Deck 9: Gene Transfer, Mutations, and Genome Evolution

Question 1

Newly replicated, and consequently ________, DNA sequences are invisible to a restriction enzyme.

A) mutated
B) restricted
C) modified
D) hemimethylated
E) single-stranded

Answer 1

D

Question 2

Which of the following bacteria requires artificial assistance to become competent to take up DNA?

A) Bacillus
B) E. coli
C) Haemophilus
D) Neisseria
E) Streptococcus

Answer 2

B

Question 3

The transformasome necessary for cell competency in Gram-positive bacteria is regulated using which of the following methods?

A) an alternative sigma factor to transcribe the necessary genes
B) a repressor protein to keep the genes turned off
C) induction in the presence of fertility factors
D) each gene has an attenuator
E) use of a restriction-modification system

Answer 3

A

Question 4

An example of vertical gene transfer is the

A) development of many genetically diverse mesorhizobia via incorporation of a 500 kB segment from a mesorhizobium.
B) uptake of beta-lactamase genes by Streptococcus pneumoniae.
C) transfer of CRISPR spacers to daughter cells during cell division.
D) transfer of a Ti plasmid from agrobacterium to a plant.
E) transfer of conjugative plasmids from one strain to another.

Question 5

During conjugation, DNA pol ________ is used for replication beginning at ________.

A) I; oriV
B) III; oriV
C) I; oriT
D) II; oriT
E) III; oriT

Question 6

Consider a semipermeable membrane that allows molecules such as DNA and proteins to pass through to the other side. This membrane is not permeable to structures such as ribosomes, viruses, and cells. The following tubes are set up with membrane in between the two compartments in each tube. Tube 1. Cells, both donors and recipients, on both sides of the membrane
Tube 2. Bacteriophage on one side of the membrane and recipient cells on the other
Tube 3. DNA on one side and recipient cells on the other side
In which of these tubes would you see a genetic process, and what is the name of that process?

A) Tube 1; conjugation
B) Tube 2; conjugation
C) Tube 3; conjugation
D) Tube 3; transduction
E) Tube 3; transformation

Question 7

During generalized recombination, ________ proteins catalyze branch migration at crossovers called ________.

A) RuvAB; Holliday junctions
B) RuvAB; duplexes
C) RecBCD; Holliday junctions
D) RecBCD; duplexes
E) RecA; duplexes

Question 8

Agrobacterium can transfer DNA to ________ using its ________.

A) E. coli; LINES
B) E. coli; Ti plasmid
C) plants; LINES
D) plants; Ti plasmid
E) plants; opines

Question 9

The process in which bacteriophages carry host DNA from one cell to another is known as

A) conjugation.
B) transformation.
C) transposition.
D) recombination.
E) transduction.

Question 10

Genomes are considered to be mosaic. Which of the following statements provides the LEAST support for this idea?

A) E. coli can receive plasmids from other strains of Gram-negative bacteria.
B) The archaeon Methanocaldococcus jannaschii has many proteins with sequence homology to proteins found in both bacteria and eukarya.
C) Agrobacterium can transfer plasmids to plants.
D) Genome sequencing and informatics has revealed a variety of homologous genes throughout the domains of life.
E) Genes from Mesorhizobium loti have been found in other new species of Mesorhizobium.

Question 11

A derivative F plasmid that contains host DNA is called an ________ plasmid.

A) F
B) F+
C) F-
D) F'
E) Hfr

Question 12

During conjugation, the DNA passes through the ________, NOT the ________.

A) membranes; pilus
B) pilus; membranes
C) pilus; phage
D) phage; pilus
E) F factor; phage

Question 13

In order to transfer, an F factor must have which of the following?

A) oriV and its own DNA polymerase
B) oriV and tra genes
C) oriT and tra genes
D) oriT and its own DNA polymerase
E) oriT, tra genes, and its own DNA polymerase

Question 14

In the figure shown below, the role of the -Me groups on the second sequence is that the methyl groups

A) direct an enzyme to cut at those sequences.
B) signal that the DNA is not foreign and thus it should not be cut.
C) signal for a transposon to excise itself.
D) signal for the sequence to be incorporated in CRISPR.
E) serve as a sequence for specialized transduction.

Question 15

CRISPR is considered an example of adaptive immunity in bacteria and archaea because it

A) methylates host DNA and destroys invading DNA.
B) requires host "pac" sites in order to destroy invading DNA.
C) minimizes damage from foreign DNA by using guide RNA similar to the invader and cas proteins to cleave the foreign DNA.
D) prevents the production of cell surface receptors that allow phages to get into the cell.
E) prevents archaeal DNA from infecting bacteria.

Question 16

The main components of CRISPR anatomy include

A) methylation sites on palindromic sequences.
B) int genes with att sites for homology.
C) inverted repeats and genes encoding transposase.
D) short direct repeats, spacers, and genes encoding cas proteins.
E) cell surface receptors.

Question 17

Competence in Gram-positive organisms is induced by

A) calcium and cold.
B) electrical currents.
C) competence factors made of peptides.
D) presence of biofilm.
E) Competence is not induced in Gram-positive bacteria.

Question 18

The difference between generalized and specialized transduction is

A) the size of the plasmids being moved.
B) the size of the phages being used.
C) that in generalized transduction, chromosomes are moved, whereas in specialized transduction, plasmids are moved.
D) that in generalized transduction, any DNA can be moved, but with specialized transduction, only certain DNA near the phage site can be moved.
E) There is no difference.

Question 19

A difference between type II restriction enzyme and type I or type III restriction enzymes is that

A) type II enzymes require shorter recognition sequences.
B) type II enzymes cut at the recognition sequence rather than elsewhere.
C) type I and III cut palindromic sequences but type II does not.
D) type I and III require different proteins for methylation and cutting.
E) type II enzymes are found only in Gram-positive bacteria.

Question 20

Bacteria have developed a "Halt! Who goes there?" approach to gene exchange to prevent unrestricted incorporation of DNA into the cell. It is called ________ and ________.

A) conjugation; recombination
B) transformation; transposition
C) restriction; modification
D) transduction; Hfr
E) mobilizable; F plasmid

Question 21

Which of the following is NOT a feature of a transposon?

A) ability to move around a genome
B) presence of inverted repeats at each end
C) the ability to transfer via a phage head
D) genes coding for a transposase activity
E) presence of antibiotic resistance genes

Question 22

Numerous human genetic diseases are caused by mutations in homologs of bacterial

A) transposons.
B) ligases.
C) integrases.
D) polymerases.
E) repair genes.

Question 23

In the figure shown below, the cause of the appearance of these bacterial colonies is ________ and is caused by ________.

A) sectoring; liver homogenate
B) pyrimidine dimers; ultraviolet light
C) reversion mutations; rat liver homogenate
D) frameshift mutations; high mutation rate
E) sectoring; high mutation rate

Question 24

The process of moving a genetic element within or between DNA molecules is

A) conjugation.
B) transduction.
C) transformation.
D) transposition.
E) reversion.

Question 25

Which of the following mutagens does NOT cause point mutations?

A) caffeine
B) 5-bromouracil
C) nitrosoguanidine
D) nitrites
E) acridine dyes

Question 26

Spontaneous mutations can be caused by

A) tautomers having altered base pairings.
B) acridine intercalating into DNA.
C) UV causing pyrimidine dimers.
D) 5-bromouracil.
E) alkylating agents.

Question 27

The reaction of cytosine, shown below, happens ________ and causes ________.

A) spontaneously; pyrimidine dimers
B) when irradiated; pyrimidine dimers
C) when treated with acridine; pyrimidine dimers
D) when irradiated; transition mutations
E) spontaneously; transition mutations

Question 28

Which of the following is the activator of the SOS response?

A) RecA
B) LexA
C) FtsZ
D) sulA
E) uvrA

Question 29

After extensive DNA damage, special DNA polymerases are expressed that sacrifice replication ________ to rescue the damaged genome.

A) initiation
B) accuracy
C) termination
D) modification
E) restriction

Question 30

Which of the following forms of transposition specifically describes the transfer of DNA from one cell to another?

A) nonreplicative
B) replicative
C) composite
D) complex
E) conjugative

Question 31

Ames used his reversion test with Salmonella to screen compounds for

A) virulence.
B) pathogenicity.
C) toxicity.
D) antibiotics.
E) mutagenicity.

Question 32

Which of the following is NOT true of a pyrimidine dimer?

A) It can be repaired by photoreactivation.
B) The pyrimidines are base-paired one to another.
C) It is produced by ultraviolet light.
D) It blocks DNA replication.
E) It blocks transcription.

Question 33

Large regions of sequence homology are required when recombining DNA molecules by ________ recombination.

A) general
B) site-specific
C) specialized
D) transposition
E) reversion

Question 34

Mutations that occur even in the absence of an added mutagen are known as ________ mutations.

A) spontaneous
B) silent
C) missense
D) nonsense
E) frameshift

Question 35

In the figure below, which type(s) of mutation(s) is/are introducing frameshifts?

A) A and B
B) C and D
C) D and E
D) A, B, and C
E) only D

Question 36

Phase variation is an example of

A) conjugation.
B) site-specific recombination.
C) general recombination.
D) transposition.
E) radiation resistance.

Question 37

Consider a culture of 1,000 cells. Each cell divides once to yield a total of 2,000 cells. A measurement of the mutation rate in this culture would be based on the total number of

A) 2,000 cells.
B) genes in the bacterium.
C) generations, which in this case is one.
D) cell divisions, which is 1,000.
E) mutations found in that culture.

Question 38

Knockout mutations can include ________ mutations and ________ mutations.

A) gain of function; loss of function
B) gain of function; missense
C) frameshift; nonsense
D) silent; nonsense
E) silent; missense

Question 39

Consider a culture of 10,000 cells that double to 20,000 cells. If measuring 100 mutations in the population, the mutation frequency would be

A) 100 mutations / ~4,500 genes = 0.022.
B) 100 mutations / 1 generation = 100.
C) 100 mutations / 20,000 cells = 0.05.
D) 100 mutations / 10,000 new cells = 0.001.
E) (100 / ~4,500 genes) / 10,000 new cells = 0.0000022.

Question 40

The experiment outlined below is a/an ________ test. The role of the rat liver homogenate is to ________.

A) pathogenicity; provide growth factors such as amino acids that the pathogen may require
B) pathogenicity; chemically modify the test chemical
C) Ames; control for spontaneous mutations
D) Ames; provide growth factors such as amino acids that the pathogen may require
E) Ames; chemically modify the test chemical

Question 41

Which of the following statements is LEAST supportive of the idea that genetic exchange between bacteria occurs in the human gastrointestinal tract?

A) the high bacterial cell density in this environment
B) the presence of mixed species and biofilms in this environment
C) the presence of dead bacteria as a source of extracellular DNA for transformation
D) the passage of antibiotic resistance genes from one bacterium to another within a patient
E) the presence of pseudogenes in bacteria

Question 42

Is an Hfr cell also considered to be F⁺? Why or why not?

Question 43

Why does a genetic experiment using recombination generally involve screening hundreds of millions of cells to find a few recombinants that form visible colonies?

Question 44

Distinguish between generalized and specialized transduction.

Question 45

The figure shown below diagrams a variety of genomic islands. What characteristics do these islands in the diagram share?

A) They code for pathogenicity.
B) They are coded on transposons.
C) They have a GC content similar to the rest of the genome.
D) They encode type II secretion systems.
E) They have direct repeats and mostly insert near a tRNA gene.

Question 46

Which of the following LEAST supports the idea of genome reduction?

A) Pseudogenes found in some organisms are no longer expressed but have homology to functional genes in other species.
B) Virulence factors are found on pathogenicity islands.
C) Pathogenic shigellae lack major regions of genes that the closely related E. coli possesses.
D) Bacteria no longer need "pseudogenes" when growing in new environments.
E) Over half of the genome of the obligate intracellular pathogen, Mycobacterium leprae, is composed of pseudogenes that are no longer needed.

Question 47

The following statements about superfamily proteins are true EXCEPT that

A) ABC (ATP-binding cassette) transporters serve as an example.
B) proteins with structural and functional similarity but low sequence homology may be considered superfamilies.
C) superfamily proteins are encoded by genes found on superfamily islands.
D) superfamily proteins are encoded by genes that have been duplicates and then mutated.
E) proteins such as HSP70 that are found in all domains of life are examples.

Question 48

Many infectious bacteria have regions of DNA coding for virulence factors. These regions are called

A) transposases.
B) pathogenicity islands.
C) inverted repeats.
D) F plasmids.
E) genome reductions.

Question 49

In the figure shown below, product A is the result of ________ and product B is the result of ________.

A) vertical gene transfer; horizontal gene transfer
B) nonreplicative transposition; replicative transposition
C) nonhomologous recombination; homologous recombination
D) missense mutation; nonsense mutation
E) generalized transduction; specialized transduction

Question 50

CRISPR is viewed as the adaptive immune system of bacteria, yet restriction/modification systems also play roles in bacterial defense. Compare and contrast how both systems protect the host.

Question 51

Compare and contrast general and site-specific recombination.

Question 52

Approximately what percentage of the 4,288 open reading frames of E. coli have no known or annotated function?

A) 10
B) 14
C) 24
D) 52
E) 70

Question 53

When a population is under threat, which of the following would spread?

A) F plasmids
B) bacteriophage
C) resistance plasmids
D) conjugative transposons
E) genome reductions

Question 54

Which of the following is evidence of gene reduction?

A) altered GC content
B) different codon usage
C) pseudogenes
D) genomic islands
E) transposons

Question 55

Describe the differences in the transformation process in Gram-positive and Gram-negative organisms.

Question 56

Phages that carry host DNA are called transducing particles. Describe how the Salmonella P22 phage accidentally packages host DNA.

Question 57

Approximately what percentage of the genome of E. coli O157:H7, which has been responsible for several outbreaks of food-borne disease, has been acquired from other species?

A) 5
B) 10
C) 25
D) 40
E) 50

Question 58

Evolution toward pathogenicity may involve

A) horizontal gene transfer.
B) gene loss.
C) gene acquisition.
D) horizontal gene transfer and gene acquisition.
E) horizontal gene transfer, gene loss, and gene acquisition.

Question 59

Describe the process whereby DNA is transferred from Agrobacterium to plants.

Question 60

Which of the following is NOT an example of a genomic island?

A) pathogenicity islands in infectious organisms
B) symbiosis islands in Mesorhizobium
C) resistance islands in Staphylococcus
D) transposition islands within bacteria
E) metabolic islands within Salmonella

Question 61

What are the differences between replicative and nonreplicative transposition?

Question 62

Why did Ames modify the test to incorporate treatment of the potential mutagen with rat liver extract?

Question 63

Describe four of the informational classes of mutations.

Question 64

Describe a frameshift mutation in terms of insertions and deletions. Does an insertion always result in a frameshift mutation? Will an insertion always render the gene product nonfunctional?

Question 65

Describe four of the error-proof DNA repair mechanisms.

Question 66

Define a pseudogene and what it is thought to represent.

Question 67

Outline any three characteristics of the human gastrointestinal tract that makes it an ideal environment for genetic exchange.

Question 68

Why is SOS repair considered to be an error-prone repair mechanism? Why would an organism use an error-prone mechanism?

Question 69

Describe the purpose of an Ames revision test and how it is performed.

Question 70

Site-specific recombination is RecA independent and requires very short regions of homology between donor and target DNA. Describe an example in either E. coli or Salmonella.

Question 71

What is transcription-coupled repair and why is it important for the cell?

Question 72

Describe two processes that may happen during the evolution toward pathogenicity.