314 Homework Questions

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

contains at least one polyprotein.

The aerated upper layer of soil is likely to have ________ concentrations of H2 for aerobic H2-oxidizing Bacteria, so these bacteria likely ________.

low / will need a chemoorganotrophic way to grow as well

In a natural population of diverse slow-growing prokaryotic cells, what type of viruses would you expect to be most common?

lytic bacteriophages

Which of the following enzymes would you expect to find in the virion of a retrovirus, but NOT in a bacteriophage?

reverse transcriptase

Horizontal gene transfer has been thoroughly documented for genes involved in

virulence and metabolic functions.

The genome sequence of an organism can provide information about the organism's __________.

genes, function, and evolutionary history

Arrange the following genetic components in the correct order.

genome, transcriptome, proteome, metabolome

Ferrous iron (Fe2+) oxidation generally occurs in environments with

high H+ concentrations

Benefits of transgenic plants include __________.

insect resistance

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

introns

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 advantage(s) of second-generation DNA sequencing compared to the Sanger method are the result of

miniaturization of reaction size and increased computer power.

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

Metabolomics

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

confers resistance to infection by viruses of the same type.

The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.

false

Which of those listed below is LEAST similar in what is being studied and concluded?

fluorescence in situ hybridization

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

post-translationally cleaved

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.

Obligate anaerobes can often use ________ electropositive redox couples than facultative anaerobes, and ________ metabolism is most common in this group as well.

lower / assimilative

Sequencing an organism's genome often leads to identification of hypothetical proteins, which are characterized as __________.

proteins that likely exist though their function is unknown

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

reporter

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

reporter genes.

The genome of retroviruses contains genes to make all of the following EXCEPT

repressor proteins.

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

phenotype

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

______________ use organic carbon as their carbon source

Heterotrophs

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.

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

frameshift mutation

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

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

false

Horizontal gene transfer in Archaea

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

Integration of Mu DNA into the host genome is essential for

both lytic and lysogenic growth.

Whether an organism is classified as a photoheterotroph or a photoautotroph depends on its

carbon source

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

cassette mutagenesis

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

chromosome, phage, or plasmid.

All of the following can act as receptors for various bacteriophages EXCEPT

cilia

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.

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

What two gases were most abundant on early Earth?

CO2 and H2

A drug designed to inhibit reverse transcriptase activity would target

retroviruses

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

Mu

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

a yeast cell

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.

When determining the number of virus particles in a suspension, why is the number obtained always less than the actual viral titer?

because all of the virus particles do not infect with 100% efficiency

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

before the entire T7 genome enters the cell.

What products would be expected to form during anoxic degradation of the seven-carbon compound benzoate following reduction and cleavage of the aromatic ring?

1 three-carbon compound and 2 two-carbon compounds

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

Within Archaea and Bacteria, one megabase pair (Mbp) of DNA encodes about ________ open reading frames.

1,000

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.

Horizontal gene transfer

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

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

_____________ is performed by obligate anaerobes that use H2 as the major electron donor; both ion pumps and substrate level phosphorylation are used to conserve energy.

Acetogenesis

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?

As terminal electron acceptors for anaerobic respiration

_______________ perform CO2 fixation and utilize CO2 as their sole carbon source

Autorophs

The introductory passage gives information about the structure and function of the Zika virus. Based on this information, what is the Baltimore class of the Zika virus?

Baltimore class IV

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).

The introductory passage describes the identification of eukaryotic signature genes in Lokiarchaeota, explaining that these suggest that bacteria were acquired by archaeal cells to give rise to the Eukarya. Prior to this event, a series of events needed to take place in order for life to arise on Earth. Put the events below into the correct order to summarize the hypothesized path from prebiotic chemistry to evolutionary diversification, beginning with the earliest event.

Biological building blocks (amino acids, nucleosides, and sugars) appeared. Self-replicating and catalytic RNA developed (the "RNA world"). Protein synthesis and protein enzymes appeared. DNA genomes developed, along with the processes of DNA replication and transcription. Lipid bilayers surrounded the earliest cells and allowed the formation of cellular compartments. Bacteria and Archaea diverged. Archaea and Eukarya diverged.

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

evolution

Alternative autotrophic routes to the Calvin cycle such as the reverse citric acid cycle and the hydroxypropionate pathway are unified in their requirement for

CO2.

_________________ use inorganic electron donors and CO2 as a carbon source

Chemolithotrophs

______________ use inorganic or organic chemicals as energy sources

Chemotrophs

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.

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.

False

Retroviruses become proviruses integrated into the host chromosome soon after infecting the host cell, and can remain there indefinitely. The provirus DNA can then be transcribed and translated by the host cell, making new retroviral RNA genomes, enzymes, and structural proteins. New retroviral virions can then assemble and bud through the host cell membrane continuously over long periods of time. What is one implication of this retroviral life cycle?

It is difficult to completely cure an animal host of the virus, since anti-retroviral drugs will only eliminate circulating virions, not proviruses.

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.

Based on your understanding of the chapter material and the information in the passage, which of the following best defines something as a virus? Are virophages a type of virus or something different?

It must have a capsid and a nucleic acid, which can be double-stranded or single-stranded, circular or linear, and DNA or RNA. Virophages are therefore a type of virus.

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.

ANME and other organisms can be methanogens or methylotrophs, depending on how they use carbon compounds. Which term best describes each of the choices below?

Methanogens: can use CO2, methyl compounds, or acetate as a substrate, produces CH4, can be autotrophs, are anaerobic archaea. Methylotrophs: includes the methanotrophs, which catabolize methane, includes the ANME, can be anaerobic or aerobic.

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

What is a specific advantage of using small subunit ribosomal RNA (SSU rRNA) gene sequences for phylogenetic analysis compared with DNA sequences?

Standard primers exist for SSU rRNA gene sequences, including universal primers.

What would be the consequence of deleting the late T4 genes?

T4 capsid proteins would not be made.

As described in the chapter, viruses vary greatly in their genetic material and structure. For example, the Zika virus is enveloped and has single-stranded RNA. One way of classifying viruses is using Baltimore classes. Based on the information in the passage and in the chapter, how could the researchers determine the Baltimore class of the Zika virus?

They could examine whether enzymes such as RNA replicase or reverse transcriptase were present. They could examine whether the virus had an RNA or a DNA genome. They could examine whether the genome was single stranded or double stranded.

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.

_____________ the study of all of the RNA produced by an organism.

Transcriptomics

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.

The SOS DNA repair system is __________.

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

A cell that lacks sulfite reductase but can still oxidize sulfur for energy could be identified by

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

Anammox is an anaerobic process that generates energy from ________ and forms N2.

ammonia and nitrite

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 of the following are the hosts for most enveloped viruses?

animals

Linking an ORF with a specific function is an example of gene

annotation

You are attempting to mutate lambda to affect whether lysis or lysogeny occurs after infection. Which mutation would INCREASE the chances of LYSOGENY over lysis?

deletion or inactivation of the cro gene

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.

Bacteriophages genomes are typically composed of

double-stranded DNA

______________ and ______________ viruses carry their own nucleic acid polymerases (called replicases) to replicate the viral genome with no DNA intermediate.

double-stranded RNA, single-stranded RNA

Gene duplication is essential to organisms because __________.

duplicate genes are more able to evolve into new genes

The cells used as hosts for cloning vectors are __________.

easy to grow and transform with engineered DNA

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.

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

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

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

_____________ viruses have replication that involves first generating a complementary DNA strand.

single-stranded DNA

_______________ viruses have genome configuration that are either plus-sense or minus-sense.

single-stranded RNA

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.

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.

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

sulfide oxidation, nitrification, and iron oxidation.

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

The most abundant genes in prokaryotic genomes are

those involved in metabolism

The introductory passage describes the way in which Vibrio cholerae bacteria obtain genes from their prey. Based on the information in the introductory passage and in the chapter, what type of gene transfer is this?

transformation

The early energy reactions used hydrogen, which is a powerful

electron donor.

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.

Redox reactions (involving electron transfer) are important to understand, but some types are commonly confused. In particular, the terms "fermentation" and "anaerobic respiration" may be used inappropriately or synonymously despite important distinctions. Drag each characteristic into the appropriate bin to indicate which metabolic process it best describes.

Aerobic H2 oxidation: often occurs most efficiently in a microaerophilic environment, often involves the hydrogenase enzyme. Fermentation: NADH produced during glycolysis donates an electron to an endogenous molecule (often organic) rather than to an electron transport chain. Anaerobic respiration: involves an electron transport chain with an exogenous terminal electron acceptor, such as CO2, SO42-, and S0, used in dissimilatory sulfate reduction. Direct electron transfer through nanowires: involves the use of electrically conductive pili that connect cytochromes.

________________________ is performed by Archaea and Bacteria and produces nitrite; Bacteria may oxidize the nitrite and nitrate.

Aerobic ammonia oxidation

Why would it be highly advantageous to a cell to form a mutualism (and eventually an endosymbiotic association) with a prokaryote capable of aerobic cellular respiration?

Aerobic cellular respiration involves an electron transport chain with oxygen as the terminal electron acceptor. This produces large amounts of ATP as the electron transport chain produces the greatest amount of ATP in cellular respiration.

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.

The introductory passage discusses how researchers learned more about the relationships between Bacteria, Archaea, and Eukarya from studying the new Archaeal phylum Lokiarchaeota.

All of these domains evolved from a shared ancestor known as LUCA.

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

Alphaproteobacteria.

What will happen to a cyanobacterium that has its photosystem II (PSII) blocked?

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 describes a polyprotein, such as the Zika virus?

An HIV virus produces a large protein that contains multiple structure proteins and a protease.

The introductory passage discusses the way that virophages interfere with the ability of megaviruses to reproduce and the possible selective benefits of this. However, there are many ways that cells attempt to survive attacks by viruses. According to the chapter, what is another way that cells have evolved to avoid viral infection?

An attachment receptor on the host cell surface that is recognized by the virus is mutated.

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?

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

_____________________ is performed by Archaea, often in sewage and in freshwater sediments; CO2 if often reduced using H2.

Anaerobic oxidation of methane (AOM)

Which objective would be best to use a Southern blot rather than a Northern blot?

Determine if a gene is present in a genome.

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.

_____________ viruses have processes of replication, transcription, and translation that are the most similar to those used by cells.

Double-stranded DNA

__________________ is the genetic material of virophages

Double-stranded DNA

T4 genes are transcribed by host RNA polymerase, yet this transcription is carefully controlled so that groups of T4 genes are transcribed in a specific order after infection. How is this accomplished?

Early and middle T4 genes encode for RNA polymerase-modifying proteins so that only phage promoters are recognized.

During infection, viruses such as the Zika virus produce proteins that can be described as early proteins or late proteins. Sort the choices below based on whether they are produced early or late in a viral infection.

Early proteins: RNA replicase, RNA polymerase, DNA polymerase, proteins that interfere with host gene expression, proteins produced in small amounts. Late proteins: capsid components, virion structural components, proteins produced in large amounts.

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.

Some viruses, especially animal viruses, have an envelope surrounding their nucleocapsid. This envelope may have viral proteins embedded in it. Why are the viral proteins more readily recognized and targeted by the immune system than the envelope?

Enveloped viruses are often coated with animal cell membrane as they leave the cell. This membrane is a major component of the viral envelope. The viral proteins are more readily recognized by the immune system, as they are more distinct from the materials normally found in and on the cells. However, the envelope can contain several types of viral components as well.

Based on the evolutionary tree shown below, RubisCO Form II and RLP beta are orthologs. RLP alpha | RLP beta Ancestral gene | | RLP ancestor | | | | | Duplicate gene | RubisCO Form II | | ____RubisCO ancestor RubisCO Form I | | RubisCO Duplicate | RubisCO Form III

False

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.

False

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

False

_________________ can be aerobic or anaerobic; only small amount of energy can be produced in acidic environments even though many of the organisms using this are acidophilic.

Ferrous iron oxidation.

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

GAATTC CTTAAG

Besides the method used by V. cholerae, other types of gene transfer exist. One important type is transduction, which can be generalized or specialized. Choose whether the following examples illustrate generalized transduction, specialized transduction, or neither.

Generalized transduction: any part of the host genome can be transferred, a relatively low percentage of cells exposed undergo transduction. Specialized transduction: it is not necessary for phages to be defective for transduction, transduced DNA is integrated into the host as part of a prophage, transduction must involve a temperate phage, only specific regions of DNA may be transduced. Both: it is accomplished by transducing particles, transduction may involve a virulent phage.

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.

____________ the study of the entire genetic makeup of an organism.

Genomics

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

____________________ a gene that is related in different species by being inherited from a common ancestor

Homologous

The introductory passage describes how Vibrio cholerae bacteria can take up genes from their prey through horizontal gene transfer. Based on the introductory passage and the material in the chapter, classify the following examples of gene transfer as horizontal gene transfer, vertical gene transfer, or neither.

Horizontal gene transfer: DNA from mature organism to mature organism, DNA from virus to mature organism, conjugation, transformation, transduction. Vertical gene transfer: DNA from parent to offspring, a gene shared by several species, inherited from a common ancestor. Neither: a gene that is different in two related species as a result of a mutated ancestral gene, transposition (by transposable elements).

As discussed above, one type of genetic analysis is multilocus sequence typing (MLST). Which of the following statements summarizes why housekeeping genes can be used in multilocus sequence typing (MLST)?

Housekeeping genes are less likely to be under environmental selection.

In studying Lokiarchaeota, researchers identified eukaryotic signature genes and used this information to better understand the relationship between archaeans and eukaryotes. Many other types of genetic analysis can be used that focus on certain types of genes. One example of this is multilocus sequence typing (MLST), which focuses on examining genes called housekeeping genes. Microbes encode both housekeeping and pathogenic genes in their genome. Drag the examples of genes to the correct bins to indicate whether they are housekeeping genes, pathogenic genes, or eukaryotic signature genes.

Housekeeping genes: membrane lipid genes, ribosomal genes, peptidoglycan synthesis genes. Pathogenic genes: endotoxin genes, exotoxin genes. Eukaryotic signature genes: membrane remodeling genes, cytoskeletal genes.

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?

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

Differentiate between persistent and latent animal virus infections.

In a persistent infection, the host cell is continually releasing new viral particles slowly. In a latent infection, there are periods of time where the virus is not replicating and creating new viral particles.

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.

Why does the structure of plant and bacterial cells illustrate the reason for having few enveloped viruses that infect these cells?

Plant and bacterial cells contain cell walls that limit the virus from budding out and obtaining the envelope.

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

Metagenomics

________________ the study of genetic material from an environmental sample.

Metagenomics

_____________ use inorganic compounds for energy and organic compounds as a carbon source

Mixotrophs

_____________ a group of organisms in a phylogeny that have a common ancestor.

Monophyletic

____________ involves the aerobic oxidation of ammonia or nitrite

Nitrification

____________ use light as an energy source and CO2 as a carbon source.

Phototrophs

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.

_______________ a gene that is related in different species by being inherited from a common ancestor and that has the same function.

Orthologs

__________ a gene that is related in different species by being inherited from a common ancestor and that has a different function (this occurs through gene duplication).

Paralogs

_____________ the study of all of the proteins produced by an organism.

Proteomics

A new virus with a similar genetic makeup to the Zika virus is found. Although the introductory passage does not describe the Zika virus life cycle in detail, it describes information about other viruses in the same Baltimore class. Based on your knowledge of other viral life cycles and the information provided in the introductory passage, which of the following do you think describes the Zika virus life cycle?

RNA replicase is used to replicate the RNA genome. The RNA genome may be transcribed directly. Polyproteins are cut by proteases to form functional products.

Viruses rely on the host cell machinery to make new viruses, but they sometimes provide their own enzymes (such as reverse transcriptase, which is an RNA-dependent DNA polymerase). Which of the following types of enzymes would a virus need to provide in order to replicate within a cell? In other words, which of these enzymes would not normally be found in a cell unless a virus provided it?

RNA replicases (RNA-dependent RNA polymerases) for RNA viruses

The Baltimore classification scheme is based on the relationship between the virus's genome and its mRNA, and the Zika virus can be classified in this way. For the following choices, indicate which viruses would fall into each classification: (1) require reverse transcriptase to copy the information in their own genome to DNA; (2) can replicate and be transcribed in the same manner as the cell's own genetic material; and (3) produce a replicative form of DNA to use for both replication and transcription.

Requires reverse transcriptase: retrovirus, double-stranded DNA viruses that have an RNA intermediate. Functions similarly to cell's own genetic material: double-stranded DNA viruses. Uses a replicative form of DNA: plus-strand DNA viruses, double-stranded RNA viruses, plus-strand RNA viruses, minus-strand RNA viruses.

_____ viruses contain an RNA-dependent DNA polymerase called reverse transcriptase that is used generate a DNA intermediate.

Retro-

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

S, and H2

_____________ and ____________ viruses replicate using DNA polymerases, either their own or from those of the host.

Single-stranded DNA, double-stranded DNA.

Based on the phylogenetic tree below, which of the following statements is FALSE? The figure shows a phylogenetic tree with 3 branches starting from a common ancestor. The first branch leads to Species F. The second branch divides into two, leading to Species B and Species C. The third branch divides into two, one for Species D and one for a new clade. The new clade is a bifurcation to species A and species E.

Species D is more closely related to species C than to species E.

As discussed in part C, horizontal gene transfer is an important process to study using sequencing and other molecular methods. There are a variety of ways in which researchers can detect genetic material that was likely introduced to a genome through horizontal gene transfer. Drag the choices below into the correct bins to indicate whether each characteristic is suggestive of horizontal gene transfer or not.

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

_____________ are organisms that accomplish the catabolism and degradation of a substance through a cooperative effort with one or more other microorganisms

Syntrophs

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.

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.

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

The RNA must be converted to cDNA.

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.

What metabolic advantage do cells have in storing the elemental sulfur byproduct from sulfide 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.

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

Photosynthetic organisms were present when Earth was primarily anoxic. Why was the appearance of cyanobacteria critical for the oxidation of the atmosphere?

The early forms of photosynthesis did not produce oxygen as a waste product.

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.

The general steps of the viral lifecycle are similar in most viruses. One major exception, however, is entry into the host cell. How does this step differ between an animal cell and E coli?

The entire virion is taken into an animal cell, but only the viral genome enters E coli.

In E. coli, the adenine in the sequence GATC is methylated by the Dam enzyme. In the same cells, a restriction endonuclease recognizes and cleaves dsDNA with the sequence GATC on either strand. Why does E. coli have these two enzymes?

The enzymes protect E. coli from infection by preferentially degrading viral or other exogenous DNA that is not methylated.

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).

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.

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.

Metabolic reactions can be assimilative or dissimilative. Which term, "assimilative" or "dissimilative," describes the reduction of sulfate by the sulfate-reducing bacteria (SRB) that have a symbiotic association with ANME?

The reduction of sulfate by SRB using electrons from ANME is dissimilative.

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.

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?

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

You isolate a bacteriophage that can replicate in E. coli. Through chemical analyses you determine that the only nucleic acid present is RNA. You isolate the RNA and put it in a test tube with all of the enzymes, amino acids, and RNAs necessary for translation. The RNA is translated directly, without being copied into a complementary strand first, and new infectious virions are made and released. What does this tell you about the bacteriophage?

The viral genome is ssRNA of the plus sense.

Virophages interfere with the life cycle of megaviruses by competing with them for replication enzymes, causing defective megaviruses to be produced. When the life cycle occurs correctly, what are the steps?

The virus attaches to the host cell, which can be mediated by cell surface receptors. Penetration of nucleic acids into the host cell and the capsid is discarded. Host cell enzymes and replication machinery are used to synthesize new viral genetic and capsid material. Newly synthesized viral genomes and capsids are assembled into complete viral particles. The hose cell lyses, releasing the newly assembled virus particles.

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).

When horizontal gene transfer occurs, an organism can obtain genes that may help it to survive and reproduce (increasing its fitness). Which of the following are some potential benefits to Vibrio cholerae bacteria of obtaining genes from their prey?

They may obtain genes that help them to more effectively infect hosts and gain antibiotic resistance while also experiencing reduced competition for nutrients.

What would likely occur if an anammox bacterium was unable to use ladderane lipids?

Toxic products of the anammox reaction could kill the cell.

The introductory passage explains that Vibrio cholerae bacteria may benefit from being able to obtain genes from their prey. What would be the best way to test whether they can benefit within one week of exposure to prey with a gene that confers resistance to ampicillin, an antibiotic that is commonly used in microbiology laboratories? Choose all of the steps that you should include.

Transfer V. cholerae that have been exposed for one week to prey lacking the resistance gene to medium with ampicillin. Transfer V. cholerae that have been exposed for one week to prey with the resistance gene to medium with ampicillin. Set up V. cholerae cultures that are susceptible to ampicillin and allow them to grow for a week in the presence of prey that have the resistance gene on medium that does not contain ampicillin. Set up V. cholerae cultures that are susceptible to ampicillin and allow them to grow for a week in the presence of prey lacking the resistance gene on medium that does not contain ampicillin.

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

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

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

True

Which of the following examples is an example of lysogenic conversion?

Vibrio cholerae bacteria produce cholera toxin when infected with a phage.

Which of the following is true about viral infection?

Viruses are very specific in which cells they infect. For a virus to be taken up by a cell, it must find a cell with appropriate receptors on the surface; it cannot be taken up by cells without the appropriate receptors.

The introductory passage describes ways that virophages use megavirus-producing factories in Amoeba to reproduce because they are unable to do so independently. Compare characteristics of viruses and virophages by dragging the characteristics into the correct bin to indicate whether each is a characteristic of virophages only, viruses only, both, or neither.

Vriophages only: They are always smaller than bacteria and archaea. They lack the genes for proteins needed to replicate themselves. Non-virophage viruses only: the genetic information of can be in the form of DNA or RNA. Both virophages and other viruses: They cannot replicate on their own. They do not belong to any of the three domains (Bacteria, Archaea and Eukarya). They have a protein capsid surrounding their nucleic acid. Neither virophages nor other viruses: They generate energy through mitochondria. They use their own ribosomes to make proteins.

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.

Some viruses have plus sense RNA genomes. Which of the following could describe one of those viruses?

a virus that contains RNA with the same nucleotide sequence as the functional mRNA that its host cell will translate to produce viral products.

When new genetic material enters a bacterial cell through conjugation, transformation, or transduction, a merodiploid cell can be formed. Does this happen with the V. cholerae bacteria?

Yes, it produces temporary merodiploid cells between the time the genetic material enters the cell and the time that recombination occurs.

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 group of microorganisms would the Calvin cycle LEAST likely be found in?

anoxygenic Chloroflexus

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

antigenic shift.

The filamentous DNA phages are unusual, because they

are released from the host without the host being lysed.

Rolling circle replication of the lambda genome differs from replication of a bacterial chromosome in that

bidirectional replication forks are not formed.

Proteomic analysis of a microbial community indicated an abundance of phycobiliproteins. Which phototrophic group is likely active and abundant in this community?

cyanobacteria

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

cytoplasm

The process by which electrons from the quinone pool are forced against the thermodynamic gradient to reduce NAD+ to NADH is called reverse

electron transport.

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 general, prokaryotic genome size is linked to its metabolism and interaction with the environment. Which type of prokaryote typically has the smallest genome?

endosymbiont

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

A poorly immunogenic vaccine often suggests the foreign proteins were not properly recognized by the immune system due to a lack of ________ necessary, which can also be engineered to occur with additional molecular manipulations.

glycosylation

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

highly conserved and universally distributed

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

Portable sequencers and other portable, efficient equipment for molecular analysis make genomic analyses easier to do in a wide range of conditions. These types of analyses can provide a great deal of information, from metabolic profiles to genome sizes. How would researchers accomplish this type of work?

isolation of genetic material. genome sequencing. genome assembly. genome annotation. determination of open reading frame. comparative genomics.

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

The T4 bacteriophage could not infect Staphylococcus aureus because this bacterium does NOT possess a

lipopolysaccharide outer membrane.

Megaviruses have a particular life cycle in which new viral particles are produced, and then the host cell lyses, although virophages can compete with them for replication enzymes. Viruses have many types of life cycles and can go through phases during which they are actively replicating and destructive to the host cell or dormant within the host cell. These life cycles differ in different types of viruses, so the cycle of megaviruses differs from those of bacteria and animals. During which part of the bacteriophage life cycle will the viral genome be replicated in synchrony with the host cell?

lysogenic

Some bacteriophage possess an enzyme similar to ________, which makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter.

lysozyme

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.

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.

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 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

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

not produce the protein being studied.

In Sanger sequencing and in many newer sequencing techniques, labeled precursors are used. What are these precursors?

primers or nucleotides that will be incorporated into the newly synthesized DNA

Which of the following is NOT included in the genome?

proteins

Gene function is annotated based on homology between the ORFs of a genome and proteins whose function has been proven experimentally. What -omic approach could help us determine the function and structure of proteins encoded by uncharacterized ORFs?

proteomics

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

qPCR

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

reduction reactions

Evolution is driven by

selection pressure applied to random mutation.

Which of the following is NOT a role of carotenoids?

to produce singlet oxygen

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

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

viral in origin

The growth of viruses in a culture is described as a one-step growth curve, because

virion numbers show no increase during intracellular replication and can only be counted after the virions burst from the host cell.