Environmental Microbiology
Chapter Exam Questions
Course Introduction
Environmental Microbiology explores the roles and interactions of microorganisms within natural and engineered environments. The course covers microbial diversity, metabolism, and ecology, focusing on processes such as nutrient cycling, biodegradation, water and soil quality, and the impact of microbes on environmental health. Students gain an understanding of how microbes respond to environmental changes, their applications in bioremediation and pollution control, and the methods used to study microbial communities in various ecosystems. The curriculum integrates laboratory techniques with current research to highlight the significance of microorganisms in maintaining and restoring environmental balance.
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Microbiology An Evolving Science 4th Edition by John W. Foster
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Page 2
Chapter 1: Microbial Life: Origin and Discovery
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Q1) What feature of bacteria facilitated the DNA revolution in the 1970s?
A) They are very small.
B) They readily recombine DNA.
C) They have very large genomes.
D) All of their genes were known.
E) They do not cause disease.
Answer: B
Q2) A microbe is commonly defined as a ________ that requires a microscope to be seen.
A) virus
B) bacterium
C) single-cellular prokaryote
D) multicellular eukaryote
E) living organism
Answer: E
Q3) How do microbes help in the extraction of minerals?
Answer: Several lithotrophic bacteria help in the rapid oxidation of minerals, which generates strong acids that expedite the breakdown of mineral ore. Currently, approximately 20% of the world's copper, as well as some uranium and zinc, is produced by bacterial leaching.
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Chapter 2: Observing the Microbial Cell
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Q1) Define a fluorophore and give three examples of how it can be used to label cells.
Answer: A fluorophore is a fluorescent molecule that can be used to stain a specimen for observation with a fluorescence microscope. Some fluorophores, such as DAPI, have affinity for certain cell chemicals. Antibodies can be labeled with fluorescent dyes and reacted with specific targets in immuno- fluorescence. Short sequences of DNA attached to a fluorophore can be used to hybridize and label target DNA.
Q2) Chlamydia trachomatis transmits infection to a new cell via A) a membrane vesicle.
B) elementary bodies.
C) amoeba.
D) host membranes.
E) the human cell.
Answer: B
Q3) List and describe three common shapes of bacteria.
Answer: Bacilli (bacillus in the singular) are rod-shaped bacteria. Cocci (singular, coccus) are spherical-shaped bacteria. Spirochetes are tightly coiled spirals or corkscrew-shaped bacteria.
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Page 4
Chapter 3: Cell Structure and Function
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Q1) All of the statements about genetic analysis of cells complementing cell fractionation are true EXCEPT that it
A) is used to identify which genes and proteins are involved in a process.
B) can be used by identifying phenotypes under a microscope.
C) can be used to identify the exact change in protein sequences giving a particular phenotype.
D) has never been used to study FtsZ.
E) can be used to study cell division.
Answer: D
Q2) A ________ is a term used to designate a single messenger RNA molecule being translated by multiple ribosomes.
A) couple
B) periplasm
C) carboxysome
D) thylakoid
E) polysome
Answer: E
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Chapter 4: Bacterial Culture, Growth, and Development
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Q1) The shortest lag period would most likely be observed in the transfer
A) from complex medium to fresh complex medium.
B) from complex medium to minimal medium.
C) to a lower temperature.
D) to a different pH.
E) to a different salt concentration.
Q2) When the population doubles during each given unit of time, the growth is
A) linear.
B) semilogarithmic.
C) exponential.
D) geometric.
E) arithmetic.
Q3) The time between inoculation and the beginning of growth is usually called the ________ phase.
A) lag
B) early log
C) late log
D) stationary
E) death
Q4) Compare and contrast complex media, synthetic media, and enriched media.
Page 6
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Chapter 5: Environmental Influences and Control of
Microbial Growth
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Q1) A bacterium that thrives in your stomach is probably a(n)
A) thermophile.
B) neutrophile.
C) alkaliphile.
D) acidophile.
E) psychrophile.
Q2) Special channels for helping water move across the membrane quickly are called A) compatible solutes.
B) osmolarity.
C) aquaporins.
D) mechanosensitive channels.
E) chaperones.
Q3) Describe one method that enables researchers to study extremophilic organisms that we cannot culture in the laboratory.
Q4) The conditions used in an autoclave may be reproduced at home in A) a rice cooker.
B) a double-boiler.
C) a microwave.
D) a pressure cooker.
E) boiling water.
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Chapter 6: Viruses
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Q1) Some viruses require an RNA-dependent RNA polymerase. What does that mean? What would you call the host cell RNA polymerase (RNA pol)? What would you call reverse transcriptase (RTase)?
Q2) Which of the following is FALSE concerning HIV?
A) It is the causative agent of AIDS.
B) It makes a DNA copy of its RNA genome.
C) Reverse transcriptase is translated from an early gene.
D) The virion contains two copies of the HIV genome.
E) The viral RNA is copied into double-stranded DNA.
Q3) Define oncogenes and oncogenic viruses, and explain how they can be used in gene therapy.
Q4) What determines the host range and tropism of a virus?
Q5) Which filamentous virus causes a fatal disease in humans and is also related to primates?
A) HIV
B) Ebola
C) smallpox
D) cowpox
E) herpes virus
Q6) How can a virus be used to transfer genes from one bacterial cell to another?
Page 8
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Chapter 7: Genomes and Chromosomes
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Q1) Besides the nucleoid, two other kinds of DNA molecules that may be present in the cytoplasm of a bacterial cell are ________ and the genomes of ________.
A) bacteriophages; pseudogenes
B) introns; bacteriophages
C) plasmids; bacteriophages
D) plasmids; introns
E) introns; exons
Q2) A nucleoid gently released from Escherichia coli appears as 30-100 tightly wound loops, each defined by anchoring
A) histones.
B) histone-like proteins.
C) transcription factors.
D) rho factors.
E) sigma factors.
Q3) Describe the functions of DNA Pol III.
Q4) When gently released from an E. coli cell, the nucleoid was found to contain 30 to100 domain loops. How are these loops kept together, and what type of studies have demonstrated their independence?
Q5) What determines the timing of DNA replication in Escherichia coli?
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Chapter 8: Transcription, Translation, and Bioinformatics
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Q1) Genes that have arisen from a duplication within a species and have evolved to carry out different functions are referred to as
A) homologs.
B) orthologs.
C) paralogs.
D) homogenous.
E) synonymous.
Q2) Explain the processes of Rho-dependent and Rho-independent termination of transcription.
Q3) Molecules of sRNA do not encode proteins but are used to ________ the stability or translation of specific mRNAs into proteins.
A) start
B) regulate C) stop
D) speed up
E) slow down
Q4) Describe how Marshal Nirenberg and Heinrich Matthaei utilized an E. coli cell lysate to figure out the genetic code.
Q5) How are folded and unfolded proteins moved from the cytoplasm to the periplasm?
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Chapter 9: Gene Transfer, Mutations, and Genome
Evolution
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Q1) Why is SOS repair considered to be an error-prone repair mechanism? Why would an organism use an error-prone mechanism?
Q2) Compare and contrast general and site-specific recombination.
Q3) Which of the following LEAST supports the idea of genome reduction?
A) Pseudogenes found in some organisms are no longer expressed but have homology to functional genes in other species.
B) Virulence factors are found on pathogenicity islands.
C) Pathogenic shigellae lack major regions of genes that the closely related E. coli possesses.
D) Bacteria no longer need "pseudogenes" when growing in new environments.
E) Over half of the genome of the obligate intracellular pathogen, Mycobacterium leprae, is composed of pseudogenes that are no longer needed.
Q4) Which of the following mutagens does NOT cause point mutations?
A) caffeine
B) 5-bromouracil
C) nitrosoguanidine
D) nitrites
E) acridine dyes
Q5) Distinguish between generalized and specialized transduction.
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Chapter 10: Molecular Regulation
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Q1) How does the AraC regulatory protein turn on transcription in the presence of arabinose?
A) With the addition of arabinose, AraC no longer dimerizes and will form a large loop by binding to araO and aria, and thus can interact with RNA polymerase to permit transcription.
B) The dimer will form a large loop by binding to araO and aria, and thus can interact with RNA polymerase to permit transcription.
C) With the addition, AraC no longer dimerizes and thus can interact with RNA polymerase to permit transcription.
D) It becomes less flexible, so that a monomer can bind to araI1 and araI2 and interact with RNA polymerase to permit transcription.
E) It becomes more flexible, so that the dimer can bind to araI1 and araI2 and interact with RNA polymerase to permit transcription.
Q2) Briefly explain two-dimensional gel electrophoresis. What is the procedure used to determine, and why are both dimensions necessary?
Q3) Explain how a repressor protein works with respect to a biosynthetic operon.
Q4) Explain a way that organisms sense and respond to their environment.
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Chapter 11: Viral Molecular Biology
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Q1) How many genomes does an HIV particle have and what is their biochemical nature?
A) two RNA molecules
B) eight RNA molecules
C) a DNA/RNA hybrid
D) a single RNA molecule
E) a DNA molecule and a noncomplementary RNA molecule
Q2) Sequences of endogenous retroviruses (HERVs) are remnants of retroviral infections. HERVs have accumulated over millions of years and comprise about 8% of the human genome. Briefly describe the evidence for the expression of HERV-K proteins and virus-like particles in the human embryo. What are the implications of HERV-K products interacting with embryonic factors?
Q3) Control proteins Cro and CII lead to lysis or lysogeny, respectively. What environmental signal in the host contributes to regulate the amount of CII by influencing the activity of the protease HflB?
A) Mg2+ ion concentrations
B) temperature
C) water availability
D) nutrient concentrations
E) helper phages
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Chapter 12: Biotechniques and Synthetic Biology
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Q1) A "buffer gate" in synthetic biology can best be described as A) a single repressor molecule (R1) that prevents the production of an output molecule (Pr1).
B) alternate input molecules (I1 or I2) that drive the production of alternative proteins (Prn).
C) a single input inducer molecule (I1) that leads to the production of a single product (Pr1).
D) kill switches.
E) a potent DNA-damaging toxin.
Q2) What is the conceptual basis of the primer extension technique?
Q3) The replacement of the genome of Mycoplasma capricolum with the modified genome of M. mycoides is considered to be a significant accomplishment because it A) demonstrates that genetic manipulation of recalcitrant organisms is impossible.
B) opens the possibility to redesign prokaryotic genomic systems.
C) enables gene editing of species.
D) merges the genomes into a hybrid.
E) creates a riboswitch board.
Q4) What are translational fusions used for? How are they constructed?
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Page 14
Chapter 13: Energetics and Catabolism
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Q1) The energy yield from fermentation is lower than from respiration because A) fermentation uses NAD+, not NADP+.
B) respiration completely oxidizes glucose to CO , resulting in greater generation of NADH and thus ATP.
C) respiration uses the TCA cycle, which has many steps that directly produce ATP or GTP.
D) fermentation shunts much of the carbon from glucose to biosynthesis.
E) fermentation relies on the glyoxylate bypass, which bypasses ATP production.
Q2) The Gibbs equation describes the relationship between the components of free energy change and can be generally expressed as
A) DG = DG° + RT ln Keq.
B) DG = DH - TDS.
C) ADP + Pi D ATP + H O.
D) K = T°C + 273.
E) DG = -2.303 RT log [C] [D] / [A] [B].
Q3) Describe the diagnostic use of sorbitol MacConkey agar to test for the presence of E. coli O157:H7.
Q4) Describe the Entner-Doudoroff (ED) pathway. What are the advantages to microorganisms that display the ED pathway?
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Chapter 14: Electron Flow in Organotrophy,
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Q1) In cytochromes, the heme group plays a key role in acquiring and transferring electrons with a(n) __________ transition.
A) Mg0/Mg2+
B) S0/S2-
C) Cu+/Cu2+
D) Fe3+/Fe2+
E) Mn0/MN +
Q2) In anaerobic soils, some yeasts and filamentous fungi can reduce nitrate to nitrite and nitrite to
A) ammonia (NH3).
B) nitric oxide (NO).
C) urea.
D) nitrogen gas (N ).
E) ammonium hydroxide (NH4OH).
Q3) Which of the following substrates is an electron donor in organotrophy?
A) Fe2+
B) succinate
C) NO
D) H
E) H O
Page 16
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Chapter 15: Biosynthesis
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Q1) Which of the following is NOT correct regarding nitrogen assimilation into biomass?
A) Different oxidation states of nitrogen require different amounts of reducing energy.
B) It is easy for living organisms to assimilate nitrogen due to its great stability.
C) Nitrogen forms must be fully reduced to NH3.
D) Only bacteria and archaea can assimilate elemental nitrogen.
E) It is expensive, requiring reducing energy and ATP.
Q2) How do cyanobacteria benefit from their heterocysts attracting heterotrophic bacteria?
Q3) Which of the following drugs is a nonribosomal peptide antibiotic?
A) erythromycin
B) penicillin
C) tetracycline
D) vancomycin
E) ciprofloxacin
Q4) How is fatty acid biosynthesis regulated in bacteria?
Q5) How does the reductive or reverse TCA cycle differ from the regular TCA cycle?
Q6) Briefly describe how NH is assimilated into biomass by bacteria.
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Chapter 16: Food and Industrial Microbiology
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Q1) Describe several physical means of food preservation.
Q2) Miso is a fermented Japanese condiment made primarily from ________, which is salted and fermented with ________ for two months.
A) cabbage; Leuconostoc
B) rice; Leuconostoc
C) cabbage; Bacillus
D) cabbage; Aspergillus oryzae
E) ground soy and rice; Aspergillus oryzae
Q3) Microorganisms are used in the production of many small molecules, such as amino acids, vitamins, and medicines. Which of the following is NOT produced by a bacterium?
A) steroids
B) L-lysine
C) vitamin B12
D) penicillin
E) tetracycline
Q4) Explain the difference between food spoilage and food poisoning.
Q5) Describe how the transportation of milk products by herders led to the formation of cheeses.
Q6) What makes a company dealing with industrial microbiology a success?
Page 18
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Chapter 17: Origins and Evolution
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Q1) Evidence of life left in the geological record is known as A) biosignatures.
B) genetic markers.
C) abiotic artifacts.
D) enzyme markers.
E) molecular weight markers.
Q2) The term "________" indicates that the members of a clade share a common ancestor, one not shared by any group outside the clade.
A) monogamy
B) monophyletic group
C) polyphyletic group
D) monoploid
E) polyploid
Q3) In the domains of life, archaea and bacteria differ from each other in that
A) archaea contain membrane-bound organelles, bacteria do not.
B) bacteria can be extreme thermophiles, archaea cannot.
C) archaea contain ester-linked membrane fatty acids, bacteria do not.
D) bacteria start protein production with formylmethionine, archaea do not.
E) bacteria have introns, archaea do not.
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Chapter 18: Bacterial Diversity
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Q1) In order to learn what makes proteins stable in thermophilic bacteria, how should the amino acids or motifs that are involved in conferring thermostability to proteins be explored?
Q2) What are oligotrophs? Provide two examples of oligotrophic bacteria.
Q3) Which of the following is NOT correct with respect to the mycoplasmas?
A) They have lost their cell wall and the S-layer through reductive evolution.
B) Their cells maintain their shape through a type of cytoskeleton.
C) When cultured on agar, their colonies have a "fried-egg" shape.
D) They are parasites of all kinds of multicellular organisms.
E) They have some of the largest bacterial genomes.
Q4) Why is it that the deep-branching thermophiles may appear to have diverged from other bacteria earlier than they actually did?
Q5) What bacterial groups use actin as a means to leave their host cells? What advantage does this type of cellular invasion provide to intracellular pathogens?
Q6) Describe three mechanisms cyanobacteria use to provide an anoxic environment for the oxygen-sensitive, nitrogen-fixation enzyme nitrogenase.
Q7) Describe the metabolic characteristics of Chlorobium species.
Q8) What is unique about the genome of Borrelia species?
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Chapter 19: Archaeal Diversity
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Q1) Why has Sulfolobus been studied so much more extensively than many archaea, and what is known about it?
Q2) With respect to pH, the ________ show the widest range of any clade.
A) crenarchaeotes
B) euryarchaeotes
C) Ancient Archaeal Group
D) nanoarchaeotes
E) methanogens
Q3) What novel adaptation would you expect undersea vent archaea to have versus archaea growing at a similar temperature in terrestrial hot springs?
A) barophily
B) thermophily
C) bacteriorhodopsin phototrophy
D) pseudopeptidoglycan
E) positively supercoiled genome
Q4) Explain how ammonia-oxidizing Thaumarchaeota gain energy and state the habitats in which they are found.
Q5) What are "vent polymerases," why are they better than previously used polymerases, and from where are they acquired?
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Chapter 20: Eukaryotic Diversity
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Q1) The oomycete ("water fungus") ________ caused the Great Irish Famine in the 1840s.
A) Opalina sp.
B) Tinea pedis
C) Phytophthora infestans
D) Amanita muscaria
E) Histoplasma capsulatum
Q2) Why are coral endosymbionts, known as zooxanthellae, important indicators of ocean health?
Q3) Trypanosomes are a group of organisms that share which of the following characteristics?
A) free-living aquatic parasites, round cell, no flagellum
B) intestinal parasites, shelled cell structure with pseudopodia
C) opportunistic parasites, multicellular with paired flagellum and apicoplast
D) obligate parasites, elongated cell with single flagellum and a kinetoplast
E) anaerobic parasites, single cellular structure with cilia
Q4) Why are sponges, jellyfish, worms, reptiles, humans, yeast, and microsporidia placed in the same eukaryotic clade?
Q5) What are choanoflagellates and what is their importance in evolutionary studies?
Page 22
Q6) Compare and contrast radiolarians and foraminiferans.
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Chapter 21: Microbial Ecology
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Q1) Much of the microbial fermentation in humans occurs in the A) stomach.
B) colon.
C) rumen.
D) small intestine.
E) esophagus.
Q2) Lakes that have dilute concentrations of nutrients are termed A) eutrophic.
B) syntrophic.
C) aphotic.
D) oligotrophic.
E) atrophic.
Q3) Which of the following organisms forms a specific mutualistic association with legumes?
A) rhizobia
B) agrobacteria
C) E. coli
D) morels
E) Vibrio sp.
Q4) Describe the initiation process for legume-rhizobium symbiosis.
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Chapter 22: Microbes in Global Elemental Cycles
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Q1) Discuss the concept of iron fertilization to remove excess CO from the atmosphere.
Q2) Which of the following is an anaerobic respiration reaction?
A) conversion of phosphine to phosphate
B) methanogenesis
C) photolysis of hydrogen sulfide to sulfur
D) precipitation of ferric iron with hydroxide
E) nitrogen fixation
Q3) Compare and contrast assimilatory and dissimilatory nitrate reduction.
Q4) The release of CO by human industry has/is ________ the rate of CO fixation globally.
A) equal to B) tripled
C) outpaced D) far less than E) decreased
Q5) Discuss the difference in environmental availability of phosphorus versus sulfur and nitrogen.
Q6) Some bacteria are responsible for degrading concrete. How do they accomplish this?
Page 24
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Chapter 23: Human Microbiota and Innate Immunity
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Q1) Which of the following definitions is mismatched?
A) extravasation-movement of leukocytes through endothelial cells into tissues
B) pus- teeming with white blood cells
C) vasoactive-chemical degradation inside a phagolysosome
D) autophagy-destruction of intracellular pathogens
E) opsonization-formation of pseudopods
Q2) Interferons are
A) high molecular weight cytokines.
B) not species specific.
C) low molecular weight cytokines.
D) not effective against polio virus.
E) not effective against influenza virus.
Q3) Explain the distinguishing characteristics of innate and adaptive immunity.
Q4) How is it that Clostrioides difficile, often a part of the normal intestinal microflora, can be the causative agent of pseudomembranous enterocolitis?
Q5) What is the biology underlying the condition of lupus? How could the symptoms of lupus be lessened on the cellular level?
Q6) Is it correct to state that bacteria introduced through a skin cut will most likely be engulfed by Langerhans cells?
Page 25
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Chapter 24: The Adaptive Immune Response
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Q1) Positive selection in T-cell education refers to
A) T-cell receptors that can bind strongly to self MHC proteins.
B) CD8 receptors that can bind strongly to self MHC proteins.
C) T-cell receptors that can bind weakly to self MHC proteins.
D) CD4 that can bind weakly to self MHC proteins.
E) B-cell receptors that bind weakly to T-cell receptors.
Q2) Bacteremia is a condition in which live bacteria enter the bloodstream, but not the cells of the body. Which form of processing would occur to stimulate a cell-mediated immune response?
A) bacterial peptide transported from cytoplasm to rER for presentation on MHC I
B) endocytosis by APC followed by presentation on MHC II
C) neutrophil phagocytosis with presentation on Fc receptor
D) cytotoxic T-cell endocytosis for presentation on CD8 receptor
E) B-cell capping for presentation on the B-cell receptor
Q3) Mycobacteria spp. have evolved a mechanism to evade adaptive immunity by
A) creating autoantibodies against activated T-cell populations.
B) triggering T- and B-cell apoptosis.
C) hiding within red blood cells of the body (similar to malarial infection).
D) inducing the production of anti-inflammatory cytokines (IL-6 and IL-10).
E) producing phagocytic chemorepellants and paralyzing neutrophils.
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Chapter 25: Microbial Pathogenesis
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Q1) Autophagy is used by a host cell to
A) activate G-proteins.
B) regulate phagocytosis.
C) scavenge nutrients from damaged organelles.
D) fight extracellular pathogens.
E) induce apoptosis.
Q2) Multivalent adhesion molecule 7, or MAM7, is a unique adhesion because it
A) is expressed late in an infection.
B) is found only in Gram-positive organisms.
C) is important in initiating infection.
D) decreases the LD50 of an organism.
E) acts as a toxin.
Q3) The toxin gene in Corynebacterium diphtheriae is located on A) the plasmid.
B) mobile genes called transposons.
C) bacterial chromosomes.
D) lysogenic phage genomes.
E) the plasma membrane.
Q4) Diphtheria toxin is a classic AB exotoxin. How does it cause host cell damage?
Q5) Define a fomite and give at least two specific examples.
Page 27
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Chapter 26: Microbial Diseases
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Q1) Most diarrheal diseases are of what origin?
A) viral
B) bacterial
C) fungal
D) archaeal
E) They can be of any origin.
Q2) Hepatitis A and B viruses both
A) are RNA viruses.
B) infect the liver.
C) can be transmitted by blood products.
D) have vaccines.
E) infect the liver and are vaccines for both viral diseases.
Q3) In urinary tract infections (UTIs), what is the implication of the ability of bacteria to actually hide urinary tract epithelial cells and form biofilms?
A) UTIs can never be cured.
B) A reservoir for reinfection is created.
C) The kidney will invariably be infected.
D) Intracellular pathogens are the etiologies for UTI.
E) The ureter is the usual route for bladder infection.
Q4) What makes uropathogenic Escherichia coli different from the other E. coli?
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Chapter 27: Antimicrobial Therapy
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Sample Questions
Q1) Most antiviral drugs approved for clinical use target viral proteins. Which of the following is NOT a targeted viral protein?
A) Cap-binding complex
B) proteases
C) polymerases
D) entry proteins
E) alpha-glucosidase
Q2) Which of the following statements about the Kirby-Bauer assay is true?
A) It is used to test multiple bacteria simultaneously on a single plate.
B) It uses serial dilutions of specific antibiotics to determine MIC.
C) Zones of inhibition that are smaller are better antibiotics than antibiotics that form larger zones.
D) It can test up to 12 different antibiotic disks at one time.
E) It cannot be correlated with in vivo tissue concentrations.
Q3) Bactericidal antibiotics include all of the following EXCEPT
A) aminoglycosides.
B) quinolones.
C) rifampins.
D) macrolides.
E) penicillins.
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Chapter 28: Clinical Microbiology and Epidemiology
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Sample Questions
Q1) Catalase-positive organisms such as ________ produce ________ as end products when exposed to hydrogen peroxide.
A) Streptomyces; KCl and CO
B) Streptococcus; H O and H O
C) Lactobacillales; CO and O
D) Stachybotrys; HOCl and H O
E) Staphylococcus; H O and O
Q2) In determining the bacterial etiology of a patient with an infection, the first laboratory test should be what, and why? What type of testing would then follow?
Q3) Shigella sonnei is the cause of an infection commonly seen in infant day-care facilities due to
A) a high prevalence of the microbe in young children.
B) its ability to contaminate and grow on plastic toys.
C) its inherent antimicrobial nature (it is bleach and cleaning-product resistant).
D) diaper changes and hands not being properly washed.
E) Gram-positive cell wall structure making the bacteria environmentally resistant.
Q4) How would a serum antibody ELISA work in the detection of Lyme disease?
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