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MB 414 > Bacterial Genetics 1 > Flashcards

Bacterial Genetics 1 Flashcards

1
Q

The best way to see what a gene does

A
  • break it and see what happens
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2
Q

the best way to tell what gene controls a process

A

break lots of genes and look for an organism that can’t do the process

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3
Q

mutation

A

change in DNA sequence

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4
Q

isogenic

A

all genes except one are the same

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5
Q

species

A

a population of microorganisms with similar characteristics

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6
Q

clone

A

a population of cells that are genetically identical

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7
Q

genotype

A

the specific set of genes present in a cell

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8
Q

phenotype

A

the collection of characteristics that are available

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9
Q

wild type strain

A
  • a recognized “type” strain, which is a clonal population of a particular species
  • has the identical genotype and phenotype
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10
Q

mutagens

A
  • chemicals
  • ionizing radiation
  • UV radiation
  • agents that increase mistakes in DNA replication
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11
Q

point mutation

A
  • change of one base to another
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12
Q

point mutation outside of protein coding region

A
  • no effect
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13
Q

silent mutation

A

codon still encodes same AA

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14
Q

missense mutation

A

codon codes for different AA

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15
Q

read through mutation

A
  • normal termination sequence is mutated and no longer stops translation
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16
Q

nonsense mutation

A

change to termination codon.

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17
Q

frameshift mutation

A
  • if one of two bases added or deleted within the coding region
  • new AA sequence downstream
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18
Q

spontaneous mutations

A
  • 1 mutation/generation
  • 10^-6 to 10^-8 per generation
  • errors not fixed in DNA replication
  • DNA damage
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19
Q

UV induced damage

A
  • wavelength less than 280 nm
  • form pyrimidine dimers
  • DNA pol will stall or skip dimer completely or misincorporate other nucleotides
  • UVA at shorter wavelengths can break backbone
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20
Q

ionizing radiation

A
  • radiation forms chemical free radical, which can cause double strand breaks in DNA
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21
Q

depurination

A
  • free radicals damage bases and cause separate of base from sugar
  • problems arise during DNA replication
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22
Q

deamination of cytosine results in

A
  • uracil

- DNA pol recognizes as thymine

23
Q

nitric oxide or nitrous acid

A

removes amine group

24
Q

oxidative damage

A
  • causes free radicals that damage DNA
  • hydroxyl group backs DNA backbone
  • done by hydrogen peroxide (H2O2)
  • Guanine to 8-oxo-guanine
25
Q

DNA pol puts what opposite of 8-oxo-G?

A
  • Adenine

- twisted 8-oxo-G looks like thymine

26
Q

Photolyse

A
  • binds to dimer and activated by visible light (340-400 nm)
  • uses energy of photon to resolve the pyrimidine dimer (monomerize dimer)
  • excision repair
  • recombination repair
27
Q

Nucleotide excision repair mediated by UvrABCD

A
  • UvrAB detects error
  • UvrC is recruited to the error
  • UvrC makes single stranded nick 8 bases 5’ to error and 4 bases 3’ to error
  • UvrD (helicase) releases the 12 base region
  • Gap filled and ligated with DNA pol and ligase
28
Q

methyl directed mismatch repair

A
  • involves MutSLH system
  • takes advantage of dam methylase to repair misincorporated based in new DNA - slow to methylate all GATC sites in genome
29
Q

steps in methyl directed mismatch repair

A
  • MutS binds to single base pair mismatches
  • MutL and MutH are then recruited to the mismatch
  • DNA is then looped through until a hemimethylated dam site (GATC) is encountered
  • MutH nicks the unmethylated strand - cuts backbone
  • MutL separates strand back to mismatch
  • DNA is unwound by UvrD and strand is chewed up
  • The gap is repaired by DNA pol I and ligase
30
Q

DNA glycosylases

A
  • cleave the sugar bond in altered or damaged nucleotides
  • recognize and remove altered or damaged nucleotides
  • nick filled by DNA pol 1 and sealed by DNA ligase
31
Q

Daughter strand repair

A
  • replication blocked by pyrimidine dimer which leaves a gap
  • the daughter strand that is correct donates its correct strand to the other daughter strand with gap at the T-T dimer.
  • mediated by recABC
32
Q

SOS response

A
  • DNA damage detected by RecA protein
  • Halts cell division - gives cells time to repair chromosome
  • induction of Polymerase V
33
Q

Polymerase V

A
  • can polymerize damaged DNA “translesion”
  • not as picky about inserting correct base as pol III
  • makes the most mistakes
34
Q

good way to make mutants

A
  • random point mutants - need a screenable phenotype

- treat with mutagen, select for phenotypes - difficult to determine where mutation has taken place

35
Q

better ways to make mutants

A
  • signature tagged mutants
  • transposable element mutation - insert randomly in gene and cause mutation. sequence known so DNA elements cloned quickly and insertion site easily identified.
36
Q

best way to make mutants

A
  • gene directed mutation
37
Q

UV light

A

cross links base pairs

38
Q

ionizing radiation

A

breaks phosphate backbone

39
Q

nitrous acid

A

deamination, altered base pairing

40
Q

H2O2

A

oxidative damage of bases

41
Q

intercolating agents

A

alter DNA causing base misincorporation

- ethidium bromide

42
Q

screenable phenotypes

A
  • temp sensitivity, motility, antibiotic resistance
43
Q

physiological phenotype

A
  • wild type - prototroph - can make histidine

- mutant - auxotroph - required histidine to grow

44
Q

replica plating

A
  • spread mutagenized cultures on plate where it’ll grow
  • transfer colonies to 2 plate - 1 with nutrient; 1 without nutrient
  • look for colony on plate with nutrient but absent in other.
45
Q

example of auxotrophic mutant

A

For example, there are auxotrophs for histidine. wild-type strain can make histidine and grow on glucose as sole carbon source.
- if the mutation is in histidinol dehydrogenase, the bacterium requires histidine to be added to the medium to grow.

46
Q

transposable elements

A
  • discrete DNA sequences that encode the proteins necessary for their movement from one site to another
  • cause large insertion in coding region that results in a mutation
  • known DNA sequence so easy to know where they went
47
Q

gene encoding transposase

A
  • cut out element from one site and integrate into a new site
48
Q

required for transposition

A
  • gene encoding transposase

- terminal target sites recognized by transposase

49
Q

three classes of transposable elements in E. coli

A
  • insertion sequences
  • transposons
  • bacteriophage Mu
50
Q

insertion sequences

A
  • a transposase gene flanked by inverted repeats

- simplest form

51
Q

transposons

A

encode a transposase as well as other genes such as drug resistance

52
Q

bacteriophage Mu

A
  • a lysogenic bacteriophage that exclusively uses transposition to replicate.
53
Q

Transposase mechanism

A
  • transposase (as dimer) recognizes inverted repeats at ends and binds, bringing them together forming paired end complex
  • double strand DNA cleavage at target sites
  • element moves as paired end circular structure to new sequence
  • cuts at target sequence and inserts at new sequence.
54
Q

Why use transpose mutagenesis

A
  • insertions can be isolated at a large number of sites on the bacterial chromosome - almost any site mutated
  • insertion mutants can be recovered at high frequency
  • a transposon insertion in a gene usually causes complete loss of function
  • the phenotype of the insertion mutation is completely linked to antibiotic resistance in genetic crosses
  • special transposons can be used to construct operon or gene fusions to reporter genes.

MB 414 (26 decks)

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