Exam #2 Study questions

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.

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.

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

contains at least one polyprotein.

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

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

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.

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

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

fluorescence in situ hybridization

Arrange the following genetic components in the correct order.

genome, transcriptome, proteome, metabolome

Metagenomics

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

Proteomics

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

Genomics

the study of the entire genetic makeup of an organism.

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.

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

not produce the protein being studied.

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

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

reverse transcriptase

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

structural proteins proteases integrase.

Double-stranded DNA

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

Single-stranded DNA

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

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.

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

1,000

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.

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.

A drug designed to inhibit reverse transcriptase activity would target

retroviruses.

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?

-The colonies may be due to recombination. & -The colonies may be due to back mutation (reversion).

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

Genetically engineered vaccines can be created by

-adding virulence genes from a pathogen to a non-virulent organism -purifying a specific subunit of a pathogen -removing virulence genes from a pathogen

Suggestive of horizontal gene transfer

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

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

-the virus must make an RNA complement from its RNA genome, and the host cell does not have the machinery for this process -the virus must carry its own RNA-dependent RNA polymerase -the viral genome must encode for RNA-dependent RNA polymerase

Plasmids are commonly used as cloning vectors because

-they can replicate independently of the chromosome -they can contain genes for antibiotic resistance used for plasmid selection -they are easily inserted into cells by transformation

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

Mu

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

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.

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

Antiviral drug are limited for DNA virus infections simply because it would be awful if we targeted the host(our) cells. DNA viruses usually rely on host cells for replication therefore a antiviral drug would destroy our cells in the process. The only way we can't target them individually would be in the early stages of un-coating or cell receptors.

Generalized transduction

Any part of the host genomecan be transferred. A relatively low percentageof cells exposed undergotransduction.

When exposed to lytic bacteriophage in laboratory, most susceptible bacteria are infected and lysed. However, after about one day after exposure, most of the bacterial population is immune to bacteriophage infection. How might this occur?

Bacteriophage infections require viral binding to specific bacterial receptors. Those include proteins, carbohydrates, lipids, glycoproteins or glycolipids. Some bacteria may mutate and lose the ability to produce these targets. As a consequence, these cells will be immune to viral infection. After one day of exposure, most susceptible cells will have been infected and killed and the immune cells will predominate in the population.

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).

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

Class IV ssRNA (+) viruses

Vertical gene transfer

DNA from parent to offspring a gene shared by several species,inherited from a common ancestor

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.

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.

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.

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.

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.

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.

Which of the following is most similar to lysogeny?

Hfr state

Chromosomal islands are presumed to have a foreign origin based upon three observations. What are these observations and how do they indicate that chromosomal islands are foreign in origin?

Horizontal gene transfer, host adaption, and virulence. They indicate a foreign origin due to them usually occurring in gram positive bacteria

What effect on bacteriophage lambda infection would a cI- mutation (no cI protein made) have?

In the absence of the cI repressor, the competing protein (Cro) would always bind to the bacteriophage regulatory sequences. As a consequence, the phage would always enter the lytic phase. The resulting plaques would appear clear rather than cloudy like the wild-type temperate virus.

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.

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

Legitimate genes and non-coding RNA may be missed.

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

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

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.

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.

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

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.

All of the following can act as receptors for various bacteriophages

Sugar transporters flagella iron transport proteins.

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

T4 capsid proteins would not be made.

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.

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

The Ms2 phage has a positive ssRNA genome equivalent to mRNA therefore it can be translated directly upon entry.

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

The RNA must be converted to cDNA.

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.

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.

Which of the following would result in a frameshift mutation?

The deletion of two nucleotides in a codon

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.

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.

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.

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

The outcome of a base pair mutation is variable because it all depends on how the codon is read. It could be read as a completely different amino acid (Missense mutation) , as if it had not been changed (normal- silent mutation), or it could not code for anything at all (nonsense mutation).

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.

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.

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.

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).

Explain why some viruses contain enzymes within the virion and others do not. Use specific examples to support your answer.

These enzymes help produce infection however they are not needed for the organism to survive. Lysozyme makes hole in the cell wall. Neuraminidases kill glycoproteins and glycolipids

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.

Specialized transduction

Transduction must involvea temperate phage. Transduced DNA is integratedinto the host as part of a prophage. It is not necessary for phages tobe defective for transduction. Only specific regions ofDNA may be transduced.

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

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

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.

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.

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.

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

annotation.

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.

Single-stranded RNA & double-stranded RNA

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

double-stranded DNA & Single-stranded DNA

____and ___ viruses replicate using DNA polymerases, either their own or from those of the host.

The SOS DNA repair system is

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

Which of the following could describe a virus?

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

An open reading frame (ORF) encodes for

a polypeptide

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

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

a yeast cell

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

agarose gel electrophoresis

Which of the following are the hosts for most enveloped viruses?

animals

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.

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

bidirectional replication forks are not formed.

Integration of Mu DNA into the host genome is essential for

both lytic and lysogenic growth.

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.

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

genes, function, and evolutionary history

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

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

confers resistance to infection by viruses of the same type.

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

cytoplasm

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.

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

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

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

frameshift mutation

Horizontal gene transfer in Archaea

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

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

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

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.

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

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

ligation transformation recombination

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

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

lytic bacteriophages

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.

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.

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

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

What is included in the genome?

noncoding regions of DNAgenes that encode RNAscoding regions of DNA

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

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

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

post-translationally cleaved

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

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

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

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.

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

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.

Metabolomics

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

Transcriptomics

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

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

Horizontal gene transfer

transformation conjugation transduction DNA from mature organismto mature organism DNA from virus tomature organism

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.

Horizontal gene transfer has been thoroughly documented for genes involved in

virulence and metabolic functions.

Retro-

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

Single-stranded RNA

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