Microbiology Exam 2 HW Questions (Chp 8-14)

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

genes, function, and evolutionary history

What is the correct order of the "-omes"

genome, transcriptome, proteome, metabolome

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

high H+ concentrations.

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

highly conserved and universally distributed

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

miniaturization of reaction size and increased computer power.

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

Evolution is driven by _____________.

selection pressure applied to random mutation.

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

D. 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? A. Trp- B. TrpC C. trp D. trpC1

D. trpC1

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

cyanobacteria

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

Which of the following populations would be most likely to demonstrate genetic drift? A. A researcher transfers bacteria into fresh medium but accidentally collects only a very small quantity of bacteria in the process. B. A large population of bacteria is grown over an extended period in a continuous culture system. C. Someone takes an extended course of antibiotics, leaving a relatively small number of surviving bacteria. D. A researcher performs a Gram stain to separate gram-positive and gram-negative bacteria. He places the gram-positive bacteria in one test tube and the gram-negative bacteria in the other.

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

Which of the following viral genomes could be directly translated to make proteins? A. Class IV ssRNA (+) viruses B. Class III dsRNA viruses C. Class I dsDNA viruses D. Class V ssRNA (-) viruses

A. Class IV ssRNA (+) viruses

Transformation and homologous recombination allow for the formation of heteroduplex DNA. Which of the following would occur during DNA replication of this molecule? A. One daughter strand is complementary to the recombinant DNA molecule, while the other daughter strand is complementary to the parent DNA molecule. B. Both daughter strands are complementary to the recombinant DNA molecule. C. Both daughter strands are complementary to the parent DNA molecule. D. None of the answers are correct.

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

Why does the structure of plant and bacterial cells illustrate the reason for having few enveloped viruses that infect these cells? A. Plant and bacterial cells contain cell walls that limit the virus from budding out and obtaining the envelope. B. Plant and bacterial cells contain cell walls that prevent viruses from being released from the cell. C. Plant and bacterial cells contain cell walls that prevent attachment of viruses. D. Plant and bacterial cells contain cell walls that prevent viral infection.

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

If the hypothesis stating viruses evolved prior to living organisms on Earth is TRUE, the first type of viruses in the world were likely A. RNA viruses B. DNA viruses C. retroviruses D. bacteriophages

A. RNA viruses

What would be the consequence of deleting the late T4 genes? A. T4 capsid proteins would not be made. B. The T4 genome would not be copied. C. T4 mRNA would not be produced. D. ATP would not be produced and the T4 genome would not be packaged into the capsid.

A. T4 capsid proteins would not be made.

A(n) ________ gene is a gene that encodes a protein that is easy to detect and assay. A. reporter B. translational C. recorder D. encoder

A. reporter

Which objective would be best to use a Southern blot rather than a Northern blot? A. Quantify expression profiles of a gene. B. Determine if a gene is present in a genome. C. Identify regulatory gene-protein interactions. D. Discover gene function.

B. Determine if a gene is present in a genome. Southern use hybridization to target DNA fragments (northern targets RNA fragments)

Which of the following is most similar to lysogeny? A. F- state B. Hfr state C. F state D. F+ state

B. Hfr state

Which of the following are the hosts for most enveloped viruses? A. Bacteria B. animals C. Archaea D. fungi

B. animals

Which of the following sequences is a palindrome, characteristic of many recognition sequences for restriction endonucleases? GTAATG CATTAC GGGGGGG CCCCCCCC GAATTC CTTAAG TTGCCGA AACGGCT

C

Genetically engineered vaccines can be created by __________. A. removing virulence genes from a pathogen B. purifying a specific subunit of a pathogen C. adding virulence genes from a pathogen to a non-virulent organism D. All of the listed responses are correct.

D. All of the listed responses are correct.

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

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? A. expression vector B. plasmid C. shuttle vector D. bacteriophage

A. expression vector

_________________ use inorganic or organic chemicals as energy sources. _________________ use organic carbon as their carbon source. _________________ use inorganic compounds for energy and organic compounds as a carbon source. _________________ perform CO2 fixation and utilize CO2 as their sole carbon source. _________________ use light as an energy source and CO2 as a carbon source. _________________ use inorganic electron donors and CO2 as a carbon source. _________________ are organisms that accomplish the catabolism and degradation of a substance through a cooperative effort with one or more other microorganisms.

1. chemotrophs 2. heterotrophs 3. mixotrophs 4. autotrophs 5. phototrophs 6. chemolithotrophs 7. syntrophs

What suggests that horizontal gene transfer has occurred?

1. identification of a DNA segment that has a distinctive GC content compared with other segments of the genome 2. identification of genes typically found in other, distantly related species 3. identification of a segment with an unusual codon bias compared with the rest of the genome

Why is a special polymerase, such as Taq polymerase, required for PCR? A. Taq polymerase is produced by an extremophile prokaryote and is able to work at relatively high temperatures. B. Taq polymerase can add complementary bases in an extremely accurate way, resulting in a very low error rate. C. Taq polymerase can add DNA or RNA, allowing amplification of DNA or RNA. D. Taq polymerase adds bases more rapidly than other polymerases, allowing very rapid amplification.

A. Taq polymerase is produced by an extremophile prokaryote and is able to work at relatively high temperatures.

Genetic recombination involving insertion sequences typically results in what type of mutation? A. frameshift mutation B. silent mutation C. base-pair substitution mutation D. base-pair deletion mutation

A. frameshift mutation

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? A. The enzymes protect E. coli from infection by preferentially degrading viral or other exogenous DNA that is not methylated. B. The enzymes cut the E. coli genome into pieces that bind to viral particles and inhibit viral replication. C. The enzymes encourage lysogeny because the cleavage sites are recognized by viral integrases. D. The enzymes increase the rate of mutation and genome rearrangement, thus increasing the likelihood that E. coli cells will mutate and become resistant to viral infection.

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

A single base substitution happens to cause a nonsense mutation early in the gene for a protein. What will be the result? A. The protein will be truncated so much that it is unlikely to function normally. B. The protein will be truncated a small amount, but is unlikely to function normally. C. The protein will be truncated a small amount, but is likely to function normally. D. The protein will be truncated a great deal, but is likely to function normally.

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

Which of the following describes a retrovirus? A. The virus uses reverse transcriptase to make DNA from an RNA template, the reverse of the normal process of gene expression. B. The viral RNA is used directly for translation; there is no need for transcription. C. Retroviruses also have a DNA genome in their capsid and go through the normal process of gene expression, unlike other viruses. D. The viral RNA genome is transcribed by RNA replicase to form a complementary RNA strand to use for translation, unlike normal gene expression.

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

Which of the following is true about viral infection? A. 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. B. Viruses can infect any cell in a particular species; it does not matter which tissue they infect as long as the species (or group of similar species) is correct. C. Viruses have what is needed to infect a host cell; they do not need anything specific from the host cell in order to cause infection and therefore can infect a wide range of cells. D. Viruses can infect any cells within a large group, but they are not more specific than that. For example, there are plant viruses that can affect many types of plants, bacteriophages that affect many types of bacteria, and animal viruses that affect a range of viruses.

A. 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.

Which of the following could describe a virus? A. a particle composed of a protein capsid surrounding single-stranded DNA B. a particle that has double-stranded RNA and only a minimal number of ribosomes C. a particle that has double-stranded DNA and only a minimal number of organelles D. a particle composed of a protein capsid surrounding single-stranded DNA and single-stranded RNA

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

Some viruses have plus sense RNA genomes. Which of the following could describe one of those viruses? A. a virus that contains RNA with the same nucleotide sequence as the functional mRNA that its host cell will translate to produce viral products B. a virus that has single-stranded DNA with the same nucleotide sequence as the functional mRNA that its host cell will translate to produce viral products C. a virus that contains RNA with the complementary nucleotide sequence to the functional mRNA that its host cells will translate to produce viral products D. a virus that has single-stranded DNA with the complementary nucleotide sequence to the functional mRNA that its host cell will translate to produce viral products

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

Rolling circle replication of the lambda genome differs from replication of a bacterial chromosome in that A. bidirectional replication forks are not formed. B. only a single strand of the genome is copied and no concatamers are formed. C. no concatamers are formed. D. only a single strand of the genome is copied.

A. bidirectional replication forks are not formed.

What method of mutagenesis would be best to determine if a gene is essential for a prokaryote? A. cassette mutagenesis B. knock-out mutagenesis C. gene disruption D. site-specific mutagenesis

A. cassette mutagenesis

Bacteriophages genomes are typically composed of A. double-stranded DNA. B. single-stranded DNA. C. single-stranded RNA. D. double-stranded RNA.

A. double-stranded DNA.

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. A. glycosylation B. glucosylation C. complex folding D. methylation

A. glycosylation

The T4 bacteriophage could not infect Staphylococcus aureus because this bacterium does NOT possess a A. lipopolysaccharide outer membrane. B. teichoic acid outer membrane. C. pili. D. flagella.

A. lipopolysaccharide outer membrane.

Some bacteriophage possess an enzyme similar to ________, which makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter. A. lysozyme B. peptidoglycanase C. nuclease D. infectase

A. lysozyme

In a natural population of diverse slow-growing prokaryotic cells, what type of viruses would you expect to be most common? A. lytic bacteriophages B. temperate bacteriophages C. icosahedral viruses D. enveloped viruses

A. lytic bacteriophages

Based on its function, which type(s) of viruses likely contain(s) a gene encoding for RNA replicase? A. positive and negative ssRNA viruses B. positive ssRNA viruses C. dsDNA and ssDNA viruses D. ssRNA and ssDNA viruses

A. positive and negative ssRNA viruses

Which of the following is NOT included in the genome? A. proteins B. genes that encode RNAs C. coding regions of DNA D. noncoding regions of DNA

A. proteins

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 A. subunit vaccines. B. purified protein administered. C. attenuated carrier viruses. D. monovalent.

A. subunit vaccines.

Proteins made by a ribosome reading through the stop codon of a transcript without their own discrete ribosome binding sites A. suggest a relatively low level of protein product is essential for the virus due to the rare frequency of these events. B. appear most abundant in archaeal viruses and relatively uncommon in bacteriophages. C. are thought to be a primitive mechanism to avoid host defenses. D. create opportunities for viruses to make different capsid proteins.

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

The growth of viruses in a culture is described as a one-step growth curve, because A. virion numbers show no increase during intracellular replication and can only be counted after the virions burst from the host cell. B. assembly and release actually occur in one step. C. the eclipse phase prevents the plating and enumeration of virions although new virions are produced at a steady rate during the eclipse phase. D. there is only one step in the viral life cycle which leads to only one replicative cycle in a culture.

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

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; Thanks to the degeneracy of the genetic code that allows for silent mutations.

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.

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.

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

Antigenic shift (segments of the RNA genome from two separate strains infecting the same cell are reassorted resulting in hybrid virions whose proteins are unrecognized by the immune system)

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

confers resistance to infection by viruses of the same type.

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

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? A. The envelope is not capable of stimulating an immune response because of its makeup. B. 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. C. Viral proteins are highly immunogenic in order to facilitate uptake by host cells, while the envelope is not important in uptake by host cells. D. Only proteins can stimulate the immune system, so the phospholipids and glycoproteins of the envelope are not immunogenic.

B. 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.

Differentiate between persistent and latent animal virus infections. A. In a latent infection, the host cell is continually releasing new viral particles slowly. In a persistent infection, there are periods of time where the virus is not replicating and creating new viral particles. B. 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. C. Persistent infections can cause transformation of the host cell, which can lead to the development of cancer. Latent infections do not cause transformation. D. Persistent infections always lead to cell lysis, while latent infections never lead to cell lysis.

B. 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.

Which of the following enzymes would you expect to find in the virion of a retrovirus, but NOT in a bacteriophage? A. methylase B. restriction enzymes C. lysozyme D. reverse transcriptase

D. reverse transcriptase

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? A. It is necessary to know something about the sequence of the DNA sample prior to amplifying a specific region. B. It requires very pure and high-quality DNA samples. C. It is more error prone than most DNA replication. D. PCR is so sensitive that contamination can easily occur.

B. It requires very pure and high-quality DNA samples.

Explain why viroids can only infect and damage plant cells, but not animal cells. A. Although both types of cells contain RNA, viroids recognize a specific receptor on the surface of plant cells. B. Plant cells contain a RNA polymerase that can copy RNA can animal cells do not. C. The genome of plant cells is made of RNA while animal cells have a DNA genome. D. Animal cells contain RNA polymerase that can copy RNA and plant cells do not.

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

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? A. The viral genome is ssRNA of the minus sense. B. The viral genome is ssRNA of the plus sense. C. The bacteriophage is a retrovirus. D. The bacteriophage is probably a new strain and should be studied further.

B. The viral genome is ssRNA of the plus sense.

When determining the number of virus particles in a suspension, why is the number obtained always less than the actual viral titer? A. because it can be difficult to accurately count all of the plaques produced by infection B. because all of the virus particles do not infect with 100% efficiency C. because the cells used for culturing the virus may become resistant to the virus D. because there may not be enough cells for each viral particle to infect

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

In T7, the proteins that inhibit the host restriction system are synthesized A. while the T7 genome is entering the cell but before it enters the nucleus. B. before the entire T7 genome enters the cell. C. in response to the T7 genome binding to the host chromosome. D. after the T7 genome is completely within the host cytoplasm.

B. before the entire T7 genome enters the cell.

The cells used as hosts for cloning vectors are __________. A. always E. coli B. easy to grow and transform with engineered DNA C. always prokaryotic D. always eukaryotic

B. easy to grow and transform with engineered DNA

Which of those listed below is LEAST similar in what is being studied and concluded? A. Northern blot B. fluorescence in situ hybridization C. GFP fusion protein D. RT-PCR

B. fluorescence in situ hybridization (FISH)

Horizontal gene transfer in Archaea A. has not been documented, thus all genetic studies of archaea are done via genomic sequencing. B. frequently occurs in nature and has been used to perform genetic studies in the laboratory as well C. is infrequent in nature and therefore difficult to use for genetic studies in the laboratory. D. frequently occurs in nature, but there are very few laboratory studies because archaea do not cause human disease.

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

Which process listed below allows genetic material to be transferred from a virus-like particle that lacks genes for its own replication? A. transformation of a linear piece of DNA B. gene transfer through a gene transfer agent C. transduction by a dsDNA phage Mu D. conjugation of an F+ plasmid

B. gene transfer through a gene transfer agent

Expression vectors are designed to ensure that ________ can be efficiently ________. A. DNA / transcribed B. mRNA / transcribed C. mRNA / translated D. DNA / translated

B. mRNA / transcribed

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? A. minimal medium + threonine B. minimal medium + streptomycin C. minimal medium D. minimal medium + streptomycin + threonine

B. minimal medium + streptomycin

To estimate the total concentration of a beneficial bacterial species in yogurt, ________ would provide the quickest results. A. RT-PCR B. qPCR C. a Southern blot D. fluorescence in situ hybridization

B. qPCR (quantitative PCR)

The genome of retroviruses contains genes to make all of the following EXCEPT A. integrase. B. repressor proteins. C. proteases. D. structural proteins.

B. repressor proteins.

How could overlapping genes in a positive ssDNA virus genome be predicted? A. Convert the positive ssDNA into negative ssDNA and search all six possible frames for genes that use part of the same sequence. B. Convert the positive ssDNA into its complementary ssDNA and search for genes in the negative ssDNA strand that also share a complementary gene in the positive strand. C. Directly search the three frames of the positive ssDNA for genes that have sequences where more than one gene is predicted. D. Convert the positive ssDNA into its complementary ssDNA and search for genes in the negative ssDNA strand for sequences used in more than one predicted gene.

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

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? A. Rolling circle replication of the viral genome ensures that the genes are available for transcription in the correct order. B. Each group of T4 genes has a different promoter that indicates the order in which they should be transcribed based on the affinity of the promoter for the host RNA polymerase. C. Early and middle T4 genes encode for RNA polymerase-modifying proteins so that only phage promoters are recognized. D. Early T4 genes encode for proteolytic enzymes that destroy the host RNA polymerase. Subsequently a viral polymerase is created that transcribes the middle and late genes in the correct order.

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

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? A. The colonies may be due to recombination. B. The colonies may be due to back mutation (reversion). C. Either A or B is possible. D. Neither A nor B is possible.

C. Either A or B is possible.

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? A. Retroviruses have a typical one-step viral growth curve, which leads to the host being overwhelmed quickly. B. Once many new virus particles are produced, the host cell will lyse to release them. C. It is difficult to completely cure an animal host of the virus, since anti-retroviral drugs will only eliminate circulating virions, not proviruses. D. Because retroviruses have multiple enzymes (reverse transcriptase, protease, and integrase), they can rapidly kill the host cell once enough of these enzymes are synthesized by the host.

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

Which of the following is TRUE of natural competence? A. It is not required for transformation. B. It commonly occurs with high efficiency in nature. C. It requires special proteins such as a cell wall autolysin. D. It cannot occur naturally in bacteria.

C. It requires special proteins such as a cell wall autolysin.

Which of the following factors has delayed the development of laboratory-based genetic systems in Archaea? A. Archaea do NOT host viruses or plasmids. B. There are no documented systems of conjugation in Archaea. C. Many archaea grow in extreme or unusual conditions that make the use of agar and traditional mutant screening techniques problematic. D. Homologous recombination does NOT occur in Archaea.

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

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? A. Temperate bacteriophages are capable of both horizontal and vertical gene transfer, allowing a wide range of ways to increase genetic diversity. Virulent bacteriophages are not capable of either. B. Temperate phages are capable of lysogeny, and their genetic material can be integrated into the host genome, causing damage rather than increasing fitness. C. Temperate phages don't immediately kill their hosts. D. Virulent phages are capable of lysogeny, and their genetic material can be integrated into the host genome, causing damage rather than increasing fitness.

C. Temperate phages don't immediately kill their hosts.

Which of the following would result in a frameshift mutation? A. The deletion of three nucleotides in a codon B. The deletion of one nucleotide from one codon and two nucleotides from the adjacent codon C. The deletion of two nucleotides in a codon D. The addition of three nucleotides between two existing codon.

C. The deletion of two nucleotides in a codon

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? A. All of the DNA strands would contain radioactive nucleotides. B. None of the DNA strands would contain radioactive nucleotides. C. 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. D. All of the DNA molecules would have one radioactive strand and one non-radioactive strand.

C. 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 filamentous DNA phages are unusual, because they A. replicate without a host. B. have linear genomes. C. are released from the host without the host being lysed. D. are released from the host without being lysed and have linear genomes.

C. are released from the host without the host being lysed.

Integration of Mu DNA into the host genome is essential for A. lytic growth. B. lysogenic growth. C. both lytic and lysogenic growth. D. neither lytic nor lysogenic growth.

C. both lytic and lysogenic growth.

Horizontal gene transfer... A. is so rare over evolutionary history that it is not considered when examining microbial evolution. B. occurs within bacterial species. C. complicates the construction of phylogenetic trees and the interpretation of specific traits in relation to evolution. D. only affects the evolution of plasmids.

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

Identifying proteases being essential for the replication of a virus would suggest the virus A. lyses its host following genome replication. B. uses at least one set of overlapping genes. C. contains at least one polyprotein. D. has a single-stranded RNA genome.

C. contains at least one polyprotein.

What makes eukaryotic transcripts easier to isolate than bacterial transcripts? A. Larger transcript size in eukaryotes enables easy size-selection methods. B. Transcripts are the most abundant RNAs in eukaryotes. C. mRNA is polyadenylated in eukaryotes. D. Eukaryotic transcripts are not methylated but their genes are often methylated.

C. mRNA is polyadenylated in eukaryotes. (unique)

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 (because they are carbon fixation pathways)

What two gases were most abundant on early Earth?

CO2 & H2

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

Carbon

If a foreign gene is cloned into an expression host, it is important that the host itself A. produce the protein in larger amounts than the vector. B. repress the genetic expression being studied. C. produce signal proteins to tag the host protein. D. not produce the protein being studied.

D. not produce the protein being studied.

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

Cytoplasm (pox viruses, dsDNA virus/Baltimore class I, are unique in that all replication events occur in the cytoplasm instead of the nucleus)

Plasmids are commonly used as cloning vectors because __________. A. they are easily inserted into cells by transformation B. they can contain genes for antibiotic resistance used for plasmid selection C. they can replicate independently of the chromosome D. All of the listed responses are correct.

D. 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 __________. A. the virus must make an RNA complement from its RNA genome, and the host cell does not have the machinery for this process B. the virus must carry its own RNA-dependent RNA polymerase C. the viral genome must encode for RNA-dependent RNA polymerase D. All of the listed responses are correct.

D. All of the listed responses are correct.

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. Lactic acid fermenters are able to generate energy in the absence of oxygen. D. An organism uses an electron transport chain with sulfur as the terminal electron acceptor.

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

Restriction endonucleases are found in nature. They are extremely useful for genetic engineering. Why do organisms produce them? A. They are involved in DNA replication in prokaryotes. B. Organisms produce them as a way of allowing new genetic material to be inserted. C. They are part of the viral life cycle and help in the assembly of new viruses. D. 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).

D. 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).

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? A. DNA-dependent DNA polymerases for DNA viruses B. DNA-dependent RNA polymerases for RNA viruses C. DNA-dependent RNA polymerases for DNA viruses D. RNA replicases (RNA-dependent RNA polymerases) for RNA viruses

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

What is the first step in constructing a metagenomic library from RNA? A. The RNA must be amplified through PCR, producing many RNA copies. B. The RNA must be inserted into plasmid vectors. C. The RNA must be screened to identify the genes of interest. D. The RNA must be converted to cDNA.

D. The RNA must be converted to cDNA.

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? A. The entire virion enters E coli, but only the nucleic acid is taken up by animal cells. B. The virion randomly attaches to E coli, but viral binding to a specific receptor is required for entry into animal cells. C. The virion fuses to the bacterial cell membrane of E coli, while the genome is injected into an animal cell. D. The entire virion is taken into an animal cell, but only the viral genome enters E coli.

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

Which of the following examples is an example of lysogenic conversion? A. T4 phages infect E. coli bacteria and are resistant to destruction by restriction enzymes. B. An RNA virus infects a cell and causes the production of new viruses. C. A lambda phage infects E. coli and enters the lytic cycle. D. Vibrio cholerae bacteria produce cholera toxin when infected with a phage.

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

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. recombination. B. ligation. C. transformation. D. a reporter gene.

D. a reporter gene.

The enzyme transposase may be coded for by insertion sequences on a A. chromosome B. phage C. plasmid D. chromosome, phage, or plasmid.

D. chromosome, phage, or plasmid.

All of the following can act as receptors for various bacteriophages EXCEPT A. Sugar transporters. B. iron transport proteins. C. flagella. D. cilia.

D. cilia.

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? A. deletion of both the cro and cI genes B. overexpression of the cro gene C. deletion or inactivation of the cI gene D. deletion or inactivation of the cro gene

D. deletion or inactivation of the cro gene

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 A. allows continual expression of the protein. B. is not able to be replicated. C. is attached to a normal cell promoter. D. is inducible.

D. is inducible.

Cloning vectors can be distinguished from expression vectors by A. having a high copy number per cell. B. carrying ori genes for replication of the cloned sequence. C. having a multiple cloning site (MCS). D. lacking a promoter site upstream of the insertion site.

D. lacking a promoter site upstream of the insertion site.

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.

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

Double-stranded DNA

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.

T/F: Bacteria that are capable of oxidizing both iron and sulfur usually have a strong preference for sulfur oxidation because it yields more energy.

False

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

False

T/F: 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

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

False

T/F: The largest cellular genomes belong to prokaryotes that are parasitic or pathogenic.

False

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.

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.

Provide 5 examples of horizontal gene transfer and 2 examples of vertical gene transfer

Horizontal gene transfer: 1. conjugation 2. transduction 3. transformation 4. DNA from mature organism to mature organism 5. DNA from virus to mature organism Vertical gene transfer: 1. DNA from parent to offspring 2. a gene shared by several species, inherited from a common ancestor

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.

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.

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 phage creates mutations in its host genome via transposition?

Mu Mu(tation)

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.

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

Post-translationally cleaved

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

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.

In photosynthesis, NADH and NADPH are produced from NAD + and NADP+ by ___________ reactions

Reduction NAD and NADP are reduced, or given electrons (often from the splitting of water), and become NADPH and NADH, which can then carry the electrons to where they need to go. Then, once those electrons are dropped off (oxidized), NADP and NAD are regenerated and the cycle begins again.

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

Retro- viruses

Which type of virus would a drug designed to inhibit reverse transcriptase activity target?

Retrovirus (or hepadnavirus)

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

S & H2

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

Single-stranded DNA

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

Single-stranded DNA; double-stranded DNA

__________________ viruses have genome configurations that are either plus-sense or minus-sense.

Single-stranded RNA

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

Single-stranded RNA; double-stranded RNA

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.

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.

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.

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.

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).

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.

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.

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 ladderane lipids aggregate in the membrane and prevent the diffusion of substances into the cytoplasm)

T/F: 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

T/F: 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

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.

The SOS DNA repair system is __________.

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

An open reading frame (ORF) encodes for

a polypeptide

Which of these organisms is likely to have the largest genome? A. a chloroplast B. an extremophile Archaean due to the demands of surviving in harsh environments C. an autotrophic bacterium D. a yeast cell

a yeast cell

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.

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

annotation

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

anoxygenic Chloroflexus

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.

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.

Gene duplication is essential to organisms because __________.

duplicate genes are more able to evolve into new genes

The early energy reactions used hydrogen, which is a powerful

electron donor

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

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

evolution

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 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.

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

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

lower / assimilative

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

You want to know whether the virulence genes present in Bordetella pertussis are evolutionarily related to genes in the less pathogenic species B. bronchisepticaor 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

The designations Phe-, Leu-, and Ser+ refer to an organism's ____________________

phenotype

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

pili

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 (ddNTPs)

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

The CRISPR system ...

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

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

reporter genes

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 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.

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

viral in origin

Horizontal gene transfer has been thoroughly documented for genes involved in ___________________

virulence and metabolic functions.