Molecular Microbiology Final Homework Questions

Due to well-developed molecular tools and careful screening designs, functional genes can be isolated directly by isolation from the environment rather than cultivating the diverse species in a microbial community. True False

True

Following uptake, transforming DNA becomes attached to a competence-specific protein that prevents it from nuclease attack until it reaches the chromosome. True False

True

Viruses

Turnover in seawater is relatively rapid; the populations are replaced within a few days or weeks. They are the most numerous biological entities in seawater. Most are inactivated by hydrolytic enzymes or sunlight.

Sulfur-reducing bacteria can cause corrosion in neutral anoxic _________________________.

aquatic environments

The filamentous DNA phages are unusual, because they

are released from the host without the host being lysed.

For organisms to be considered members of the same species, they must __________.

be genetically and phenotypically cohesive

Sulfate-reducing bacteria produce ______________________________, a chemically corrosive compound, as a product of their metabolism.

hydrogen sulfide

With increased levels of oxidizable materials, the biochemical oxygen demand (BOD) will A. increase. B. decrease. C. remain the same. D. increase or decrease depending on the nature of the materials involved.

increase

metagenomics

the study of all of the genetic material of all organisms in a particular habitat

The genes for 16S rRNA are used to determine genetic relatedness amongst microbes because __________.

these highly conserved genes are of adequate length to show deep relationships

Bacterial abundance (102 to 108) and generation times (days to centuries) vary by many orders of magnitude in the deep subsurface mainly due to __________. A. nutrient limitations B. variations in water availability C. oxygen levels D. temperatures

nutrient limitations

Which of the following is the correct abbreviation for a mutation in a gene that synthesizes one of the enzymes involved in tryptophan production?

trpC1

Genomic analyses can be used to determine

phylogenetic classification and metabolic characteristics of newly discovered microbes

steps of genomic analysis

1- isolation of genetic material 2- genome sequencing 3- genome assembly 4- genome annotation, determination of open reading frame 6- comparative genomics

Explain why viroids can only infect and damage plant cells, but not animal cells.

Plant cells contain a RNA polymerase that can copy RNA can animal cells do not.

If a bacterium carrying a plasmid that confers resistance to ampicillin is placed into medium without ampicillin, it may

lose the plasmid because there is no selection for ampicillin resistance.

Genome assembly relies on

overlap of a large numbers of short sequences.

Fungi growing on building materials can produce _________________________, which gradually breaks down stone.

oxalic acid

The genes encoding green fluorescent protein (GFP) and β-galactosidase are typically used in cloning as

reporter genes.

Aerobic secondary treatment is usually best for ________ wastewater. A. agricultural B. chemical C. industrial D. residential

residential

The designations Phe-, Leu-, and Ser+ refer to an organisms

phenotype.

New organic compounds are produced from inorganic substrates by _________________________ (such as plants) and __________________________.

photolithotrophs; chemolithotrophs

Oxygen did not accumulate in the early atmosphere until it reacted with reduced materials, especially ________, in the oceans.

ferrous iron

The conversion of light into chemical energy is called photoautotrophy. True False

False

Some sulfur-oxidizing bacteria can simultaneously reduce nitrate, which enables them to grow anaerobically. True False

True

You are studying 12 new isolates from the human skin. Their average nucleotide identity for shared orthologous genes is 97%.The isolates would most likely be

classified as individual strains of the same species.

most wastewater treatment facilities employ methods designed to detect each pathogenic organism that may be present in a given sample. True False

false

In anoxic environments, organic compounds are cycled back to carbon dioxide and methane by __________. A. glycolysis B. metabolism C. cellular respiration D. fermentation

fermentation

A drug designed to inhibit reverse transcriptase activity would target

retroviruses.

Which of the following features are common to transformation, transduction, and conjugation? (1) unidirectional transfer of genes (2) incomplete gene transfer (3) homologous recombination (4) meiosis occurring in the recipient

1, 2, 3

Sequencing with devices such as the MinION can be used to study individual organisms. However, researchers sometimes also study the genetics of an entire community in an environmental sample (metagenomics) without distinguishing individual organisms. Why would researchers study the metagenome of an entire community in this way rather than separating out individual species?

-The microbial community may be more complex. -The researchers may be interested in determining DNA contributions from different sources (such as viruses and dead bacteria).

Not suggestive of horizontal gene transfer

-identification of a high GC content within the entire genome -identification of a high number of metabolic genes -identification of an unusually large genome

Suggestive of horizontal gene transfer

-identification of genes typically found in other, distantly related species -identification of a DNA segment that has a distinctive GC content compared with other segments of the genome -identification of a segment with an unusual codon bias compared with the rest of the genome

A NASA ecologist wants to design an instrument to send to Mars on the next space probe to determine whether living organisms ever carried out carbon fixation on that planet. Suggest an assay that she could use on Martian soil samples. A. 34S/35S stable isotope analysis B. NanoSIMS C. MAR-FISH D. 13C/12C stable isotope analysis

13C/12C stable isotope analysis

Genes encoding ________ are widely used as target genes in molecular biodiversity studies. A. ATPases B. DNA polymerase III C. RNA polymerase D. 16S rRNA

16S rRNA

A soil clump has an oxic (oxygen containing) zone containing aerobic and facultatively aerobic organotrophs, and an anoxic zone containing fermentative bacteria, sulfate reducers, and denitrifyers. This soil clump has at least __________ different habitats, __________ different communities and __________ different guilds. A. 2, 2, 20 B. 5, 5, 20 C. 5, 2, 5 D. 2, 2, 5

2, 2, 5

Bacteria

A common genus is Pelagibacter;Some types found in the photic zone carry out aerobic photosynthesis;Based upon current knowledge, they are the predominant prokaryotes above 1000 m.

Which of the following populations would be most likely to demonstrate genetic drift?

A researcher transfers bacteria into fresh medium but accidentally collects only a very small quantity of bacteria in the process.

The genetic code has many important characteristics. For example, a specific codon always means the same thing in a particular species. Codons mean the same thing in most species (even though there are some exceptions). In some cases, a particular amino acid can be specified by more than one codon (the genetic code is degenerate). Which of the following answers describes an example of the degenerate nature of the code?

AUU, AUC, and AUA all code for Ile

What are activity measurements? A. Activity measurements are an example of metagenomics, which can be used when genetic analysis is difficult. B. Activity measurements are any measurements taken in situ. C. Activity measurements are collective estimates of the physiological reactions in an entire microbial community. D. Activity measurements are any measurements taken in vitro.

Activity measurements are collective estimates of the physiological reactions in an entire microbial community.

Genetically engineered vaccines can be created by __________.

All of the listed responses are correct.

Plasmids are commonly used as cloning vectors because __________.

All of the listed responses are correct.

Transcription in a virus that has an RNA genome is more complex than in a DNA-based virus because __________.

All of the listed responses are correct.

Culture-independent methods

Allows the detection of genetic fragments, not just genes from entire organisms.Not all microbes grow in one culture medium; knowing all species may be important.Genetic analysis allows identification of genetic material regardless of growth requirements.

Molecular sequencing suggests that mitochondria arose from a group of prokaryotic organisms within the

Alphaproteobacteria.

Describe three characteristics of an ideal cloning host for genetic engineering.

An ideal host must be an organism that can be cultivated and grown in the lab with ease. The host must also have a stable genetic makeup such that mutations can be inserted and observed. The host must be able to susceptible to transformation so that the mutations can be inserted and replicated.

The term "respiration" is often used more broadly than is strictly accurate. The term "anaerobic respiration" may sound counterintuitive, but many different molecules can serve as electron donors or electron acceptors for prokaryotes. Which of the examples below is the best example of anaerobic respiration? A. Many organisms use an electron transport chain with oxygen as the terminal electron acceptor to generate relatively large quantities of ATP. B. Purple bacteria use a type of photosynthesis that does not generate oxygen. C. An organism uses an electron transport chain with sulfur as the terminal electron acceptor. D. Lactic acid fermenters are able to generate energy in the absence of oxygen.

An organism uses an electron transport chain with sulfur as the terminal electron acceptor.

Inorganic compounds can be reduced by microbes either for biosynthesis (assimilatory reductions) or for energy metabolism (dissimilative reductions) purposes. What is the role of the inorganic compound that is reduced in dissimilative reductions? A. As electron donors for anaerobic respiration B. As electron carriers for any type of respiration C. As sources of elemental substances for use in making proteins or nucleic acids D. As terminal electron acceptors for anaerobic respiration

As terminal electron acceptors for anaerobic respiration

Because there is low availability of organic material or reduced inorganic energy sources, the ___________________________________ in these ecosystems is low.

BOD (biochemical oxygen demand)

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).

Which is the most toxic form of mercury? A. Hg0 B. CH3Hg+ C. Hg2+ D> Hg4+

CH3Hg+

Which product of anoxic sewage treatment can be used to heat and power an entire water treatment facility? A. CH4 B. H2 C. O2 D. CO2

CH4

What two gases were most abundant on early Earth?

CO2 and H2

Decomposition of organic carbon ultimately results in the formation of __________. A. CO2 plus CH4 in aerobic environments and CH4 in anoxic environments B. CH4 in aerobic environments and CO2 in anoxic environments C. CO2 in aerobic environments and CH4 in anoxic environments D. CO2 in aerobic environments and CO2 plus CH4 in anoxic environments

CO2 in aerobic environments and CO2 plus CH4 in anoxic environments

Alternative autotrophic routes to the Calvin cycle such as the reverse citric acid cycle and the hydroxypropionate pathway are unified in their requirement for A. organic compound(s) formed. B. coenzyme A. C. NAD(P)H. D. CO2.

CO2.

________ use inorganic electron donors released from deep-sea hydrothermal vents. A. Photolithotrophs B. Chemolithotrophs C. Photoheterotrophs D. Chemoheterotrophs

Chemolithotrophs

Which of the following viral genomes could be directly translated to make proteins?

Class IV ssRNA (+) viruses

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.

Consider the following experiment. First, large populations of two mutant strains of Escherichia coli are mixed, each requiring a different, single amino acid. After plating them onto a minimal medium, 45 colonies grew. Which of the following may explain this result?

Either A or B is possible.

Determine why some prokaryotes have less DNA but more genes than eukaryotes.

Eukaryotes have more introns in their chromosomes.

What is the difference between an F+ and an Hfr bacterium?

F+ bacteria have a nonintegrated F plasmid, while Hfr bacteria have an F plasmid that is integrated into their main chromosome.

Bacteria that are capable of oxidizing both iron and sulfur usually have a strong preference for sulfur oxidation because it yields more energy. True False

False

Bacterial mating (or conjugation) is a bidirectional process where nucleic acids (DNA or RNA) are transferred between two cells. True False

False

Chemoheterotrophic bacteria are primary producers. True False

False

Cyclic di-guanosine monophosphate is upregulated as Pseudomonas aeruginosa cells are declining. True False

False

Functional differences can be observed by using 16S rRNA gene phylogenetics of a microbial community. True False

False

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? A. 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. B. Flask A would contain ammonium utilizers and flask B would contain nitrogen fixers that could not tolerate the presence of ammonium. C. Flask A would contain nitrogen fixers that could not tolerate the presence of ammonium; flask B would contain ammonium utilizers. D. Flask A would contain ammonium utilizers, and flask B would contain nitrogen fixers that could grow without the presence of ammonium.

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 sequences is a palindrome, characteristic of many recognition sequences for restriction endonucleases?

GAATTC CTTAAG

Which fluorescent molecule enables visualization of living microorganisms? A. DAPI B. SYBR® Green C. acridine orange D. GFP

GFP

What are some advantages and limitations of using biofuels, and why are genetically engineered microbes more useful for their production than naturally occurring microbes?

Genetically engineered microbes, specifically those formed from nonedible plant material, are more desirable for use as they use natural fermentation processes to form biofuels instead of fossil fuels. The fossil fuels are limited resources as they cannot be synthesized, in contrast biofuels can be formed from natural processes of fermentation. One drawback is that they may require some modification in order to be effective. Overall, the use of biofuels is more efficient, cost-effective, and sustainable over a long period of time.

It is hypothesized that early photosynthesis was anoxygenic. Think about the role of oxygen in photosynthesis as carried out by green plants, green algae, and cyanobacteria (as opposed to modern organisms that use anoxygenic photosynthesis). What would have been different in anoxygenic photosynthesis (or is different in modern organisms that use anoxygenic photosynthesis)?

Green plants, green algae, and cyanobacteria split H2O to replace an excited electron in noncyclic photophosphorylation. Oxygen is released into the atmosphere. In anoxygenic photosynthesis, a different molecule (such as H2S) is split and a different product (such as sulfur) is released.

Which of the following is most similar to lysogeny?

Hfr state

What reaction is catalyzed by mercuric reductase? A. CH3HgCH3 to Hg2+ B. Hg4+ to Hg2+ C. Hg2+ to Hg0 D. CH3Hg+ to Hg2+

Hg2+ to Hg0

Some hydrogen oxidizers synthesize two forms of the enzyme hydrogenase, one that is embedded in the cytoplasmic membrane and one that is soluble in the cytoplasm. Other hydrogen oxidizers get by with only one form of hydrogenase. Given the roles of each type of hydrogenase, what are the implications for the latter type of organism? A. Hydrogen oxidizers that contain only a soluble hydrogenase can oxidize H2 to make NADH for autotrophy, but cannot use electrons from H2 for energy generation by oxidative phosphorylation. B. There is no difference. The two forms of hydrogenases are redundant. C. Hydrogen oxidizers with only a membrane-integrated hydrogenase cannot donate electrons to the electron transport chain to generate energy by oxidative phosphorylation. D. Hydrogen oxidizers with only membrane-integrated hydrogenases must use reverse electron transport to reduce NAD+ to NADH for autotrophy.

Hydrogen oxidizers with only membrane-integrated hydrogenases must use reverse electron transport to reduce NAD+ to NADH for autotrophy.

Why are there so few antiviral drugs available for DNA virus infections? What viral processes would these drugs most likely target?

In order for antiviral drugs to target viral DNA to prevent or treat infections, the antiviral drugs must be able to bind to the virus and inhibit certain processes. This is problematic in the case of viruses as they contain different components of genetic material including DNA and RNA. They also utilize mechanism of the host cell in order to replicate and infect the organism, therefore antiviral drugs must be able to cease replication of the virus but prevent death of the host cell, which is difficult to create especially in eukaryotes which only have DNA and any antiviral drugs would also inhibit the synthesis of DNA in nonhost cells; hence the few antiviral drugs available for DNA virus infections. Therefore, antiviral drugs must target the virus in the binding processes before insertion of DNA into the host cell.

How would you label and separate the DNA of unknown methylotrophs in a sample? A. Incubate the sample with 13C-methane. B. Hybridize the DNA to FISH probes. C. Use T-RFLP to identify the methylotroph DNA in the sample. D. Use DGGE to separate the strands of DNA in the sample.

Incubate the sample with 13C-methane.

The Ames test is commonly used to test whether a particular chemical is mutagenic. When you conduct an Ames test, you need two groups of plates. One group of plates contains bacteria that are exposed to the chemical of interest, while the other plates contain bacteria that are not exposed to the chemical. Why is the latter group needed if you are just interested in the rate of mutation caused by the chemical?

It is important to compare the rate of mutations with the chemical to the normal background mutation rate. Mutations occur spontaneously even without the presence of a mutagen.

Which of the following is TRUE of natural competence?

It requires special proteins such as a cell wall autolysin.

The polymerase chain reaction, PCR, has revolutionized molecular genetics. Despite all of the advantages of PCR, it does have limitations. Which of the following is NOT a limitation of PCR?

It requires very pure and high-quality DNA samples.

A computer program recognizes an ORF by looking for ribosomal binding sites, start codons, and stop codons with an appropriate number of nucleotides between each element. What is a drawback of this approach?

Legitimate genes and non-coding RNA may be missed.

Which of the following factors has delayed the development of laboratory-based genetic systems in Archaea?

Many archaea grow in extreme or unusual conditions that make the use of agar and traditional mutant screening techniques problematic.

The introductory passage describes the way that microbes can produce CH4 and CO2 in melting permafrost, especially in saturated, anoxic depressions. Although other types may also be present, what microbes are most likely present to make these products in these conditions? A. A pure culture of syntrophic bacteria is probably present. B. Methanogens are probably present as they produce CH4 and CO2 in anoxic environments. C. Methanotrophs are probably present as they produce CH4 and CO2. D. Sulfate-reducing bacteria are probably present as they are important in anoxic environments.

Methanogens are probably present as they produce CH4 and CO2 in anoxic environments.

Some microbial transformations of mercury yield more toxic forms of mercury, including the most toxic form, methylmercury (CH3Hg+). Which of the following properties of methylmercury in an aquatic ecosystem would be most problematic for humans? A. Methylmercury accumulates in animal muscle and is biomagnified in the food chain. B. Methylmercury is water-soluble. C. Methylmercury is a neurotoxin. D. Methylmercury absorbs readily through the skin.

Methylmercury accumulates in animal muscle and is biomagnified in the food chain.

Archaea

Most of these living below 1000 m are thought to be ammonia oxidizers. Below 1000 m the most common phylum is Thaumarchaeota. They increase to near 50% of total prokaryotes below 1000 m.

Of the phages listed below, which creates mutations in its host genome via transposition?

Mu

A farmer wants to stock small fish in a pond on his property, but the water looks a bit murky to him. He asks a microbiologist friend to analyze the pond water to see if fish could survive there. The microbiologist finds that the water has a very high BOD. Should she tell the farmer to stock the pond with fish? A. Yes; the pond is likely to be aerated. B. Yes; the pond water is high in nutrition for the fish. C. No; the pond is likely to be anoxic. D. No; the pond water is toxic.

No; the pond is likely to be anoxic.

Transformation and homologous recombination allow for the formation of heteroduplex DNA. Which of the following would occur during DNA replication of this molecule?

One daughter strand is complementary to the recombinant DNA molecule, while the other daughter strand is complementary to the parent DNA molecule.

It is hypothesized that early photosynthesis was anoxygenic. If so, what was the effect of the appearance of organisms using oxygenic photosynthesis?

Organisms using oxygenic photosynthesis release oxygen into the atmosphere, causing an increase in the oxygen in the atmosphere and allowing for the development of aerobes.

The most abundant prokaryotic organism in the ocean is of the ________ genus. A. Puniceispirillum B. Roseobacter C. Pelagibacter D. Prochlorococcus

Pelagibacter

________ are the main primary producers in freshwater environments. A. Heterotrophic microorganisms B. Chemolithotrophic microorganisms C. Viral microorganisms D. Phototrophic microorganisms

Phototrophic microorganisms

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.

After transcription, mRNA may undergo significant editing. Compare and contrast RNA editing in prokaryotes and eukaryotes and connect how these differences affect genome size and gene content.

Post-transcriptional editing of mRNA differs greatly between prokaryotes and eukaryotes. Prokaryotes have no post-transcriptional modification, while eukaryotes have capping at the 5' end, poly A tail, and splicing of introns. Prokaryotes are lacking in introns. Both strands will have untranslated regions at the 3' and 5' ends. Due to the complexity of the eukaryotic cell the genetic material present in the exons would be greater than that present in the prokaryotic exons. The mechanisms required for translation would also require more complex systems, in eukayotes (capping, poly A tail) such that translation can occur at the poly A tail. Typically the larger the genome the more introns present in the genome which indicates a larger need for intron splicing.

According to bacterial abundance studies done so far on soils, the ________ represent the most abundant phylum. A. Acidobacteria B. Actinobacteria C. Firmicutes D. Proteobacteria

Proteobacteria

Phylogenetic analyses of marine prokaryotic diversity in both shallow and deep-sea marine sediments have found that both types of sediments are dominated by A. Chloroflexi. B. Planctomycetes. C. Proteobacteria. D. Firmicutes.

Proteobacteria.

Culture-dependent methods

Provides living microbes for further testing and analysis. Allows isolation of individual species, not a mixed species assemblage. Provides living microbes for further testing and analysis. Prevents risk of missing an unusual species due to lack of appropriate PCR primers.

In DNA replication in vivo, RNA primers are used. However, researchers used DNA primers instead in the lab because DNA primers are more stable. Why might this be the case?

RNA has a relatively short half-life compared with DNA and does not need to be as stable to perform its functions in the cell.

If the hypothesis stating viruses evolved prior to living organisms on Earth is TRUE, the first type of viruses in the world were likely

RNA viruses.

Chemical reactions involving ________ have been proposed as energy-yielding reactions for the earliest organisms on Earth.

S, and H2

A small farm pond containing many species of microorganisms (bacteria, cyanobacteria, algae, and protozoa) was perturbed when runoff from a manure pile entered the pond. The added nutrients soon turned the water green due to a bloom of cyanobacteria. How did this affect the microbial community in the pond? A. Species richness increased and species abundance decreased. B. Species richness increased and species abundance increased. C. Species richness decreased and species abundance decreased. D. Species richness decreased and species abundance increased.

Species richness decreased and species abundance increased.

________________ reducers can also take up electrons directly from Fe.

Sulfate

One hypothesis that has been proposed to explain the development of viruses suggests that viruses were beneficial because they allowed for rapid gene transfer, especially in prokaryotic cells, and therefore increased genetic diversity. Temperate viruses could have increased horizontal gene transfer between prokaryotic cells and potentially increased their fitness. With respect to this hypothesis, why would it matter whether the bacteriophages were temperate or virulent?

Temperate phages don't immediately kill their hosts.

Explain why the viral genome of the MS2 phages can be immediately translated. What type of genome must it have for this to be the case?

The MS2 phages can be immediately translated as they have plus-sense RNA which can be immediately translated as the virus utilizes RNA. As both the phages and the viruses utilize RNA, the mechanisms to transcribe are the same and the phage's genetic material can be incorporated through the use of reverse transcriptase.

What is the first step in constructing a metagenomic library from RNA?

The RNA must be converted to cDNA.

When analyzing the sequence of genes similar to ones already known, why is the amino acid sequence of the protein more important than the DNA sequence?

The amino acid sequence codes for the function of the proteins. While codon bias exists the sequence of the amino acids are even more essential as this is where the mutations occur which change the sequence and thus function of the protein. Furthermore, DNA sequences are required for the inheritance of the offspring. In contrast, protein sequences are required for the maintenance of the individual organism which makes the amino acid sequence less prone to changes. ( Some nt changes don't change the amino acid sequences and will thus have no effect on protein function. Looking at changes in amino acid sequence means you're looking at changes that could lead to a change in function and therefore may be subject to natural selection.)

Researchers discover a new species of bacterium that has an unusual metabolism. However, it has biochemical and morphological similarities to other species. What is the most comprehensive and effective approach to determine how to classify these bacteria?

The bacteria should be classified by using genomic analyses to construct phylogenies.

Why is the biological species concept useful for Eukarya but not meaningful for Archaea and Bacteria? How are prokaryotic species defined?

The biological species concept is useful for Eukarya as the species meets the requirements of fundamentally diverse units that are genetically and phenotypically similar. This concept is less useful for the distinction between Bacteria and Archaea as they contain strains with much genetic and phenotypic similarity. Furthermore, Bacteria and Archaea share a recent common ancestor and cannot be separately monophyletic. The degree of relatedness between the two groups would cause overlapping in defining specific species and their origin. Prokaryotic species can be loosely defined as organisms lacking membrane bound organelles, cell wall, and containing 70S ribosomes.

Microbial species have a core genome and a pan genome. What is the difference between the two?

The core genome is a set of genes shared by all members of a species, while the pan genome includes the core genes as well as genes that are not shared by all members.

Which of the following would result in a frameshift mutation?

The deletion of two nucleotides in a codon

How do viability stains usually distinguish between living cells and dead cells? A. The dyes fluorescence is quenched by dead cells. B. The chemical stain is taken up by living cells and once metabolized becomes fluorescent. C. The chemical fluoresces only when bound to ribosomes that are actively synthesizing proteins. D. The dye specifically targets intact cytoplasmic membranes.

The dye specifically targets intact cytoplasmic membranes.

Although it is important to study the organisms that live in the abyssal and hadal zones, researchers can often more easily study organisms that live closer to the ocean's surface, which do not require the use of remotely operated vehicles and similar equipment for sampling. The photic zone is the region in which the light intensity is sufficient for photosynthesis to occur. In the open ocean of tropical and subtropical regions, the photic zone is dominated by several ecotypes of the bacterium Prochlorococcus. Each ecotype dominates a particular depth range of the photic zone. Which of the following reasons are thought to be responsible for this phenomenon? Choose all correct answers. A. The ecotypes vary in ability to compete for different nitrogen and phosphorus sources. B. The genetic material in all ecotypes is nearly 100% the same. C. Some ecotypes are predominantly chemoorganoheterotrophic. D. The ecotypes differ in ability to photosynthesize and compete effectively at different light intensities. E. The ecotypes differ in their response to extreme pressures.

The ecotypes vary in ability to compete for different nitrogen and phosphorus sources. The ecotypes differ in ability to photosynthesize and compete effectively at different light intensities.

Which statement is TRUE about the fluid from the hydrothermal vents? A. The fluid contains large amounts of oxidized inorganic materials. B. The fluid contains large amounts of reduced inorganic materials. C. The fluid usually contains about equal amounts of organic and inorganic material. D. The fluid contains large amounts of organic material.

The fluid contains large amounts of reduced inorganic materials.

Functional analysis of the genome of a prokaryote shows that 20% of the genome is for metabolism, 1 % for biosynthesis of amino acids, 8% for peptide ABC transporters, and 2% for replication. What can you determine about the environment in which this organism lives?

The organism lives in an environment rich in organic material, particularly amino acids and proteins.

Rhodobacter cells perform photosynthesis in the presence of light and grow heterotrophically in the dark. After being cultured in total darkness for multiple generations, phenotypic and genotypic changes occur. What phenotypic changes occur and what evolutionary processes are driving them?

The phenotypic change would be involve heterotrophic growth as a primary mechanism of energy derivation rather than photosynthetic derivation of energy causing a loss of the mechanisms over time. The evolutionary processes driving these changes would be the lack of a need for the photosynthetic apparatus as it is energetically expensive. Natural selection would streamline this process in addition to the selection pressures of the environment, requiring an organism capable of heterotrophic growth in the dark.

A single base substitution happens to cause a nonsense mutation early in the gene for a protein. What will be the result?

The protein will be truncated so much that it is unlikely to function normally.

Chlorophyll and bacteriochlorophyll pigment molecules absorb light energy for photosynthesis. Each specific version of these molecules absorbs a different range of wavelengths of light, allowing different species of phototrophs to coexist by partitioning their use of the light spectrum. What controls the absorption spectrum of each particular chlorophyll/bacteriochlorophyll? A. The number of tetrapyrrole rings linked together alters the absorption spectrum. B. The exact orientation of the pigment molecule in the membrane (on the membrane surface, inner membrane or transmembrane) alters the absorption spectrum. C. The various substituents on the tetrapyrrole ring alter the absorption properties of the pigments. D. The specific metal ion in the center of the tetrapyrrole ring alters the absorption spectrum.

The various substituents on the tetrapyrrole ring alter the absorption properties of the pigments.

Which of the following describes a retrovirus?

The virus uses reverse transcriptase to make DNA from an RNA template, the reverse of the normal process of gene expression.

Some bacteria have unusually high mutation rates. Is there an adaptive reason why they might have such high mutation rates?

These bacteria may be able to adapt rapidly to a new environment (e.g., an environment with an antibiotic).

Why is the outcome of a base-pair substitution mutation variable? List and describe the possible outcomes of a base-pair substitution mutation in your answer.

There are three different outcomes a base-pair substitution could incite. A base-pair substitution involves the change of one base pair within the genome. The first type of base-pair substitution involves replacing a base-pair within the codon with another which codes for the same amino acid due to the redundancy of the code. This is known as a silent mutation which changes the genotype of the organism but not the phenotype. This type of mutation typically occurs in the third base-pair position. For example, AUU codes for Ile, if a mutation where to occur in the third position of the base-pair changing AUU to AUC the genetic code would change but the sequence would still code for Ile. The second type of base-pair substitution involves substituting a base-pair within the codon with another that does not cause the same amino acid to be coded for. This is known as missense mutation which, involves the change of both the genotype of the organism and the phenotype. For example, AUU codes for Ile, if a mutation where to occur in the second position of the base-pair changing AUU to ACU the genetic code would change but the sequence would still code for Thr. The third type of base-pair substitution involves substituting a base-pair within the codon with another that does not cause an amino acid to be coded for, instead a stop codon is formed. This is known as a nonsense mutation as the needed codon formations are often incomplete an result in no or incorrect production. For example, AUU codes for Ile, if a two mutations where to occur in the first and second position of the base-pair changing AUU to UAG the genetic code would now read a stop codon and the sequence would be terminated. This is a problem if the mutation is at the beginning of the sequence as few or no polypeptides will be formed.

Researchers using molecular analyses, including sequencing technology, may be interested in studying horizontal gene transfer because it plays such an important role in microbial evolution. Genome sequencing has led to insights about this type of genetic transfer between a wide range of organisms, even in very different taxa. This is another area in which portable, inexpensive sequencing will expand the research that can be done. If a researcher wanted to understand whether a particular species of non-pathogenic bacteria had obtained genes via horizontal gene transfer, which of the following would be true?

They should focus their attention on metabolic genes.

What would likely occur if an anammox bacterium was unable to use ladderane lipids? A. Ammonium rather than ammonia would be used due to ammonia toxicity to other cellular processes within the anammoxosome. B. It would require a different source for carbon assimilation. C. Toxic products of the anammox reaction could kill the cell. D. Rates of anammox would be considerably slower due to a lack of localized metabolism.

Toxic products of the anammox reaction could kill the cell.

Why is U4+ a preferred form of uranium over U6+? A. Uranite is insoluble; U4+ is soluble. B. U6+ is insoluble, which makes it difficult to work with. C. U4+ is insoluble, so it will not contaminate groundwater. D. U4+ is soluble, so it can move from its initial site to other places and be diluted by groundwater.

U4+ is insoluble, so it will not contaminate groundwater.

What is the most important advantage of Pfu polymerase over Taq polymerase?

Unlike Taq polymerase, Pfu polymerase has proofreading activity

Some viruses are associated with cancer. There are a variety of ways in which viruses may affect a cell in a way that may lead to the formation of a tumor. Based on your knowledge of the life cycles of viruses and of molecular genetics, what is one way that this might happen?

Viral genetic material inserts into a host genome, placing a promoter in a new location and turning on a gene that had previously been turned off.

Design an experiment using -omic methods to test how Escherichia coli adapts to different growth temperatures.

We could perform and experiment to demonstrate the transcriptomics of the E. coli strain. Transcriptomics would analyze the transcription mechanisms of the strain as well as the RNA under the specific growth conditions. From this study we could determine which genes are transcribed in order for the strain to survive in different growth temperatures. In order to perform the experiment, we would utilize microarrays. These fix and array in a known sequence/pattern. Next the fluoresently labeled DNA is identify and the hybridized DNA/RNA is measured. These measurements can be used to analyze the total gene expression of the strain, thus indicating the strain's ability to adapt to different growth temperatures.

One group of chemical mutagens includes the base analogs. How do these lead to mutations?

When replication occurs, complementary base pairing may fail because the base analog may not be treated in the same way as the base that it replaced.

Why would using nitrogenous fertilizer near a body of water affect the organisms in the body of water? A. When runoff enters the body of water, the nitrogen level significantly increases, which decreases the activity of the microorganisms there and upsets the balance of the ecosystem. B. When runoff enters the body of water, the nitrogen level significantly decreases, which increases the activity of the microorganisms there and upsets the balance of the ecosystem. C. When runoff enters the body of water, the nitrogen level significantly increases, which increases the activity of the microorganism there and upsets the balance of the ecosystem. D. It would not affect the organisms in the water, only those in the soil where the fertilizer is applied.

When runoff enters the body of water, the nitrogen level significantly increases, which increases the activity of the microorganism there and upsets the balance of the ecosystem.

Many restriction enzymes produce sticky ends, which are very useful for genetic engineering. What makes the ends sticky?

When the restriction enzyme cuts, it cuts the two strands of a double-stranded DNA molecule unevenly. This produces overhanging DNA nucleotides on each fragment. These overhanging fragments are complementary to each other or to other fragments produced using the same restriction enzyme.

When measuring microbial community metabolic activity, __________ is always necessary. A. radioisotopes B. a killed control C. DNA extraction and sequencing D. enrichment culture

a killed control

The SOS DNA repair system is __________.

a last-ditch effort to prevent cell death from major chromosomal damage

Which of the following could describe a virus?

a particle composed of a protein capsid surrounding single-stranded DNA

An open reading frame (ORF) encodes for

a polypeptide.

Inserting a kanamycin resistance cassette into a catabolic operon to confirm the gene is essential in degradation of a particular compound would involve all of the following EXCEPT

a reporter gene.

Which of these organisms is likely to have the largest genome?

a yeast cell

The ocean has mitigated the impact of anthropogenic carbon dioxide production by A. absorbing 500 billion tons of atmospheric carbon dioxide. B. storing 600 billion tons of organic carbon. C. absorbing over 80% of the trapped heat energy. D. absorbing 500 billion tons of atmospheric carbon dioxide and over 80% of the trapped heat energy.

absorbing 500 billion tons of atmospheric carbon dioxide and over 80% of the trapped heat energy.

A cell that lacks sulfite reductase but can still oxidize sulfur for energy could be identified by A. adenosine phosphosulfate reductase coupled with substrate-level phosphorylation. B. electrons being transferred to cytochrome c prior to shuttling them into the electron transport chain. C. identifying an alternative quinone, flavoprotein, or cytochrome. D. quantifying the release of sulfate byproduct.

adenosine phosphosulfate reductase coupled with substrate-level phosphorylation.

To verify a gene was cloned into a vector successfully, sequencing the vector as well as ________ are commonly performed.

agarose gel electrophoresis

While most of the oil spilled into the Gulf of Mexico from the Deepwater Horizon drilling rig in 2010 has disappeared, some of the oil spilled from the Exxon Valdez oil tanker into Prince William Sound, Alaska, in 1989 still remains in the coastal sand and sediments. What possible differences in these two spills could account for the different rates of petroleum degradation? A. the amount of oil spilled and the seawater salts composition B. the types of bacteria present and the amount of oxygen in the water C. ambient temperatures and the types of hydrocarbons present D. seawater salt composition and types of bacteria

ambient temperatures and the types of hydrocarbons present

Anammox is an anaerobic process that generates energy from ________ and forms N2. A. ammonia and nitrate B. ammonia and nitrite C. ammonium D. ammonia

ammonia and nitrite

Which are the most dominant chemolithotrophs in pelagic waters? A. ammonia-oxidizing Archaea B. Prochlorococcus C. ammonia-oxidizing Bacteria D. sulfate-reducing Bacteria

ammonia-oxidizing Archaea

Many organisms release ammonium (NH4+) from degradation of nitrogen-containing organic materials. This process is referred to as ________________________.

ammonification

Analyses of sulfur isotopes have been used as evidence against life on the Moon, because the sulfides in lunar rocks have A. an isotope composition most similar to marine sulfate, which is enriched in 34S. B. an isotope composition most similar to marine mud, which is enriched in 34S. C. exactly equal amounts of 34S and 32S. D. an isotope composition most similar to igneous rocks.

an isotope composition most similar to igneous rocks.

Phosphorus-accumulating organisms are used in ____________________________________________________ in enhanced biological phosphorus removal.

anaerobic reactors of tertiary wastewater treatment

A process that results in anaerobic ammonia (NH3) oxidation, uses nitrite (NO2-) as the electron acceptor, and produces N2 as the product is the ___________________ reaction.

anammox

Chromosomal islands are similar to plasmids __________.

because both elements contain nonessential genes

In T7, the proteins that inhibit the host restriction system are synthesized

before the entire T7 genome enters the cell.

An organism living in the bottommost region of a body of water is described as being A. litoral. B. benthic. C. pelagic. D. neritic.

benthic.

All of the following are true of biofilms EXCEPT that __________. A. biofilms are composed of only one species at a time B. biofilms form on virtually all submerged surfaces in nature C. biofilm formation and dispersal are regulated processes D. biofilms protect organisms from antibiotics

biofilms are composed of only one species at a time

According to the RNA world hypothesis, which of the following was the correct sequence of developments?

biological building blocks (e.g., amino acids, sugars, and nucleosides), then RNA (including catalytic and self-replicating RNA), then protein synthesis, then DNA, then lipid bilayers surrounding early cellular life

Integration of Mu DNA into the host genome is essential for

both lytic and lysogenic growth.

Increases in atmospheric carbon dioxide concentrations leads to acidification of the oceans as CO2 dissolves in the water and forms carbonic acid. This acidification is predicted to have a major effect on the carbon cycle, as well as the calcium and silica cycles, due to the roles of Ca+ and Si in __________. A. building the shells and frustules of microscopic algae and some animals B. the formation of fossil fuels C. the formation of carbonate rocks D. mercury oxidation

building the shells and frustules of microscopic algae and some animals

The calcium cycle is tightly coupled to the A. phosphorus cycle through calcium phosphate formation in sediments and rocks. B. silica cycle through calcium silicate formation in coastal ocean sediments. C. nitrogen cycle because nitrogenase requires calcium ions. D. carbon cycle through calcium carbonate formation in ocean waters.

carbon cycle through calcium carbonate formation in ocean waters.

Whether an organism is classified as a photoheterotroph or a photoautotroph depends on its A. energy source. B. carbon source. C. carbon and energy sources. D. oxygen requirements.

carbon source.

The element(s) that have proven most useful for stable isotope studies are A. carbon only. B. nitrogen only. C. sulfur only. D. carbon, sulfur, and sometimes nitrogen.

carbon, sulfur, and sometimes nitrogen.

What method of mutagenesis would be best to determine if a gene is essential for a prokaryote?

cassette mutagenesis

The microbes that decompose permafrost carbon to release CH4 and CO2 are most specifically examples of ____________________________.

chemoorganotrophs

The 140 kbp genome containing many short repeats, ribosomal RNA genes, one RNA polymerase gene (rpo) and one RubisCO gene (rbcL) is most likely from a(n)

chloroplast.

The enzyme transposase may be coded for by insertion sequences on a

chromosome, phage, or plasmid.

The production of a functional gene product by transforming bacteria that lack a lacZ gene with a plasmid containing a lacZ gene is known as

complementation.

Horizontal gene transfer

complicates the construction of phylogenetic trees and the interpretation of specific traits in relation to evolution.

Lysogeny probably carries a strong selective advantage for the host cell because it

confers resistance to infection by viruses of the same type.

Compared with today, the temperature on Earth during its first half-billion years was probably

considerably warmer.

The strategy for bioremediation of large sites contaminated by inorganic pollutants like toxic metals and radionuclides is usually to __________. A. completely remove the contaminants from the site B. completely oxidize the pollutants to carbon dioxide and water C. contain the pollutants by converting them into a less mobile form D. break down the pollutants to less harmful products

contain the pollutants by converting them into a less mobile form

Identifying proteases being essential for the replication of a virus would suggest the virus

contains at least one polyprotein.

What has occurred when organisms share a trait that was NOT inherited from a common ancestor?

convergent evolution

Proteomic analysis of a microbial community indicated an abundance of phycobiliproteins. Which phototrophic group is likely active and abundant in this community? A. eukaryotic phototrophs B. cyanobacteria C. prochlorophytes D. green bacteria

cyanobacteria

Sudden nutrient perturbations in an environment generally ________ the overall prokaryotic diversity. A. replicate B. maintain C. increase D. decrease

decrease

The use of nitrate (NO3-) as an electron acceptor with formation of multiple gaseous end products (N2, N2O, or NO) is ____________________.

denitrification

You work for a biotechnology company that uses Streptomyces strains to produce pharmaceutical products. A phage has infected and killed some of your Streptomyces strains during production, resulting in dramatically decreased yields. To protect the strains from infection you propose to:

design and insert CRISPR spacer sequences into the genomes of your strains that are complementary to the genomes of the phages that are infecting the cultures.

By isolating total community RNA, using reverse transcriptase to make cDNA copies of it, and then sequencing the cDNA, ecologists can __________. A. determine the community metabolic activity at the moment of sampling B. determine the community genomic potential at the moment of sampling C. determine the community genome translation at the moment of sampling D. determine the community genome expression at the moment of sampling

determine the community genome expression at the moment of sampling

Lysis of marine algae and cyanobacteria releases the major osmoregulatory solute, dimethylsulfoniopropionate (DMSP), which is degraded into the most abundant organic S compound in nature, ________. A. dimethyl sulfide (CH3-S-CH3) B. hydrogen sulfide (H2S) C. elemental sulfur (So) D. gypsum (CaSO4)

dimethyl sulfide (CH3-S-CH3)

Geobacter sulfurreducens uses its pili to form direct connections with insoluble ferric iron particles. As the organism carries out respiration, the Fe3+ is acting as a(n) __________. A. electron donor B. carbon source C. micronutrient D. electron acceptor

electron acceptor

The early energy reactions used hydrogen, which is a powerful

electron donor.

Phylogenetic analysis of microbial communities in nature using various PCR techniques has revealed that only a minority of phylotypes have been cultured from the environment and the most common phylotypes have not been grown in in the laboratory. This is due in part to __________. A. lack of sufficient sampling of the community B. enrichment bias C. the uncultured organisms' being rare in the community D. poor technique

enrichment bias

Which of the following techniques can link prokaryotic phylogeny and metabolic function? A. stable isotope probing only B. DAPI staining C. environmental genomics and stable isotope probing D. environmental genomics only

environmental genomics and stable isotope probing

A change in allele frequencies in a set of organisms over time is called __________.

evolution

What technique(s) can be used to characterize the phylogenetic composition of a microbial community without culturing any of the members? A. stable isotope techniques B. green fluorescent protein tagging C. radioisotope experiments D. fluorescent in situ hybridization (FISH)

fluorescent in situ hybridization (FISH)

Genetic recombination involving insertion sequences typically results in what type of mutation?

frameshift mutation

Horizontal gene transfer in Archaea

frequently occurs in nature and has been used to perform genetic studies in the laboratory as well.

Metatranscriptomics and metaproteomics are favored over metagenomics when ________ is of more interest than ________. A. gene presence / function or gene expression B. phylogeny / gene presence C. gene presence / phylogeny D. function or gene expression / gene presence

function or gene expression / gene presence

Microarrays are useful for assessing A. gene expression only. B. gene expression and the presence of specific rRNA sequences. C. enzyme activity. D. the presence of specific rRNA sequences only.

gene expression and the presence of specific rRNA sequences.

Which process listed below allows genetic material to be transferred from a virus-like particle that lacks genes for its own replication?

gene transfer through a gene transfer agent

The conditions of nutrient availability, pressure, and temperature result in long _________________________ and thus slow __________________________.

generation times, growth rates

Metagenomics is a more sensitive analysis of community diversity than rRNA-based analyses because __________. A. rRNA genes are not found in all of the organisms present in the environment B. genes do not have to be amplified by PCR before being sequenced C. the extraction of the DNA from the environmental samples is more efficient D. more clone libraries can be assembled

genes do not have to be amplified by PCR before being sequenced

Ammonia-oxidizing bacteria are found on the outside of ___________ used in AST.

granules

The general term for organisms that have to use preformed organic molecules is____________, whereas the general term for those that can use CO2 to synthesize organic molecules are ________________.

heterotrophs; autotrophs

Ferrous iron (Fe2+) oxidation generally occurs in environments with A. high H+ concentrations. B. alkaline conditions. C. high oxygen content. D. little or no light present.

high H+ concentrations.

Genomic analysis of Prochlorococcus has revealed A. the presence of bacteriorhodopsin. B. that no regions are shared between cultured representatives and environmental populations. C. high levels of gene conservation between cultured representatives and environmental populations. D. complete congruence of genes and genome structure within the same phylotype.

high levels of gene conservation between cultured representatives and environmental populations.

Microorganisms inhabiting the abyssal and hadal zones must be able to thrive under......

high pressures. These environments contain piezophilic and extremely piezophilic archaeans and bacteria.

The pan genome of a microbial species is constantly changing because of

horizontal gene transfer.

Agricultural application of nitrogen fertilizer A. increases global warming by increasing microbial respiration in agricultural soils. B. reduces global warming by increasing the storage of carbon dioxide in plant biomass. C. increases global warming by increasing the production of nitrous oxide (N2O) by denitrification in agricultural soils. D. has little to no effect on the carbon cycle.

increases global warming by increasing the production of nitrous oxide (N2O) by denitrification in agricultural soils.

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 EXCEPT __________. A. production of intercellular signaling molecules B. formation of cell surface attachment proteins C. initiation of flagella formation D. initiation of extracellular polysaccharide production

initiation of flagella formation

Benefits of transgenic plants include __________.

insect resistance

One of the more formidable obstacles to mammalian gene cloning is the presence of

introns.

Chemical mutagens, UV radiation, and ionizing radiation all increase mutation rates, but they have different mechanisms. Which type of mutagen would be best suited for creating large deletions and rearrangements within a genome?

ionizing radiation

The primary metal sulfides emitted from the black smokers are ________ sulfides. A. iron B. zinc C. magnesium D. copper

iron

If a protein that could be toxic to the expression host needs to be expressed in large quantities, then it is best to select an expression vector that

is inducible.

Which approach would help to identify biologically produced sulfur in a sediment sample? A. microelectrodes B. microautoradiography C. enrichment D. isotopic fractionation

isotopic fractionation

Transcriptome analysis is useful in relation to genome analysis because

it analyzes RNA, thus it reveals which genes are expressed under different conditions.

Cloning vectors can be distinguished from expression vectors by

lacking a promoter site upstream of the insertion site.

In DNA cloning, fragments of DNA need to be joined together (e.g., to add a fragment into a vector). What common enzyme is used for this process?

ligase

If a foreign gene is cloned into an expression host, it is important that the host itself

not produce the protein being studied.

The aerated upper layer of soil is likely to have ________ concentrations of H2 for aerobic H2-oxidizing Bacteria, so these bacteria likely ________. A. high / thrive in such conditions by not competing with chemoorganotrophs B. low / will need a chemoorganotrophic way to grow as well C. low / do not occur in such habitats D. high / generate important reducing equivalents as byproducts for other microorganisms in the soil

low / will need a chemoorganotrophic way to grow as well

Obligate anaerobes can often use ________ electropositive redox couples than facultative anaerobes, and ________ metabolism is most common in this group as well. A. lower / dissimilative B. lower / assimilative C. higher / dissimilative D. higher / assimilative

lower / assimilative

Expression vectors are designed to ensure that ________ can be efficiently ________.

mRNA / transcribed

What makes eukaryotic transcripts easier to isolate than bacterial transcripts?

mRNA is polyadenylated in eukaryotes.

Secondary disinfection of drinking water is necessary to A. kill Cryptosporidium and other resistant pathogens. B. neutralize taste- and odor-producing organic compounds. C. prevent the formation of biofilms on pipes in the water distribution system. D. maintain sufficient residual in the water distribution system to inhibit microbial growth.

maintain sufficient residual in the water distribution system to inhibit microbial growth.

From the aquatic systems below, where are heterotrophic Bacteria the most abundant? A. open ocean B. deep sea C. Sargasso Sea D. marine coastal waters

marine coastal waters

Just by knowing that a particular organism is an archaean, it is possible to predict that its genome ___________________________________ those of most Bacteria.

may contain more unidentified genes than

Both deletions and insertions occur during the evolution of microbial genomes. Insertions bring in new genes that may be useful for the cell. Deletions

may increase fitness of a microorganism by eliminating unneeded genes.

If a researcher wanted to compare the enzymatic capacity to degrade compounds in a water column at various depths under a specific set of conditions, which would be the most useful approach?

metaproteomics

The two major forms of carbon that remain following microbial degradation are A. lignin and fossil fuels. B. methane, organic matter, and fossil fuels. C. methane and carbon dioxide. D. organic matter and hydrocarbons.

methane and carbon dioxide.

Some types of bacteria are commonly found as biofilms. Which of the following are likely to be found in biofilms? microbes in pipes in drinking water distribution systems bacteria on the dry outer surface of an oil pipe, facing the air the microbes growing on granules used in aerobic granular sludge technology the microbes on rocks used in secondary wastewater treatment Staphylococcus aureus in the air from shed human skin within a house

microbes in pipes in drinking water distribution systems the microbes on rocks used in secondary wastewater treatment

Examples of Aquatic; aerobic environment at pH 7

microbes in water undergoing primary wastewater treatment

Examples of Aquatic; anoxic environment with pH 7

microbes in water undergoing secondary wastewater treatment in a sludge digester

Examples of aquatic with relatively aerobic outer layer and relatively anaerobic outer layer and relatively anaerobic inner layer; variable pH

microbes on granules used in AGS technology

Chemolithotrophs are used in leaching through oxidation of materials in ______________.

mines

Which taxonomic tool would scientists use if they wanted to determine if an outbreak of food poisoning was caused by a particular strain of a pathogen?

multilocus sequence typing

The addition of two bases to the genome of a prokaryote would be most damaging if located __________.

near the beginning of the coding region of a protein

Ecological theory states that for every organism there is at LEAST one ________, and the microenvironment where the organism is most successful is called the ________. A. prime niche / niche B. niche / prime niche C. community / population D. population / community

niche / prime niche

To prevent the souring of crude oil, ________ is added to oil well injection water to encourage ________ instead of ________. A. nitrate / nitrate reduction / sulfate reduction B. oxygen / aerobic respiration / sulfate reduction C. sulfate / sulfate reduction / nitrate reduction D. sulfate / sulfate reduction / fermentation

nitrate / nitrate reduction / sulfate reduction

Both ammonium (NH4+) and nitrate (NO3-) are assimilated by primary producers, but ammonium is the preferred form of nitrogen for fertilizers used in agriculture because __________. A. ammonium is converted to nitrate by microbial nitrification B. nitrate leaches out of soils easily due to its negative charge C. ammonium does not cause eutrophication (algal blooms) if it enters aquatic ecosystems D. ammonium leaches out of soils easily due to its positive charge

nitrate leaches out of soils easily due to its negative charge

The aerobic process that uses ammonium (NH4+) as an energy source is referred to as ____________________.

nitrification

metabolic processes of oxic environments

nitrification; sulfide oxidation

Rates of NH3 oxidation in nature are probably controlled by archaeal ___________.

nitrifiers

Many nutrient cycles are coupled and changes in one cycle will affect another. This means that a change in the amount of carbon dioxide fixed is intimately affected by the amount of __________. A. oxygen available in an ecosystem B. hydrogen available in an ecosystem C. methane available in an ecosystem D. nitrogen available in an ecosystem

nitrogen available in an ecosystem

An assimilatory process in which N2 is converted to ammonia (NH3) for incorporation into organic nitrogen-containing molecules is ______________________________.

nitrogen fixation

What role does Acidithiobacillus ferrooxidans play in the copper leaching process? A. oxidation of sulfide to sulfate B. reduction of sulfate to sulfide C. reduction of oxidized iron (Fe3+) to reduced iron (Fe2+) D. oxidation of reduced iron (Fe2+) to oxidized iron (Fe3+)

oxidation of reduced iron (Fe2+) to oxidized iron (Fe3+)

Which of the following is the first, or initiator, reaction in acid mine drainage and leaching? A. microbial sulfate reduction B. oxidation of reduced sulfides to sulfate and the release of reduced iron (Fe2+) C. rapid spontaneous reduction of oxidized iron (Fe3+) D. rapid oxidation of sulfides to sulfate by oxidized iron (Fe3+)

oxidation of reduced sulfides to sulfate and the release of reduced iron (Fe2+)

Nitrification and anammox both A. oxidize ammonia, but nitrification uses O2 as an electron acceptor and anammox uses NO2-. B. create nitrogen gas, but nitrification is aerobic while anammox is anaerobic. C. are aerobic processes, but nitrification produces NO3- and annamox produces N2 gas. D. occur in soils at neutral pH.

oxidize ammonia, but nitrification uses O2 as an electron acceptor and anammox uses NO2-.

Epsilonproteobacteria are most dominant in hydrothermal vents because they A. reduce nitrogen. B. bind divalent cations. C. oxidize sulfide and sulfur as electron donors. D. use oxygen as electron acceptors.

oxidize sulfide and sulfur as electron donors.

Enzymes that incorporate oxygen into compounds are called __________. A. hydrolase B. oxygenases C. hydrogenases D. dehydrogenases

oxygenases

You want to know whether the virulence genes present in Bordetella pertussis are evolutionarily related to genes in the less pathogenic species B. bronchiseptica or if the virulence genes were acquired via horizontal gene transfer. What characteristic(s) would you compare to answer this question?

percentage of GC content and codon usage

Which of the following can be completely degraded to carbon dioxide by microorganisms? A. petroleum B. uranium C. petroleum and chlorinated organics D. chlorinated organics

petroleum and chlorinated organics

Genes that retain their function yet change over evolutionary time as organisms diverge are called orthologs. Organisms with identical or very similar orthologous genes belong to the same __________. A. ribotype B. genotype C. phenotype D. phylotype

phylotype

Thirty organisms containing the same phylogenetic marker, with identical or similar orthologous genes, are all considered to be within the same A. phylogenetic tree. B. phylotype. C. functional group. D. species.

phylotype.

The F (fertility) plasmid contains a set of genes that encode for the ________ proteins that are essential in conjugative transfer of DNA.

pili

Based on its function, which type(s) of viruses likely contain(s) a gene encoding for RNA replicase?

positive and negative ssRNA viruses

Polyproteins made from human viruses such as poliovirus must be ________ in order to yield the required functional units of the virus.

post-translationally cleaved

Nitrous oxide (N2O) is a A. direct product of ammonification. B. potent greenhouse gas that is a product of denitrification. C. direct product ofnitrogen fixation. D. potent greenhouse gas that is a product of nitrification.

potent greenhouse gas that is a product of denitrification.

Deep sea ocean ecosystems in the region of hydrothermal vents typically have much higher biomass with greater presence of larger eukaryotic organisms than other deep sea ecosystems. Which of the following is most responsible for this difference? A. presence of substantial amounts of highly reduced inorganic compounds and methane B. greater O2 content in regions around hydrothermal vents C. temperature differences D. pressure differences E. much greater numbers of photosynthetic organisms

presence of substantial amounts of highly reduced inorganic compounds and methane

The pan genome of a species is the genomic content that is

present in one or more strains of the same species.

Deep sea organisms live in habitats that are characterized by high ____________ and low ___________________.

pressures, temperatures

Using a host defective in proteases is likely to be necessary when

producing a small protein.

Opportunistic pathogens such as Legionella, Pseudomonas, and Mycobacterium species have the ability to grow within ________, which may enhance their ability to survive in water distribution systems. A. human saliva B. protists C. UV irradiated water D. fish

protists

Staining methods are suitable for obtaining A. quantitative information from natural samples. B. information about physiology from natural samples. C. phylogenetic information from natural samples. D. neither qualitative nor quantitative information from natural samples.

quantitative information from natural samples.

Mobile DNA elements are more common in the genomes of

rapidly evolving species.

The CRISPR system

recognizes foreign DNA sequences that have previously entered the cell and directs the Cas proteins to destroy them.

In photosynthesis, NADH and NADPH are produced from NAD + and NADP+ by A. reduction reactions. B. oxidation reactions. C. both oxidation and reduction reactions. D. neither oxidation nor reduction reactions.

reduction reactions.

As a microbiologist, you have been asked to advise a town council on the possible ways to remove PCB contaminants from the local groundwater. Which microbial process is most likely to have bioremediation potential in this case? A. containment and stabilization B. reductive dechlorination C. aerobic dechlorination D. leaching

reductive dechlorination

Ecologically, which transformation is most important in degrading chlorinated xenobiotics? A. dechlorination B. oxidative chlorination C. reductive dechlorination D. chlorination

reductive dechlorination

A(n) ________ gene is a gene that encodes a protein that is easy to detect and assay.

reporter

An engineer working for the Peace Corps is helping a small town in Africa design a drinking water purification system. The raw water supply from the nearby river has high levels of suspended solids, dissolved organic carbon, and bacterial load. What would be the most effective order for the water treatment processes? A. sedimentation, disinfection, coagulation, filtration B. disinfection, sedimentation, coagulation, filtration C. sedimentation, coagulation, filtration, disinfection D. filtration, coagulation, sedimentation, disinfection

sedimentation, coagulation, filtration, disinfection

Enrichment cultures are often effective for isolating bacteria from complex communities in natural samples because they __________. A. select both for and against certain bacteria B. select against certain bacteria C. select for certain bacteria D. do not select for or against any bacteria; they help every organism to grow

select both for and against certain bacteria

Evolution is driven by

selection pressure applied to random mutation.

The overall purpose of DGGE is to A. separate genes of the same length that have different sequences, resulting in different denaturation profiles. B. separate genes that differ in length. C. measure the activity of cells that use DGGE as an energy source. D. detect cells that utilize a specific radiolabeled substrate.

separate genes of the same length that have different sequences, resulting in different denaturation profiles.

Consider a mutation in which the change is from UAC to UAU. Both codons specify the amino acid tyrosine. Which type of point mutation is this?

silent mutation

The number of Roseobacter in the ocean describes A. species prevalence. B. species richness. C. species abundance. D. species diversity.

species abundance.

Proteins made by a ribosome reading through the stop codon of a transcript without their own discrete ribosome binding sites

suggest a relatively low level of protein product is essential for the virus due to the rare frequency of these events.

Which group of organisms is thought to be responsible for the corrosion of submerged metal structures and pipelines? A. hydrocarbon-degrading anaerobes B. acidophilic iron-oxidizers C. sulfate reducers D. fermentative microorganisms

sulfate reducers

H2S that these newly described organisms use is at the highest concentration in anoxic marine habitats because ____________________________ produce it as an end product of anaerobic respiration, oxidizing H2 or small organic compounds with sulfate as the terminal electron acceptor.

sulfate-reducing bacteria

metabolic processes of anoxic environments

sulfate-reduction; meghan-genesis; iron reduction

The oxic atmosphere created conditions that led to the evolution of various new metabolic pathways, such as

sulfide oxidation, nitrification, and iron oxidation

Which metabolic strategy is most common in chemolithotrophic mats? A. nitrate reduction B. ammonia oxidation C. sulfur oxidation D. iron oxidation

sulfur oxidation

In "crown corrosion," hydrogen sulfide can also be oxidized to ____________________________, which reacts with free lime in the concrete to corrode concrete sewer pipes.

sulfuric acid

Based on your knowledge of hydrocarbon degradation, what factors most likely limited the rate of petroleum degradation after the Exxon Valdez oil spill off the coast of Alaska? A. temperature and inorganic nutrient concentrations B. salt concentration C. temperature D. inorganic nutrient concentrations

temperature and inorganic nutrient concentrations

Industrial production of nitrogenous fertilizers from N2 now equals or exceeds the amount of nitrogen fixation carried out by microbes in the biosphere. The resulting increase in primary production is an example of the fact that __________. A. the C and N cycles are closely coupled B. synthetic fertilizers work better than natural N sources for primary production C. N is generally not a limiting nutrient for primary production D. there is a fixed quantity of N on Earth

the C and N cycles are closely coupled

One important difference between the C, N, and S cycles and the P, Ca, and Si cycles is that A. the P, Ca, and Si cycles do NOT involve microbial activity. B. P, Ca, and Si are NOT cycled in terrestrial environments. C. the P, Ca, and Si cycles are NOT affected by global warming or other human activity. D. the P, Ca, and Si cycles do NOT involve redox changes or gaseous forms that can alter Earths atmospheric chemistry.

the P, Ca, and Si cycles do NOT involve redox changes or gaseous forms that can alter Earths atmospheric chemistry.

Microbial leaching of valuable metals from low-concentration ores is carried out in open-air leaching dumps for copper recovery, but in closed bioreactors for gold recovery because __________. A. the bioreactor prevents release of toxic waste products from gold-containing ores B. the bioreactor prevents the loss of any valuable gold C. more oxygen is required for copper leaching D. the microbes used for gold leaching are obligate anaerobes

the bioreactor prevents release of toxic waste products from gold-containing ores

What was the LUCA?

the last organism prior to the divergence of bacteria and archaea

Microorganisms were probably restricted to the oceans and subsurface environments until

the ozone layer was made.

Microbes that thrive in acidic environments seem to have "cost free" ATP energy available to them due to the pre-existing H+ gradient across the cytoplasmic membrane. However, this is not entirely true because __________. A. the protons entering the cell must be consumed to prevent the cytoplasm from becoming too acidic; therefore electrons are required as H+ are combined with O2 to form water B. the protons from the acidic environment cannot be used for ATP production because they did not come from the inside of the cell C. the protons would have to be pumped back out of the cell as fast as they came in through the ATPase, so as to avoid acidifying the cytoplasm. Therefore, no net energy would be captured D. it requires energy to pump the protons into the cell to form the ATP

the protons entering the cell must be consumed to prevent the cytoplasm from becoming too acidic; therefore electrons are required as H+ are combined with O2 to form water

metabolomics

the study of all intermediates and small molecules produced by reactions within an organism

transcriptomics

the study of all of the RNA produced by an organism

In the soil, oxygen concentrations are highly variable even within a soil particle. The center of the particle may be anoxic even if the outer portions are oxygen rich. In this context, facultative anaerobes could be found A. in the center of the particle. B. throughout the particle. C. in the middle regions of the particle. D. at the surface of the particle.

throughout the particle.

For what purpose would a microbial ecologist use a microsensor? A. to quantify the uptake of a radioactive material B. to determine the expression of a particular gene in a microbial community C. to determine the concentration of cells in small increments in a sediment or water column D. to determine the concentration of O2, N2O, or other chemical species in small increments in a sediment or water column

to determine the concentration of O2, N2O, or other chemical species in small increments in a sediment or water column

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

Which of the following is NOT a role of carotenoids? A. to produce singlet oxygen B. photoprotection C. to quench toxic oxygen species D. as accessory pigments

to produce singlet oxygen

RNA-Seq analysis is a method aimed at defining a(n)

transcriptome.

Special pair is the name given to the ________ in the photochemical complex of the purple bacteria. A. two quinones B. two reaction centers C. two bacteriochlorophyll b molecules D. two bacteriochlorophyll a molecules

two bacteriochlorophyll a molecules

Compared with pure cultures grown in the lab, microbes in nature usually experience a wider range of environmental conditions, more variation in conditions over time, and more contact with other organisms. Therefore, the same organism in nature will __________. A. typically grow slower than in pure culture B. typically grow faster than in pure culture C. typically grow only on surfaces D. carry out completely different metabolisms than in pure culture

typically grow slower than in pure culture

Single-cell genomics may help us A. predict which microbes will be abundant based on the environmental conditions. B. understand the physiology of uncultured microbes. C. develop better enrichment culture methods. D. understand the physiology of uncultured microbes and develop better enrichment culture methods.

understand the physiology of uncultured microbes and develop better enrichment culture methods.

Radioisotopes are useful when A. very high sensitivity is required. B. the fate of portions of particular molecules need to be followed. C. turnover rates need to be determined. D. very high sensitivity is required, turnover rates need to be determined, and the fate of portions of particular molecules need to be followed.

very high sensitivity is required, turnover rates need to be determined, and the fate of portions of particular molecules need to be followed.

A surprising finding of environmental metagenomic studies is that a majority of genes in the environment are

viral in origin

Chromosomal islands contain clusters of genes for

virulence, biodegradation of pollutants, and symbiotic relationships.

When DNA is transferred into a prokaryotic cell it may

be degraded by enzymes, replicate independent of the host chromosome, or recombine with the host chromosome.

What products would be expected to form during anoxic degradation of the seven-carbon compound benzoate following reduction and cleavage of the aromatic ring? A. 1 three-carbon compound and 1 four-carbon compound B. 1 three-carbon compound and 2 two-carbon compounds C. 2 three-carbon compounds and CO2 D. 3 two-carbon compounds and CO2

1 three-carbon compound and 2 two-carbon compounds

Typically ________ of ORFs in a genome cannot clearly be assigned a function. These ORFs are usually assigned and predicted to encode hypothetical proteins.

30%

Assuming exposure to the same climate, which of the following aquatic systems would be most stratified? A. 300 m deep freshwater lake B. 20 m deep freshwater river C. 50 m deep marine water fjord D. 200 m deep saltwater lake

300 m deep freshwater lake

After analysis of a phototrophic microbe from a local pond, sulfur granules, bacteriochlorophyll a, and quinones were detected. What sort of microbe is this? How would it most likely generate ATP and NADH when growing phototrophically?

A phototrophic microbe is capable of performing photosynthesis, but with the presence of sulfur granules we can infer there is a use of sulfur within the system. Sulfur can be incorporated into anoxygenic photosynthetic organisms derivation of energy as sulfur replaces the splitting of water, which generates electrons, as an electron donor. The purple sulfur bacteria is one type of bacteria which is capable of this anoxygenic photosynthesis. The presence of bacteriochlorophyll-a confirms the presence of photosynthetic pigments. Quinones are electron carriers which aid in respiration of microbes. Therefore, this organism would most likely generate ATP and NADH anaerobically through anoxygenic photosynthesis. (The presence of the structures indicated that this organism uses H2S for respiration and is most consistent with a purple anoxygenic phototroph. One example is Oscillatoria limnetica. These organisms generate a proton motive force via a cyclic photorespiratory electron transport system. This can be used to produce chemical energy with a membrane ATPase. The reduced quinones in this respiratory chain are not able to form NADH directly. Therefore, reverse electron transport is used by coupling proton reentry to the reduction of the cofactor.)

Compare and contrast denitrification and the anammox reaction. Where in the environment are these reactions most important? Why are these reactions important to society?

Anammox reactions involve the oxidation of ammonia through the use of nitrite as an electron acceptor in order to produce nitrogen gas within anoxic environments. Denitrification reactions involve nitrate as an electron acceptor in order to produce N2, N2O, and NO within oxygenic environments. These reactions are essential in order to remove fixed nitrogen within aqueous environments. Furthermore, in certain environments the continuous denitrification may cause a shortage of nitrite.

What will happen to a cyanobacterium that has its photosystem II (PSII) blocked? A. Anoxygenic photosynthesis only using photosystem I (PSI) could occur by using cyclic photophosphorylation and an alternative electron donor such as H2S. B. Photons will generate excessive reactive oxygen species and the cyanobacterium will die as a consequence. C. It will die from being unable to obtain energy for photosynthesis. D. Additional electron acceptors, such as NADP+, will be required to oxidize oxygen and overcome the lost PSII process.

Anoxygenic photosynthesis only using photosystem I (PSI) could occur by using cyclic photophosphorylation and an alternative electron donor such as H2S.

Which of the following hypotheses could be tested using microautoradiography fluorescence in situ hybridization (MAR-FISH)? A. Archaea are the main autotrophs in marine water samples taken 300 m below the surface of the ocean. B. The ammonia monooxygenase gene is present in members of the phylum Verrucomicrobium. C. Bacteriorodopsin uses light energy to translocate protons. D. The microbial community of agricultural soils is more phylogenetically diverse than the microbial community of native prairie soils.

Archaea are the main autotrophs in marine water samples taken 300 m below the surface of the ocean.

Steps between Soluble Fe2+ and Mn2+ and Soluble Fe2+ and Mn2+

Diffusion from anoxic to toxic region Oxidation of soluble forms Metal oxides and hydroxides precipitate Oxidized metals return to sediments Bacteria use oxidized metals as electron acceptors

How could overlapping genes in a positive ssDNA virus genome be predicted?

Directly search the three frames of the positive ssDNA for genes that have sequences where more than one gene is predicted.

In order to replicate its genome, a positive-strand RNA virus must produce a complete negative-strand RNA molecule that serves as the template for protein synthesis. True False

False

Methanogens, among other compounds, use alcohols and fatty acids to synthesize methane gas in anoxic environments. True False

False

Phototrophic organisms in SIP experiments are often observed releasing 14CO2 as a way of measuring photosynthetic activity. True False

False

Reductive dechlorination involves chlorinated organic compounds serving as electron donors and releasing the chloride in inorganic forms. True False

False

Examples of Aquatic; acidic

Ferroplasma (a type of Archaean that is aerobic and can oxidize iron)

Two tubes are inoculated from the same tube containing a bacterial culture. The cultures are then transferred every day for 2 months. All of the media and growth conditions are the same in every tube. After 2 months of cultivation, the fitness and genotype frequencies of the populations in the two tubes are compared. The fitness of the two cultures is the same, but the genotype frequencies are very different in the two cultures. How is this possible?

Genetic drift within the small populations in the test tubes resulted in different genotype frequencies.

Some mercury-resistant bacteria can convert toxic forms of mercury to less toxic forms using the mer operon under transcriptional regulation the merR protein. What molecule would you predict binds to merR to cause it to act as a repressor or as an activator of transcription for this operon? A. NADH B. Hg2+ C. H0 D. MerP periplasmic binding protein

Hg2+

Based on the table of average intron frequency given below, predict the relative order of genome size for these four eukaryotic organisms. Organism Average Intron Frequency Cryptosporidium parvum 0 Plasmodium falciparum 1 Arabidopsis thaliana 5 Homo sapiens 8

Homo sapiens > Arabidopsis thaliana > Plasmodium falciparum > Cryptosporidium parvum

What is the major reservoir of stable nitrogen? A. N2 B. NH4 C. NO D. NO3-

N2

Microbes have important effects on their environment. For example, the microbes used in AST are important in oxidizing ammonia to nitrite and then reducing nitrite to nitrogen gas. This reduces the nitrogen content of the water that could otherwise stimulate unwanted microbial growth. Other microbes have different effects on their environment and understanding these is important to protecting human structures as well as using bacteria for processes such as AST. During conventional wastewater treatment, bacteria are also used to reduce the amount of organic and inorganic materials so that the water no longer supports substantial microbial growth. During secondary wastewater treatment, bacteria within sludge digesters break down organic materials into fatty acids H2 and CO2. These products are fermented to acetate, CO2 and H2. Finally, archaeans ferment acetate to form methane and carbon dioxide. Just by knowing this information, what is true of the bacteria used in sludge digesters? A. Some are methanogens. B. They are capable of anaerobic metabolism. C. They are capable of forming slime layers. D. They are sulfate-reducing bacteria.

Some are methanogens. They are capable of anaerobic metabolism.

Why are some xenobiotics biodegraded slower than crude oil and petroleum products? A. Only cometabolic microbial processes degrade xenobiotics. B. Xenobiotics were designed to inhibit microbial growth. C. Chlorinated compounds are so toxic that biodegradation is not possible. D. Some xenobiotics are novel compounds that differ from naturally occurring chemicals, thus microorganisms have not yet evolved to effectively degrade them.

Some xenobiotics are novel compounds that differ from naturally occurring chemicals, thus microorganisms have not yet evolved to effectively degrade them.

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 at relatively high temperatures.

What metabolic advantage do cells have in storing the elemental sulfur byproduct from sulfide oxidation? A. The byproduct can be used for other biosynthetic pathways that use sulfur, such as Rieske Fe-S proteins. B. The cells avoid producing transport energy waste to secrete the sulfur. C. Sulfur decreases the intracellular acidification for non-acid-tolerant sulfide oxidizers. D. The byproduct serves as an electron reserve for subsequent oxidation.

The byproduct serves as an electron reserve for subsequent oxidation.

During conjugation, if an Hfr cell is mated with an F- cell, why will the F- cell remain F-?

The cells would not stay in contact long enough for the entire Hfr genome to be transferred.

Photooxidation reactions can lead to the production of toxic forms of oxygen and the destruction of the photosynthetic apparatus. True False

True

For living cells and for some viruses, genome replication is semiconservative. However, some viruses use rolling circle replication to generate new copies of their genomes. If replication occurs in the presence of radioactive nucleotides, you can distinguish the old strands (not radioactive) from the new strands (radioactive). Which pattern would you expect to see after several rounds of DNA genome replication using rolling circle replication?

The new DNA molecules would contain only radioactive nucleotides; the old DNA strand used as a template would have no radioactive nucleotides, but its complimentary strand would now be radioactive.

If the biochemical oxygen demand (BOD) of a lake is very high, how will that affect the aquatic life in the lake? A. There will be less oxygen available for the aquatic life due to the microbial activity. B. The BOD does not have an impact on available oxygen in the lake. C. There will be more oxygen available for the aquatic life but much less oxygen available to the microbial populations. D. There will be more oxygen available for the aquatic life due to the microbial activity.

There will be less oxygen available for the aquatic life due to the microbial activity.

In a culture of bacteria, there are some individuals that are unable to synthesize histidine. What is the best and most likely description of how these individuals differ from the other bacteria in the culture?

They differ in their genotype and in their phenotype.

Many viruses that infect humans may illicit a strong immune response causing additional harmful effects, so the discovery of a virus that can induce an immune response without causing harm made it attractive for vaccine development. True False

True

A monooxygenase can always be distinguished from a dioxygenase by incorporating only one oxygen atom from O2 into the substrate rather than both. True False

True

Abiotic oxidation of Fe2+ requires oxygen and occurs rapidly when the pH is near 7. True False

True

Bacteria that degrade aromatic compounds with reductions steps rather than oxygenase activity prior to ring fission are likely to be anaerobes. True False

True

Beta-oxidation exclusively removes two carbons at a time to catabolize fatty acids regardless of the carbon chain length. True False

True

Chemolithotrophs that obtain electrons from donors such as sulfide use the same electron transport chains to obtain energy as chemoorganotrophs. True False

True

A chemical that comes from outside the ecosystem is referred to as a(n) ________ chemical. A. lithotrophic B. pleomorphic C. synthropic D. allochthonous

allochthonous

Phylogenetic trees for bacteria are constructed by which of the following?

analyzing molecular similarities and then using computer algorithms or optimality criteria to construct phylogenetic trees showing hypothesized evolutionary relationships

Which group of microorganisms would the Calvin cycle LEAST likely be found in? A. chemolithotrophic Bacteria B. cyanobacteria C. purple Bacteria D. anoxygenic Chloroflexus

anoxygenic Chloroflexus

When two different influenza viruses infect the same cell, their segmented genomes can undergo reassortment which will result in

antigenic shift.

Lignin is a complex polymer of methoxylated ________ compounds and is present in ________. A. oil / fossil fuels B. aromatic / vascular plant material C. mineral / rocks D. silica / aquatic environments

aromatic / vascular plant material

Sulfide is toxic to respiring organisms, because it can combine with metals present in ________ that serve a critical function in respiration. A. glycolysis enzymes B. oxidases C. NADH D. cytochromes

cytochromes

In designing a drug to inhibit poxvirus, the compound should localize in the hosts ________ to be most effective.

cytoplasm

Sarah has cloned a gene that codes for the protein EN. EN breaks down cellulose. She wants to collect a large concentration of this protein for research. Which vector should she choose for best results?

expression vector

The earliest photosynthetic microbes, before the cyanobacterial lineage developed, oxidized substances other than water. What was produced by these microbes instead of oxygen?

elemental sulfur

In an agar dilution tube, microbial colonies grow A. on the surface, but some creep down the sides away from the surface. B. at the bottom of the tube. C. embedded in the agar, rather than growing on the surface. D. on the sides of the tube, although some may be at the surface.

embedded in the agar, rather than growing on the surface.

Bacteria used to help break down fiber and cellulose in anaerobic environments are found in __________________________________________________.

enclosed waste water tanks

When compared with Bacteria, species of Archaea seem to devote a higher percentage of their genomes to genes encoding proteins involved in

energy and coenzyme production.

Environmental damage due to acid mine drainage occurs only once ores containing pyrite (FeS2) are __________. A. reduced from Fe3+ to Fe2+ oxidation states B. increased in temperature to at least 50 degrees C. C. mixed with other toxic metals like lead and cadmium D. exposed to oxygen and water

exposed to oxygen and water

Arrange the following genetic components in the correct order.

genome, transcriptome, proteome, metabolome

What characteristics make a gene a good candidate for determining the evolutionary relationships between organisms?

highly conserved and universally distributed

Genes from different sources that are related in sequence due to shared evolutionary ancestry are called ________ genes, and groups of such genes are known as ________.

homologous / gene families

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 __________. A. is highly conserved over evolutionary time B. has more genes than mRNA C. is easier to extract from samples D. is made by cells only at certain times

is highly conserved over evolutionary time

Just by knowing that a bacterium is a autotroph, it is possible to predict that its genome_____________ than those of average heterotrophs.

is larger than

Just by knowing that N. equitans is a parasite, it is possible to predict that its genome _____________ than those of most other hyperthermophiles.

is smaller than

The metabolic diversity of photosynthetic bacteria stems from different A. chlorophylls they can have and organic compounds they can produce. B. unrelated taxa capable of photosynthesis. C. light-harvesting complexes, electron donors, and organic compounds they produce. D. bacteriochlorophylls and pigments they contain.

light-harvesting complexes, electron donors, and organic compounds they produce.

Based on comparative studies of agricultural soils or polluted soils compared with undisturbed soils, disturbance of soil microbial communities tends to lead to __________. A. no change in microbial community composition B. lower prokaryotic diversity C. greater microbial metabolic activity D. higher microbial abundance

lower prokaryotic diversity

Carbon dioxide and methane are potent greenhouse gases, with methane having 20 times more warming potential in the atmosphere than CO2. As global warming progresses, there is the real possibility that increased temperatures on land and in the oceans will lead to a positive feedback effect leading to accelerated warming. From the carbon reservoirs listed below with their percentage of the total carbon on Earth, what would be the most dangerous potential source of C that could be released to potentiate further warming? A. oceans and terrestrial biosphere (0.053%) B. methane hydrates (0.014%) C. fossil fuels (0.006%) D. rocks and sediments (99.5%)

methane hydrates (0.014%)

You have performed the following mating experiment using Hfr and F-strains of Escherichia coli: Hfr (thr+ leu+ gal+ strs) × F- (thr- leu- gal- strr). Which of the following selective media would you use to score recombinant colonies?

minimal medium + streptomycin

Which technique would be used to estimate the concentration of naturally occurring Escherichia coli in a wastewater sample? A. laser tweezers method B. most probable number (MPN) method C. agar dilution tube method D. cell tagging using GFP method

most probable number (MPN) method

Deep sea sediments are typically ___________________, having very low nutrient availability.

oligotrophic

To estimate the total concentration of a beneficial bacterial species in yogurt, ________ would provide the quickest results.

qPCR

Phylogenetic stains, such as those used in phylogenetic FISH, hybridize with A. ribosomal RNA. B. mitochondrial DNA. C. nuclear DNA. D. RNA polymerase.

ribosomal RNA.

Biomass generation due to heterotrophic organisms is called ________ production. A. regulatory B. secondary C. auxotrophic D. primary

secondary

What would the result be when a soil is supplemented with S0? A. syntrophic utilization of sulfite B. organic carbon production due to anaerobes C. dimethyl sulfide production due to mixotrophs D. soil acidification due to chemolithotrophs

soil acidification due to chemolithotrophs

You would like to test the hypothesis that ammonia-oxidizing Archaea are more active and abundant than ammonia-oxidizing Bacteria in coastal marine water. What technique(s) or experiment(s) could you use to test this hypothesis? A. stable isotope probing using 15N labeled ammonia B. fluorescent in situ hybridization (FISH) C. stable isotope ratios of ammonia and nitrite D. environmental proteomics

stable isotope probing using 15N labeled ammonia

Recognizing pathogens that contain multiple unique proteins which enable the human immune system to recognize just one and mount an effective response has opened the door on development of some vaccines only being

subunit vaccines.

proteomics

the study of all of the proteins produced by an organism

genomics

the study of the entire genetic makeup of an organism