# The Eukaryotes of Microbiology

## Parasitic Helminths

### Learning Objectives

By the end of this section, you will be able to:
1. Explain why we include the study of parasitic worms within the discipline of microbiology
2. Compare the basic morphology of the major groups of parasitic helminthes
3. Describe the characteristics of parasitic nematodes, and give an example of infective eggs and infective larvae
4. Describe the characteristics of parasitic trematodes and cestodes, and give examples of each
5. Identify examples of the primary causes of infections due to nematodes, trematodes, and cestodes
6. Classify parasitic worms according to major groups

Parasitic helminths are animals that are often included within the study of microbiology because many species of these worms are identified by their microscopic eggs and larvae. There are two major groups of parasitic helminths: the roundworms (Nematoda) and flatworms (Platyhelminthes). Of the many species that exist in these groups, about half are parasitic and some are important human pathogens. As animals, they are multicellular and have organ systems. However, the parasitic species often have limited digestive tracts, nervous systems, and locomotor abilities. Parasitic forms may have complex reproductive cycles with several different life stages and more than one type of host. Some are monoecious, having both male and female reproductive organs in a single individual, while others are dioecious, each having either male or female reproductive organs.

### Nematoda (Roundworms)

Phylum Nematoda (the roundworms) is a diverse group containing more than 15,000 species, of which several are important human parasites (). These unsegmented worms have a full digestive system even when parasitic. Some are common intestinal parasites, and their eggs can sometimes be identified in feces or around the anus of infected individuals.  is the largest nematode intestinal parasite found in humans; females may reach lengths greater than 1 meter. A. lumbricoides is also very widespread, even in developed nations, although it is now a relatively uncommon problem in the United States. It may cause symptoms ranging from relatively mild (such as a cough and mild abdominal pain) to severe (such as intestinal blockage and impaired growth).
Of all nematode infections in the United States, pinworm (caused by ) is the most common. Pinworm causes sleeplessness and itching around the anus, where the female worms lay their eggs during the night.  and T. cati are nematodes found in dogs and cats, respectively, that can be transmitted to humans, causing toxocariasis. Antibodies to these parasites have been found in approximately 13.9% of the U.S. population, suggesting that exposure is common.Won K, Kruszon-Moran D, Schantz P, Jones J. “National seroprevalence and risk factors for zoonotic Toxocara spp. infection.” In: Abstracts of the 56th American Society of Tropical Medicine and Hygiene; Philadelphia, Pennsylvania; 2007 Nov 4-8. Infection can cause larval migrans, which can result in vision loss and eye inflammation, or fever, fatigue, coughing, and abdominal pain, depending on whether the organism infects the eye or the viscera. Another common nematode infection is hookworm, which is caused by  (the New World or North American hookworm) and  (the Old World hookworm). Symptoms of hookworm infection can include abdominal pain, diarrhea, loss of appetite, weight loss, fatigue, and anemia.
Trichinellosis, also called trichinosis, caused by , is contracted by consuming undercooked meat, which releases the larvae and allows them to encyst in muscles. Infection can cause fever, muscle pains, and digestive system problems; severe infections can lead to lack of coordination, breathing and heart problems, and even death. Finally, heartworm in dogs and other animals is caused by the nematode  which is transmitted by mosquitoes. Symptoms include fatigue and cough; when left untreated, death may result.

### Platyhelminths (Flatworms)

Phylum Platyhelminthes (the platyhelminths) are flatworms. This group includes the flukes, tapeworms, and the turbellarians, which include planarians. The flukes and tapeworms are medically important parasites ().
The flukes (trematodes) are nonsegmented flatworms that have an oral sucker () (and sometimes a second ventral sucker) and attach to the inner walls of intestines, lungs, large blood vessels, or the liver. Trematodes have complex life cycles, often with multiple hosts. Several important examples are the liver flukes ( and ), the intestinal fluke (), and the oriental lung fluke (). Schistosomiasis is a serious parasitic disease, considered second in the scale of its impact on human populations only to malaria. The parasites  mansoni, S. haematobium, and S. japonicum, which are found in freshwater snails, are responsible for schistosomiasis (). Immature forms burrow through the skin into the blood. They migrate to the lungs, then to the liver and, later, other organs. Symptoms include anemia, malnutrition, fever, abdominal pain, fluid buildup, and sometimes death.
The other medically important group of platyhelminths are commonly known as tapeworms (cestodes) and are segmented flatworms that may have suckers or hooks at the scolex (head region) (). Tapeworms use these suckers or hooks to attach to the wall of the small intestine. The body of the worm is made up of segments called proglottids that contain reproductive structures; these detach when the gametes are fertilized, releasing gravid proglottids with eggs. Tapeworms often have an intermediate host that consumes the eggs, which then hatch into a larval form called an oncosphere. The oncosphere migrates to a particular tissue or organ in the intermediate host, where it forms cysticerci. After being eaten by the definitive host, the cysticerci develop into adult tapeworms in the host's digestive system ().  (the beef tapeworm) and T. solium (the pork tapeworm) enter humans through ingestion of undercooked, contaminated meat. The adult worms develop and reside in the intestine, but the larval stage may migrate and be found in other body locations such as skeletal and smooth muscle. The beef tapeworm is relatively benign, although it can cause digestive problems and, occasionally, allergic reactions. The pork tapeworm can cause more serious problems when the larvae leave the intestine and colonize other tissues, including those of the central nervous system.  is the largest human tapeworm and can be ingested in undercooked fish. It can grow to a length of 15 meters. , the dog tapeworm, can parasitize humans and uses dogs as an important host.

### Key Concepts and Summary

1. Helminth parasites are included within the study of microbiology because they are often identified by looking for microscopic eggs and larvae.
2. The two major groups of helminth parasites are the roundworms (Nematoda) and the flatworms (Platyhelminthes).
3. Nematodes are common intestinal parasites often transmitted through undercooked foods, although they are also found in other environments.
4. Platyhelminths include tapeworms and flukes, which are often transmitted through undercooked meat.

### Multiple Choice

### Fill in the Blank

### Short Answer

### Critical Thinking


# The Eukaryotes of Microbiology

## Fungi

### Learning Objectives

By the end of this section, you will be able to:
1. Explain why the study of fungi such as yeast and molds is within the discipline of microbiology
2. Describe the unique characteristics of fungi
3. Describe examples of asexual and sexual reproduction of fungi
4. Compare the major groups of fungi in this chapter, and give examples of each
5. Identify examples of the primary causes of infections due to yeasts and molds
6. Identify examples of toxin-producing fungi
7. Classify fungal organisms according to major groups
The fungi comprise a diverse group of organisms that are heterotrophic and typically saprozoic. In addition to the well-known macroscopic fungi (such as mushrooms and molds), many unicellular yeasts and spores of macroscopic fungi are microscopic. For this reason, fungi are included within the field of microbiology.
Fungi are important to humans in a variety of ways. Both microscopic and macroscopic fungi have medical relevance, with some pathogenic species that can cause mycoses (illnesses caused by fungi). Some pathogenic fungi are opportunistic, meaning that they mainly cause infections when the host’s immune defenses are compromised and do not normally cause illness in healthy individuals. Fungi are important in other ways. They act as decomposers in the environment, and they are critical for the production of certain foods such as cheeses. Fungi are also major sources of antibiotics, such as penicillin from the fungus .

### Characteristics of Fungi

Fungi have well-defined characteristics that set them apart from other organisms. Most multicellular fungal bodies, commonly called molds, are made up of filaments called hyphae. Hyphae can form a tangled network called a mycelium and form the thallus (body) of fleshy fungi. Hyphae that have walls between the cells are called septate hyphae; hyphae that lack walls and cell membranes between the cells are called nonseptate or coenocytic hyphae). ().
In contrast to molds, yeasts are unicellular fungi. The budding yeasts reproduce asexually by budding off a smaller daughter cell; the resulting cells may sometimes stick together as a short chain or pseudohypha ().
Some fungi are dimorphic, having more than one appearance during their life cycle. These dimorphic fungi may be able to appear as yeasts or molds, which can be important for infectivity. They are capable of changing their appearance in response to environmental changes such as nutrient availability or fluctuations in temperature, growing as a mold, for example, at 25 °C (77 °F), and as yeast cells at 37 °C (98.6 °F). This ability helps dimorphic fungi to survive in diverse environments. Two examples of dimorphic yeasts are the human pathogens Histoplasma capsulatum and Candida albicans. H. capsulatum causes the lung disease histoplasmosis, and C. albicans is associated with vaginal yeast infections, oral thrush, and candidiasis of the skin ().
There are notable unique features in fungal cell walls and membranes. Fungal cell walls contain chitin, as opposed to the cellulose found in the cell walls of plants and many protists. Additionally, whereas animals have cholesterol in their cell membranes, fungal cell membranes have different sterols called ergosterols. Ergosterols are often exploited as targets for antifungal drugs.
Fungal life cycles are unique and complex. Fungi reproduce sexually either through cross- or self-fertilization. Haploid fungi form hyphae that have gametes at the tips. Two different mating types (represented as “+ type” and “– type”) are involved. The cytoplasms of the + and – type gametes fuse (in an event called plasmogamy), producing a cell with two distinct nuclei (a dikaryotic cell). Later, the nuclei fuse (in an event called karyogamy) to create a diploid zygote. The zygote undergoes meiosis to form spores that germinate to start the haploid stage, which eventually creates more haploid mycelia (). Depending on the taxonomic group, these sexually produced spores are known as zygospores (in Zygomycota), ascospores (in Ascomycota), or basidiospores (in Basidiomycota) ().
Fungi may also exhibit asexual reproduction by mitosis, mitosis with budding, fragmentation of hyphae, and formation of asexual spores by mitosis. These spores are specialized cells that, depending on the organism, may have unique characteristics for survival, reproduction, and dispersal. Fungi exhibit several types of asexual spores and these can be important in classification.

### Fungal Diversity

The fungi are very diverse, comprising seven major groups. Not all of the seven groups contain pathogens. Some of these groups are generally associated with plants and include plant pathogens. For example, Urediniomycetes and Ustilagomycetes include the plant rusts and smuts, respectively. These form reddish or dark masses, respectively, on plants as rusts (red) or smuts (dark). Some species have substantial economic impact because of their ability to reduce crop yields. Glomeromycota includes the mycorrhizal fungi, important symbionts with plant roots that can promote plant growth by acting like an extended root system. The Glomeromycota are obligate symbionts, meaning that they can only survive when associated with plant roots; the fungi receive carbohydrates from the plant and the plant benefits from the increased ability to take up nutrients and minerals from the soil. The Chytridiomycetes (chytrids) are small fungi, but are extremely ecologically important. Chytrids are generally aquatic and have flagellated, motile gametes; specific types are implicated in amphibian declines around the world. Because of their medical importance, we will focus on Zygomycota, Ascomycota, Basidiomycota, and Microsporidia.  summarizes the characteristics of these medically important groups of fungi.
The Zygomycota (zygomycetes) are mainly saprophytes with coenocytic hyphae and haploid nuclei. They use sporangiospores for asexual reproduction. The group name comes from the zygospores that they use for sexual reproduction (), which have hard walls formed from the fusion of reproductive cells from two individuals. Zygomycetes are important for food science and as crop pathogens. One example is  (), an important bread mold that also causes rice seedling blight.  is a genus of fungi that can potentially cause necrotizing infections in humans, although most species are intolerant of temperatures found in mammalian bodies ().
The Ascomycota include fungi that are used as food (edible mushrooms, morels, and truffles), others that are common causes of food spoilage (bread molds and plant pathogens), and still others that are human pathogens. Ascomycota may have septate hyphae and cup-shaped fruiting bodies called ascocarps. Some genera of Ascomycota use sexually produced ascospores as well as asexual spores called conidia, but sexual phases have not been discovered or described for others. Some produce an ascus containing ascospores within an ascocarp ().
Examples of the Ascomycota include several bread molds and minor pathogens, as well as species capable of causing more serious mycoses. Species in the genus Aspergillus are important causes of allergy and infection, and are useful in research and in the production of certain fermented alcoholic beverages such as Japanese sake. The fungus , a contaminant of nuts and stored grains, produces an aflatoxin that is both a toxin and the most potent known natural carcinogen.  is of particular use in genetics research because the spores produced by meiosis are kept inside the ascus in a row that reflects the cell divisions that produced them, giving a direct view of segregation and assortment of genes ().  produces the antibiotic penicillin ().
Many species of ascomycetes are medically important. A large number of species in the genera , , and  are dermatophytes, pathogenic fungi capable of causing skin infections such as athlete’s foot, jock itch, and ringworm.  is a dimorphic fungus that can cause blastomycosis, a respiratory infection that, if left untreated, can become disseminated to other body sites, sometimes leading to death. Another important respiratory pathogen is the dimorphic fungus  (), which is associated with birds and bats in the Ohio and Mississippi river valleys.  causes the serious lung disease Valley fever. , the most common cause of vaginal and other yeast infections, is also an ascomycete fungus; it is a part of the normal microbiota of the skin, intestine, genital tract, and ear (). Ascomycetes also cause plant diseases, including ergot infections, Dutch elm disease, and powdery mildews.
 yeasts, including the baker’s yeast S. cerevisiae, are unicellular ascomycetes with haploid and diploid stages (). This and other Saccharomyces species are used for brewing beer.
The Basidiomycota (basidiomycetes) are fungi that have basidia (club-shaped structures) that produce basidiospores (spores produced through budding) within fruiting bodies called basidiocarps (). They are important as decomposers and as food. This group includes rusts, stinkhorns, puffballs, and mushrooms. Several species are of particular importance. , a fungus commonly found as a yeast in the environment, can cause serious lung infections when inhaled by individuals with weakened immune systems. The edible meadow mushroom, Agricus campestris, is a basidiomycete, as is the poisonous mushroom Amanita phalloides, known as the death cap. The deadly toxins produced by A. phalloides have been used to study transcription.
Finally, the Microsporidia are unicellular fungi that are obligate intracellular parasites. They lack mitochondria, peroxisomes, and centrioles, but their spores release a unique polar tubule that pierces the host cell membrane to allow the fungus to gain entry into the cell. A number of microsporidia are human pathogens, and infections with microsporidia are called microsporidiosis. One pathogenic species is , which can cause symptoms such as diarrhea, cholecystitis (inflammation of the gall bladder), and in rare cases, respiratory illness.

### Key Concepts and Summary

1. The fungi include diverse saprotrophic eukaryotic organisms with chitin cell walls
2. Fungi can be unicellular or multicellular; some (like yeast) and fungal spores are microscopic, whereas some are large and conspicuous
3. Reproductive types are important in distinguishing fungal groups
4. Medically important species exist in the four fungal groups Zygomycota, Ascomycota, Basidiomycota, and Microsporidia
5. Members of Zygomycota, Ascomycota, and Basidiomycota produce deadly toxins
6. Important differences in fungal cells, such as ergosterols in fungal membranes, can be targets for antifungal medications, but similarities between human and fungal cells make it difficult to find targets for medications and these medications often have toxic adverse effects

### Multiple Choice

### Fill in the Blank

### Short Answer

### Critical Thinking


# The Eukaryotes of Microbiology

## Algae

### Learning Objectives

By the end of this section, you will be able to:
1. Explain why algae are included within the discipline of microbiology
2. Describe the unique characteristics of algae
3. Identify examples of toxin-producing algae
4. Compare the major groups of algae in this chapter, and give examples of each
5. Classify algal organisms according to major groups
The algae are autotrophic protists that can be unicellular or multicellular. These organisms are found in the supergroups Chromalveolata (dinoflagellates, diatoms, golden algae, and brown algae) and Archaeplastida (red algae and green algae). They are important ecologically and environmentally because they are responsible for the production of approximately 70% of the oxygen and organic matter in aquatic environments. Some types of algae, even those that are microscopic, are regularly eaten by humans and other animals. Additionally, algae are the source for agar, agarose, and carrageenan, solidifying agents used in laboratories and in food production. Although algae are typically not pathogenic, some produce toxins. Harmful algal blooms, which occur when algae grow quickly and produce dense populations, can produce high concentrations of toxins that impair liver and nervous-system function in aquatic animals and humans.
Like protozoans, algae often have complex cell structures. For instance, algal cells can have one or more chloroplasts that contain structures called pyrenoids to synthesize and store starch. The chloroplasts themselves differ in their number of membranes, indicative of secondary or rare tertiary endosymbiotic events. Primary chloroplasts have two membranes—one from the original cyanobacteria that the ancestral eukaryotic cell engulfed, and one from the plasma membrane of the engulfing cell. Chloroplasts in some lineages appear to have resulted from secondary endosymbiosis, in which another cell engulfed a green or red algal cell that already had a primary chloroplast within it. The engulfing cell destroyed everything except the chloroplast and possibly the cell membrane of its original cell, leaving three or four membranes around the chloroplast. Different algal groups have different pigments, which are reflected in common names such as red algae, brown algae, and green algae.
Some algae, the seaweeds, are macroscopic and may be confused with plants. Seaweeds can be red, brown, or green, depending on their photosynthetic pigments. Green algae, in particular, share some important similarities with land plants; however, there are also important distinctions. For example, seaweeds do not have true tissues or organs like plants do. Additionally, seaweeds do not have a waxy cuticle to prevent desiccation. Algae can also be confused with cyanobacteria, photosynthetic bacteria that bear a resemblance to algae; however, cyanobacteria are prokaryotes (see Nonproteobacteria Gram-negative Bacteria and Phototrophic Bacteria).
Algae have a variety of life cycles. Reproduction may be asexual by mitosis or sexual using gametes.

### Algal Diversity

Although the algae and protozoa were formerly separated taxonomically, they are now mixed into supergroups. The algae are classified within the Chromalveolata and the Archaeplastida. Although the Euglenozoa (within the supergroup Excavata) include photosynthetic organisms, these are not considered algae because they feed and are motile.
The dinoflagellates and stramenopiles fall within the Chromalveolata. The dinoflagellates are mostly marine organisms and are an important component of plankton. They have a variety of nutritional types and may be phototrophic, heterotrophic, or mixotrophic. Those that are photosynthetic use chlorophyll a, chlorophyll c2, and other photosynthetic pigments (). They generally have two flagella, causing them to whirl (in fact, the name dinoflagellate comes from the Greek word for “whirl”: dini). Some have cellulose plates forming a hard outer covering, or theca, as armor. Additionally, some dinoflagellates produce neurotoxins that can cause paralysis in humans or fish. Exposure can occur through contact with water containing the dinoflagellate toxins or by feeding on organisms that have eaten dinoflagellates.
When a population of dinoflagellates becomes particularly dense, a red tide (a type of harmful algal bloom) can occur. Red tides cause harm to marine life and to humans who consume contaminated marine life. Major toxin producers include  and , both of which cause paralytic shellfish poisoning. Another species, , is known as a fish killer because, at certain parts of its life cycle, it can produce toxins harmful to fish and it appears to be responsible for a suite of symptoms, including memory loss and confusion, in humans exposed to water containing the species.
The stramenopiles include the golden algae (Chrysophyta), the brown algae (Phaeophyta), and the diatoms (Bacillariophyta). Stramenopiles have chlorophyll a, chlorophyll c, and fucoxanthin as photosynthetic pigments. Their storage carbohydrate is chrysolaminarin. While some lack cell walls, others have scales. Diatoms have frustules, which are outer cell walls of crystallized silica; their fossilized remains are used to produce diatomaceous earth, which has a range of uses such as filtration and insulation. Additionally, diatoms can reproduce sexually and asexually, and the male gametes of centric diatoms have flagella providing directed movement to seek female gametes for sexual reproduction.
Brown algae (Phaeophyta) are multicellular marine seaweeds. Some can be extremely large, such as the giant kelp (). They have leaf-like blades, stalks, and structures called holdfasts that are used to attach to substrate. However, these are not true leaves, stems, or roots (). Their photosynthetic pigments are chlorophyll a, chlorophyll c, β-carotene, and fucoxanthine. They use laminarin as a storage carbohydrate.
The Archaeplastids include the green algae (Chlorophyta), the red algae (Rhodophyta), another group of green algae (Charophyta), and the land plants. The Charaphyta are the most similar to land plants because they share a mechanism of cell division and an important biochemical pathway, among other traits that the other groups do not have. Like land plants, the Charophyta and Chlorophyta have chlorophyll a and chlorophyll b as photosynthetic pigments, cellulose cell walls, and starch as a carbohydrate storage molecule.  is a green alga that has a single large chloroplast, two flagella, and a stigma (eyespot); it is important in molecular biology research ().
 is a nonmotile, large, unicellular alga, and  is an even larger unicellular green alga. The size of these organisms challenges the idea that all cells are small, and they have been used in genetics research since Joachim Hämmerling (1901–1980) began to work with them in 1943. Volvox is a colonial, unicellular alga (). A larger, multicellular green alga is Ulva, also known as the sea lettuce because of its large, edible, green blades. The range of life forms within the Chlorophyta—from unicellular to various levels of coloniality to multicellular forms—has been a useful research model for understanding the evolution of multicellularity. The red algae are mainly multicellular but include some unicellular forms. They have rigid cell walls containing agar or carrageenan, which are useful as food solidifying agents and as a solidifier added to growth media for microbes.

### Key Concepts and Summary

1. Algae are a diverse group of photosynthetic eukaryotic protists
2. Algae may be unicellular or multicellular
3. Large, multicellular algae are called seaweeds but are not plants and lack plant-like tissues and organs
4. Although algae have little pathogenicity, they may be associated with toxic algal blooms that can and aquatic wildlife and contaminate seafood with toxins that cause paralysis
5. Algae are important for producing agar, which is used as a solidifying agent in microbiological media, and carrageenan, which is used as a solidifying agent

### Multiple Choice

### Fill in the Blank

### Short Answer


# The Eukaryotes of Microbiology

## Lichens

### Learning Objectives

By the end of this section, you will be able to:
1. Explain why lichens are included in the study of microbiology
2. Describe the unique characteristics of a lichen and the role of each partner in the symbiotic relationship of a lichen
3. Describe ways in which lichens are beneficial to the environment
No one has to worry about getting sick from a lichen infection, but lichens are interesting from a microbiological perspective and they are an important component of most terrestrial ecosystems. Lichens provide opportunities for study of close relationships between unrelated microorganisms. Lichens contribute to soil production by breaking down rock, and they are early colonizers in soilless environments such as lava flows. The cyanobacteria in some lichens can fix nitrogen and act as a nitrogen source in some environments. Lichens are also important soil stabilizers in some desert environments and they are an important winter food source for caribou. Finally, lichens produce compounds that have antibacterial effects, and further research may discover compounds that are medically useful to humans.

### Characteristics

A lichen is a combination of two organisms, a green alga or cyanobacterium and fungus, living in a symbiotic relationship. Whereas algae normally grow only in aquatic or extremely moist environments, lichens can potentially be found on almost any surface (especially rocks) or as epiphytes (meaning that they grow on other plants).
In some ways, the symbiotic relationship between lichens and algae seems like a mutualism (a relationship in which both organisms benefit). The fungus can obtain photosynthates from the algae or cyanobacterium and the algae or cyanobacterium can grow in a drier environment than it could otherwise tolerate. However, most scientists consider this symbiotic relationship to be a controlled parasitism (a relationship in which one organism benefits and the other is harmed) because the photosynthetic organism grows less well than it would without the fungus. It is important to note that such symbiotic interactions fall along a continuum between conflict and cooperation.
Lichens are slow growing and can live for centuries. They have been used in foods and to extract chemicals as dyes or antimicrobial substances. Some are very sensitive to pollution and have been used as environmental indicators.
Lichens have a body called a thallus, an outer, tightly packed fungal layer called a cortex, and an inner, loosely packed fungal layer called a medulla (). Lichens use hyphal bundles called rhizines to attach to the substrate.

### Lichen Diversity

Lichens are classified as fungi and the fungal partners belong to the Ascomycota and Basidiomycota. Lichens can also be grouped into types based on their morphology. There are three major types of lichens, although other types exist as well. Lichens that are tightly attached to the substrate, giving them a crusty appearance, are called crustose lichens. Those that have leaf-like lobes are foliose lichens; they may only be attached at one point in the growth form, and they also have a second cortex below the medulla. Finally, fruticose lichens have rounded structures and an overall branched appearance.  shows an example of each of the forms of lichens.

### Key Concepts and Summary

1. Lichens are a symbiotic association between a fungus and an algae or a cyanobacterium
2. The symbiotic association found in lichens is currently considered to be a controlled parasitism, in which the fungus benefits and the algae or cyanobacterium is harmed
3. Lichens are slow growing and can live for centuries in a variety of habitats
4. Lichens are environmentally important, helping to create soil, providing food, and acting as indicators of air pollution

### Multiple Choice

### Short Answer


# Acellular Pathogens

## Introduction

Public health measures in the developed world have dramatically reduced mortality from viral epidemics. But when epidemics do occur, they can spread quickly with global air travel. In 2009, an outbreak of H1N1 influenza spread across various continents. In early 2014, cases of Ebola in Guinea led to a massive epidemic in western Africa. This included the case of an infected man who traveled to the United States, sparking fears the epidemic might spread beyond Africa.
Until the late 1930s and the advent of the electron microscope, no one had seen a virus. Yet treatments for preventing or curing viral infections were used and developed long before that. Historical records suggest that by the 17th century, and perhaps earlier, inoculation (also known as variolation) was being used to prevent the viral disease smallpox in various parts of the world. By the late 18th century, Englishman Edward Jenner was inoculating patients with cowpox to prevent smallpox, a technique he coined vaccination.S. Riedel “Edward Jenner and the History of Smallpox and Vaccination.”
Today, the structure and genetics of viruses are well defined, yet new discoveries continue to reveal their complexities. In this chapter, we will learn about the structure, classification, and cultivation of viruses, and how they impact their hosts. In addition, we will learn about other infective particles such as viroids and prions.


# Acellular Pathogens

## Viruses

### Learning Objectives

By the end of this section, you will be able to:
1. Describe the general characteristics of viruses as pathogens
2. Describe viral genomes
3. Describe the general characteristics of viral life cycles
4. Differentiate among bacteriophages, plant viruses, and animal viruses
5. Describe the characteristics used to identify viruses as obligate intracellular parasites
Despite their small size, which prevented them from being seen with light microscopes, the discovery of a filterable component smaller than a bacterium that causes tobacco mosaic disease (TMD) dates back to 1892.H. Lecoq. “[Discovery of the First Virus, the Tobacco Mosaic Virus: 1892 or 1898?].”  At that time, Dmitri Ivanovski, a Russian botanist, discovered the source of TMD by using a porcelain filtering device first invented by Charles Chamberland and Louis Pasteur in Paris in 1884. Porcelain Chamberland filters have a pore size of 0.1 µm, which is small enough to remove all bacteria ≥0.2 µm from any liquids passed through the device. An extract obtained from TMD-infected tobacco plants was made to determine the cause of the disease. Initially, the source of the disease was thought to be bacterial. It was surprising to everyone when Ivanovski, using a Chamberland filter, found that the cause of TMD was not removed after passing the extract through the porcelain filter. So if a bacterium was not the cause of TMD, what could be causing the disease? Ivanovski concluded the cause of TMD must be an extremely small bacterium or bacterial spore. Other scientists, including Martinus Beijerinck, continued investigating the cause of TMD. It was Beijerinck, in 1899, who eventually concluded the causative agent was not a bacterium but, instead, possibly a chemical, like a biological poison we would describe today as a toxin. As a result, the word virus, Latin for poison, was used to describe the cause of TMD a few years after Ivanovski’s initial discovery. Even though he was not able to see the virus that caused TMD, and did not realize the cause was not a bacterium, Ivanovski is credited as the original discoverer of viruses and a founder of the field of virology.
Today, we can see viruses using electron microscopes () and we know much more about them. Viruses are distinct biological entities; however, their evolutionary origin is still a matter of speculation. In terms of taxonomy, they are not included in the tree of life because they are acellular (not consisting of cells). In order to survive and reproduce, viruses must infect a cellular host, making them obligate intracellular parasites. The genome of a virus enters a host cell and directs the production of the viral components, proteins and nucleic acids, needed to form new virus particles called virions. New virions are made in the host cell by assembly of viral components. The new virions transport the viral genome to another host cell to carry out another round of infection.  summarizes the properties of viruses.

### Hosts and Viral Transmission

Viruses can infect every type of host cell, including those of plants, animals, fungi, protists, bacteria, and archaea. Most viruses will only be able to infect the cells of one or a few species of organism. This is called the host range. However, having a wide host range is not common and viruses will typically only infect specific hosts and only specific cell types within those hosts. The viruses that infect bacteria are called bacteriophages, or simply phages. The word phage comes from the Greek word for devour. Other viruses are just identified by their host group, such as animal or plant viruses. Once a cell is infected, the effects of the virus can vary depending on the type of virus. Viruses may cause abnormal growth of the cell or cell death, alter the cell’s genome, or cause little noticeable effect in the cell.
Viruses can be transmitted through direct contact, indirect contact with fomites, or through a vector: an animal that transmits a pathogen from one host to another. Arthropods such as mosquitoes, ticks, and flies, are typical vectors for viral diseases, and they may act as mechanical vectors or biological vectors. Mechanical transmission occurs when the arthropod carries a viral pathogen on the outside of its body and transmits it to a new host by physical contact. Biological transmission occurs when the arthropod carries the viral pathogen inside its body and transmits it to the new host through biting.
In humans, a wide variety of viruses are capable of causing various infections and diseases. Some of the deadliest emerging pathogens in humans are viruses, yet we have few treatments or drugs to deal with viral infections, making them difficult to eradicate.
Viruses that can be transmitted from an animal host to a human host can cause zoonoses. For example, the avian influenza virus originates in birds, but can cause disease in humans. Reverse zoonoses are caused by infection of an animal by a virus that originated in a human.

### Viral Structures

In general, virions (viral particles) are small and cannot be observed using a regular light microscope. They are much smaller than prokaryotic and eukaryotic cells; this is an adaptation allowing viruses to infect these larger cells (see ). The size of a virion can range from 20 nm for small viruses up to 900 nm for typical, large viruses (see ). Recent discoveries, however, have identified new giant viral species, such as Pandoravirus salinus and Pithovirus sibericum, with sizes approaching that of a bacterial cell.N.
In 1935, after the development of the electron microscope, Wendell Stanley was the first scientist to crystallize the structure of the tobacco mosaic virus and discovered that it is composed of RNA and protein. In 1943, he isolated , which contributed to the development of an influenza (flu) vaccine. Stanley’s discoveries unlocked the mystery of the nature of viruses that had been puzzling scientists for over 40 years and his contributions to the field of virology led to him being awarded the Nobel Prize in 1946.
As a result of continuing research into the nature of viruses, we now know they consist of a nucleic acid (either RNA or DNA, but never both) surrounded by a protein coat called a capsid (see ). The interior of the capsid is not filled with cytosol, as in a cell, but instead it contains the bare necessities in terms of genome and enzymes needed to direct the synthesis of new virions. Each capsid is composed of protein subunits called capsomeres made of one or more different types of capsomere proteins that interlock to form the closely packed capsid.
There are two categories of viruses based on general composition. Viruses formed from only a nucleic acid and capsid are called naked viruses or nonenveloped viruses. Viruses formed with a nucleic-acid packed capsid surrounded by a lipid layer are called enveloped viruses (see ). The viral envelope is a small portion of phospholipid membrane obtained as the virion buds from a host cell. The viral envelope may either be intracellular or cytoplasmic in origin.
Extending outward and away from the capsid on some naked viruses and enveloped viruses are protein structures called spikes. At the tips of these spikes are structures that allow the virus to attach and enter a cell, like the influenza virus hemagglutinin spikes (H) or enzymes like the neuraminidase (N) influenza virus spikes that allow the virus to detach from the cell surface during release of new virions. Influenza viruses are often identified by their H and N spikes. For example, H1N1 influenza viruses were responsible for the pandemics in 1918 and 2009,J. Cohen. “What’s Old Is New: 1918 Virus Matches 2009 H1N1 Strain.  H2N2 for the pandemic in 1957, and H3N2 for the pandemic in 1968.
Viruses vary in the shape of their capsids, which can be either helical, polyhedral, or complex. A helical capsid forms the shape of tobacco mosaic virus (TMV), a naked helical virus, and Ebola virus, an enveloped helical virus. The capsid is cylindrical or rod shaped, with the genome fitting just inside the length of the capsid. Polyhedral capsids form the shapes of poliovirus and rhinovirus, and consist of a nucleic acid surrounded by a polyhedral (many-sided) capsid in the form of an icosahedron. An icosahedral capsid is a three-dimensional, 20-sided structure with 12 vertices. These capsids somewhat resemble a soccer ball. Both helical and polyhedral viruses can have envelopes. Viral shapes seen in certain types of bacteriophages, such as T4 phage, and poxviruses, like vaccinia virus, may have features of both polyhedral and helical viruses so they are described as a complex viral shape (see ). In the bacteriophage complex form, the genome is located within the polyhedral head and the sheath connects the head to the tail fibers and tail pins that help the virus attach to receptors on the host cell’s surface. Poxviruses that have complex shapes are often brick shaped, with intricate surface characteristics not seen in the other categories of capsid.

### Classification and Taxonomy of Viruses

Although viruses are not classified in the three domains of life, their numbers are great enough to require classification. Since 1971, the International Union of Microbiological Societies Virology Division has given the task of developing, refining, and maintaining a universal virus taxonomy to the International Committee on Taxonomy of Viruses (ICTV). Since viruses can mutate so quickly, it can be difficult to classify them into a genus and a species epithet using the binomial nomenclature system. Thus, the ICTV’s viral nomenclature system classifies viruses into families and genera based on viral genetics, chemistry, morphology, and mechanism of multiplication. To date, the ICTV has classified known viruses in seven orders, 96 families, and 350 genera. Viral family names end in -viridae (e.g, Parvoviridae) and genus names end in −virus (e.g., Parvovirus). The names of viral orders, families, and genera are all italicized. When referring to a viral species, we often use a genus and species epithet such as Pandoravirus dulcis or Pandoravirus salinus.
The Baltimore classification system is an alternative to ICTV nomenclature. The Baltimore system classifies viruses according to their genomes (DNA or RNA, single versus double stranded, and mode of replication). This system thus creates seven groups of viruses that have common genetics and biology.
Aside from formal systems of nomenclature, viruses are often informally grouped into categories based on chemistry, morphology, or other characteristics they share in common. Categories may include naked or enveloped structure, single-stranded (ss) or double-stranded (ds) DNA or ss or ds RNA genomes, segmented or nonsegmented genomes, and positive-strand (+) or negative-strand (−) RNA. For example, herpes viruses can be classified as a dsDNA enveloped virus; human immunodeficiency virus (HIV) is a +ssRNA enveloped virus, and tobacco mosaic virus is a +ssRNA virus. Other characteristics such as host specificity, tissue specificity, capsid shape, and special genes or enzymes may also be used to describe groups of similar viruses.  lists some of the most common viruses that are human pathogens by genome type.

### Classification of Viral Diseases

While the ICTV has been tasked with the biological classification of viruses, it has also played an important role in the classification of diseases caused by viruses. To facilitate the tracking of virus-related human diseases, the ICTV has created classifications that link to the International Classification of Diseases (ICD), the standard taxonomy of disease that is maintained and updated by the World Health Organization (WHO). The ICD assigns an alphanumeric code of up to six characters to every type of viral infection, as well as all other types of diseases, medical conditions, and causes of death. This ICD code is used in conjunction with two other coding systems (the Current Procedural Terminology, and the Healthcare Common Procedure Coding System) to categorize patient conditions for treatment and insurance reimbursement.
For example, when a patient seeks treatment for a viral infection, ICD codes are routinely used by clinicians to order laboratory tests and prescribe treatments specific to the virus suspected of causing the illness. This ICD code is then used by medical laboratories to identify tests that must be performed to confirm the diagnosis. The ICD code is used by the health-care management system to verify that all treatments and laboratory work performed are appropriate for the given virus. Medical coders use ICD codes to assign the proper code for procedures performed, and medical billers, in turn, use this information to process claims for reimbursement by insurance companies. Vital-records keepers use ICD codes to record cause of death on death certificates, and epidemiologists used ICD codes to calculate morbidity and mortality statistics.

### Key Concepts and Summary

1. Viruses are generally ultramicroscopic, typically from 20 nm to 900 nm in length. Some large viruses have been found.
2. Virions are acellular and consist of a nucleic acid, DNA or RNA, but not both, surrounded by a protein capsid. There may also be a phospholipid membrane surrounding the capsid.
3. Viruses are obligate intracellular parasites.
4. Viruses are known to infect various types of cells found in plants, animals, fungi, protists, bacteria, and archaea. Viruses typically have limited host ranges and infect specific cell types.
5. Viruses may have helical, polyhedral, or complex shapes.
6. Classification of viruses is based on morphology, type of nucleic acid, host range, cell specificity, and enzymes carried within the virion.
7. Like other diseases, viral diseases are classified using ICD codes.

### Multiple Choice

### True/False

### Fill in the Blank

### Short Answer

### Critical Thinking


# Acellular Pathogens

## The Viral Life Cycle

### Learning Objectives

By the end of this section, you will be able to:
1. Describe the lytic and lysogenic life cycles
2. Describe the replication process of animal viruses
3. Describe unique characteristics of retroviruses and latent viruses
4. Discuss human viruses and their virus-host cell interactions
5. Explain the process of transduction
6. Describe the replication process of plant viruses
All viruses depend on cells for reproduction and metabolic processes. By themselves, viruses do not encode for all of the enzymes necessary for viral replication. But within a host cell, a virus can commandeer cellular machinery to produce more viral particles. Bacteriophages replicate only in the cytoplasm, since prokaryotic cells do not have a nucleus or organelles. In eukaryotic cells, most DNA viruses can replicate inside the nucleus, with an exception observed in the large DNA viruses, such as the poxviruses, that can replicate in the cytoplasm. With a few exceptions, RNA viruses that infect animal cells replicate in the cytoplasm. An important exception that will be highlighted later is Influenza virus.

### The Life Cycle of Viruses with Prokaryote Hosts

The life cycle of bacteriophages has been a good model for understanding how viruses affect the cells they infect, since similar processes have been observed for eukaryotic viruses, which can cause immediate death of the cell or establish a latent or chronic infection. Virulent phages typically lead to the death of the cell through cell lysis. Temperate phages, on the other hand, can become part of a host chromosome and are replicated with the cell genome until such time as they are induced to make newly assembled viruses, or progeny viruses.

### The Lytic Cycle

During the lytic cycle of virulent phage, the bacteriophage takes over the cell, reproduces new phages, and destroys the cell. T-even phage is a good example of a well-characterized class of virulent phages. There are five stages in the bacteriophage lytic cycle (see ). Attachment is the first stage in the infection process in which the phage interacts with specific bacterial surface receptors (e.g., lipopolysaccharides and OmpC protein on host surfaces). Most phages have a narrow host range and may infect one species of bacteria or one strain within a species. This unique recognition can be exploited for targeted treatment of bacterial infection by phage therapy or for phage typing to identify unique bacterial subspecies or strains. The second stage of infection is entry or penetration. This occurs through contraction of the tail sheath, which acts like a hypodermic needle to inject the viral genome through the cell wall and membrane. The phage head and remaining components remain outside the bacteria.
The third stage of infection is biosynthesis of new viral components. After entering the host cell, the virus synthesizes virus-encoded endonucleases to degrade the bacterial chromosome. It then hijacks the host cell to replicate, transcribe, and translate the necessary viral components (capsomeres, sheath, base plates, tail fibers, and viral enzymes) for the assembly of new viruses. Polymerase genes are usually expressed early in the cycle, while capsid and tail proteins are expressed later. During the maturation phase, new virions are created. To liberate free phages, the bacterial cell wall is disrupted by phage proteins such as holin or lysozyme. The final stage is release. Mature viruses burst out of the host cell in a process called lysis and the progeny viruses are liberated into the environment to infect new cells.

### The Lysogenic Cycle

In a lysogenic cycle, the phage genome also enters the cell through attachment and penetration. A prime example of a phage with this type of life cycle is the lambda phage. During the lysogenic cycle, instead of killing the host, the phage genome integrates into the bacterial chromosome and becomes part of the host. The integrated phage genome is called a prophage. A bacterial host with a prophage is called a lysogen. The process in which a bacterium is infected by a temperate phage is called lysogeny. It is typical of temperate phages to be latent or inactive within the cell. As the bacterium replicates its chromosome, it also replicates the phage’s DNA and passes it on to new daughter cells during reproduction. The presence of the phage may alter the phenotype of the bacterium, since it can bring in extra genes (e.g., toxin genes that can increase bacterial virulence). This change in the host phenotype is called lysogenic conversion or phage conversion. Some bacteria, such as Vibrio cholerae and Clostridium botulinum, are less virulent in the absence of the prophage. The phages infecting these bacteria carry the toxin genes in their genome and enhance the virulence of the host when the toxin genes are expressed. In the case of V. cholera, phage encoded toxin can cause severe diarrhea; in C. botulinum, the toxin can cause paralysis. During lysogeny, the prophage will persist in the host chromosome until induction, which results in the excision of the viral genome from the host chromosome. After induction has occurred the temperate phage can proceed through a lytic cycle and then undergo lysogeny in a newly infected cell (see ).

### Transduction

Transduction occurs when a bacteriophage transfers bacterial DNA from one bacterium to another during sequential infections. There are two types of transduction: generalized and specialized transduction. During the lytic cycle of viral replication, the virus hijacks the host cell, degrades the host chromosome, and makes more viral genomes. As it assembles and packages DNA into the phage head, packaging occasionally makes a mistake. Instead of packaging viral DNA, it takes a random piece of host DNA and inserts it into the capsid. Once released, this virion will then inject the former host’s DNA into a newly infected host. The asexual transfer of genetic information can allow for DNA recombination to occur, thus providing the new host with new genes (e.g., an antibiotic-resistance gene, or a sugar-metabolizing gene). Generalized transduction occurs when a random piece of bacterial chromosomal DNA is transferred by the phage during the lytic cycle. Specialized transduction occurs at the end of the lysogenic cycle, when the prophage is excised and the bacteriophage enters the lytic cycle. Since the phage is integrated into the host genome, the prophage can replicate as part of the host. However, some conditions (e.g., ultraviolet light exposure or chemical exposure) stimulate the prophage to undergo induction, causing the phage to excise from the genome, enter the lytic cycle, and produce new phages to leave host cells. During the process of excision from the host chromosome, a phage may occasionally remove some bacterial DNA near the site of viral integration. The phage and host DNA from one end or both ends of the integration site are packaged within the capsid and are transferred to the new, infected host. Since the DNA transferred by the phage is not randomly packaged but is instead a specific piece of DNA near the site of integration, this mechanism of gene transfer is referred to as specialized transduction (see ). The DNA can then recombine with host chromosome, giving the latter new characteristics. Transduction seems to play an important role in the evolutionary process of bacteria, giving them a mechanism for asexual exchange of genetic information.

### Life Cycle of Viruses with Animal Hosts

Lytic animal viruses follow similar infection stages to bacteriophages: attachment, penetration, biosynthesis, maturation, and release (see ). However, the mechanisms of penetration, nucleic-acid biosynthesis, and release differ between bacterial and animal viruses. After binding to host receptors, animal viruses enter through endocytosis (engulfment by the host cell) or through membrane fusion (viral envelope with the host cell membrane). Many viruses are host specific, meaning they only infect a certain type of host; and most viruses only infect certain types of cells within tissues. This specificity is called a tissue tropism. Examples of this are demonstrated by the poliovirus, which exhibits tropism for the tissues of the brain and spinal cord, or the influenza virus, which has a primary tropism for the respiratory tract.
Animal viruses do not always express their genes using the normal flow of genetic information—from DNA to RNA to protein. Some viruses have a dsDNA genome like cellular organisms and can follow the normal flow. However, others may have ssDNA, dsRNA, or ssRNA genomes. The nature of the genome determines how the genome is replicated and expressed as viral proteins. If a genome is ssDNA, host enzymes will be used to synthesize a second strand that is complementary to the genome strand, thus producing dsDNA. The dsDNA can now be replicated, transcribed, and translated similar to host DNA.
If the viral genome is RNA, a different mechanism must be used. There are three types of RNA genome: dsRNA, positive (+) single-strand (+ssRNA) or negative (−) single-strand RNA (−ssRNA). If a virus has a +ssRNA genome, it can be translated directly to make viral proteins. Viral genomic +ssRNA acts like cellular mRNA. However, if a virus contains a −ssRNA genome, the host ribosomes cannot translate it until the −ssRNA is replicated into +ssRNA by viral RNA-dependent RNA polymerase (RdRP) (see ). The RdRP is brought in by the virus and can be used to make +ssRNA from the original −ssRNA genome. The RdRP is also an important enzyme for the replication of dsRNA viruses, because it uses the negative strand of the double-stranded genome as a template to create +ssRNA. The newly synthesized +ssRNA copies can then be translated by cellular ribosomes.
An alternative mechanism for viral nucleic acid synthesis is observed in the retroviruses, which are +ssRNA viruses (see ). Single-stranded RNA viruses such as HIV carry a special enzyme called reverse transcriptase within the capsid that synthesizes a complementary ssDNA (cDNA) copy using the +ssRNA genome as a template. The ssDNA is then made into dsDNA, which can integrate into the host chromosome and become a permanent part of the host. The integrated viral genome is called a provirus. The virus now can remain in the host for a long time to establish a chronic infection. The provirus stage is similar to the prophage stage in a bacterial infection during the lysogenic cycle. However, unlike prophage, the provirus does not undergo excision after splicing into the genome.

### Persistent Infections

Persistent infection occurs when a virus is not completely cleared from the system of the host but stays in certain tissues or organs of the infected person. The virus may remain silent or undergo productive infection without seriously harming or killing the host. Mechanisms of persistent infection may involve the regulation of the viral or host gene expressions or the alteration of the host immune response. The two primary categories of persistent infections are latent infection and chronic infection. Examples of viruses that cause latent infections include herpes simplex virus (oral and genital herpes), varicella-zoster virus (chickenpox and shingles), and Epstein-Barr virus (mononucleosis). Hepatitis C virus and HIV are two examples of viruses that cause long-term chronic infections.

### Latent Infection

Not all animal viruses undergo replication by the lytic cycle. There are viruses that are capable of remaining hidden or dormant inside the cell in a process called latency. These types of viruses are known as latent viruses and may cause latent infections. Viruses capable of latency may initially cause an acute infection before becoming dormant.
For example, the varicella-zoster virus infects many cells throughout the body and causes chickenpox, characterized by a rash of blisters covering the skin. About 10 to 12 days postinfection, the disease resolves and the virus goes dormant, living within nerve-cell ganglia for years. During this time, the virus does not kill the nerve cells or continue replicating. It is not clear why the virus stops replicating within the nerve cells and expresses few viral proteins but, in some cases, typically after many years of dormancy, the virus is reactivated and causes a new disease called shingles (). Whereas chickenpox affects many areas throughout the body, shingles is a nerve cell-specific disease emerging from the ganglia in which the virus was dormant.
Latent viruses may remain dormant by existing as circular viral genome molecules outside of the host chromosome. Others become proviruses by integrating into the host genome. During dormancy, viruses do not cause any symptoms of disease and may be difficult to detect. A patient may be unaware that he or she is carrying the virus unless a viral diagnostic test has been performed.

### Chronic Infection

A chronic infection is a disease with symptoms that are recurrent or persistent over a long time. Some viral infections can be chronic if the body is unable to eliminate the virus. HIV is an example of a virus that produces a chronic infection, often after a long period of latency. Once a person becomes infected with HIV, the virus can be detected in tissues continuously thereafter, but untreated patients often experience no symptoms for years. However, the virus maintains chronic persistence through several mechanisms that interfere with immune function, including preventing expression of viral antigens on the surface of infected cells, altering immune cells themselves, restricting expression of viral genes, and rapidly changing viral antigens through mutation. Eventually, the damage to the immune system results in progression of the disease leading to acquired immunodeficiency syndrome (AIDS). The various mechanisms that HIV uses to avoid being cleared by the immune system are also used by other chronically infecting viruses, including the hepatitis C virus.

### Life Cycle of Viruses with Plant Hosts

Plant viruses are more similar to animal viruses than they are to bacteriophages. Plant viruses may be enveloped or non-enveloped. Like many animal viruses, plant viruses can have either a DNA or RNA genome and be single stranded or double stranded. However, most plant viruses do not have a DNA genome; the majority have a +ssRNA genome, which acts like messenger RNA (mRNA). Only a minority of plant viruses have other types of genomes.
Plant viruses may have a narrow or broad host range. For example, the citrus tristeza virus infects only a few plants of the Citrus genus, whereas the cucumber mosaic virus infects thousands of plants of various plant families. Most plant viruses are transmitted by contact between plants, or by fungi, nematodes, insects, or other arthropods that act as mechanical vectors. However, some viruses can only be transferred by a specific type of insect vector; for example, a particular virus might be transmitted by aphids but not whiteflies. In some cases, viruses may also enter healthy plants through wounds, as might occur due to pruning or weather damage.
Viruses that infect plants are considered biotrophic parasites, which means that they can establish an infection without killing the host, similar to what is observed in the lysogenic life cycles of bacteriophages. Viral infection can be asymptomatic (latent) or can lead to cell death (lytic infection). The life cycle begins with the penetration of the virus into the host cell. Next, the virus is uncoated within the cytoplasm of the cell when the capsid is removed. Depending on the type of nucleic acid, cellular components are used to replicate the viral genome and synthesize viral proteins for assembly of new virions. To establish a systemic infection, the virus must enter a part of the vascular system of the plant, such as the phloem. The time required for systemic infection may vary from a few days to a few weeks depending on the virus, the plant species, and the environmental conditions. The virus life cycle is complete when it is transmitted from an infected plant to a healthy plant.

### Viral Growth Curve

Unlike the growth curve for a bacterial population, the growth curve for a virus population over its life cycle does not follow a sigmoidal curve. During the initial stage, an inoculum of virus causes infection. In the eclipse phase, viruses bind and penetrate the cells with no virions detected in the medium. The chief difference that next appears in the viral growth curve compared to a bacterial growth curve occurs when virions are released from the lysed host cell at the same time. Such an occurrence is called a burst, and the number of virions per bacterium released is described as the burst size. In a one-step multiplication curve for bacteriophage, the host cells lyse, releasing many viral particles to the medium, which leads to a very steep rise in viral titer (the number of virions per unit volume). If no viable host cells remain, the viral particles begin to degrade during the decline of the culture (see ).

### Key Concepts and Summary

1. Many viruses target specific hosts or tissues. Some may have more than one host.
2. Many viruses follow several stages to infect host cells. These stages include attachment, penetration, uncoating, biosynthesis, maturation, and release.
3. Bacteriophages have a lytic or lysogenic cycle. The lytic cycle leads to the death of the host, whereas the lysogenic cycle leads to integration of phage into the host genome.
4. Bacteriophages inject DNA into the host cell, whereas animal viruses enter by endocytosis or membrane fusion.
5. Animal viruses can undergo latency, similar to lysogeny for a bacteriophage.
6. The majority of plant viruses are positive-strand ssRNA and can undergo latency, chronic, or lytic infection, as observed for animal viruses.
7. The growth curve of bacteriophage populations is a one-step multiplication curve and not a sigmoidal curve, as compared to the bacterial growth curve.
8. Bacteriophages transfer genetic information between hosts using either generalized or specialized transduction.

### Multiple Choice

### Fill in the Blank

### Short Answer

### Critical Thinking


# Acellular Pathogens

## Isolation, Culture, and Identification of Viruses

### Learning Objectives

By the end of this section, you will be able to:
1. Discuss why viruses were originally described as filterable agents
2. Describe the cultivation of viruses and specimen collection and handling
3. Compare in vivo and in vitro techniques used to cultivate viruses
At the beginning of this chapter, we described how porcelain Chamberland filters with pores small enough to allow viruses to pass through were used to discover TMV. Today, porcelain filters have been replaced with membrane filters and other devices used to isolate and identify viruses.

### Isolation of Viruses

Unlike bacteria, many of which can be grown on an artificial nutrient medium, viruses require a living host cell for replication. Infected host cells (eukaryotic or prokaryotic) can be cultured and grown, and then the growth medium can be harvested as a source of virus. Virions in the liquid medium can be separated from the host cells by either centrifugation or filtration. Filters can physically remove anything present in the solution that is larger than the virions; the viruses can then be collected in the filtrate (see ).

### Cultivation of Viruses

Viruses can be grown in vivo (within a whole living organism, plant, or animal) or in vitro (outside a living organism in cells in an artificial environment. Flat horizontal cell culture flasks (see (a)) are a common vessel used for in vitro work. Bacteriophages can be grown in the presence of a dense layer of bacteria (also called a bacterial lawn) grown in a 0.7 % soft agar in a Petri dish or flat (horizontal) flask (see (b)). As the phage kills the bacteria, many plaques are observed among the cloudy bacterial lawn.
Animal viruses require cells within a host animal or tissue-culture cells derived from an animal. Animal virus cultivation is important for 1) identification and diagnosis of pathogenic viruses in clinical specimens, 2) production of vaccines, and 3) basic research studies. In vivo host sources can be a developing embryo in an embryonated bird’s egg (e.g., chicken, turkey) or a whole animal. For example, most of the influenza vaccine manufactured for annual flu vaccination programs is cultured in hens’ eggs.
The embryo or host animal serves as an incubator for viral replication (see ). Location within the embryo or host animal is important. Many viruses have a tissue tropism, and must therefore be introduced into a specific site for growth. Within an embryo, target sites include the amniotic cavity, the chorioallantoic membrane, or the yolk sac. Viral infection may damage tissue membranes, producing lesions called pox; disrupt embryonic development; or cause the death of the embryo.
For in vitro studies, various types of cells can be used to support the growth of viruses. A primary cell culture is freshly prepared from animal organs or tissues. Cells are extracted from tissues by mechanical scraping or mincing to release cells or by an enzymatic method using trypsin or collagenase to break up tissue and release single cells into suspension. Because of anchorage-dependence requirements, primary cell cultures require a liquid culture medium in a Petri dish or tissue-culture flask so cells have a solid surface such as glass or plastic for attachment and growth. Primary cultures usually have a limited life span. When cells in a primary culture undergo mitosis and a sufficient density of cells is produced, cells come in contact with other cells. When this cell-to-cell-contact occurs, mitosis is triggered to stop. This is called contact inhibition and it prevents the density of the cells from becoming too high. To prevent contact inhibition, cells from the primary cell culture must be transferred to another vessel with fresh growth medium. This is called a secondary cell culture. Periodically, cell density must be reduced by pouring off some cells and adding fresh medium to provide space and nutrients to maintain cell growth. In contrast to primary cell cultures, continuous cell lines, usually derived from transformed cells or tumors, are often able to be subcultured many times or even grown indefinitely (in which case they are called immortal). Continuous cell lines may not exhibit anchorage dependency (they will grow in suspension) and may have lost their contact inhibition. As a result, continuous cell lines can grow in piles or lumps resembling small tumor growths (see ).
An example of an immortal cell line is the HeLa cell line, which was originally cultivated from tumor cells obtained from Henrietta Lacks, a patient who died of cervical cancer in 1951. HeLa cells were the first continuous tissue-culture cell line and were used to establish tissue culture as an important technology for research in cell biology, virology, and medicine. Prior to the discovery of HeLa cells, scientists were not able to establish tissue cultures with any reliability or stability. More than six decades later, this cell line is still alive and being used for medical research. See Eye on Ethics: The Immortal Cell Line of Henrietta Lacks to read more about this important cell line and the controversial means by which it was obtained.

### Detection of a Virus

Regardless of the method of cultivation, once a virus has been introduced into a whole host organism, embryo, or tissue-culture cell, a sample can be prepared from the infected host, embryo, or cell line for further analysis under a brightfield, electron, or fluorescent microscope. Cytopathic effects (CPEs) are distinct observable cell abnormalities due to viral infection. CPEs can include loss of adherence to the surface of the container, changes in cell shape from flat to round, shrinkage of the nucleus, vacuoles in the cytoplasm, fusion of cytoplasmic membranes and the formation of multinucleated syncytia, inclusion bodies in the nucleus or cytoplasm, and complete cell lysis (see ).
Further pathological changes include viral disruption of the host genome and altering normal cells into transformed cells, which are the types of cells associated with carcinomas and sarcomas. The type or severity of the CPE depends on the type of virus involved.  lists CPEs for specific viruses.

### Hemagglutination Assay

A serological assay is used to detect the presence of certain types of viruses in patient serum. Serum is the straw-colored liquid fraction of blood plasma from which clotting factors have been removed. Serum can be used in a direct assay called a hemagglutination assay to detect specific types of viruses in the patient’s sample. Hemagglutination is the agglutination (clumping) together of erythrocytes (red blood cells). Many viruses produce surface proteins or spikes called hemagglutinins that can bind to receptors on the membranes of erythrocytes and cause the cells to agglutinate. Hemagglutination is observable without using the microscope, but this method does not always differentiate between infectious and noninfectious viral particles, since both can agglutinate erythrocytes.
To identify a specific pathogenic virus using hemagglutination, we must use an indirect approach. Proteins called antibodies, generated by the patient’s immune system to fight a specific virus, can be used to bind to components such as hemagglutinins that are uniquely associated with specific types of viruses. The binding of the antibodies with the hemagglutinins found on the virus subsequently prevent erythrocytes from directly interacting with the virus. So when erythrocytes are added to the antibody-coated viruses, there is no appearance of agglutination; agglutination has been inhibited. We call these types of indirect assays for virus-specific antibodies hemagglutination inhibition (HAI) assays. HAI can be used to detect the presence of antibodies specific to many types of viruses that may be causing or have caused an infection in a patient even months or years after infection (see ). This assay is described in greater detail in Agglutination Assays.

### Nucleic Acid Amplification Test

Nucleic acid amplification tests (NAAT) are used in molecular biology to detect unique nucleic acid sequences of viruses in patient samples. Polymerase chain reaction (PCR) is an NAAT used to detect the presence of viral DNA in a patient’s tissue or body fluid sample. PCR is a technique that amplifies (i.e., synthesizes many copies) of a viral DNA segment of interest. Using PCR, short nucleotide sequences called primers bind to specific sequences of viral DNA, enabling identification of the virus.
Reverse transcriptase-PCR (RT-PCR) is an NAAT used to detect the presence of RNA viruses. RT-PCR differs from PCR in that the enzyme reverse transcriptase (RT) is used to make a cDNA from the small amount of viral RNA in the specimen. The cDNA can then be amplified by PCR. Both PCR and RT-PCR are used to detect and confirm the presence of the viral nucleic acid in patient specimens.

### Enzyme Immunoassay

Enzyme immunoassays (EIAs) rely on the ability of antibodies to detect and attach to specific biomolecules called antigens. The detecting antibody attaches to the target antigen with a high degree of specificity in what might be a complex mixture of biomolecules. Also included in this type of assay is a colorless enzyme attached to the detecting antibody. The enzyme acts as a tag on the detecting antibody and can interact with a colorless substrate, leading to the production of a colored end product. EIAs often rely on layers of antibodies to capture and react with antigens, all of which are attached to a membrane filter (see ). EIAs for viral antigens are often used as preliminary screening tests. If the results are positive, further confirmation will require tests with even greater sensitivity, such as a western blot or an NAAT. EIAs are discussed in more detail in EIAs and ELISAs.

### Key Concepts and Summary

1. Viral cultivation requires the presence of some form of host cell (whole organism, embryo, or cell culture).
2. Viruses can be isolated from samples by filtration.
3. Viral filtrate is a rich source of released virions.
4. Bacteriophages are detected by presence of clear plaques on bacterial lawn.
5. Animal and plant viruses are detected by cytopathic effects, molecular techniques (PCR, RT-PCR), enzyme immunoassays, and serological assays (hemagglutination assay, hemagglutination inhibition assay).

### Multiple Choice

### Fill in the Blank

### Short Answer

### Critical Thinking


# Acellular Pathogens

## Viroids, Virusoids, and Prions

### Learning Objectives

By the end of this section, you will be able to:
1. Describe viroids and their unique characteristics
2. Describe virusoids and their unique characteristics
3. Describe prions and their unique characteristics
Research attempts to discover the causative agents of previously uninvestigated diseases have led to the discovery of nonliving disease agents quite different from viruses. These include particles consisting only of RNA or only of protein that, nonetheless, are able to self-propagate at the expense of a host—a key similarity to viruses that allows them to cause disease conditions. To date, these discoveries include viroids, virusoids, and the proteinaceous prions.

### Viroids

In 1971, Theodor Diener, a pathologist working at the Agriculture Research Service, discovered an acellular particle that he named a viroid, meaning “virus-like.” Viroids consist only of a short strand of circular RNA capable of self-replication. The first viroid discovered was found to cause potato tuber spindle disease, which causes slower sprouting and various deformities in potato plants (see ). Like viruses, potato spindle tuber viroids (PSTVs) take control of the host machinery to replicate their RNA genome. Unlike viruses, viroids do not have a protein coat to protect their genetic information.
Viroids can result in devastating losses of commercially important agricultural food crops grown in fields and orchards. Since the discovery of PSTV, other viroids have been discovered that cause diseases in plants. Tomato planta macho viroid (TPMVd) infects tomato plants, which causes loss of chlorophyll, disfigured and brittle leaves, and very small tomatoes, resulting in loss of productivity in this field crop. Avocado sunblotch viroid (ASBVd) results in lower yields and poorer-quality fruit. ASBVd is the smallest viroid discovered thus far that infects plants. Peach latent mosaic viroid (PLMVd) can cause necrosis of flower buds and branches, and wounding of ripened fruit, which leads to fungal and bacterial growth in the fruit. PLMVd can also cause similar pathological changes in plums, nectarines, apricots, and cherries, resulting in decreased productivity in these orchards, as well. Viroids, in general, can be dispersed mechanically during crop maintenance or harvesting, vegetative reproduction, and possibly via seeds and insects, resulting in a severe drop in food availability and devastating economic consequences.

### Virusoids

A second type of pathogenic RNA that can infect commercially important agricultural crops are the virusoids, which are subviral particles best described as non–self-replicating ssRNAs. RNA replication of virusoids is similar to that of viroids but, unlike viroids, virusoids require that the cell also be infected with a specific “helper” virus. There are currently only five described types of virusoids and their associated helper viruses. The helper viruses are all from the family of Sobemoviruses. An example of a helper virus is the subterranean clover mottle virus, which has an associated virusoid packaged inside the viral capsid. Once the helper virus enters the host cell, the virusoids are released and can be found free in plant cell cytoplasm, where they possess ribozyme activity. The helper virus undergoes typical viral replication independent of the activity of the virusoid. The virusoid genomes are small, only 220 to 388 nucleotides long. A virusoid genome does not code for any proteins, but instead serves only to replicate virusoid RNA.
Virusoids belong to a larger group of infectious agents called satellite RNAs, which are similar pathogenic RNAs found in animals. Unlike the plant virusoids, satellite RNAs may encode for proteins; however, like plant virusoids, satellite RNAs must coinfect with a helper virus to replicate. One satellite RNA that infects humans and that has been described by some scientists as a virusoid is the hepatitis delta virus (HDV), which, by some reports, is also called hepatitis delta virusoid. Much larger than a plant virusoid, HDV has a circular, ssRNA genome of 1,700 nucleotides and can direct the biosynthesis of HDV-associated proteins. The HDV helper virus is the hepatitis B virus (HBV). Coinfection with HBV and HDV results in more severe pathological changes in the liver during infection, which is how HDV was first discovered.

### Prions

At one time, scientists believed that any infectious particle must contain DNA or RNA. Then, in 1982, Stanley Prusiner, a medical doctor studying scrapie (a fatal, degenerative disease in sheep) discovered that the disease was caused by proteinaceous infectious particles, or prions. Because proteins are acellular and do not contain DNA or RNA, Prusiner’s findings were originally met with resistance and skepticism; however, his research was eventually validated, and he received the Nobel Prize in Physiology or Medicine in 1997.
A prion is a misfolded rogue form of a normal protein (PrPc) found in the cell. This rogue prion protein (PrPsc), which may be caused by a genetic mutation or occur spontaneously, can be infectious, stimulating other endogenous normal proteins to become misfolded, forming plaques (see ). Today, prions are known to cause various forms of transmissible spongiform encephalopathy (TSE) in human and animals. TSE is a rare degenerative disorder that affects the brain and nervous system. The accumulation of rogue proteins causes the brain tissue to become sponge-like, killing brain cells and forming holes in the tissue, leading to brain damage, loss of motor coordination, and dementia (see ). Infected individuals are mentally impaired and become unable to move or speak. There is no cure, and the disease progresses rapidly, eventually leading to death within a few months or years.
TSEs in humans include kuru, fatal familial insomnia, Gerstmann-Straussler-Scheinker disease, and Creutzfeldt-Jakob disease (see ). TSEs in animals include mad cow disease, scrapie (in sheep and goats), and chronic wasting disease (in elk and deer). TSEs can be transmitted between animals and from animals to humans by eating contaminated meat or animal feed. Transmission between humans can occur through heredity (as is often the case with GSS and CJD) or by contact with contaminated tissue, as might occur during a blood transfusion or organ transplant. There is no evidence for transmission via casual contact with an infected person.  lists TSEs that affect humans and their modes of transmission.
Prions are extremely difficult to destroy because they are resistant to heat, chemicals, and radiation. Even standard sterilization procedures do not ensure the destruction of these particles. Currently, there is no treatment or cure for TSE disease, and contaminated meats or infected animals must be handled according to federal guidelines to prevent transmission.

### Key Concepts and Summary

1. Other acellular agents such as viroids, virusoids, and prions also cause diseases. Viroids consist of small, naked ssRNAs that cause diseases in plants. Virusoids are ssRNAs that require other helper viruses to establish an infection. Prions are proteinaceous infectious particles that cause transmissible spongiform encephalopathies.
2. Prions are extremely resistant to chemicals, heat, and radiation.
3. There are no treatments for prion infection.

### Multiple Choice

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### Short Answer

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# Microbial Biochemistry

## Introduction

The earth is estimated to be 4.6 billion years old, but for the first 2 billion years, the atmosphere lacked oxygen, without which the earth could not support life as we know it. One hypothesis about how life emerged on earth involves the concept of a “primordial soup.” This idea proposes that life began in a body of water when metals and gases from the atmosphere combined with a source of energy, such as lightning or ultraviolet light, to form the carbon compounds that are the chemical building blocks of life. In 1952, Stanley Miller (1930–2007), a graduate student at the University of Chicago, and his professor Harold Urey (1893–1981), set out to confirm this hypothesis in a now-famous experiment. Miller and Urey combined what they believed to be the major components of the earth’s early atmosphere—water (H2O), methane (CH4), hydrogen (H2), and ammonia (NH3)—and sealed them in a sterile flask. Next, they heated the flask to produce water vapor and passed electric sparks through the mixture to mimic lightning in the atmosphere (). When they analyzed the contents of the flask a week later, they found amino acids, the structural units of proteins—molecules essential to the function of all organisms.


# Microbial Biochemistry

## Organic Molecules

### Learning Objectives

By the end of this section, you will be able to:
1. Identify common elements and structures found in organic molecules
2. Explain the concept of isomerism
3. Identify examples of functional groups
4. Describe the role of functional groups in synthesizing polymers
Biochemistry is the discipline that studies the chemistry of life, and its objective is to explain form and function based on chemical principles. Organic chemistry is the discipline devoted to the study of carbon-based chemistry, which is the foundation for the study of biomolecules and the discipline of biochemistry. Both biochemistry and organic chemistry are based on the concepts of general chemistry, some of which are presented in Appendix A.

### Elements in Living Cells

The most abundant element in cells is hydrogen (H), followed by carbon (C), oxygen (O), nitrogen (N), phosphorous (P), and sulfur (S). We call these elements macronutrients, and they account for about 99% of the dry weight of cells. Some elements, such as sodium (Na), potassium (K), magnesium (Mg), zinc (Zn), iron (Fe), calcium (Ca), molybdenum (Mo), copper (Cu), cobalt (Co), manganese (Mn), or vanadium (V), are required by some cells in very small amounts and are called micronutrients or trace elements. All of these elements are essential to the function of many biochemical reactions, and, therefore, are essential to life.
The four most abundant elements in living matter (C, N, O, and H) have low atomic numbers and are thus light elements capable of forming strong bonds with other atoms to produce molecules (). Carbon forms four chemical bonds, whereas nitrogen forms three, oxygen forms two, and hydrogen forms one. When bonded together within molecules, oxygen, sulfur, and nitrogen often have one or more “lone pairs” of electrons that play important roles in determining many of the molecules’ physical and chemical properties (see Appendix A). These traits in combination permit the formation of a vast number of diverse molecular species necessary to form the structures and enable the functions of living organisms.
Living organisms contain inorganic compounds (mainly water and salts; see Appendix A) and organic molecules. Organic molecules contain carbon; inorganic compounds do not. Carbon oxides and carbonates are exceptions; they contain carbon but are considered inorganic because they do not contain hydrogen. The atoms of an organic molecule are typically organized around chains of carbon atoms.
Inorganic compounds make up 1%–1.5% of the dry weight of living cells. They are small, simple compounds that play important roles in the cell, although they do not form cell structures. Most of the carbon found in organic molecules originates from inorganic carbon sources such as carbon dioxide captured via carbon fixation by microorganisms.

### Organic Molecules and Isomerism

Organic molecules in organisms are generally larger and more complex than inorganic molecules. Their carbon skeletons are held together by covalent bonds. They form the cells of an organism and perform the chemical reactions that facilitate life. All of these molecules, called biomolecules because they are part of living matter, contain carbon, which is the building block of life. Carbon is a very unique element in that it has four valence electrons in its outer orbitals and can form four single covalent bonds with up to four other atoms at the same time (see Appendix A). These atoms are usually oxygen, hydrogen, nitrogen, sulfur, phosphorous, and carbon itself; the simplest organic compound is methane, in which carbon binds only to hydrogen ().
As a result of carbon’s unique combination of size and bonding properties, carbon atoms can bind together in large numbers, thus producing a chain or carbon skeleton. The carbon skeleton of organic molecules can be straight, branched, or ring shaped (cyclic). Organic molecules are built on chains of carbon atoms of varying lengths; most are typically very long, which allows for a huge number and variety of compounds. No other element has the ability to form so many different molecules of so many different sizes and shapes.
Molecules with the same atomic makeup but different structural arrangement of atoms are called isomers. The concept of isomerism is very important in chemistry because the structure of a molecule is always directly related to its function. Slight changes in the structural arrangements of atoms in a molecule may lead to very different properties. Chemists represent molecules by their structural formula, which is a graphic representation of the molecular structure, showing how the atoms are arranged. Compounds that have identical molecular formulas but differ in the bonding sequence of the atoms are called structural isomers. The monosaccharides glucose, galactose, and fructose all have the same molecular formula, C6H12O6, but we can see from  that the atoms are bonded together differently.
Isomers that differ in the spatial arrangements of atoms are called stereoisomers; one unique type is enantiomers. The properties of enantiomers were originally discovered by Louis Pasteur in 1848 while using a microscope to analyze crystallized fermentation products of wine. Enantiomers are molecules that have the characteristic of chirality, in which their structures are nonsuperimposable mirror images of each other. Chirality is an important characteristic in many biologically important molecules, as illustrated by the examples of structural differences in the enantiomeric forms of the monosaccharide glucose or the amino acid alanine ().
Many organisms are only able to use one enantiomeric form of certain types of molecules as nutrients and as building blocks to make structures within a cell. Some enantiomeric forms of amino acids have distinctly different tastes and smells when consumed as food. For example, L-aspartame, commonly called aspartame, tastes sweet, whereas D-aspartame is tasteless. Drug enantiomers can have very different pharmacologic affects. For example, the compound methorphan exists as two enantiomers, one of which acts as an antitussive (dextromethorphan, a cough suppressant), whereas the other acts as an analgesic (levomethorphan, a drug similar in effect to codeine).
Enantiomers are also called optical isomers because they can rotate the plane of polarized light. Some of the crystals Pasteur observed from wine fermentation rotated light clockwise whereas others rotated the light counterclockwise. Today, we denote enantiomers that rotate polarized light clockwise (+) as s, and the mirror image of the same molecule that rotates polarized light counterclockwise (−) as the . The d and l labels are derived from the Latin words dexter (on the right) and laevus (on the left), respectively. These two different optical isomers often have very different biological properties and activities. Certain species of molds, yeast, and bacteria, such as , , and  spp., respectively, can only metabolize one type of optical isomer; the opposite isomer is not suitable as a source of nutrients. Another important reason to be aware of optical isomers is the therapeutic use of these types of chemicals for drug treatment, because some microorganisms can only be affected by one specific optical isomer.

### Biologically Significant Functional Groups

In addition to containing carbon atoms, biomolecules also contain functional groups—groups of atoms within molecules that are categorized by their specific chemical composition and the chemical reactions they perform, regardless of the molecule in which the group is found. Some of the most common functional groups are listed in . In the formulas, the symbol R stands for “residue” and represents the remainder of the molecule. R might symbolize just a single hydrogen atom or it may represent a group of many atoms. Notice that some functional groups are relatively simple, consisting of just one or two atoms, while some comprise two of these simpler functional groups. For example, a carbonyl group is a functional group composed of a carbon atom double bonded to an oxygen atom: C=O. It is present in several classes of organic compounds as part of larger functional groups such as ketones, aldehydes, carboxylic acids, and amides. In ketones, the carbonyl is present as an internal group, whereas in aldehydes it is a terminal group.

### Macromolecules

Carbon chains form the skeletons of most organic molecules. Functional groups combine with the chain to form biomolecules. Because these biomolecules are typically large, we call them macromolecules. Many biologically relevant macromolecules are formed by linking together a great number of identical, or very similar, smaller organic molecules. The smaller molecules act as building blocks and are called monomers, and the macromolecules that result from their linkage are called polymers. Cells and cell structures include four main groups of carbon-containing macromolecules: polysaccharides, proteins, lipids, and nucleic acids. The first three groups of molecules will be studied throughout this chapter. The biochemistry of nucleic acids will be discussed in Biochemistry of the Genome.
Of the many possible ways that monomers may be combined to yield polymers, one common approach encountered in the formation of biological macromolecules is dehydration synthesis. In this chemical reaction, monomer molecules bind end to end in a process that results in the formation of water molecules as a byproduct:
 shows dehydration synthesis of glucose binding together to form maltose and a water molecule.  summarizes macromolecules and some of their functions.

### Key Concepts and Summary

1. The most abundant elements in cells are hydrogen, carbon, oxygen, nitrogen, phosphorus, and sulfur.
2. Life is carbon based. Each carbon atom can bind to another one producing a carbon skeleton that can be straight, branched, or ring shaped.
3. The same numbers and types of atoms may bond together in different ways to yield different molecules called isomers. Isomers may differ in the bonding sequence of their atoms (structural isomers) or in the spatial arrangement of atoms whose bonding sequences are the same (stereoisomers), and their physical and chemical properties may vary slightly or drastically.
4. Functional groups confer specific chemical properties to molecules bearing them. Common functional groups in biomolecules are hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.
5. Macromolecules are polymers assembled from individual units, the monomers, which bind together like building blocks. Many biologically significant macromolecules are formed by dehydration synthesis, a process in which monomers bind together by combining their functional groups and generating water molecules as byproducts.

### Multiple Choice

### True/False

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