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Microbiology Quiz 1 > Microbio 3-26 genetics > Flashcards

Microbio 3-26 genetics Flashcards

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1
Q

What is the structure of the genome in bacteria?

A

haploid (single copies), double-stranded, circular DNA molecule

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2
Q

What type of replication does the bacterial undergo?

A

semi-conservative replication and bidirectional (form the Ori)

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3
Q

How many genes does the bacterial genome encode for?

A

~4000 genes

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4
Q

Define silent mutations.

A

mutation that does not give rise to a change in phenotype

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5
Q

Why are some mutations silent?

A

1) the genetic code is degenerate 2) conservative changes in a.a. may not affect the function (ie non-polar -> non-polar)

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6
Q

What are point mutations?

A

mutations that are single base pair changes

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7
Q

What are transition mutations?

A

point mutation in a codon that results in a purine -> purine conversion and a pyrimidine -> pyrimidine conversion

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8
Q

What are transversion mutations?

A

point mutation in a codon that results in a purine -> pyrimidine conversion, and vice versa.

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9
Q

What is missense mutation?

A

point mutation that changes the codon from one a.a. to another a.a.

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10
Q

What is a nonsense mutation?

A

point mutation that changes the codon to a stop codon

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11
Q

What is a deletion mutation?

A

removal of one or more nucleotides

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12
Q

What is an insertion mutation?

A

addition of one or more nucleotides

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13
Q

What is a frameshift mutation?

A

shift in reading frame caused by an insertion or deletion of nucleotides

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14
Q

What is a null mutation?

A

mutation in a gene that leads to its not being transcribed into RNA and/or translated into a functional protein product

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15
Q

What is a revertant? What is the difference between a true revertant and a suppressor revertant?

A

mutation that restores a WT phenotype. True: reversal of original mutation. Suppressor: mutation that occur at a second site (gene or different location of the same gene that restores WT phenotype)

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16
Q

What is an auxotroph?

A

mutation that renders the bacteria unable to synthesize an essential metabolite (a.a.); cannot grow on minimal media, must be grown on media supplemented with metabolite

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17
Q

What is a prototroph?

A

a WT bacterium that can grow on minimal medium.

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18
Q

How would you analyze auxotrophic mutants?

A

use penicillin enrichment since auxotrophs will not grow in minimal medium containing pencillin whereas prototrophs will grow and be killed (penicillin only kills growing cells). Grow on enrich medium and make a replica plates on minimal medium and look for colonies that did not grow (auxotrophs won’t grow)

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19
Q

How do antibiotic resistant strains arise?

A

1) mutation that results in antibiotic resistance (selective presure). 2) transfer of antibiotic resistance gene.

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20
Q

What is the adaptation theory (Lamarkism)? Can this theory be applied to antibiotic resistant bacteria? If not, what theory would be appropriate?

A

Adaptation theory: organisms ability to adapt to changes in the environment and adjust accordingly over time. This theory has nothing to do with antibiotic resistant bacteria. The more appropriate theory to be applied to antibiotic resistant bacteria is Darwin’s - survival of the fittest.

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21
Q

How does antibiotic resistant organisms arise?

A

under the selective pressure imposed by antibiotic treatment - only the resistant organisms are able to survive and over time become the principal component of the new population

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22
Q

What are conditional mutants?

A

mutations that exhibit a mutant phenotype only under certain conditions.

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23
Q

Temperature senstive mutations are what type of mutations? What is the difference between permissive and non-permissive temperatures?

A

Conditional mutants (mutations that exhibit a mutant phenotype only under certain conditions). Permissive temperatures - mutation allows protein to assume a normal conformation. Non-permissive temperature - mutant phenotype is observed.

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24
Q

What is general (homologous) recombination?

A

requires extensive DNA homology for two genetic elements to recombine.

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25
Q

What is site-specific recombination?

A

requires only a small region of DNA homology for two genetic elements to recombine.

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26
Q

What is illegitimate recombination?

A

requires no DNA homology for two genetic elements to recombine; occurs at a very low frequency (ex: non-homologous recombination, transposition)

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27
Q

Why is SSU rRNA good way to study mixed populations of bacteria? How would you go about detecting SSU rRNA?

A

small subunit (SSU) ribosomal RNA analysis - where the sequene is highly conserved but has enough variability to have a unique sequence for most species. Amplify the sample using PCR and analyze population using sequencing or on a DNA array

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28
Q

What does whole genome sequencing used to reveal in bacteria? What type of bacteria is it most useful for?

A

virulence genes (pathogenesis-related genes) and metabolic tendencies (potential weaknesses) of bacteria. Most useful to identifying virulene genes in obligate intracellular and difficult-to-culture pathogens

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29
Q

What is a bacteriophage?

A

bacterial viruses; simplest life form consisting of a nucleic acid genome surrounded by a protein coat

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30
Q

What is the structure of a bacteriophage

A

genome (RNA or DNA) within a protein shell (capsid)

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31
Q

What is the shape of bacteriophage nucleocapsid?

A

Icosahedral or helical

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32
Q

How big is the bacteriophage genome?

A

10-150 genes

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33
Q

How can you grow bacteriophage?

A

bacteriophage are grown by infecting an ACTIVELY growing bacterial culture. The bacteriophage can reproduce and cause host cell lysis and subsequent release of progeny phage.

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34
Q

How can you quantify bacteriophage?

A

plaque assay - where phage are placed on a lawn of sensitive bacteria. Their growth will produce a plaque (circular zone of bacterial death)

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35
Q

What causes the a clear plaque? Turbid plaque?

A

Clear plaque - caused by virulent phage (lytic infection). Turbid plaque - caused by temperate phage (has a choice between lytic or lysogenic infection)

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36
Q

What is the virulent/lytic lifecycle of a phage?

A

involves phage multiplication, host cell lysis, and release of newly formed phage

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37
Q

What is the lysogenic lifecycle of a phage?

A

does not result in the production of progeny phage or bacterial killing. Instead, the phage DNA becomes integrated into the host chromosome and propagated as a prophage when the bacteria divides

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38
Q

What is a prophage?

A

phage (viral) genome that has inserted/integrated into the circular bacterial DNA or extrachromosomal plasmid

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39
Q

What is a temperate phage? What is an example?

A

phage that can follow either the lytic or lysogenic pathway. Bacteriophage lambda.

40
Q

What are the steps of a virulent DNA phage?

A

1) Adsorption - binding of phage coat protein to cell membrane receptors. 2) Introduction of the DNA into cell; coat protein stays out. 3) Inhibition of host transcription and transcription of phage DNA. 4) Replication of phage DNA. 5) Synthesis of phage capsid proteins. 6) Morphogenesis and packaging of the phage genomes. 7) Host cell lysis and release.

41
Q

T/F Phage replicates via binary fission

A

False. Only the phage genome enters the cell and turns it into a phage factory, where viral components are synthesized and assembled into mature phage particles late in infection

42
Q

Following injection of its DNA, bacteriophage lambda makes a choice to undergo lytic or lysogenic infection. What happens in either case? What causes the phage to go from a lysogenic -> lytic cycle?

A

temperate phage (it can undergo a lytic or lysogenic infection). In a lysogenic infection, the phage genome circularizes and integrates into specific sites in the bacterial chromosome “prophage”. Under stress (ie UV damage), the prophage excises and undergoes a lytic cycle.

43
Q

What mechanisms are present that keep a prophage in the lysogenic stage? What happens when the bacterium undergoes stress? (ie starvation, UV)

A

The prophage expresses a repressor of expression of all the genes required for lytic infection, so the prophage is carried along as a passenger in the bacterial chromosme. Under host-cell stress (ie starvation, UV), the repressor protein is inactivated and the prophage excises and undergoes a lytic cycle.

44
Q

What is complementation test used for?

A

used to determine the number of independent genetic elements in a series of mutants with the same phenotype.

45
Q

If two mutants phages are coinfected into a bacterial strain, what does the genome of both look like if complementation does occur? If it does not occur?

A

if the genome of both phages are both mutated at the same loci, then no progeny phage is produced. However, if both phages are mutated at different loci (or genes), then progeny phage is produced because the two genomes “complement” each other in that the WT of one genome makes up for mutation in the other

46
Q

What would be the rationale if two mutants fail to complement each other?

A

they lie in the same gene or the SAME complementation group.

47
Q

What would be the rationale if two mutants complement each other?

A

they represent two mutations that reside in different genes and falls into TWO complementation groups

48
Q

If two mutants fail to complement each other, are they in the same or different complementation group?

A

SAME

49
Q

If two mutants complements each other, are they in the same or different complementation group?

A

DIFFERENT

50
Q

What is the difference between restriction enzymes and modification enzymes?

A

RE: protects bacteria against against bacteriophage infection by degrading the foreign dna. ME: modifies its own DNA to protect it from degradation by restriction enzymes

51
Q

What are transposable genetic elements?

A

transposons are mobile genetic elements that are integrated into the bacterial genome and are capable of jumping from one location to another.

52
Q

Transposons have these type of sequences that allow them to integrate at random locations.

A

insertion sequences (IS)

53
Q

What type of integration do transposons undergo?

A

non-homologous (illegitimate) recombination - does not requre any sequence homology for integration

54
Q

What does the insertion sequences encode for?

A

transposase enzyme that facilitates non-homologous (illegitimate) recombination

55
Q

What is the simplest form of a transposon? What gene(s) do most transposons carry?

A

simplest form: one that contains only insertion sequences (IS). Most carry an antibiotic resistance gene or a toxin gene that is flanked by IS

56
Q

Why would transposons be of any medical relevance?

A

Most carry an antibiotic resistance gene or a toxin gene that is flanked by insertion sequences (IS), which permits the movement of these genes from the bacteria to a conjugal plasmid, which it can efficiently move to another bacteria during conjugation

57
Q

What are the 3 mechanisms of gene transfer in bacteria?

A

transformation, transduction, and conjugation

58
Q

What is transformation?

A

transfer of genetic information to a bacterium following the uptake of naked DNA from the extracellular environment

59
Q

What is transduction?

A

transfer of a gene from one bacteria to another by a phage that has mistakenly replaced a part or all of its genome with some of the host DNA

60
Q

What is conjugation?

A

it’s basically how bacteria mate. In other words, it’s sexual reproduction, but in bacteria. it is the transfer of genetic information that requires direct cell-cell contact (ex: conjugal plasmids, transfer of genes via Hfr strains)

61
Q

What is Hfr?

A

high frequency of transfer. It is bacterium with a conjugative plasmid (often the F plasmid) integrated into its genomic DNA and, upon conjugation with a F− cell, attempt to transfer their entire DNA through the mating bridge “sex pilus”

62
Q

How does transformation occur?

A

DNA binds to the bacterial membrane and enters the cell. If its chromosomal DNA, it undergoes homologous recombination with the host chromosome. If its plasmid DNA, it replicates autonomously (independent of the chromosome)

63
Q

What is competence?

A

ability of bacteria to be transformed. E coli can be made competent by treatment with CaCl2 or by electroporation

64
Q

What are two types of transduction?

A

general (transfer of a random region of DNA) and specialized transduction (transfer of a specific region of DNA)

65
Q

What is generalized transduction? How does it occur?

A

transfer of a random region of bacterial host DNA (donor) to another bacterium (recipient); results from the mistaken encapsidation of a random piece of host chromsomal DNA fragment into phage particles.

66
Q

What is specialized transduction? How does it occur?

A

transfer of a specific region of bacterial host DNA (donor) into another bacterium (recipient). Temperate phage integrates into the host cell chromosome at a specific location and during the transition from lysogeny to lytic growth, the prophage excises incorrectly, leaving behind some of its own genome and acquiring a limited set of bacterial genes near the integration site.

67
Q

What is the difference between generalized and specialized transduction in terms of the genetic information that they carry?

A

generalized: phage contains only bacterial host DNA. Specialized: phage contains bacterial + phage DNA

68
Q

T/F Closely linked markers have a higher % to be cotransduced (generalized transduction)

A

True.

69
Q

How would you create a linkage map for generalized transduction?

A

Closely linked markers have a higher % to be cotransduced, and a HIGHER % of colonies that have the marker indicate that genes are CLOSER together, whereas a LOWER % indicate that the genes are spaced further apart.

70
Q

What is the F factor?

A

a plasmid that can transfer genes from a donor strain bearing a F factor (F+) to a recipient (F-) strain

71
Q

What is the R factor?

A

R factor are conjugative plasmids that encode resistance to various antibiotics.

72
Q

Why are bacteriocidins?

A

Bacteriocidins are plasmids that encode for narrow spectrum of antibiotics called bacteriocins, which bacteria use against each other

73
Q

What are the structural features of plasmids? (3)

A

circular, dsDNA, supercoiled

74
Q

Why are plasmids capable of autonomous replication?

A

because they have their own origin of replication, but note that the replication and transcription enzymes are provided by the host cell.

75
Q

How is the copy # of a plasmid regulated?

A

the copy # is controlled by a plasmid-encoded repressor of replication that binds at the site of replication initiation.

76
Q

What is the average copy # of a plasmid?

A

None. Certain plasmids have a low copy # whereas others have a high copy #

77
Q

What are plasmid incompatability groups?

A

classification scheme based on the inability of related plasmids to be propagated stably in the same cell (thus only compatible plasmids can be rescued in transconjugants)

78
Q

What determines the plasmid incompatability group?

A

Inc is based on plasmids inability to coexist in the same cell. Plasmids that share the SAME mechanism that control copy # CANNOT coexist stably in the same host cell because the plasmid is able to replicate faster or has some other advantage will be represented disproportionately

79
Q

T/F plasmids often contain insertion sequence (IS) elements

A

True. The plasmids have the ability to insert themselves randomly into any DNA molecule via transposition

80
Q

What is the F plasmid?

A

a plasmid that encodes proteins (ie tra) required for conjugative transfer of DNA

81
Q

How does a F plasmid transferred from one cell to another?

A

through a conjugation bridge (encoded by the F-plasmid) mediates cell:cell contact. This is also known as “sex pilus”

82
Q

T/F F+ strain can initiate pilus contact with only an F- strain.

A

True.

83
Q

What allows F plasmids to integrate into the host chromosome to form an Hfr strain?

A

IS elements allow integration of F plasmid into host cell to form an HFr strain

84
Q

Why are R factors medically relevant?

A

R factor are conjugative plasmids that encode various antibiotics genes flanked by IS elements. These elements allow various resistant R factors to form, since they allow single resistance genes to move into plasmids that already carry other resistance genes.

85
Q

T/F In conjuation, the genetic information transferred between two parents is equal.

A

False. The exchange of genetic information is unequal.

86
Q

What are some properties of conjugation?

A

1) sexual reproduction, 2) unequal exchange of genetic information between parents, 3) unidirectional transfer of genetic information between F+ (donor) and F- (recipient), 4) transfer requires cell-to-cell contact.

87
Q

How does integration of the F plasmid into the host genome (to form an Hfr plasmid) occur?

A

via homologous recombination between IS elements or by IS-mediated transposition of the entire F plasmid

88
Q

What is the difference a F plasmid and a F’ plasmid?

A

F plasmid that encodes proteins required for conjugal transfer of genetic information from one cell another. F’ plasmid is formed when the F plasmid integrates into the bacterial genome, but excises out with adjacent chromosomal genes to form a hybrid plasmid (F’)

89
Q

What are the steps of Hfr transfer?

A

1) pilus formation. 2) nicking of the transfer of origin and strand transfer. 3) DNA replication to make ss -> ds. 4) pilus ruptures and cells separate. 5) homologous recombination to integrate transferred DNA into recipient genome.

90
Q

How would you create a genome map for generalized transduction?

A

map by INTERRUPTED MATING of Hfr to F- strain at various times by physically breaking the pilus. Know that genes are transferred at a FIXED-order, with genes near the origin of transfer (oriT) transferred first.

91
Q

What are resistance transfer factors (RTFs)?

A

RTFs are conjugal plasmids that carry SEVERAL antibiotic resistance genes

92
Q

What is R100?

A

a RTF (resistance transfer factor)/conjugal plasmid that carry antibiotic resistance genes

93
Q

What are RTFs capable of?

A

interspecies transfer (between different genre of enteric bacteria)

94
Q

What allow genes from one R factor to be transmitted to another R factor?

A

in most cases, the resistance genes are flanked by IS sequences, which allows the resistance genes to move from one location to another.

95
Q

Why is it important that when a patient starts a course of antibiotics, they should finish the full course?

A

treatment with a sub-inhibitory dose of antibiotic causes the emergence of cells with high resistance. These cells contain RTFs with multiple copies of resistance genes that have arisen by gene duplication (often by transposition) and thus a sub-inhibitory dose of antibiotic may not be enough to kill the bacteria

Microbiology Quiz 1 (6 decks)

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