Microbiology Exam 3
Spirochete
a slender, tightly coiled, gram-negative bacterium of the phylum Spirochaetes characterized by possession of endoflagella used for motility
Which of the following choices is a typical target for the integration of chromosomal islands
a tRNA gene
Dissimilative sulfur-reducer
an anaerobic or facultatively aerobic microorganism that conserves energy through the reduction of S0 but cannot reduce SO4-2
Yeast artificial chromosome (YAC)
an artificial chromosome with a yeast origin of replication and a centromere sequence
Biofilm
an attached polysaccharide matrix containing bacterial cells
Denaturing gradient gel electrophoresis (DGGE)
an electrophoretic technique capable of separating nucleic acid fragments of the same size that differ in base sequence
Oxygen minimun zone (OMZ)
an oxygen-depleted region of intermediate depth in the marine water column
What enzyme is present in the cells of chemolithotrophs that use H2 as the sole electron donor
hydrogenase
Which of the following is NOT an environmental suitable for growth of purple sulfur bacteria
hydrothermal vents suitable environments -salt marshes -lakes -sulfur springs
What is the genome-wide study of structure, function, and regulation of an organism's proteins called
proteomics
Which of the following statements about phylochips is correct
they can be made to carry probes targeting genes that encode a key metabolic function
By isolating total community RNA, using reverse transcriptase to make cDNA copies of it, and then sequencing the cDNA, ecologists can
determine the community genome expression at the moment of sampling
What percentage of microbial diversity currently exists in the form of laboratory cultures
less than 0.1%
Automated sequencing techniques require only one lane on an electrophoresis gel rather than four. What is one method that makes this possible
each base is identified with a different fluorescence color
What enzyme is used in metatranscriptomics to convert total community RNA to DNA for analysis
reverse transcriptase
Hydrothermal vents
warm or hot water-emitting springs associated with crustal spreading centers on the seafloor
The rhizosphere is
the soil immediately surrounding the root of a plant
Microbiota
the types of organisms present in an environmental habitat, such as the human skin or the human gastrointestinal tract
Bioinformatics
the use of computational tools of acquire, analyze, store, and access DNA and protein sequences
Epilimnion
the warmer and less dense surface waters of a stratified lake
Gas vesicles in cyanobacteria are used by the organisms for what purpose
they allow the cells to adjust their buoyancy to maintain a certain depth in the water column
A recombinant cell
is a cell that receives DNA from an outside source and incorporates it into its own
Cyanobacteria
prokaryotic oxygenic phototrophs containing chlorophyll a and phycobilins
All of the following are true of biofilms
-biofilms form on virtually all submerged surfaces in nature -biofilms protect organisms from antibiotics -biofilm formation and dispersal are regulated processes EXCEPT: -biofilms are composed of only one species at a time
Fluorescent in situ hybridization (FISH) can be used to determine
-how many Salmonella typhimurium cells are present in a sample of unpasteurized apple juice -whether a specific piece of mRNA is being produced -the phylogenetic diversity of an environmental sample
To be successful, an enrichment culture for an environment isolate must take into account
-pH -osmotic conditions -nutrients
Initiation of biofilm formation in many organisms is at least in part regulated by c-di-GMP, which alters gene expression and enzyme activity leading to all of the following
-production of intracellular signaling molecules -initiation of extracellular polysaccharide production -formation of cell surface attachment proteins EXCEPT -initiation of flagella formation
Streptomyces are unique because
-some can produce antibodies -most produce spores -they produce hyphae similar to fungi
Proteome
-the total set of proteins encoded by a genome -the total protein complement of an organism under a given set of conditions
Plasmids are commonly used as cloning vectors because
-they can contain genes for antibiotic resistance used for plasmid selection -they can replicate independently of the chromosome -they are easily inserted into cells by the transformation
In which direction does DNA polymerase synthesize the new DNA strand
5' to 3'
Which of the following methods utilizes a fluorescently labeled oligonucleotide primer for DNA amplification
ARISA
The substrate Xgal is used to detect
B-galactosidase
The F plasmid has been used to construct cloning vectors called
BACs
Infants who are exclusively breast fed have a microbiota enriched in
Bifidobacterium
What is the technique called that uses a fluorescently labeled tyramide molecule as a substrate for a single oligonucleotide conjugated to peroxidase
CARD-FISH
Which of the following methods allows for the genetic studies of very slow-growing prokaryotic organisms
CARD-FISH
Southern blotting is a method of hybridization used to identify a target
DNA fragment
Complementary DNA (cDNA)
DNA made from an RNA template during the reverse transcription PCR (RT-PCR) procedure
Electrophoresis can be used to separate molecules by size, shape, and charge. When DNA samples are run in an electrophoresis gel, the different bands produced generally represent fragments of different sizes. Why is the size of the fragment the most critical factor in determining how far it migrates on a gel when DNA fragments are compared
DNA moves toward a positive charge due to the negative charge on its phosphate groups. The charge is consistent because all DNA nucleotides have a single phosphate group rather than having more diverse patterns of charges. Because the charge is relatively consistent, size is the most important factor determining how far fragments move
In a single-cell genomics, what type of DNA polymerase is used in multiple displacement amplification
DNA polymerase from a bacteriophage
Which of the following methods is NOT commonly used to obtain a pure culture of a microorganism
FISH
Which microbe colonizes the stomach of over 50% of the world's population
Helicobacter pylori
Which of the following organisms is responsible for keeping the pH of the adult female vagina acidic
Lactobacillus acidophilus
The genome of which of the following organisms probably arose through genome duplications
Saccharomyces
The oral cavity is dominated by
Streptococcus
Which of the following bacteria is implicated in causing dental caries
Streptococcus mutans
Why is a special polymerase, such as Taq polymerase, required for PCR
Taq polymerase is produced by an extremophile prokaryote and is able to work to relatively high temperatures
Open reading frame (ORF)
a sequence of DNA or RNA that could be translated to give a polypeptide
Chromosomal island (genomic island)
a bacterial chromosome region of foreign origin that contains clustered genes for some extra property such as virulence of symbiosis
Pathogenicity island
a bacterial chromosome region of foreign origin that contains clustered genes of virulence
Bacterial artificial chromosome (BAC)
a circular artificial chromosome with a bacterial origin or replication
Convergent evolution
a circumstance where a trait or set of traits that are similar in form and/or function between two organisms are not inherited from a shared ancestor (that is, traits that are similar but not homologous)
Orthologs
a gene in one organism that is similar to a gene in another organism because of descent form a common ancestor
Winogradsky column
a glass column packed with mud and overlaid with water to mimic an aquatic environment, in which various bacteria develop over a period of months
Purple non sulfur bacteria
a group of phototrophic bacteria that contain bacteriochlorophyll a or b and Q0type reaction centers, and that grow best as photoheterotrophs
Purple sulfur bacteria
a group of phototrophic bacteria that contain bacteriochlorophylls a or b, Q-type reaction center, and can oxidize H2S as photosynthetic electron donor
Southern blot
a hybridization procedure where DNA is the target and RNA or DNA is the probe
Northern blot
a hybridization procedure where RNA is the target and DNA or RNA is the probe
Which of the following statements is FALSE
dental plaque is formed by the action of fungi TRUE: -dental caries are caused by decalcification of the tooth -the outside layer of the tooth is enamel -acidic glycoproteins from saliva promote bacterial attachment to the tooth
Which of the following is the initial step in culture-independent analysis of microbial populations
extraction of total community DNA
Budding is a form of reproduction whereby prokaryotic microbes can reproduce sexually
false
The ecological diversity of microbes is largely dependent on their complex morphological and structural diversity
false
The in vitro alteration of genetic material is known as
genetic engineering
Aerobic methylotrophs are most likely to be found
in water and soil
Which of the following antimicrobial substances are contained in saliva
lysozyme
The best choice for estimating the viable cell number of a water sample would be the
most probable number technique
Which technique would you use to change the amino acid serine to the amino acid arginine
site-directed mutagenesis
Microarray
small, solid supports to which genes or portions of genes are affixed and arrays spatially in a known pattern (also called gene chips)
Microbial diversity in an ecosystem can be expressed as the number of different species present, which is termed
species richness
DNA molecules that have short, single-stranded overhands are said to have
sticky ends
Metagenomics
the genomic analysis of pooled DNA or RNA from environmental sample containing organisms that have not been isolated; same as environmental genomics
What might be a reason that a researcher would decide to use Northern blotting instead of Southern blotting
to determine the extent to which a gene is being transcribed in a particular tissue
Heterologous expression
transcription and translation of a gene or genes from one organism in a different organism
What do scientists call the entire complement of RNA produced under a given set of conditions
transcriptome
Which of the following is an example of horizontal gene transfer in bacteria
transduction, conjugation, and transformation
What is the hallmark of all horizontal gene transfers
transfer of DNA between organisms of the same generation
Budding bacteria form new cell wall material at a single point rather than throughout the whole cell
true
In a phylogeny, which two organisms would be most likely to be placed closest together after a node based only on the information given
two organisms that appear to have different lifestyles but that are both very similar genetically to a common ancestor
These organisms carry our anoxygenic photosynthesis using H2S as an electron donor and deposit the resulting sulfur outside the cell
green sulfur bacteria
Microbes in the colon are primarily
obligate anaerobes
What is the niche called in which an organism is the most successful
prime niche
In bacteria, DNA modification enzymes modify
host DNA to protect it from host restriction enzymes
Which organisms are considered primary producers
oxygenic phototrophs
In cyanobacteria, gas vesicles are used to regulate ________ in response to light intensity
buoyancy
In which type of procedure is a sample ionized and vaporized by a laser and then accelerated through the time of flight analyzer
MALDI mass spectrometry
In the Sanger method of DNA sequencing, how are DNA chains randomly terminated in reactions using DNA polymerase
by having a small amount of dideoxyribonucleoside triphosphate in the reaction
Probiotic
a live microorganism that, when administered in adequate amounts, confers a health benefit on the host
Fluorescent in situ hybridization (FISH)
a method of employing a fluorescent dye covalently bonded to a specific nucleic acid probe for identifying or tracking organisms in the environment
Dissimilative sulfur-oxidizer
a microorganism that gains energy for growth through oxidation of reduced sulfur compounds
DAPI
a nonspecific fluorescent dye that stains DNA in microbial cells; used to obtain total cell numbers in natural samples
Enrichment bias
a problem with enrichment cultures in which "weed" species tend to dominate in the enrichment, often to the exclusion of the most abundant or ecologically significant organisms in the inoculum
Microsensor
a small glass sensor or electrode for measuring pH or specific compounds such as O2, H2S or NO3- that can be immersed into a microbial habitat at microscale intervals
Nucleic acid probe
a strand of nucleic acid that can be used to hybridize with a complementary stand of nucleic acid in a mixture; one of the two strands is labeled
Gel electrophoresis
a technique for separation of nucleic acid molecules by passing an electric current through a gel made of agarose or polysaccharide
MAR-FISH
a technique that combines identification of microorganisms with measurement of metabolic activities
Microbial mat
a thick, layered, diverse community nourishes either by light in a hypersaline or an extremely hot aquatic environment, in which cyanobacteria are essential; or by chemolithotrophs growing on the surface of sulfide-rich marine sediments
Which of these organisms is likely to have the largest genome
a yeast cell
You would like to determine the rate of production of carbon dioxide in a specific microbial habitat. How could you do this without growing the microorganisms in the lab
by using a microsensor
Most microbes found in the oral cavity during the first year are
aerotolerant anaerobes
Dysbiosis
an altercation of imbalance of an individual's microbiome relative to the normal, healthy state, primarily observed in the microbiota of the digestive tract or the skin
Green non sulfur bacteria
anoxygenic phototrophs containing chlorosomes, Q-type photosynthetic reaction centers, bacteriochlorophylls a and c as light-harvesting cholorphylls, and typically growing best as photoheterotrophs
A cloned gene expressing its protein product can be identified using
antibodies to the protein
Fluorescent protein
any of a large group of proteins that fluoresce different colors, including the green fluorescent protein, for tracking genetically modified organisms and determining conditions that induce the expression of specific genes
Restriction endonucleases are found in nature. They are extremely useful for genetic engineering. Why do organisms produce them
because they cut only at specific sequences in DNA, they are useful in cutting harmful DNA (such as viral DNA) without harming the organism that produces them (which can protect those sequences in its own DNA)
In addition to the determination of microbial activities, what is a second major component of microbial ecology
biodiversity
What bacterial signaling molecules promotes a sessile lifestyle that is consistent with biofilm formation
c-di-GMP
Which of the following dyes is NOT a fluorescent DNA stain
crystal violet
What is the primary difference between dissimilative sulfur reducers and dissimilative sulfur oxidizers
dissimilative sulfur oxidizers use sulfur compounds as an energy source, while dissimilative sulfur reducers use sulfur compounds as terminal electron acceptors
Disruption of the homeostasis between the gut microbiota and the host is called
dysbiosis
Phylogenetic analysis of microbial communities in nature using various PCR techniques has revealed that only a minority of phylotypes have been cultures from the environment and the most common phylotypes have not been grown in the laboratory. This is due to
enrichment bias
Determine why some prokaryotes have less DNA but more genes than eukaryotes
eukaryotes have more introns in their chromosomes
When Beijerinck enriched for nitrogen fixers, he inoculated soil into two types of liquid media: one containing mineral salts and mannitol but no nitrogen source (flask A), and one containing mineral salts, mannitol, and an ammonium salt (flask B). After incubation in the presence of air, what types of organisms did he expect to find in each flask
flask A would contain nitrogen fixers that could grow both without ammonium; flask B would not contain nitrogen fixers but would contain organisms that could use ammonium
Which of the following techniques would you use to sort cells from a biodiverse sample for subsequent growth and characterization
fluorescence-activated cell sorting
Metagenomics is a more sensitive analysis of community diversity than rRNA-based analyses because
genes do not have to be amplified by PCR before being sequenced
The genome sequence of an organism can provide information about the organism's
genes, function, and evolutionary history
Which of the following regarding gut enterotypes is true
gut enterotypes may influence an individual's response to diet or drugs
Which of the following technical breakthroughs has enabled the development of metagenomics
high-throughput DNA sequencing
The intensity of a signal in Northern blotting tells one
how much RNA is present in the sample
When a known single-stranded DNA probe is mixed with unknown nucleic acid sequences to look for similarity, it is called
hybridization
Horizontal gene transfer refers to the transfer of genes from one organism to another, as occurs during conjugation between bacteria. How does this differ from vertical gene transfer
in horizontal gene transfer, genes are transferred from one mature adult organism to another. In vertical gene transfer, genes are transferred from adults to offspring
Which of the following statements concerning Helicobacter pylori is FALSE
infection with H. pylori is always asymptomatic TRUE: -infection with H. pylori is a major risk factor for ulcers -H. pylori can persist in the gastric mucosa -H. pylori can be transmitted orally between family members
Antibiotic use early in life increases the risk of which of the following
inflammatory bowel disease
The phylogenetic diversity analysis of complex microbial communities often targets small subunit (SSU) ribosomal RNA genes. This is because rRNA is found in all organisms and
is highly conserved over evolutionary time
Why is DNA polymerase from Thermus aquaticus ideal for PCR
it can withstand the high temperatures associated with PCR
Lyme disease is a common arthropod-borne disease caused by the spirochete Borrelia burgdorferi. Which of the following best describes B. burgdorferi
it has a flexible spiral shape with endoflagella
Members of the Bacteroidetes and the Firmicutes dominate the normal microbiota of the
large intestine
In terms of microbial diversity, what would you expect to find when examining a sample of ice water obtained from the North Pole
low species richness and high species abundance
Which of the following instruments is able to identify small molecules metabolites from cells
mass spectrometer
What is the analysis of pooled environmental DNA or RNA called
metagenomics
Select the option that lists the steps necessary for PCR analysis of a microbial community in the correct order
microbial sample collection; DNA extraction; PCR of target genes; sorting by electrophoresis; analysis
Spirochetes have an unusual flagellum called an endoflagellum. How does it differ from other flagella
most flagella extend beyond the cell wall, but endoflagella are completely located within the periplasm
In an ecosystem, what provides the energy for heterotrophic organisms
newly synthesized organic matter
Chemolithotrophs that are able to grow by consuming ammonia are called
nitrifiers
Codon bias
nonrandom usage of multiple codons encoding the same amino acid
Bacterial abundance (10^2 to 10^8) and generation times (days to centuries) vary by many orders of magnitude in the deep subsurface mainly due to
nutrient limitations
Phylotype
one or more organisms with the same or related sequences of a phylogenetic marker gene
Consider the following two statements: (1) it is impossible to distinguish live cells from dead using a microscope (2) all microorganisms can be stained by acridine orange
only statement (2) is correct
Which of the following would best describe a group of genes found in one organism that are similar due to gene duplication
paralogs
Which feature of Cyanobacteria contributes to their importance in shaping the Earth's atmosphere
photosystem
Microarrays that have been designed to screen samples for specific groups of bacteria are called
phylochips
What are evolutionary relationships between different microorganisms called
phylogenetic diversity
You are interested in trying to determine the function of a particular gene in a common bacterium (meaning that it has a haploid genome). To do this, could you use a knockout mutation
possibly; it would depend on whether the gene was essential for survival and on whether you could create a diploid bacteria as well
What are the short DNA fragments called that are used to initiate DNA synthesis in the Sanger dideoxy sequencing method
primers
What types of organisms inhabit deep subsurface aquifers
prokaryotes
Sequencing an organism's genome often leads to identification of hypothetical proteins, which are characterized as
proteins that likely exist through their function is unknown
Enrichment cultures are often effective for isolation bacteria from complex communities in natural samples because they
select both for and against certain bacteria
Agarose gel electrophoresis is used to
separate DNA fragments by size
Which of the following are NOT found in the bottom layers of a stratified freshwater lake
strictly aerobic microorganisms
In a Winogradsky column, which of the following determines which organisms are enriched from the environment
substrate
Which of the following steps in biofilm formation comes before the others
surface adhesion -loss of flagella -formation of water channels -polysaccharide formation
Polymerase chain reaction (PCR)
the artificial amplification of a DNA sequence by repeated cycles of strand separation and replication
Which of the following is NOT a resource that influences microbial growth
the availability of water resources: -the presence of oxygen -the amount of organic carbon -the amount of phosphate
Which of the following statements about bacterial biofilms is NOT correct
the cells within a biofilm maintain an independent existence correct: -biofilms typically contain several porous layers -biofilms may contain one or two species or, more commonly, several species of bacteria -biofilms are functional microbial communities and not just the cells trapped in sticky matrix
Genomics
the discipline that maps, sequences, analyzes, and compared genomes
What are the electron donor and acceptor for the species that are found in the chemolithotrophic microbial mats off the coasts of Chile and Peru
the donor is H2S and the acceptor is nitrate
Gene duplication is thought to have had a significant influence on the evolution of microbes because
the duplicated gene can be mutated, possibly leading to a useful new gene function or product, while the original copy can still perform its original (and possibly essential) genetic function
Researchers observed one positive spot on phylogenetic microarray to which oligonucleotides complementary to 16S rRNA form 50 different species of Lactobacillus were attached and then probed with DNA amplified from en environmental sample. What conclusions can the researchers confidently make from this experiment
the environmental sample contained at least one species of Lactobacillus, and the amount of diversity related to other microorganisms is unknown
Hybridization
the joining of two single-stranded nucleic acid molecules by complementary base pairing for form a double-stranded hybrid DNA or DNA-RNA molecule
Normal microflora can be found in all of these regions EXCEPT
the lower respiratory tract can be found: -the inside of the nose the surface of the skin -the interior of the mouth
Microautoradiography (MAR)
the measurement of the uptake of radioactive substrates by visually observing the cells in an exposed photographic emulsion
Mobilome
the mobile genetic elements in a genome
Which of the following factors does NOT influence the types of microbial activities in an ecosystem
the noise levels in an ecosystem do influence -population sizes -species composition -the physiological state of the microorganisms in each habitat
An example of T7 expression vector is
the pET series of vectors
Core genome
the part of a genome shared by all strains of a species
What is the key difference between the purple sulfur bacteria and the purple non sulfur bacteria
the possible electron donors used for photosynthesis
Which of the following choices can indicate horizontal gene transfer
the presence of genes that encode proteins typically found only in distantly relates species
Species abundance
the proportion of each species in a community
Rhizosphere
the region immediately adjacent to plant roots
All of the following are problems that arise when expressing a mammalian gene in a bacterium EXCEPT that
introns in the mammalian cDNA need to be removed are problems: -mammalian genes can be toxic to a bacterial host cell -mammalian genes require a bacterial promoter -mammalian proteins often require post-translational modification
Bacteria will benefit as part of a biofilm because
it allows them to remain in a favorable niche
Microbial ecology
the study of microorganisms in their natural environments
Most-probable-number (MPN) technique
the serial dilution of a natural sample to determine the highest dilution yielding growth
Which of the following statements is FALSE
the stomach is a sterile environment because of its low pH TRUE: -antibiotics kill the normal intestinal microflora -microbial fermentation takes place in the colon -intestinal microflora are influences by a person's diet
Biogeochemistry
the study of biologically mediated chemical transformations in the environment
Human microbiome
the total microbial content in and on the human body
Species richness
the total number of different species present in a community
Pan genome
the totality of genes present in the different strains of a species
Horizontal gene transfer
the transfer of genes between cells through a process uncoupled from reproduction
In a body of freshwater, the transition between the warmer upper layers and the colder lower layers of water is called the
thermocline
What is the function of primers in PCR
they provide 3' end for the DNA polymerase
Which terminology is used to describe how a transcription factor, RNA, and an enzyme associate to move an organism towards a nutritional source
interactome
Which of the following statements is FALSE for purple sulfur bacteria
the sulfur produced is deposited only outside the cell TRUE -hydrogen sulfide is an electron donor for autotrophic growth hydrogen sulfide is oxidized to sulfur and then to sulfate autotrophy is supported by the reactions of the Calvin cycle
Metagenome
the total genetic complement of all the cells present in a particular environment
All of the following are characteristics that often make plasmids ideal cloning vectors EXCEPT that
they can be recombined with large fragments of DNA and still be extremely stable true: -they are stably maintained in host cells and in high numbers so large quantities of product can be manufactured -they contain a region with single cut sites for many restriction endonucleases so foreign material can be easily inserted -they are composed of relatively few base pairs, which makes the DNA easy to isolate and manipulate