Microbiology, 2021

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1162 C • Metabolic Pathways Calvin-Benson Cycle Figure C9 The Calvin-Benson cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic molecule, 3-PGA. In stage 2, the organic molecule is reduced using electrons supplied by NADPH. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the cycle can continue. Only one carbon dioxide molecule is incorporated at a time, so the cycle must be completed three times to produce a single three-carbon GA3P molecule, and six times to produce a six-carbon glucose molecule. Access for free at openstax.org.
APPENDIX D Taxonomy of Clinically Relevant Microorganisms Bacterial Pathogens D • Taxonomy of Clinically Relevant Microorganisms 1163 The following tables list the species, and some higher groups, of pathogenic Eubacteria mentioned in the text. The classification of Bacteria, one of the three domains of life, is in constant flux as relationships become clearer through sampling of genetic sequences. Many groups at all taxonomic levels still have an undetermined relationship with other members of the phylogenetic tree of Bacteria. Bergey’s Manual of Systematics of Archaea and Bacteria maintains a published list and descriptions of prokaryotic species. The tables here follow the taxonomic organization in the Bergey’s Manual Taxonomic Outline. 1 We have divided the species into tables corresponding to different bacterial phyla. The taxonomic rank of kingdom is not used in prokaryote taxonomy, so the phyla are the subgrouping below domain. Note that many bacterial phyla not represented by these tables. The species and genera are listed only under the class within each phylum. The names given to bacteria are regulated by the International Code of Nomenclature of Bacteria as maintained by the International Committee on Systematics or Prokaryotes. Phylum Actinobacteria Class Genus Species Related Diseases Corynebacterium diphtheriae Diphtheria Gardnerella vaginalis Bacterial vaginosis Micrococcus Opportunistic infections Actinobacteria Mycobacterium bovis Tuberculosis, primarily in cattle Mycobacterium leprae Hansen’s disease Mycobacterium tuberculosis Tuberculosis Propionibacterium acnes Acne, blepharitis, endophthalmitis Table D1 Phylum Bacteroidetes Class Genus Species Related Diseases Bacteroidia Porphyromonas Periodontal disease 1 Bergey’s Manual Trust. Bergey’s Manual of Systematics of Archaea and Bacteria, Taxonomic Outline. 2012. http://www.bergeys.org/outlines.html
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Microbiology SENIOR CONTRIBUTING AU
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OPENSTAX OpenStax provides free, pe
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Contents Preface 1 CHAPTER 1 An Inv
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9.2 Oxygen Requirements for Microbi
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18.1 Overview of Specific Adaptive
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Appendix C Metabolic Pathways 1155
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Preface 1 PREFACE Welcome to Microb
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Preface 3 that often confer critica
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Preface 5 further. Our features inc
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Preface 7 and science, and pursues
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CHAPTER 1 An Invisible World Figure
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1.1 • What Our Ancestors Knew 11
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1.2 • A Systematic Approach 17 Th
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1.2 • A Systematic Approach 19 Fi
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1.2 • A Systematic Approach 21 Ta
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1.3 • Types of Microorganisms 23
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1 • Summary 31 SUMMARY 1.1 What O
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1 • Review Questions 33 17. The p
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CHAPTER 2 How We See the Invisible
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2.1 • The Properties of Light 37
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2.1 • The Properties of Light 39
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2.2 • Peering Into the Invisible
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2.3 • Instruments of Microscopy 4
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2.4 • Staining Microscopic Specim
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2 • Review Questions 71 REVIEW QU
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CHAPTER 3 The Cell Figure 3.1 Micro
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3.1 • Spontaneous Generation 75 F
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3.2 • Foundations of Modern Cell
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3.3 • Unique Characteristics of P
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3.4 • Unique Characteristics of E
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3 • Summary 125 SUMMARY 3.1 Spont
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3 • Review Questions 127 3. Which
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3 • Review Questions 129 Critical
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CHAPTER 4 Prokaryotic Diversity Fig
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4.1 • Prokaryote Habitats, Relati
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4.2 • Proteobacteria 139 for or s
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4.2 • Proteobacteria 141 Class Al
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4.2 • Proteobacteria 143 Class Be
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4.2 • Proteobacteria 145 Figure 4
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4.2 • Proteobacteria 147 Class Ga
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4.3 • Nonproteobacteria Gram-Nega
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4.4 • Gram-Positive Bacteria 157
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4.6 • Archaea 167 The class Therm
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4.6 • Archaea 169 thus is a livin
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4 • Summary 171 SUMMARY 4.1 Proka
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4 • Review Questions 173 REVIEW Q
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4 • Review Questions 175 39. Expl
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CHAPTER 5 The Eukaryotes of Microbi
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5.1 • Unicellular Eukaryotic Para
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Figure 5.7 5.1 • Unicellular Euka
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5.2 • Parasitic Helminths 193 hel
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5.2 • Parasitic Helminths 195 Fig
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5.2 • Parasitic Helminths 197 Fig
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5.2 • Parasitic Helminths 199 MIC
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5.3 • Fungi 201 Figure 5.25 Multi
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5.3 • Fungi 203 Figure 5.27 zygos
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5.3 • Fungi 205 diploid stages (F
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5.3 • Fungi 207 Figure 5.32 prese
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5.3 • Fungi 209 MICRO CONNECTIONS
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5.4 • Algae 211 and other photosy
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5.5 • Lichens 213 Figure 5.37 Chl
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5.5 • Lichens 215 marina. (b) Thi
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5 • Review Questions 217 REVIEW Q
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CHAPTER 6 Acellular Pathogens Figur
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6.1 • Viruses 221 assembly of vir
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6.1 • Viruses 223 Viral Structure
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6.1 • Viruses 225 Figure 6.5 (a)
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6.1 • Viruses 227 LINK TO LEARNIN
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6.2 • The Viral Life Cycle 229 on
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6.2 • The Viral Life Cycle 231 Fi
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6.2 • The Viral Life Cycle 237 by
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6.2 • The Viral Life Cycle 239 Ca
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6.3 • Isolation, Culture, and Ide
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6.4 • Viroids, Virusoids, and Pri
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6.4 • Viroids, Virusoids, and Pri
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6 • Summary 253 SUMMARY 6.1 Virus
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6 • Review Questions 255 18. A/an
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CHAPTER 7 Microbial Biochemistry Fi
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7.1 • Organic Molecules 259 Figur
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7.1 • Organic Molecules 261 Figur
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7.2 • Carbohydrates 263 and the m
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7.2 • Carbohydrates 265 Figure 7.
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7.3 • Lipids 267 Figure 7.11 Star
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7.3 • Lipids 269 Figure 7.13 This
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7.3 • Lipids 271 Figure 7.15 Five
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7.4 • Proteins 273 Figure 7.17 Am
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7.4 • Proteins 275 Figure 7.19 Re
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7.4 • Proteins 277 Figure 7.23 Pr
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7.5 • Using Biochemistry to Ident
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7.5 • Using Biochemistry to Ident
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7 • Review Questions 283 as hormo
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7 • Review Questions 285 19. A tr
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CHAPTER 8 Microbial Metabolism Figu
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8.1 • Energy, Matter, and Enzymes
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8.2 • Catabolism of Carbohydrates
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8.3 • Cellular Respiration 301 8.
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8.3 • Cellular Respiration 303 Fi
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8.4 • Fermentation 305 If respira
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8.4 • Fermentation 307 Common Fer
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8.5 • Catabolism of Lipids and Pr
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8.6 • Photosynthesis 311 independ
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8.6 • Photosynthesis 313 Oxygenic
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8.7 • Biogeochemical Cycles 315 L
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8.7 • Biogeochemical Cycles 317 N
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8.7 • Biogeochemical Cycles 319 F
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8.7 • Biogeochemical Cycles 321 F
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8 • Summary 323 oxygen as the fin
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8 • Review Questions 325 4. To wh
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8 • Review Questions 327 Matching
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CHAPTER 9 Microbial Growth Figure 9
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9.1 • How Microbes Grow 331 and a
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9.1 • How Microbes Grow 333 The G
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9.1 • How Microbes Grow 335 Susta
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9.1 • How Microbes Grow 337 chang
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9.1 • How Microbes Grow 339 Figur
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9.1 • How Microbes Grow 341 trans
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9.1 • How Microbes Grow 343 micro
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9.2 • Oxygen Requirements for Mic
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9.3 • The Effects of pH on Microb
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9.4 • Temperature and Microbial G
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9.4 • Temperature and Microbial G
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9.5 • Other Environmental Conditi
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9.6 • Media Used for Bacterial Gr
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9 • Summary 361 SUMMARY 9.1 How M
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9 • Review Questions 363 7. Filam
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9 • Review Questions 365 Matching
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9 • Review Questions 367 Critical
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CHAPTER 10 Biochemistry of the Geno
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10.1 • Using Microbiology to Disc
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10.2 • Structure and Function of
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10 • Summary 401 SUMMARY 10.1 Usi
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10 • Review Questions 403 3. Whic
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10 • Review Questions 405 Short A
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CHAPTER 11 Mechanisms of Microbial
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11.1 • The Functions of Genetic M
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11.2 • DNA Replication 411 Figure
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11.2 • DNA Replication 413 Figure
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11.2 • DNA Replication 415 strand
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11.2 • DNA Replication 417 telome
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11.3 • RNA Transcription 419 Figu
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11.3 • RNA Transcription 421 the
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11.4 • Protein Synthesis (Transla
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11.5 • Mutations 429 Effects of M
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11.5 • Mutations 431 In recent ye
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11.5 • Mutations 433 Figure 11.20
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11.5 • Mutations 435 formation of
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11.6 • How Asexual Prokaryotes Ac
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11.7 • Gene Regulation: Operon Th
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11 • Summary 457 SUMMARY 11.1 The
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11 • Summary 459 undamaged DNA st
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11 • Review Questions 461 11. Whi
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11 • Review Questions 463 46. ___
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71. The following figure is from Mo
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CHAPTER 12 Modern Applications of M
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12.1 • Microbes and the Tools of
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12.2 • Visualizing and Characteri
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12.3 • Whole Genome Methods and P
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12.3 • Whole Genome Methods and P
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12.4 • Gene Therapy 499 Figure 12
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12.4 • Gene Therapy 501 overall w
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12 • Summary 503 SUMMARY 12.1 Mic
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12 • Review Questions 505 11. The
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CHAPTER 13 Control of Microbial Gro
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13.1 • Controlling Microbial Grow
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13.2 • Using Physical Methods to
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13.3 • Using Chemicals to Control
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13.4 • Testing the Effectiveness
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13 • Summary 553 commonly used to
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13 • Review Questions 555 12. Ble
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CHAPTER 14 Antimicrobial Drugs Figu
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14.1 • History of Chemotherapy an
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14.1 • History of Chemotherapy an
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14.2 • Fundamentals of Antimicrob
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14.2 • Fundamentals of Antimicrob
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14.3 • Mechanisms of Antibacteria
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14.4 • Mechanisms of Other Antimi
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14.5 • Drug Resistance 591 Common
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14.5 • Drug Resistance 593 negati
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14.5 • Drug Resistance 595 Clavul
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14.7 • Current Strategies for Ant
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14.7 • Current Strategies for Ant
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14 • Summary 605 cells. • Becau
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14 • Review Questions 609 50. Why
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CHAPTER 15 Microbial Mechanisms of
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15.1 • Characteristics of Infecti
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15.2 • How Pathogens Cause Diseas
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15.3 • Virulence Factors of Bacte
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15.4 • Virulence Factors of Eukar
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15.4 • Virulence Factors of Eukar
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15 • Review Questions 647 protect
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15 • Review Questions 649 Critica
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CHAPTER 16 Disease and Epidemiology
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16.1 • The Language of Epidemiolo
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16.1 • The Language of Epidemiolo
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16.2 • Tracking Infectious Diseas
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16.3 • Modes of Disease Transmiss
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16.4 • Global Public Health 673 C
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16.4 • Global Public Health 675 S
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16 • Summary 677 SUMMARY 16.1 The
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16 • Review Questions 679 Matchin
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16 • Review Questions 681 20. Wha
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CHAPTER 17 Innate Nonspecific Host
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17.1 • Physical Defenses 685 Over
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17.1 • Physical Defenses 687 know
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17.1 • Physical Defenses 689 Figu
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17.2 • Chemical Defenses 691 Phys
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17.2 • Chemical Defenses 693 sali
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17.2 • Chemical Defenses 695 prod
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17.2 • Chemical Defenses 697 Figu
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17.2 • Chemical Defenses 699 Clin
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17.3 • Cellular Defenses 701 Hema
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17.3 • Cellular Defenses 703 stra
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17.3 • Cellular Defenses 705 Clin
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17.3 • Cellular Defenses 707 Figu
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17.4 • Pathogen Recognition and P
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17.4 • Pathogen Recognition and P
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17.5 • Inflammation and Fever 713
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17 • Summary 719 SUMMARY 17.1 Phy
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17 • Review Questions 721 8. Hist
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17 • Review Questions 723 Short A
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CHAPTER 18 Adaptive Specific Host D
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18.1 • Overview of Specific Adapt
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18.2 • Major Histocompatibility C
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18.3 • T Lymphocytes and Cellular
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18.4 • B Lymphocytes and Humoral
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18.4 • B Lymphocytes and Humoral
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18.5 • Vaccines 751 pathogen—bu
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18.5 • Vaccines 753 Eye on Ethics
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18.5 • Vaccines 755 for Disease C
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18.5 • Vaccines 757 Classes of Va
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18 • Summary 759 SUMMARY 18.1 Ove
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18 • Review Questions 761 5. MHC
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18 • Review Questions 763 20. Mat
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CHAPTER 19 Diseases of the Immune S
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19.1 • Hypersensitivities 767 Fig
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19.1 • Hypersensitivities 769 bin
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19.1 • Hypersensitivities 771 mec
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19.1 • Hypersensitivities 775 CHE
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19.1 • Hypersensitivities 777 Cli
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19.1 • Hypersensitivities 779 MIC
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19.2 • Autoimmune Disorders 783 t
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19.2 • Autoimmune Disorders 785 F
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19.2 • Autoimmune Disorders 787 M
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19.2 • Autoimmune Disorders 789 F
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19.3 • Organ Transplantation and
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19.4 • Immunodeficiency 793 and m
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19.4 • Immunodeficiency 795 CHECK
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19.5 • Cancer Immunobiology and I
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19 • Summary 799 SUMMARY 19.1 Hyp
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19 • Review Questions 801 13. All
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CHAPTER 20 Laboratory Analysis of t
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20.1 • Polyclonal and Monoclonal
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20.2 • Detecting Antigen-Antibody
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20.3 • Agglutination Assays 823 a
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20.3 • Agglutination Assays 825 F
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20.3 • Agglutination Assays 827 e
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20.3 • Agglutination Assays 829 s
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20.4 • EIAs and ELISAs 831 Mechan
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20.4 • EIAs and ELISAs 833 Figure
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20.4 • EIAs and ELISAs 837 • Wh
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20.5 • Fluorescent Antibody Techn
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20 • Review Questions 849 20.4 EI
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20 • Review Questions 851 15. Sup
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CHAPTER 21 Skin and Eye Infections
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21.1 • Anatomy and Normal Microbi
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21.2 • Bacterial Infections of th
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21.3 • Viral Infections of the Sk
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21.4 • Mycoses of the Skin 881 se
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21.4 • Mycoses of the Skin 883 fr
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21.4 • Mycoses of the Skin 885 Fi
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21.5 • Protozoan and Helminthic I
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21.5 • Protozoan and Helminthic I
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21 • Summary 891 SUMMARY 21.1 Ana
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CHAPTER 22 Respiratory System Infec
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22.3 • Viral Infections of the Re
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22.4 • Respiratory Mycoses 931 ha
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22.4 • Respiratory Mycoses 933 Fi
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22.4 • Respiratory Mycoses 935 re
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Figure 22.29 22.4 • Respiratory M
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22 • Review Questions 939 200 vir
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CHAPTER 23 Urogenital System Infect
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23.5 • Fungal Infections of the R
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23.6 • Protozoan Infections of th
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23 • Summary 975 SUMMARY 23.1 Ana
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CHAPTER 24 Digestive System Infecti
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24.2 • Microbial Diseases of the
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24.4 • Viral Infections of the Ga
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24.6 • Helminthic Infections of t
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24 • Summary 1033 SUMMARY 24.1 An
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CHAPTER 25 Circulatory and Lymphati
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25.1 • Anatomy of the Circulatory
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25.1 • Anatomy of the Circulatory
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25.3 • Viral Infections of the Ci
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Page 1085 and 1086:
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Page 1089 and 1090:
Figure 25.26 25.3 • Viral Infecti
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25.4 • Parasitic Infections of th
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Page 1095 and 1096:
Page 1097 and 1098:
Page 1099 and 1100:
Page 1101 and 1102:
Page 1103 and 1104:
25 • Review Questions 1089 • To
Page 1105 and 1106:
25 • Review Questions 1091 Critic
Page 1107 and 1108:
CHAPTER 26 Nervous System Infection
Page 1109 and 1110:
26.1 • Anatomy of the Nervous Sys
Page 1111 and 1112:
26.1 • Anatomy of the Nervous Sys
Page 1113 and 1114:
26.2 • Bacterial Diseases of the
Page 1115 and 1116:
Page 1117 and 1118:
Page 1119 and 1120:
Page 1121 and 1122:
Page 1123 and 1124:
Page 1125 and 1126: 26.2 • Bacterial Diseases of the
Page 1127 and 1128: 26.3 • Acellular Diseases of the
Page 1137 and 1138: Figure 26.19 26.3 • Acellular Dis
Page 1139 and 1140: 26.4 • Fungal and Parasitic Disea
Page 1147 and 1148: 26 • Review Questions 1133 are fa
Page 1149 and 1150: 26 • Review Questions 1135 Matchi
Page 1151 and 1152: 26 • Review Questions 1137 59. Th
Page 1153 and 1154: A • Fundamentals of Physics and C
Page 1163 and 1164: B • Mathematical Basics 1149 APPE
Page 1165 and 1166: B • Mathematical Basics 1151 Mult
Page 1167 and 1168: B • Mathematical Basics 1153 The
Page 1169 and 1170: C • Metabolic Pathways 1155 APPEN
Page 1171 and 1172: C • Metabolic Pathways 1157 Entne
Page 1173 and 1174: C • Metabolic Pathways 1159 Figur
Page 1175: C • Metabolic Pathways 1161 Elect
Page 1179 and 1180: D • Taxonomy of Clinically Releva
Page 1191 and 1192: E • Glossary 1177 APPENDIX E Glos
Page 1193 and 1194: E • Glossary 1179 destruction by
Page 1195 and 1196: E • Glossary 1181 pollutants from
Page 1197 and 1198: E • Glossary 1183 chromosome disc
Page 1199 and 1200: E • Glossary 1185 cysts are forme
Page 1201 and 1202: E • Glossary 1187 occurring ectop
Page 1203 and 1204: E • Glossary 1189 molecules of DN
Page 1205 and 1206: E • Glossary 1191 glycoprotein co
Page 1207 and 1208: E • Glossary 1193 image point is
Page 1209 and 1210: E • Glossary 1195 discontinuously
Page 1211 and 1212: E • Glossary 1197 infection cause
Page 1213 and 1214: E • Glossary 1199 target cells by
Page 1215 and 1216: E • Glossary 1201 intact ribosome
Page 1217 and 1218: E • Glossary 1203 point source sp
Page 1219 and 1220: E • Glossary 1205 complexes forme
Page 1221 and 1222: E • Glossary 1207 antibody is fir
Page 1223 and 1224: E • Glossary 1209 the number of c
Page 1225 and 1226: E • Glossary 1211 the reciprocal
Page 1227 and 1228:
E • Glossary 1213 vector animal (
Page 1229 and 1230:
1215 ANSWER KEY Chapter 1 1. D 2. D
Page 1231 and 1232:
1217 B 18. A, C, B 19. peristalsis
Page 1233 and 1234:
Index 1219 INDEX Symbols +ssRNA 237
Page 1235 and 1236:
Index 1221 antigen-presenting cells
Page 1237 and 1238:
Index 1223 Bordetella 142 Bordetell
Page 1239 and 1240:
Index 1225 chromosomes 372, 394 chr
Page 1241 and 1242:
Index 1227 de Duve 113 dead zone 35
Page 1243 and 1244:
Index 1229 Enteroinvasive E. coli (
Page 1245 and 1246:
Index 1231 Gardnerella vaginalis 47
Page 1247 and 1248:
Index 1233 shunt 298 Hfr cell 443 H
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Index 1235 iron lungs 1118 iron-sul
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Index 1237 maturation 230 mature na
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Index 1239 Health 501 National Noti
Page 1255 and 1256:
Index 1241 patterns (PAMPs) 710 pat
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Index 1243 primary lymphoid tissue
Page 1259 and 1260:
Index 1245 596, 1048, 1051, 1051 ri
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Index 1247 sterilant 511, 541 steri
Page 1263 and 1264:
Index 1249 toxigenicity 633 toxin 6
Page 1265:
Index 1251 water activity 522 water
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Microbiology, 2021

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