Microbiology Chapter 3: The Cell PDF

CHAPTER 3 The Cell FIGURE 3.1 Microorganisms vary visually in their size and shape, as can be observed microscopically; but they also vary in invisible ways, such as in their metabolic capabilities. (credit a, e, f: modification of work by Centers for Disease Control and Prevention; credit b: modif...

CHAPTER 3 The Cell FIGURE 3.1 Microorganisms vary visually in their size and shape, as can be observed microscopically; but they also vary in invisible ways, such as in their metabolic capabilities. (credit a, e, f: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by NIAID; credit c: modification of work by CSIRO; credit d: modification of work by “Microscopic World”/YouTube) CHAPTER OUTLINE 3.1 Spontaneous Generation 3.2 Foundations of Modern Cell Theory 3.3 Unique Characteristics of Prokaryotic Cells 3.4 Unique Characteristics of Eukaryotic Cells INTRODUCTION Life takes many forms, from giant redwood trees towering hundreds of feet in the air to the tiniest known microbes, which measure only a few billionths of a meter. Humans have long pondered life’s origins and debated the defining characteristics of life, but our understanding of these concepts has changed radically since the invention of the microscope. In the 17th century, observations of microscopic life led to the development of the cell theory: the idea that the fundamental unit of life is the cell, that all organisms contain at least one cell, and that cells only come from other cells. Despite sharing certain characteristics, cells may vary significantly. The two main types of cells are prokaryotic cells (lacking a nucleus) and eukaryotic cells (containing a well-organized, membrane-bound nucleus). Each type of cell exhibits remarkable variety in structure, function, and metabolic activity (Figure 3.1). This chapter will focus on the historical discoveries that have shaped our current understanding of microbes, including their origins and their role in human disease. We will then explore the distinguishing structures found in prokaryotic and eukaryotic cells. 74 3 The Cell 3.1 Spontaneous Generation LEARNING OBJECTIVES By the end of this section, you will be able to: Explain the theory of spontaneous generation and why people once accepted it as an explanation for the existence of certain types of organisms Explain how certain individuals (van Helmont, Redi, Needham, Spallanzani, and Pasteur) tried to prove or disprove spontaneous generation CLINICAL FOCUS Part 1 Barbara is a 19-year-old college student living in the dormitory. In January, she came down with a sore throat, headache, mild fever, chills, and a violent but unproductive (i.e., no mucus) cough. To treat these symptoms, Barbara began taking an over-the-counter cold medication, which did not seem to work. In fact, over the next few days, while some of Barbara’s symptoms began to resolve, her cough and fever persisted, and she felt very tired and weak. What types of respiratory disease may be responsible? Jump to the next Clinical Focus box Humans have been asking for millennia: Where does new life come from? Religion, philosophy, and science have all wrestled with this question. One of the oldest explanations was the theory of spontaneous generation, which can be traced back to the ancient Greeks and was widely accepted through the Middle Ages. The Theory of Spontaneous Generation The Greek philosopher Aristotle (384–322 BC) was one of the earliest recorded scholars to articulate the theory of spontaneous generation, the notion that life can arise from nonliving matter. Aristotle proposed that life arose from nonliving material if the material contained pneuma (“spirit” or “breath”). As evidence, he noted several instances of the appearance of animals from environments previously devoid of such animals, such as the seemingly sudden 1 appearance of fish in a new puddle of water. This theory persisted into the 17th century, when scientists undertook additional experimentation to support or disprove it. By this time, the proponents of the theory cited how frogs simply seem to appear along the muddy banks of the Nile River in Egypt during the annual flooding. Others observed that mice simply appeared among grain stored in barns with thatched roofs. When the roof leaked and the grain molded, mice appeared. Jan Baptista van Helmont, a 17th century Flemish scientist, proposed that mice could arise from rags and wheat kernels left in an open container for 3 weeks. In reality, such habitats provided ideal food sources and shelter for mouse populations to flourish. However, one of van Helmont’s contemporaries, Italian physician Francesco Redi (1626–1697), performed an experiment in 1668 that was one of the first to refute the idea that maggots (the larvae of flies) spontaneously generate on meat left out in the open air. He predicted that preventing flies from having direct contact with the meat would also prevent the appearance of maggots. Redi left meat in each of six containers (Figure 3.2). Two were open to the air, two were covered with gauze, and two were tightly sealed. His hypothesis was supported when maggots developed in the uncovered jars, but no maggots appeared in either the gauze-covered or the tightly sealed jars. He concluded that maggots could only form when flies were allowed to lay eggs in the meat, and that the maggots were the offspring of flies, not the product of spontaneous generation. 1 K. Zwier. “Aristotle on Spontaneous Generation.” http://www.sju.edu/int/academics/cas/resources/gppc/pdf/Karen%20R.%20Zwier.pdf Access for free at openstax.org  3.1 Spontaneous Generation 75 FIGURE 3.2 Francesco Redi’s experimental setup consisted of an open container, a container sealed with a cork top, and a container covered in mesh that let in air but not flies. Maggots only appeared on the meat in the open container. However, maggots were also found on the gauze of the gauze-covered container. In 1745, John Needham (1713–1781) published a report of his own experiments, in which he briefly boiled broth 2 infused with plant or animal matter, hoping to kill all preexisting microbes. He then sealed the flasks. After a few days, Needham observed that the broth had become cloudy and a single drop contained numerous microscopic creatures. He argued that the new microbes must have arisen spontaneously. In reality, however, he likely did not boil the broth enough to kill all preexisting microbes. Lazzaro Spallanzani (1729–1799) did not agree with Needham’s conclusions, however, and performed hundreds of 3 carefully executed experiments using heated broth. As in Needham’s experiment, broth in sealed jars and unsealed jars was infused with plant and animal matter. Spallanzani’s results contradicted the findings of Needham: Heated but sealed flasks remained clear, without any signs of spontaneous growth, unless the flasks were subsequently opened to the air. This suggested that microbes were introduced into these flasks from the air. In response to Spallanzani’s findings, Needham argued that life originates from a “life force” that was destroyed during Spallanzani’s extended boiling. Any subsequent sealing of the flasks then prevented new life force from entering and causing spontaneous generation (Figure 3.3). FIGURE 3.3 (a) Francesco Redi, who demonstrated that maggots were the offspring of flies, not products of spontaneous generation. (b) John Needham, who argued that microbes arose spontaneously in broth from a “life force.” (c) Lazzaro Spallanzani, whose experiments with broth aimed to disprove those of Needham. CHECK YOUR UNDERSTANDING Describe the theory of spontaneous generation and some of the arguments used to support it. Explain how the experiments of Redi and Spallanzani challenged the theory of spontaneous generation. 2 E. Capanna. “Lazzaro Spallanzani: At the Roots of Modern Biology.” Journal of Experimental Zoology 285 no. 3 (1999):178–196. 3 R. Mancini, M. Nigro, G. Ippolito. “Lazzaro Spallanzani and His Refutation of the Theory of Spontaneous Generation.” Le Infezioni in Medicina 15 no. 3 (2007):199–206. 76 3 The Cell Disproving Spontaneous Generation The debate over spontaneous generation continued well into the 19th century, with scientists serving as proponents of both sides. To settle the debate, the Paris Academy of Sciences offered a prize for resolution of the problem. Louis Pasteur, a prominent French chemist who had been studying microbial fermentation and the causes of wine spoilage, accepted the challenge. In 1858, Pasteur filtered air through a gun-cotton filter and, upon microscopic examination of the cotton, found it full of microorganisms, suggesting that the exposure of a broth to air was not introducing a “life force” to the broth but rather airborne microorganisms. Later, Pasteur made a series of flasks with long, twisted necks (“swan-neck” flasks), in which he boiled broth to sterilize it (Figure 3.4). His design allowed air inside the flasks to be exchanged with air from the outside, but prevented the introduction of any airborne microorganisms, which would get caught in the twists and bends of the flasks’ necks. If a life force besides the airborne microorganisms were responsible for microbial growth within the sterilized flasks, it would have access to the broth, whereas the microorganisms would not. He correctly predicted that sterilized broth in his swan-neck flasks would remain sterile as long as the swan necks remained intact. However, should the necks be broken, microorganisms would be introduced, contaminating the flasks and allowing microbial growth within the broth. Pasteur’s set of experiments irrefutably disproved the theory of spontaneous generation and earned him the prestigious Alhumbert Prize from the Paris Academy of Sciences in 1862. In a subsequent lecture in 1864, Pasteur articulated “Omne vivum ex vivo” (“Life only comes from life”). In this lecture, Pasteur recounted his famous swan- neck flask experiment, stating that “…life is a germ and a germ is life. Never will the doctrine of spontaneous 4 generation recover from the mortal blow of this simple experiment.” To Pasteur’s credit, it never has. 4 R. Vallery-Radot. The Life of Pasteur, trans. R.L. Devonshire. New York: McClure, Phillips and Co, 1902, 1:142. Access for free at openstax.org  3.2 Foundations of Modern Cell Theory 77 FIGURE 3.4 (a) French scientist Louis Pasteur, who definitively refuted the long-disputed theory of spontaneous generation. (b) The unique swan-neck feature of the flasks used in Pasteur’s experiment allowed air to enter the flask but prevented the entry of bacterial and fungal spores. (c) Pasteur’s experiment consisted of two parts. In the first part, the broth in the flask was boiled to sterilize it. When this broth was cooled, it remained free of contamination. In the second part of the experiment, the flask was boiled and then the neck was broken off. The broth in this flask became contaminated. (credit b: modification of work by “Wellcome Images”/Wikimedia Commons) CHECK YOUR UNDERSTANDING How did Pasteur’s experimental design allow air, but not microbes, to enter, and why was this important? What was the control group in Pasteur’s experiment and what did it show? 3.2 Foundations of Modern Cell Theory LEARNING OBJECTIVES By the end of this section, you will be able to: Explain the key points of cell theory and the individual contributions of Hooke, Schleiden, Schwann, Remak, and Virchow Explain the key points of endosymbiotic theory and cite the evidence that supports this concept Explain the contributions of Semmelweis, Snow, Pasteur, Lister, and Koch to the development of germ theory While some scientists were arguing over the theory of spontaneous generation, other scientists were making discoveries leading to a better understanding of what we now call the cell theory. Modern cell theory has two basic 78 3 The Cell tenets: All cells only come from other cells (the principle of biogenesis). Cells are the fundamental units of organisms. Today, these tenets are fundamental to our understanding of life on earth. However, modern cell theory grew out of the collective work of many scientists. The Origins of Cell Theory The English scientist Robert Hooke first used the term “cells” in 1665 to describe the small chambers within cork that he observed under a microscope of his own design. To Hooke, thin sections of cork resembled “Honey-comb,” or “small Boxes or Bladders of Air.” He noted that each “Cavern, Bubble, or Cell” was distinct from the others (Figure 3.5). At the time, Hooke was not aware that the cork cells were long dead and, therefore, lacked the internal structures found within living cells. FIGURE 3.5 Robert Hooke (1635–1703) was the first to describe cells based upon his microscopic observations of cork. This illustration was published in his work Micrographia. Despite Hooke’s early description of cells, their significance as the fundamental unit of life was not yet recognized. Nearly 200 years later, in 1838, Matthias Schleiden (1804–1881), a German botanist who made extensive microscopic observations of plant tissues, described them as being composed of cells. Visualizing plant cells was relatively easy because plant cells are clearly separated by their thick cell walls. Schleiden believed that cells formed through crystallization, rather than cell division. Theodor Schwann (1810–1882), a noted German physiologist, made similar microscopic observations of animal tissue. In 1839, after a conversation with Schleiden, Schwann realized that similarities existed between plant and animal tissues. This laid the foundation for the idea that cells are the fundamental components of plants and animals. In the 1850s, two Polish scientists living in Germany pushed this idea further, culminating in what we recognize today as the modern cell theory. In 1852, Robert Remak (1815–1865), a prominent neurologist and embryologist, published convincing evidence that cells are derived from other cells as a result of cell division. However, this idea was questioned by many in the scientific community. Three years later, Rudolf Virchow (1821–1902), a well- respected pathologist, published an editorial essay entitled “Cellular Pathology,” which popularized the concept of cell theory using the Latin phrase omnis cellula a cellula (“all cells arise from cells”), which is essentially the second 5 tenet of modern cell theory. Given the similarity of Virchow’s work to Remak’s, there is some controversy as to which scientist should receive credit for articulating cell theory. See the following Eye on Ethics feature for more about this controversy. 5 M. Schultz. “Rudolph Virchow.” Emerging Infectious Diseases 14 no. 9 (2008):1480–1481. Access for free at openstax.org  3.2 Foundations of Modern Cell Theory 79 EYE ON ETHICS Science and Plagiarism Rudolf Virchow, a prominent, Polish-born, German scientist, is often remembered as the “Father of Pathology.” Well known for innovative approaches, he was one of the first to determine the causes of various diseases by examining their effects on tissues and organs. He was also among the first to use animals in his research and, as a result of his work, he was the first to name numerous diseases and created many other medical terms. Over the course of his career, he published more than 2,000 papers and headed various important medical facilities, including the Charité – Universitätsmedizin Berlin, a prominent Berlin hospital and medical school. But he is, perhaps, best remembered for his 1855 editorial essay titled “Cellular Pathology,” published in Archiv für Pathologische Anatomie und Physiologie, a journal that Virchow himself cofounded and still exists today. Despite his significant scientific legacy, there is some controversy regarding this essay, in which Virchow proposed the central tenet of modern cell theory—that all cells arise from other cells. Robert Remak, a former colleague who worked in the same laboratory as Virchow at the University of Berlin, had published the same idea 3 years before. Though it appears Virchow was familiar with Remak’s work, he neglected to credit Remak’s ideas in his essay. When Remak wrote a letter to Virchow pointing out similarities between Virchow’s ideas and his own, Virchow was dismissive. In 1858, in the preface to one of his books, Virchow wrote that his 1855 publication was just an editorial piece, not a scientific paper, and thus there was no need to cite Remak’s work. By today’s standards, Virchow’s editorial piece would certainly be considered an act of plagiarism, since he presented Remak’s ideas as his own. However, in the 19th century, standards for academic integrity were much less clear. Virchow’s strong reputation, coupled with the fact that Remak was a Jew in a somewhat anti-Semitic political climate, shielded him from any significant repercussions. Today, the process of peer review and the ease of access to the scientific literature help discourage plagiarism. Although scientists are still motivated to publish original ideas that advance scientific knowledge, those who would consider plagiarizing are well aware of the serious consequences. In academia, plagiarism represents the theft of both individual thought and research—an offense that can 6 7 8 9 destroy reputations and end careers. FIGURE 3.6 (a) Rudolf Virchow (1821–1902) popularized the cell theory in an 1855 essay entitled “Cellular Pathology.” (b) The idea that all cells originate from other cells was first published in 1852 by his contemporary and former colleague Robert Remak (1815–1865). 6 B. Kisch. “Forgotten Leaders in Modern Medicine, Valentin, Gouby, Remak, Auerbach.” Transactions of the American Philosophical Society 44 (1954):139–317. 7 H. Harris. The Birth of the Cell. New Haven, CT: Yale University Press, 2000:133. 8 C. Webster (ed.). Biology, Medicine and Society 1840-1940. Cambridge, UK; Cambridge University Press, 1981:118–119. 9 C. Zuchora-Walske. Key Discoveries in Life Science. Minneapolis, MN: Lerner Publishing, 2015:12–13. 80 3 The Cell CHECK YOUR UNDERSTANDING What are the key points of the cell theory? What contributions did Rudolf Virchow and Robert Remak make to the development of the cell theory? Endosymbiotic Theory As scientists were making progress toward understanding the role of cells in plant and animal tissues, others were examining the structures within the cells themselves. In 1831, Scottish botanist Robert Brown (1773–1858) was the first to describe observations of nuclei, which he observed in plant cells. Then, in the early 1880s, German botanist Andreas Schimper (1856–1901) was the first to describe the chloroplasts of plant cells, identifying their role in starch formation during photosynthesis and noting that they divided independent of the nucleus. Based upon the chloroplasts’ ability to reproduce independently, Russian botanist Konstantin Mereschkowski (1855–1921) suggested in 1905 that chloroplasts may have originated from ancestral photosynthetic bacteria living symbiotically inside a eukaryotic cell. He proposed a similar origin for the nucleus of plant cells. This was the first articulation of the endosymbiotic hypothesis, and would explain how eukaryotic cells evolved from ancestral bacteria. Mereschkowski’s endosymbiotic hypothesis was furthered by American anatomist Ivan Wallin (1883–1969), who began to experimentally examine the similarities between mitochondria, chloroplasts, and bacteria—in other words, to put the endosymbiotic hypothesis to the test using objective investigation. Wallin published a series of papers in the 1920s supporting the endosymbiotic hypothesis, including a 1926 publication co-authored with Mereschkowski. Wallin claimed he could culture mitochondria outside of their eukaryotic host cells. Many scientists dismissed his cultures of mitochondria as resulting from bacterial contamination. Modern genome sequencing work supports the dissenting scientists by showing that much of the genome of mitochondria had been transferred to the host cell’s 10 11 nucleus, preventing the mitochondria from being able to live on their own. Wallin’s ideas regarding the endosymbiotic hypothesis were largely ignored for the next 50 years because scientists were unaware that these organelles contained their own DNA. However, with the discovery of mitochondrial and chloroplast DNA in the 1960s, the endosymbiotic hypothesis was resurrected. Lynn Margulis (1938–2011), an American geneticist, published her ideas regarding the endosymbiotic hypothesis of the origins of mitochondria and 12 chloroplasts in 1967. In the decade leading up to her publication, advances in microscopy had allowed scientists to differentiate prokaryotic cells from eukaryotic cells. In her publication, Margulis reviewed the literature and argued that the eukaryotic organelles such as mitochondria and chloroplasts are of prokaryotic origin. She presented a growing body of microscopic, genetic, molecular biology, fossil, and geological data to support her claims. 10 T. Embley, W. Martin. “Eukaryotic Evolution, Changes, and Challenges.” Nature Vol. 440 (2006):623–630. 11 O.G. Berg, C.G. Kurland. “Why Mitochondrial Genes Are Most Often Found in Nuclei.” Molecular Biology and Evolution 17 no. 6 (2000):951–961. 12 L. Sagan. “On the Origin of Mitosing Cells.” Journal of Theoretical Biology 14 no. 3 (1967):225–274. Access for free at openstax.org  3.2 Foundations of Modern Cell Theory 81 Again, this hypothesis was not initially popular, but mounting genetic evidence due to the advent of DNA sequencing supported the endosymbiotic theory, which is now defined as the theory that mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host (Figure 3.7). With Margulis’ initial endosymbiotic theory gaining wide acceptance, she expanded on the theory in her 1981 book Symbiosis in Cell Evolution. In it, she explains how endosymbiosis is a major driving factor in the evolution of organisms. More recent genetic sequencing and phylogenetic analysis show that mitochondrial DNA and chloroplast DNA are highly related to their bacterial counterparts, both in DNA sequence and chromosome structure. However, mitochondrial DNA and chloroplast DNA are reduced compared with nuclear DNA because many of the genes have moved from the organelles into the host cell’s nucleus. Additionally, mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, rather than to the eukaryotic ribosomes of their hosts. Last, the binary fission of these organelles strongly resembles the binary fission of bacteria, as compared with mitosis performed by eukaryotic cells. Since Margulis’ original proposal, scientists have observed several examples of bacterial endosymbionts in modern-day eukaryotic cells. Examples include the endosymbiotic bacteria found within the guts 13 14 of certain insects, such as cockroaches, and photosynthetic bacteria-like organelles found in protists. FIGURE 3.7 According to the endosymbiotic theory, mitochondria and chloroplasts are each derived from the uptake of bacteria. These bacteria established a symbiotic relationship with their host cell that eventually led to the bacteria evolving into mitochondria and chloroplasts. CHECK YOUR UNDERSTANDING What does the modern endosymbiotic theory state? What evidence supports the endosymbiotic theory? The Germ Theory of Disease Prior to the discovery of microbes during the 17th century, other theories circulated about the origins of disease. For example, the ancient Greeks proposed the miasma theory, which held that disease originated from particles emanating from decomposing matter, such as that in sewage or cesspits. Such particles infected humans in close proximity to the rotting material. Diseases including the Black Death, which ravaged Europe’s population during the Middle Ages, were thought to have originated in this way. In the 11th Century, Persian physician Ibn Sina 13 A.E. Douglas. “The Microbial Dimension in Insect Nutritional Ecology.” Functional Ecology 23 (2009):38–47. 14 J.M. Jaynes, L.P. Vernon. “The Cyanelle of Cyanophora paradoxa: Almost a Cyanobacterial Chloroplast.” Trends in Biochemical Sciences 7 no. 1 (1982):22–24. 82 3 The Cell (sometimes referred to as Avicenna) proposed that tuberculosis was likely spread by people's breath when in close proximity. Arab physician Ibn Zuhr, writing in about 1155, documented that the common skin condition scabies was caused by tiny mites that bored into the skin. Though scabies mites are about half a millimeter long (and therefore not technically microscopic) and their skin tunnels are often visible, Ibn Zuhr's discovery gave more evidence that unseen substances or creatures caused diseases. In 1546, Italian physician Girolamo Fracastoro proposed, in his essay De Contagione et Contagiosis Morbis, that seed-like spores may be transferred between individuals through direct contact, exposure to contaminated clothing, or through the air. We now recognize Fracastoro as an early proponent of the germ theory of disease, which states that diseases may result from microbial infection. However, in the 16th century, Fracastoro’s ideas were not widely accepted and would be largely forgotten until the 19th century. In 1847, Hungarian obstetrician Ignaz Semmelweis (Figure 3.8) observed that people who gave birth in hospital wards staffed by physicians and medical students were more likely to suffer and die from puerperal fever after childbirth (10%–20% mortality rate) than were people in wards staffed by midwives (1% mortality rate). Semmelweis observed medical students performing autopsies and then subsequently carrying out vaginal examinations on living patients without washing their hands in between. He suspected that the students carried disease from the autopsies to the patients they examined. His suspicions were supported by the untimely death of a friend, a physician who contracted a fatal wound infection after a postmortem examination of a woman who had died of a puerperal infection. The dead physician’s wound had been caused by a scalpel used during the examination, and his subsequent illness and death closely paralleled that of the dead patient. Although Semmelweis did not know the true cause of puerperal fever, he proposed that physicians were somehow transferring the causative agent to their patients. He suggested that the number of puerperal fever cases could be reduced if physicians and medical students simply washed their hands with chlorinated lime water before and after examining every patient. When this practice was implemented, the maternal mortality rate in people cared for by physicians dropped to the same 1% mortality rate observed among people cared for by midwives. This demonstrated that handwashing was a very effective method for preventing disease transmission. Despite this great success, many discounted Semmelweis’s work at the time, and physicians were slow to adopt the simple procedure of handwashing to prevent infections in their patients because it contradicted established norms for that time period. FIGURE 3.8 Ignaz Semmelweis (1818–1865) was a proponent of the importance of handwashing to prevent transfer of disease between patients by physicians. Around the same time Semmelweis was promoting handwashing, in 1848, British physician John Snow conducted studies to track the source of cholera outbreaks in London. By tracing the outbreaks to two specific water sources, both of which were contaminated by sewage, Snow ultimately demonstrated that cholera bacteria were transmitted via drinking water. Snow’s work is influential in that it represents the first known epidemiological study, and it resulted in the first known public health response to an epidemic. The work of both Semmelweis and Snow clearly refuted the prevailing miasma theory of the day, showing that disease is not only transmitted through the air but also through contaminated items. Access for free at openstax.org  3.2 Foundations of Modern Cell Theory 83 Although the work of Semmelweis and Snow successfully showed the role of sanitation in preventing infectious disease, the cause of disease was not fully understood. The subsequent work of Louis Pasteur, Robert Koch, and Joseph Lister would further substantiate the germ theory of disease. While studying the causes of beer and wine spoilage in 1856, Pasteur discovered properties of fermentation by microorganisms. He had demonstrated with his swan-neck flask experiments (Figure 3.4) that airborne microbes, not spontaneous generation, were the cause of food spoilage, and he suggested that if microbes were responsible for food spoilage and fermentation, they could also be responsible for causing infection. This was the foundation for the germ theory of disease. Meanwhile, British surgeon Joseph Lister (Figure 3.9) was trying to determine the causes of postsurgical infections. Many physicians did not give credence to the idea that microbes on their hands, on their clothes, or in the air could infect patients’ surgical wounds, despite the fact that 50% of surgical patients, on average, were dying of 15 postsurgical infections. Lister, however, was familiar with the work of Semmelweis and Pasteur; therefore, he insisted on handwashing and extreme cleanliness during surgery. In 1867, to further decrease the incidence of postsurgical wound infections, Lister began using carbolic acid (phenol) spray disinfectant/antiseptic during surgery. His extremely successful efforts to reduce postsurgical infection caused his techniques to become a standard medical practice. A few years later, Robert Koch (Figure 3.9) proposed a series of postulates (Koch’s postulates) based on the idea that the cause of a specific disease could be attributed to a specific microbe. Using these postulates, Koch and his colleagues were able to definitively identify the causative pathogens of specific diseases, including anthrax, tuberculosis, and cholera. Koch’s “one microbe, one disease” concept was the culmination of the 19th century’s paradigm shift away from miasma theory and toward the germ theory of disease. Koch’s postulates are discussed more thoroughly in How Pathogens Cause Disease. FIGURE 3.9 (a) Joseph Lister developed procedures for the proper care of surgical wounds and the sterilization of surgical equipment. (b) Robert Koch established a protocol to determine the cause of infectious disease. Both scientists contributed significantly to the acceptance of the germ theory of disease. CHECK YOUR UNDERSTANDING Compare and contrast the miasma theory of disease with the germ theory of disease. How did Joseph Lister’s work contribute to the debate between the miasma theory and germ theory and how did this increase the success of medical procedures? CLINICAL FOCUS Part 2 After suffering a fever, congestion, cough, and increasing aches and pains for several days, Barbara suspects 15 Alexander, J. Wesley. “The Contributions of Infection Control to a Century of Progress” Annals of Surgery 201:423-428, 1985. 84 3 The Cell that she has a case of the flu. She decides to visit the health center at her university. The PA tells Barbara that her symptoms could be due to a range of diseases, such as influenza, bronchitis, pneumonia, or tuberculosis. During her physical examination, the PA notes that Barbara’s heart rate is slightly elevated. Using a pulse oximeter, a small device that clips on her finger, he finds that Barbara has hypoxemia—a lower-than-normal level of oxygen in the blood. Using a stethoscope, the PA listens for abnormal sounds made by Barbara’s heart, lungs, and digestive system. As Barbara breathes, the PA hears a crackling sound and notes a slight shortness of breath. He collects a sputum sample, noting the greenish color of the mucus, and orders a chest radiograph, which shows a “shadow” in the left lung. All of these signs are suggestive of pneumonia, a condition in which the lungs fill with mucus (Figure 3.10). FIGURE 3.10 This is a chest radiograph typical of pneumonia. Because X-ray images are negative images, a “shadow” is seen as a white area within the lung that should otherwise be black. In this case, the left lung shows a shadow as a result of pockets in the lung that have become filled with fluid. (credit left: modification of work by “Christaras A”/Wikimedia Commons) What kinds of infectious agents are known to cause pneumonia? Jump to the next Clinical Focus box. Go back to the previous Clinical Focus box. Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 85 FIGURE 3.11 (credit “swan-neck flask”: modification of work by Wellcome Images) 3.3 Unique Characteristics of Prokaryotic Cells LEARNING OBJECTIVES By the end of this section, you will be able to: Explain the distinguishing characteristics of prokaryotic cells Describe common cell morphologies and cellular arrangements typical of prokaryotic cells and explain how cells maintain their morphology Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function Compare the distinguishing characteristics of bacterial and archaeal cells Cell theory states that the cell is the fundamental unit of life. However, cells vary significantly in size, shape, structure, and function. At the simplest level of construction, all cells possess a few fundamental components. These include cytoplasm (a gel-like substance composed of water and dissolved chemicals needed for growth), which is contained within a plasma membrane (also called a cell membrane or cytoplasmic membrane); one or more chromosomes, which contain the genetic blueprints of the cell; and ribosomes, organelles used for the production of proteins. Beyond these basic components, cells can vary greatly between organisms, and even within the same multicellular organism. The two largest categories of cells—prokaryotic cells and eukaryotic cells—are defined by major differences in several cell structures. Prokaryotic cells lack a nucleus surrounded by a complex nuclear membrane and generally have a single, circular chromosome located in a nucleoid. Eukaryotic cells have a nucleus surrounded 16 by a complex nuclear membrane that contains multiple, rod-shaped chromosomes. All plant cells and animal cells are eukaryotic. Some microorganisms are composed of prokaryotic cells, whereas 16 Y.-H.M. Chan, W.F. Marshall. “Scaling Properties of Cell and Organelle Size.” Organogenesis 6 no. 2 (2010):88–96. 86 3 The Cell others are composed of eukaryotic cells. Prokaryotic microorganisms are classified within the domains Archaea and Bacteria, whereas eukaryotic organisms are classified within the domain Eukarya. The structures inside a cell are analogous to the organs inside a human body, with unique structures suited to specific functions. Some of the structures found in prokaryotic cells are similar to those found in some eukaryotic cells; others are unique to prokaryotes. Although there are some exceptions, eukaryotic cells tend to be larger than prokaryotic cells. The comparatively larger size of eukaryotic cells dictates the need to compartmentalize various chemical processes within different areas of the cell, using complex membrane-bound organelles. In contrast, prokaryotic cells generally lack membrane-bound organelles; however, they often contain inclusions that compartmentalize their cytoplasm. Figure 3.12 illustrates structures typically associated with prokaryotic cells. These structures are described in more detail in the next section. FIGURE 3.12 A typical prokaryotic cell contains a cell membrane, chromosomal DNA that is concentrated in a nucleoid, ribosomes, and a cell wall. Some prokaryotic cells may also possess flagella, pili, fimbriae, and capsules. Common Cell Morphologies and Arrangements Individual cells of a particular prokaryotic organism are typically similar in shape, or cell morphology. Although thousands of prokaryotic organisms have been identified, only a handful of cell morphologies are commonly seen microscopically. Figure 3.13 names and illustrates cell morphologies commonly found in prokaryotic cells. In addition to cellular shape, prokaryotic cells of the same species may group together in certain distinctive arrangements depending on the plane of cell division. Some common arrangements are shown in Figure 3.14. Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 87 FIGURE 3.13 (credit “Coccus” micrograph: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit “Coccobacillus” micrograph: modification of work by Janice Carr, Centers for Disease Control and Prevention; credit “Spirochete” micrograph: modification of work by Centers for Disease Control and Prevention) 88 3 The Cell FIGURE 3.14 In most prokaryotic cells, morphology is maintained by the cell wall in combination with cytoskeletal elements. The cell wall is a structure found in most prokaryotes and some eukaryotes; it envelopes the cell membrane, protecting the cell from changes in osmotic pressure (Figure 3.15). Osmotic pressure occurs because of differences in the concentration of solutes on opposing sides of a semipermeable membrane. Water is able to pass through a semipermeable membrane, but solutes (dissolved molecules like salts, sugars, and other compounds) cannot. When the concentration of solutes is greater on one side of the membrane, water diffuses across the membrane from the side with the lower concentration (more water) to the side with the higher concentration (less water) until the concentrations on both sides become equal. This diffusion of water is called osmosis, and it can cause extreme osmotic pressure on a cell when its external environment changes. The external environment of a cell can be described as an isotonic, hypertonic, or hypotonic medium. In an isotonic medium, the solute concentrations inside and outside the cell are approximately equal, so there is no net movement of water across the cell membrane. In a hypertonic medium, the solute concentration outside the cell exceeds that inside the cell, so water diffuses out of the cell and into the external medium. In a hypotonic medium, the solute concentration inside the cell exceeds that outside of the cell, so water will move by osmosis into the cell. This causes the cell to swell and potentially lyse, or burst. The degree to which a particular cell is able to withstand changes in osmotic pressure is called tonicity. Cells that have a cell wall are better able to withstand subtle changes in osmotic pressure and maintain their shape. In hypertonic environments, cells that lack a cell wall can become dehydrated, causing crenation, or shriveling of the cell; the plasma membrane contracts and appears scalloped or notched (Figure 3.15). By contrast, cells that possess a cell wall undergo plasmolysis rather than crenation. In plasmolysis, the plasma membrane contracts and detaches from the cell wall, and there is a decrease in interior volume, but the cell wall remains intact, thus allowing Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 89 the cell to maintain some shape and integrity for a period of time (Figure 3.16). Likewise, cells that lack a cell wall are more prone to lysis in hypotonic environments. The presence of a cell wall allows the cell to maintain its shape and integrity for a longer time before lysing (Figure 3.16). FIGURE 3.15 In cells that lack a cell wall, changes in osmotic pressure can lead to crenation in hypertonic environments or cell lysis in hypotonic environments. FIGURE 3.16 In prokaryotic cells, the cell wall provides some protection against changes in osmotic pressure, allowing it to maintain its shape longer. The cell membrane is typically attached to the cell wall in an isotonic medium (left). In a hypertonic medium, the cell membrane detaches from the cell wall and contracts (plasmolysis) as water leaves the cell. In a hypotonic medium (right), the cell wall prevents the cell membrane from expanding to the point of bursting, although lysis will eventually occur if too much water is absorbed. CHECK YOUR UNDERSTANDING Explain the difference between cell morphology and arrangement. What advantages do cell walls provide prokaryotic cells? The Nucleoid All cellular life has a DNA genome organized into one or more chromosomes. Prokaryotic chromosomes are typically circular, haploid (unpaired), and not bound by a complex nuclear membrane. Prokaryotic DNA and DNA-associated 90 3 The Cell proteins are concentrated within the nucleoid region of the cell (Figure 3.17). In general, prokaryotic DNA interacts with nucleoid-associated proteins (NAPs) that assist in the organization and packaging of the chromosome. In bacteria, NAPs function similar to histones, which are the DNA-organizing proteins found in eukaryotic cells. In archaea, the nucleoid is organized by either NAPs or histone-like DNA organizing proteins. FIGURE 3.17 The nucleoid region (the area enclosed by the green dashed line) is a condensed area of DNA found within prokaryotic cells. Because of the density of the area, it does not readily stain and appears lighter in color when viewed with a transmission electron microscope. Plasmids Prokaryotic cells may also contain extrachromosomal DNA, or DNA that is not part of the chromosome. This extrachromosomal DNA is found in plasmids, which are small, circular, double-stranded DNA molecules. Cells that have plasmids often have hundreds of them within a single cell. Plasmids are more commonly found in bacteria; however, plasmids have been found in archaea and eukaryotic organisms. Plasmids often carry genes that confer advantageous traits such as antibiotic resistance; thus, they are important to the survival of the organism. We will discuss plasmids in more detail in Mechanisms of Microbial Genetics. Ribosomes All cellular life synthesizes proteins, and organisms in all three domains of life possess ribosomes, structures responsible for protein synthesis. However, ribosomes in each of the three domains are structurally different. Ribosomes, themselves, are constructed from proteins, along with ribosomal RNA (rRNA). Prokaryotic ribosomes are found in the cytoplasm. They are called 70S ribosomes because they have a size of 70S (Figure 3.18), whereas eukaryotic cytoplasmic ribosomes have a size of 80S. (The S stands for Svedberg unit, a measure of sedimentation in an ultracentrifuge, which is based on size, shape, and surface qualities of the structure being analyzed). Although they are the same size, bacterial and archaeal ribosomes have different proteins and rRNA molecules, and the archaeal versions are more similar to their eukaryotic counterparts than to those found in bacteria. FIGURE 3.18 Prokaryotic ribosomes (70S) are composed of two subunits: the 30S (small subunit) and the 50S (large subunit), each of which are composed of protein and rRNA components. Inclusions As single-celled organisms living in unstable environments, some prokaryotic cells have the ability to store excess nutrients within cytoplasmic structures called inclusions. Storing nutrients in a polymerized form is advantageous because it reduces the buildup of osmotic pressure that occurs as a cell accumulates solutes. Various types of inclusions store glycogen and starches, which contain carbon that cells can access for energy. Volutin granules, also called metachromatic granules because of their staining characteristics, are inclusions that store polymerized inorganic phosphate that can be used in metabolism and assist in the formation of biofilms. Microbes known to contain volutin granules include the archaea Methanosarcina, the bacterium Corynebacterium diphtheriae, and the unicellular eukaryotic alga Chlamydomonas. Sulfur granules, another type of inclusion, are found in sulfur bacteria of the genus Thiobacillus; these granules store elemental sulfur, which the bacteria use for metabolism. Occasionally, certain types of inclusions are surrounded by a phospholipid monolayer embedded with protein. Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 91 Polyhydroxybutyrate (PHB), which can be produced by species of Bacillus and Pseudomonas, is an example of an inclusion that displays this type of monolayer structure. Industrially, PHB has also been used as a source of biodegradable polymers for bioplastics. Several different types of inclusions are shown in Figure 3.19. FIGURE 3.19 Prokaryotic cells may have various types of inclusions. (a) A transmission electron micrograph of polyhydroxybutryrate lipid droplets. (b) A light micrograph of volutin granules. (c) A phase-contrast micrograph of sulfur granules. (d) A transmission electron micrograph of gas vacuoles. (e) A transmission electron micrograph of magnetosomes. (credit b, c, d: modification of work by American Society for Microbiology) Some prokaryotic cells have other types of inclusions that serve purposes other than nutrient storage. For example, some prokaryotic cells produce gas vacuoles, accumulations of small, protein-lined vesicles of gas. These gas vacuoles allow the prokaryotic cells that synthesize them to alter their buoyancy so that they can adjust their location in the water column. Magnetotactic bacteria, such as Magnetospirillum magnetotacticum, contain magnetosomes, which are inclusions of magnetic iron oxide or iron sulfide surrounded by a lipid layer. These allow cells to align along a magnetic field, aiding their movement (Figure 3.19). Cyanobacteria such as Anabaena cylindrica and bacteria such as Halothiobacillus neapolitanus produce carboxysome inclusions. Carboxysomes are composed of outer shells of thousands of protein subunits. Their interior is filled with ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. Both of these compounds are used for carbon metabolism. Some prokaryotic cells also possess carboxysomes that sequester functionally related enzymes in one location. These structures are considered proto-organelles because they compartmentalize important compounds or chemical reactions, much like many eukaryotic organelles. Endospores Bacterial cells are generally observed as vegetative cells, but some genera of bacteria have the ability to form endospores, structures that essentially protect the bacterial genome in a dormant state when environmental conditions are unfavorable. Endospores (not to be confused with the reproductive spores formed by fungi) allow some bacterial cells to survive long periods without food or water, as well as exposure to chemicals, extreme temperatures, and even radiation. Table 3.1 compares the characteristics of vegetative cells and endospores. 92 3 The Cell Characteristics of Vegetative Cells versus Endospores Vegetative Cells Endospores Sensitive to extreme temperatures Resistant to extreme temperatures and radiation and radiation Gram-positive Do not absorb Gram stain, only special endospore stains (see Staining Microscopic Specimens) Normal water content and enzymatic Dehydrated; no metabolic activity activity Capable of active growth and Dormant; no growth or metabolic activity metabolism TABLE 3.1 The process by which vegetative cells transform into endospores is called sporulation, and it generally begins when nutrients become depleted or environmental conditions become otherwise unfavorable (Figure 3.20). The process begins with the formation of a septum in the vegetative bacterial cell. The septum divides the cell asymmetrically, separating a DNA forespore from the mother cell. The forespore, which will form the core of the endospore, is essentially a copy of the cell’s chromosomes, and is separated from the mother cell by a second membrane. A cortex gradually forms around the forespore by laying down layers of calcium and dipicolinic acid between membranes. A protein coat then forms around the cortex while the DNA of the mother cell disintegrates. Further maturation of the endospore occurs with the formation of an outermost exosporium. The endospore is released upon disintegration of the mother cell, completing sporulation. FIGURE 3.20 (a) Sporulation begins following asymmetric cell division. The forespore becomes surrounded by a double layer of membrane, a cortex, and a protein coat, before being released as a mature endospore upon disintegration of the mother cell. (b) An electron micrograph of a Carboxydothermus hydrogenoformans endospore. (c) These Bacillus spp. cells are undergoing sporulation. The endospores have been visualized using Malachite Green stain. (credit b: modification of work by Jonathan Eisen) Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 93 Endospores of certain species have been shown to persist in a dormant state for extended periods of time, up to 17 thousands of years. However, when living conditions improve, endospores undergo germination, reentering a vegetative state. After germination, the cell becomes metabolically active again and is able to carry out all of its normal functions, including growth and cell division. Not all bacteria have the ability to form endospores; however, there are a number of clinically significant endospore- forming gram-positive bacteria of the genera Bacillus and Clostridium. These include B. anthracis, the causative 18 agent of anthrax, which produces endospores capable of surviving for many decades ; C. tetani (causes tetanus); C. difficile (causes pseudomembranous colitis); C. perfringens (causes gas gangrene); and C. botulinum (causes botulism). Pathogens such as these are particularly difficult to combat because their endospores are so hard to kill. Special sterilization methods for endospore-forming bacteria are discussed in Control of Microbial Growth. CHECK YOUR UNDERSTANDING What is an inclusion? What is the function of an endospore? Plasma Membrane Structures that enclose the cytoplasm and internal structures of the cell are known collectively as the cell envelope. In prokaryotic cells, the structures of the cell envelope vary depending on the type of cell and organism. Most (but not all) prokaryotic cells have a cell wall, but the makeup of this cell wall varies. All cells (prokaryotic and eukaryotic) have a plasma membrane (also called cytoplasmic membrane or cell membrane) that exhibits selective permeability, allowing some molecules to enter or leave the cell while restricting the passage of others. The structure of the plasma membrane is often described in terms of the fluid mosaic model, which refers to the ability of membrane components to move fluidly within the plane of the membrane, as well as the mosaic-like composition of the components, which include a diverse array of lipid and protein components (Figure 3.21). The plasma membrane structure of most bacterial and eukaryotic cell types is a bilayer composed mainly of phospholipids formed with ester linkages and proteins. These phospholipids and proteins have the ability to move laterally within the plane of the membranes as well as between the two phospholipid layers. FIGURE 3.21 The bacterial plasma membrane is a phospholipid bilayer with a variety of embedded proteins that perform various functions 17 F. Rothfuss, M Bender, R Conrad. “Survival and Activity of Bacteria in a Deep, Aged Lake Sediment (Lake Constance).” Microbial Ecology 33 no. 1 (1997):69–77. 18 R. Sinclair et al. “Persistence of Category A Select Agents in the Environment.” Applied and Environmental Microbiology 74 no. 3 (2008):555–563. 94 3 The Cell for the cell. Note the presence of glycoproteins and glycolipids, whose carbohydrate components extend out from the surface of the cell. The abundance and arrangement of these proteins and lipids can vary greatly between species. Archaeal membranes are fundamentally different from bacterial and eukaryotic membranes in a few significant ways. First, archaeal membrane phospholipids are formed with ether linkages, in contrast to the ester linkages found in bacterial or eukaryotic cell membranes. Second, archaeal phospholipids have branched chains, whereas those of bacterial and eukaryotic cells are straight chained. Finally, although some archaeal membranes can be formed of bilayers like those found in bacteria and eukaryotes, other archaeal plasma membranes are lipid monolayers. Proteins on the cell’s surface are important for a variety of functions, including cell-to-cell communication, and sensing environmental conditions and pathogenic virulence factors. Membrane proteins and phospholipids may have carbohydrates (sugars) associated with them and are called glycoproteins or glycolipids, respectively. These glycoprotein and glycolipid complexes extend out from the surface of the cell, allowing the cell to interact with the external environment (Figure 3.21). Glycoproteins and glycolipids in the plasma membrane can vary considerably in chemical composition among archaea, bacteria, and eukaryotes, allowing scientists to use them to characterize unique species. Plasma membranes from different cells types also contain unique phospholipids, which contain fatty acids. As described in Using Biochemistry to Identify Microorganisms, phospholipid-derived fatty acid analysis (PLFA) profiles can be used to identify unique types of cells based on differences in fatty acids. Archaea, bacteria, and eukaryotes each have a unique PFLA profile. Membrane Transport Mechanisms One of the most important functions of the plasma membrane is to control the transport of molecules into and out of the cell. Internal conditions must be maintained within a certain range despite any changes in the external environment. The transport of substances across the plasma membrane allows cells to do so. Cells use various modes of transport across the plasma membrane. For example, molecules moving from a higher concentration to a lower concentration with the concentration gradient are transported by simple diffusion, also known as passive transport (Figure 3.22). Some small molecules, like carbon dioxide, may cross the membrane bilayer directly by simple diffusion. However, charged molecules, as well as large molecules, need the help of carriers or channels in the membrane. These structures ferry molecules across the membrane, a process known as facilitated diffusion (Figure 3.23). Active transport occurs when cells move molecules across their membrane against concentration gradients (Figure 3.24). A major difference between passive and active transport is that active transport requires adenosine triphosphate (ATP) or other forms of energy to move molecules “uphill.” Therefore, active transport structures are often called “pumps.” FIGURE 3.22 Simple diffusion down a concentration gradient directly across the phospholipid bilayer. (credit: modification of work by Mariana Ruiz Villareal) Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 95 FIGURE 3.23 Facilitated diffusion down a concentration gradient through a membrane protein. (credit: modification of work by Mariana Ruiz Villareal) FIGURE 3.24 Active transport against a concentration gradient via a membrane pump that requires energy. (credit: modification of work by Mariana Ruiz Villareal) Group translocation also transports substances into bacterial cells. In this case, as a molecule moves into a cell against its concentration gradient, it is chemically modified so that it does not require transport against an unfavorable concentration gradient. A common example of this is the bacterial phosphotransferase system, a series of carriers that phosphorylates (i.e., adds phosphate ions to) glucose or other sugars upon entry into cells. Since the phosphorylation of sugars is required during the early stages of sugar metabolism, the phosphotransferase system is considered to be an energy neutral system. Photosynthetic Membrane Structures Some prokaryotic cells, namely cyanobacteria and photosynthetic bacteria, have membrane structures that enable them to perform photosynthesis. These structures consist of an infolding of the plasma membrane that encloses photosynthetic pigments such as green chlorophylls and bacteriochlorophylls. In cyanobacteria, these membrane structures are called thylakoids; in photosynthetic bacteria, they are called chromatophores, lamellae, or chlorosomes. Cell Wall The primary function of the cell wall is to protect the cell from harsh conditions in the outside environment. When present, there are notable similarities and differences among the cell walls of archaea, bacteria, and eukaryotes. The major component of bacterial cell walls is called peptidoglycan (or murein); it is only found in bacteria. Structurally, peptidoglycan resembles a layer of meshwork or fabric (Figure 3.25). Each layer is composed of long chains of alternating molecules of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). The structure of the long chains has significant two-dimensional tensile strength due to the formation of peptide bridges that 96 3 The Cell connect NAG and NAM within each peptidoglycan layer. In gram-negative bacteria, tetrapeptide chains extending from each NAM unit are directly cross-linked, whereas in gram-positive bacteria, these tetrapeptide chains are linked by pentaglycine cross-bridges. Peptidoglycan subunits are made inside of the bacterial cell and then exported and assembled in layers, giving the cell its shape. Since peptidoglycan is unique to bacteria, many antibiotic drugs are designed to interfere with peptidoglycan synthesis, weakening the cell wall and making bacterial cells more susceptible to the effects of osmotic pressure (see Mechanisms of Antibacterial Drugs). In addition, certain cells of the human immune system are able “recognize” bacterial pathogens by detecting peptidoglycan on the surface of a bacterial cell; these cells then engulf and destroy the bacterial cell, using enzymes such as lysozyme, which breaks down and digests the peptidoglycan in their cell walls (see Pathogen Recognition and Phagocytosis). FIGURE 3.25 Peptidoglycan is composed of polymers of alternating NAM and NAG subunits, which are cross-linked by peptide bridges linking NAM subunits from various glycan chains. This provides the cell wall with tensile strength in two dimensions. The Gram staining protocol (see Staining Microscopic Specimens) is used to differentiate two common types of cell wall structures (Figure 3.26). Gram-positive cells have a cell wall consisting of many layers of peptidoglycan totaling 30–100 nm in thickness. These peptidoglycan layers are commonly embedded with teichoic acids (TAs), 19 carbohydrate chains that extend through and beyond the peptidoglycan layer. TA is thought to stabilize peptidoglycan by increasing its rigidity. TA also plays a role in the ability of pathogenic gram-positive bacteria such as Streptococcus to bind to certain proteins on the surface of host cells, enhancing their ability to cause infection. In addition to peptidoglycan and TAs, bacteria of the family Mycobacteriaceae have an external layer of waxy mycolic acids in their cell wall; as described in Staining Microscopic Specimens, these bacteria are referred to as acid-fast, since acid-fast stains must be used to penetrate the mycolic acid layer for purposes of microscopy (Figure 3.27). 19 T.J. Silhavy, D. Kahne, S. Walker. “The Bacterial Cell Envelope.” Cold Spring Harbor Perspectives in Biology 2 no. 5 (2010):a000414. Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 97 FIGURE 3.26 Bacteria contain two common cell wall structural types. Gram-positive cell walls are structurally simple, containing a thick 20 layer of peptidoglycan with embedded teichoic acid external to the plasma membrane. Gram-negative cell walls are structurally more complex, containing a thin layer of peptidoglycan and an outer membrane containing lipopolysaccharide. (credit: modification of work by “Franciscosp2”/Wikimedia Commons) FIGURE 3.27 (a) Some gram-positive bacteria, including members of the Mycobacteriaceae, produce waxy mycolic acids found exterior to their structurally-distinct peptidoglycan. (b) The acid-fast staining protocol detects the presence of cell walls that are rich in mycolic acid. Acid-fast cells are stained red by carbolfuschin. (credit a: modification of work by “Franciscosp2”/Wikimedia Commons; credit b: modification of work by Centers for Disease Control and Prevention) 21 Gram-negative cells have a much thinner layer of peptidoglycan (no more than about 4 nm thick ) than gram- positive cells, and the overall structure of their cell envelope is more complex. In gram-negative cells, a gel-like matrix occupies the periplasmic space between the cell wall and the plasma membrane, and there is a second lipid bilayer called the outer membrane, which is external to the peptidoglycan layer (Figure 3.26). This outer membrane is attached to the peptidoglycan by murein lipoprotein. The outer leaflet of the outer membrane contains the molecule lipopolysaccharide (LPS), which functions as an endotoxin in infections involving gram-negative bacteria, contributing to symptoms such as fever, hemorrhaging, and septic shock. Each LPS molecule is composed of Lipid A, a core polysaccharide, and an O side chain that is composed of sugar-like molecules that comprise the external face of the LPS (Figure 3.28). The composition of the O side chain varies between different species and strains of bacteria. Parts of the O side chain called antigens can be detected using serological or immunological tests to identify specific pathogenic strains like Escherichia coli O157:H7, a deadly strain of bacteria that causes bloody diarrhea and kidney failure. 20 B. Zuber et al. “Granular Layer in the Periplasmic Space of Gram-Positive Bacteria and Fine Structures of Enterococcus gallinarum and Streptococcus gordonii Septa Revealed by Cryo-Electron Microscopy of Vitreous Sections.” Journal of Bacteriology 188 no. 18 (2006):6652–6660 21 L. Gana, S. Chena, G.J. Jensena. “Molecular Organization of Gram-Negative Peptidoglycan.” Proceedings of the National Academy of Sciences of the United States of America 105 no. 48 (2008):18953–18957. 98 3 The Cell FIGURE 3.28 The outer membrane of a gram-negative bacterial cell contains lipopolysaccharide (LPS), a toxin composed of Lipid A embedded in the outer membrane, a core polysaccharide, and the O side chain. Archaeal cell wall structure differs from that of bacteria in several significant ways. First, archaeal cell walls do not contain peptidoglycan; instead, they contain a similar polymer called pseudopeptidoglycan (pseudomurein) in which NAM is replaced with a different subunit. Other archaea may have a layer of glycoproteins or polysaccharides that serves as the cell wall instead of pseudopeptidoglycan. Last, as is the case with some bacterial species, there are a few archaea that appear to lack cell walls entirely. Glycocalyces and S-Layers Although most prokaryotic cells have cell walls, some may have additional cell envelope structures exterior to the cell wall, such as glycocalyces and S-layers. A glycocalyx is a sugar coat, of which there are two important types: capsules and slime layers. A capsule is an organized layer located outside of the cell wall and usually composed of polysaccharides or proteins (Figure 3.29). A slime layer is a less tightly organized layer that is only loosely attached to the cell wall and can be more easily washed off. Slime layers may be composed of polysaccharides, glycoproteins, or glycolipids. Glycocalyces allows cells to adhere to surfaces, aiding in the formation of biofilms (colonies of microbes that form in layers on surfaces). In nature, most microbes live in mixed communities within biofilms, partly because the biofilm affords them some level of protection. Biofilms generally hold water like a sponge, preventing desiccation. They also protect cells from predation and hinder the action of antibiotics and disinfectants. All of these properties are advantageous to the microbes living in a biofilm, but they present challenges in a clinical setting, where the goal is often to eliminate microbes. Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 99 FIGURE 3.29 (a) Capsules are a type of glycocalyx composed of an organized layer of polysaccharides. (b) A capsule stain of Pseudomonas aeruginosa, a bacterial pathogen capable of causing many different types of infections in humans. (credit b: modification of work by American Society for Microbiology) The ability to produce a capsule can contribute to a microbe’s pathogenicity (ability to cause disease) because the capsule can make it more difficult for phagocytic cells (such as white blood cells) to engulf and kill the microorganism. Streptococcus pneumoniae, for example, produces a capsule that is well known to aid in this bacterium’s pathogenicity. As explained in Staining Microscopic specimens, capsules are difficult to stain for microscopy; negative staining techniques are typically used. An S-layer is another type of cell envelope structure; it is composed of a mixture of structural proteins and glycoproteins. In bacteria, S-layers are found outside the cell wall, but in some archaea, the S-layer serves as the cell wall. The exact function of S-layers is not entirely understood, and they are difficult to study; but available evidence suggests that they may play a variety of functions in different prokaryotic cells, such as helping the cell withstand osmotic pressure and, for certain pathogens, interacting with the host immune system. CLINICAL FOCUS Part 3 After diagnosing Barbara with pneumonia, the PA writes her a prescription for amoxicillin, a commonly- prescribed type of penicillin derivative. More than a week later, despite taking the full course as directed, Barbara still feels weak and is not fully recovered, although she is still able to get through her daily activities. She returns to the health center for a follow-up visit. Many types of bacteria, fungi, and viruses can cause pneumonia. Amoxicillin targets the peptidoglycan of bacterial cell walls. Since the amoxicillin has not resolved Barbara’s symptoms, the PA concludes that the causative agent probably lacks peptidoglycan, meaning that the pathogen could be a virus, a fungus, or a bacterium that lacks peptidoglycan. Another possibility is that the pathogen is a bacterium containing peptidoglycan but has developed resistance to amoxicillin. How can the PA definitively identify the cause of Barbara’s pneumonia? What form of treatment should the PA prescribe, given that the amoxicillin was ineffective? Jump to the next Clinical Focus box. Go back to the previous Clinical Focus box. Filamentous Appendages Many bacterial cells have protein appendages embedded within their cell envelopes that extend outward, allowing interaction with the environment. These appendages can attach to other surfaces, transfer DNA, or provide movement. Filamentous appendages include fimbriae, pili, and flagella. 100 3 The Cell Fimbriae and Pili Fimbriae and pili are structurally similar and, because differentiation between the two is problematic, these terms 22 23 are often used interchangeably. The term fimbriae commonly refers to short bristle-like proteins projecting from the cell surface by the hundreds. Fimbriae enable a cell to attach to surfaces and to other cells. For pathogenic bacteria, adherence to host cells is important for colonization, infectivity, and virulence. Adherence to surfaces is also important in biofilm formation. The term pili (singular: pilus) commonly refers to longer, less numerous protein appendages that aid in attachment to surfaces (Figure 3.30). A specific type of pilus, called the F pilus or sex pilus, is important in the transfer of DNA between bacterial cells, which occurs between members of the same generation when two cells physically transfer or exchange parts of their respective genomes (see How Asexual Prokaryotes Achieve Genetic Diversity). FIGURE 3.30 Bacteria may produce two different types of protein appendages that aid in surface attachment. Fimbriae typically are more numerous and shorter, whereas pili (shown here) are longer and less numerous per cell. (credit: modification of work by American Society for Microbiology) MICRO CONNECTIONS Group A Strep Before the structure and function of the various components of the bacterial cell envelope were well understood, scientists were already using cell envelope characteristics to classify bacteria. In 1933, Rebecca Lancefield proposed a method for serotyping various β-hemolytic strains of Streptococcus species using an agglutination assay, a technique using the clumping of bacteria to detect specific cell-surface antigens. In doing so, Lancefield discovered that one group of S. pyogenes, found in Group A, was associated with a variety of human diseases. She determined that various strains of Group A strep could be distinguished from each other based on variations in specific cell surface proteins that she named M proteins. Today, more than 80 different strains of Group A strep have been identified based on M proteins. Various strains of Group A strep are associated with a wide variety of human infections, including streptococcal pharyngitis (strep throat), impetigo, toxic shock syndrome, scarlet fever, rheumatic fever, and necrotizing fasciitis. The M protein is an important virulence factor for Group A strep, helping these strains evade the immune system. Changes in M proteins appear to alter the infectivity of a particular strain of Group A strep. Flagella Flagella are structures used by cells to move in aqueous environments. Bacterial flagella act like propellers. They are stiff spiral filaments composed of flagellin protein subunits that extend outward from the cell and spin in solution. The basal body is the motor for the flagellum and is embedded in the plasma membrane (Figure 3.31). A hook region connects the basal body to the filament. Gram-positive and gram-negative bacteria have different basal body configurations due to differences in cell wall structure. Different types of motile bacteria exhibit different arrangements of flagella (Figure 3.32). A bacterium with a singular flagellum, typically located at one end of the cell (polar), is said to have a monotrichous flagellum. An example of a 22 J.A. Garnetta et al. “Structural Insights Into the Biogenesis and Biofilm Formation by the Escherichia coli Common Pilus.” Proceedings of the National Academy of Sciences of the United States of America 109 no. 10 (2012):3950–3955. 23 T. Proft, E.N. Baker. “Pili in Gram-Negative and Gram-Positive Bacteria—Structure, Assembly and Their Role in Disease.” Cellular and Molecular Life Sciences 66 (2009):613. Access for free at openstax.org  3.3 Unique Characteristics of Prokaryotic Cells 101 monotrichously flagellated bacterial pathogen is Vibrio cholerae, the gram-negative bacterium that causes cholera. Cells with amphitrichous flagella have a flagellum or tufts of flagella at each end. An example is Spirillum minor, the cause of spirillary (Asian) rat-bite fever or sodoku. Cells with lophotrichous flagella have a tuft at one end of the cell. The gram-negative bacillus Pseudomonas aeruginosa, an opportunistic pathogen known for causing many infections, including “swimmer’s ear” and burn wound infections, has lophotrichous flagella. Flagella that cover the entire surface of a bacterial cell are called peritrichous flagella. The gram-negative bacterium E. coli shows a peritrichous arrangement of flagella. FIGURE 3.31 The basic structure of a bacterial flagellum consists of a basal body, hook, and filament. The basal body composition and arrangement differ between gram-positive and gram-negative bacteria. (credit: modification of work by “LadyofHats”/Mariana Ruiz Villareal) FIGURE 3.32 Flagellated bacteria may exhibit multiple arrangements of their flagella. Common arrangements include monotrichous, amphitrichous, lophotrichous, or peritrichous. Directional movement depends on the configuration of the flagella. Bacteria can move in response to a variety of environmental signals, including light (phototaxis), magnetic fields (magnetotaxis) using magnetosomes, and, most commonly, chemical gradients (chemotaxis). Purposeful movement toward a chemical attractant, like a food source, or away from a repellent, like a poisonous chemical, is achieved by increasing the length of runs and decreasing the length of tumbles. When running, flagella rotate in a counterclockwise direction, allowing the bacterial cell to move forward. In a peritrichous bacterium, the flagella are all bundled together in a very streamlined way (Figure 3.33), allowing for efficient movement. When tumbling, flagella are splayed out while rotating in a clockwise direction, creating a looping motion and preventing meaningful forward movement but reorienting the cell toward the direction of the attractant. When an attractant exists, runs and tumbles still occur; however, the length of runs is longer, while the length of the tumbles is reduced, allowing overall movement toward the higher concentration of the attractant. When no chemical gradient exists, the lengths of runs and tumbles are more equal, and overall movement is more random (Figure 3.34). 102 3 The Cell FIGURE 3.33 Bacteria achieve directional movement by changing the rotation of their flagella. In a cell with peritrichous flagella, the flagella bundle when they rotate in a counterclockwise direction, resulting in a run. However, when the flagella rotate in a clockwise direction, the flagella are no longer bundled, resulting in tumbles. FIGURE 3.34 Without a chemical gradient, flagellar rotation cycles between counterclockwise (run) and clockwise (tumble) with no overall directional movement. However, when a chemical gradient of an attractant exists, the length of runs is extended, while the length of tumbles is decreased. This leads to chemotaxis: an overall directional movement toward the higher concentration of the attractant. CHECK YOUR UNDERSTANDING What is the peptidoglycan layer and how does it differ between gram-positive and gram-negative bacteria? Compare and contrast monotrichous, amphitrichous, lophotrichous, and peritrichous flagella. Access for free at openstax.org  3.4 Unique Characteristics of Eukaryotic Cells 103 3.4 Unique Characteristics of Eukaryotic Cells LEARNING OBJECTIVES By the end of this section, you will be able to: Explain the distinguishing characteristics of eukaryotic cells Describe internal and external structures of eukaryotic cells in terms of their physical structure, chemical structure, and function Identify and describe structures and organelles unique to eukaryotic cells Compare and contrast similar structures found in prokaryotic and eukaryotic cells Describe the processes of eukaryotic mitosis and meiosis, and compare to prokaryotic binary fission Eukaryotic organisms include protozoans, algae, fungi, plants, and animals. Some eukaryotic cells are independent, single-celled microorganisms, whereas others are part of multicellular organisms. The cells of eukaryotic organisms have several distinguishing characteristics. Above all, eukaryotic cells are defined by the presence of a nucleus surrounded by a complex nuclear membrane. Also, eukaryotic cells are characterized by the presence of membrane-bound organelles in the cytoplasm. Organelles such as mitochondria, the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes are held in place by the cytoskeleton, an internal network that supports transport of intracellular components and helps maintain cell shape (Figure 3.35). The genome of eukaryotic cells is packaged in multiple, rod-shaped chromosomes as opposed to the single, circular-shaped chromosome that characterizes most prokaryotic cells. Table 3.2 compares the characteristics of eukaryotic cell structures with those of bacteria and archaea. FIGURE 3.35 An illustration of a generalized, single-celled eukaryotic organism. Note that cells of eukaryotic organisms vary greatly in terms of structure and function, and a particular cell may not have all of the structures shown here. 104 3 The Cell Summary of Cell Structures Cell Structure Prokaryotes Eukaryotes Bacteria Archaea Size ~0.5–1 μm ~0.5–1 μm ~5–20 μm Surface area-to- High High Low volume ratio Nucleus No No Yes Genome Single Single chromosome Multiple chromosomes characteristics chromosome Circular Linear Circular Haploid Haploid or diploid Haploid Contains histones Contains histones Lacks histones Cell division Binary fission Binary fission Mitosis, meiosis Membrane lipid Ester-linked Ether-linked Ester-linked composition Straight-chain Branched isoprenoids Straight-chain fatty acids fatty acids Bilayer or monolayer Sterols Bilayer Bilayer Cell wall Peptidoglycan, or Pseudopeptidoglycan, or Cellulose (plants, some composition None Glycopeptide, or algae) Polysaccharide, or Chitin (fungi) Protein (S-layer), or Silica (some algae) None Most others lack cell walls Motility Rigid spiral flagella Rigid spiral flagella composed Flexible flagella and cilia structures composed of flagellin of archaeal flagellins composed of microtubules Membrane- No No Yes bound organelles Endomembrane No No Yes (ER, Golgi, lysosomes) system Ribosomes 70S 70S 80S in cytoplasm and rough ER 70S in mitochondria, chloroplasts TABLE 3.2 Access for free at openstax.org  3.4 Unique Characteristics of Eukaryotic Cells 105 Cell Morphologies Eukaryotic cells display a wide variety of different cell morphologies. Possible shapes include spheroid, ovoid, cuboidal, cylindrical, flat, lenticular, fusiform, discoidal, crescent, ring stellate, and polygonal (Figure 3.36). Some eukaryotic cells are irregular in shape, and some are capable of changing shape. The shape of a particular type of eukaryotic cell may be influenced by factors such as its primary function, the organization of its cytoskeleton, the viscosity of its cytoplasm, the rigidity of its cell membrane or cell wall (if it has one), and the physical pressure exerted on it by the surrounding environment and/or adjoining cells. FIGURE 3.36 Eukaryotic cells come in a variety of cell shapes. (a) Spheroid Chromulina alga. (b) Fusiform shaped Trypanosoma. (c) Bell- shaped Vorticella. (d) Ovoid Paramecium. (e) Ring-shaped Plasmodium ovale. (credit a: modification of work by NOAA; credit b, e: modification of work by Centers for Disease Control and Prevention) CHECK YOUR UNDERSTANDING Identify two differences between eukaryotic and prokaryotic cells. Nucleus Unlike prokaryotic cells, in which DNA is loosely contained in the nucleoid region, eukaryotic cells possess a nucleus, which is surrounded by a complex nuclear membrane that houses the DNA genome (Figure 3.37). By containing the cell’s DNA, the nucleus ultimately controls all activities of the cell and also serves an essential role in reproduction and heredity. Eukaryotic cells typically have their DNA organized into multiple linear chromosomes. The DNA within the nucleus is highly organized and condensed to fit inside the nucleus, which is accomplished by wrapping the DNA around proteins called histones. 106 3 The Cell FIGURE 3.37 Eukaryotic cells have a well-defined nucleus surrounded by a nuclear membrane. The nucleus of this mammalian lung cell is located in the bottom right corner of the image. The large, dark, oval-shaped structure within the nucleus is the nucleolus. Although most eukaryotic cells have only one nucleus, exceptions exist. For example, protozoans of the genus Paramecium typically have two complete nuclei: a small nucleus that is used for reproduction (micronucleus) and a large nucleus that directs cellular metabolism (macronucleus). Additionally, some fungi transiently form cells with two nuclei, called heterokaryotic cells, during sexual reproduction. Cells whose nuclei divide, but whose cytoplasm does not, are called coenocytes. The nucleus is bound by a complex nuclear membrane, often called the nuclear envelope, that consists of two distinct lipid bilayers that are contiguous with each other (Figure 3.38). Despite these connections between the inner and outer membranes, each membrane contains unique lipids and proteins on its inner and outer surfaces. The nuclear envelope contains nuclear pores, which are large, rosette-shaped protein complexes that control the movement of materials into and out of the nucleus. The overall shape of the nucleus is determined by the nuclear lamina, a meshwork of intermediate filaments found just inside the nuclear envelope membranes. Outside the nucleus, additional intermediate filaments form a looser mesh and serve to anchor the nucleus in position within the cell. FIGURE 3.38 In this fluorescent microscope image, all the intermediate filaments have been stained with a bright green fluorescent stain. The nuclear lamina is the intense bright green ring around the faint red nuclei. Eukaryotes are able to multiply through asexual reproduction, during which a single parent cell becomes two identical daughter cells. This process of clonal reproduction is called mitosis. Although mitosis may sound similar to asexual binary fission in prokaryotes, the processes are very different. In contrast to the single chromosome in most prokaryotes, eukaryotic cells possess multiple chromosomes that must be replicated and strategically divided between daughter cells. Therefore, mitosis is a much more complex cellular process than binary fission. The eukaryotic cell cycle is an ordered and carefully regulated series of events involving cell growth, DNA replication, and cell division to produce two clonal daughter cells. One “turn” or cycle of the cell cycle consist of two general phases: interphase and the mitotic phase. (Figure 3.39). During interphase, the cell is not dividing, but rather is undergoing normal growth processes and DNA is replicated preparing for cell division. The three stages of Access for free at openstax.org  3.4 Unique Characteristics of Eukaryotic Cells 107 interphase are called G1, S, and G2. FIGURE 3.39 The cell cycle consists of interphase and the mitotic phase. During interphase, the cell grows and the nuclear DNA is duplicated. Interphase is followed by the mitotic phase. During the mitotic phase, the duplicated chromosomes are segregated and distributed into daughter nuclei. The cytoplasm is usually divided as well, resulting in two daughter cells. (attribution: Biology 2e, Rice University, OpenStax, under CC BY 4.0 license) The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, move to opposite poles of the cell, and then are divided into two identical daughter cells. The first portion of the mitotic phase is called karyokinesis, or nuclear division. Karyokinesis is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure 3.40). The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into the two daughter cells. LINK TO LEARNING Go to this University of Arizona website about the stages of mitosis (https://openstax.org/l/CellCycleMito) to learn more. 108 3 The Cell FIGURE 3.40 Karyokinesis (or mitosis) is divided into five stages—prophase, prometaphase, metaphase, anaphase, and telophase. The pictures at the bottom were taken by fluorescence microscopy (hence, the black background) of cells artificially stained by fluorescent dyes: blue fluorescence indicates DNA (chromosomes) and green fluorescence indicates microtubules (spindle apparatus). (attribution: Biology 2e, Rice University, OpenStax, under CC BY 4.0 license) In addition to the mitotic asexual reproduction described above, most eukaryotic microorganisms also have the option of sexual reproduction involving meiosis. Although mitosis and meiosis both require DNA replication, nuclear division, and share procedural similarities, there are important differences between the process and outcomes (Figure 3.41). Access for free at openstax.org  3.4 Unique Characteristics of Eukaryotic Cells 109 FIGURE 3.41 Meiosis and mitosis are both preceded by one cycle of DNA replication; however, meiosis includes two nuclear divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells resulting from mitosis are diploid and identical to the parent cell. (credit: Biology 2e, Rice University, OpenStax, under CC BY 4.0 license) In contrast to the single nuclear division that completes mitosis, meiosis involves two separate nuclear divisions. Rather than creating two clonal daughter cells, the goal of meiosis is to create four genetically-distinct gametes, with each gamete possessing half the number of chromosomes found in the original cell. This strategic chromosome reduction is essential for the fertilization that occurs during sexual reproduction to produce in a zygote with a full complement of chromosomes. Nucleolus The nucleolus is a dense region within the nucleus where ribosomal RNA (rRNA) biosynthesis occurs. In addition, the nucleolus is also the site where assembly of ribosomes begins. Preribosomal complexes are assembled from rRNA and proteins in the nucleolus; they are then transported out to the cytoplasm, where ribosome assembly is completed (Figure 3.42). 110 3 The Cell FIGURE 3.42 (a) The nucleolus is the dark, dense area within the nucleus. It is the site of rRNA synthesis and preribosomal assembly. (b) Electron micrograph showing the nucleolus. Ribosomes Ribosomes found in eukaryotic organelles such as mitochondria or chloroplasts have 70S ribosomes—the same size as prokaryotic ribosomes. However, nonorganelle-associated ribosomes in eukaryotic cells are 80S ribosomes, composed of a 40S small subunit and a 60S large subunit. In terms of size and composition, this makes them distinct from the ribosomes of prokaryotic cells. The two types of nonorganelle-associated eukaryotic ribosomes are defined by their location in the cell: free ribosomes and membrane-bound ribosomes. Free ribosomes are found in the cytoplasm and serve to synthesize water-soluble proteins; membrane-bound ribosomes are found attached to the rough endoplasmic reticulum and make proteins for insertion into the cell membrane or proteins destined for export from the cell. The differences between eukaryotic and prokaryotic ribosomes are clinically relevant because certain antibiotic drugs are designed to target one or the other. For example, cycloheximide targets eukaryotic action, whereas 24 chloramphenicol targets prokaryotic ribosomes. Since human cells are eukaryotic, they generally are not harmed by antibiotics that destroy the prokaryotic ribosomes in bacteria. However, sometimes negative side effects may occur because mitochondria in human cells contain prokaryotic ribosomes. Endomembrane System The endomembrane system, unique to eukaryotic cells, is a series of membranous tubules, sacs, and flattened disks that synthesize many cell components and move materials around within the cell (Figure 3.43). Because of their larger cell size, eukaryotic cells require this system to transport materials that cannot be dispersed by diffusion alone. The endomembrane system comprises several organelles and connections between them, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles. 24 A.E. Barnhill, M.T. Brewer, S.A. Carlson. “Adverse Effects of Antimicrobials via Predictable or Idiosyncratic Inhibition of Host Mitochondrial Components.” Antimicrobial Agents and Chemotherapy 56 no. 8 (2012):4046–4051. Access for free at openstax.org  3.4 Unique Characteristics of Eukaryotic Cells 111 FIGURE 3.43 The endomembrane system is composed of a series of membranous intracellular structures that facilitate movement of materials throughout the cell and to the cell membrane. Endoplasmic Reticulum The endoplasmic reticulum (ER) is an interconnected array of tubules and cisternae (flattened sacs) with a single lipid bilayer (Figure 3.44). The spaces inside of the cisternae are called lumen of the ER. There are two types of ER, rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER). These two different types of ER are sites for the synthesis of distinctly different types of molecules. RER is studded with ribosomes bound on the cytoplasmic side of the membrane. These ribosomes make proteins destined for the plasma membrane (Figure 3.44). Following synthesis, these proteins are inserted into the membrane of the RER. Small sacs of the RER containing these newly synthesized proteins then bud off as transport vesicles and move either to the Golgi apparatus for further processing, directly to the plasma membrane, to the membrane of another organelle, or out of the cell. Transport vesicles are single-lipid, bilayer, membranous spheres with hollow interiors that carry molecules. SER does not have ribosomes and, therefore, appears “smooth.” It is involved in biosynthesis of lipids, carbohydrate metabolism, and detoxification of toxic compounds within the cell. FIGURE 3.44 The rough endoplasmic reticulum is studded with ribosomes for the synthesis of membrane proteins (which give it its rough appearance). Golgi Apparatus The Golgi apparatus was discovered within the endomembrane system in 1898 by Italian scientist Camillo Golgi (1843–1926), who developed a novel staining technique that showed stacked membrane structures within the cells of Plasmodium, the causative agent of malaria. The Golgi apparatus is composed of a series of membranous disks called dictyosomes, each having a single lipid bilayer, that are stacked together (Figure 3.45). Enzymes in the Golgi apparatus modify lipids and proteins transported from the ER to the Golgi, often adding carbohydrate components to them, producing glycolipids, glycoproteins, or proteoglycans. Glycolipids and glycoproteins are often inserted into the plasma membrane and are important for signal recognition by other cells or infectious particles. Different types of cells can be distinguished from one another by the structure and arrangement of the glycolipids and glycoproteins contained in their plasma membranes. These glycolipids and glycoproteins commonly also serve as cell surface receptors. 112 3 The Cell Transport vesicles leaving the ER fuse with a Golgi apparatus on its receiving, or cis, face. The proteins are processed within the Golgi apparatus, and then additional transport vesicles containing the modified proteins and lipids pinch off from th