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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
Q

insertions and deletions

A

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

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26
Q

mutation rates

A

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

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27
Q

Mutagens

A

agents that increase mutation rates

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28
Q

three types of mutagens

A

chemical, physical, biological

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29
Q

chemical mutagens

A

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
Q

types of chemical modifications

A

alkylating agents and intercalating agents

31
Q

intercalating agents

A

chemical mutation that cause frameshift mutations, push two bps apart
trigger insertions or deletions

32
Q

alkylating agents

A

introduce changes in replicating or nonreplicating DNA

33
Q

horizontal (lateral) gene transfer

A

gene movement between cells that are not descendants

34
Q

what does horizontal gene transfer cause

A

quick acquisition of new characteristics
fuels metabolic diversity

35
Q

three fates of DNA after horizontal gene transfer

A

degradation, replication by itself (viruses), recombination with host genome

36
Q

genetic recombinations

A

physical exchange of DNA between genetic elements

37
Q

homologous recombination

A

causes genetic exchange between homologous DNA from two sources
drives crossing over

38
Q

genetic transformation

A

free DNA is incorporated into a recipient cell and brings about genetic change
typical size: 10 genes/10k nucleotides

39
Q

competence

A

a cell that can take up DNA and be transformed
in bacteria, can be linked to pili

40
Q

competence regulation

A

transformation
responds to cell density so not all cells become competent

41
Q

electroporation

A

high voltage electrical pulses used to force cells to take up DNAm, key in gene cloning

42
Q

Transduction

A

transfer of DNA from one cell to another by a bacteriophage
occurs in bacteria and archaea

43
Q

modes of transduction

A

generalized and specialized

44
Q

generalized transduction

A

DNA from any portion of host genome packaged inside virion
donor genes cannot replicate independently
will be lost without recombination

45
Q

specialized transduction

A

DNA from specific region of host chromosome is integrated directly into virus genome, usually replaces viral genes
homologous recom. can occur

46
Q

examples of transduction

A

multiple antibiotic resistance genes in salmonella, shiga like toxins in e. coli, virulence factors in vibrio cholerae, photosynthetic genes in cyanobacteria

47
Q

process of general transduction

A

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
Q

process of specialized transduction

A

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
Q

benefits of transduction

A

allows cell to become immune to future infection by same phage
selective value for host because of resistance to further infection

50
Q

gene transfer agents

A

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
Q

conjugation

A

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
Q

conjugative plasmid

A

~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
Q

Mobile DNA

A

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
Q

transposable elements in bacteria

A

insertion sequences and transposons
encode transposase
contain short inverted repeats at ends required for transposition

55
Q

genetic engineering

A

using in vitro techniques to alter genetic material in the laboratory

56
Q

genetic engineering techniques

A

restriction enzymes, gel electrophoresis, nucleic acid hybridization, nucleic acid probes, molecular cloning, cloning vectors

57
Q

nucleic acid hybridiztion

A

base pairing of single strands of DNA or RNA from two sources

58
Q

nucleic acid probe

A

segment of single stranded DNA with predetermined identity used in hybridization

59
Q

southern blot

A

hybridization procedure where DNA is in gel and probe is RNA or DNA

60
Q

northern plot

A

gel contains RNA

61
Q

applications of PCR

A

phylogenetic studies, surveying different groups of environmental organisms, amplifying small amounts of DNA, identifying specific bacteria, looking for a specific gene

62
Q

molecular cloning

A

isolation and incorporation of a piece of DNA into a vector so it can be replicated and manipulated

63
Q

three steps of gene cloning

A
  1. isolation and fragmentation of source DNA
  2. insertion of DNA fragment into cloning vector
  3. introduction of cloned DNA into host organism
64
Q

environmental gene mining

A

isolation of enzymes with industrial applications

65
Q

examples of environmental gene mining

A

enzymes with resistance to industrial conditions (high temperatures, high or low ph, oxidizing conditions), enzymes with combinations of properties (heat stable lipases)

66
Q

genome editing (CRISPR and CAS9)

A

add mutations to genomes that can be passed through generations

67
Q

CRISPR

A

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
Q

viroids

A

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
Q

CAS proteins

A

obtain and store segments of foreign DNA as spacers
recognize and destroy foreign DNA

68
Q

diseases caused by viroids

A

potato spindle tuber, chrysanthemum stunt, avocado sunblotch, coconut cadang-cadang
hepatitis D

68
Q

examples of TSEs

A

scrapie, chronic wasting disease, bovine spongiform encephalopathy (mad cow disease), feline spongiform encephalopathy, creutzfeldt-jakob disease
possibly alzheimer’s and type II diabetes

69
Q

prions

A

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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