into the environment and decompose almost any large organic molecule to smaller ones that are absorbable. There is probably no natural organic molecule that cannot be digested by at least one bacterial species. Bacteria play a critical role in recycling matter and making inorganic molecules available to photosynthesizers.
Heterotrophic bacteria may be either free-living or symbiotic, meaning that they form (1) mutualistic (both partners benefit), (2) commensalistic (one partner benefits, the other is not harmed), or (3) parasitic (one partner benefits, the other is harmed) relationships. Mutualistic bacteria that live in human intestines release vitamins K and B12, which we can use to help produce blood components. In the stomachs of cows and goats, special mutualistic prokaryotes digest cellulose, enabling these animals to feed on grass.
Commensalism often occurs when one population modifies the environment in such a way that a second population benefits. Obligate anaerobes can live in our intestines only because the bacterium Escherichia coli uses up the available oxygen. The parasitic bacteria cause diseases, as discussed on the next page.
Environmental and Medical Importance of Bacteria
Bacteria in the EnvironmentFor an ecosystem to sustain its populations, the chemical elements available to living things must eventually be recycled. A fixed and limited amount of elements are available to living things—the rest are either buried too deep in the Earth’s crust or present in forms that are not usable. All living organisms, including producers, consumers, and decomposers, are involved in the important process of cycling elements to sustain life (see Fig. 1.4). Bacteria are decomposers that digest dead organic remains and return inorganic nutrients to producers. Without the work of decomposers, life would soon come to a halt.
While decomposing, bacteria perform reactions needed for biogeochemical cycling, such as for the carbon and nitrogen cycles. Let’s examine how bacteria participate in the nitrogen cycle. Plants are unable to fix atmospheric nitrogen (N2), but they need a source of ammonia or nitrate in order to produce proteins. Bacteria in the soil can fix atmospheric nitrogen and/or change nitrogen compounds into forms that plants can use. In addition, mutualistic bacteria live in the root nodules of soybean, clover, and alfalfa plants where they reduce atmospheric nitrogen to ammonia, which is used by plants (Fig. 17.12). Without the work of bacteria, nitrogen would not be available for plants to produce proteins, nor available to animals that feed on plants or other animals.
Bioremediation is the biological cleanup of an environment that contains harmful chemicals called pollutants. To help correct the situation, the vast ability of bacteria to break down almost any substance, including sewage, is being exploited (Fig. 17.13a). People have added thousands of tons of slowly degradable pesticides and herbicides, nonbiodegradable detergents, and plastics to the environment. Strains of bacteria are being developed specifically for cleaning up these particular types of pollutants. Some strains have been used to remove Agent Orange, a potent herbicide, from soil samples, and dual cultures of two types of bacteria have been shown to degrade PCBs, chemicals formerly used as coolants and lubricants. The occasional oil spill spoils beaches and kills wildlife. The ability of bacteria to degrade petroleum has been improved by biotechnology and the addition of a growth-
promoting fertilizer (Fig. 17.13b). Without the fertilizer, the lack of nitrogen and phosphate in seawater limits their growth.

Bacteria in Food Science and BiotechnologyA wide variety of food products are created through the action of bacteria (Fig. 17.14). Under anaerobic conditions, bacteria carry out fermentation, which results in a variety of alcohols and acids. One of these acids is lactate, a product that pickles cucumbers, curdles milk into cheese, and gives these foods their characteristic tangy flavor. Other bacterial fermentations can produce flavor compounds, such as the propionic acid in Swiss cheese. Bacterial fermentation is also useful in the manufacture of such products as vitamins and antibiotics—in fact, most antibiotics known today were discovered in soil bacteria.
As you know, biotechnology can be used to alter the genome and the products generated by bacterial cultures. Bacteria can be genetically engineered to produce medically important products such as insulin, human growth hormone, and vaccines against a number of human diseases. The natural ability of bacteria to perform all manner of reactions is also enhanced through biotechnology. 
Bacterial Diseases in HumansMicrobes that can cause disease are called pathogens. Pathogens are able to (1) produce a toxin, and/or (2) adhere to surfaces, and sometimes (3) invade organs or cells. 
Toxins are small organic molecules, or small pieces of protein or parts of the bacterial cell wall that are released when bacteria die. Toxins are poisonous, and bacteria that produce a toxin usually cause serious diseases. In almost all cases, the growth of the microbes themselves does not cause disease; the toxins they release cause disease. When someone steps on a rusty nail, bacteria may be introduced deep into damaged tissue. The damaged area does not have good blood flow and can become anaerobic. Clostridium tetani, the cause of tetanus, proliferates under these conditions. The bacteria never leave the site of the wound, but the tetanus toxin they produce does move throughout the body. This toxin prevents the relaxation of muscles. In time, the body contorts because all the muscles have contracted. Eventually, the person suffocates. 
Adhesion factors allow a pathogen to bind to certain cells, and this determines which organs or cells of the body will be its host. Shigella dysenteriae produces a toxin, but it is also able to stick to the intestinal wall, which makes it a more life-threatening cause of dysentery. Also, invasive mechanisms that give a pathogen the ability to move through tissues and into the bloodstream result in a more medically significant disease than if it were localized. Usually a person can recover from food poisoning caused by Salmonella. But some strains of Salmonella have virulence factors that allow the bacteria to penetrate the lining of the colon and move beyond this organ. Typhoid fever, a life-threatening disease, can then result. 
Because bacteria are cells in their own right, a number of antibiotic compounds are active against bacteria and are widely prescribed. Most antibacterial compounds fall within two classes: those that inhibit protein biosynthesis and those that inhibit cell wall biosynthesis. Erythromycin and tetracyclines can inhibit bacterial protein biosynthesis because bacterial ribosomes function somewhat differently than eukaryotic ribosomes. Cell wall biosynthesis inhibitors generally block the formation of peptidoglycan, the substance found in the bacterial cell wall. Penicillin, ampicillin, and fluoroquinolone (such as Cipro) inhibit bacterial cell wall biosynthesis without harming animal cells. 
One problem with antibiotic therapy has been increasing bacterial resistance to antibiotics. When penicillin was first introduced, less than 3% of Staphylococcus aureus strains were resistant to it. Now, due to natural selection, 90% or more are resistant. 
Archaea
As previously discussed in Chapter 16, scientists currently propose that the tree of life contains three domains: Archaea, Bacteria, and Eukarya. Because archaea and some bacteria are found in extreme environments (hot springs, thermal vents, salt basins), they may have diverged from a common ancestor relatively soon after life began. Later, the eukarya are believed to have split off from the archaeal line of descent. Archaea and eukarya share some of the same ribosomal proteins (not found in bacteria), initiate transcription in the same manner, and have similar types of tRNA.
Structure and Function
The plasma membranes of archaea contain unusual lipids that allow them to function at high temperatures. The archaea have also evolved -diverse cell wall types, which facilitate their survival under extreme conditions. The cell walls of archaea do not contain peptidoglycan as do the cell walls of bacteria. In some archaea, the cell wall is largely composed of polysaccharides, and in others, the wall is pure protein. A few have no cell wall.
Archaea have retained primitive and unique forms of metabolism. The ability to form methane, is one type of metabolism that is performed only by some archaea, called methanogens. Most archaea are chemoautotrophs (see page 272), and few are photosynthetic. This suggests that chemoautotrophy predated photo-autotrophy during the evolution of prokaryotes. Archaea are sometimes mutualistic or even commensalistic, but none are parasitic—that is, archaea are not known to cause infectious diseases.
Types of Archaea
Archaea are often discussed in terms of their unique habitats. The methanogens (methane makers) are found in anaerobic environments, such as in swamps, marshes, and the intestinal tracts of animals. They couple the production of methane (CH4) from hydrogen gas (H2) and carbon dioxide to the formation of ATP (Fig. 17.15). This methane, which is also called biogas, is released into the atmosphere where it contributes to the greenhouse effect and global warming. About 65% of the methane in our atmosphere is produced by methanogenic archaea.
The halophiles require high salt concentrations for growth (usually 12–15%; by contrast, the ocean is about 3.5% salt). Halophiles have been isolated from highly saline environments such as the Great Salt Lake in Utah, the Dead Sea, solar salt ponds, and hypersaline soils (Fig. 17.16). These archaea have evolved a number of mechanisms to survive in high-salt environments. They depend on a pigment related to the rhodopsin in our eyes to absorb light energy for the purpose of pumping chloride and another similar type pigment for the purpose of synthesizing ATP.
A third major type of archaea are the thermo-acidophiles (Fig. 17.17). These archaea are isolated from extremely hot, acidic environments such as hot springs, geysers, submarine thermal vents, and around volcanoes. They reduce sulfur to sulfides and survive best at temperatures above 80°C; some can even grow at 105°C (remember that water boils at 100°C)! Metabolism of sulfides results in acidic sulfates and these bacteria grow best at pH 1 to 2.
17.4		The Protists
Like ancient creatures from another planet, the protists inhabit the oceans and other watery environments of the world. Their morphological diversity is their most outstanding feature—unicellular diatoms are encrusted in silica “hatboxes”; dinoflagellates have plates of armor; and ciliates shaped like slippers have complex structures. 
Many protists are unicellular, but all are eukaryotes with a nucleus and a wide range of organelles. It is widely held that the organelles of eukaryotic cells arose from close symbiotic associations between bacteria and primitive eukaryotes (Fig. 17.18). This so-called endosymbiotic hypothesis is supported by the presence of double membranes around mitochondria and chloroplasts. Also, these organelles have their own genomes, although incomplete, and their ribosomal genes point to bacterial origins. The mitochondria appear closely related to certain bacteria, and  the chloroplasts are most closely related to cyanobacteria. 
To explain the diversity of protists, we can well imagine that once the eukaryotic cell arose, it provided the opportunity for many different lineages to begin. Some unicellular protists have organelles not seen in other eukaryotes. For example, food is digested in food vacuoles, and excess water is expelled when contractile vacuoles discharge their contents. 
Protists also possibly give us insight into the evolution of a multicellular organism with differentiated tissues. Some protists are a colony of single cells, with certain cells specialized to produce eggs and sperm, and others are multicellular, with tissues specialized for various purposes. Perhaps the first type of organization preceded the second in a progression toward multicellular organisms. 
General Biology of Protists
The complexity and diversity of protists make it -difficult to classify them. The variety of protists is so great that it’s been suggested they could be split into more than a dozen kingdoms. Due to limited space, this text groups the phyla according to modes of nutrition. 
Traditionally, the term algae means aquatic photosynthesizer. At one time, botanists classified algae as plants because they contain chlorophyll a and carry on photosynthesis. In aquatic environments, algae are a part of the phytoplankton, photosynthesizers that lie suspended in the water. They are producers, which serve as a source of food for other organisms and pour oxygen into the environment. In terrestrial systems, algae are found in soils, on rocks, and in trees. One type of alga is a symbiote of animals called corals, which depend on them for food as they build the coral reefs of the world. Others partner with fungi in lichens capable of living in harsh terrestrial environments. 
The definition of a protozoan as a unicellular chemoheterotroph explains why protozoans were originally classified with the animals. Often a protozoan has some form of locomotion, either by flagella, pseudopods, or cilia. In aquatic environments, protozoans are a part of the zooplankton, suspended microscopic heterotrophs that serve as a food source for animals. While most are free-living, some protozoans are human pathogens, often causing diseases of the blood. In many cases, their complex life cycles inhibit the development of suitable treatments. 
There is still one other group of protists: the slime molds and water molds. These creatures are chemoheterotrophs, but the slime molds ingest their food in the same manner as the protozoan called an amoeba, while the water molds are saprotrophic, like fungi. 
Algae
The green alga Chlamydomonas serves as our model for algal structure (Fig. 17.19). The most conspicuous organelle in the algal cell is the chloroplast. Algal chloroplasts share many features with those of plants, and the two groups likely share a common origin; for example, the photosynthetic pigments are housed in thylakoid membranes. Not surprisingly, then, algae perform photosynthesis in the same manner as plants. Pyrenoids are organelles found in algae that are active in starch storage and metabolism. Vacuoles are seen in algae, along with mitochondria. Algae generally have a cell wall, and many produce a slime layer that can be harvested and used for food processing. Some algae are nonmotile, while others possess flagella. 
Algae can reproduce asexually or sexually in most cases. Asexual reproduction can occur by binary fission, as in bacteria. Some proliferate by forming flagellated spores called zoospores, while others simply fragment, with each fragment becoming a progeny alga. Sexual reproduction generally requires the formation of gametes that combine to form a zygote.
One traditional way to classify algae is based on the color of the pigments in their chloroplasts: green algae, red algae, golden-brown algae, and brown algae (Fig. 17.20). The green algae are most closely related to plants, and they are commonly represented by three species: Chlamydomonas; colonial Volvox, a large, hollow sphere with dozens to hundreds of cells; and Spirogyra, a filamentous alga in which the chloroplasts form a green spiral ribbon. The coralline red algae deposit calcium carbonate in their cell walls and contribute to the formation of coral reefs. The golden-brown algae are represented by the diatoms, which have a hatbox structure with each half an elaborate shell composed of silica. The green algae, red algae, and brown algae include the multicellular seaweeds. 
The Protozoans
Protozoans are unicellular, but their cells are very complex. Many of the functions we normally associate with the organs of multicellular organisms are performed by organelles in protozoans. Some protozoans have more than one nucleus. In some cases, the two nuclei are identical in size and function. Other protozoans, such as Paramecium, have a large macronucleus and a small micronucleus (Fig. 17.21). The macronucleus produces mRNA and directs metabolic functions. The micronucleus is important for reproduction. Protozoans usually reproduce asexually by binary fission. 
Protozoans are heterotrophic, and many feed by engulfing food particles. Phagocytic vacuoles act as their “stomachs” into which digestive enzymes and acid are added. Secretory vacuoles release enzymes that may enhance any pathogenicity. Contractile vacuoles permit osmoregulation, particularly in fresh water. 
The various protozoans shown in Figure 17.22 illustrate that they are usually motile. The ciliates, so named because they move by cilia, are represented by Paramecium, and the amoeboids by amoebas, which move by cytoplasmic extensions called pseudopods. The radiolarians and foraminiferans are two types of marine amoeboids with calcium carbonate skeletons important in limestone formations—including the White Cliffs of Dover in Britain. The amoeba Entamoeba histolytica causes amoebic dysentery. The zooflagellates, which move by flagella, also cause diseases. In this group, a trypanosome is the cause of African sleeping sickness, a blood disease that cuts off circulation to the brain. In the United States, Giardia lamblia contaminates water supplies and causes severe diarrhea. Apicomplexans, commonly called sporozoans because they produce spores, are unlike other protozoan groups because they are not motile. One genus, Plasmodium, causes malaria, the most widespread and dangerous protozoan disease. Malaria is transmitted by a mosquito. Toxoplasmosis, another protozoan disease, is commonly transmitted by cats. 
Slime Molds and Water Molds
In forests and woodlands, slime molds feed on, and therefore help dispose of, dead plant material. They also feed on bacteria, keeping their population sizes under control. Water molds decompose remains but are also significant parasites of plants and animals in ecosystems. Slime molds and water molds were once classified as fungi, but unlike fungi, all have flagellated cells at some time during their life cycles. Only the water molds have a cell wall, but it contains cellulose, not the chitin of fungal cell walls. Both slime molds and water molds form spores, each a small, single-celled reproductive body capable of becoming a new organism. The spores of water molds are flagellated, but those of slime molds are windblown. 
Although grouped together here, slime molds and water molds may be more closely related to the amoeboids than to each other. Indeed, the vegetative state of the slime molds is mobile and amoeboid, and like the amoeboids, they ingest their food by phagocytosis. 
Plasmodial Slime MoldsUsually, plasmodial slime molds exist as a plasmodium—a diploid, multinucleated, cytoplasmic mass enveloped by a slime sheath that creeps along, phagocytizing decaying plant material in a forest or agricultural field. At times unfavorable to growth, such as during a drought, the plasmodium develops many sporangia. A sporangium is a reproductive structure that produces spores resistant to dry conditions. When favorable moist conditions return, the spores germinate, releasing a flagellated cell or an amoeboid cell. Eventually, two of them fuse to form a zygote that feeds and grows, producing a multinucleated plasmodium once again. Figure 17.23 shows the life cycle of a plasmodial slime mold.
The Chapter in Review
Summary
17.1		The Viruses
Viruses are noncellular particles.
Structure
	•	Viruses have at least two parts: an outer capsid composed of protein subunits and an inner core of nucleic acid, either DNA or RNA.
	•	Animal viruses are either naked (no outer envelope) or they have an outer membranous envelope.
Reproduction
Viruses are obligate intracellular parasites that can reproduce only inside living cells. Bacteriophages can have a lytic or lysogenic life cycle.
The lytic cycle consists of these steps:
	•	Attachment
	•	Penetration
	•	Biosynthesis
	•	Maturation
	•	Release
In the lysogenic cycle, viral DNA is integrated into bacterial DNA for an indefinite period of time, but it can undergo the last three steps of the lytic cycle at any time.
Plant Viruses
Crops and garden plants are subject to viral infections. Not all viruses are deadly, but over time they debilitate a plant.
Animal Viruses
The reproductive cycle in animal viruses has the same steps as in a bacteriophage, with modifications if the virus has an envelope, in which case: 
	•	Fusion or endocytosis brings virus into cell.
	•	Uncoating is needed to free the genome from the capsid.
	•	Budding releases the viral particles from the cell.
HIV, the AIDS virus, is an RNA retrovirus. These viruses have an enzyme, reverse transcriptase, which carries out reverse transcription. This produces cDNA, which replicates, forming a double helix that becomes integrated into host DNA.
Drug Control of Human Viral Diseases
Antiviral drugs are structurally similar to a nucleotide and interfere with viral genome synthesis. HIV protease inhibitors block enzymes required for maturation of viral proteins.
17.2		Viroids and Prions
Viroids are naked (not covered by a capsid) strands of RNA that can cause disease. 
Prions are protein molecules that have a misshapen tertiary structure. Prions cause such diseases as CJD in humans and mad cow disease in cattle when they cause other proteins of their own kind to also become misshapen.
17.3		The Prokaryotes
The bacteria and archaea are prokaryotes. Prokaryotes lack a nucleus and most of the other cytoplasmic organelles found in eukaryotic cells.
General Biology of Bacteria
Bacterial Structure
	•	Structure can be rods (bacilli), spheres (cocci), and curved or spiral (vibrio, spirillum, or spirochete).
	•	Single, closed circle of double-stranded DNA (chromosome) is in a nucleoid.
	•	Flagellum is unique and rotates, causing the organism to spin.
	•	Cell wall contains peptidoglycan.
Bacterial Reproduction and Survival
	•	Reproduction is asexual by binary fission.
	•	Genetic recombination occurs by means of conjugation, transformation, and transduction.
	•	Endospore formation allows bacteria to survive an unfavorable environment.
	•	Endospores are extremely resistant to destruction; the genetic material can thereby survive unfavorable conditions.
Bacterial Nutrition
	•	Bacteria can be autotrophic. Cyanobacteria are photoautotrophs—they photosynthesize, as do plants. Chemoautotrophs oxidize inorganic compounds, such as hydrogen gas, hydrogen sulfide, and ammonia, to acquire energy to make their own food. Chemoautotrophs are chemosynthesizers that support communities at deep-sea vents.
	•	Like animals, most bacteria are chemoheterotrophs (heterotrophs), but they are saprotrophic decomposers. Many heterotrophic prokaryotes are symbiotic. The mutualistic nitrogen-fixing bacteria live in nodules on the roots of legumes.
Environmental and Medical Importance of Bacteria
Bacteria in the Environment
	•	As decomposers, bacteria keep inorganic nutrients cycling in ecosystems.
	•	The reactions they perform keep the nitrogen cycle going.
	•	Bacteria play an important role in bioremediation.
Bacteria in Food Science and Biotechnology
	•	Bacterial fermentations are important in the production of foods.
	•	Genetic engineering allows bacteria to produce medically important products.
Bacteria Diseases in Humans
	•	Bacterial pathogens that can cause diseases are able to: (1) produce a toxin, (2) adhere to surfaces, and (3) sometimes invade organs or cells.
	•	Indiscriminate antibiotic therapy has led to bacterial resistance to some antibiotics.
Archaea 
The archaea (domain Archaea) are a second type of prokaryote. Some characteristics of archaea are:
	•	They appear to be more closely related to the eukarya than to the bacteria. 
	•	They do not have peptidoglycan in their cell walls, as do the bacteria, and they share more biochemical characteristics with the eukarya than do bacteria.
	•	They are well known for living under harsh conditions, such as anaerobic marshes (methanogens), salty lakes (halophiles), and sulfur springs (thermoacidophiles).
17.4		The Protists
General Biology of Protists
	•	Protists are eukaryotes. Endosymbiotic events may account for the presence of mitochondria and chloroplasts in eukaryotic cells. Some are multicellular with differentiated tissues.
	•	Protists have great ecological importance because in largely aquatic environments they are the producers (algae) or sources (algae and protozoans) of food for other organisms.
Algae
	•	Algae possess chlorophylls. They store reserve food as starch and have cell walls, as do plants.
	•	Algae are divided according to their pigments, being either green, brown, golden-brown, or red. Many are unicellular, but the green, red, and brown algae include multicellular seaweeds.
Protozons
	•	Protozoans are heterotrophic and usually motile by means of cilia (paramecia), pseudopods (amoebas), or flagella (zooflagellates).
	•	Sporozoans cause diseases, including malaria, the most serious protozoan disease.
	•	A zooflagellates (trypanosome) causes African sleeping sickness; Giardia causes severe diarrhea. 
Slime Molds and Water Molds
	•	Slime molds are decomposers in forests and woodlands.
	•	Water molds have cell walls of cellulose, which distinguish them from fungi.
Thinking Scientifically
	1.	The bacterium Agrobacterium tumefasciens is a plant pathogen. When it infects a plant, it transforms the plant’s genome with a set of bacterial genes. These genes code for a bacterial food supply and for proteins that encourage plant cell proliferation, providing a home for the bacteria. Plant genetic engineers have taken advantage of this property to introduce foreign genes into plants. Suggest how they might do this without creating diseased plants. 
	2.	If a plant is genetically engineered to produce the capsid protein of a virus, it becomes resistant to that virus. However, these transgenic plants are not resistant if you infect them with the RNA of the virus. How, and when in the infection process, do you suppose this resistance mechanism is acting? 
Testing Yourself
Choose the best answer for each question.
	1.	A virus contains
	a. a cell wall. 
	b. a plasma membrane.
	c. nucleic acid.
	d. cytoplasm.
	e. More than one of these are correct.
	2.	Label the parts of a virus in the following illustration.
	3.	The five stages of the lytic cycle occur in this order:
	a. penetration, attachment, release, maturation, biosynthesis
	b. attachment, penetration, release, biosynthesis, maturation
	c. biosynthesis, attachment, penetration, maturation, release
	d. attachment, penetration, biosynthesis, maturation, release
	e. penetration, biosynthesis, attachment, maturation, release
	4.	Animal viruses
	a. contain both DNA and RNA.
	b. sometimes have an envelope.
	c. sometimes infect bacteria.
	d. do not reproduce inside cells.
	5.	The enzyme that is unique to retroviruses is
	a. reverse transcriptase.	c. DNA gyrase.
	b. DNA polymerase.	d. RNA polymerase.
	6.	Which of these is mismatched?
	a. amoeboids—pseudopods	c. algae—variously colored
	b. sporozoans—disease agents	d. slime molds—trypanosomes
	7.	Which of the following statements about viroids is false?
	a. They are composed of naked RNA.
	b. They cause plant diseases.
	c. They have a broader range of hosts than most viruses.
	d. They die once they reproduce.
	8.	Prion proteins cause disease when they
	a. enlarge in size.	c. change shape.
	b. break into small pieces.	d. interact with DNA.
	9.	Bacterial cells contain
	a. ribosomes.	d. vacuoles.
	b. nuclei.	e. More than one of these are 
	c. mitochondria.		correct.
	10.	The primary producers at deep-sea vents are
	a. heterotrophs.	c. chemoautotrophs.
	b. symbionts.	d. photoautotrophs.
For questions 11–15, determine which type of organism is being described. Each answer in the key may be used more than once. 
Key:
	a. bacteria
	b. archaea
	c. both bacteria and archaea
	d. neither bacteria nor archaea
	11.	Peptidoglycan in cell wall.
	12.	Methanogens. 
	13.	Sometimes parasitic.
	14.	Contain a nucleus.
	15.	Plasma membrane contains lipids.
	16.	Unlike plants, algae contain
	a. chloroplasts.	d. pyrenoids.
	b. vacuoles.	e. cell walls.
	c. mitochondria.
	17.	Label the parts of a paramecium in the following illustration.
Go to www.mhhe.com/maderessentials for more quiz questions.
Bioethical Issue
The Food and Drug Administration (FDA) estimates that physicians annually write 50 million unnecessary prescriptions for antibiotics to treat viral infections. Of course, these antibiotics are ineffective against viruses. Furthermore, the frequent exposure of bacteria to these drugs has resulted in the development of numerous strains with antibiotic resistance. Doctors may prescribe antibiotics because patients demand them. In addition, if the cause of the illness is not known, it is safer to prescribe an antibiotic that turns out to be ineffective than to withhold the antibiotic when it would have helped. The FDA has, therefore, initiated a new policy requiring manufacturers to label antibiotics with precautions about their misuse. 
Do you think this type of labeling information will educate consumers enough to significantly reduce the inappropriate use of antibiotics? Physicians already know about the dangers of antibiotic resistance, but may prescribe them anyway. This is probably due, in large part, to the fact that they are liable for erring on the side of withholding an antibiotic but not for inappropriately prescribing one. Should physicians be held more accountable for prescribing antibiotics? If so, how?
Understanding the Terms
algae (sing., alga)276
amoeboid278
archaea275
bacteria270
bacteriophage267
binary fission271
bioremediation273
brown algae277
capsid266
chemoautotroph272
chemoheterotroph272
ciliate278
conjugation272
cyanobacteria272
emerging virus269
endospore272
flagella271
foraminiferan278
golden-brown algae277
green algae277
halophile275
lysogenic cycle267
lytic cycle267
methanogen275
nucleoid271
pathogen274
peptidoglycan271
photoautotroph272
plasmid271
prion270
prokaryote270
protist276
protozoan276
pseudopod278
radiolarian278
red algae277
retrovirus268
saprotroph272
slime mold279
sporozoan278
symbiotic273
thermoacidophile275
transduction272
transformation272
trypanosome278
viroid270
virus266
water mold279
zooflagellate278
Match the terms to these definitions:
a.	_______________	Phage life cycle in which the infected bacterium does not immediately produce phage. 
b.	_______________	RNA animal virus with a DNA stage. 
c.	_______________	Proteinaceous infectious particle. 
d.	_______________	Type of molecule found in a bacterial cell wall. 
e.	_______________	Method of asexual reproduction in bacteria. 

Preventing transmission is the key to protecting yourself from infectious diseases. 
Fear of polio (above) and AIDS (right) can cause us to modify our behavior.
Isolation of victims helps keep tuberculosis (above) and leprosy (below) at bay.
Figure 17.2Bacteriophage lambda ().
The micrograph shows many viral particles attached to a bacteriophage and the blow-up shows how DNA from a virus enters a bacterium.
Figure 17.3Lytic and lysogenic cycles of a virus called lambda.
a. In the lytic cycle, viral particles escape when the cell is lysed (broken open). b. In the lysogenic cycle, viral DNA is integrated into host DNA. At some time in the future, the lysogenic cycle can be followed by the last three steps of the lytic cycle.
Figure 17.1Adenovirus anatomy.
Typical of viruses, adenoviruses have a nucleic acid core and a coat of protein, the so-called capsid. Note the projections called spikes—they help a virus enter a cell. 
Figure 17.6Emerging diseases.
Emerging diseases, such as those noted here according to their country of origin, are new or demonstrate increased prevalence. These disease-causing agents may have acquired new virulence factors, or environmental factors may have encouraged their spread to an increased number of hosts. Avian influenza (bird flu) is a new emerging disease.
Figure 17.5Reproduction of HIV.
HIV, the virus that causes AIDS, goes through the steps noted in the boxes. Because HIV is a retrovirus with an RNA genome, the enzyme reverse transcriptase is utilized to produce a DNA copy of the genome, called cDNA. After cDNA undergoes replication, DNA integrates its genome into host DNA. 
Figure 17.4Infected tobacco plant.
Mottling and a distorted leaf shape are typical of a viral infection 
in plants.
Check Your Progress
	1.	All viruses contain what two components? 
	2.	
Contrast a lytic with a lysogenic viral life cycle. 
	3.	List ways in which viruses can move among plants.
	4.	What happens when animal viruses bud from the host cell? 
	5.	Describe the significance of reverse transcriptase for retroviruses. 
Answers:1. All viruses are composed of an outer capsid made of protein and an inner core of DNA or RNA.2. In the lytic cycle, the bacterium is used to immediately produce more virus particles. In the lysogenic cycle, the phage is latent, but it may at some point be stimulated to enter the lytic cycle.
3. Insect vectors, gardening tools, seeds, and pollen.4. They acquire an outer envelope, which in part consists of the host plasma membrane.  
5. Retroviruses have an RNA genome. They use the enzyme reverse transcriptase to make a DNA copy of their genome. When this replicates, the double helix can integrate into the host cell genome and become latent. 
Check Your Progress
	1.	Contrast a viroid with a prion.
	2.	Prions cause disease. Why then can proteins that become prions be found in healthy brains?
Answers:1. A viroid is composed of naked RNA, while a prion is composed of protein.2. Prions are derived from normal proteins that have become prions due to a change in shape. 
Check Your Progress
	1.	List the two types of prokaryotes.
	2.	
List the three shapes of bacteria.
	3.	Describe the chromosome of a bacterium.
Answers:1. Bacteria and archaea.2. Spherical (cocci), rod (bacilli), and spiral (spirillum).3. A single, closed circle of double-stranded DNA.
Figure 17.9Flagella.
Each flagellum of a bacterium contains a basal body, a hook, and a filament. Arrows here indicate that the hook (and filament) rotates 360°. Flagella rotating counterclockwise result in forward motion of the bacterium; a clockwise rotation causes the bacterium to move backward.
Figure 17.8Shapes of bacteria. 
a. Streptococci, which exist as chains of cocci, cause a number of illnesses, including strep throat. b. Escherichia coli, which lives in your intestine, is a rod-shaped bacillus. c. Treponema pallidum, the cause of syphilis, is a spirochete. 
Figure 17.7Kuru.
Kuru is a fatal prion disease that infected the Fore (pronounced for-ay), a tribe of the remote highlands of Papua New Guinea, prior to the 1950s. Following their death, family members were ritualistically cooked and eaten, with the closest female relatives and children usually consuming the brain, the organ most likely to pass on kuru. A misshapen protein is the causative agent of all prion diseases, whether they occur in animals (e.g., mad cow disease) or in humans (e.g., kuru, CJD). The inset shows a diseased monkey brain. 
Figure 17.12Nodules of a legume.
Although some free-living bacteria carry on nitrogen fixation, those of the genus Rhizobium invade the roots of legumes, with the resultant formation of nodules. Here the bacteria convert atmospheric nitrogen to an organic nitrogen that the plant can use. These are nodules on the roots of a soybean plant.
Figure 17.13Bioremediation.
a. Bacteria have been used for many years in sewage treatment plants to break down human wastes. b. Increasingly, the ability of bacteria to break down pollutants is being researched and enhanced. Here technicians are relying on bacteria to clean up an oil spill. 
Figure 17.10Bacterial reproduction and survival.
a, b. When conditions are favorable to growth, prokaryotes divide to multiply. c. Formation of endospores allows bacteria to survive unfavorable environmental conditions. 
Figure 17.11Bacterial autotrophs.
a. Cyanobacteria are photoautotrophs that photosynthesize in the same manner as plants—they split water and release oxygen. 
b. Certain chemoautotrophic bacteria live inside tubeworms, where they produce organic compounds without the need of sunlight. In this way they help support ecosystems at hydrothermal vents deep in the ocean. 
Figure 17.15Methanogen habitat and structure.
a. A swamp where methanogens live. b. Micrograph of Methano--sarcina mazei, a methanogen.
Figure 17.16Halophile habitat and structure.
a. Great Salt Lake, Utah, where halophiles live. b. Micrograph of Halobacterium salinarium, a halophile.
Figure 17.17Thermoacidophile habitat and structure.
a. Boiling springs and geysers in Yellowstone National Park where thermoacidophiles live. b. Micrograph of Sulfolobus acidocaldarius, a thermoacidophile. (The dark central region has yet to be identified and could be an artifact of staining.) 
Figure 17.14Bacteria in food processing. 
Bacteria and fungi (see Chapter 18) are used to help produce food products. Fungal fermentation results in carbon dioxide and alcohol, which help produce bread and wine, respectfully. Bacterial fermentation results in acids that give some types of cheeses their characteristic taste.
Check Your Progress
	1.	Explain how bacteria reproduce asexually.
	2.	List the three ways in which genetic recombination can occur in bacteria.
	3.	Describe the function of endospores in bacteria.
	4.	Contrast photoautotrophs with chemoautotrophs.
	5.	Describe a significant role of bacteria in the nitrogen cycle that is beneficial to plants and animals.
	6.	Describe the modes of action of the two major classes of antibiotics.
Answers:1. The single chromosome copies itself, and the two copies are pulled apart as the cell enlarges. The cell is then partitioned into two cells, with a chromosome in each one.2. Conjugation, transformation, and transduction.3. Endospores allow bacteria to survive harsh conditions and disperse to new places.4. Photoautotrophs use energy from the sun to produce sugars, while chemoautotrophs use high-energy electrons from chemicals.5. Bacteria in nodules and the soil change nitrogen to a form plants can use. Animals acquire organic nitrogen from plants or from animals that have fed on plants.6. One class inhibits cell wall biosynthesis, while the other inhibits protein biosynthesis.
Check Your Progress
List the features of mitochondria and chloroplasts that support the endosymbiotic hypothesis.
Answer:Double membrane, the presence of DNA, and ribosomal genes similar to those of bacteria.
Figure 17.19Chlamydomonas.
Chlamydomonas, a green alga, has the organelles and other possible structures typical of a motile algal cell. 
Figure 17.20Algal diversity.
a. Acetabularia, a unicellular green alga; b. Bossiella, a coralline red alga; c. Fucus, a brown alga; d. Licmorpha, a stalked diatom; e. Chlamydomonas, a unicellular green alga; 
f. Volvox, a colonial green alga with daughter colonies 
inside; g. Spirogyra, a filamentous green alga 
undergoing conjugation to form zygotes; h. Ceratium, 
an armored dinoflagellate; i. Macrocystis, a brown alga; 
j. Sargassum, a brown alga.

Figure 17.18Evolution of the eukaryotic cell.
Invagination of the plasma membrane could account for the formation of the nucleus and certain other organelles. The endosymbiotic hypothesis suggests that mitochondria and chloroplasts are derived from prokaryotes that were taken up by a much larger eukaryotic cell. 
Figure 17.23Plasmodial slime molds.
As long as conditions are favorable, plasmodial slime molds exist as multinucleated diploid plasmodium that creeps along the forest floor phagocytizing organic remains. When conditions become unfavorable, sporangia form where meiosis produces haploid spores, structures that can survive unfavorable times. Spores germinate to release independent haploid cells. Fusion of these cells produces a zygote that becomes a mature plasmodium once again.
Figure 17.21A paramecium.
A paramecium is a ciliate, a type of complex protozoan that moves by cilia. 
Figure 17.22Protozoan diversity.
a. Entamoeba invadens, a parasitic amoeba; b. Globigerina sp., a foraminiferan; c. Plasmodium sp., a sporozoan that causes malaria (several are seen here infecting a red blood cell); 
d. Trypanosoma brucei, a zooflagellate that causes African sleeping sickness; e. Giardia lamblia, a zooflagellate that causes severe diarrhea.
Check Your Progress
	1.	Compare and contrast algae with protozoans.
	2.	List the major features of protozoans.
	3.	Describe the significance of slime molds in terrestrial ecosystems.
Answers:1. Both algae and protozoans are protists, but algae are autotrophs, while protozoans are heterotrophs.2. Protozoans are unicellular, may have more than one nucleus, reproduce asexually via binary fission, and are phagocytes.3. Slime molds feed on bacteria and decaying plant material.

Comparison of Viruses and Prokaryotes	

Characteristic of Life	Viruses	Prokaryotes	
Consist of cell	No	Yes	
Metabolize	No 	Yes	
Respond to stimuli	No	Yes	
Multiply	Yes
(always inside living cell)	Yes
(usually independently)	
Evolve	Yes	Yes	

8,000
b. 
Rod-shaped E. coli
10,500
a. Sphere-shaped streptococci
c. Spirochete, T. pallidum
b.Amoeboids
Zooflagellates
Sporozoan