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Throughout *Microbiology*, you will find features that engage students by taking selected topics a step further. Our features include:
**Clinical Focus.** Each chapter has a multi-part clinical case study that follows the story of a fictional patient. The case unfolds in several realistic episodes placed strategicall... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Preface**",
"Header 3": "**Engaging Feature Boxes**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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Our art program is designed to enhance students' understanding of concepts through clear and effective illustrations, diagrams, and photographs. Detailed drawings, comprehensive lifecycles, and clear micrographs provide visual reinforcement for concepts.
!... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Preface**",
"Header 3": "**Comprehensive Art Program**",
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**Learning Objectives.** Every section begins with a set of clear and concise learning objectives that are closely aligned to the content and Review Questions.
**Summary.** The Summary distills the information in each section into a series of concise bullet points. Key Terms in the Summary are bold-faced for emphasis... | {
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"Header 2": "**Materials That Reinforce Key Concepts**",
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#### **Nina Parker (Content Lead), Shenandoah University**
Dr. Nina Parker received her BS and MS from the University of Michigan, and her PhD in Immunology from Ohio University. She joined Shenandoah University's Department of Biology in 1995 and serves as Associate Professor, teaching general microbiology, medical ... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Materials That Reinforce Key Concepts**",
"Header 3": "**About the Authors Senior Contributing Authors**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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Summer Allen, Brown University Ann Auman, Pacific Lutheran University Graciela Brelles-Mariño, Universidad Nacional de la Plata Myriam Alhadeff Feldman, Lake Washington Institute of Technology Paul Flowers, University of North Carolina–Pembroke Clifton Franklund, Ferris State University Ann Paterson, Williams Baptist U... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Materials That Reinforce Key Concepts**",
"Header 3": "**Contributing Authors**",
"token_count": 623,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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From boiling thermal hot springs to deep beneath the Antarctic ice, microorganisms can be found almost everywhere on earth in great quantities. Microorganisms (or microbes, as they are also called) are small organisms. Most are so small that they cannot be seen without a microscope.
Most microorganisms are harmless t... | {
"Header 1": "**An Invisible World**",
"Header 2": "**Introduction**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **Learning Objectives**
- Describe how our ancestors improved food with the use of invisible microbes
- Describe how the causes of sickness and disease were explained in ancient times, prior to the invention of the microscope
- Describe key historical events associated with the birth of microbiology
Most peopl... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.1 What Our Ancestors Knew**",
"token_count": 1292,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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Prehistoric humans had a very limited understanding of the causes of disease, and various cultures developed different beliefs and explanations. While many believed that illness was punishment for angering the gods or was simply the result of fate, archaeological evidence suggests that prehistoric people attempted to t... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.1 What Our Ancestors Knew**",
"Header 3": "**The Iceman Treateth**",
"token_count": 276,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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Several ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. This is especially evident in historical attempts to contain the spread of disease. For example, the Bible refers to the practice of quarantining people with leprosy and other diseases, su... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.1 What Our Ancestors Knew**",
"Header 3": "**Early Notions of Disease, Contagion, and Containment**",
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While the ancients may have suspected the existence of invisible "minute creatures," it wasn't until the invention of the microscope that their existence was definitively confirmed. While it is unclear who exactly invented the microscope, a Dutch cloth merchant named Antonie van Leeuwenhoek (1632–1723) was the first to... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.1 What Our Ancestors Knew**",
"Header 3": "**The Birth of Microbiology**",
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**Taxonomy** is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1... | {
"Header 1": "**An Invisible World**",
"Header 2": "**The Science of Taxonomy**",
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Sometimes these names reflect some distinctive trait of the organism; in other cases, microorganisms are named after the scientists who discovered them. The archaeon *Haloquadratum walsbyi* is an example of both of these naming schemes. The genus, *Haloquadratum*, describes the microorganism's saltwater habitat (*halo*... | {
"Header 1": "**An Invisible World**",
"Header 2": "**The Science of Taxonomy**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **Learning Objectives**
- List the various types of microorganisms and describe their defining characteristics
- Give examples of different types of cellular and viral microorganisms and infectious agents
- Describe the similarities and differences between archaea and bacteria
- Provide an overview of the field ... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
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**Bacteria** are found in nearly every habitat on earth, including within and on humans. Most bacteria are harmless or helpful, but some are **pathogens**, causing disease in humans and other animals. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. Most bacteria have c... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
"Header 3": "**Prokaryotic Microorganisms**",
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The domain Eukarya contains all eukaryotes, including uni- or multicellular eukaryotes such as protists, fungi, plants, and animals. The major defining characteristic of eukaryotes is that their cells contain a nucleus.
#### **Protists**
**Protists** are unicellular eukaryotes that are not plants, animals, or fungi... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
"Header 3": "**Eukaryotic Microorganisms**",
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Multicellular parasitic worms called **helminths** are not technically microorganisms, as most are large enough to see without a microscope. However, these worms fall within the field of microbiology because diseases caused by helminths involve microscopic eggs and larvae. One example of a helminth is the guinea worm, ... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
"Header 3": "**Helminths**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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**Microbiology** is a broad term that encompasses the study of all different types of microorganisms. But in practice, microbiologists tend to specialize in one of several subfields. For example, **bacteriology** is the study of bacteria; **mycology** is the study of fungi; **protozoology** is the study of protozoa; **... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
"Header 3": "**Microbiology as a Field of Study**",
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#### **[1.1 What Our Ancestors Knew](#page-25-0)**
• **Microorganisms** (or **microbes**) are living organisms that are generally too small to be seen without a microscope.
- Throughout history, humans have used microbes to make fermented foods such as beer, bread, cheese, and wine.
- Long before the invention of t... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
"Header 3": "**Summary**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **Multiple Choice**
- **1.** Which of the following foods is NOT made by fermentation?
- a. beer
- b. bread
- c. cheese
- d. orange juice
- **2.** Who is considered the "father of Western medicine"?
- a. Marcus Terentius Varro
- b. Thucydides
- c. Antonie van Leeuwenhoek
- d. Hippocrates
- **3.** Who was the fir... | {
"Header 1": "**An Invisible World**",
"Header 2": "**1.3 Types of Microorganisms**",
"Header 3": "**Review Questions**",
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**Figure 2.1** Different types of microscopy are used to visualize different structures. Brightfield microscopy (left) renders a darker image on a lighter background, producing a clear image of these *Bacillus anthracis* cells in cerebrospinal fluid (the rod-shaped bacterial cells are surr... | {
"Header 1": "**How We See the Invisible World**",
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When we look at a rainbow, its colors span the full spectrum of light that the human eye can detect and differentiate. Each hue represents a different frequency of visible light, processed by our eyes and brains and rendered as red, orange, yellow, green, or one of the many other familiar colors that have always been a... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Introduction**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **Learning Objectives**
- Identify and define the characteristics of electromagnetic radiation (EMR) used in microscopy
- Explain how lenses are used in microscopy to manipulate visible and ultraviolet (UV) light
Visible light consists of electromagnetic waves that behave like other waves. Hence, many of the p... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.1 The Properties of Light**",
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Light waves interact with materials by being reflected, absorbed, or transmitted. **Reflection** occurs when a wave bounces off of a material. For example, a red piece of cloth may reflect red light to our eyes while absorbing other colors of light. **Absorbance** occurs when a material captures the energy of a light w... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.1 The Properties of Light**",
"Header 3": "**Interactions of Light**",
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Visible light is just one form of electromagnetic radiation (EMR), a type of energy that is all around us. Other forms of EMR include microwaves, X-rays, and radio waves, among others. The different types of EMR fall on the electromagnetic spectrum, which is defined in terms of wavelength and frequency. The spectrum of... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.1 The Properties of Light**",
"Header 3": "**Electromagnetic Spectrum and Color**",
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Microscopes magnify images and use the properties of light to create useful images of small objects. **Magnification** is defined as the ability of a lens to enlarge the image of an object when compared to the real object. For example, a magnification of 10⨯ means that the image appears 10 times the size of the object ... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.1 The Properties of Light**",
"Header 3": "**Magnification, Resolution, and Contrast**",
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Read this **[article \(https://www.openstax.org/l/22aperture\)](https://www.openstax.org/l/22aperture)** to learn more about factors that can increase or decrease the numerical aperture of a lens.
Even when a microscope has high resolution, it can be difficult to distinguish small stru... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.1 The Properties of Light**",
"Header 3": "**Link to Learning**",
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Antonie van Leeuwenhoek, sometimes hailed as "the Father of Microbiology," is typically credited as the first person to have created microscopes powerful enough to view microbes (**[Figure 2.9](#page-60-0)**). Born in the city of Delft in the Dutch Republic, van Leeuwenhoek began his career selling fabrics. However, he... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.2 Peering Into the Invisible World**",
"Header 3": "**Early Microscopes**",
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#### **Learning Objectives**
- Identify and describe the parts of a brightfield microscope
- Calculate total magnification for a compound microscope
- Describe the distinguishing features and typical uses for various types of light microscopes, electron microscopes, and scanning probe microscopes
The early pioneers... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.3 Instruments of Microscopy**",
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Many types of microscopes fall under the category of light microscopes, which use light to visualize images. Examples of light microscopes include brightfield microscopes, darkfield microscopes, phase-contrast microscopes, differential interference contrast microscopes, fluorescence microscopes, confocal scanning laser... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Light Microscopy**",
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Similar to a photographic negative, the spirochetes appear bright against a dark background. (credit: Centers for Disease Control and Prevention)
• Identify the key differences between brightfield and darkfield microscopy.
#### **Clinical Focus**
#### **Part 2**
Wound infections li... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Light Microscopy**",
"token_count": 1967,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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(credit a: modification of work by Centers for Disease Control and Prevention; credit b: modification of work by Centers for Disease Control and Prevention)
• Why must fluorochromes be used to examine a specimen under a fluorescence microscope?
#### **Confocal Microscopes**
Whereas o... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Light Microscopy**",
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The maximum theoretical resolution of images created by light microscopes is ultimately limited by the wavelengths of visible light. Most light microscopes can only magnify 1000⨯, and a few can magnify up to 1500⨯, but this does not begin to approach the magnifying power of an **electron microscope (EM)**, which uses s... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Light Microscopy**",
"Header 3": "**Electron Microscopy**",
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A **scanning probe microscope** does not use light or electrons, but rather very sharp probes that are passed over the surface of the specimen and interact with it directly. This produces information that can be assembled into images with magnifications up to 100,000,000⨯. Such large magnifications can be used to obser... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Light Microscopy**",
"Header 3": "**Scanning Probe Microscopy**",
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Example: Ebola virus | | | |
| Scanning (SEM) | Uses electron beams to visualize surfaces; useful to observe the three-dimensional surface details of specimens. <b>Example:</b> Campylobactor jejuni ... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Light Microscopy**",
"Header 3": "**Scanning Probe Microscopy**",
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In clinical settings, light microscopes are the most commonly used microscopes. There are two basic types of preparation used to view specimens with a light microscope: wet mounts and fixed specimens.
The simplest type of preparation is the **wet mount**, in which the specimen is placed on the slide in a drop of liqu... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.4 Staining Microscopic Specimens**",
"Header 3": "**Preparing Specimens for Light Microscopy**",
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The **Gram stain procedure** is a differential staining procedure that involves multiple steps. It was developed by Danish microbiologist Hans Christian Gram in 1884 as an effective method to distinguish between bacteria with different types of cell walls, and even today it remains one of the most frequently used stain... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.4 Staining Microscopic Specimens**",
"Header 3": "**Gram Staining**",
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Acid-fast staining is another commonly used, differential staining technique that can be an important diagnostic tool. An **acid-fast stain** is able to differentiate two types of gram-positive cells: those that have waxy mycolic acids in their cell walls, and those that do not. Two different methods for acid-fast stai... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.4 Staining Microscopic Specimens**",
"Header 3": "**Acid-Fast Stains**",
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Certain bacteria and yeasts have a protective outer structure called a capsule. Since the presence of a capsule is directly related to a microbe's virulence (its ability to cause disease), the ability to determine whether cells in a sample have capsules is an important diagnostic tool. Capsules do not absorb most basic... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**2.4 Staining Microscopic Specimens**",
"Header 3": "**Capsule Staining**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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Flagella (singular: flagellum) are tail-like cellular structures used for locomotion by some bacteria, archaea, and eukaryotes. Because they are so thin, flagella typically cannot be seen under a light microscope without a specialized **flagella staining** technique. Flagella staining thickens the flagella by first app... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Flagella Staining**",
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Samples to be analyzed using a TEM must have very thin sections. But cells are too soft to cut thinly, even with diamond knives. To cut cells without damage, the cells must be embedded in plastic resin and then dehydrated through a series of soaks in ethanol solutions (50%, 60%, 70%, and so on). The ethanol replaces th... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Flagella Staining**",
"Header 3": "**Preparing Specimens for Electron Microscopy**",
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Samples for fluorescence and confocal microscopy are prepared similarly to samples for light microscopy, except that the dyes are fluorochromes. Stains are often diluted in liquid before applying to the slide. Some dyes attach to an antibody to stain specific proteins on specific types of cells (immunofluorescence); ot... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Flagella Staining**",
"Header 3": "**Preparation and Staining for Other Microscopes**",
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#### **[2.1 The Properties of Light](#page-53-0)**
- Light waves interacting with materials may be **reflected**, **absorbed**, or **transmitted**, depending on the properties of the material.
- Light waves can interact with each other (**interference**) or be distorted by interactions with small objects or openings ... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Flagella Staining**",
"Header 3": "**Summary**",
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#### **Multiple Choice**
- **1.** Which of the following has the highest energy?
- a. light with a long wavelength
- b. light with an intermediate wavelength
- c. light with a short wavelength
- d. It is impossible to tell from the information given.
- **2.** You place a specimen under the microscope and notice that ... | {
"Header 1": "**How We See the Invisible World**",
"Header 2": "**Flagella Staining**",
"Header 3": "**Review Questions**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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**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: modificatio... | {
"Header 1": "**The Cell**",
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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 sin... | {
"Header 1": "**The Cell**",
"Header 2": "**Introduction**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **Learning Objectives**
• 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
H... | {
"Header 1": "**The Cell**",
"Header 2": "**3.1 Spontaneous Generation**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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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 ... | {
"Header 1": "**The Cell**",
"Header 2": "**3.1 Spontaneous Generation**",
"Header 3": "**Disproving Spontaneous Generation**",
"token_count": 724,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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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 ... | {
"Header 1": "**The Cell**",
"Header 2": "**3.2 Foundations of Modern Cell Theory**",
"Header 3": "**The Origins of Cell Theory**",
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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 ea... | {
"Header 1": "**The Cell**",
"Header 2": "**3.2 Foundations of Modern Cell Theory**",
"Header 3": "**Endosymbiotic Theory**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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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... | {
"Header 1": "**The Cell**",
"Header 2": "**The Germ Theory of Disease**",
"token_count": 1934,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **Learning Objectives**
- 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 p... | {
"Header 1": "**The Cell**",
"Header 2": "**3.3 Unique Characteristics of Prokaryotic Cells**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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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](#page-113-0)** names and illustrates cell morphologies co... | {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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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 proteins are concentrated within the **nucleoid** region of the cell (**[Figure 3.17](#page-116-0... | {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"Header 3": "**The Nucleoid**",
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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... | {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"Header 3": "**Plasmids**",
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"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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 ... | {
"Header 1": "**The Cell**",
"Header 2": "**Common Cell Morphologies and Arrangements**",
"Header 3": "**Inclusions**",
"token_count": 775,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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 form... | {
"Header 1": "**The Cell**",
"Header 2": "**Endospores**",
"token_count": 1034,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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 va... | {
"Header 1": "**The Cell**",
"Header 2": "**Endospores**",
"Header 3": "**Plasma Membrane**",
"token_count": 1996,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
These peptidoglycan layers are commonly embedded with teichoic acids (TAs), carbohydrate chains that extend through and beyond the peptidoglycan layer.[19] 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... | {
"Header 1": "**The Cell**",
"Header 2": "**Endospores**",
"Header 3": "**Plasma Membrane**",
"token_count": 1167,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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... | {
"Header 1": "**The Cell**",
"Header 2": "**Glycocalyces and S-Layers**",
"token_count": 889,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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.
#### **Fimbriae and Pili**
... | {
"Header 1": "**The Cell**",
"Header 2": "**Glycocalyces and S-Layers**",
"Header 3": "**Filamentous Appendages**",
"token_count": 1905,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Explain the distinguishing characteristics of eukaryotic cells
- Describe internal and external structures of prokaryotic cells in terms of their physical structure, chemical structure, and function
- Identify and describe structures and organelles unique to eukaryotic cells
- Compare a... | {
"Header 1": "**The Cell**",
"Header 2": "**3.4 Unique Characteristics of Eukaryotic Cells**",
"token_count": 1142,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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](#page-134-0)**). Some eukaryotic cells are irregular in shape, and some are capable of ch... | {
"Header 1": "**The Cell**",
"Header 2": "**Cell Morphologies**",
"token_count": 1032,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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 m... | {
"Header 1": "**The Cell**",
"Header 2": "**Cell Morphologies**",
"Header 3": "**Ribosomes**",
"token_count": 309,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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 3.40](#page-137-0)**). Because of their larger cell size, eukaryotic cells require this system to transport mate... | {
"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"token_count": 1733,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Eukaryotic cells have an internal cytoskeleton made of **microfilaments**, **intermediate filaments**, and **microtubules**. This matrix of fibers and tubes provides structural support as well as a network over which materials can be transported within the cell and on which organelles can be anchored (**[Figure 3.44](#... | {
"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"Header 3": "**Cytoskeleton**",
"token_count": 2056,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
It also contains mitochondrial DNA and 70S ribosomes. Invaginations of the inner membrane, called cristae, evolved to increase surface area for the location of biochemical reactions. The folding patterns of the cristae differ among various types of eukaryotic cells and are used to distinguish different eukaryotic organ... | {
"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"Header 3": "**Cytoskeleton**",
"token_count": 865,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The plasma membrane of eukaryotic cells is similar in structure to the prokaryotic plasma membrane in that it is composed mainly of phospholipids forming a bilayer with embedded peripheral and integral proteins (**[Figure 3.51](#page-146-0)**). These membrane components move within the plane of the membrane according t... | {
"Header 1": "**The Cell**",
"Header 2": "**Endomembrane System**",
"Header 3": "**Plasma Membrane**",
"token_count": 1361,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Some eukaryotic cells use **flagella** for locomotion; however, eukaryotic flagella are structurally distinct from those found in prokaryotic cells. Whereas the prokaryotic flagellum is a stiff, rotating structure, a eukaryotic flagellum is more like a flexible whip composed of nine parallel pairs of microtubules surro... | {
"Header 1": "**The Cell**",
"Header 2": "**Flagella and Cilia**",
"token_count": 2017,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.
- The **smooth endoplasmic reticulum** plays a role in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds. The **rough endoplasmic reticulum** contains membrane-bound 80S ribosomes that synthesize proteins destin... | {
"Header 1": "**The Cell**",
"Header 2": "**Flagella and Cilia**",
"token_count": 533,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Multiple Choice**
- **1.** Which of the following individuals argued in favor of the theory of spontaneous generation?
- a. Francesco Redi
- b. Louis Pasteur
- c. John Needham
- d. Lazzaro Spallanzani
- **2.** Which of the following individuals is credited for definitively refuting the theory of spontaneous ge... | {
"Header 1": "**The Cell**",
"Header 2": "**Flagella and Cilia**",
"Header 3": "**Review Questions**",
"token_count": 1973,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
**Figure 4.1** The bacterium *Shewanella* lives in the deep sea, where there is little oxygen diffused in the water. It is able to survive in this harsh environment by attaching to the sea floor and using long appendages, called "nanocables," to sense oxygen. (credit a: modification of w... | {
"Header 1": "**Prokaryotic Diversity**",
"token_count": 241,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Scientists have studied prokaryotes for centuries, but it wasn't until 1966 that scientist Thomas Brock (1926–) discovered that certain bacteria can live in boiling water. This led many to wonder whether prokaryotes may also live in other extreme environments, such as at the bottom of the ocean, at high altitudes, or i... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Introduction**",
"token_count": 248,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Prokaryotes are ubiquitous. They can be found everywhere on our planet, even in hot springs, in the Antarctic ice shield, and under extreme pressure two miles under water. One bacterium, *Paracoccus denitrificans*, has even been shown to survive when scientists removed it from its native environment (soil) and used a c... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.1 Prokaryote Habitats, Relationships, and Microbiomes**",
"Header 3": "**Prokaryote Habitats and Functions**",
"token_count": 1929,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
As we have learned, prokaryotic microorganisms can associate with plants and animals. Often, this association results in unique relationships between organisms. For example, bacteria living on the roots or leaves of a plant get nutrients from the plant and, in return, produce substances that protect the plant from path... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Symbiotic Relationships**",
"token_count": 2045,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Assigning prokaryotes to a certain species is challenging. They do not reproduce sexually, so it is not possible to classify them according to the presence or absence of interbreeding. Also, they do not have many morphological features. Traditionally, the classification of prokaryotes was based on their shape, staining... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Symbiotic Relationships**",
"Header 3": "**Taxonomy and Systematics**",
"token_count": 1937,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of each class within the phylum Proteobacteria: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria
- Give an example of a bacterium in each class of Proteobacteria
In 1987, the American microbiologi... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.2 Proteobacteria**",
"token_count": 244,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The first class of Proteobacteria is the **Alphaproteobacteria**. The unifying characteristic of this class is that they are **oligotroph**s, organisms capable of living in low-nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil.
Among the Alphaproteobacteria are two taxa, chl... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.2 Proteobacteria**",
"Header 3": "**Alphaproteobacteria**",
"token_count": 1434,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Unlike Alphaproteobacteria, which survive on a minimal amount of nutrients, the class **Betaproteobacteria** are **eutroph**s (or copiotrophs), meaning that they require a copious amount of organic nutrients. Betaproteobacteria often grow between aerobic and anaerobic areas (e.g., in mammalian intestines). Some genera ... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.2 Proteobacteria**",
"Header 3": "**Betaproteobacteria**",
"token_count": 933,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The most diverse class of gram-negative bacteria is **Gammaproteobacteria**, and it includes a number of human pathogens. For example, a large and diverse family, *Pseudomonaceae*, includes the genus *Pseudomonas*. Within this genus is the species *P. aeruginosa*, a pathogen responsible for diverse infections in variou... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Gammaproteobacteria**",
"token_count": 2011,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
pneumophila<br>causes Legionnaires disease |
| Methylomonas | Gram-negative<br>bacillus ... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Gammaproteobacteria**",
"token_count": 1061,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The smallest class of Proteobacteria is **Epsilonproteobacteria**, which are gram-negative microaerophilic bacteria (meaning they only require small amounts of oxygen in their environment). Two clinically relevant genera of Epsilonproteobacteria are *Campylobacter* and *Helicobacter*, both of which include human pathog... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**Gammaproteobacteria**",
"Header 3": "**Epsilonproteobacteria**",
"token_count": 638,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Spirochetes are characterized by their long (up to 250 μm), spiral-shaped bodies. Most **spirochetes** are also very thin, which makes it difficult to examine gram-stained preparations under a conventional brightfield microscope. Darkfield fluorescent microscopy is typically used instead. Spirochetes are also difficult... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 3": "**Spirochetes**",
"token_count": 637,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The gram-negative nonproteobacteria of the genera *Cytophaga*, *Fusobacterium*, and *Bacteroides* are classified together as a phylum and called the **CFB group**. Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA. They are rod-shap... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 3": "*Cytophaga***,** *Fusobacterium***, and** *Bacteroides*",
"token_count": 471,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The Planctomycetes are found in aquatic environments, inhabiting freshwater, saltwater, and brackish water. Planctomycetes are unusual in that they reproduce by budding, meaning that instead of one maternal cell splitting into two equal daughter cells in the process of binary fission, the mother cell forms a bud that d... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 3": "**Planctomycetes**",
"token_count": 692,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The **phototrophic bacteria** are a large and diverse category of bacteria that do not represent a taxon but, rather, a group of bacteria that use sunlight as their primary source of energy. This group contains both Proteobacteria and nonproteobacteria. They use solar energy to synthesize ATP through photosynthesis. Wh... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 3": "**Phototrophic Bacteria**",
"token_count": 2006,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Phototrophic Bacteria**
| Phylum | Class | Example<br>Genus or<br>Species | Common<br>Name | Oxygenic or<br>Anoxygenic | Sulfur<br>Deposition |
|---------------------------|---------------------|--------------------------------|-------------------------------... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria**",
"Header 3": "**Phototrophic Bacteria**",
"token_count": 326,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of each category of high G+C and low G+C gram-positive bacteria
- Identify similarities and differences between high G+C and low G+C bacterial groups
- Give an example of a bacterium of high G+C and low G+C group commonly associated with each category
Prok... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "4.4 Gram-Positive Bacteria",
"token_count": 345,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The name Actinobacteria comes from the Greek words for *rays* and *small rod*, but Actinobacteria are very diverse. Their microscopic appearance can range from thin filamentous branching rods to coccobacilli. Some Actinobacteria are very large and complex, whereas others are among the smallest independently living orga... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "4.4 Gram-Positive Bacteria",
"Header 3": "**Actinobacteria: High G+C Gram-Positive Bacteria**",
"token_count": 2030,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Clinical Focus**
#### **Part 3**
Based on her symptoms, Marsha's doctor suspected that she had a case of tuberculosis. Although less common in the United States, tuberculosis is still extremely common in many parts of the world, including Nigeria. Marsha's work there in a medical lab likely exposed her to ... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "4.4 Gram-Positive Bacteria",
"Header 3": "**Actinobacteria: High G+C Gram-Positive Bacteria**",
"token_count": 2020,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
**Figure 4.22** This SEM of *Staphylococcus aureus* illustrates the typical "grape-like" clustering of cells. (credit: modification of work by Centers for Disease Control and Prevention)
*S. epidermidis*, whose main habitat is the human skin, is thought to be nonpathogenic for humans... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "4.4 Gram-Positive Bacteria",
"Header 3": "**Actinobacteria: High G+C Gram-Positive Bacteria**",
"token_count": 1981,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of deeply branching bacteria
- Give examples of significant deeply branching bacteria
On a phylogenetic tree (see **[A Systematic Approach](#page-32-0)**), the trunk or root of the tree represents a common ancient evolutionary ancestor, often called the la... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.5 Deeply Branching Bacteria**",
"token_count": 1091,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Describe the unique features of each category of Archaea
- Explain why archaea might not be associated with human microbiomes or pathology
- Give common examples of archaea commonly associated with unique environmental habitats
Like organisms in the domain Bacteria, organisms of the d... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.6 Archaea**",
"token_count": 1219,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The phylum Euryarchaeota includes several distinct classes. Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane. They can l... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.6 Archaea**",
"Header 3": "**Euryarchaeota**",
"token_count": 2009,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.
- Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.
- Some pho... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.6 Archaea**",
"Header 3": "**Euryarchaeota**",
"token_count": 925,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Multiple Choice**
- **1.** The term prokaryotes refers to which of the following?
- a. very small organisms
- b. unicellular organisms that have no nucleus
- c. multicellular organisms
- d. cells that resemble animal cells more than plant cells
- **2.** The term microbiota refers to which of the following?
- a... | {
"Header 1": "**Prokaryotic Diversity**",
"Header 2": "**4.6 Archaea**",
"Header 3": "**Review Questions**",
"token_count": 1989,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
**Figure 5.1** Malaria is a disease caused by a eukaryotic parasite transmitted to humans by mosquitos. Micrographs (left and center) show a sporozoite life stage, trophozoites, and a schizont in a blood smear. On the right is depicted a primary defense against mosquito-borne illnesses l... | {
"Header 1": "**The Eukaryotes of Microbiology**",
"token_count": 237,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Although bacteria and viruses account for a large number of the infectious diseases that afflict humans, many serious illnesses are caused by eukaryotic organisms. One example is malaria, which is caused by *Plasmodium*, a eukaryotic organism transmitted through mosquito bites. Malaria is a major cause of morbidity (il... | {
"Header 1": "**The Eukaryotes of Microbiology**",
"Header 2": "**Introduction**",
"token_count": 434,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
#### **Learning Objectives**
- Summarize the general characteristics of unicellular eukaryotic parasites
- Describe the general life cycles and modes of reproduction in unicellular eukaryotic parasites
- Identify challenges associated with classifying unicellular eukaryotes
- Explain the taxonomic scheme used for uni... | {
"Header 1": "**The Eukaryotes of Microbiology**",
"Header 2": "**5.1 Unicellular Eukaryotic Parasites**",
"token_count": 744,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The word *protist* is a historical term that is now used informally to refer to a diverse group of microscopic eukaryotic organisms. It is not considered a formal taxonomic term because the organisms it describes do not have a shared evolutionary origin. Historically, the protists were informally grouped into the "anim... | {
"Header 1": "**The Eukaryotes of Microbiology**",
"Header 2": "**5.1 Unicellular Eukaryotic Parasites**",
"Header 3": "**Characteristics of Protists**",
"token_count": 1414,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The protists are a **polyphyletic** group, meaning they lack a shared evolutionary origin. Since the current taxonomy is based on evolutionary history (as determined by biochemistry, morphology, and genetics), protists are scattered across many different taxonomic groups within the domain Eukarya. Eukarya is currently ... | {
"Header 1": "**The Eukaryotes of Microbiology**",
"Header 2": "**5.1 Unicellular Eukaryotic Parasites**",
"Header 3": "**Taxonomy of Protists**",
"token_count": 1987,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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