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Microbio 310 > Chapter 9 & 10: Subviral Agents > Flashcards

Chapter 9 & 10: Subviral Agents Flashcards

1
Q

Mutation

A

heritable change in genome
can lead to change in properties of an organism, can be beneficial, detrimental or have no effect

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2
Q

prokaryotes accumulate mutations ______ because of _________ growth

A

quickly, exponential

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3
Q

horizontal gene transfer

A

generates larger changes (than mutations)

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4
Q

2 factors thats fuel evolution

A

mutation and genetic exchange

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5
Q

bacteria can/cannot exchange genes

A

can

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6
Q

genomes of cells

A

contain double stranded DNA

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7
Q

viral genomes

A

contain double or single stranded DNA or RNA

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8
Q

wild-type strain

A

isolated from nature, refer to individual or one gene

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9
Q

mutant

A

cell/virus derived from wild type that carries genotype change

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10
Q

genome

A

nucleotide sequence

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11
Q

selectable mutations

A

contain an advantage, progeny cells outcompete parent, easy to detect and can be used as a genetic tool

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12
Q

example of selectable mutations

A

antibiotic resistance

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13
Q

non selectable mutations

A

do not contain an advantage, may still change phenotype, very hard to detect

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14
Q

example of non selectable mutation

A

color loss in pigmented organism

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15
Q

Ways to isolate mutants

A

selection and screening

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16
Q

spontaneous mutations

A

occur without external intervention, most result from errors by DNA polymerase during replication

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17
Q

induced muations

A

caused environmentally or deliberately, can result from exposure to radiation or chemicals that modify DNA

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18
Q

point mutations

A

change in only one base pair, occurs via single bp substitution, phenotypic change depends on location

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19
Q

types of base pair mutations

A

missense, nonsense, silent

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20
Q

silent mutations

A

do not affect sequence of amino acids due to degeneracy
no change in phenotype
almost always change in third base (in reading frame) of codon

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21
Q

missense mutation

A

changes sequence of amino acids
may alter activity

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22
Q

nonsense mutation

A

causes a stop codon where it doesn’t belong, results in truncated protein
lacks normal activity

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23
Q

frameshift mutation

A

single (or double) bp deletion or insertion that results in shift of reading frame
scrambles entire protein
can lead to a premature stop codon

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24
Q

insertion/deletion of three base pairs

A

adds or deletes an entire codon/amino acid, usually not as bad

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25
insertions and deletions
can result in gain or loss off 100s to 1000s of bps, results in complete loss of gene function, can be lethal may arise from errors during recombinations large insertions may be from transposable elements
26
mutation rates
in microorganisms, 10^-6 to 10^-7 per kb (single gene is ~1kb) eukaryotes 10 fold lower DNA viruses 100-1000x higher RNA viruses even higher
27
Mutagens
agents that increase mutation rates
28
three types of mutagens
chemical, physical, biological
29
chemical mutagens
nucleotide base analogs: resemble nucleotide bases but have faulty base pairing (lack 3, -OH leading to chain termination) replication errors occur at higher frequencies results in mismatched base incorporation cause chemical modifications
30
types of chemical modifications
alkylating agents and intercalating agents
31
intercalating agents
chemical mutation that cause frameshift mutations, push two bps apart trigger insertions or deletions
32
alkylating agents
introduce changes in replicating or nonreplicating DNA
33
horizontal (lateral) gene transfer
gene movement between cells that are not descendants
34
what does horizontal gene transfer cause
quick acquisition of new characteristics fuels metabolic diversity
35
three fates of DNA after horizontal gene transfer
degradation, replication by itself (viruses), recombination with host genome
36
genetic recombinations
physical exchange of DNA between genetic elements
37
homologous recombination
causes genetic exchange between homologous DNA from two sources drives crossing over
38
genetic transformation
free DNA is incorporated into a recipient cell and brings about genetic change typical size: 10 genes/10k nucleotides
39
competence
a cell that can take up DNA and be transformed in bacteria, can be linked to pili
40
competence regulation
transformation responds to cell density so not all cells become competent
41
electroporation
high voltage electrical pulses used to force cells to take up DNAm, key in gene cloning
42
Transduction
transfer of DNA from one cell to another by a bacteriophage occurs in bacteria and archaea
43
modes of transduction
generalized and specialized
44
generalized transduction
DNA from any portion of host genome packaged inside virion donor genes cannot replicate independently will be lost without recombination
45
specialized transduction
DNA from specific region of host chromosome is integrated directly into virus genome, usually replaces viral genes homologous recom. can occur
46
examples of transduction
multiple antibiotic resistance genes in salmonella, shiga like toxins in e. coli, virulence factors in vibrio cholerae, photosynthetic genes in cyanobacteria
47
process of general transduction
host DNA gets accidentally packaged into bacteriophage, forms transducing particle that is defective and cannot cause viral lytic infection upon lysis, transducing particles and normal virons released most cells receive virus, some get transducing particles that may recombine low efficiency: one in 10^6 to 10^8 cells transduced
48
process of specialized transduction
phage genomes is integrated at specific site, viral replication under control of bacterial host chromosome upon induction, viral DNA separates via process that reverses integration sometimes excises incorrectly and takes adjacent host genes along with it, which can be transferred to another cell limited amount of host DNA able to replace phage DNA, helper phages can assist in mixed infection, fewer phage specific genes needed extremely efficient transfer
49
benefits of transduction
allows cell to become immune to future infection by same phage selective value for host because of resistance to further infection
50
gene transfer agents
defective bacteriophages that transfer DNA between prokaryotic cells result from prokaryotes hijacking defective viruses specifically for DNA exchange resemble tiny tailed bacteriophages contain random small pieces of host DNA do not produce viral plaques found in many bacteria and some archaea synthesis regulated by cell may have evolved as mechanism for protected gene dispersion
51
conjugation
horizontal gene transfer that requires cell to cell contact occurs between related cells donor cell: contains conjugative plasmid recipient cell: does not have plasmid other genetic elements may be mobilized
52
conjugative plasmid
~99kbp circular DNA molecule, contains genes that regulate DNA replication, other transposable elements that allow plasmid to integrate into host cell, TRA genes that encode transfer function
53
Mobile DNA
discrete segments of DNA that move as a unit from one location to another within other DNA molecules most are transposable elements, move by transposition, extremely abundant
54
transposable elements in bacteria
insertion sequences and transposons encode transposase contain short inverted repeats at ends required for transposition
55
genetic engineering
using in vitro techniques to alter genetic material in the laboratory
56
genetic engineering techniques
restriction enzymes, gel electrophoresis, nucleic acid hybridization, nucleic acid probes, molecular cloning, cloning vectors
57
nucleic acid hybridiztion
base pairing of single strands of DNA or RNA from two sources
58
nucleic acid probe
segment of single stranded DNA with predetermined identity used in hybridization
59
southern blot
hybridization procedure where DNA is in gel and probe is RNA or DNA
60
northern plot
gel contains RNA
61
applications of PCR
phylogenetic studies, surveying different groups of environmental organisms, amplifying small amounts of DNA, identifying specific bacteria, looking for a specific gene
62
molecular cloning
isolation and incorporation of a piece of DNA into a vector so it can be replicated and manipulated
63
three steps of gene cloning
1. isolation and fragmentation of source DNA 2. insertion of DNA fragment into cloning vector 3. introduction of cloned DNA into host organism
64
environmental gene mining
isolation of enzymes with industrial applications
65
examples of environmental gene mining
enzymes with resistance to industrial conditions (high temperatures, high or low ph, oxidizing conditions), enzymes with combinations of properties (heat stable lipases)
66
genome editing (CRISPR and CAS9)
add mutations to genomes that can be passed through generations
67
CRISPR
clustered regularly interspaced short palindromic repeats type of prokaryotic immune system region of bacterial chromosome containing DNA sequences similar to foreign DNA (spacers) alternating with identical repeated sequences
68
viroids
infectious RNA molecules that lack a protein coat smallest known pathogens cause plant diseases small, circular ssRNA molecules do not encode proteins, dependent on host encoded enyzmes
68
CAS proteins
obtain and store segments of foreign DNA as spacers recognize and destroy foreign DNA
68
diseases caused by viroids
potato spindle tuber, chrysanthemum stunt, avocado sunblotch, coconut cadang-cadang hepatitis D
68
examples of TSEs
scrapie, chronic wasting disease, bovine spongiform encephalopathy (mad cow disease), feline spongiform encephalopathy, creutzfeldt-jakob disease possibly alzheimer's and type II diabetes
69
prions
infectious proteins whose extracellular form contains no nucleic acid cause transmissible spongiform encephalopathies host cell contains gene that encodes native form of prion protein that is found in healthy animals prion misfolding results in neurological symptoms of disease

Microbio 310 (6 decks)

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