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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
generalized transduction
lytic phage packing host DNA defective phage
26
specialized transduction
temperate phages host DNA near site of insertion is excised
27
phage conversion
alteration of phenotype by prophages
28
implications of being prophage +
could make a harmless microbe pathenogenic
29
how do prokaryotes defend themselves
mutating receptors programmed cell death phase exclusion (modified DNA to prevent replication) restriction enzymes (endonucleases)
30
CRISPR
seeks and destroys foreign nucleic acid sequences allows for adaptive immunity based on previous infections contains CAS proteins to degrade DNA
31
evolution
change in heritable characteristics within a population over time requires a change in genome and a process changing frequency
32
evolution is NOT
survival of fittest winner takes all process progress towards improvement slow and gradual
33
homologue define and subclasses
share common ancestor paralogue and orthologue
34
paralogue
share ancestor different functions divergent evolution
35
orthologue
share ancestor same functions parallel evolution
36
analogue
share no ancestors have common function convergent evolution
37
genomic island
insertion of horizontally acquired gene clusters in the genome
38
pathogenicity island
violence factor added to genomic island
39
pangenome
collection of genes within 1 species core genome + accessory genome
40
core genome
genes present in all members
41
accessory genome
extra genes present in some of the members
42
only way to get new genes
horizontal gene transfer
43
genetic drift
change in mutation frequency over time
44
natural selection
survival of the fittest one line repeatedly surviving over others
45
bottleneck event
reduction in population size due to non selective event natural disaster new population is not representative of the old
46
founder effect
new population being started by an unrepresentative group
47
red queen hypothesis
coevolution between competing species pressure to keep bringing ne DNA in
48
evolutionary arms race
pressure on host to resist infection pressure on pathogen to overcome defenses
49
court jester hypothesis
competition has small impact environment has large impact
50
green beard effect
alike help eachother kin recognition
51
black queen hypothesis
natural selection drives genes lost reductive evolution theory
52
biotechnology
science of using living systems to benefit humankind
53
recombinant DNA
form of genetic engineering of gluing DNA from multiple sources together into a sequence
54
cloning plasmids
use vectors to carry DNA fragments multicloning sites slection markers (antibiotic resistance) reporter genes
55
multicloning sites
sequences recognized by restriction enzymes
56
selection markers
antibiotic resitance
57
inducible promoters
strong repression
58
process of amplifying DNA
thermostable polymerase (split) primers (fix at area) and dNTPs (building blocks
59
how can mutations be introduced
site directed mutagenesis CRISPR gene editing
60
sticky ends
unmatched base pairs
61
net charge of DNA
negative
62
how to visualize DNA
agar solution and a negative current to push fragment different distances based on length
63
fluroescent tags
attach to denatured DNA to find specific segments and mark them
64
how can bact, euk, and plant cells transform
bact: addition of new DNA euk: electric current pushing recombinant DNA into the cell plant: bacteria getting in a hyjacking
65
second generation sequencing
enzymes to add fluorescent tags to nucleotides to determine DNA sequence
66
pyrosequencing
sequencing by synthesis with luciferase
67
illumina
sequencing by reversible terminator chemistry fluorescent tags are removable
68
third generation sequencing
single molecule sequencing allowing measurement of epigenetic modification
69
PacBio
DNA passing through an immobilized polymerase with fluorescent nucleotides in real time
70
nanopore
no amplification or labeling required DNA passes through a pore disrupting electric current which is measured
71
best method for sequencing entire bacterial chromosome
nanopore
72
how to visualize proteins
SDS denaturing them making uniformly negative to travel through solution
73
genomics
studies DNA
74
transcriptome
RNA
75
proteome
proteins
76
metabolome
sugars, nucleotides, amino acids, lipids
77
how were genomes sequenced prior to 2005 since then?
sanger sequencing massive parallel sequencing, single molecule sequencing
78
bioinformatic analysis
uses annotation to find the open reading frame
79
genomic studies infers
proteins encoded by a bacteria pan genome genomic/pathogenicity island
80
qPCR
real time measures amount of double RNA with on strand fluorescence or release of fluorescence
81
digital PCR
not real time measures number of molecules
82
how is proteomics primarily done
mass spectrometry genome is sequenced to predict protein gel electrophoresis proteins are cut out to be identified
83
northern blot
RNA
83
western blot
proteins
84
southern blot
DNA
85
expression plasmids
used to express gene and produce protein multiclong sites selection maker inducible promoter tagg for purification

BMSC 210 (10 decks)

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