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

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.

Answer 2

A

Question 3

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

Answer 3

A

Question 4

During conjugation, __________ is used for replication beginning at __________.

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

Question 5

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 6

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 7

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 8

The process of importing free DNA into cells is known as:

A) transposition
B) conjugation
C) specialized transduction
D) generalized transduction
E) transformation

Question 9

The transfer of F factor in E. coli from one donor cell to a __________ cell results in two __________ cells.

A) donor; donor
B) recipient; recipient
C) donor; recipient
D) recipient; donor
E) recipient; Hfr

Question 10

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 gens turned off
C) induction in the presence of fertility factors
D) each gene has an attenuator
E) use of a restriction-modification system

Question 11

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

Question 12

The recipient of Hfr conjugation __________ becomes an F⁺ or Hfr cell.

A) never
B) rarely
C) frequently
D) usually
E) never

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

A derivative F plasmid that contains host DNA is called an:

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

Question 15

Interrupted mating involves breaking __________ bridges using a blender.

A) transformation
B) transduction
C) conjugation
D) transposition
E) bacteriophage

Question 16

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 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

F factor contains how many origins of replication?

A) one
B) two
C) three
D) four
E) none

Question 19

Restriction enzymes are categorized into three types based on all of the following EXCEPT:

A) the number of subunits in the enzyme
B) the phages that are susceptible to their activity
C) the cofactors required for activity
D) where the DNA cleavage sites are located
E) whether the enzyme methylates the host DNA

Question 20

Approximately how long does it take for an Hfr strain to transfer its entire chromosome?

A) 30 minutes
B) 60 minutes
C) 100 minutes
D) 180 minutes
E) 300 minutes

Question 21

A synonymous substitution is a(n):

A) inversion
B) deletion
C) silent mutation
D) insertion
E) missense mutation

Question 22

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 23

A __________ colony is the result of a high mutation rate.

A) colored
B) wrinkled
C) large
D) sectored
E) convex

Question 24

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

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

Question 25

Which of the following forms of DNA repair is error-prone?

A) base excision
B) methyl mismatch
C) SOS repair
D) nucleotide excision
E) photoreactivation

Question 26

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 27

Ames used his reversion test with Salmonella to screen compounds for:

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

Question 28

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 29

Which of the following requires no homology between donor and recipient DNA molecules?

A) phage integration
B) phase variation
C) site-specific recombination
D) transposition
E) general recombination

Question 30

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 31

Recent experiments have suggested that human DNA known as __________ has been transferred to __________.

A) Ti plasmid; Wolbachia
B) Ti plasmid; Neisseria
C) LINES; Salmonella
D) LINES; Neisseria
E) F factor; Neisseria

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

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 34

A loss-of-function mutation could NOT be caused by:

A) frameshift mutation
B) nonsense mutation
C) silent mutation
D) knockout mutation
E) insertion mutation

Question 35

RecA molecules are also called __________ because they are able to scan DNA molecules for homology and align the homologous regions, forming a triplex DNA molecule.

A) recombinases
B) integrases
C) polymerases
D) synaptases
E) transposases

Question 36

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

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

Question 37

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 38

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 39

Which of the following mutagens does not cause point mutations?

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

Question 40

Phase variation is an example of:

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

Question 41

Name two traits that have been genetically engineered into plants. How were genes for these activities incorporated into the plant genome? Why is this method more advantageous than typical plant breeding?

Question 42

Approximately what percent 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 43

How is the Ames reversion test performed, and what is it used to determine?

Question 44

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 45

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 46

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

Question 47

Which of the following genes belongs to the so-called flexible gene pool?

A) ribosome
B) cell envelope
C) antibiotic resistance
D) DNA replication
E) metabolic pathways

Question 48

__________ are designed to spread when a population is facing danger.

A) F plasmids
B) Bacteriophage
C) Resistance plasmids
D) Conjugative transposons
E) Genome reductions

Question 49

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

Question 50

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 51

Approximately what percent 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 52

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 53

__________ is the process of moving a genetic element within or between DNA molecules.

A) Conjugation
B) Transduction
C) Transformation
D) Transposition
E) Reversion

Question 54

Define what it means for genes to be cotransduced. What does it tell you about the location of these genes and why?

Question 55

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 56

Evolution toward pathogenicity may involve:

A) horizontal gene transfer
B) gene loss
C) gene acquisition
D) A and C
E) all of the above

Question 57

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

Question 58

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 59

Why is genetic recombination advantageous to an organism?

Question 60

How do bacterial cells protect themselves from invading foreign DNA? Why aren't the bacteria harmed by this process?

Question 61

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

Question 62

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

Question 63

What are the differences between replicative and nonreplicative transposition?

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

When a nonpermissive strain of Salmonella was infected with a P22 phage carrying a tetracycline resistance gene, the Salmonella still became resistant at a high frequency. How did this happen and what suggested this was the case?

Question 66

Describe four of the error-proof DNA repair mechanisms.

Question 67

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

Question 68

Describe four of the informational classes of mutations.

Question 69

Define a pseudogene and what it is thought to represent.

Question 70

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