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This course provides an introduction to the fundamental concepts of microbiology with a focus on topics relevant to health sciences. Students will explore the structure, function, classification, and growth of microorganisms, including bacteria, viruses, fungi, and parasites. Emphasis is placed on the roles of these microbes in health and disease, mechanisms of pathogenicity, host immune responses, and methods for controlling microbial growth in clinical settings. The course also covers the principles of aseptic technique, infection control, antimicrobial therapy, and emerging infectious diseases, equipping students with essential knowledge for understanding and preventing the spread of infectious agents in healthcare environments.
Recommended Textbook Microbiology An Evolving Science 4th Edition by John W. Foster
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Q1) Viruses are
A) infectious agents that infect exclusively multicellular organisms.
B) noncellular particles that take over the metabolism of a cell to generate more virus particles.
C) pathogens that replicate in complex growth media.
D) cellular particles that belong to the archaea domain.
E) microbes that consist of lipid membrane-enclosed genomes.
Answer: B
Q2) All of the following are true about penicillin EXCEPT that it
A) was discovered by Alexander Fleming.
B) was an accidental discovery.
C) is produced by a bacterium.
D) was the first antibiotic used by humans.
E) was purified by Florey and Chain.
Answer: C
Q3) Define "attenuation" and describe some mechanisms used to attenuate pathogens.
Answer: Attenuation results in a weakened organism that will not produce full-blown disease but will generate immunity. Answers for mechanisms may vary, but heat treatment or aging for various periods or natural attenuation in the host are mentioned in the chapter.
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Q1) Which two components of the Gram stain form a complex that is retained by Gram-positive cells?
A) crystal violet and iodine
B) safranin and iodine
C) crystal violet and safranin
D) alcohol and safranin
E) alcohol and iodine
Answer: A
Q2) Increasing the refractive index of the medium between the object and the objective lens increases
A) refraction.
B) reflection.
C) magnification.
D) resolution.
E) wavelength.
Answer: D
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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Q1) E. coli and Sinorhizobium cell-surface proteins enable colonization of ________ and ________, respectively.
A) the human intestinal epithelium; animal skin
B) legume plants; the human intestinal epithelium
C) the human intestinal epithelium; legume plants
D) legume plants; animal skin
E) cantaloupe; spinach
Answer: C
Q2) The z-ring is
A) made up of an actin-like polymer.
B) involved in segregation of two to four nucleoids.
C) controlled by a nutrient-dependent regulator.
D) involved in replication but not cytokinesis.
E) involved in preventing transcription of noncoding regions of DNA.
Answer: C
Q3) Describe the types of molecules that can move through a membrane via passive diffusion.
Answer: Small uncharged molecules such as water, oxygen, and carbon dioxide can move through a membrane via passive diffusion.
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Q1) Define the terms "viable" and "viable but unculturable." Why are so many environmental organisms believed to be viable but unculturable?
Q2) You are measuring growth in a bacterial culture. The number of viable cells remains constant, and when you check the medium, you find that the carbon source has been used up. In which phase of growth is the culture?
A) lag
B) early log
C) late log
D) stationary
E) death
Q3) Why do some members of a biofilm community live deep within the biofilm?
A) They are not flagellated.
B) They produce fewer exopolysaccharides.
C) They were the first organisms to initiate attachment.
D) Antibiotics do not penetrate deep into biofilms.
E) Oxygen does not penetrate deep into biofilms.
Q4) Compare and contrast complex media, synthetic media, and enriched media.
Q5) Describe the differences between batch culture and growth in a chemostat. What are the advantages of a chemostat?
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Q1) A measure of the number of solute molecules in solution and is inversely related to water activity is known as
A) osmolarity.
B) hypertonic.
C) hypotonic.
D) isotonic.
E) d-value.
Q2) Which of the following is true of microbes and their membranes?
A) They are relatively permeable to protons.
B) Protons can leak through directly when the difference in intracellular and extracellular pH is very high.
C) Membrane-permeant organic acids can prevent the leakage of protons.
D) They are able to change the pH optima of their enzymes.
E) Acidophiles use Na+/H+ antiporters to remove internal protons.
Q3) What alkaliphile do pink flamingos eat, and how is it involved in making the flamingo pink?
Q4) Why is death a logarithmic function and not an instantaneous event upon treatment?
Page 7
Q5) How are some organisms able to survive temporary exposures to elevated temperatures?
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Q1) A key factor in the evolution of killer strains of influenza is that they
A) only have eight genes.
B) have an RNA genome.
C) contain reverse transcriptase.
D) have a segmented genome.
E) have a circular chromosome.
Q2) What is NOT a difficulty of culturing viruses?
A) tropism for particular tissue
B) tissue culture may not show organ property
C) loss of virulence
D) able to observe a large population
E) need a double culture of host cell and viruses
Q3) 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
Q4) Discuss the role that marine viruses play in carbon balance.
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Q1) Which of the following are DNA chain-terminator molecules and were used in the original biochemical approach to DNA sequencing devised by Frederick Sanger in the 1970s?
A) 2'-Deoxyribonucleotides
B) 3'-Deoxyribonucleotides
C) 2', 3'-Dideoxyribonucleotides
D) 2'-Deoxyuridine and 2'-deoxyadenosine
E) Uridine and adenosine
Q2) The main replication DNA polymerase in E. coli is Pol III. What type of bonds do DNA polymerases form?
A) aminoacyl-tRNA
B) peptide
C) phosphodiester
D) hydrogen
E) disulfide
Q3) In addition to primases and polymerases, name three other proteins required for initiation and elongation during replication. Describe their functions.
Q4) Describe how the name of bacterial genes and their gene product are denoted.
Q5) Describe the functions of DNA Pol III.
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Q1) What feature of eukaryotes makes annotation more difficult?
Q2) Which of the following are required for the termination of translation?
A) sRNAs
B) degrons
C) TolC proteins
D) release factors
E) ubiquitins
Q3) Post-translational modification to achieve function does NOT involve A) adenylation.
B) phosphorylation.
C) acetylation.
D) removal of formylmethionine.
E) ubiquitination.
Q4) Explain how a type I secretion system works. Are the secreted proteins ever in periplasmic space?
Q5) Where is the Shine-Dalgarno sequence located and what is it responsible for?
Q6) How does mRNA compare to the template and nontemplate DNA strand?
Q7) Name two antibiotics that affect transcription and explain their mode of action.
Q9) Explain the process of transcription initiation. Page 10
Q8) What are the functions of the different types of RNA molecules?
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Evolution
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Q1) Phages that carry host DNA are called transducing particles. Describe how the Salmonella P22 phage accidentally packages host DNA.
Q2) The transformasome necessary for cell competency in Gram-positive bacteria is regulated using which of the following methods?
A) an alternative sigma factor to transcribe the necessary genes
B) a repressor protein to keep the genes turned off
C) induction in the presence of fertility factors
D) each gene has an attenuator
E) use of a restriction-modification system
Q3) Competence in Gram-positive organisms is induced by
A) calcium and cold.
B) electrical currents.
C) competence factors made of peptides.
D) presence of biofilm.
E) Competence is not induced in Gram-positive bacteria.
Q4) Why is SOS repair considered to be an error-prone repair mechanism? Why would an organism use an error-prone mechanism?
Q5) Compare and contrast general and site-specific recombination.
Q6) Is an Hfr cell also considered to be F ? Why or why not?
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Q1) Quorum sensing plays a role in interspecies communications. Describe the relationship between green seaweed Enteromorpha and Vibrio anguillarum bacterial cells in biofilms, and explain how Escherichia coli was used to understand this interaction.
Q2) What is diauxic growth and why does it occur?
Q3) A transmembrane sensor kinase protein senses an environmental condition outside ________ bacteria or in the periplasm of a(n) ________ bacteria.
A) Gram-positive; Gram-negative
B) Gram-negative; Gram-positive
C) prokaryotic; eukaryotic
D) prokaryotic; archaean
E) Gram-positive; acid-fast
Q4) Which form of control is the LEAST reversible and MOST drastic?
A) posttranslational control
B) control of transcription
C) alterations of DNA sequence
D) translational control
E) mRNA stability
Q5) Describe what happens to the lac operon in the presence of both lactose and glucose.
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Q1) Describe the several features of lentivectors. What are their molecular sources?
Q2) 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
Q3) The reverse transcriptase complex is a crucial enzyme for retroviruses. Which catalytic activity does reverse transcriptase have?
A) RNA-dependent RNA synthesis
B) RNA degradation via RNase H
C) DNA-dependent DNA synthesis
D) RNA-dependent DNA synthesis
E) DNA-dependent RNA synthesis
Q4) Why is it advantageous to use lentivectors to treat diseases that affect nondividing cells?
Q5) Describe the replication process of the human immunodeficiency virus (HIV).
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Q1) The uses for phage display include all the following EXCEPT
A) antibody fragments cloned from synthetic sources.
B) the identification of high-affinity peptides that bind to attachment proteins of some eukaryotic viruses and effectively block viral infection.
C) antibody fragments cloned from natural sources.
D) collections of mutant enzymes to be tested for activity.
E) directed evolution projects.
Q2) Noise in synthetic biology is a result of the A) ara operon.
B) lac operon.
C) dual-feedback oscillator.
D) fluctuation of gene expression among single-cells in a population.
E) oscillatory genetic circuit.
Q3) How do operon fusions reveal transcriptional control of a target gene?
Q4) What is synthetic biology? Provide an example of its potential applications.
Q5) What is the conceptual basis of the primer extension technique?
Q6) Describe the difference between autoradiography and phosphor imaging.
Q7) Briefly explain how real-time polymerase chain reaction (PCR) works.
Q9) How is the concept of "logic gates" used in synthetic biology? Page 15
Q8) Describe the use of a primary and secondary antibody in a western blot.
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Q1) Which of the following phenomena is sufficient to transport nutrients to cells that lack chemotactic motility?
A) active, ATP-dependent transport
B) diffusion
C) turbulent flow
D) quorum sensing
E) biofilm formation
Q2) Treponema pallidum, the causative agent of syphilis, was shown to be lacking a TCA cycle. Explain the significance of this finding.
Q3) The enzyme pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to pyruvate; the phosphate group is transferred to ADP to form ATP. This reaction is an example of
A) ATP synthesis by substrate-level phosphorylation.
B) the use of a proton concentration gradient by [H+]-ATPases to synthesize ATP.
C) ATP coupled to FADH oxidation.
D) a P-Type ATPase activity.
E) oxidative phosphorylation.
Q4) What is the phosphotransferase system (PTS) and why is the advantage for a microbial cell to have a PTS?
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Q1) Which of the following is FALSE regarding dehalorespiration?
A) It is a type of hydrogenotrophy.
B) Cl- can be removed from toxic compounds by dehalorespiration.
C) Nitrogen (N ) is a by-product of dehalorespiration.
D) Halogenated organic molecules serve as electron acceptors for H .
E) Hydrogenotrophs can be used in bioremediation.
Q2) Ferroplasma acidarmanus produces large amounts of sulfuric acid through
A) oxidation of Cu+ with Cu(NO3)2.
B) oxidation of FeS2 with Fe3+ and H O.
C) oxidation of Fe3O with Fe2+.
D) oxidation of H S with H O.
E) reduction of SO with H .
Q3) What is dissimilatory metal reduction? How is it different from assimilatory metal reduction? Is there application of the dissimilatory metal reduction phenomenon?
Q4) What are methanotrophs? What is their role in the global carbon cycle?
Q5) Why and how is it that mitochondria have only a single electron transport system (ETS), unlike many bacteria?
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Q6) How does photosystem I allow Chlorobium and other green sulfur bacteria to live near deep-sea vents?

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Q1) Which of the following pathways is NOT a route for CO assimilation?
A) reductive acetyl-CoA pathway
B) gluconeogenesis pathway
C) hydroxypropionate cycle
D) reductive pentose phosphate cycle
E) reverse TCA cycle
Q2) Rubisco catalyzes which of the following reactions?
A) \( \mathrm{CO}_{2}+ \) ribulose 1,5 -bisphosphate \( \rightarrow 2,3 \)-phosphoglycerate
B) \( \mathrm{HCO}_{3}{ }^{-}+ \)acetyl-CoA \( \rightarrow \) malonyl-CoA + NADPH \( \triangle 3 \)-hydroxypropionate
C) \( \mathrm{H}_{2} \mathrm{~S}+ \) light \( \rightarrow \mathrm{S}^{0}+2 \mathrm{H}^{+}+2 \mathrm{e}^{-} \)
D) Ribulose-1,5-bisphosphate \( +\mathrm{CO}_{2}{ }^{-} \rightarrow \) Fructose- 1,6 -bisphosphate
E) 2-carboxy-3-ketoarabinitol-1,5-bisphosphate \( \rightarrow \) G3P
Q3) How do ammonium and oxygen regulate the expression of nitrogen fixation genes?
Q4) It is thought that the Calvin cycle appeared after the divergence of the three domains of life. What supports this hypothesis?
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Q1) The most common food-borne cause of death in the United States is A) norovirus.
B) Salmonella enterica.
C) Campylobacter sp.
D) Clostridium botulinum.
E) Escherichia coli O157:H7.
Q2) Another term for food contamination is
A) rancid.
B) putrefacation
C) food poisoning.
D) food spoilage.
E) putrefied.
Q3) The following are desirable characteristics of an industrial strain, EXCEPT A) efficient gene transfer system.
B) susceptibility to large DNA rearrangements.
C) inexpensive growth and maintenance.
D) safe, non-pathogenic.
E) easy harvesting of product.
Q4) Explain the difference between food spoilage and food poisoning.
Q5) Describe several physical means of food preservation.
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Q1) During the Long-Term Evolution Experiment (LTEE), investigators found a Cit strain of Escherichia coli that allowed fast growth on citrate buffer after 33,000 generations. The ability to catabolize citrate evolved at this time through
A) acquiring the ability to exploit new ecological niches.
B) becoming pathogens.
C) becoming dependant on a symbiotic partner's resources.
D) becoming pathogens and becoming dependent on a symbiotic partner's resources.
E) losing the ability to exploit new ecological niches.
Q2) What trait do all cells on Earth NOT have in common?
A) double-stranded DNA
B) cell wall of varying composition
C) universal gene code, common ancestral rRNAs, and elongation factors
D) common ancestral functional domains in proteins
E) cytoplasm, an aqueous compartment enclosed by a membrane
Q3) The elements that formed initial microbial life originated from A) oceans.
B) lightning.
C) supernovas.
D) the sun.
E) ozone.
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Q1) Some Gram-negative bacteria branch more deeply from the proteobacteria than the five Greek-lettered classes do from each other. Which phyla listed below is deep-branching Gram-negative?
A) Thermotogo
B) Aquifex
C) Flavobacteria
D) Protobacteria
E) Chlorobi
Q2) Bacteroidetes are important components of what ecosystem?
A) Antarctic brine lakes
B) the termite gut
C) hydrothermal springs
D) the human gut
E) acid mines
Q3) What distinguishes bacterial cell walls from those in archaea and eukarya?
Q4) Discuss the chemical nature of mycolic acids and some of the traits they confer to organisms that possess them.
Q5) Describe the unique way in which spirochetes can be isolated from other environmental species. What makes this possible?
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Q1) The energy-yielding process of ________ occurs only in the archaea.
A) fermentation
B) sulfur oxidation
C) hydrogen oxidation
D) methanogenesis
E) anaerobic respiration
Q2) Why has Sulfolobus been studied so much more extensively than many archaea, and what is known about it?
Q3) Nitrosopumilus maritimus is able to oxidize
A) nitrate.
B) ammonia.
C) sulfide.
D) sulfate.
E) methane.
Q4) Which organism has a periplasmic space containing membrane vesicles?
A) Desulfurococcus sp.
B) Ignicoccus sp.
C) Methanosarcina sp.
D) Methanothermus sp.
E) Pyrodictium sp.

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Q1) What are protists? What is the current status of the classification of protists? What is the difference between protozoa and protists?
Q2) Amebas that have filopodial movement structures can be found in which categories?
A) trypanosomes and metamonads
B) diatoms and algae
C) dinoflagellates and apicomplexans
D) cellular and plasmodial slime molds
E) radiolarians and foraminiferans
Q3) Dinoflagellates are marine phototrophs responsible for the toxic red tide blooms. What pigments confer the red color to these organisms?
A) rhodopsin
B) tannins
C) anthocyanins
D) chlorophylls
E) carotenoids
Q4) Describe how the life cycle of the slime mold Dictyostelium discoideum is dependent upon prokaryotic organisms.
Q5) What are choanoflagellates and what is their importance in evolutionary studies?
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Q1) Name two factors that differentiate aquatic and terrestrial ecosystems and explain how they affect food cycles in these systems.
Q2) Which region of marine habitat refers to the microscopic interface between water and air?
A) pelagic zone
B) neuston
C) euphotic zone
D) aphotic zone
E) benthic zone
Q3) A holobiont is defined as an
A) organism that benefits while providing no benefit or a hidden benefit to its host.
B) interaction that harms one partner nonspecifically without an intimate symbiosis.
C) organism that forms an intimate relationship with another, where both benefit.
D) entity composed of multiple types of organisms, including microbes.
E) intimate relationship in which one member benefits while harming a host.
Q4) Explain how viruses select for increased diversity of microbial plankton in the oceans.
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Q1) Describe the difference between a source, sink, and reservoir of an element.
Q2) What are the major limitations to nitrogen fixation? How do organisms overcome these limitations?
Q3) Jupiter's moon ________ is a candidate for extraterrestrial life due to its subsurface oceans.
A) Io
B) Europa
C) Titan
D) Mimas
E) Deimos
Q4) Astrobiology is the study of life in the universe. Why might our rDNA probes NOT be appropriate to detect extraterrestrial life?
Q5) Increased ________ is NOT needed to terraform Mars.
A) greenhouse gases
B) temperature
C) pH
D) air pressure
E) oxygen
Q6) What types of evidence suggest the past existence of water on Mars?
Q7) Compare and contrast assimilatory and dissimilatory nitrate reduction.
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Q1) Which of the following two organisms are commonly used as probiotics?
A) Streptococcus mutans and Lactobacillus acidophilus
B) Bacteroides and Lactobacillus acidophilus
C) Enterococcus and Enterobacter species
D) Bifidobacterium and Lactobacillus acidophilus
E) Diphtheroids and Fusobacterium species
Q2) How can differences in gut microbiota account for obesity and leanness in humans?
Q3) Which of the following creates a channel in target cell membranes?
A) complement
B) defensins
C) natural killer cells
D) complement and defensins
E) complement, defensins, and natural killer cells
Q4) IFN-gamma protects the host by
A) inducing dsRNA endonucleases.
B) interfering directly with viral replication.
C) having an immunomodulatory role.
D) inducing fever at the hypothalamus.
E) blocking adhesion of pathogens.
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Q1) An example of an antigen that could stimulate naïve B-cell proliferation and differentiation without the help of a T cell would be a(n) ________ molecule from
A) lipopolysaccharide; Proteus vulgaris
B) plasmid DNA; Yersinia pestis
C) protein A; Staphylococcus aureus
D) anthrax toxin; Bacillus anthracis
E) porin protein; Escherichia coli
Q2) A complete T-cell receptor on a helper T cell contains both the antigen-binding receptor molecule and a ________ protein for signal transduction.
A) CD8
B) CD3 complex
C) MHC I
D) MHC II
E) CD28
Q3) X-linked hyper IgM syndrome (XHIM) is an immunodeficiency disorder caused by mutations of the gene encoding CD154. Why is this disease characterized by recurrent infections (starting in childhood) and elevated serum levels of IgM?
Q4) Detail the benefits and predict possible risks of vaccinations.
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Q1) Which of the following species causes whooping cough?
A) Streptococcus mutans
B) Staphylococcus aureus
C) Bordetella pertussis
D) Neisseria gonorrhoeae
E) Mycoplasma
Q2) The likely mode of transmission of a bacterial disease in which incidence increases with a prolonged warm summer is
A) direct transmission.
B) airborne transmission.
C) insect vector transmission.
D) common source fomite.
E) sexual transmission.
Q3) Biofilms play a major role in enhancing bacterial virulence because
A) biofilm strains are mutants.
B) the exopolymer matrix is highly toxic and mutagenic.
C) biofilm bacteria are intracellular pathogens.
D) bacteria in biofilms are more resistant to antimicrobials and phagocytosis.
E) low bacteria density does not alert the human immune system.
Q4) Diphtheria toxin is a classic AB exotoxin. How does it cause host cell damage?
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Q1) Which of the following diseases is likely to increase in incidence if global warming continues unabated?
A) Streptococcal pharyngitis
B) Lyme disease
C) syphilis
D) gonorrhea
E) hepatitis B
Q2) Describe epigenetic silencing and the role it plays in malaria.
Q3) Helicobacter pylori is thought to cause cancer through A) toxin production.
B) inducing superantigens.
C) neutralizing acid pH, which allows anaerobes to grow.
D) injecting the CagA protein into gastric epithelial cells.
E) adhering with pili to the oropharygeal epithelium.
Q4) 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.
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Q1) A negative structural mutation in the norA gene in Staphylococcus aureus could have the effect of
A) decreased protein synthesis.
B) increased bacterial conjugation.
C) decreased drug resistance.
D) increased uptake of beta-lactams.
E) decreased rate of clonal division.
Q2) Bactericidal antibiotics include all of the following EXCEPT A) aminoglycosides.
B) rifampin.
C) macrolides.
D) subcutaneous isoniazidchloramphenicol.
E) quinolones.
Q3) Minimal inhibitory concentration, or MIC, is ________ concentration of a drug that will prevent the growth of an organism.
A) the average
B) the lowest
C) the highest
D) the midline
E) any
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Sample Questions
Q1) 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.
Q2) Which of the following criteria is NOT required in order for a mosquito-borne virus to become endemic in a new location?
A) A person infected elsewhere must travel to the new area.
B) A local mosquito must bite a person who has the disease in order to spread it to someone else.
C) The virus must move from an Aedes mosquito to another insect vector.
D) The virus must move from the local mosquito to a local animal that can then serve as a reservoir.
E) The local mosquito must bite another human in that area and give him or her the disease.
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