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Microbiology - Advanced Microbiology - Advanced Douglas Wilkin, Ph.D. Niamh Gray-Wilson Say Thanks to the Authors Click http://www.ck12.org/saythanks (No sign in required) AUTHORS Douglas Wilkin, Ph.D. To access a customizable version of this book, as well as other Niamh Gray-Wilson interactive content, visit www.ck12.org EDITOR Douglas Wilkin, Ph.D. CK-12 Foundation is a non-profit organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-source, collaborative, and web-based compilation model, CK-12 pioneers and promotes the creation and distribution of high-quality, adaptive online textbooks that can be mixed, modified and printed (i.e., the FlexBook® textbooks). Copyright © 2016 CK-12 Foundation, www.ck12.org The names “CK-12” and “CK12” and associated logos and the terms “FlexBook®” and “FlexBook Platform®” (collectively “CK-12 Marks”) are trademarks and service marks of CK-12 Foundation and are protected by federal, state, and international laws. Any form of reproduction of this book in any format or medium, in whole or in sections must include the referral attribution link http://www.ck12.org/saythanks (placed in a visible location) in addition to the following terms. Except as otherwise noted, all CK-12 Content (including CK-12 Curriculum Material) is made available to Users in accordance with the Creative Commons Attribution-Non-Commercial 3.0 Unported (CC BY-NC 3.0) License (http://creativecommons.org/ licenses/by-nc/3.0/), as amended and updated by Creative Com- mons from time to time (the “CC License”), which is incorporated herein by this reference. Complete terms can be found at http://www.ck12.org/about/ terms-of-use. Printed: January 24, 2016 www.ck12.org Chapter 1. Microbiology - Advanced CHAPTER 1 Microbiology - Advanced CHAPTER OUTLINE 1.1 Prokaryotes - Advanced 1.2 Prokaryote Classification - Advanced 1.3 Prokaryote Structure and Function - Advanced 1.4 Gram Stain Identification - Advanced 1.5 Prokaryote Intracellular Structures - Advanced 1.6 Prokaryote Extracellular Structures - Advanced 1.7 Introduction to Archaea - Advanced 1.8 Introduction to Bacteria - Advanced 1.9 Prokaryote Nutrition and Metabolism - Advanced 1.10 Prokaryote Habitats - Advanced 1.11 Prokaryote Growth and Reproduction - Advanced 1.12 Symbiotic Relationships of Prokaryotes - Advanced 1.13 Human Uses of Prokaryotes - Advanced 1.14 Prokaryotes and Research - Advanced 1.15 Bacterial Diseases - Advanced 1.16 Prokaryotic Infections - Advanced 1.17 Preventions and Treatments for Bacterial Diseases - Advanced 1.18 Emerging and Reemerging Diseases - Advanced 1.19 Control of Bacteria - Advanced 1.20 Microbiology of Viruses - Advanced 1.21 Virus Characteristics - Advanced 1.22 Virus Structure - Advanced 1.23 Virus Discovery - Advanced 1.24 Virus Classification - Advanced 1.25 Virus Origins - Advanced 1.26 Virus Replication - Advanced 1.27 Lytic Cycle - Advanced 1.28 Lysogenic Cycle - Advanced 1.29 Viral Disease - Advanced 1.30 Control of Viruses - Advanced 1.31 Viruses in Research - Advanced 1.32 Prions and Viroids - Advanced 1.33 References 1 www.ck12.org Introduction Can you guess what type of organism is pictured here? Are they fat green worms on a red leaf? Here’s a clue: there are more organisms like these than any other on Earth. Here’s another clue: each organism consists of a single cell without a nucleus. And lastly, there are more of these types of organisms in your mouth than people on the planet. The specific organism depicted here are bacteria called Salmonella. If the word Salmonella rings a bell, that’s probably because Salmonella causes human diseases such as food poisoning. Many other types of bacteria also cause human diseases. But not all bacteria are harmful to people. In fact, we could not survive without many of the trillions of bacteria that live in or on the human body. You will learn why when you read this chapter. 2 www.ck12.org Chapter 1. Microbiology - Advanced 1.1 Prokaryotes - Advanced • Define and describe prokaryotic organisms. If you had to guess what these cells represent, what would you say? Single-celled organisms with a few flagella. If your first guess was some sort of prokaryotic organism, that would be correct. And if you could see inside, what would be missing? Prokaryotes Have you ever eaten cheese, yogurt, or pickled vegetables or had to take antibiotics? Have you ever had acne or a sore throat? If so, you have both benefited and suffered from the existence of prokaryotes. They are tiny and are sometimes bothersome, but the world would be a very different place without them. Prokaryotes are single-celled organisms without a nucleus. It is the lack of a nucleus that is the major distinction between prokaryotic cells and eukaryotic cells. Prokaryotic cells also lack other membrane-bound organelles, but they do contain ribosomes. Recall that ribosomes are not surrounded by a membrane. Prokaryotes are the most numerous organisms on Earth. Most are too small to be seen with the naked eye. Because of their tiny size, the existence of prokaryotes was unknown until Anton van Leeuwenhoek first saw tiny cells with his microscope in the late 17th century. Since then, prokaryotes have been found almost everywhere on Earth. They are found in sea water, in animals’ intestines, on your skin, and even in rocks deep beneath the Earth’s crust. Scientists estimate that life on Earth developed between 3 and 4 billion years ago and that the first types of cells were prokaryotes, possibly similar to those that live in an environment comparable to that shown in the Figure 1.1. 3 1.1. Prokaryotes - Advanced www.ck12.org Prokaryotes can survive on this planet just fine without us, but conversely, we could not survive without prokaryotes. Modern day bacteria and archaea comprise the two prokaryotic kingdoms. FIGURE 1.1 The landscape of early Earth was hot and acidic and may have looked a little like Mammoth Hot Springs in Yellowstone National Park. Scientists believe that prokaryotic organisms, possibly similar to the ones living in the hot springs today, were the first organisms on Earth. Vocabulary • eukaryotic cells: Cells typical of multi-celled organisms; they have a nucleus and membrane bound organelles and are usually larger than prokaryotic cells. • organelle: A structure within the cytoplasm of a cell that performs a specific function. They may be enclosed within a membrane. • prokaryote: An organism that has neither a cell nucleus nor any organelles that are surrounded by a mem- brane; bacteria are prokaryotes. • prokaryotic cells: Cells typical of simple single-celled organisms, such as bacteria; they lack a nucleus and other membrane bound organelles. Summary • Prokaryotes are single-celled organisms without a nucleus. Practice Use this resource to answer the questions that follow. • http://www.hippocampus.org/HippoCampus/Biology?loadLeftClass=Course&loadLeftId=37&loadTopicId=39 66 1. What is the major distinct characteristic of a prokaryote? 4 www.ck12.org Chapter 1. Microbiology - Advanced 2. Where are prokaryotes found? List some example environments. 3. How does other life benefit from prokaryotes? What process do prokaryotes carry out that is beneficial to other life? 4. How did ancient prokaryotes change the early Earth’s atmosphere? Practice Answers 1. A prokaryote does not have a nucleus nor membrane bound organelles. 2. Bacteria are found in a very diverse range of environments. Archaea are found in extreme environments, including locations with excessive heat, cold, salinity, pH and pressure. Archaea are often found in more temperate environments as well. 3. Prokaryotes benefit other life through carrying out photosynthetic processes. They also play a significant role in nitrogen, sulfur, and carbon cycles. 4. Cyanobacteria are believed to have developed photosynthetic processes which increased the levels of oxygen in early Earth’s atmosphere. Review 1. What are prokaryotic organisms? 2. What is the distinguishing feature between prokaryotic cells and all other cells? 3. Name some important beneficial human uses of prokaryotes. Review Answers 1. Prokaryotes are single-celled organisms which do not have a nucleus. 2. Prokaryotic cells are distinguished from other cells through their lack of both a nucleus and membrane-bound organelles. 3. Prokaryotic organisms are necessary for the production of various foods, as well as the production of antibi- otics. 5 1.2. Prokaryote Classification - Advanced www.ck12.org 1.2 Prokaryote Classification - Advanced • Outline the relationship between bacteria, archaea, and eukaryotes. What do all these organisms have in common? They are all bacteria. But more than that, they are all common bacteria that infect humans. Notice that they have different shapes and sizes. Classification and Evolution of Prokaryotes Even though prokaryotes are tiny organisms, they differ greatly in where they live, what they use for food, and their DNA sequences. In the past, scientists classified prokaryotes into two groups, called Eubacteria and Archaebac- teria. The kingdom Eubacteria was made up of the “everyday” bacteria, such as the ones that make milk sour, decompose dead organic matter, and, on occasion, make people sick. The kingdom Archaebacteria was made up of a strange group of microorganism that scientists found in extremely hot, acidic, or salty environments. In the late 1970s two American scientists, Carl Woese and George Fox, proposed that archaebacteria were not just "weird" bacteria, but instead were a distinct group of organisms that are very different from bacteria. Their idea was based on their investigations of certain prokaryotic DNA and RNA sequences. 6 www.ck12.org Chapter 1. Microbiology - Advanced Genome Changes Over Time The DNA sequence in the genome of organisms changes slowly over time. Certain sequences of DNA change more slowly than other sequences do. These stable sequences usually contain genes that code for molecules involved in important processes, such as protein synthesis.
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