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