BioCh21.docx

Phenomenon The plot could come from a horror movie. They are silent, invisible, always in the background. At first, they do no harm. Then something small happens. Perhaps a new animal arrives in the neighborhood, one that becomes their ideal host, and they stop being harmless. What are "they"? They...

Phenomenon The plot could come from a horror movie. They are silent, invisible, always in the background. At first, they do no harm. Then something small happens. Perhaps a new animal arrives in the neighborhood, one that becomes their ideal host, and they stop being harmless. What are "they"? They are the microscopic organisms, or microbes, with whom we share this planet. In fact, these organisms actually dominate the planet. They are found everywhere, from the cleanest home to the most extreme environments on earth Most of the time, their actions are harm­ less or even helpful. In nature, they help to recycle dead organic material, such as when they break down a dead tree to help enrich the soil. Microbes known as bacteria also live closely with plants and animals. In fact, the human body may be home to more bacterial cells than human cells! Centuries ago, Europeans first made their way into North and South America. They brought horses and guns, both of which were unknown to the native peoples. Unwittingly, they also brought along microscopic cargo that was to prove far deadlier than any weapon. For the first time, Native Americans were exposed to the infectious diseases small­ pox, cholera, and influenza. The Europeans had lived with these diseases for centuries, but the native peoples had not, andhadno immunity to them. The toll was devastating. These microscopic pathogens laid waste to indigenous civilizations in just decades. Some diseases, such as Zika and Ebola, are caused by viruses. Others, such as cholera, are caused by bacteria that infect food and drinking water. Malaria-among the deadliest killers of children-is the result of a unicellular eukaryote carried by mosquitoes in tropical regions In many cases, modern medicine has developed effective ways to cure or prevent these diseases. Yet that has not always pre­ vented these diseases from breaking out of the background to produce mass epidemics. Sometimes a disease spreads so quickly that it is out of control before public health authori­ ties realize it has become a problem. For oth­ ers, preventive measures like vaccines have become so effective that people lose sight of just how dangerous these diseases can be. And tragically, many poor and underdevel­ oped regions of the world lack the resources to prevent the spread of disease and to react effectively when an epidemic threatens. What are the types of microscopic organ­ isms responsible for such diseases and how do they differ from one another? Just as importantly, how can understanding these microbes help us to control them and to pre­ vent new outbreaks of disease? How do viruses reproduce? What happens after a virus infects a cell? How do viruses cause disease? Can viruses be considered living things? VOCABULARY virus • capsid • lytic infection • bacteriophage lysogenic infection • prophage • retrovirus Imagine that you have been presented with a great puzzle. Farmers have begun to lose their valuable tobacco crop to a disease that causes infected leaves to wither and die, killing the plants. You take leaves from a diseased plant and crush them to produce a liquid extract. You place a few drops of that liquid on the leaves of healthy plants. A few days later, these leaves also turn yellow and die. You use a light microscope to look for a germ that might cause the disease, but none can be seen. In fact, when even the tiniest of cells are filtered out of the liquid, a drop of it still causes the dis­ ease. You figure the liquid must contain disease-causing agents so small that they are not visible under the microscope and can pass right through the filter. What do you do next? How do you deal with something invisible but deadly? What Is a Virus? If you think you know the answer to this puzzle, congratulations! You're walking in the footsteps of a 28-year-old Russian biologist, Dmitri lvanovski. In 1892, lvanovski showed that the cause of this plant disease-called tobacco mosaic disease-was found in the liquid extracted from infected plants. But what was in the liquid? Discovery of Viruses In 1897, Dutch scientist Martinus Beijerinck suggested that tiny particles in the juice caused the dis­ ease, and he named these particles viruses, after a Latin word for "poison." Then, in 1935, the American biochemist Wendell Stanley isolated crystals of tobacco mosaic virus. Living organisms do not crystallize, so Stanley inferred that viruses were not truly alive. This is a conclusion that biologists still recognize as being valid today. A virus is a nonliving particle made of proteins, nucleic acids, and sometimes lipids. Viruses can reproduce only by infecting living cells Structure and Composition Viruses are very different from living cells, and are so small they can be seen only with the aid of a powerful electron microscope. Viruses differ widely in terms of size and structure, as you can see in Figure 21-1. Viruses contain genetic information in the form of RNA or DNA, surrounded by a protein coat known as a capsid. Some viruses, such as the influenza virus, also have a membrane surrounding the capsid. The simplest viruses con­ tain only a few genes, whereas the most complex may have hundreds. CHECK POINT Explain How did scientists conclude that viruses are not alive? T4Bacteriophage Tobacco Mosaic Virus Influenza Virus How Do Viruses Differ in Structure? Make models of two of the viruses shown in Figure 21-1. Label the parts of each of your virus models. Measure and record the length of each of your virus models in centimeters. Convert the length of each model into nanome­ ters by using the following formula: 1 cm = 10 million nm. Measure the actual length of each virus you modeled. Divide the length of each model by the length of the actual virus to determine how much larger each model is than the virus it represents. Viral Infections If you have access to a personal computer, you may know that they can easily be infected by pieces of code known as computer viruses. These usually enter a computer system by trickery, masquerading as an email attachment or an application program. Once they gain entry to a system, they can "reproduce" by making copies of their own code, and can even spread to other computers by instructing the operating system to send these copies to other computers on a network. The viruses that infect living cells work in ways that are remarkably similar to this, as described in Figure 21-2. To enter a host cell, most viruses have proteins on their surfaces that bind to receptors on a cell. These proteins "trick" the cell to take in the virus. Once inside the cell, the virus makes copies of itself that can spread to other cells, sometimes destroying the host cell in the process. Nearly every type of organism, whether plant, animal, or bacterium, can be infected by viruses. After a virus has entered a host cell, what happens? Inside living cells, viruses use their genetic information to reproduce. Some viruses replicate immediately, while others initially persist in an inactive state within the host. These two patterns of infection are called lytic infection and lysogenic infection respectively. How Viruses Enter Living CellsViruses gain entry to cells by "tricking" their hosts. First the host cell. takes in the virus, and then it follows the harmful instructions the virus contains. Lytic Infection In a lytic infection, a virus enters a bacterial cell, makes copies of itself, and causes the cell to burst, or lyse. T4, a bac­ terial virus, or bacteriophage, causes just such an infection. The virus binds to the surface of a bacterium, injects its DNA into the cell, and then begins to make messenger RNA (mRNA) from its own genes. These mRNAs are translated into proteins that act like a molecular wrecking crew, chopping up the cell's DNA. Under the control of viral genes, the host cell now makes thou­ sands of copies of viral nucleic acid and capsid proteins, enabling the virus to reproduce. Before long, the infected cell lyses, releasing hundreds of virus particles that may go on to infect other cells. Lysogenic Infection Some bacterial viruses, including the bacteriophage lambda, cause a 1lysogenic infection, in which a host cell is not immediately taken over. Instead, the viral nucleic acid is inserted into the host cell's DNA, where it is replicated along with the host DNA without damaging the host. Bacteriophage DNA that becomes embedded in the bacterial host's DNA is called a prophage. That DNA may remain in the host genome for many generations. Influences from the environment­ including radiation, heat, and certain chemicals-trigger the prophage to become active. It then removes itself from the host cell DNA and reproduces by forming new virus particles. The lysogenic infection now becomes an active lytic infection, as shown in Figure 21-3. The details of viral infection in eukaryotic cells differ in many ways from infections of bacteria. However, the basic patterns are similar. A Closer Look at Two RNA Viruses About 70 percent of viruses contain RNA rather than DNA. In humans, RNA viruses cause a wide range of infections, from relatively mild colds to influenza and AIDS. Certain kinds of cancer also begin with an infection by viral RNA. The Common Cold What happens when you get a cold? Cold viruses attack with a very simple, fast-acting infection, as shown in Figure 21-4. A virus settles on a cell, often in the lining of the nose, and is brought inside the cell. The host cell's ribosomes translate the viral RNA into capsids and other viral proteins. These proteins assemble around copies of viral RNA, and within eight hours, the host cell releases hundreds of new virus particles to infect other cells. Common Cold Infection Mechanism Once the cold virus has pen­ etrated the host's cells, it uses the host's cellular machinery to replicate itself. HIV The deadly disease called acquired immune deficiency syn­ drome (AIDS) is caused by an RNA virus called human immunodefi­ ciency virus (HIV), shown in Figure 21-5. HIV belongs to a group of RNA viruses that are called retroviruses. The genetic information of a retrovirus is copied from RNA to DNA, and may become inserted into the DNA of the host cell. Retroviral infections are similar to lysogenic infections of bacteria. The viral genes may remain inactive for many cell cycles before making new virus particles and damaging the cells of the host's immune system. Once activated, HIV begins to destroy the very cells that would normally fight infections HIV Infection Mechanism In contrast to the cold virus, a retrovirus such as HIV makes a DNA copy of itself that inserts into the host's DNA. There, it may remain inactive for many cell cycles. Viral Diseases Viruses produce disease by disrupting the body's normal homeosta­ sis. Figure 21-6 lists some commonly known human diseases caused by viruses. Viruses produce serious animal and plant diseases as well. Disease Mechanism In many viral infections, viruses attack and destroy certain cells in the body, causing the symptoms of the associated disease. Poliovirus, for example, destroys cells in the ner­ vous system, producing paralysis. Other viruses cause infected cells to change their patterns of growth and development, sometimes leading to cancer. Viruses cause disease by directly destroying living cells or by affecting cellular processes in ways that upset homeostasis. Prevention and Treatment Many viral diseases can be pre­ vented by vaccines prepared from weakened or inactivated virus particles. Vaccines stimulate the body's immune system to recognize and destroy such viruses before they can cause disease. Personal hygiene matters, too. Studies show that cold and flu viruses are often transmitted by hand-to-mouth contact, so washing your hands often as well as covering your mouth when you cough or sneeze can help prevent the spread of viruses. While viral diseases are very difficult to treat, in recent years limited progress has been made in developing a handful of antiviral drugs that attack specific viral enzymes that host cells do not have. These treatments include an antiviral medication that can help speed recovery from the flu virus, and others that have helped prolong the lives of people infected with HIV Commonly Known Human Viral Diseases Some commonly known human viral diseases are shown in the table below. You may have had some of these diseases, or you may have only heard about some on the news Viruses and Cells Viruses must infect living cells in order to grow and reproduce, taking advantage of the nutrients and cellular machinery of their hosts. This means that all viruses are parasites. Parasites depend entirely upon other living organisms for their existence, harming these organisms in the process. Despite the fact that they are not alive, viruses have many of the characteristics of living things. After infecting living cells, viruses can reproduce, regulate gene expression, and even evolve. In fact, viral evolution is one of the reasons we need a new flu shot every year. A comparison of the principal differences between cells and viruses is shown in Figure 21-7. Although viruses are smaller and simpler than the smallest cells, it is unlikely that they were the first organisms. Because viruses are dependent upon living organisms, it seems more likely that viruses developed after living cells. In fact, the first viruses may have evolved from the genetic material of living cells. Viruses have continued to evolve, along with the cells they infect, for billions of years. Imagine living all your life as a member of what you believe is the only family on your street. Then, one morning, you open the front door and see neighbors tending their gardens and children walking to school. Where did all the people come from? What if the answer turned out to be that they had always been there-you just hadn't seen them? When the microscope was first invented, we humans had just such a shock. Suddenly, the street was very crowded! Microorganisms like bacteria are all around us-in fact, they even live inside our bodies. What Are Prokaryotes? Microscopic life covers nearly every square centimeter of Earth. The smallest and most abundant of these microorganisms are pro aryotes (pro KAR ee ohts)-unicellular organisms that lack a nucleus. Unlike eukaryotes, the DNA of prokaryotes is located directly in the cytoplasm. For many years, most prokaryotes were simply called "bacteria." Today, however, biologists divide prokaryotes into two very distinct groups: Bacteria and Archaea. These groups are as different from each other as both are from eukaryotes. Prokaryotes are clas­ sified as Bacteria or Archaea-two of the three domains of life. Eukarya is the third domain. The domain Bacteria corresponds to the kingdom Eubacteria. The domain Archaea corresponds to the kingdom Archaebacteria. Bacteria The larger of the two domains of prokaryotes is Bacteria. Bacteria include a range of organisms with lifestyles so different that biologists do not agree on exactly how to classify them within the group. Bacteria live almost everywhere, in fresh water, in salt water, on land, and on and within the bodies of humans and other eukaryotes. HS-LS1-1: Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells, HS-LS4•1: Communicate scientific information that common ancestry and biological evolution are supported by multiple lines of empirical evidence. EP&Clb: Students should be developing an understanding that the ecosystem seNices provided by natural systems are essential to human life and to the functioning of our economies and cultures. Bacteria are usually surrounded by a cell wall that protects the cell from injury and determines its shape. The cell walls of bacteria contain peptidoglycan-a polymer of sugars and amino acids that surrounds the cell membrane. Some bacteria, such as E. coli, shown in Figure 21-8, have a second membrane outside the peptidoglycan wall that makes the cell especially resistant to damage. In addition, some prokaryotes have flagella that they use for movement, or pili (singular: pilus), which in E. coli serve mainly to anchor the bacterium to a surface or to other bacteria. Archaea Under a microscope, , Archaea look very similar to Bacteria. Both are equally small, lack nuclei, and have cell walls, but there are important differences. The cell walls of Archaea lack pep­ tidoglycan and their membranes contain different lipids. Also, the DNA sequences of key Archaea genes are more like those of eukary­ otes than those of bacteria. Many Archaea live in extremely harsh environments. One group of Archaea produce methane gas and five in environments with little or no oxygen, such as thick mud or the digestive tracts of animals. Other Archaea live in extremely salty environments, such as Utah's Great Salt Lake, or in hot pools where temperatures approach the boiling point of water, such as the one shown in Figure 21-9. Bacilli Cocci Spirilla Prokaryotic Shapes Prokaryotes usually have one of these three basic shapes: bacilli, cocci, or spirilla. Structure and Function of Prokaryotes Because prokaryotes are so small, it may seem hard to tell them apart. Prokaryotes vary in their size and shape, in the way they move, and in the way they obtain and release energy. Prokaryotes range in size from 1 to 5 micrometers, making them much smaller than most eukaryotic cells. Prokaryotes come in a variety of shapes, as shown in Figure 21-10. Rod-shaped prokaryotes are called bacilli (buh SIL eye). Spherical prokaryotes are called cocci (KAHK sy). Spiral and corkscrew-shaped prokaryotes are called spirilla (spy RIL uh). You can also distinguish prokaryotes by whether they move and how they move. Some prokaryotes do not move at all. Others are propelled by flagella. Some glide slowly along a layer of slimelike material they secrete. Nutrition and Metabolism Like all organisms, prokaryotes need a supply of chemical energy, or food. They release energy from food molecules by cellular respiration, fermentation, or both. The diverse ways prokaryotes obtain and release energy are compared in Figure 21-11. Energy Capture and Release by Prokaryotes Prokaryotes vary in the way they capture energy and in the way they release it. Growth, Reproduction, and Recombination Most prokaryotes reproduce by the process of binary fission, shown in Figure 21-12. In this process, the cell replicates its DNA and then divides in half to produce two identical cells. Because binary fission does not involve the exchange or recombination of genetic informa­ tion, it is a form of asexual reproduction. When conditions are favor­ able, some prokaryotes can grow and divide as often as once every 20 minutes! When growth conditions become unfavorable, many prokaryotic cells form an endospore-a thick internal wall that encloses the DNA and a portion of the cytoplasm. Endospores can remain dormant for months or even years. The ability to form endospores makes it possible for some prokaryotes to survive very harsh conditions. The bacterium Bacillus anthracis, which causes the disease anthrax, is one such bacterium. As in any organism, adaptations that increase the survival and reproduction of a particular prokaryote are favored. Recall that in organisms that reproduce sexually, genes are shuffled and recom­ bined during meiosis. But many prokaryotes reproduce asexually. So, how do their populations evolve? Mutations Mutations are one of the main ways prokaryotes evolve. Recall that mutations are heritable changes in DNA. In prokaryotes, mutations are inherited by daughter cells produced by binary fission. Conjugation Many prokaryotes exchange genetic information by a process called conjugation. During conjugation, a hollow bridge forms between two bacterial cells, and genetic material, usually in the form of a plasmid, moves from one cell to the other. Many plas­ mids carry genes that enable bacteria to survive in new environments or to resist antibiotics that might otherwise prove fatal. This transfer of genes increases genetic diversity in populations of prokaryotes. Prokaryotes in the Environment You may remember the star actors in the last movie you saw, but have you ever thought about a film's behind-the-scene production crew? Prokaryotes are just like those unseen workers. Prokaryotes are essential in maintaining every aspect of the ecological bal­ ance of the living world. In addition, some species have specific uses in human industry. Decomposers Every living thing depends on a supply of raw materials for its survival. By breaking down, or decomposing, dead organisms, prokaryotes supply raw materials to the environment. Bacterial decomposers are also essential to industrial sewage treat­ ment, helping to produce purified water and chemicals that can be used as fertilizers. Producers Photosynthetic prokaryotes are among the most important producers on the planet. The tiny cyanobacterium Prochlorococcus (Figure 21-13) alone may account for more than half of the primary production in the open ocean. Food chains every­ where are dependent upon prokaryotes as producers of food and biomass. Nitrogen Fixers All organisms need nitrogen to grow. But while nitrogen gas (N2) makes up 80 percent of Earth's atmosphere, only a few organisms-all of them prokaryotes-can convert N2 into use- ful forms. This process, known as nitrogen fixation, provides up to 90 percent of the nitrogen used by other organisms. Some plants have vital symbiotic relationships with nitrogen-fixing prokaryotes. As shown in Figure 21-13, the bacterium Rhizobium grows in nodules, or knobs, on the roots of legume plants such as clover and soybean. The Rhizobium bacteria within these nodules convert nitrogen in the air into the nitrogen compounds essential for plant growth. In effect, these plants have fertilizer factories in their roots! Human Uses of Prokaryotes Prokaryotes, especially bacteria, are used in the production of a wide variety of foods and other com­ mercial products. For example, yogurt is produced by the bacterium Lactobacillus. Some bacteria can even digest petroleum and remove human-made waste products and poisons from water. Others are used to synthesize drugs and chemicals through the techniques of genetic engineering. The Microbiome Bacteria live just about everywhere, but one of their favorite places turns out to be the human body. Bacteria live on the skin, on the hair, inside the mouth and nose, and especially inside our digestive systems. In a typical human intestine there may be as many as 30 trillion bacteria belonging to 150 different species. Throughout the body these organisms form what scientists now call the "microbiome," a huge collection of prokaryotic genomes that rivals the human genome in size and complexity. Ecological Roles Played by Prokaryotes Prokaryotes play many impor­ tant roles in the environment. Cyanobacteria in the ocean (top) provide oxygen to the atmo­ sphere and food for ocean food chains. Rhizobium nodules on soybean roots (bottom) convert atmospheric nitrogen into useful compounds. This great diversity of microorganisms helps us to digest food, synthesizes certain vitamins, and maintains a balance that is impor­ tant to good health. There is growing evidence that disorders such as diabetes, obesity, and even cancer can be linked to abnormal microbiomes. An emerging area of medical science is now dedicated to understanding and correcting imbalances in the microbiome Bacterial Diseases We share this planet with prokaryotes and viruses, and most of the time we are never aware of our relationships with them. Often, these relationships are highly beneficial, but in a few cases, sharing simply doesn't work-and disease is the result. Disease-causing agents are called pathogens. Although patho­ gens can come from any taxonomic group, nearly all known prokary­ otic pathogens are bacteria. The French chemist Louis Pasteur was the first person to show convincingly that bacteria cause disease. Pasteur helped to establish what has become known as the germ theory of disease when he showed that bacteria were responsible for a number of human and animal diseases. Disease Mechanisms Bacteria produce disease in one of two general ways. Bacteria disrupt health and cause disease by destroying living cells or by releasing chemicals that upset homeostasis. Some bacteria destroy living cells and tissues of the infected organism directly, while some cause the immune system to overreact, causing it to attack the body's own tissues. Other bacte­ ria release toxins (poisons) that interfere with the normal activity of the host. Figure 21-14 lists some common human diseases caused by bacteria. Controlling Bacteria Although most bacteria are harmless, and many are beneficial, the everyday risks of any person acquiring a bac­ terial infection are great enough to warrant efforts to control bacterial growth. Some methods of controlling bacteria are shown in Figure 21-15. Preventing Bacterial Diseases Many bacterial diseases can be prevented by stimulating the body's immune system with vaccines. A accine is a preparation of weakened or killed pathogens or inactivated toxins. When injected into the body, a vaccine prompts the body to produce immunity to a specific disease. Immunity is the body's ability to recognize and destroy pathogens before they cause disease. Treating Bacterial Diseases A number of drugs can be used to attack a bacterial infection. These drugs include antibiotics, such as penicillin and tetracycline, that block the growth and reproduction of bacteria. Antibiotics disrupt proteins or cell processes that are spe­ cific to bacterial cells. In this way, they do not harm the host's cells. "Superbugs" When first introduced in the 1940s, penicillin, an antibiotic derived from fungi, was a miracle drug. Conquest of bacte­ rial diseases seemed to be in sight. Within a few decades, however, penicillin lost much of its effectiveness, as have other antibiotics. The culprit is evolution. Natural selection and the widespread use of anti­ biotics have led to the emergence of antibiotic resistance. Physicians now must fight "superbugs" that are resistant to multiple antibiotics. One example is methicillin-resistant Staphylococcus aureus, known as MRSA (pronounced MURS uh), which can cause infections that are especially difficult to control. MRSA skin infections can be spread by close contact, including the sharing of personal items such as towels and athletic gear. In hospitals, MRSA bacteria can infect surgical wounds and spread from patient to patient. Problem How can you track the outbreak of a disease? Suppose doctors in the United States have noticed an increase in the number of cases of cholera, a serious intestinal disease caused by bacteria. You are an epidemiologist, who studies the causes of diseases and how they spread. In this lab, you will try to determine how the cholera outbreak began and whether the number of cases is increasing or decreasing. You can find this lab in your digital course. Emerging Disease A previously unknown disease that appears in a popula- tion for the first time or a well-known disease that suddenly becomes harder to control is called an emerging disease. To Native Americans, the smallpox virus that Europeans brought to the new world was just such a disease. In 1521, an epidemic of this viral disease so weakened the mighty Aztec empire that Spaniard Hernan Cortes was able to conquer what is now Mexico with just a few hundred soldiers. Similar epidemics ravaged the Native American populations of New England as well in the early 1600s. The Threat Today Emerging diseases remain a threat today. Figure 21-16 shows locations worldwide where specific emerging diseases have broken out in recent years. Changes in lifestyle and com­ merce have made the health disruptions caused by emerging diseases even more of a threat. One recent example is the Zika virus, named for the forest in Uganda, Africa, where it was first discovered in monkeys. Over several decades, this mosquito-borne virus made the jump to humans, spreading across central Africa to Southeast Asia, and then to islands in the Pacific Ocean. Finally, in 2015, it emerged for the first time in South America. Because the population had no immunity to the virus, it spread quickly. In Brazil, there was a sudden increase in serious birth defects among children born to mothers who had been infected with the virus. Once the serious nature of the threat from Zika became known, public health officials moved quickly to try to stop the spread of the virus and the mosquitoes that carry it. Because viruses replicate so quickly, their genetic makeup can change rapidly, sometimes allowing a virus to evolve in ways that enables it to jump from one species to another. Researchers have evidence that this is how the virus that causes AIDS originated, moving from nonhuman primates into humans. Public health officials are especially worried about the flu virus. This RNA virus infects cells in the respiratory system, and can lead to severe illness and even death, especially among the elderly. Gene shuffling among different flu viruses infecting wild and domesticated bird populations has led to the emergence of a dangerous "bird flu." This bird flu is similar to the flu that spread worldwide and killed mil­ lions of people in 1918. In a few cases, bird flu has indeed infected humans, and health officials warn that a major "jump" into the human population remains possible in the future. Prions In 1972, American scientist Stanley Prusiner became inter­ ested in scrapie, an infectious disease in sheep, the exact cause of which was unknown. At first, he suspected a viral cause, but experi­ ments revealed clumps of tiny protein particles in the brains of infected sheep. Prusiner called these particles prions, short for "protein infec­ tious particles." Although prions were first discovered in sheep, many animals, including humans, can become infected with prions. Prions are formed when a protein known as PrP is improperly folded. Prions them­ selves can cause PrP proteins to misfold, producing even more prions. An accumulation of prions can damage nerve cells. Describe the characteristics of the two kingdoms of prokaryotes. In what ways do prokaryotes differ from one another? List three ecological roles of prokaryotes What are two ways that bacteria cause disease? Why are emerging diseases of particular concern?