Microbiology Chapter 9 HW

Which type of DNA uptake is dependent on viruses? Choose one: A. Transduction B. Transformation C. Recombination D. Conjugation

A Transduction requires bacteriophages, viruses that infect bacteria, to transfer DNA. Conjugation, the direct transfer of DNA from one bacterial cell to another, and transformation, the uptake of DNA from the environment, do not rely on viruses.

The process of importing free DNA from the environment into cells is called Choose one: A. transformation. B. transcription. C. conjugation. D. transduction.

A Transformation is the uptake of DNA from the environment. Conjugation requires cell-cell contact, transduction is mediated through a bacteriophage, and transcription is the production of an RNA complementary to a DNA template.

Transposable elements differ from plasmids in that only plasmids Choose one: A. may exist autonomously, not integrated into host DNA. B. consist of double-stranded DNA. C. may code for antibiotic resistance. D. may be transmitted horizontally from one bacterium into another.

A Transposable elements may "jump" from one DNA molecule to another, but they do not replicate independently as plasmids can. Both plasmids and transposable elements are comprised of dsDNA and both may code for antibiotic resistance. Conjugative transposons may be transmitted horizontally.

In bacteria, a partially diploid strain may result from Choose one or more: A. acquisition of an F' factor. B. specialized transduction. C. generalized transduction. D. acquisition of F factor. E. natural transformation (not electroporation).

A & B Partial diploids allow microbiologists to study dominance of mutant alleles and aspects of chromosome organization. They also accelerate evolution because the bacteria are able to freely "experiment" with the second allele (while having the security of a backup copy of the gene).

Part 1 What are the basic parts of an insertion sequence? Choose one or more: A. two flanking inverted repeats B. random DNA of 100-200 bp C. coding region for polymerase D. ligase gene E. target sequence F. transposase coding region

A & F These simple elements catalyze their own movement in and out of host chromosomes, but are incapable of autonomous replication.

Uptake of foreign DNA can benefit a prokaryotic cell by serving as a source of which of the following? Choose one or more: A. novel genes B. repair material C. quorum sensing signals D. terminal electron acceptors E. nutrition

A, B, & E Exogenous DNA may be used as a source of carbon and energy for heterotrophs, or as a source of new genes that increase the cell's relative fitness. DNA from a genetically similar cell could also aid in DNA repair by reciprocal exchange with a homologous region. However, DNA nucleotides are highly reduced carbon molecules, which makes them good electron donors, but poor acceptors. Finally, DNA is not used as a quorum sensing signal. Instead, depending on the species, this process is mediated by small, freely diffusible "autoinducers" or small peptides.

Part 3 Why is it incorrect to refer to conjugation as bacterial sex? Choose one or more: A. It does not involve gametes. B. It does not require physical contact. C. The transferred DNA is not required for normal cellular function. D. The recipient is haploid for the transferred genes. E. The transferred DNA cannot replicate.

A, C, & D It is somewhat ironic, though, that after receiving an F factor, the newly converted F+ cell is in increased danger of viral attack. This is because the MS2 bacteriophage specifically binds to the pilus encoded by F factor. In this way, the F factor acts somewhat like a sexually transmitted disease!

Which type of DNA uptake is dependent on transferable plasmids? Choose one: A. Transformation B. Conjugation C. Recombination D. Transduction

B A transferable plasmid is needed when one cell directly transfers DNA to another cell as occurs in conjugation. Transformation, the uptake of DNA from the environment, and transduction, the acquisition of a gene from a bacteriophage, do not require a transferable plasmid.

Consider conjugation in E. coli. In which of the following matings would chromosomal genes most likely be transferred? Choose one: A. F+ x F- B. Hfr x F- C. F' x F+ D. F- x F- E. Hfr x F+

B Also, during conjugation, the orientation of the integrated F factor will determine which of the flanking chromosomal genes are transferred first.

CRISPR uses pieces of phage DNA incorporated into the genome Choose one: A. to direct specialized transduction. B. as the source of an RNA that will guide Cas proteins to cleave the foreign DNA. C. as a replicative transposon site. D. to direct restriction enzyme activity to cleave foreign DNA with homologous sequences.

B CRISPR is a kind of immune system, where foreign DNA is inserted as spacers in the clustered repeats. The DNA is transcribed and the resulting RNA guide associates with a Cas protein to complex with homologous sequences on a foreign piece of DNA to cleave it.

In 1928, a physician named Frederick Griffith was investigating the virulence of Streptococcus pneumoniae. He first determined that mice exposed to an encapsulated strain of S. pneumoniae (which formed smooth colonies) died. Mice infected with a nonencapsulated strain (which formed rough colonies) lived. In a now-famous experiment, he coinjected mice with heat-killed cells of virulent S. pneumoniae and cells from a live nonencapsulated strain. Amazingly, the mice died and a live virulent strain was recovered that formed smooth colonies. It was later discovered that Choose one: A. the mice had subclinical infections of S. pneumoniae and became sick during the experiment. B. the live cells were transformed with DNA from the dead virulent cells. C. the dead virulent cells were resurrected once inside the living host. D. the injected cell preparations were contaminated with live virulent S. pneumoniae. E. the live harmless cells mutated into a virulent strain once in the mice.

B It was later demonstrated that DNA from the dead cells contained a gene for the protective polysaccharide capsule that transformed the "rough" harmless strain into the "smooth" phenotype characteristic of the pathogenic form.

Identify the form of horizontal gene transfer depicted here. Choose one: A. transduction B. conjugation C. binary fission D. electroporation E. transformation

B This image captures the initiation of conjugation, whereby a cell carrying a conjugative plasmid (such as F factor) produces a sex pilus that attaches to receptors on a cell lacking the plasmid.

Association of RecA with an incoming piece of foreign DNA is required for a cell to do which of the following? Choose one: A. degrade one strand of a dsDNA molecule B. swap the incoming DNA with a homologous region on the chromosome C. metabolize the DNA as a food source D. transcribe the DNA into mRNA E. maintain the DNA as a plasmid

B This strategy can serve as a repair mechanism to replace a damaged region of DNA, or as a way to experiment with a slightly different version of an existing gene.

How does a transposon differ from an insertion sequence? Choose one: A. It contains two IS sequences flanking one or more genes. B. It is capable of nonreplicative transposition, while an IS sequence is not. C. It contains one or more genes in addition to transposase. D. It lacks inverted repeats. E. It carries at least one antibiotic resistance gene.

C And similar to insertion sequences, transposons have inverted repeats at either end of the element.

All of the following are potential mechanisms of horizontal gene transfer except Choose one: A. specialized transduction. B. transformation. C. binary fission. D. conjugation. E. generalized transduction.

C Binary division is a form of vertical gene transfer because the genetic material is passed from parent to progeny.

Which of the following is not a mechanism of horizontal gene transfer in bacteria? Choose one: A. transduction B. transformation C. binary fission D. conjugation

C Binary fission is a common form of asexual reproduction in bacteria and is not a mechanism of horizontal gene transfer.

Which of the following is an example of horizontal gene transfer in bacteria that requires cell-to-cell contact? Choose one: A. transduction B. transformation C. conjugation D. binary fission

C Conjugation is a process by which bacteria transfer DNA via formation of a pilus. This process requires cell-to-cell contact.

Which of the following is an example of horizontal transmission? Choose one: A. PCR B. Cell division C. Transformation D. Mitosis

C Horizontal transmission is the passage of genes from one organism to another via a non-reproductive process. This transfer can be accomplished via transformation. Mitosis is the division of the chromosome sets in eukaryotes prior to cell division. Cell division then distributes the DNA to the offspring of the original cell, which is an example of vertical transmission. PCR is a technique to amplify a specific DNA fragment.

Part 3 Transposases are multifunctional enzymes. During nonreplicative transposition, the transposase does all of the following except Choose one: A. excise insertion element creating double-stranded break in donor strand. B. nick donor DNA to produce free 3' OH on either side of insertion sequence. C. fill in single-stranded gaps that occur in the target region of the recipient DNA. D. bind to donor DNA and bring the ends of the insertion element together. E. mediate attack of 3' OH ends of insertion element into new target DNA.

C The insertion sequence-encoded transposase mediates almost the entire process of nonreplicative transposition. Synthesis of DNA in single-stranded gap regions and ligation of nicks in target DNA are the only steps catalyzed by host enzymes (DNA polymerase and ligase, respectively).

The CRISPR system Choose one: A. facilitates recombination through a complex system of proteins and clustered repeats. B. promotes horizontal gene transfer following exposure to antibiotics. C. unwittingly replicates bacteriophage DNA. D. is a type of immunity that directs degradation of foreign DNA upon repeat exposure. E. randomly causes double-stranded breaks in any incoming DNA.

D The presence or absence of a functional CRISPR region can also influence how easily some bacteria (such as Streptococcus) are transformed by exogenous DNA. In other cases, Cas proteins prevent lysogenized Pseudomonas aeruginosa from joining biofilm communities, and they affect the ability of Legionella pneumophila to infect amoebas.

Select the true statement regarding the relationship between genotype and phenotype. Choose one: A. The phenotype represents the entire genome of an organism. B. Only genes that produce proteins are considered part of an organism's genotype. C. Some mutations will cause a change in the genotype, while others will not. D. Any change in the genotype will be reflected in the phenotype. E. The phenotype reflects only the portion of the genotype that is expressed.

E Accordingly, heritable changes in the genotype (mutations) may or may not result in an observable change in the phenotype. Usually it is the location, rather than the size, of the mutation that matters.

Which specific feature of replicative transposition distinguishes it from nonreplicative transposition? Choose one: A. The target sequence is replicated as a result. B. It induces replication of the host chromosome. C. Only the DNA internal to the inverted repeats of the transposon is replicated. D. It happens during replication of the chromosome. E. During replicative transposition, the entire transposon is replicated.

E The process actually involves formation of a cointegrate molecule, which is then resolved into separate donor and recipient molecules by recombination.

Part 2 Upon successful completion of conjugation, the donor cell is _____ and the recipient cell is _____ . - F+ - HFr - F' - F-

F+, F+ At the completion of conjugation, DNA polymerase III in the donor cell has replaced the strand that was transferred. DNA ligase reseals the nick at the oriT site, which restores the integrity of the molecule, and the cell retains its F+ status. This cell can now transfer its F factor to other F- cells in the population.

Sort the following features according to whether they apply to generalized transduction, specialized transduction, or both. - Some resultant phages carry only host DNA. - Individual phages contain a mixture of phage and host DNA. - Certain host genes are packaged at a high frequency. - Genes from transducing phages can recombine with DNA in a new host. - This process may result from infection by a lytic phage. - All chromosomal genes have an equal chance of being packaged in to a phage. - This process requires integration of phage DNA into the host chromosome. - This process requires infection by a bacteriophage. - Resulting phages can be transduced into new cells (may require a helper phage).

Generalized: Some resultant phages carry only host DNA. All chromosomal genes have an equal chance of being packaged into a phage. This process may result from infection by a lytic phage. Specialized: Certain host genes are packaged at a high frequency. Individual phages contain a mixture of phage and host DNA. This process requires integration of phage DNA into the host chromosome. Both: Genes from transducing phages can recombine with DNA in a new host. Resulting phages can be transduced into new cells (may require a helper phage). This process requires integration of phage DNA into the host chromosome. Remember that in both cases, the vast majority of phages are completely normal. In generalized transduction, less than 1% of phages contain host DNA, and an even smaller percentage of lysogenic cells contain incorrectly excised phage. Still, small numbers become significant and meaningful when considering the large numbers of bacteria present in these populations.

Part 1 Correctly order the following steps in bacterial conjugation from start to finish. - A sex pilus is formed that joins an F+ cell to an F- cell. - The sex pilus retracts, and relaxosome forms. - The F factor is nicked at oriT, and one strand starts to transfer into the recipient. - The transferred DNA strand circularizes and completes replication. - DNA polymerase III synthesizes a replacement strand in the donor.

I. A sex pilus is formed that joins an F+ cell to an F- cell. II. The sex pilus retracts, and a relaxosome forms. III. The F factor is nicked at oriT, and one strand starts to transfer into the recipient. IV. DNA Pol III synthesizes a replacement strand in the donor. V. The transferred DNA strand circularizes and completes replication. In addition to mediating its own dissemination through a population, conjugative plasmids such as F factor can mobilize other plasmids that do not contain all the genes necessary for self-transfer.

Part 2 Sort the following events according to whether they occur in replicative transposition, nonreplicative transposition, or both: - Insertion sequence "jumps" into recipient DNA. - DNA polymerase fills in gaps. - Donor DNA retains a copy of insertion sequence. - Transposase is required. - Hairpin structures form on each end of insertion sequence. - Donor DNA loses insertion sequence. - DNA ligase seals nicks. - Target sequence gets duplicated. - Recombination separates donor and target DNAs.

Replicative: Donor DNA retains a copy of insertion sequence. Recombination separates donor and target DNAs. Nonreplicative: Hairpin structures form on each end of insertion sequence. Insertion sequence "jumps" into recipient DNA. Donor DNA loses insertion sequence. Both: DNA polymerase fills in gaps. Transposase is required. Target sequence gets duplicated. DNA ligase seals nicks. Replicative and nonreplicative transposition differ primarily in the fate of the donor DNA. In replicative transposition, the donor molecule remains intact, and following recombination with the recipient, each molecule contains a copy of the insertion element. In nonreplicative transposition, the process of excising the insertion element creates a double-stranded break in the donor DNA. At the same time, each end of the insertion sequences forms a hairpin, which is then nicked prior to movement into new target DNA. Both types of transposition require transposase encoded by the insertion element. Host DNA polymerase inserts nucleotides into single-stranded gaps in the donor DNA that are then sealed by ligase. At the conclusion of both types of transposition, replicated target sequences are produced on each side of the newly inserted DNA. You may want to review the video for a better understanding of each type of transposition.

You have a strain of ampicillin-resistant Escherichia coli and a strain of ampicillin-sensitive Enterobacter. You mix the strains together and leave them overnight. In the morning, you discover that the Enterobacter is now resistant to ampicillin as well. Now you must decide what experiments you could do to determine the mechanism of genetic exchange (transformation, conjugation, or transduction). Assume there was no experimental error overnight (i.e., no contamination), and keep in mind that only small particles (like DNA and viruses) will remain suspended in cell-free extract. Consider the descriptions of genetic exchange methods below and match each description to the proper type of exchange. - This method can occur with cell-free extract only and is not affected by DNase. - This method of DNA exchange cannot occur using the recipient cells mixed with cell-free extract only. - This method would be affected by DNase, an enzyme that can degrade naked DNA that is unprotected.

Transformation: This method would be affected by DNase, an enzyme that can degrade naked DNA that is unprotected. Conjugation: This method of DNA exchange cannot occur using the recipient cells mixed with cell-free extract only. Transduction: This method can occur with cell-free extract only and is not affected by DNase. These three mechanisms of gene exchange can be distinguished by whether cell-cell contact is required and whether the mechanism is sensitive or resistant to DNA-degrading DNAse.