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Biology & Life Science
Q:
Which process listed below does NOT require homologous recombination to maintain the new genetic material in the recipient cell?
A) conjugation of an F+ plasmid
B) gene transfer through a genetic transfer agent
C) transduction by a dsDNA phage Mu
D) transformation of a linear piece of DNA
Q:
A mutation that readily reverses to restore the original parental type would most likely be due to a(n)
A) deletion.
B) insertion.
C) point mutation.
D) frameshift mutation.
Q:
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?
A) silent mutation
B) nonsense mutation
C) missense mutation
D) frameshift mutation
Q:
A mutant that has a nutritional requirement for growth is an example of a(n)
A) autotroph.
B) auxotroph.
C) heterotroph.
D) organotroph.
Q:
How might mutations in the dnaQ sequence, whose enzyme is involved in DNA proofreading, be beneficial for a microbe in a highly competitive and dynamic community?
Q:
The CRISPR system is said to protect or preserve genome integrity in prokaryotic cells by acting as a type of "immune system." Explain how the CRISPR system works and its limitations.
Q:
A mutant you made in the laboratory with 5-bromouracil suddenly regains the wild-type phenotype. You discuss this phenomenon with your advisor and colleagues, and they suggest you try transposon mutagenesis to avoid this problem and create stable mutants. Why would mutants created with 5-bromouracil be more likely to regain the wild-type phenotype than mutants created via transposon mutagenesis?
Q:
How does the SOS system simultaneously fix damage DNA and increase the mutation rate? How does the SOS system increase the survival of microorganisms?
Q:
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.
Q:
Discuss the importance of homologous recombination and transposition in natural horizontal gene transfer and evolution. Be sure to define all of the terms you use and connect them together logically in your answer.
Q:
Consider the map shown below of a portion of a prokaryotic genome. How might the elements indicated affect the stability and structure of the genome? Assume that IS2 encodes for a transposase that catalyzes conservative transposition. Re-draw the genome map to illustrate your prediction if necessary.
| IS2 |__gene1 gene2 gene3 | IS2 | geneA geneB geneC| IS2 | geneD | IS2 | geneX
Q:
Compare and contrast generalized transduction with specialized transduction.
Q:
Explain how electroporation works and the significance of the procedure for genetic experiments.
Q:
Design an experiment (including controls) to determine if a new kitchen chemical cleaner is mutagenic. Include in your answer how you would interpret the results.
Q:
Archaea have a unique form of conjugation involving cytoplasmic bridges for bidirectional transfer of DNA.
Q:
A typical mutation rate for a bacterium is in the range of 10-6 to 10-9 per kbp.
Q:
Intercalating agents, like acridine orange and ethidium bromide, lead to mutagenesis by pushing DNA base pairs apart, which can lead to insertions or deletions.
Q:
Penicillin selection is a positive selection for the isolation of mutants with growth factor requirements.
Q:
All Hfr strains possess an F factor integrated into the host chromosome.
Q:
Toxigenicity in Corynebacterium diphtheriae is due to phage conversion.
Q:
Insertion sequences are found on both ends of transposons and encode for transposase.
Q:
Proteins and nucleic acids absorb light maximally at 260 nm; hence, proteins protect cells from UV effects.
Q:
Lysogeny is essential for the virulence of many pathogenic bacterial strains.
Q:
Many Bacteria isolated from nature are natural lysogens.
Q:
In specialized transduction, as exemplified by lambda phage in E. coli, transduction occurs at high efficiency for only a restricted group of genes near the insertion site of lambda.
Q:
In specialized transduction, virtually any genetic marker can be transferred from donor to recipient.
Q:
In transformation experiments using a variety of Bacteria, it has been noted that essentially all of the cells in a population can become competent.
Q:
Transposons can be found on many genetic elements, including plasmids, chromosomes, and viral genomes.
Q:
The use of transposons to generate mutations is a convenient way to create bacterial mutations in the laboratory.
Q:
In a prokaryotic genome, either insertion elements OR transposons are present, but both are never present at the same time.
Q:
When the F factor is integrated, all Hfr strains have the origin of replication functioning in the same direction.
Q:
Most plasmids are circular rather than linear.
Q:
Almost all plasmids are double-stranded DNA.
Q:
Laboratory-based genetic systems have been difficult to develop for Archaea, because they do NOT naturally undergo conjugation or transduction.
Q:
Bacterial mating (or conjugation) is a bidirectional process where nucleic acids (DNA or RNA) are transferred between two cells.
Q:
The evolutionary significance of phage conversion likely stems from an effective alteration of host cells.
Q:
Following uptake, transforming DNA becomes attached to a competence-specific protein that prevents it from nuclease attack until it reaches the chromosome.
Q:
When UV radiation damage occurs, DNA repair occurs only in the absence of template instruction.
Q:
UV radiation is a useful tool in producing mutants of microbial cultures.
Q:
The CRISPR system
A) facilitates homologous recombination through a complex system of proteins and clustered repeats.
B) recognizes foreign DNA sequences that have previously entered the cell and directs the Cas proteins to destroy them.
C) repairs DNA and increases DNA damage tolerance during times of stress.
D) synthesizes gene transfer agents during stationary phase.
Q:
High-efficiency natural transformation
A) is common in Bacteria and Archaea.
B) requires specialized DNA uptake, DNA binding, and integration proteins.
C) is only common in Archaea.
D) usually involves plasmids.
Q:
Integration of linear transforming DNA into the chromosome
A) is not required for the expression for the transformed genes.
B) is catalyzed by the RecA gene.
C) almost never occurs because restriction endonuclease will degrade the DNA before it is integrated.
D) only occurs in laboratory-based systems in artificial competent cells.
Q:
The process in which related DNA sequences from two different sources are exchanged is called
A) transduction.
B) phage conversion.
C) reversion.
D) homologous recombination.
Q:
When DNA is transferred into a prokaryotic cell it may
A) be degraded by enzymes.
B) replicate independent of the host chromosome.
C) recombine with the host chromosome.
D) be degraded by enzymes, replicate independent of the host chromosome, or recombine with the host chromosome.
Q:
If a bacterium carrying a plasmid that confers resistance to ampicillin is placed into medium without ampicillin, it may
A) gain resistance to other antibiotics.
B) transfer resistance to other cultures in the laboratory.
C) undergo a reversion mutation.
D) lose the plasmid because there is no selection for ampicillin resistance.
Q:
The designations Phe-, Leu-, and Ser+ refer to an organism's
A) plasmid type.
B) genotype.
C) phenotype.
D) mutation type.
Q:
The F (fertility) plasmid contains a set of genes that encode for the ________ proteins that are essential in conjugative transfer of DNA.
A) pili
B) SOS repair
C) transduction
D) transformation
Q:
When damaged or single-stranded DNA activates the RecA protein, the RecA protein stimulates the cleavage of LexA. This results in
A) repression of polymerase V and activation of endonuclease.
B) activation of the Hfr system.
C) derepression of the SOS system.
D) increased transduction and recombination.
Q:
Microinsertions and microdeletions often result in ________ mutations.
A) auxotrophic
B) advantageous
C) silent
D) frameshift
Q:
The SOS system repairs DNA that has gaps, breaks, and other lesions by
A) cutting DNA from other parts of the genome and pasting it into the gaps or damaged areas.
B) stabilizing single-stranded DNA until the next round of normal replication.
C) using specialized DNA polymerases that will synthesize a new DNA strand even if there is not a normal complementary DNA strand to act as a template.
D) using available mRNA and a special RNA-dependent DNA polymerase to fill in the gaps and replace damaged DNA.
Q:
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?
A) chemical mutagens
B) UV radiation
C) ionizing radiation
D) Chemical, UV, and ionizing radiation would create large deletions and rearrangements if used in a very high dose.
Q:
Mutation rates are similar in Bacteria and Archaea, yet certain stressful conditions mutation rates increase. Why is the mutation rate not constant and close to zero all of the time?
A) Increased mutation rates can be advantageous in rapidly changing environments because some random mutations may be useful for survival.
B) Microorganisms carefully control the mutation rate of their DNA to match the environmental conditions and maximize evolution.
C) The increased mutation rate under stressful conditions is an indication that the microorganisms can no longer replicate their DNA properly and are about to die.
D) Constant mutation rates would halt evolution completely.
Q:
Hfr means high frequency of ________, and these cells are capable of transferring genes from their ________ to other cells.
A) transformation / chromosome
B) transduction / plasmids
C) recombination / chromosome
D) transduction / chromosome
Q:
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
A) introduce gene transfer agents into the Streptomyces cultures to transfer antibiotic resistance genes into your Streptomyces strains.
B) 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.
C) infect the Streptomyces strains with a helper phage that will help the strains resist infection.
D) transform the Streptomyces strains with plasmids encoding antibody proteins that will protect them from phage infection.
Q:
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.
Q:
Which of the following factors has delayed the development of laboratory-based genetic systems in Archaea?
A) There are no documented systems of conjugation in Archaea.
B) Homologous recombination does NOT occur in Archaea.
C) Archaeado NOT host viruses or plasmids.
D) Many archaea grow in extreme or unusual conditions that make the use of agar and traditional mutant screening techniques problematic.
Q:
The SOS regulatory system is activated by
A) the activity of DNA polymerase IV.
B) DNA damage.
C) transcription of LexA.
D) repression of RecA.
Q:
Genetic recombination involving insertion sequences typically results in what type of mutation?
A) base-pair substitution mutation
B) silent mutation
C) frameshift mutation
D) base-pair deletion mutation
Q:
In the bacterial world, a gene located on which of the following would be the LEAST likely to be transferred?
A) R factor
B) F+
C) the phage Mu
D) the chromosome
Q:
Which of the following is most similar to lysogeny?
A) Hfr state
B) F+ state
C) F- state
D) F' state
Q:
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
A) 1, 2, 3
B) 1, 2
C) 3, 4
D) 1, 2, 4
Q:
Consider conjugation in Escherichia coli. In which of the following matings would chromosomal genes be transferred most frequently?
A) F+ F-
B) F- F-
C) Hfr F-
D) Hfr F+
Q:
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
A) complementation.
B) mitosis.
C) transfection.
D) reversion.
Q:
A deleterious mutation in recA results in
A) a decrease in specific recombination.
B) a decrease in homologous recombination.
C) an increase in homologous recombination.
D) no change in either general or specific recombination.
Q:
A "point mutation" refers to mutations involving
A) a base-pair substitution.
B) the gain of a base pair (microinsertion).
C) the deletion of a base pair (microdeletion).
D) a substitution, deletion, or addition of one base-pair.
Q:
A strain of an organism with an increased mutation rate is known as a(n)
A) adaptive mutagen strain.
B) hypermutable or mutator strain.
C) encoded dnaQ system.
D) phenotypic variation.
Q:
The enzyme transposase may be coded for by insertion sequences on a
A) chromosome.
B) phage.
C) plasmid.
D) chromosome, phage, or plasmid.
Q:
Transposition is a(n)
A) homologous recombination event.
B) analogous recombination event.
C) site-specific recombination event.
D) general recombination event.
Q:
All Hfr strains integrate into the chromosome at
A) the same locus.
B) several specific sites.
C) the same locus most of the time, although there may be some variation.
D) loci that cannot be accurately determined.
Q:
F- strains of Escherichia coli
A) do not have an F factor.
B) have the F factor as a plasmid.
C) have an integrated F factor.
D) transfer the F factor to other strains at a high frequency.
Q:
F+ strains of Escherichia coli
A) do not have an F factor.
B) have the F factor as a plasmid.
C) have an integrated F factor.
D) transfer the F factor to recipient cells at a high frequency.
Q:
Hfr strains of Escherichia coli
A) do not possess an F factor.
B) have the F factor as a plasmid.
C) have an integrated F factor.
D) transfer the complete F factor to recipient cells at a high frequency.
Q:
Homologous recombination has been observed in
A) Archaea.
B) Bacteria.
C) Eukarya.
D) Archaea, Bacteria, andEukarya.
Q:
Which of the following would NOT be a trait of a resistance plasmid?
A) It may carry antibiotic resistance genes.
B) It may carry heavy metal resistance genes.
C) It increases the host's growth rate.
D) It may undergo genetic recombination.
Q:
Plasmids that govern their own transfer are known as
A) transformable.
B) transmutable.
C) conjugative.
D) transfective.
Q:
Defend why the discovery of prions and viroids changes our view on what it takes to be an infectious particle. Be sure to explain the feature of each that distinguishes them from traditional viruses.
Q:
Why are phylogenetic studies of viruses more challenging than Bacteria? Explain how genes are selected in viruses for phylogeny and the constraints those create.
Q:
Why is so much emphasis placed on the genomic composition (e.g., ssRNA, dsDNA) of individual viruses. Provide examples to support your explanation.
Q:
Explain why the viral genome of the MS2 phage can be immediately translated. What type of genome must it have for this to be the case?
Q:
Describe one use of bacteriophage Mu for a bacterial geneticist, and explain why it is useful.