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Chapter 1: An Invisible World * = Correct answer Multiple Choice

1. Which of the following is true of the microbial world? A. All microbes are harmful. B. Humans could survive without microbes. C. Many microbes are helpful.* D. Most microbes are pathogenic. Difficulty: Easy ASM Standard: 23, 24 2. Which of the following is when humans first suspected the existence of microbes? A. during the Industrial Revolution B. in prehistoric times* C. in the last century D. within the last 500 years Difficulty: Easy ASM Standard: 23 3. Which individual first observed unicellular organisms, which he called “animalcules,” using a microscope he developed? A. Robert Koch B. Louis Pasteur C. Thucydides D. Antonie van Leeuwenhoek* Difficulty: Easy ASM Standard: 6 4. To reduce the risk of open flame from Bunsen burners, microbiologists are increasingly using which of the following devices for easy, rapid benchtop sterilization of small pieces of equipment? A. autoclaves B. ethylene oxide C. incubators

D. microincinerators* Difficulty: Easy ASM Standard: 36

5. The Swedish botanist known for having developed an important biological classification system is which of the following people? A. Ernst Haeckel B. Carolus Linnaeus* C. Louis Pasteur D. Robert Whittaker Difficulty: Easy ASM Standard: N/A 6. Which kingdom was the only one found in Empire Prokaryota? A. Animalia B. Fungi C. Monera* D. Protista Difficulty: Easy ASM Standard: N/A 7. Which are the three currently accepted domains? A. Archaea, Bacteria, and Eukarya* B. Archaea, Prokaryota, and Eukaryota C. Bacteria, Fungi, and Protista D. Bacteria, Prokaryota, and Eukarya Difficulty: Easy ASM Standard: N/A 8. Which two taxonomic units are typically used to identify an organism when using binomial nomenclature? A. domain and kingdom B. genus and family C. genus and species* D. phylum and class Difficulty: Easy ASM Standard: N/A 9. Which of the following is not true about the process of fermentation? A. It can help preserve foods, preventing spoilage. B. It converts sugars to organic acids, alcohols, and/or gases such as carbon dioxide.

C. It is carried out exclusively by unicellular eukaryotes such as yeast.* D. It is used to make foods such as cheese and bread. Difficulty: Moderate ASM Standard: 11, 23, 26

10. The Romans may have reduced their risk of waterborne infectious diseases by using which of the following? A. a variety of pharmaceutical products B. aqueducts and a sewer system* C. prophylactic antibiotics D. quarantine of people with leprosy Difficulty: Moderate ASM Standard: 23 11. For which of the following is Thucydides known? A. developing an effective sewer system in ancient Greece, helping to reduce levels of disease in cities B. observing microbes, using a microscope, for the first time, even distinguishing between bacteria and fungi C. proposing that disease was caused by microorganisms D. realizing that people who had been infected by the Athenian plague had immunity to reinfection* Difficulty: Moderate ASM Standard: 23, 31 12. Ernst Haeckel proposed a classification system consisting of which of the following subgroups? A. five kingdoms B. four kingdoms* C. two domains and three kingdoms D. two domains and five kingdoms Difficulty: Moderate ASM Standard: N/A 13. Viruses not included in phylogenetic trees for which of the following reasons? A. It is too difficult to observe their characteristics. B. They are acellular and nonliving.* C. They do not have any genes, which prevents genetic analysis. D. They lack a nucleus. Difficulty: Moderate ASM Standard: 5 14. Which is the best description of the primary purpose of a phylogeny? A. Phylogenies show all the alterative names for each species. B. Phylogenies show all the common names for each species. C. Phylogenies show evolutionary relatedness between organisms.*

D. Phylogenies show interactions between species in a shared habitat. Difficulty: Moderate ASM Standard: 5 15. Current phylogenetic analyses include which of the following? A. information from a range of sources, including morphological, genetic, and biochemical data* B. information on visible similarities only C. information regarding how to classify organisms on the basis of external morphological characteristics and visible behaviors D. varied morphological and structural characteristics, with preference for leaving historical classifications to prevent confusion Difficulty: Moderate ASM Standard: 5 16. Diatoms are classified within which of the following domains? A. Archaea B. Bacteria C. Eukarya* D. Prokaryota Difficulty: Moderate ASM Standard: N/A 17. Horizontal gene transfer involves which of the following? A. any transfer of genes in a laboratory setting B. the transfer of genes from a virus to a bacterium or vice versa but not any other form of gene transfer C. the transfer of genes from one individual to another, including from one species to another, but not from parent to offspring* D. the transfer of genes from parent to offspring Difficulty: Moderate ASM Standard: 2, 4 18. Bacteria are generally identified to species by using which of the following? A. a combination of genetic, biochemical, and microscopic approaches* B. a combination of microscopic and physiological approaches, but not genetics C. primarily characteristics such as motility that can be visualized using microscopy D. primarily morphological characteristics of individual cells Difficulty: Moderate ASM Standard: 34, 36

19. For taxonomic classification of microbes, serological tests typically are used to do which of the following? A. determine complete genome sequences for microbes B. identify proteins on the basis of their reaction with specific antibodies* C. run analyses to identify whether particular genes are present D. visualize microbial external morphology Difficulty: Moderate ASM Standard: 34, 36 20. Which of the following is true of bacterial strains? A. They are closely related subtypes within a bacterial species that may or may not have similar properties.* B. They are informal bacterial groupings used for medical distinctions but not recognized for classification purposes. C. They are more distantly related to each other than are members of a single bacterial species. D. They are very similar bacteria with almost identical properties. Difficulty: Moderate ASM Standard: 5 21. Bergey’s Manual of Systematic Bacteriology is used primarily as which of the following?

A. a guide to bacterial shapes B. a historical account of changes in classification techniques C. a list and characterization of all known medically relevant microbes D. a reference for bacterial classification* Difficulty: Moderate ASM Standard: 34 22. Which of the following indicates how bacteria and viruses typically compare in size? A. Bacteria are indistinguishable from viruses. B. Bacteria are much larger than viruses.* C. Bacteria are much smaller than viruses. D. Bacteria are similar in size to viruses. Difficulty: Easy ASM Standard: N/A 23. Viruses are classified as which of the following? A. Archaea B. Bacteria C. Eukarya D. distinct from the three-domain system*

Difficulty: Moderate ASM Standard: 4 24. Which of the following is not a curved bacterial shape? A. bacillus* B. spirillum C. spirochete D. vibrio Difficulty: Easy ASM Standard: 34 25. Based just on the name, which of the following groups of bacteria contains entirely species that consume organic compounds for food? A. cyanobacteria B. green nonsulfur bacteria C. green sulfur bacteria D. nonphotosynthetic bacteria* Difficulty: Moderate ASM Standard: 11, 13, 20 26. Chitin cell walls are characteristic of which taxonomic group? A. algae B. archaea C. bacteria D. fungi* Difficulty: Moderate ASM Standard: 20 27. Yeasts are which of the following? A. a type of algae B. a type of protist C. any unicellular microbe D. unicellular fungi* Difficulty: Moderate ASM Standard: 20 28. The cell walls of archaeans often contain which of the following substances? A. cellulose B. chitin C. peptidoglycan D. pseudopeptidoglycan*

Difficulty: Moderate ASM Standard: 20 29. Which of the following is not true of archaeans? A. Some species live on the human body. B. They are genetically distinct from bacteria. C. They are only found in extreme environments.* D. They have substantial metabolic differences from bacteria. Difficulty: Difficult ASM Standard: 20 30. Which of the following is not true of algae? A. All the algae are classified together in one similar group closely related to green plants.*

B. Ingredients made from algae, including carrageenan, are used in food products. C. They are being used to develop biofuels. D. They are sometimes multicellular. Difficulty: Moderate ASM Standard: 20, 23, 26 31. Oral thrush is caused by which type of organism? A. algae B. bacteria C. fungi* D. protists

Difficulty: Moderate ASM Standard: 23 32. Mycotoxins are produced by which type of organism? A. archaeans B. heterotrophic protists C. molds* D. protozoans Difficulty: Moderate ASM Standard: 23 33. Which of the following is not a common use of fungi? A. the production of alcoholic beverages B. the production of carrageenan* C. the production of cyclosporine D. the production of penicillin

Difficulty: Moderate ASM Standard: 20, 23, 26 34. The guinea worm is best described as which of the following? A. a helminthic parasite transmitted by consuming contaminated water* B. a type of mold that grows into a worm-like shape and produces antimicrobial chemicals

C. a type of protist found in water that has not been properly treated D. a type of protozoan that is unusual because it is multicellular Difficulty: Moderate ASM Standard: 23 35. Which of the following is true of the genetics of viruses? A. Viruses always contain DNA and force host cells to produce RNA. B. Viruses always contain DNA and RNA. C. Viruses always contain RNA and force host cells to produce DNA. D. Viruses can contain either DNA or RNA, but not both.* Difficulty: Moderate ASM Standard: N/A True/False 36. All organisms studied in the field of microbiology are visible only with a microscope. Answer: False Difficulty: Easy ASM Standard: N/A 37. Older scientific names are typically derived from Latin. Answer: True Difficulty: Easy ASM Standard: N/A 38. Animal cells are generally about the same size as bacterial cells. Answer: False Difficulty: Easy ASM Standard: N/A 39. Researchers studying a 5300-year-old mummy discovered in the 1990s think he may have been trying to use a fungus to treat his illnesses. Answer: True Difficulty: Easy

ASM Standard: 23, 26 40. Analyses of rRNA genes suggest that Archaea, Bacteria, and Eukarya evolved from a common ancestor. Answer: True Difficulty: Moderate ASM Standard: 5 41. The average size of a typical virus is approximately 100 nm. Answer: True Difficulty: Moderate ASM Standard: N/A 42. When a scientific name is used repeatedly, both the genus and species must always be written out in full to avoid confusion. Answer: False Difficulty: Moderate ASM Standard: N/A 43. Taenia saginata is a type of fungus that causes disease. Answer: False Difficulty: Moderate ASM Standard: 23 Matching 44. Match each type of microbiological tool with the best definition. A. loop i. tool used to transfer microbes from one location to another B. media ii. liquid, solid, or gel that contains nutrients to aid microbial growth C. microincinerator iii. tool used to sterilize equipment D. Petri plate iv. container used to grow microbial cultures Answers: A. i., B. ii., C. iii., D. iv. Difficulty: Easy ASM Standard: 36 45. Match the bacterial shape with the illustration.

(credit micrograph “i”: modification of work by Janice Haney Carr, Centers for Disease Control and Prevention; credit micrograph “iii”: modif ication of work by Centers f or Disease Control and Prevention)

Answers: A. v., B. i., C. iv., D. iii., E. ii. Difficulty: Easy ASM Standard: 34 46. Match each type of microbe with the best description. A. algae i. a very broad, informal grouping of organisms that do not fit into other eukaryotic kingdoms and that may be photosynthetic or nonphotosynthetic B. fungi ii. a diverse, informal subgroup of organisms that may move using cilia, flagella, or pseudopodia C. protists iii. a group of photosynthetic organisms with cellulose cell walls D. protozoa iv. a group of nonphotosynthetic organisms that usually have cell walls containing chitin Answers: A. iii., B. iv., C. i., D. ii. Difficulty: Moderate ASM Standard: 2 47. Match each subfield of microbiology with the most appropriate example. A. bacteriology i. the study of how antibodies are released in response to a pathogen B. immunology ii. the study of how fungi cause disease in plants C. mycology iii. the study of the classification of bacilli D. parasitology iv. the study of how to reduce the rate of guinea worm infections E. protozoology v. the study of heterotrophic protists

Answers: A. iii., B. i., C. ii., D. iv., E. v. Difficulty: Moderate ASM Standard: 23 48. Match each taxonomic group with its domain. You will use some options more than once.

A. algae i. Archaea B. halophiles ii. Bacteria C. helminths iii. Eukarya D. spirochetes Answers: A. iii., B. i., C. iii., D. ii. Difficulty: Moderate ASM Standard: 2 49. Match each causative agent with the associated classification. A. Dracunculus medinensis i. protist B. Ebola ii. fungus C. Giardia lamblia iii. helminth D. yeast iv. virus Answers: A. iii., B. iv., C. i., D. ii. Difficulty: Difficult ASM Standard: 23 Fill in the Blank 50.

was a Greek physician who posited that natural causes, not supernatural forces, caused disease. Answer: Hippocrates Difficulty: Easy ASM Standard: 23

51.

is the science of identifying, naming, and classifying living organisms. Answer: Taxonomy Difficulty: Easy ASM Standard: N/A

52. Fermentation by yeast produces ethanol and gas. Answer: carbon dioxide Difficulty: Moderate ASM Standard: 11, 26

53. Carl Woese and George Fox sequenced and analyzed wide range of organisms to build their phylogenetic tree. Answer: rRNA (or ribosomal RNA)

from a

Difficulty: Moderate ASM Standard: 4, 5 54. The archaebacteria are now called . Answer: Archaea Difficulty: Moderate ASM Standard: N/A 55. The genus of Halobacterium salinarum is . Answer: Halobacterium Difficulty: Easy ASM Standard: N/A 56. is the standard reference book that provides guidance onidentifying and classifying prokaryotes. Answer: Bergey’s Manual of Determinative Bacteriology Difficulty: Moderate ASM Standard: 34 57. There are nanometers in 520 meters. Answer: 520,000,000,000 Difficulty: Moderate ASM Standard: 29 58. The thermophilic genus Thermoproteus includes extremophiles classified in the domain . Answer: Archaea

Difficulty: Difficult ASM Standard: 5 59. The cytoplasmic extensions used by some protists to move are called . Answer: pseudopods Difficulty: Moderate ASM Standard: N/A Short Answer

60. What is horizontal gene transfer? Sample Answer: Horizontal gene transfer is the transfer of genetic material between two organisms that are not related as parent and offspring. Difficulty: Easy ASM Standard: 2 61. How are newly discovered organisms named? Sample Answer: Newly discovered organisms are usually given names that describe their characteristics and/or that honor a particular individual. The names are generally Latin, Greek, or English. Difficulty: Easy ASM Standard: 5 62. How do protozoa move? Sample Answer: Protozoa can move using structures such as pseudopods, flagella, and cilia. They may also be carried by the water in which they live. Difficulty: Easy ASM Standard: N/A 63. Why are formal scientific names based on a standardized system more useful than simple names that just describe characteristics, such as “orange cat-like animal”? Sample Answer: Organisms may have similar characteristics, especially in closely related species. By having a formal naming system, it is possible to clearly distinguish organisms so that people around the world can identify exactly which organism is being discussed.

Difficulty: Moderate ASM Standard: N/A 64. What are at least four types of products made using fermentation? Sample Answer: Fermentation is used to make alcoholic products, cheese, yogurts, pickled vegetables, and bread. Difficulty: Easy ASM Standard: 11, 23, 26 65. What is the Hippocratic Oath? Sample Answer: The Hippocratic Oath is an oath taken by new doctors to pledge their willingness to follow certain ethical guidelines, such as avoiding causing harm to their patients. Difficulty: Moderate ASM Standard: N/A31

66. Which famous scientist developed a vaccine for rabies? Sample Answer: Louis Pasteur developed a vaccine for rabies.

Difficulty: Moderate ASM Standard: 14, 23 67. Why is most milk pasteurized before it is sold? Sample Answer: Pasteurization helps reduce the number of microbes associated with spoilage and disease, keeping milk safe to drink longer than if it is not pasteurized.

Difficulty: Moderate ASM Standard: 14, 23 68. What are helminths and why are they medically important? Sample Answer: Helminths are worms. They are eukaryotes. They can be human parasites.

Difficulty: Moderate ASM Standard: 14, 23 69. Why is it often preferable to use a microincinerator rather than a Bunsen burner? Sample Answer: Bunsen burners have an open flame, whereas microincinerators do not; therefore, it is safer to use a microincinerator. Difficulty: Moderate ASM Standard: 14, 36 70. How do scientists decide how to organize organisms in a phylogenetic tree? Sample Answer: Phylogenies show evolutionary relationships. To develop a phylogenetic tree, scientists examine a variety of characteristics, including biochemical, morphological, and genetic characteristics, to determine the most likely relationships between organisms. Genetic data are especially important in determining these relationships in modern phylogenetic trees. Difficulty: Moderate ASM Standard: 5 71. What is the difference in how DNA is stored within the cells of prokaryotes versus eukaryotes? Sample Answer: Eukaryotes have a true membrane-bound nucleus and prokaryotes do not.

Difficulty: Moderate ASM Standard: 9

72. What does it m ean to say that som e photosynthetic bacteria, including som e green sulfur bacteria, are anoxygenic? Consider the word parts in “anoxygenic” if you are not sure. Sample Answer: Anoxygenic means that they do not generate oxygen.

Difficulty: Difficult ASM Standard: 11 73. Who published Systema Naturae and what did it present? Sample Answer: Systema Naturae was published by Carolus Linnaeus to present his taxonomic system. Difficulty: Difficult ASM Standard: N/A 74. Of the three domains, which is/are known to contain some human pathogens? Sample Answer: Bacteria and Eukarya contain some species that are human pathogens. No known archaeal pathogens have been identified. Difficulty: Moderate ASM Standard: 23 Brief Essay Essay Question Rubric RATING Failing Criteria for evaluati on

Answer does not provide an argument. Answer contains inaccuracies. Writing is poor and contains numerous grammatical mistakes and misspellings.

Below Average Answer fails to provide examples to support an argument. Writing is poor and grammatical errors are common. Answer is somewhat incoherent.

Competent

Advanced

Answer provides an argument with one or two examples that support it. Writing is acceptable for the college level but may contain one or two grammatical mistakes or misspellings.

Answer clearly provides an argument with two or more excellent examples that support it; student makes the argument clearly and eloquently. Answer is well organized and free of grammatical errors and misspellings. 3

0 1 2 POINT VALUE Assume rating/grading scale for the question ranges from 0 to 3 points.

75. Explain why some scientists think that it may be more appropriate to describe a “web of life” instead of a “tree of life.” Answer: Student answers will vary but should include components of the following. A tree suggests straightforward pathways of evolution from one branch to another. Because horizontal gene transfer is common, this does not fully represent the complexity involved in evolution. A web would better show ways genes can be transferred from one taxonomic group to another. Difficulty: Moderate ASM Standard: 5 76. Halobacterium salinarum is classified in the domain Archaea. Why does its name suggest it is a bacterium? This answer is not in the textbook chapter, so you should speculate based on your understanding of taxonomy. Answer: Student answers will vary but should include the following. This species was identified before the domain Archaea was recognized. As a result, it was previously considered a bacterium and given a bacterial name. Difficulty: Moderate ASM Standard: N/A 77. Consider the phylogenetic tree below. Explain how it shows the relationships between Bacteria, Archaea, and Eukarya, and their common ancestor. Of these three groups, which two are more closely related and how can you tell from the figure?

(credit: modification of work by Eric Gaba) Answer: Student answers will vary but should include the following. The lines leading to Bacteria, Archaea, and Eukarya branch from the same root, meaning they all share a common ancestor. Archaea and Eukarya branch more closely together than either branches with

Bacteria, suggesting that they diverged from each other more recently than they diverged from a common ancestor that had previously branched from Bacteria.

Difficulty: Difficult ASM Standard: 5 78. In the textbook chapter, there is information about efforts to eradicate the guinea worm. What are some factors that have allowed these efforts to be relatively successful, with only 126 cases reported in 2014, compared with efforts to eradicate other diseases such as hantavirus, carried by rodents, and rabies, carried by a variety of wild animals?

Answer: Student answers will vary but should include components of the following. Guinea worm is transmitted in contaminated water. Thus, efforts to improve water sanitation can be very effective in reducing infections. Other diseases have different mechanisms of transmission. Diseases such as rabies are found in wild animals and it would be difficult to treat or vaccinate all infected animals. Difficulty: Difficult ASM Standard: 14, 23, 31

Chapter 2: How We See the Invisible World * = Correct answer Multiple Choice 1. Which term is used to refer to a wave’s rate of vibration? A. amplitude B. frequency* C. trough D. wavelength Difficulty: Easy ASM Standard: N/A 2. On the figure, which letter represents a refracted ray of light?

A. A B. B C. C D. D* Difficulty: Easy ASM Standard: N/A 3. On the electromagnetic spectrum, which type of wave has the shortest wavelength? A. cosmic ray* B. infrared ray C. ultraviolet ray D. visible light Difficulty: Moderate ASM Standard: N/A 4. Dyes are often used during microscopy to increase which of the following? A. contrast* B. magnification

C. motility D. resolution Difficulty: Easy ASM Standard: 32 5. Which of the following was the first to use the term “cells”? A. Robert Hooke* B. Robert Koch C. Carolus Linnaeus D. Antonie van Leeuwenhoek Difficulty: Easy ASM Standard: N/A 6. Which of the following is the typical magnification of an object viewed using a 10× ocular lens and a 100× objective lens on a brightfield microscope? A. 1× B. 10× C. 100× D. 1000×* Difficulty: Moderate ASM Standard: 32 7. Most modern microscopes have two eyepieces, meaning that they are which of the following? A. binocular* B. monocular C. oil immersion D. trinocular Difficulty: Easy ASM Standard: 32 8. An annular stop is used for which type of microscopy? A. confocal B. darkfield C. fluorescence D. phase contrast* Difficulty: Easy ASM Standard: 32 9. Which of the following is the specific name for a stain that colors the background but not the specimen?

A. acid-fast stain B. counterstain C. differential stain D. negative stain* Difficulty: Easy ASM Standard: 32 10. Which type of microscopy would work best for viewing internal cell structures? A. atomic force microscopy B. scanning electron microscopy C. scanning tunneling microscopy D. transmission electron microscopy* Difficulty: Moderate ASM Standard: 32 11. The Gram-staining procedure is best described as which of the following? A. complex staining B. differential staining* C. negative staining D. simple staining Difficulty: Easy ASM Standard: 32 12. When there is a substantial difference in refractive index between two materials, which of the following describes what will happen to light passing from one material to the other? A. It will fail to be refracted. B. It will undergo a large amount of refraction.* C. It will undergo a small amount of refraction. D. It will undergo a variable amount of refraction. Difficulty: Moderate ASM Standard: N/A 13. In microscopy, the focal length refers to which of the following? A. a description of the wavelength needed for an image to be in focus B. a measure of the amount of refraction produced by a lens C. a measure of the thickness of the lens needed for an image to be in focus D. the distance to the image point (at which all light entering a lens is parallel)* Difficulty: Moderate ASM Standard: 32 14. Which of the following are pigments used in microscopy to absorb and reflect light? A. chromatographs

B. chromophores* C. oilophores D. photophores Difficulty: Easy ASM Standard: N/A 15. Negative staining is the standard approach used to visualize which structure(s)? A. capsules* B. endospores C. flagella D. nucleoid regions Difficulty: Moderate ASM Standard: 6, 32 16. Which is a standard mordant used in flagella staining? A. basic fuchsin B. iodine C. safranin D. tannic acid* Difficulty: Moderate ASM Standard: 6, 32 17. Which of the following pairs are common acid-fast staining techniques? A. Gram and Kinyoun B. negative and Schaeffer-Fulton C. Ziehl-Neelsen and Kinyoun* D. Ziehl-Neelsen and Schaeffer-Fulton Difficulty: Moderate ASM Standard: 32 18. Which is the primary stain used in the Ziehl-Neelsen technique? A. acid-alcohol B. carbolfuchsin* C. crystal violet D. methylene blue Difficulty: Moderate ASM Standard: 32 19. Which is the correct order of steps in Gram staining? A. crystal violet stain, ethanol decolorization, Gram’s iodine mordant, safranin counterstain B. crystal violet stain, Gram’s iodine mordant, ethanol decolorization, safranin counterstain*

C. ethanol stain, crystal violet rinse, safranin counterstain, Gram’s iodine mordant D. safranin stain, Gram’s iodine mordant, ethanol decolorization, crystal violet counterstain Difficulty: Easy ASM Standard: 32 20. It is important to fix bacterial smears on a slide for which of the following reasons? A. to attach them to the slide* B. to cause swelling of the cell to make interior structures more visible C. to enhance the uptake of stains D. to provide a nutrient medium to sustain the bacteria Difficulty: Easy ASM Standard: 32 21. Which of the following is not commonly used for chemical fixation? A. acetic acid B. ethanol C. glutaraldehyde D. iodine* Difficulty: Moderate ASM Standard: 32 22. Which of the following is not involved in preparing a bacterial slide for Gram staining? A. allowing the sample to dry on the slide B. fixing the specimen to the slide C. placing a smear on the slide D. preparing a wet mount* Difficulty: Moderate ASM Standard: 32 23. Which of the following most specifically refers to stains with positively charged chromophores? A. acid-fast dyes B. acidic dyes C. basic dyes* D. positive dyes Difficulty: Moderate ASM Standard: 32 24. Which of the following most specifically refers to a stain that dyes a specimen rather than the background? A. counterstain

B. mordant C. negative stain D. positive stain* Difficulty: Moderate ASM Standard: 32 25. Which of the following describes the difference between the Ziehl-Neelsen and Kinyoun acid-fast staining techniques? A. The Ziehl-Neelsen technique uses a counterstain and the Kinyoun technique does not. B. The Ziehl-Neelsen technique uses an acidic dye and the Kinyoun technique does not. C. The Ziehl-Neelsen technique uses heat and the Kinyoun technique does not.* D. The Ziehl-Neelsen technique uses two dyes and the Kinyoun technique does not. Difficulty: Moderate ASM Standard: 32 26. Which of the following described the difference between gram-positive and gram-negative cells that causes them to stain differently after Gram staining? A. Gram-positive cells have a mycolic acid layer in their cell walls that holds in stain, whereas gram-negative cells lack this layer. B. Gram-positive cells have capsules and gram-negative cells have S layers. C. Gram-positive cells have thicker cell membranes than gram-negative cells. D. Gram-positive cells have thicker peptidoglycan layers in their cell walls than do gramnegative cells.* Difficulty: Moderate ASM Standard: 7, 32, 34, 36 27. Which of the following would not potentially cause a gram-positive cell to appear gramnegative after Gram staining? A. counterstaining with crystal violet instead of safranin* B. exposing the cells to ethanol for too long C. using older bacterial cultures D. using safranin as a primary stain Difficulty: Moderate ASM Standard: 32, 34, 36 28. Which of the following does not cause the probe to move up and down above the specimen in atomic force microscopy? A. chemical bonding B. electrostatic forces C. van der Waals forces D. variations in current*

Difficulty: Difficult ASM Standard: 32 29. Quantum tunneling of electrons is important in the mechanism underlying which microscope type? A. AFM B. SEM C. STM* D. TEM Difficulty: Moderate ASM Standard: 32 30. Which of the following is the chemical in some bacterial cells’ walls that makes themresist decolorization after acid-fast staining? A. acetic acid B. mycolic acid* C. peptidoglycan D. phospholipid Difficulty: Moderate ASM Standard: 32 31. Gram staining is useful for bacterial identification. Which of the following is another way it is most useful? A. Knowing Gram staining results allows a researcher to know which organisms abacterium can infect. B. Knowing Gram staining results allows a researcher to select the appropriate growth medium for optimal bacterial growth. C. Knowing Gram staining results is helpful in choosing an effective antibiotic.* D. Knowing Gram staining results is helpful in understanding a bacterium’s metabolic requirements. Difficulty: Difficult ASM Standard: 7, 23 32. Which of the following is not true regarding capsule staining? A. Capsules are typically stained using basic dyes.* B. Capsule staining does not require heat fixation in advance. C. Capsule staining requires careful selection of a stain that can stain the capsule itself. D. Capsule staining typically involves negative staining. Difficulty: Difficult ASM Standard: 7, 23 33. Because endospores are difficult to stain, which of the following is generally needed?

A. Heat must be used to make the endospore take up stain. B. Mycolic acid must be added to encourage the endospore to take up stain. C. Negative staining must be used to stain endospores because they do not absorb stain.* D. The cells must be cooled to make the endospore more brittle prior to staining. Difficulty: Difficult ASM Standard: 7, 32 34. When endospores are stained using the Schaeffer-Fulton method, which of the following correctly describes how they appear after staining? A. The endospore appears green within a pink cell, because only the endospore retained the primary stain.* B. The entire cell appears green because the endospore surrounds all the vegetative material. B. The entire cell appears pink because the endospore surrounds all the vegetative material. C. The entire cell appears pink except for a clear area representing the endospore. Difficulty: Moderate ASM Standard: 6, 7, 32 35. Specimens for TEM are prepared by doing which of the following? A. dehydrating the specimen in ethanol and then coating it in a material that will repel electrons B. sputter coating with a substance such as gold to repel electrons C. using an ultramicrotome to cut very thin sections from samples embedded in plastic resin* D. using chemical fixation, followed by standard staining techniques such as the Gram stain Difficulty: Difficult ASM Standard: 32 True/False 36. In fluorescence, emitted photons have the same amount of energy as absorbed photons. Answer: False Difficulty: Easy ASM Standard: N/A 37. A microscope with very high magnification and low resolution would allow you toclearly see small structures. Answer: False Difficulty: Easy ASM Standard: 6 38. The difference between a simple microscope and a compound microscope is that the latter only has one lens.

Answer: False Difficulty: Easy ASM Standard: N/A 39. Flagella staining is very useful for diagnostic purposes in medical settings. Answer: False Difficulty: Moderate ASM Standard: 7, 32 40. The transmission electron microscope and scanning electron microscope produce very similar images, but the former can be show three-dimensional external structures. Answer: False Difficulty: Moderate ASM Standard: 6, 32 41. Differential interference contrast microscopy produces three-dimensional images of specimens. Answer: True Difficulty: Moderate ASM Standard: 32 42. During specimen preparation for transmission electron microscopy, the specimensare dehydrated in alcohol and embedded in plastic resin. Answer: True Difficulty: Difficult ASM Standard: 32 43. In atomic force microscopy, the movement of the probe tip is determined using Hooke’slaw of elasticity. Answer: True Difficulty: Difficult ASM Standard: 32 Matching 44. Match each term with the best definition. A. amplitude i. electromagnetic radiation within certain parameters B. frequency ii. the height of a wave peak or depth of a wave trough C. visible light iii. the rate of vibration of a wave D. wavelength iv. the distance between two wave peaks

Answers: A. ii., B. iii., C. i., D. iv. Difficulty: Easy ASM Standard: N/A 45. Match each term with the best definition. A. absorbance i. Light waves change direction when they enter a new medium. B. diffraction ii. Two waves interact. C. interference iii. A wave travels through something. D. refraction iv. A material captures light energy. E. transmission v. Light bends or scatters as it interacts with objects or openings. Answers: A. iv., B. v., C. ii., D. i., E. iii. Difficulty: Moderate ASM Standard: N/A 46. Match each type of microscope with a common use for that microscope type. A. brightfield i. commonly used clinically; helpful in distinguishing living from dead cells, finding molecules within a cell, and for immunostaining B. darkfield ii. widely used and easily available; used for examining common protists, bacteria, and tissues; stains are often needed C. fluorescence iii. uses an annular stop, refraction, and interference to produce relatively high-resolution images without stains D. phase contrast iv. used to examine an image produced with light that hits a specimen indirectly owing to the use of an opaque light stop; often used to view living microorganisms without stains E. two-photon v. often used to penetrate thick specimens, such as biofilms, with long-wavelength light Answers: A. ii., B. iv., C. i., D. iii., E. v. Difficulty: Difficult ASM Standard: 32 47. Match each type of microscopy with the best description. A. atomic force microscopy i. measures changes in current as a probe is moved at a constant height over a specimen B. scanning electron ii. measures variations in the height of a probe moving microscopy over the specimen; height variations occur to maintain a constant current C. scanning tunneling iii. yields images from electrons produced by an electron microscopy beam hitting the surface of a sputter-coated specimen D. transmission electron iv. produces images from electrons that pass through a microscopy very thin specimen, allowing internal structures to be visualized Answers: A. ii., B. iii., C. i., D. iv. Difficulty: Moderate

ASM Standard: 32 48. Match the staining procedure with the chemicals used. A. acid-fast stain i. crystal violet, iodine, ethanol, safranin B. capsule stain ii. tannic acid or potassium alum, pararosaniline or basic fuchsin C. endospore stain iii. carbolfuchsin, acid alcohol, and methylene blue D. flagella stain iv. malachite green, safranin E. Gram stain v. India ink or nigrosin, sometimes with positive staining Answers: A. iii., B. v., C. iv., D. ii., E. i. Difficulty: Moderate ASM Standard: 32 49. The choices describe possible scenarios and outcomes from Gram staining with standard stains (e.g., crystal violet and safranin). Match the scenario with the most likely outcome. A. A gram-negative cell is stained, but i. The cell will probably appear pink, which will the ethanol step is skipped. not correctly indicate its cell wall structure. B. A gram-positive cell with a severely ii. The cell will appear pink. damaged cell wall is stained. C. A healthy gram-negative cell is iii. The cell will appear purple/violet. stained. D. A healthy gram-positive cell is iv. The cell will probably appear purple/violet, stained. which will not correctly indicate its cell wall structure. Answers: A. iv., B. i., C. ii., D. iii. Difficulty: Difficult ASM Standard: 6, 32 Fill in the Blank 50. Compared with air, water has a(n) Answer: higher

refractive index.

Difficulty: Easy ASM Standard: N/A 51. The electron microscope produces high-resolution images of three-dimensional surface structures of sputter-coated specimens. Answer: scanning Difficulty: Moderate ASM Standard: 32 52. Robert Hooke published compound microscopes. Answer: Micrographia

, in which he described his observations of cork via

Difficulty: Easy ASM Standard: N/A 53.

microscopy uses an opaque stop, is useful for viewing living organisms without using stains, and produces images with a dark background. Answer: Darkfield Difficulty: Moderate ASM Standard: 32

54. Acid-fast bacteria have Answer: mycolic acids

in their cell walls that retain carbolfuschin stain.

Difficulty: Moderate ASM Standard: 6, 7, 32 55. In acid-fast staining, cells that are not acid-fast usually appear Answer: blue

Difficulty: Moderate ASM Standard: 32 56. During preparation of specimens for scanning electron microscopy, specimens areoften sputter coated with or a similar material. Answer: gold Difficulty: Moderate ASM Standard: 32 57. Negative staining of capsules is commonly done using India ink or Answer: nigrosin

Difficulty: Moderate ASM Standard: 6 32 58. An acid-fast staining technique similar to the Ziehl-Neelsen technique is called the technique. Answer: Kinyoun Difficulty: Moderate ASM Standard: 32 59. When an object is relatively small relative to a wavelength of light, diffraction is than if an object is relatively large. Answer: larger

Difficulty: Difficult ASM Standard: 32 Short Answer 60. Why is the resolution of a microscope image important? Sample Answer: A high-resolution image is clear because you can distinguish between points. If the image is low resolution, then it is fuzzy and individual structures are more difficult to see. Difficulty: Easy ASM Standard: 32 61. Who is believed to have developed the first microscopes that allowed microbes to be viewed? Sample Answer: Antonie van Leeuwenhoek is believed to have developed the first microscopes that allowed microscopes to be viewed. Difficulty: Easy ASM Standard: N/A 62. What is the name of the lens that focuses light from a microscope light source onto the specimen on the stage? Sample Answer: The lens that focuses light on the slide is called the condenser. Difficulty: Easy ASM Standard: N/A 63. Would you use immersion oil at high magnification or low magnification? Sample Answer: Immersion oil is used to view specimens at high magnification with a light microscope and only with objective lenses that are designed for oil immersion. Difficulty: Easy ASM Standard: 32 64. What is the difference between fluorescence and phosphorescence? Sample Answer: In both fluorescence and phosphorescence, a material absorbs energy from light and then emits it again at a lower energy level. However, there is a delay between light absorbance and the emission of lower energy photons in phosphorescence that does not occur in fluorescence. Difficulty: Difficult ASM Standard: N/A 65. Which lens will produce an image with greater resolution: one with a higher numerical aperture or one with a lower numerical aperture? Why?

Sample Answer: A higher numerical aperture produces an image with greater resolution, because more light can be gathered by the lens. Difficulty: Moderate ASM Standard: 32 66. How does immersion oil improve the resolution of a microscope image? Sample Answer: Immersion oil has a similar refractive index to glass. When light passes from the specimen into air, it is refracted and some is lost rather than passing through the objective. When there is oil between the specimen and the objective lens, more light enters the objective lens rather than being lost, and the image resolution is greater. Difficulty: Moderate ASM Standard: N/A 67. For what type of microscopy is an opaque light stop used, and what is its function? Sample Answer: In darkfield microscopy, an opaque stop is placed between the light source (illuminator) and the condenser lens. The stop blocks light from the illuminator from hitting the specimen directly. This means light does not hit the specimen directly and only refracted or reflected light reaches the objective, producing a bright specimen on a dark background. Difficulty: Moderate ASM Standard: N/A 68. Why is it sometimes advantageous to avoid using stains when viewing microorganisms? Sample Answer: Most stains or the process of staining can kill the specimen. It is often advantageous to view microorganisms without stains when one wishes to observe them alive (e.g., to observe their motility). Difficulty: Moderate ASM Standard: N/A 69. What is another name for differential interference contrast microscopy? Sample Answer: Differential interference contrast microscopy is also called Nomarski optics. Difficulty: Moderate ASM Standard: N/A 70. What are some common fluorochromes used in fluorescence microscopy? Sample Answer: Some common fluorochromes are Texas red, FITC, DAPI, and acridine orange. Difficulty: Moderate ASM Standard: 32 71. In immunofluorescence, what are secondary antibodies used for?

Sample Answer: Secondary antibodies bind to primary antibodies, which bind to a an antigen (i.e., a protein, sometimes as part of a pathogen) in indirect immunofluorescence assays. Difficulty: Moderate ASM Standard: 32 72. Why is it important to embed specimens in plastic resin during their preparation for TEM? Sample Answer: TEM specimens must be very thin for internal structures to be visible. An ultramicrotome is used to cut thin sections for this purpose. By embedding the specimens in plastic before cutting them, it is easier to prevent them from being damaged and compressed while being cut. Ethanol is used to help the plastic resin penetrate the cell. Difficulty: Difficult ASM Standard: 32 73. Why can electron microscopes achieve higher resolutions than light microscopes? Sample Answer: Resolution is higher when there are shorter wavelengths. The beams of electrons used by electron microscopes have shorter wavelengths than the light waves used by light microscopes. Difficulty: Difficult ASM Standard: 32 74. Why do microscopes have rheostats? What is adjusted by adjusting a microscope’s rheostat? Sample Answer: A microscope rheostat is used to adjust the amount of light on the specimen. This is important to have the optimal amount of light to view the specimen. Having too much or too little light makes the specimen difficult to see clearly. Difficulty: Difficult ASM Standard: 32 Brief Essay Essay Question Rubric RATING Failing Criteria for evaluati on

Answer does not provide an argument. Answer contains inaccuracies. Writing is poor and contains numerous grammatical

Below Average Answer fails to provide examples to support an argument. Writing is poor and grammatical errors are common. Answer is

Competent

Advanced

Answer provides an argument with one or two examples that support it. Writing is acceptable for the college level but may contain one or

Answer clearly provides an argument with two or more excellent examples that support it; student makes the argument clearly and eloquently.

mistakes and misspellings.

somewhat incoherent.

two grammatical mistakes or misspellings.

Answer is well organized and free of grammatical errors and misspellings.

0 1 2 3 POINT VALUE Assume rating/grading scale for the question ranges from 0 to 3 points. 75. Explain how direct and indirect immunofluorescence assays differ, including an explanation of why indirect immunofluorescence is more commonly used. Answer: Student answers will vary but should include the following. Direct immunofluorescence involves the use of an antibody that is attached to a fluorochrome. When the antibody binds to an antigen, the fluorochrome is visible under the fluorescence microscope and allows the location of the antigen to be visualized. In indirect immunofluorescence, a primary antibody lacking a fluorochrome binds to an antibody. Then, a secondary antibody containing a fluorochrome binds to the primary antibody. Because more than one secondary antibody may bind to a primary antibody, indirect immunofluorescence increases sensitivity and can make it easier to visualize the specimen. This is an important reason to choose indirect immunofluorescence even though direct immunofluorescence requires fewer steps. Difficulty: Moderate ASM Standard: 32, 36 76. You prepare a slide of a bacterial sample by placing bacteria on a slide and examining it under a brightfield microscope. However, it is difficult to see the bacteria because the contrast is low. What are at least two ways you could increase the contrast? Answer: Student answers will vary but should include the following. There are several ways you could increase the contrast. You could add a stain, choosing one that would likely stain the structures or cells of interest. You could also use a different form of microscopy, such as darkfield or phase contrast. Another option is to adjust the amount of light on the slide using the diaphragm and/or rheostat. Other options are also possible. Difficulty: Moderate ASM Standard: 32 77. Explain some advantages of two-photon microscopy, and explain why this typeof microscopy is not more commonly used. Answer: Student answers will vary but should include the following. Two-photon microscopy is especially valuable for penetrating thicker materials, such as biofilms. It also uses lower-energy light that is less damaging to living tissues than some other forms of microscopy. This means it can be used to obtain high-resolution images of living organisms and tissues. However, the technology is still not widely used because it is very expensive. Difficulty:

Moderate ASM Standard: 32 78. There is some debate over who invented the microscope. Explain why this debate exists and what factors help some individuals get more credit for their roles than others. Answer: Student answers will vary but should include components of the following. Multiple people worked on early microscopes, including Galileo. Antonie van Leeuwenhoek and Robert Hooke receive considerable credit for their microscopes and observations. However, it is possible that Hans Janssen and Zaccharias Janssen should receive more credit. There is considerable uncertainty about their exact work. A major reason for this is that Leeuwenhoek and Hooke published their work. Because the Janssens did not, much less is known about their work. Difficulty: Difficult ASM Standard: 31 79. Many microbes live in biofilm communities and understanding these communities is important for a variety of reasons. For example, understanding biofilm formation within wounds and medical devices is important for improving patient outcomes. What are ways that light microscopy, confocal microscopy, fluorescence microscopy, electron microscopy, and two-photon microscopy can be used to study biofilms? Answer: Student answers will vary but should include components of the following. Although light microscopes are easily available, biofilm architecture is difficult to examine under light microscopy because biofilms are too thick to easily examine throughout their structure with light microscopes without cutting and disrupting the biofilm. Confocal microscopy can be helpful in providing three-dimensional images of thicker structures, such as biofilms, but still have lower resolution than two-photon microscopes. Additionally, fluorescent stains can be used with confocal microscopy to enhance visibility with these three-dimensional images. Even without the depth of confocal microscopy, fluorescence microscopy is helpful in identifying the locations of specific molecules or cells. Electron microscopy allows high magnifications, but the specimens are distorted and can’t be viewed alive. Two-photon microscopes are especially useful because thick biofilm specimens can be viewed without distortion, but these microscopes are too expensive for general use. Difficulty: Difficult ASM Standard: 32 This file is copyright 2017, Rice University. All rights reserved.

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Chapter 3: The Cell * = Correct answer Multiple Choice 1. The idea that life could appear from nonliving materials was called which of the following? A. the cell theory B. the cellular genesis theory C. the theory of biogenesis D. the theory of spontaneous generation* Difficulty: Easy ASM Standard: N/A 2. The first known use of epidemiology to trace the source of a disease outbreak was the identification of contaminated water as the cause of cholera transmission in London. Which of the following was the physician who accomplished this? A. Joseph Lister B. John Needham C. Ignaz Semmelweis D. John Snow* Difficulty: Easy ASM Standard: N/A 3. Which of the following is a series of steps for determining the causative agent of a particular disease? A. Koch’s postulates* B. Lister’s checklists C. Pasteur’s principles D. Semmelweis’ guidelines Difficulty: Easy ASM Standard: 23 4. Which scientist performed an elegant series of experiments that finally and definitively disproved the theory of spontaneous generation? A. John Needham B. Louis Pasteur* C. Francesco Redi D. Jan Baptista van Helmont Difficulty: Easy Page 36A of S M17Standard:

N/A

5. Prokaryotes are classified into which domain(s)? A. Domain Archaea only B. Domain Bacteria only C. Domains Archaea and Bacteria only* D. Domains Bacteria and Eukarya only Difficulty: Moderate ASM Standard: N/A 6. Which term refers to a curved rod? A. bacillus B. coccus C. spirillum D. vibrio* Difficulty: Easy ASM Standard: N/A 7. When a bacterial cell with a cell wall is placed in salt water with a higher-solute concentration than the cell cytoplasm, the cell will undergo which of the following? A. crenation B. crenolysis C. lysis D. plasmolysis* Difficulty: Moderate ASM Standard: 8, 22 8. The bacterial chromosome located in which of the following? A. the capsule B. the nucleoid region* C. the nucleus D. the thylakoids Difficulty: Easy ASM Standard: N/A 9. Which scientist thought spontaneous generation had occurred in flasks of broth after the broth had been boiled? A. John Needham* B. Louis Pasteur C. Francesco Redi D. Jan Baptista van Helmont Difficulty: Moderate ASM Standard: N/A Page 37 of 17

10. Which of the following is not evidence for the endosymbiotic theory? A. Chloroplasts and mitochondria contain ribosomes that resemble prokaryotic ribosomes. B. Chloroplasts and mitochondria contain their own DNA that resembles prokaryotic DNA. C. Chloroplasts and mitochondria have structures that resemble prokaryotic cell walls.* D. Chloroplasts and mitochondria reproduce using binary fission, like prokaryotic cells. Difficulty: Moderate ASM Standard: 1 11. Which physician realized that doctors were causing maternal deaths by failing to wash their hands while assisting during childbirth? A. Girolamo Fracastoro B. Joseph Lister C. Louis Pasteur D. Ignaz Semmelweis* Difficulty: Easy ASM Standard: 23 12. How did Joseph Lister dramatically improve surgical outcomes? A. by developing new antibiotics B. by developing new ways to circulate air within surgical facilities C. by using phenol as an antiseptic and disinfectant during surgery* D. by using vaccination against communicable diseases Difficulty: Easy ASM Standard: 14, 23 13. Sporulation generally occurs under which of the following circumstances? A. when conditions are unfavorable or there are insufficient nutrients* B. when microbes are exposed to a new, favorable environment C. when microbes are under little stress and can become dormant D. when resources become highly abundant Difficulty: Moderate ASM Standard: 8, 22 14. Which of the following is not a difference between endospores and vegetative cells? A. Vegetative cells are metabolically active, whereas endospores are dormant. B. Vegetative cells are more resilient due to their metabolic activities, whereas endospores are more sensitive to change.* C. Vegetative cells normally have enzyme activity, whereas endospores do not show enzymatic activity.

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D. Vegetative cells stain easily using normal staining protocols, whereas endospores are difficult to stain without special endospore stains. Difficulty: Moderate ASM Standard: 8 15. Immediately following asymmetric cell division during sporulation, which of the following structures contains the DNA and goes on to develop into an endospore? A. cortex B. forespore* C. hindspore D. spore coat Difficulty: Moderate ASM Standard: 8 16. Which of the following gives the correct order of the stages of sporulation? A. Cortex formation, formation of a double layer of membrane, DNA replication, spore release B. DNA replication, formation of a double layer of membrane, cortex formation, spore release* C. DNA replication, spore release, cortex formation, formation of a double layerof membrane D. Formation of a double layer of membrane, DNA replication, spore release, cortex formation Difficulty: Moderate ASM Standard: 8 17. Which of the following is not a clinically significant, spore-forming bacterium? A. Bacillus anthracis B. Clostridium botulinum C. Clostridium difficile D. Escherichia coli* Difficulty: Moderate ASM Standard: 8 18. All cells have which of the following? A. capsule B. cell membrane* C. cell wall D. nucleus Difficulty: Moderate ASM Standard: 8 Page 39 of 17

19. Which term refers to proteins that extend across the plasma membrane from one side to the other? A. glycoproteins B. lipoproteins C. peripheral proteins D. transmembrane proteins* Difficulty: Moderate ASM Standard: N/A 20. In which types of organisms are phospholipids with branched chains common? A. archaea* B. bacteria C. eukaryotes D. all of the above Difficulty: Moderate ASM Standard: N/A 21. The lipopolysaccharide molecule is an important component of the cell membranes of which organisms? A. archaeans B. eukaryotes C. gram-negative bacteria* D. gram-positive bacteria Difficulty: Moderate ASM Standard: 8, 23 22. Capsules and slime layers are examples of which type of structure? A. cell walls B. glycocalyces* C. peptidoglycan layers D. S-layers Difficulty: Moderate ASM Standard: 8 23. Bacteria use flagella to move purposefully toward or away from a chemical by which of the following? A. having alternating runs and tumbles of equal lengths B. increasing the length of runs and decreasing the length of tumbles* C. increasing the length of tumbles and decreasing the length of runs D. using only runs

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