Introduction to Microbiology FINAL STUDY GUIDE_LATEST,100% CORRECT

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1. Define microbiology? 1. Where do you find microorganisms? 2. How many microorganisms are estimated to be on Earth? 3. How long have microorganisms been on Earth? 4. Are the majority of micro ... organisms beneficial or harmful? 5. Do good or bad microorganisms get the most publicity? Why? 6. How do microorganisms impact our lives through the following: A. Disease B. Agriculture C. Food D. Energy E. Bioremediation F. Biotechnology 7. What are microorganisms made of? Structure & Function 1. Name six characteristics of living cells. 2. Who was the first to use a microscope to see microorganisms? What did he see? What type of microscopy did he use? 3. Who was the first to use a microscope to see bacteria? How do we know he saw bacteria? 4. What type of microscopy did he use? 5. What are the four types of light microscopy? 6. What must be done to a microorganism to be able to see it with brightfield light microscopy? 7. Which types of light microscopy allow you to view a live sample? 8. What is the maximum resolution of a compound light microscope? Describe what that value means in practical terms when viewing a specimen. 9. What are the two types of electron microscopy? When would you use one type instead of the other? 10. What is the maximum resolution of an electron microscope? 11. What is the smallest microbial cell size discovered thus far? Would this cell have a high or low surface area-to-volume ratio compared to an average eukaryotic cell? 12. What is the significance of a cell having a high surface area-to-volume ratio? 13. Discuss the problems a cell might have it were less than 0.2microns. 14. Compare and contrast a prokaryotic microbial cell and eukaryotic microbial cell. 15. What microorganisms have a phospholipid bilayer form their cytoplasmic membrane? 16. What microorganisms have a lipid monolayer form their cytoplasmic membrane? 17. Contrast the phospholipid bilayer with the lipid monolayer? What molecules make up each? What are the different linkages characteristic of each? 18. What advantage would microorganisms with a lipid monolayer have over those with a lipid bilayer? 19. What are the functions of the cytoplasmic membrane? 20. Where is the cell wall located relative to the cytoplasmic membrane? 21. What Bacteria lack a cell wall? 22. What are most Bacteria cell walls made of? 23. The amount of peptidoglycan in the cell walls of Bacteria distinguishes what types of Bacteria? 24. Describe the peptidoglycan structure. The glycosidic bond between the two N-acetyl-glucose sugars in peptidoglycan can be cleaved by what enzyme? What is the significance of using that enzyme to cleave that bond? 25. Describe what would happen if a bacterial cell were put in a solution with lysozyme added? 26. Describe the Gram-positive cell wall. 27. What is function of teichoic acids and lipoteichoic acids? 28. Describe the Gram-negative cell wall. 29. What is the lipopolysaccharide layer? 30. What part of the LPS is toxic? When is it toxic? 31. Compare and contrast Archaea pseudomurein and Bacteria peptidoglycan. 32. What types of cell walls are found in Archaea species? 33. What types of cell walls are found in Eukarya species? 34. What are the functions of the cell wall? How does the structure of a cell wall suit the functions? 35. What are fimbriae? What does a prokaryotic cell do with fimbriae? 36. What is a pilus? What does a prokaryotic cell do with a pilus? 37. Where would an S-layer be found? What purpose does it serve? 38. Can all Bacteria form a capsule? 39. What is a capsule made of? How does a capsule’s composition suit its function? 40. Slime is made for what purpose? 41. What type of microorganisms make slime? 42. Movement using slime secretion is called what? 43. What are the 3 main parts of the prokaryotic flagellum? What is the purpose of each? 44. Compare and contrast a prokaryotic and eukaryotic flagellum. 45. Would you expect a Bacteria and Archaea flagellum to be the same or different? 46. Identify the two types of flagellation. Describe the movement of a polar flagellated prokaryotic cell. 47. Describe the movement of a peritrichous flagellated prokaryotic cell. 48. What are taxes? Give 3 examples of taxes. 1. Describe an experiment to demonstrate chemotaxis. 2. Describe an experiment to demonstrate phototaxis. 3. Describe an experiment to demonstrate aerotaxis. 49. What does a cell use to sense the environment? 50. What are 2 other ways that a cell can move other than gliding and flagella? 51. Describe how a cyanobacterium could move to obtain optimum wavelengths of light for photosynthesis. 52. Where do Gram-negative purple sulfur bacteria store sulfur? 53. What does the carboxysome store for some bacteria and cyanobacteria? 54. Describe the process of sporulation. 55. How does the structure of an endospore help it to be a survival structure? 56. Where are endospores formed? Does this vary depending on the microorganism? 57. Describe the process of germination: 58. What age is the oldest known endospore to have germinated? Where was the endospore found? 59. What are the organelles of a eukaryotic cell? What is the purpose of each organelle? 60. Describe the flow of information within the cell for a digestive enzyme starting with the DNA in the nucleus. 61. Are viruses living cells? 62. What is a virus made of? 63. What are the two forms of a virus? In which form does the virus do harm? 64. Describe the genome of a virus. How do viral genomes differ from the genomes of living cells known today? 65. What part of a virus gives the nucleocapsid its helical or icosahedral symmetry? 66. What is a viral envelope? To what cell structure is the viral envelope similar? 67. What does it mean for a virus to have complex structure? 68. Distinguish between a viroid and a prion. Are they living? Are they viruses? 69. Describe the possible mechanism by which a prion causes disease. Genetics 1. In what form (single or double stranded, linear or circular) are most prokaryotic genomes? 2. In what form (single or double stranded, linear or circular) are most eukaryotic genomes? - 3. Describe the process of replication. How does replication differ in bacteria versus eukaryotes? Where does replication occur in the cell? What is the outcome of replication? 4. What is the origin of replication? How many are there? Name the enzymes involved in replication and what they do during replication. - Describe the process of transcription. How does transcription differ in bacteria versus eukaryotes? Where does transcription occur in the cell? What is the outcome of transcription? What strand of the double stranded (ds) DNA is transcribed – 5’ to 3’ or 3’ to 5’? 5. Compare and contrast prokaryotic sigma factor with eukaryotic transcription factors. How would a single gene be transcribed in a bacterial cell? 6. How would a single gene be transcribed in a eukaryotic cell? 7. How would multiple genes of an operon be transcribed in a bacterial cell? 8. Are operons found in eukaryote genomes? 9. Using the arg operon, describe enzyme repression. A. When is the repressor bound to the operator? B. Under what condtions does transcription of the arg operon occur? C. What is the outcome of transcribing the arg operon? 10. Using the lac operon, describe enzyme induction. A. When is the repressor bound to the operator? B. Under what condtions does transcription of the lac operon occur? C. What is the outcome of transcribing the lac operon? 11. How does a repressor protein inhibit the synthesis of a specific mRNA? 12. How does a negatively controlled operon differ than a positively controlled operon? 13. Using the lac operon, describe catabolite repression. 14. How is the lac operon regulated by both catabolite repression and enzyme induction? 15. Is catabolite repression of the lac operon positive or negative control of transcription? - When faced with several sugars as possible carbon sources, do E. coli cells use all of them at the same time or is there a preference and order to their use? 16. Using the mal operon, describe positive control of transcription. A. Under what conditions does transcription of the mal operon occur? B. What is the outcome of transcribing the mal operon? 17. How does an activator protein differ from a repressor protein? 18. Describe the process of translation. How does translation differ in bacteria versus a eukaryote? Where does translation occur in the cell? What is the outcome of translation? 19. In what direction does the ribosome translate mRNA – 5’ to 3’ or 3’ to 5’ ? 20. If you were given a ribonucleotide (ss mRNA) sequence how would you find the open reading frame? Find AUG start codon and go to stop codon (UAA,UGA,UAG) 21. If you were given a nucleotide (ds DNA) sequence how would you find the open reading frame? Translate to RNA sequence, find start codon, find stop codon What three types of RNA are used for translation? tRNA, mRNA, and ribosomes 22. How does the ribosome differ in bacteria versus eukaryotes? 23. What part of the ribosome is used to determine which amino acid gets added to the polypeptide? 24. What amino acid does AUG code for in bacteria and eukaryotes? 25. How do nonsense codons signal translation to stop? - 26. Describe a way to get a lot of protein from a single mRNA transcript. Metabolism 1. What is a redox reaction? 2. What happens to a molecule that is reduced? 3. What happens to a molecule that is oxidized?. 4. What does an electron carrier do? 5. How can NAD+ act as an electron carrier? 6. How can NADH act as an electron carrier? 7. What are examples of short term energy storage molecules? 8. What are examples of long term energy storage molecules? How is each considered an energy storage molecule? 9. Where does a chemoorganotroph get its energy and electrons? 10. Where does a chemolithotroph get its energy and electrons? 11. What type of phosphorylation occurs in glycolysis to make ATP? 12. What type of phosphorylation occurs in fermentation to make ATP? 13. What type of phosphorylation occurs in respiration to make ATP? 14. What type of phosphorylation occurs in photosynthesis to make ATP? 15. What molecules can be fermented? 16. What is syntrophy? When is Syntrophomonas capable of fermenting butyrate? What role would a methanogen play in helping Syntrophomonas ferment butyrate? 17. If glucose is fermented, where does the ATP come from? What type of phosphorylation generated that ATP? What happens to pyruvate? Why is it necessary for pyruvate to be reduced to lactate or other fermention product? 18. Describe homolactic fermentation of glucose. What microorganisms are capable of this type of fermentation? 19. Describe heterolactic fermentation of glucose. What microorganisms are capable of this type of fermentation? 20. What are the differences between homolactic and heterolactic fermentation? 21. Describe mixed acid fermentation. What microorganisms are capable of this type of fermentation? Would a broth culture of Escherichia coli fermenting glucose have an acidic (low), neutral, or alkaline (high) pH? 22. Describe butanediol fermentation. What microorganisms are capable of this type of fermentation? Would a broth culture of Enterobacter aerogenes fermenting glucose have an acidic (low), neutral, or alkaline (high) pH? 23. How could you tell if an organism did mixed acid fermentation or butanediol fermentation? 24. How is ATP made in a hydrogenosome? What product of glycolysis is used to make ATP in the hydrogenosome? What kind of microorganism has hydrogenosome? What organelle do these microbes lack? 25. What product of glycolysis feeds the citric acid cycle? 26. Does the citric acid oxidize or reduce pyruvate to carbon dioxide? 27. Where do the NADH and FADH generated by redox reactions of the citric acid cycle go? 28. What are the intermediates of the citric acid cycle, such as oxalacetate and α-ketoglutarate used for? 29. Aerobic and anerobic respiration differ in what way? 30. What is the terminal electron acceptor for aerobic respiration? 31. What is the terminal electron acceptor for anaerobic respiration? 32. List 4 protein electron carriers. How many electrons and protons can each accept and donate? 33. Name a very common group of non-protein electron carriers. How many electrons and protons can it accept and donate? 34. Which electron carriers contribute to the proton motive force needed to make ATP? 35. What are the components of an electron transport chain? What is the purpose (the outcome) of an electron transport chain? 36. In a eukaryotic cell, in what organelle would an electron transport chain be located? In what membrane? On which side of the membrane will protons accumulate? On which side of the membrane will ATP be made? 37. In a prokaryotic cell, in what membrane would an electron transport chain be located? On which side of the membrane will protons accumulate? On which side of the membrane will ATP be made? 38. Facultative aerobes like E. coli have the ability to do aerobic respiration (Fig. 21.14a), anaerobic respiration (Fig. 21.14b), and fermentation (Fig. 15.23a). Which form of metabolism will E. coli use in an oxic environment? Which form of metabolism will E. coli use in an anoxic environment? Which form of metabolism used by E. coli can be thought of as a back-up way to make ATP, to be used when the others cannot be used? 39. What term is used to describe the use of a proton motive force to generate ATP? 40. In what way is the ATP synthase similar to bacterial flagella? 41. What is the energy source for a phototroph? 42. Name the pigments responsible for harvesting light energy for phototrophs. Where are these pigments located in a eukaryotic cell? In a prokaryotic cell? 43. What pigment resides in the photosynthetic reaction centers in an anoxygenic phototroph? 44. What pigment resides in the photosynthetic reaction centers in an oxygenic phototroph? 45. What do antenna pigments do? 46. Compare and contrast anoxygenic and oxygenic photosynthesis. 47. What is the initial electron donor to anoxygenic photosynthesis? 48. What is the initial electron donor to oxygenic photosynthesis? 49. How is oxygen generated in oxygenic photosynthesis? 50. How is NADH generated in anoxygenic photosynthesis? 51. How is NADH generated in oxygenic photosynthesis? 52. What process can use the NADH generated by anoxygenic and oxygenic photosynthesis? 53. Name a model organism used to study anoxygenic photosynthesis. 54. Name a prokaryotic model organism used to study oxygenic photosynthesis. 55. Name a eukaryotic model organism used to study oxygenic photosynthesis. 56. List all catabolic processes discussed in class. 57. The short term energy (ATP) generated by these catabolic processes is used for what? 58. Where can organisms get there carbon? 59. What name is given to an organism that can take carbon dioxide from the air other organic compounds? 60. Where do heterotrophs get their carbon? 61. Explain why the Calvin-Benson cycle is often referred to as the dark reaction of photosynthesis. 62. If we split the term photosynthesis into “photo” and “synthesis,” which would be used to describe the Calvin-Benson cycle? 63. The Calvin-Benson cycle is used by autotrophs to make . 64. What is the initial reaction of the Calvin-Benson cycle? 65. RubisCO fixes carbon dioxide (1 carbon) by binding it and ribulose 1,5-bisphosphate (5 carbons) to form two 3-carbon molecules of . 66. RubisCO is an acronym. What does it stand for? What other molecule besides carbon dioxide can RubisCO bind? How could this be a problem? 67. What is the purpose of the Calvin-Benson cycle? 68. What is the purpose of the reverse citric acid pathway? 69. What is the purpose of the hydroxypropionate pathway? 70. What is the purpose of the acetyl-CoA pathway? 71. How are sugars made? What catabolic process is used? What catabolic process is used in reverse? 72. What are pentose sugars made from? 73. Use ADPG to explain “activated glucose”. How does this activated glucose provide the energy to add the glucose onto a polysaccharide of glucose like glycogen, starch, or cellulose? Microbial Growth Highlighted questions are from articles 1. Distinguish between macronutrients and micronutrients. 2. Give at least 6 examples of macronutrients. 3. Give at least 4 examples of micronutrients. 4. How do growth factors differ from macronutrients and micronutrients? 5. Name the 5 groups describing an organism’s relationship to oxygen. 6. What type of broth can be used to determine an organism’s oxygen requirement? What does this broth contain that makes it possible to determine an organism’s oxygen requirement? 7. You inoculate the following organisms into tubes containing thioglycolate broth. Where would you expect to see growth in the tube? a. Obligate aerobe – b. Obligate anaerobe – c. Facultative aerobe – d. Microaerophile – e. Aerotolerate anaerobe 8. What accommodations need to be made to grow an aerobe in the lab? 9. What accommodations need to be made to grow an anaerobe in the lab? 10. During what process are toxic oxygen molecules generated? 11. How does an organism protect themselves from toxic oxygen molecules? 12. What enzyme combinations would detoxify superoxide (O2 )? In what organisms might those combinations be found? 13. Where can an organism get nitrogen? 14. Name a molecule that requires phosphorus. Where can a cell get phosphorus? 15. Name a molecule that requires sulfur. Where can a cell get sulfur? 16. Name a molecule that requires potassium. Where can a cell get potassium? 17. Name a molecule that requires magnesium. Where can a cell get magnesium? 18. Name a molecule that requires iron. What specialized molecule allows some organisms to sequester iron? What are two examples of siderophores? 19. Name a structure that requires calcium. Where can a cell get calcium? (See Table 5.1) 20. Name a structure that requires sodium. Where can a cell get sodium? (See Table 5.1) Can sodium motive force (instead of a proton motive force) be used by some organisms to generate ATP? 21. Define growth as it pertains to microorganisms. 22. What is the most common process by which prokaryotes grow? 23. What genomic event must take place before a cell divides? 24. What proteins are required to move the copies of DNA to opposite sides of the dividing cell? 25. Following DNA replication, what must form for cell division to continue? 26. What proteins form the divisome? Where are these proteins located? How does there location correlate with where division will begin? 27. Does the divisome move? 28. FtsZ protein has similar amino acid sequence to what eukaryotic cytoskeletal protein? 29. As the cell elongates new cell wall is laid down at certain sites determined by the location of what protein? 30. As the cell elongates holes are made in the existing cell wall to make room for new cell wall material. What enzyme makes these holes? What happens if these holes are not quickly filled with new cell wall material? If a cell lacks FtsI proteins, what will happen once these holes are made? 31. How does the new peptidoglycan precursor differ from existing cell wall peptidoglycan? 32. How does the new peptidoglycan precursor get to the expanding cell wall? 33. What makes bactoprenol a good molecule to transport the new peptidoglycan precursor across the cytoplasmic membrane? 34. FstI proteins catalyze what reaction? 35. What happens to the peptidoglycan precursor during transpeptidation? 36. In binary fission, where is new well wall added relative to the divisome? 37. Describe simple budding. How is simple budding different than binary fission? Give an example of a prokaryotic microorganism that divides by simple budding. Give an example of a eukaryotic microorganism that divides by simple budding. 38. Describe budding by hyphae. How is the new cell different than the parent cell? What is a swarmer cell capable of doing? Give an example of a prokaryotic microorganism that divides by budding by hyphae. 39. Describe cell division in stalked bacteria. How is the new cell different than the parent cell? Give an example of a prokaryotic microorganism that divides this way. 40. Compare and contrast cell division in stalked bacteria and budding by hyphae. 41. Describe the growth cycle. Do the growth phases always occur in the order presented in figure 6.10? 42. If you use a loopful of turbid culture of E.coli in stationary phase to inoculate a new broth culture, at what growth phase will the cells start? 43. If you use a loopful of turbid culture of E.coli in exponential phase to inoculate a new broth culture, at what growth phase will the cells start? 44. If you use a loopful of turbid culture of E.coli in lag phase to inoculate a new broth culture, at what growth phase will the cells start? Would it matter if the new broth culture was the same medium (same composition) or different medium? 45. Plot on a graph what the growth cycle would look like during the entire process described here: You grow an E.coli culture in glucose broth. Once it reaches stationary phase presumably due to consumption of all the glucose, you add additional glucose. 46. During exponential growth cells predictably . 47. Explain why generation time is often referred to as doubling time. 48. Graph the exponential growth examples on semilogarithmic graph paper, both of which are posted on Moodle. Be able to determine from the graphs, the generation time, how many cells after a period of time, and at what time would there be a certain number of cells. 49. Describe an everyday situation in which exponential growth would be relevant. 50. Know when to use N=N 2n. Be able to calculate the final cell number (N) if given the initial cell number and number of generations of growth. Be able to calculate the initial cell number (N0) if given the final cell number and number of generations of growth. 51. Know when to use g=t/n. Be able to calculate the generation time (g) if given the time of exponential growth and number of generations. Be able to calculate the amount of time of exponential growth (t) if given the generation time and number of generations. Be able to calculate the number of generations (n) if given the time of exponential growth and generation time. 52. Give an example of a batch culture. 53. How does a batch culture differ from a chemostat culture? 54. What can be controlled in a chemostat that allows for a continuous culture to be maintained? 55. What are the two types of cell counts? When would you use one type of cell count over the other? 56. What instrument is used for a total cell count? 57. Viable counts can be done in what 2 ways? 58. What procedure usually precedes a plate count? Why is this done? 59. What property of the culture is being measured by turbidity measurements? 60. What instrument is used for a turbidity measurement? 61. Turbidity is measure in units. 62. What exactly is the spectrophotometer measuring? 63. Be able to interpret a graph of turbidimetric measurements as shown in figure 6.17b. 64. What does a standard curve represent? 65. Describe the procedure for creating a standard curve. 66. Graph the standard curve examples on plain graph paper, both of which are posted on Moodle. From the graphs, be able to determine the optical density of a certain number of cells. 67. Distinguish between species richness and abundance. 68. In what type of environment would you expect to have specie richness? 69. In what type of environment would you expect to have specie abundance? 70. In the real world, how do microbes live? …as pure cultures?. 71. What term refers to where a microorganism lives? 72. List 3 reasons microbes sometimes grow differently in the lab than they do in their natural habitat? 73. Where do biofilms form? 74. Why do biofilms form? What advantages does living in a biofilm offer a microorganism? 75. List the stages of biofilm formation. What happens during each stage? At what stage would the biofilm look like a mushroom? 76. What problems are caused by biofilms? 77. Why are antimicrobial agents usually ineffective against biofilms? 78. Name a signal molecule released by some microbes to encourage biofilm formation. 80. How do acylated homoserine lactones promote biofilm formation? 81. What quorum sensing signaling molecule does Psuedomonas aeruginosa use? 82. Does Staphylococcus aureus use the same signaling molecule as P. aeruginosa? 83. What is absent from Delisea pulchra? What chemical is responsible for this? 84. How do furanones prevent biofilm formation? What stage of biofilm formation do furanones prevent? 85. Name a researcher who studies biofilms. Name at least one thing she discovered. In what bacteria did she discover this? 86. What can Vibrio fischeri and Vibrio harveyi do when enough cells get together? 87. What can Vibrio cholerae do when enough cells are present? 88. Are bacteria capable of knowing the cell next to them is like them or not? 89. What micronutrient is found in AI-2? 90. Where are most terrestrial microbes found? 91. In aquatic environments, what types of microbes are found the upper depths and at the surface? 92. In aquatic environments, what types of microbes are found the lower depths? 93. Describe the events that take place in a river after the introduction of sewage or other high-nitrogen or high-phosphorus input. (see Figure 23.9) 94. What happens to the oxygen concentration after the introduction of sewage or other high-nitrogen or high-phosphorus input? What microbes cause this? What metabolic process is responsible? When will the oxygen concentration return to previous levels? What microbes are responsible for this? What metabolic process is responsible? 95. What is “nonpoint pollution” referring to? 96. Where does fecal contamination of American beaches primarily come from? 97. Where would you find oxygenic phototrophs like cyanobacteria and algae within an aquatic environment? 98. Where would you find anoxygenic phototrophs like the purple and green sulfur bacteria within an aquatic environment? Why are they located here? 99. Where in the water column do phototrophs, chemoorganotrophs, and chemolithotrophs each reside in a marine (i.e. an ocean) environment? 100. What are terms used to describe an organism’s requirement for elevated pressure? 101. Describe the environmental conditions in the deep sea. 102. What structures on the ocean floor provide warmth and inorganic nutrients to organisms that live down there? 103. Where does the carbon dioxide come from that autotrophs use in the deep sea? 104.Define mutualism. Describe an example of a mutualistic relationship in the deep sea. 105.Do viruses require a living host cell? 106. Is it common for a virus to be able to infect across domains (Bacteria, Archaea, Eukarya)? 107. Name the two kinds of prokaryotic virus. Give an example of each. 108. What are the five steps in virulent phage life cycle? 109. What are the steps in a temperate phage life cycle? How does the life cycle of a temperate phage differ from a virulent phage? 110. What term is used to describe the alternative pathway that temperate phages have? 111. What term is used to describe the temperate virus when it is incorporated into the DNA of the host cell? 112. What term is used to describe a host cell harboring a prophage? 113. Name two repressor proteins that determine whether bacteriophage lambda enters lysogeny. What does each repressor protein do? 114. If both CI and Cro are simultaneously made by the virus, then how will levels of CI and Cro differ? . 115.Under what host cell conditions, would lambda enter lysogeny? Will CI or Cro protein concentration be higher? 116. Under what host cell conditions, would lambda enter the lytic cycle? Will CI or Cro protein concentration be higher? 117. Name and describe the 4 types of animal viruses. Which animal virus is similar to a virulent bacteriophage? Which animal virus is similar to a temperate bacteriophage? 118.What is the most infamous human retrovirus? 119. Describe of the structure of a typical retrovirus. 120. What is the genome of a retrovirus? RNA or DNA? Single-stranded or double-stranded? 121. What 3 enzymes are packaged inside the nucleocapsid of a retrovirus? What does each of these enzymes do for the virus? 122.Describe the retroviral replication cycle. At which points are reverse transcriptase, integrase and protease needed? 123. Name the 3 regions of the retroviral genome. Name and give the purpose of the proteins made from each region. 124. With no translational machinery (ribosomes, tRNAs) encoded by the virus, how does the virus makes its proteins? . 125. How do new retrovirus virions leave the host cell? 126. Where does the envelope come from that surrounds some viruses, like retroviruses? 127. How is the viral envelope similar to the host cells cytoplasmic membrane? 128. How is the viral envelope different from the host cells cytoplasmic membrane? Control of Microbial Growth 1. Describe two ways prokaryotes defend against viral infection. 2. What type of DNA is susceptible to restriction endonuclease cleavage? 3. Will restriction be effective against RNA viruses? Against ssDNA viruses? 4. How can viruses avoid host defenses? 5. What occurs during the latent period of viral replication? (see Fig. 10.9). 6. Describe RNA interference. What type (animal, prokaryotic, DNA, RNA, etc.) of virus is this effective against? 7. What is the primary way for humans to control the spread of viruses? 8. What kind of drugs can be used to treat viral infections? What do these medicines target? Can antibiotics be used to treat viral infections? 9. Who is Louis Pasteur? What hypothesis did he disprove? 10. Is pasteurization the same as sterilization? 11. List the 4 methods of physical sterilization. Which is most widely used? 12. Why can’t heat be used to sterilize everything? 13. The temperature needed for heat sterilization depends on the temperature of growth for an organism. 14. Define decimal reduction time. Would the decimal reduction time be more quickly achieved at lower or higher temperatures? 15. What equipment is used to heat sterilize? 16. How does an autoclave sterilize? 17. What factors determine the amount of autoclave time needed for sterilization? 18. List 4 factors that increase heat resistance. 19. What are the different types of radiation used for sterilization? 20. Which kind of radiation is more lethal? Why? 21. Compare the damage done by UV versus ionizing radiation. 22. How does filter sterilization work? 23. How do depth filters differ from membrane filters? 24. What is commonly sterilized by depth filters? 25. What is commonly sterilized by membrane filters? 26. Distinguish cidal agents from static agents. 27. Compare and contrast bacteriocidal agents and bacteriolytic agents in general. (Use Fig. 27.9) 28. Primarily what are chemical antimicrobial agents used for by various industries such as paper, petroleum, air conditioning? 29. Who is credited with the discovery that sterilizing surgical instruments increased the survival rate of surgery patients? 30. List the 4 categories of chemical antimicrobial agents used to control microorganisms considered to be harmful to humans. Give an example of each. (See Table 27.4) 31. Who was the first to coin the term “chemotherapy”? 32. Who is credited with the discovery of the first chemotherapeutic agent? What was it? What was it used to treat? Did it meet the criteria of selective toxicity? 33. How does a chemotherapeutic agent differ from an antiseptic? 34. In general, how do synthetic chemotherapeutic agents differ from antibiotics? 35. Give examples of synthetic chemotherapeutic agents. 36. How does the sulfa drug, sulfanilamide, disrupt folic acid synthesis in bacteria? 37. How does isoniazid disrupt mycolic acid synthesis in Mycobacterium? 38. How does 5-bromouracil alter the DNA in bacteria? 39. What is the mode of action for quinolones? 40. What is the origin of all antibiotics? 41. What term is used to describe the range of effectiveness for an antibiotic? 42. In general, distinguish broad spectrum antibiotics from narrow spectrum antibiotics. 43. What class of antibiotics has the broadest spectrum of activity? 44. Name an antibiotic with a narrow spectrum of activity. 45. What was the first antibiotic discovered? Who discovered it? What microorganism makes it? What microorganisms is it effective against? What class of antibiotics does it fall under? 46. Who won the Nobel Prize for mass producing penicillin G? What historical event was taking place at that time giving great significance to the mass production to penicillin G? 47. What is the mode of action of β-lactam antibiotics? Are β-lactam antibiotics bacteriocidal, bacteriolytic, or bacteriostatic? What enzyme is capable of destroying β-lactam antibiotics with an accessible β-lactam ring? 48. What are the 2 main types of β-lactam antibiotics? 49. What is the origin of cephalosporin? 50. Name the 2 fungal-derived antibiotics. 51. List 6 bacteria-derived antibiotics. What is the mode of action of each? What microorganisms are they effective against? 52. What genus of bacteria is responsible for most antibiotics? Name another genus of bacteria we get antibiotics from. 53. List 5 resistant mechanisms and for each an example of an antibiotic that the resistant mechanism is used against. 54. Describe how chromosomal mutation can make a bacterium resistant to an antibiotic. 55. Describe how resistance plasmids can make a bacterium resistant to an antibiotic. 56. Describe how a virus can make a bacterium resistant to an antibiotic. 57. What kinds of proteins are encoded for by genes on resistant plasmids? 58. If humans were not on Earth, would antibiotic resistance still occur? 59. Having antibiotic resistance allows a bacterium to…? 60. What soil microorganisms would take over if it weren’t for other microorganisms having mechanisms of bacterial resistance? 61. How do humans impact microbial drug resistance? 62. Look at figure 27.28a, for which antibiotic are there more resistant fecal strains of bacteria. Explain why there are more resistant strains of bacteria to those antibiotics that are used most. 63. How long does it take for resistant strains of a bacterium to emerge once an antibiotic is being used by the public 64. List at least 3 things you as a consumer of antibiotics can do to help minimize your impact on microbial drug resistance. 65. List at least 3 things medical physicians can do to help minimize your impact on microbial drug resistance. 66. Why did pharmaceutical companies in the 1980s cut back on searching for new antibiotics? What is the lesson to be learned from this mistake? 67. Why must we continue to discover new antimicrobial compounds? DIVERSITY 1. How old is the Earth? 2. What is used to date the Earth to be that old? 3. Evidence for microbial life are found in rocks that date back 3.5 billion years ago. 4. What are stromatolites? At what time during Earth’s history were all beaches likely covered in stromatolites? 5. What event occurred between 2.2-2.8 billion years ago? What effects did it have on the planet? What kind of microorganisms were involved? 6. How did the banded iron formations form? 7. Was the first cell prokaryotic or eukaryotic? 8. What theory explains the origin of the eukaryotic mitochondria and chloroplast? 9. Forming the primitive mitochondria there was symbiotic uptake of a cell with what type of metabolism? 10. Forming the primitive chloroplast there was symbiotic uptake of what kind of cell? 11. Provide support for the mitochondria and chloroplasts having bacterial origins. 12. Describe the hydrogen hypothesis. 13. The sequence of what nucleic acid is compared to determine the evolutionary relationship between organisms? 14. Phylogenetic trees represent what type of relationship? 15. Answer the following questions using the phylogenetic tree below. a. To which organism is B most closely related? b. To which organism is C most closely related? c. Which organism is the most recent descent from the ancestor at internal node 2? d. Which organism could be the outgroup? 16. Traditionally what phenotypic analyses were done to compare organisms? Are these still used today? 17. Use information on GC ratio, DNA:DNA hybridization and 16S/18S rRNA sequence to answer the following questions. a. What are the criteria for determining an organism is a new genus? i. . b. What are the criteria for determining an organism is a new species? 18. What is the GC ratio of an organism? 19. What is the principle behind DNA:DNA hybridization? 20. An endoribonuclease is an enzyme that digests (cuts) RNA. For what test would this be used? 21. In ribotyping, if you see the same pattern of bands on gel for your organism and the positive control organism, then what would be your conclusion? 22. How does multilocus sequence typing differ from 16S/18S rRNA sequence comparision? What is it useful for distinguishing between? 23. What is a biochemical analysis that will allow you to distinguish between two organisms? 24. Can determining the fatty acid composition of an organism be useful in identifying the organism? 25. List the taxonomic hierarchy. 26. What 2 things must a scientist do in order for a newly identified microorganism to be formally recognized by the scientific community? HOST MICROBE INTERACTIONS 1. Prior to birth, in the womb, were you sterile? 2. Where do the microorganisms come from that first colonize a newborn human? . 3. What decides which microorganisms become resident flora for the newborn human? 4. Where does the Escherichia coli come from that colonizes the gastrointestinal tract? Why would a newborn baby in a developing country likely be colonized by E. coli much sooner than a newborn baby in the United States or other developed nation? 5. Do human pathogens colonize a newborn? What prevents them from causing disease? What would allow them to cause disease? 6. Distinguish between infection and disease. 7. Where does infection begin? Where on the human body can you find places like this? 8. What prevents all places and surfaces of the human body from being colonized by microorganisms? 9. Name four places in the human body that are sterile (microbe-free). 10. Where on the skin do microbes colonize? In what ways are these places similar to mucosal surfaces? Why is the surface of the epidermis microbe free except for the occasional transient? 11. What glands are responsible to harboring microbes that cause body odor? 12. List the 4 most commonly found microbial genera resident of the skin. Are these Gram-positive or Gram-negative? Which is the cause of acne? 13. Are the majority of skin microflora resident or transient? . 14. What Gram-negative bacterium commonly colonizes the skin? 15. List environmental and human host factors that influence skin microflora composition. 16. Upon entering your mouth perhaps on a piece of food, a bacterium would be exposed to what in your saliva that could destroy the bacterium? How could a microbe survive exposure to the enzymes in your saliva to make it to your stomach? 17. How does the microflora of the mouth differ before and after tooth formation? 18. What are the main microbes to colonize the mouth prior to tooth formation? After tooth formation? Why is there a change in the microflora before and after tooth formation? 19. What are biofilms on the surface of teeth called? 20. Describe how Streptococci form dental plaque and provide for other microbes to join the biofilm. 21. Explain how anaerobic microbes predominant the mouth despite their being a constant influx of oxygen from breathing. 22. How does dental plaque result in dental caries? 23. Upon ingestion of sucrose, describe how Streptococci form dental caries. 24. How can dental caries be prevented? What can be used to clean the surface of teeth? What can be used to clean between teeth and in the gingival crevices? . 25. How does fluoride help prevent dental caries? 26. What 2 species of Streptococci primarily colonize teeth? 27. If there were no more toothbrushes or dental floss or fluorine left on Earth, what could Americans do to prevent dental caries? 28. Find 2 things you eat or drink regularly that contain sucrose. (Read the label of your food/drink to determine if it has sucrose or look up the food/drink online.) 29. Would dental caries be considered infectious disease? Why? 30. How does the microflora that colonizes your gastrointestinal tract get there in the first place? 31. What organ is a chemical barrier to microbial growth? 32. What makes the stomach unfriendly to microbes? 33. What is the most common microbe found in the stomach? 34. Besides pH what factor influences the stomach microflora composition? Do beef-eaters and vegetarians have the same microflora? 35. What is the primary difference between the stomach and the end of the small intestine that allows for larger numbers of microbes to be present in the small intestine? 36. What is the oxygen requirement for most microbes living in the small and large intestines? . 37. Are the small and large intestines oxic or anoxic environments? 38. What is another name for the colon that tells you what the microbes are metabolically doing there? 39. How much bacteria per gram of fecal content is in the colon? 40. The symbiotic relationship humans have with some of their intestinal flora is mutualistic. How do each benefit? 41. Name 4 gases produced by microorganisms in the human intestine? Do any of these have an odor? 42. Back in human time before fire, did humans contribute to global warming? 43. What percentage of feces is bacteria? Are the bacteria dead or alive or some of both? 44. Is the large intestine like a batch culture or a chemostat? 45. What is the growth rate of bacteria in the intestine lumen? 46. 10,000,000,000,000 What does this number represent? 47. Describe what antibiotics do to your intestinal microflora 48. Due to proximity to the exit of the gastrointestinal tract, many microbes that inhabit the gastrointestinal tract find their way to what other area of the body? 49. What part of the urogenital tract is sterile? What part is colonized? 50. What lactic acid bacteria used to make yogurt is resident flora of the human female vagina? How does this microorganism affect the pH of the vagina? During the lifetime of a human female when would Lactobacillus acidophilus expect to be resident of the vagina? 51. How do birth control pills effect the pH of the vagina? What are the microbial consequences? 52. What part of the respiratory tract is sterile? 53. What 2 opportunistic pathogens often colonize the upper respiratory tract? Why do they not cause disease most of the time? 54. What type of cells line the respiratory tract? How do these cells help prevent microbes from reaching the lower respiratory tract? 55. Smoking damages the ciliated epithelium of the respiratory tract. What occurs due to this loss of function? Smokers cough in an attempt to do what? Are smokers more susceptible to microbial infections of the lower respiratory tract? 56. Following exposure to a pathogen, list the events of pathogenesis. 57. List 4 adherence factors and an example of each. 58. Describe invasion. 59. Colonization is also known as microbial _growth_. Is microbial colonization dependent on location in the body? 60. What type of virulence factors are siderophores? 61. Distinguish between localized and systemic bacterial infection. Which would be easier to treat with antibiotics? 62. Is bacteremia a localized or systemic infection? 63. Adherence, invasion, colonization are the steps describing infection. To cause disease what must happen? 64. Define toxicity and give an example of a toxin causing disease. 65. Define invasiveness and give an example of an invasive factor helping a microorganisms cause disease. 66. What is the lethal dose50? 67. How many cells of a virulent human pathogen like Streptococcus pneumoniae are needed to kill? 68. Describe the phenomenon of attenuation. How does a virulent strain become attenuated? Is an attenuated strain still deadly? 69. Viruses and bacteria can be attenuated. Attenuated viruses are given as vaccines of common childhood viruses that are deadly or that cause major harm to the human body. 70. Distinguish between exotoxins, enterotoxins and endotoxins. 71. Describe what a cytolytic exotoxin does to be toxic and give an example of cytolytic toxin. 72. Describe how an AB exotoxin is toxic and give 3 examples of an AB exotoxin. 73. Describe how an enterotoxin is toxic and give 2 examples of enterotoxins. What is the main symptom associated with disease caused by an enterotoxin? 74. Describe how an endotoxin is toxic and give an example of an endotoxin. What group of bacteria produce endotoxins? 75. List 4 risk factors that increase a person’s susceptibility to infection. 76. List 8 barriers that provide natural resistance to infection by pathogens. (see fig. 28.25) 77. Provide an explanation for Clostridium tetani causing tetanus if introduced into a deep puncture wound but not causing any harm if ingested. 78. Provide an explanation for Salmonella causing gastroenteritis if ingested but not causing any harm if introduced in a puncture wound. 79. Provide an explanation for why a mosquito can transmit malaria but a cockroach cannot. 80. Provide an explanation for why HIV is harmless on your skin but potentially lethal in your blood. Immunology 1. Name the leukocytes. 2. Name the phagocytes. Name the lymphocytes. 3. Where do all leukocytes come from? 4. What body fluid systems transport immune cells throughout the body? 5. What is the first line of internal defense against pathogens? 6. What do Natural Killer cells do? How do they kill? 7. What do phagocytes do in innate immunity? 8. What do phagocytes have on their cell surface to recognize pathogens? 9. What part of a pathogen is recognized by a phagocyte? 11. What immune response precedes the adaptive immune response? 12. What signaling proteins from the innate immune response activate B and T cells? 13. Describe the events that take place following a macrophage encountering a foreign protein. 14. What part of Gram-negative bacteria stimulates an immune response? 15. Tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1) are what type of signaling proteins? 16. What can happen if too much TNF-alpha and IL-1 are made? 17. To what Drosophila melanogaster protein is part of IL-1 similar? 18. What do Toll proteins do in Drosophila? 19. Are there any Toll-like proteins in human in which the full-length human protein is similar to Toll? 20. What does the acronym TLR stand for? 21. How many human TLRs are there? 22. Where are TLRs located? 24. What does TLR3 recognize? 25. What does TLR4 recognize? 26. What does TLR5 recognize? 27. In general, what do TLRs recognize? 28. Name 6 other organisms besides humans that have an innate immune response. 29. What immune cells have Toll-like receptors? 30. What would a mutation in TLR4 that abolishes TLR4 activity prevent an immune cell from doing? 31. A drug that is a TLR4 activator would be capable of doing what to the inflammatory response? 32. What potential is there in inhibiting TLRs for treating certain autoimmune diseases? 33. What positive effect would a TLR inhibitor have on someone with an autoimmune inflammatory disease like rheumatoid arthritis? 34. What negative effect would a TLR inhibitor have on someone with an autoimmune inflammatory disease like rheumatoid arthritis? 35. How could activating TLRs aid in making a more effective vaccine? 36. What is an adjuvant? 37. What would be a negative consequence of activating TLRs? 38. Is phagocytosis sufficient to kill a pathogen? What does the phagocyte do to kill the pathogen? 39. What is a lysosome? What proteins are found inside a lysosome? What are these proteins use for? What other molecules are in the lysosome that are used to damage pathogens? 40. Why are the contents of a lysosome contained within the lysosome instead of free in the cytoplasm of the phagocyte? 41. What reaction follows phagocytosis? i 42. Is inflammation harmful or helpful to the immune response? 43. What cells make chemokines? 44. Chemokines are chemoattractants. What do they attract? 45. What cells make cytokines? What is an example of a cytokine? 46. What do cytokines do? 47. In what ways can a pathogen protect itself from phagocytosis? 48. List the 3 properties of adaptive immunity and give an example of each. 49. Explain the T-cell selection process. 50. What T-cell characteristics are selected for in the thymus? 51. Who coined the term autoimmunity? 52. What cells are proactive in helping the body get rid of immune cells that inappropriately interact with the body’s own tissues? 53. What were T-regs originally named before they were even identified as CD25+ regulatory T cells? How was this original name descriptive of what the T-regs do? 54. What cytokine promotes T-reg function? 55. What transcription factor is found in abundance in T-regs? 56. Mutant mice with an inactive Foxp3 protein also lack what type of immune cell? 57. If humans have a mutant Foxp3, what is the outcome? Does it matter if you are male or female? Why? 58. Absence of T-regs causes what disease in mice? 59. In your intestines, what organisms do T-regs allow your body to tolerate? 60. Chronic infection by Helicobacter pylori in the stomach could be from what action of T-regs? 61. How might T-regs play a role in pregnant women in helping to protect the development fetus? 62. What level of T-reg activity could be a cause of spontaneous abortion? 63. Describe how T-regs could be used to help organ transplantation? (see fig.) 64. Removal of some T-regs holds promise as a therapy for what kind of diseases? 65. List 2 challenges to the developing medicines targeted at T-regs. How are these challenges being overcome? 66. Is it possible to turn ordinary T-cells into T-regs? How? 67. What type of leukocytes are involved in cell-mediated immunity? 68. What type of T-Cells are involved in cell-mediated immunity? 69. What type of leukocytes are involved in antibody-mediated immunity? 70. What type of T-Cells are involved in antibody-mediated immunity 71. When would T-cytotoxic cells be used? 72. What type of MHC protein is recognized by a T-cytotoxic cell? 73. When would T-helper 1 cells be used? 74. What type of MHC protein is recognized by a T-helper 1 cell? 75. When would T-helper 2 cells be used? 76. What type of MHC protein is recognized by a T-helper 2 cell? 77. Describe the events that take place when a T-cytotoxic cell is activated. 78. Describe the events that take place when a T-helper 1 cell is activated. 79. Describe the events that take place when a T-helper 2 cell is activated. 80. What do MHC proteins, T-cell receptors and antibodies all have in common? 81. What are the 5 classes of antibodies? How is each defined? 82. What are kappa and lambda? 83. How are the light chains and heavy chains of an antibody connected? 85. Overall, how many types of antibodies are possible to make? 86. Describe the antibody-mediated immune response that occurs the first time you are exposed to an antigen. 87. What types of cells are made in response to initial antigen exposure? What do these cells do? 88. How do plasma cells differ from memory cells? 89. Describe the antibody-mediated immune response that occurs the second time you are exposed to an antigen. How does this differ from the initial antigen exposure immune response? 90. Describe the antibody-mediated immune response that occurs the third, fourth, fifth, etc. time you are exposed to an antigen. 91. Describe what the antibodies released from plasma cells do. 92. What are complement proteins used for? 93. What immune responses use complement proteins? 94. Describe classical complement activation. 95. Describe alternate complement activation. 96. How do the classical and alternative complement activation pathways differ? How are they the same? 97. Define hypersensitivity with regard to the immune system. 98. Describe the four types of hypersensitivities. 99. Why is Type I called immediate hypersensitivity? 100. What common name is used to describe a Type I hypersensitivity? 101. What name is given to the antigen that elicits a Type I hypersensitivity? 102. What occurs during initial allergen exposure? (see fig. 30.5) 103. What occurs during second and subsequent allergen exposure? (see last part of fig. 30.5) 104.Name some things that can be done to treat the symptoms of an allergic response. 105.Why is Type IV also known as delayed hypersensitivity? 106.How does Type IV differ from Type I hypersensitivity? 107. Are antibodies involved in a Type IV hypersensitive response? 108. What is main symptom associated with a Type IV hypersensitive response? 109.Can a pathogen elicit a hypersensitive response? 110.Name at least 3 things that can elicit a Type IV hypersensitive response. 111.What do Type II and III hypersensitivities have in common? 112.Describe what occurs during a Type II hypersensitive response. 113.Describe what occurs during a Type III hypersensitive response. 114.What class of hypersensitivities do drug reactions (for example to penicillin) fall under? 115.What are superantigens? 116.How do superantigens elicit an abnormal immune response? 117.What is the main symptom associated with superantigen exposure? 118.Compare and contrast active and passive immunities. 119.Compare and contrast natural and artificial active immunities. 120. Compare and contrast natural and artificial passive immunities. 121. What type of immunity do vaccinations provide? (active, passive, natural, artificial) 122. What did the English physician Edward Jenner do? 123.Describe the concept of herd immunity. 124.What percentage of the population needs to be vaccinated to have herd immunity to measles? 125.Describe 7 kinds of vaccines. 126.Which vaccines contain no live pathogens? 127.Which vaccines contain live pathogens? Microbial Diseases 1. Perhaps make a table to answer these questions: a. To what diseases are we vaccinated against in early childhood? b. What causes each of these diseases? c. How are these pathogens transmitted? d. How does the pathogen cause disease? (virulence factors) e. What immune response (innate, cell-mediated, antibody-mediated, innate and cell-mediated, innate and antibody- mediated, all three) is there to these pathogens? 2. Many airborne-transmitted pathogens cause what type of infections? [Show More]

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