Unit 1 The Microbes: Their History, Diversity, and Structure

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1 Unit 1 The Microbes: Their History, Diversity, and Structure Unit 1- page 1

2 FOM Chapter 1 - Microbiology: Then and Now Preview: In Chapter 1, we examine the discovery of microorganisms, and recognize how some of these microscopic living creatures were identified with disease and disease transmission. In fact, some of these disease encounters still challenge microbiology today. Chapter Learning Objectives: After you have reviewed all of Unit workbook materials, you should be able to: [Answer these in your own words] Outline the contributions Antony van Leeuwenhoek made to our knowledge of microorganisms. Define a miasma. Summarize the epidemiological work of Semmelweis and Snow and explain how their work dealt a blow to the miasma idea of infectious disease. Identify the major contribution Pasteur, Lister, and Koch each made to the germ theory of disease during the Golden Age of microbiology KEY CONCEPT 1.1 The Discovery of Microbes Leads to Questioning Their Origins The First Living Organisms Appeared About 3.8 Billion Years Ago Earth formed (4.5 bya) bya = billions of years ago mya = millions of years ago 3.8 bya 700 to 500 mya Land plants and animals appear 200,000 ya First humans appear Beginning of agriculture ( civilization ) 5,000 ya Unit 1 page 2

3 Microscopy Discovery of the Very Small Miasmas cause disease 2,100 ya Leeuwenhoek ( s) 400 ya Invention of the microscope 350 ya Unit 1- page 3

4 KEY CONCEPT 1.2 Disease Transmission Can Be Prevented 350 ya Ignaz Semmelweis (1850) Disease: 170 ya Development of Epidemiology Source: Chain of transmission: Prevent transmission: John Snow (1854) Disease: Source: Chain of transmission: Prevent transmission: Unit 1 page 4

5 KEY CONCEPT 1.3 The Classical Golden Age of Microbiology Reveals the Germ 170 ya Pasteur (1860s) Lister (1865) 150 to 130 ya Koch s Postulates Koch (1876) Unit 1- page 5

6 KEY CONCEPT 1.4 With the Discovery of Microbes, the Microbial World Expands Chapter Learning Objectives: After you have reviewed all of Unit 1.4 workbook materials, you should be able to: [Answer these in your own words] Define an organism and a microorganism. Identify the organisms and agents that compose the microbial menagerie and assign the organisms as prokaryotes or eukaryotes. Identify the disciplines within microbiology. Briefly describe the human microbiota. Unit 1 page 6

7 The Microbial Menagerie Today Unit 1- page 7

8 There Are Several Disciplines of Microbiology Human microbiota Unit 1 page 8

9 KEY CONCEPT 1.6 The Third Golden Age of Microbiology Is Now Chapter Learning Objectives: After you have reviewed all of Unit 1.6 workbook materials, you should be able to: [Answer these in your own words] Name five challenges facing microbiology today. Describe the four epidemiological disease patterns and then explain why these patterns are important to public health today. Microbiology Continues to Face Many Challenges Global Mortality from Infectious Disease 2015 Unit 1- page 9

Public health: Investigating Disease Patterns --- Today Infectious disease surveillance is a continuing job for the Centers for Disease Control and Prevention (CDC) as well as for state health

10 Public health: Investigating Disease Patterns --- Today Infectious disease surveillance is a continuing job for the Centers for Disease Control and Prevention (CDC) as well as for state health agencies, including the Division of Epidemiology and Disease Control within the Arizona Department of Health Services. Morbidity number Morbidity rate Mortality number Mortality rate Importance of such studies to public health Unit 1 page 10

11 Student Test Prep Study Set 1a Chapter 1 Microbiology: Then and Now Vocabulary [A strong vocabulary often means a better grade] agar animalcule antisepsis bacterium (pl. bacteria) epidemiology eukaryotic fungus (pl. fungi) germ miasma microorganism (microbe) organism pathogen prokaryotic protist pure culture virus Infectious Diseases [Diseases covered in this study set] Listeriosis Listeria monocytogenes (bacterium) Childbed (puerperal) fever Streptococcus pyogenes (bacterium) Cholera Vibrio cholerae (bacterium) Short Answer Questions [Answer these in your own words] Besides the Chapter Learning Objectives for Chapter 1, after understanding the unit material and textbook readings, you should be able to: 1. Support the statement Viruses are not microorganisms. 2. Refute the statement All microbes are pathogens. Chapter Self-Test [Refer to the end of Chapter 1 in FOM 11e, pp ] STEP A: REVIEW OF FACTS AND TERMS Multiple Choice: 1, 4, 6, 7, 13, and 15 True-False: 17, 18, and 21 STEP B: CONCEPT REVIEW Question 27 STEP C: APPLICATIONS AND PROBLEM SOLVING - None STEP D: QUESTIONS FOR THOUGHT AND DISCUSSION Questions 37 MicroPuzzlers The crossword puzzles provide an opportunity to test your microbiology vocabulary. Most terms in the puzzle relate to the microbiology class, assigned readings, and the indicated Study Set. Unit 1- page 11

12 MICROPUZZLER 01 Study Set 1a: Chapter 1 ACROSS 2. The rate refers to the total illnesses per 100,000 individuals 4. One observed by Leeuwenhoek 8. Infectious diseases that have recently appeared for the first time 11. The belief that foul air caused disease 13. The environment where Pasteur said germs existed 14. resistance is a major challenge facing medicine today 15. He proved the germ theory of disease 17. The common term for a microorganism 18. He believed germs were responsible for surgical infections 20. One of the fathers of epidemiology 21. The theory states that some microorganisms cause infectious disease 22. The study of the origin and transmission of disease 26. The only nonorganism in the microbial menagerie 27. Solidifying agent used to grow microbes The bacterial disease studied by John Snow 31. A microbe resistant to many antibiotics 32. He proposed the germ theory of disease 33. A disease-causing organism 34. A foodborne disease 35. Healthy parts of the body lacking a microbiota are said to be this DOWN 1. A yeast or mold 3. The use of biological agents to cause disease upon a large population The number refers to the total deaths in a population 6. Most scientists believe change may affect the frequency and distribution of infectious diseases globally 7. A member of the eukaryotic group of organisms 9. Koch s associated a specific disease with a specific pathogen 10. A prokaryotic organism 11. Microorganisms normally found on and in the human body 12. The study of fungi 16. An infectious disease with a resurgence in resistant forms 19. An organism without a cell nucleus 23. The type of diseases studied in BIO Yeasts and protists are these 25. The method of preventing infection, as in surgery 28. Semmelweis looked for the source of childbed 30. A living entity made of one or more cells 32. The type of culture perfected by Koch Unit 1 page 12

13 MICROPUZZLER 02 Knowledge review only: Chapter 2 ACROSS 1. Found in cell membranes 3. Formed in a chemical reaction 5. The kinds and amounts of atoms in a chemical is called the formula 7. A single-stranded polynucleotide having the base uracil 9. A ph of 4 is considered 10. Proteins are built from acids 12. A six-carbon sugar like glucose 14. DNA and RNA are a type of acid 15. Organic compound composed of carbon, hydrogen, and oxygen atoms that build sugars and starches 18. A hydrophobic, organic compound 20. A complex carbohydrate like starch or glycogen 22. In all cells, water acts as a 23. A type of lipid that can be saturated or unsaturated 24. A negatively charged atom DOWN 1. The most abundant and diverse compound in all cells 2. A monosaccharide 3. A measure of acidity 4. The atomic element in all organic molecules 6. The starting material for a chemical reaction 8. A sugar such as sucrose or lactose 11. A chain of amino acids 12. Two or more atoms held together by covalent bonds 13. A charged atom 16. The genetic material of all organisms 17. A negatively charged atomic particle 19. A positively charged atomic particle 21. A substance dissolved in water Unit 1 page 13

14 FOM Chapter 3 Concepts and Tools for Studying Microorganisms Preview: In Chapter 3, we will examine the concepts of microorganism complexity, interrelationships, and nomenclature. We then consider the microscope and the staining techniques to visualize microbial cells. KEY CONCEPT 3.1 Prokaryotes Are Not Simple, Primitive Organisms Chapter Learning Objectives: After you have reviewed all of Unit 3.1 workbook materials, you should be able to: [Answer these in your own words] Identify shared organizational patterns between bacterial cells and eukaryotic microbial cells. Discuss why prokaryotic cells are so small. Identify the structures and processes typical of a bacterial cell and a eukaryotic microbial cell. Explain how mitochondria and chloroplasts evolved and identify their similar characteristics to bacterial cells. Prokaryotic and Eukaryotic Cells Share Organizational Patterns Yet Have Structural Distinctions Shared organizational patterns and behaviors Homeostasis and metabolism Biofilms and multicellular communities Pseudomonas aeruginosa and cystic fibrosis Unit 1 page 14

15 Why Are Bacterial Cells So Small When Compared to Eukaryotic Cells? 1µm Unit 1 page 15

16 Microbial Structure and Cell Processes Have Some Similarities but Important Differences [FOM 11/e: pp ] A Comparison of Bacterial and Eukaryotic Cells Structure or Process Bacterial cell Eukaryotic cell Comments Cell nucleus DNA in the form of chromosomes Nuclear envelope Cell (plasma) membrane Cytoplasm Ribosomes Endomembrane system Endoplasmic reticulum, Golgi apparatus, lysosomes NO Mitochondria Cellular respiration Chloroplasts Photosynthesis Cell wall YES SOME No cell walls on animal cells What structures and processes are universal to all organisms? Unit 1 page 16

17 Mitochondria and Chloroplasts Once Were Free-Living Bacterial Cells Endosymbiont theory Unit 1 page 17

2 workbook materials, you should be able to: [Answer these in your own words] Describe the three areas of taxonomy.

18 KEY CONCEPT 3.2 Classifying Microorganisms Reveals Relationships Between Organisms Chapter Learning Objectives: After you have reviewed all of Unit 3.2 workbook materials, you should be able to: [Answer these in your own words] Describe the three areas of taxonomy. Identify the domains in the tree of life and describe the organisms in each domain. Discuss how organisms are given scientific names. Taxonomy Attempts to Define and Name Organisms 1. Classification arranges organisms into groups The Three-Domain System Tree of Life Unit 1 page 18

19 2. Nomenclature gives scientific names to organisms Binomial system 3. Identification assigns organisms to a known group Unit 1 page 19

20 KEY CONCEPT 3.3 Microscopy Is Used to Visualize the Structure of Cells Chapter Learning Objectives: After you have reviewed all of Unit 3.3 workbook materials, you should be able to: [Answer these in your own words] Identify the units of measurement for cells, cell parts, and viruses. Contrast magnification and resolution with a microscope. Explain why contrast is important to microscopy. Distinguish between the two basic types of staining techniques used to provide contrast with light microscopy. Identify the maximum magnification and the resolution limit of the light microscope, the transmission electron microscope, and the scanning electron microscope. Many Microbial Agents Are in the Micrometer Size Range Micrometer Nanometer Light Microscopy Is Used to Observe Most Organisms Magnification Resolution Unit 1 page 20

21 Staining Techniques Provide Contrast Contrast Advantages: Microscope field Staining Techniques Simple stain Differential stain Electron Microscopy Provides Detailed Images of Cells, Cell Parts, and Viruses Transmission electron microscope Scanning electron microscope Unit 1 page 21

22 Student Test Prep Exam Study Set 1b Chapter 3 Concepts and Tools for Studying Microorganisms Vocabulary [A strong vocabulary often means a better grade] Archaea Bacteria biofilm cell (plasma) membrane cell wall chromosome cytoplasm differential stain DNA dye endosymbiosis Eukarya genus (pl. genera) Gram stain homeostasis micrometer (µm) morphology nanometer (nm) ribosome RNA simple stain species specific epithet taxonomy Short Answer Questions [Answer these in your own words] Besides the Chapter Learning Objectives for Chapter 3, after understanding the unit material and textbook readings, you should be able to: 1. You have discovered a new type of microbe never seen before. What types of questions might a taxonomist ask about this microbe? Chapter Self-Test [Refer to the end of Chapter 3 in FOM 11e, pp ] STEP A: REVIEW OF FACTS AND TERMS Multiple Choice: 1, 3, 8, and 10 Matching: 11, 12, 15-17, and 19 STEP B: CONCEPT REVIEW Statements STEP C: APPLICATIONS AND PROBLEMS: None STEP D: QUESTIONS FOR THOUGHT AND DISCUSSION Questions 29 Unit 1 page 22

23 MICROPUZZLER 03 Study Set 1b: Chapter 3 Across 1. Made up of the genus and specific epithet 3. The evolutionary process that gave rise to the mitochondrion and chloroplast 5. The property of enlarging an image 9. One of the prokaryotic domains 11. An energy structure missing from prokaryotic cells 12. The type of staining that uses one dye 14. Organisms lacking a cell nucleus The specific is part of a species name 18. Proteinsynthesizing machine found in all cells 20. 1/1,000 of a micrometer 21. The metric unit used to measure bacterial cells 23. Most bacterial cells have an outer covering called the cell 26. The microscope magnifies up to 1000X 28. A cell surrounds all cells 29. An important property of a microscope 30. The science dealing with the cataloging of organisms Down 1. The type of electron microscope that produces a 3Dlike image 2. A cell s internal contents 4. The genetic instructions for all organisms 6. A type of differential stain 7. The electron microscope that looks at thin sections of a cell 8. The first word of a binomial name 10. The Gram stain is an example of a staining procedure 13. The fungi and protists are in this domain 14. A multicellular group of bacterial species 15. DNA is organized into this thread-like structure 17. The property of staying the same 19. The scientific term that refers to cell shape 22. Needed to easily see an object against a white background 24. The tree of has three domains 25. The substance used to color cells for contrast 27. Only members of the Eukarya have a nucleus Unit 1 page 23

FOM Chapter 4 Structure and Organization of Prokaryotic Cells Preview: In Chapter 4, we first survey the shapes and arrangements of bacterial cells.

24 FOM Chapter 4 Structure and Organization of Prokaryotic Cells Preview: In Chapter 4, we first survey the shapes and arrangements of bacterial cells. Then, we examine bacterial cell structure, including the cell surface structures and the common internal compartments. KEY CONCEPT 4.1 Prokaryotes Can Be Distinguished by Their Cell Shape and Arrangements Chapter Learning Objectives: After you have reviewed all of Unit 4.1 workbook materials, you should be able to: [Answer these in your own words] Identify the shapes (morphologies) and arrangements (or forms) for typical bacterial cells. Variations in Cell Shape (Morphology) and Cell Arrangement Exist Unit 1 page 24

25 KEY CONCEPT 4.2 Bacterial and Archaeal Cells Have an Organized Cell Structure Cell Structure Organizes Cell Function An idealized bacterial cell Name Associated with G+, G, or both Chemical composition (i.e., carbohydrate, lipid, protein, DNA/RNA) Function(s): some involved with pathogenesis Identify structure in Pommervillian drawing Represents ½ Gram + and ½ Gram Unit 1 page 25

26 KEY CONCEPT 4.4 Most Prokaryotic Cells Have a Cell Envelope Chapter Learning Objectives: After you have reviewed all of Unit 4.4 workbook materials, you should be able to: [Answer these in your own words] Identify the structures forming the bacterial cell envelope. Describe the general characteristics of the bacterial cell wall. Compare and contrast the structure and parts of the gram-positive cell wall with those of the gram-negative cell wall in bacterial cells. Explain in what ways the bacterial cell membrane is similar to and unique from the eukaryotic plasma membrane. Bacterial cell envelope The Bacterial Cell Wall Is a Tough and Protective External Shell Cell wall characteristics Association Chemical composition Function Unit 1 page 26

27 Gram-positive wall Unit 1 page 27

28 Gram-negative wall The Cell Membrane Represents a Selectively Permeable Barrier Additional functions Unit 1 page 28

29 KEY CONCEPT 4.3 Cell Surface Structures Interact with the Environment Chapter Learning Objectives: After you have reviewed all of Unit 4.3 workbook materials, you should be able to: [Answer these in your own words] Identify the association, chemical composition, and roles of the (a) pili and (b) glycocalyx. Explain the role of the bacterial flagella. Unit 1 page 29

30 Flagella (sing. flagellum) Provide Motility Chemotaxis Unit 1 page 30

31 Identification Summary: Cell Envelope and External Structures Unit 1 page 31

32 KEY CONCEPT 4.5 The Cell Cytoplasm Is Packed with Internal Structures Chapter Learning Objectives: After you have reviewed all of Unit 4.5 workbook materials, you should be able to: [Answer these in your own words] Discuss the chemical makeup of the bacterial cell cytoplasm. Explain the difference between the genetic content of the bacterial nucleoid and cytoplasmic plasmids. Distinguish between the other subcompartments that can be found in the bacterial cytoplasm. The Cell Cytoplasm Is Primarily Water in a Gel-Like State Cell association Chemical composition Function The Nucleoid Represents a Subcompartment Containing the Chromosome Cell association Chemical composition Function Unit 1 page 32

33 Plasmids Are Found in Many Bacterial and Archaeal Cells Cell association Chemical composition Function Other Subcompartments Exist in the Cell Cytoplasm Ribosomes Cell association Chemical composition Function Inclusions Cell association Chemical composition Function Unit 1 page 33

34 Identification Summary: Cell Cytoplasm and Internal Structures Unit 1 page 34

35 Student Test Prep Study Set 1c Chapter 4 Structure and Organization of Prokaryotic Cells Vocabulary [A strong vocabulary often means a better grade] bacillus (pl. bacilli) capsule/slime layer cell envelope cell membrane cell wall chemotaxis coccus (pl. cocci) cytoplasm genome glycan inclusion lipopolysaccharide (LPS) lysozyme nucleoid outer membrane pathogenesis penicillin peptidoglycan periplasm plasmid porin ribosome slime layer spiral spirillum (pl. spirilla) spirochete teichoic acid tetrad vegetative cell vibrio Short Answer Questions [Answer these in your own words] Besides the Chapter Learning Objectives for Chapter 4, after understanding the unit material and textbook readings, you should be able to: 1. Identify the (a) association, (b) chemical composition, and (c) function(s) for each of the following structures in gram-positive and/or gram-negative bacterial cells: cell membrane, flagellum, glycocalyx, inclusion, nucleoid, periplasm, pilus, plasmid, and ribosome. Chapter Self-Test [Refer to the end of Chapter 4 in FOM 11e, pp ] STEP A: REVIEW OF FACTS AND TERMS Multiple Choice: Questions 1, 3-6, Label Identification: 16 (A-G, I-M) STEP B: CONCEPT REVIEW Descriptions 17 (for bacterial cells only), STEP C: APPLICATIONS AND PROBLEMS Question 23 and 24 STEP D: QUESTIONS FOR THOUGHT AND DISCUSSION Question 26 Unit 1 page 35

36 MICROPUZZLER 04 Study Set 1c: Chapter 4 Across 2. A sphericalshaped cell 6. Gram- cell walls have teichoic acid 9. The region between the cell membrane and the outer membrane 12. A metabolizing, non-reproductive bacterial cell 13. The stain is an example of a differential stain 14. Gram-positive cell walls have many layers of 16. Independent loop of DNA in some bacterial cells 18. An antibiotic that works best on a gram-positive cells 24. The glycan molecules are a type of 27. Part of the bacterial cell envelope (2 words) 29. A rod-shaped bacterial cell 31. Only gram-negative cells have a/an membrane 32. One of the disaccharides in the peptidoglycan 33. A unique membrane protein found in gramnegative walls 34. A corkscrewshaped bacterial cell 35. A member of the bacterial or archaeal domain Down 1. The cell s interior 3. One of the three basic bacterial cell shapes 4. Spiral-shaped bacterial cells 5. A cell structure used for motility 7. The motility involving the movement of a cell toward chemicals, such as nutrients 8. A packet of four bacterial cells 10. Bacterial shape can be identified after a staining procedure 11. Similar to a slime layer in function General term for a carbohydrate layer used for attachment 17. The cell wall prevents lysis 19. A storage body in many bacterial cells 20. The outer half of the outer membrane (abbr.) 21. Gram- cells appear orange-pink after Gram staining 22. A bacterial protein structure used for attachment 23. All bacterial cells have a cell 25. Where proteins are built 26. A human-produced molecule causing gram-positive cells to swell and burst 28. The location of the bacterial genome 30. A curved rod is called this Unit 1 page 36

37 UNIT 1 EXAM Unit 1 page 37

Introductory Microbiology Dr. Hala Al Daghistani

Introductory Microbiology Dr. Hala Al Daghistani Why Study Microbes? Microbiology is the branch of biological sciences concerned with the study of the microbes. 1. Microbes and Man in Sickness and Health