Lecture 10: Bacterial Variation and Bacterial Mobilome Flashcards
1
Q
What are the two primary ways that bacterial variation occurs?
A
Phenotypic variation
Genotypic variation
2
Q
____: the entirety of all genetic info in an organism - all chromosomes and extrachromosomal elements
____: the complete listing of all genes present in an organism
A
Genome
Genotype
3
Q
____: the complete listing of all physical features than an organism expresses
A
Phenotype
4
Q
____: A DNA/RNA molecule that controls its own replication and , therefore, is capable of self-duplication
A
Replicon
5
Q
____: replicons present in a cell, excluding host cell DNA; includes: plasmids and bacteriophages
A
Extra Chromosomal Elements
6
Q
_____: the total of all mobile genetic elements in a genome
A
Mobilome
7
Q
Elements that move within a genome (e.g transposons) are the major constituents of the mobilome in ____
A. prokaryotes
B. eukaryotes
A
B. eukaryotes
8
Q
In ___, mobile genetic elements that can move between genomes (plasmids and bacteriophages) are also important part of the mobilome
A. prokaryotes
B. eukaryotes
A
A. prokaryotes
9
Q
True or False: For any organism, the complete and total potential phenotype is limited to/determined by organism’s genotype
A
True
10
Q
_____: the situation in which ALL cells in a POPULATION respond to environmental stimuli in the SAME fashion and produce a new/altered phenotype via: expression of a gene(s)
Is genotypic change needed for this to occur?
A
Phenotypic variation
No
11
Q
True or False: Capsule production by Cryptococcus neoformans is an example of phenotypic variation
A
True
12
Q
_______: When genome of one or more cells is/are altered
A. Phenotypic Variation
B. Genotypic Variation
A
B. Genotypic Variation
13
Q
____: ability of bacteria to detect the size of the own population
A
Quorum sensing
14
Q
What are the two ways that genotypic variation occur?
A
- Mutation (internal change): change in nucleotide sequence
- Horizontal gene transfer (acquisition of gene from external source- from donor to recipient)
15
Q
True or False: Mutations rarely occur, but since bacteria are found in large populations, net effect can be significant
A
True
16
Q
Horizontal gene transfer is also known as _____ and it generates diversity and facilitates spread of advantageous genes
A
DNA recombination
17
Q
The horizontal transfer (external acquisition) of genetic material from one bacterial cell (the donor) to another cell (the recipient) can occur by one of three general mechanisms:
1.
2.
3.
A
- Transformation
- Conjugation
- Transduction
18
Q
Horizontal genetic transfer and exchange in bacteria involves transfer of either:
1.
2.
3.
A
- plasmid
- virus
- transposon
19
Q
____: Uptake of “naked” exogenous DNA (plasmid or portion of chromosome fragment) by recipient cell
A. Transformation
B. Transduction
C. Translation
A
A. Transformation
20
Q
The ____ cell chromosomal genes encode for the mechanism of transformation
A. Donor Cell
B. Recipient Cell
A
B. Recipient Cell
21
Q
For transformation to occur, which cell must be in a state of competence (meaning ready to acquire naked DNA)
A. recipient cell
B. donor cell
A
A. recipient cell
22
Q
In transformation, the ___ cell lyses, releasing DNA
A. Donor Cell
B. Recipient Cell
A
A. Donor Cell
23
Q
What are the two limitations of Transformation?
A
- Not all bacterial genomes are competent
- Need a chromosomal segment for integration/recombination to occur - plasmid DNA does not require this though
24
Q
What is the significance of conjugation and transformation?
A
Results in the transfer of antibiotic resistance and virulence factors among bacteria
25
___: Horizontal gene transfer of DNA from donor bacterial cell to a recipient bacterial cell via a mechanism encoded by a conjugative (transmissible) plasmid present in donor cell; it involves CELL TO CELL contact
A. Conjugation
B. Translation
C. Transformation
A. Conjugation
26
True or False: Cell to cell contact is essential in conjugation
True
27
True or False: During conjugation, a RNA copy of the conjugative plasmid is transferred from donor to recipient cell during plasma RNA replication
False - DNA
28
During conjugation, both single stranded DNA strands (in mom and daughter cell) are made ____ and process is complete
double stranded
29
What is a limitation for conjugation?
Conjugative plasmids have host ranges
30
____: the horizontal transfer of genetic information (chromosomal or plasmid DNA) from one bacterium to another via bacteriophage (bacterial virus)
Transduction
31
What are the two types of phages?
1. The lytic (virulent) phage
2. The temperate phage
32
___ infects bacterial host cell, replicates, then kills the bacterium (via: lysis), thereby releasing new progeny to infect other cells
A. The lytic (virulent) phage
B. The temperate phage
A. The lytic (virulent) phage
33
_____ infects host cell. However, after it enters cytoplasms of host cell, it has two options:
1. go through normal lytic cycle
2. become latent virus (prophage) - replicates in synchrony with bacterial DNA and is passed to daughter cells.
From here, phage can either a) remain in cytoplasm or b) integrate into the bacterial chromosome
A. The lytic (virulent) phage
B. The temperate phage
B. The temperate phage
34
The latent virus (prophage) will do one of which two things?
1.
2.
1. Remain in cytoplasm
2. Reintegrate/insert into host cell DNA
35
True or False: The latent virus will always lead prophage DNA to replicate in synchrony with host cell DNA, leading it to it being passed onto daughter cells
True
36
Antigenic variation of Type IV pilus of N.gonnorhoea: from silent loci to express loci is an example of ____
phenotypic variation
37
True or False: Transformation, acceptance of DNA from donor is not specific
True
38
True or False: For transformation, the donor’s DNA can be chromosomal or plasmid, but must be free/naked DNA
True
39
True or False: In conjugation, contact
between donor and
recipient is not required
False - it IS required!
40
In conjugation, transfer of a
conjugative plasmid,
start from the ____ end
of the nicked DN
A. 5’ end
B. 3' end
A. 5’ end
41
In conjugation, transfer of ‘nick DNA’ occurs during ____
DNA replication
42
True or False: In conjugation, both ssDNA strands (from donor and
recipient cell) remain single stranded!
False - are made dsDNA
43
True or False: There is specific host range for conjugative plasmid
True
44
If possessing latent phage, the
bacterial cell is said to be _____
lysogenized
45
What are the two types of transduction?
1. Generalized
2. Specialized
46
True or False: Generalized transduction is mediated by both lytic and temperate bacteriophage
True
47
Why are ALL donor genes equally likely to be transferred/transduced
during generalized transduction?
Host chromosome is broken down into fragments
48
Random fragment of bacterial DNA is accidentally encapsulated in a phage protein coat. This best describes which type of transduction:
A. Generalized Transduction
B. Specific Transduction
A. Generalized Transduction
49
In generalized transduction, all regions of the bacterial chromosome can be transduced, but only bacterial _____ (no phage DNA!!) will be in transducing particles
chromosomal DNA
50
True or False: Transfer of drug resistance in Staphylo is an example of generalized transduction
True
51
Prophage integrates into bacterial chromosome and, occasionally, prophage DNA is incorrectly excised, taking adjoining specific bacterial DNA with it.
This best explains:
A. Generalized Transduction
B. Specialized Transduction
B. Specialized Transduction
52
In specialized transduction, the transducing particles carry both host ___ DNA and ___ DNA
host chromosomal DNA; phage DNA
53
True or False: In both generalized and specialized transduction, the recombinants have the same genotype from both the donor and recipient
False - in both cases, they have a genotype that is UNALIKE both donor or recipient
54
In ____, transducing phage infects new host cell (after phage replicants) where recombinant (cross over) can occur
A. Generalized Transduction
B. Specialized Transduction
C. Both generalized and specialized transduction
C. Both generalized and specialized transduction
55
The host range of the phages is a limitation of both ___ and ___
transduction and conjugation
56
Significance of transduction?
Resulted in the transfer of abx resistance and virulence factors among bacteria (e.g toxin)
57
True or False: In generalized transduction, donor genes are likely to be transferred unequally
False - in generalized transduction, ALL donor genes are EQUALLY likely to be transferred
58
Specialized transduction is only mediated only by which bacteriophages?
A. Lytic (virulent) phage
B. Temperate phage
B. Temperate phages
59
In specialized transduction, transducing particles carry both host ___ DNA and ___ DNA
chromosomal; phage
60
True or False: In both GENERALIZED and SPECIALIZED transduction, RECOMBINATION can occur and create genotypes different from either the donor or recipient
True
61
When a recipient bacterium exhibits a NEW PHENOTYPE due to the acquisition of a prophage (latent bacteriophage), ____ ____ occurs.
A. Phagic conversion
B. Lysogenic converstion
B. Lysogenic conversion
62
Acquisition of antibiotic resistance; diphtheria toxin acquired by Corynebacterium; and SPE acquired by streptococcus are all examples of _____
lysogenic conversion
63
____: double stranded covalently closed circular DNA molecules that reside in bacterial cytoplasm
Plasmid
64
True or False: Plasmids are extrachromosomal elements but are unable to insert into the chromosome
False - they are ECE and can insert into the chromosome
65
True or False: Plasmids encode traits that are not essential fro viability and replicate independent of chromosome (replicon)
True
66
____ provide mechanism for horizontal gene transfer within population of microbes and typically provides selective advantage under a given environmental state
Plasmids
67
True or False: Plasmids require direct, mechanical transfer by conjugation or the intentional uptake of genetic element by transformation
True
68
True or False: Plasmids smaller than 7.5 kb pairs are usually:
1) non-conjugative
2) have high copy numbers
3) rely on bacterial host to provide some fxtions require for replication
Larger plasmids (>40 kb) are usually:
1) conjugative
2) have small copy numbers
3) code for ALL functions required for their replication
True
69
Plasmids be easily purified and used as ___
vectors
70
What three ways can plasmids be transferred?
1. Conjugation
2. Transformation
3. Transduction (rare)
71
________: plasmids that mediate conjugation. These plasmids are usually LARGE and have all the genes necessary for autonomous replication + for transfer of DNA to recipient (genes for sex pilus)
_____: Non-conjugative plasmids are those that cannot mediate conjugation. They are usually smaller than conjugative plasmids and they lack one or more of the genes needed for transfer of DNA
A. Conjugative plasmids
B. Non-conjugative plasmids
C. Fertility plasmids
A. Conjugative plasmids
B. Non-conjugative plasmids
72
What are five phenotypic plasmids?
1. Fertility plasmids (F Factor)
2. Bacteriocinogenic plasmids (col factor)
3. Resistance plasmids (R Factors)
4. Degradative plasmids
5. Virulence plasmids
73
_____: plasmids that have genes which code for substances that kill other bacteria. These substances are called colicins or bacteriocins.
A. Fertility Plasmid (F Factors)
B. Resistance Plasmids
(R Factors)
C. Bacteriocinogenic Plasmids (col factor)
C. Bacteriocinogenic Plasmids (col factor)
74
Which plasmids carry antibiotic resistance genes?
A. Fertility Plasmid (F Factors)
B. Resistance Plasmids
(R Factors)
C. Bacteriocinogenic Plasmids (col factor)
D. Degradative Plasmids
B. Resistance Plasmids
(R Factors)
75
Which plasmids enable digestion of unusual substances (e.g toluene or salicylic acid)?
A. Fertility Plasmid (F Factors)
B. Resistance Plasmids
(R Factors)
C. Bacteriocinogenic Plasmids (col factor)
D. Degradative Plasmids
D. Degradative Plasmids
76
True or False: Virulence plasmids turn the bacterium into a pathogen (siderophores for iron uptake, toxins)
True
77
What are the 3 medically important properties of
pathogens?
1. Antibiotic resistance
2. Toxins producing
- heat-labile/heat-stable enterotoxins of E coli
-exfoliative toxin of Staphylococcus aureus,
-Neurotoxin of Clostridium
3. Synthesis of cell surface structures required for adherence/colonization
78
____ is a useful method for assessing possible relatedness of clinical isolates of particular bacterial species, based on size of plasmids
Plasmid profiles
79
What is a positive match in a plasmid profile?
Strains of the same organism that have SAME number and SIZE plasmids
80
True or False: Strains with different NUMBERS of and SIZES of plasmids are not epidemiologically related
True
81
True or False: Plasmids encoding ZFN could be used to deliver therapeutic gene to pre-selective chromosomal site, offer way to cause SITE SPECIFIC ds break to DNA genome and cause homo recomb
True
82
____: segments of DNA that can move within genome or plasmids and are widespread among prok/euk/viruses
Transposons
83
Unlike plasmids, transposons do not contain genetic info necessary for their own ___(meaning transposons are NOT replicons!)
replication
84
What does replication of transposon depend on?
Physical integration with a genome replicon
85
True or False: Transposons may cause mutation and increased or decreased amount of DNA in genome
True
86
___: an enzyme that catalyzes insertion of transposon at new site
Transposase
87
True or False: The inverted terminal repeat flanks the coding region for the transposase; it marks point at which transposon in removed or reinserted into genome
True
88
What is a diagnostic feature of mobile genetic elements?
A. Transposase
B. Target Site Repeat
B. Target site repeats
89
What insertion elements make up a transposon?
1. Transposase
-Gene producing an enzyme that catalyzes insertion of transposon at new site
2. Inverted Terminal Repeat
- Flanks coding region for transposase
- Marks point at which transposon is removed or reinserted into genome
3. Target Site Repeats/Direct Repeats
- Short stretch of genomic DNA that's repeated on either side of insertion element
-Diagnostic feature of mobile genetic elements!
90
True or False: Transposons have a low specificity to insertion site
True
91
92
kkk
93
Which transposon corresponds to bacteria and consists only of DNA that moves directly from place to place?
A. Class I
B. Class II
C. Class III
B. Class II
94
___ transposons carry genes for specialized
functions such as antibiotic resistance and are flanked by IE
Complex
95
How does one detect genetic exploitation of transposons?
Selection of specialized genetic info (e.g antibiotic resistance) that they carry
96
Dissemination of transposons throughout a population is made possible by insertion of ___ into plasmid
Plasmids are transferred among bacterial cells primarily via ____
transposon; conjugation
97
98
True or False: Bacterial Transposons (Class 2) use cut and paste process (whereby transposons is cut out of location and inserted into new location)
True
99
True or False: Class I transposons are known to be involved in changes in traits, such as: colony morphology, pigmentation, antigenic features
False - class II
100
Transposon that carry a selectable marker
(such as antibiotic resistance) has been used to make random mutations in the
genome of pathogen. This is known as: _____ ______.
transposon mutagenesis
101
True or False: When transposons are used for research, the mutants are screened for loss of virulence
due to interruption by the transposon. This also serves a marker to locate the gene of
interest.
True
102
True or False: In medically important bacteria, genes that
determine production of adherence antigens,
toxins, or other virulence factors, or specify
resistance to one or more antibiotics, are
often located in complex transposons
True
103
When a transposon is incorporated into a
plasmid, it can leave the host cell and move
to another cell, which is one way to spread
______
virulence factor
104
How are Pathogenicity Islands (PI) acquired?
They encode genes that contribute to the ___ of the pathogen
horizontal gene transfer; virulence
105
True or False: PI's are incorporated in the genome of PATHOGENIC bacteria but are
usually absent from NON-PATHOGENIC
organisms of the same or closely related
species
True
106
Which genes are associated with Pathogenicity Islands?
A. mRNA
b. tRNA
c. gRNA
d. nuclear cDNA
b. tRNA (target site for integration of DNA)
107
Pathogenicity Islands contain high levels of which two nucleotides (___ and ____) and are flanked by ___ repeats (sequence of bases at two ends are the same)
guanosine and cytosine; direct
Note: given then they are flanked by direct repeats, they have features of transposons
108
What features do pathogenicity islands share with transposons?
1. Carry functional genes
2. May move from one tRNA locus to another on the chromosome or plasmid
109
What type of bacteria are PI's predominately found in?
A. Gram (+)
B. Gram (-)
C. Archea
B. Gram (-)
110
True or False: Typical examples of PI's are: adhesins, toxins, iron uptake systems, invasins
True
111
Do genomic islands play a role in microbial evolution?
Yes!
112
____: DNA/RNA viruses that infect bacteria
Bactriophage
113
Many different genomic islands have been discovered in a variety of pathogenic as well
as non-pathogenic bacteria acquired by
_________
horizontal gene transfer
114
Viral DNA (prophage) either:
1) integrates into host cell chromosome
2) functions as a ___ in the bacterial cytoplasm
plasmid
115
Bacteria with latent phages (have prophages) are said to be ___
lysosgenized
116
A typical genomic island (GEI) is flanked by ____ structures
direct repeat (DR)
117
Typically, GEIs carry multiple functional and fragmented _____ (IS) elements and other mobility-related genes
insertion sequence
118
Antigenic variation of Type IV Pilus of N. Gonorrhea from silent to expressed loci is an example of ____ variation
phenotypic variation
119
True or False: Conjugation involves cell:cell contact while transduction occurs via bacteriophage (bacterial virus)
True
120
Transformation, Transduction, and Conjugation all have what three things in common?
External and unilateral transfer of genetic information
121
True or False: For transformation to occur, acceptance of DNA from donor is specific
False - non-specific
122
For transformation to occur, donor's DNA can be chromosomal or plasmid. However, what type of DNA must it be?
A. double stranded
B. free/naked
C. induceable
B. free/naked
123
True or False: Transformation can occur naturally but cannot be induced using artificial means
False - can be done naturally or artificially
124
What is being transferred during conjugation?
Conjugative plasmid
125
If a bacterial cell contains a latent phage, the cell is said to be _____
lysogenized
126
Which phage replicates using both lytic and lysogenic cycles?
Temperate Phage
127
Specialized transduction is mediated by only _____, which integrates into the host cell DNA
temperate bacteriophage
128
True or False: In generalized transduction, the genes that are transferred are only the ones that lie close to point of insertion of the prophage
False - this occurs with specialized transduction
129
"Pathogen error" is associated with _____ transduction while ______ is due to "snipping error" due to prophage making a mistake and, ultimately, carrying a portion of donor DNA with them
Generalized Transduction; Specialized Transduction
130
True or False: Lysogenic conversion is limited by host range of phage
True
131
Which plasmid mediates conjugation and is large (has all genes needed for autonomous replication and transfer of DNA to recipient)
A. Conjugative Plasmid
B. Non-Conjugative Plasmid
A. Conjugative Plasmid
132
___ plasmid are transferred during conjugation while ____ plasmids carry antibiotic resistance genes
Fertility plasmid (F Factor); Resistance plasmids (R Factor)
133
_____ Transposons (Class II) cut themselves out from their original location and insert themselves somewhere else in the genome. ___ Transposons (Class I) make a copy of themselves that inserts into a new location, leaving original transposon intact
A. DNA; RNA
B. RNA; DNA
C. DNA; DNA
D. RNA; DNA
A. DNA; RNA
134
A typical genomic island is flanked by _____ and carry multiple functional and fragmented insertion sequences
direct repeat structures
135
True or False: Some bacteriophages exist in latent states (prophage)
True
- No harm to bacterial cell
136
For bacteriophages, the viral DNA (prophage) either integrates into ____ chromosome or exists as an extrachromosomal ____ in bacterial cytoplasm
host cell chromosome; plasmid
