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BMSC 210 > Module 6 > Flashcards

Module 6 Flashcards

Genetics, evolution, and biotechnology

1
Q

how do bacteria acquire genetic diversity

A

evolution and adaptation via vertical and horizontal gene transfer

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2
Q

vertical gene transfer

A

new mutations

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3
Q

horizontal gene transfer

A

gene exchange
acquisition
selfish genetic elements
conjugation(contact)
transduction(phages)
transformation(environment)

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4
Q

mutations

A

changes in nucleotide sequence which are heritable

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5
Q

mutations result in
can be ___,___,____

A

phenotype variation (behaviour/protein activity)
neutral (not observable)
beneficial (gain in function)
detrimental (loss of function)

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6
Q

error rate of replication

A

1 in every 10^-6 to 10^-7 base pairs
low is good
need some for evolution

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7
Q

increasers of mutation rate

A

stresses (nutrient/environment)
mutagens (lab/natural)

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8
Q

non selectable mutations

A

neutral or detrimental
select by screening >10000 colonies

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9
Q

replica plating

A

use velvet to stamp colonies onto a new medium to see which live or die

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10
Q

how to measure mutagenic potential

A

ames test
ability of a chemical to revert an auxotroph
inc colonies = incr mutagenic potential

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11
Q

point mutations

A

changes in mRNA which can be substitution, deletion, insertion

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12
Q

silent mutations

A

sub of third base of a codon changing wobble position not AA

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13
Q

missense mutations

A

sub the first or second base of a codon changing a single AA

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14
Q

non sense mutation

A

stop codon is coded prematurely

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15
Q

indel mutation

A

insertion or deletion

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16
Q

frameshift mutation

A

removed 1-2 bases shifting the reading frame

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17
Q

reversion

A

second mutation correcting the first

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18
Q

revertant

A

phenotype that is being restored

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19
Q

transformation

A

genetic transfer of free DNA through cell lysis

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20
Q

competent cells

A

take up DNA, maybe as food

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21
Q

conjugation

A

genetic transfer requiring cell to cell contact (conjugative pili)

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22
Q

plasmid +

A

cell that is the donor and gives genetic info in conjugation

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23
Q

plasmid -

A

cell that is the receptor of genetic info in conjugation

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24
Q

transduction

A

viral
phages pick up DNA and transfer dna to a new host

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25
Q

generalized transduction

A

lytic phage
packing host DNA
defective phage

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26
Q

specialized transduction

A

temperate phages
host DNA near site of insertion is excised

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27
Q

phage conversion

A

alteration of phenotype by prophages

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28
Q

implications of being prophage +

A

could make a harmless microbe pathenogenic

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29
Q

how do prokaryotes defend themselves

A

mutating receptors
programmed cell death
phase exclusion (modified DNA to prevent replication)
restriction enzymes (endonucleases)

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30
Q

CRISPR

A

seeks and destroys foreign nucleic acid sequences
allows for adaptive immunity based on previous infections
contains CAS proteins to degrade DNA

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31
Q

evolution

A

change in heritable characteristics within a population over time
requires a change in genome and a process changing frequency

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32
Q

evolution is NOT

A

survival of fittest
winner takes all process
progress towards improvement
slow and gradual

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33
Q

homologue define and subclasses

A

share common ancestor
paralogue and orthologue

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34
Q

paralogue

A

share ancestor
different functions
divergent evolution

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35
Q

orthologue

A

share ancestor
same functions
parallel evolution

36
Q

analogue

A

share no ancestors
have common function
convergent evolution

37
Q

genomic island

A

insertion of horizontally acquired gene clusters in the genome

38
Q

pathogenicity island

A

violence factor added to genomic island

39
Q

pangenome

A

collection of genes within 1 species
core genome + accessory genome

40
Q

core genome

A

genes present in all members

41
Q

accessory genome

A

extra genes present in some of the members

42
Q

only way to get new genes

A

horizontal gene transfer

43
Q

genetic drift

A

change in mutation frequency over time

44
Q

natural selection

A

survival of the fittest
one line repeatedly surviving over others

45
Q

bottleneck event

A

reduction in population size due to non selective event
natural disaster
new population is not representative of the old

46
Q

founder effect

A

new population being started by an unrepresentative group

47
Q

red queen hypothesis

A

coevolution between competing species
pressure to keep bringing ne DNA in

48
Q

evolutionary arms race

A

pressure on host to resist infection
pressure on pathogen to overcome defenses

49
Q

court jester hypothesis

A

competition has small impact
environment has large impact

50
Q

green beard effect

A

alike help eachother
kin recognition

51
Q

black queen hypothesis

A

natural selection drives genes lost
reductive evolution theory

52
Q

biotechnology

A

science of using living systems to benefit humankind

53
Q

recombinant DNA

A

form of genetic engineering of gluing DNA from multiple sources together into a sequence

54
Q

cloning plasmids

A

use vectors to carry DNA fragments
multicloning sites
slection markers (antibiotic resistance)
reporter genes

55
Q

multicloning sites

A

sequences recognized by restriction enzymes

56
Q

selection markers

A

antibiotic resitance

57
Q

inducible promoters

A

strong repression

58
Q

process of amplifying DNA

A

thermostable polymerase (split)
primers (fix at area)
and dNTPs (building blocks

59
Q

how can mutations be introduced

A

site directed mutagenesis
CRISPR gene editing

60
Q

sticky ends

A

unmatched base pairs

61
Q

net charge of DNA

A

negative

62
Q

how to visualize DNA

A

agar solution and a negative current to push fragment different distances based on length

63
Q

fluroescent tags

A

attach to denatured DNA to find specific segments and mark them

64
Q

how can bact, euk, and plant cells transform

A

bact: addition of new DNA
euk: electric current pushing recombinant DNA into the cell
plant: bacteria getting in a hyjacking

65
Q

second generation sequencing

A

enzymes to add fluorescent tags to nucleotides to determine DNA sequence

66
Q

pyrosequencing

A

sequencing by synthesis with luciferase

67
Q

illumina

A

sequencing by reversible terminator chemistry
fluorescent tags are removable

68
Q

third generation sequencing

A

single molecule sequencing allowing measurement of epigenetic modification

69
Q

PacBio

A

DNA passing through an immobilized polymerase with fluorescent nucleotides in real time

70
Q

nanopore

A

no amplification or labeling required
DNA passes through a pore disrupting electric current which is measured

71
Q

best method for sequencing entire bacterial chromosome

A

nanopore

72
Q

how to visualize proteins

A

SDS denaturing them making uniformly negative to travel through solution

73
Q

genomics

A

studies DNA

74
Q

transcriptome

A

RNA

75
Q

proteome

A

proteins

76
Q

metabolome

A

sugars, nucleotides, amino acids, lipids

77
Q

how were genomes sequenced prior to 2005
since then?

A

sanger sequencing
massive parallel sequencing, single molecule sequencing

78
Q

bioinformatic analysis

A

uses annotation to find the open reading frame

79
Q

genomic studies infers

A

proteins encoded by a bacteria
pan genome
genomic/pathogenicity island

80
Q

qPCR

A

real time
measures amount of double RNA with on strand fluorescence or release of fluorescence

81
Q

digital PCR

A

not real time
measures number of molecules

82
Q

how is proteomics primarily done

A

mass spectrometry
genome is sequenced to predict protein
gel electrophoresis
proteins are cut out to be identified

83
Q

northern blot

A

RNA

83
Q

western blot

A

proteins

84
Q

southern blot

A

DNA

85
Q

expression plasmids

A

used to express gene and produce protein
multiclong sites
selection maker
inducible promoter
tagg for purification

BMSC 210 (10 decks)

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