Micro Fall Bacterial Genetics

Front 1

gram + or -

e coli
staph areus

Back 1

neg
posit

Front 2

recall these terms

antigen
immunogen
epitope

Back 2

Antigen: anything that binds to AB, TCR, MHC

Immunogen: binds AND elicits a response

The AG determinatn, the part that BINDS

Front 3

what genetic material are we talking about when we say there has been a mutation in surface AG of a pathogen

Back 3

the chromosomal DNA

Front 4

if there has been a change in the H or O AG of E coli what has happened? what is the result

Back 4

example of a chromosomal mutation, leads to a NEW immune response to a familiar microbe

Front 5

why is it so important that bugs can change theri surface AG by mutation?

Back 5

bc it means that they have a totally new epitope and the famiiliar bug excites out immune response in a NEW way

Front 6

what are the 3 mechs that can introduce AG mutation? what bigs do it?

Back 6

1. AG drift: bacterial, virus (gradual change)

2. AG shift: virus (abrupt change)

3. AG switching: bacteria,
protozoa, fungi
-phase variation
-gene conversion

Front 7

what is a gradual change that bacterial and viruses do to change their AG

what about abrupt change done by virus

whats the one where you can change the AG but the genes themselves dont change

Back 7

AG drift

AG shift

AG switching via 1. phase variation or 2. Gene conversion

Front 8

what are the 2 types of AG switcging

Back 8

phase variation
gene conversion

**its a way for bacteria, protozoa, and fungi to change their AG to the bug has a new way to excite the immune system. The genes stay constant but they are rearranges/shuffled to get a new combo

Front 9

what is AG drift

Back 9

slow change over time due to accumulations of mutations

over time leads to an unlimited number of distinct strains of bug

**ex E coli O157:H7 there are 157 strains that can pair with 7 dig flagella, each has a unique epitope and the same old bug needs to be recognized 157 times

Front 10

mitations in what lead to AG drift in influenza

Back 10

mutations in the H (Hemaglutinin) AG

**AG drift is the accumulations over time that lead to an unlimited number of distinct epitopes that elicit a new immune response

Front 11

what is AG shift

Back 11

a RAPID change in viral DNA that makes a NEW SUBTYPE of bug. can lead to a pandemic

**influenza A can infected lots of sources (us, pig, bird) and when there is AG shift a bird stain gets into the human strain, its a totally new thing we havent seen before

Front 12

what can lead to pandemics

Back 12

AG shifts

*influenza A, lots of sources, can make new subtype that in brand new to humans. its a fast dramatic reassortment

Front 13

what this an example of...

Human Viron H5N2 and Bird Viron H7N1 mix and form H5N1

Back 13

AG shift

**influenza A can let new subtypes of virua get in us and create pandemic

Front 14

why do we get pandemics, why do we get yearly flu vaccines

Back 14

pandemig: AG shift

yearly vaccine: ag drift

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what is AG switching

Back 15

the DNA is constant but there is a rearrangement in expression to evade the hosts immune system- they continuously change epitopes

2 ways
- Phase Variation: on off
-Gene Conversion

Front 16

what is phase variation

Back 16

its a type of AG switching that turns things on and off (gene is always part of genome)

ex. gene for surface AG, finbrea (adherance)/pili, flagella (motility) LPS

**can have inversion of DNA to prevent trsncrription or instability of mRNA

Front 17

if a bug evades us by turning its flagellum. LPS, finbrea or somehting else off what mech has it used

Back 17

phase variation of AG switching

**gene is constant it just turns it on or off

Front 18

what are 2 wyas phase variation is regulated

Back 18

1. recombinase will INVERT the DNA to turn it on/off for transcription

2. stability of mRNA

Front 19

the bug no longer had a flagellum when it found a suitable environment to live in the host. what happened

Back 19

AG switch, phase variation

**prbly inversion of the promotor region of the gene to stop expression of the fimbrea bc it no longer needed to move around. perhaps it turned on fimbrea so that it could adhere. it may have also affected the stability of mRNA products

Front 20

what does UPEC e coli do?

Back 20

uropathogenic e coli

it goes phase variation of AG switching

ON: it makes lots of fimbrea to attach to the bladder during colinization

OFF: no finbrea made and we find bugs in the pee

Front 21

what is gene conversion

Back 21

type of AG switching

**changes EPITOPE bc of recombination within specific groups of genes

Front 22

what is the cool thing that nisseria gonorrhoea does to evade us

Back 22

gene conversion (AG switching)

**it has lots of pilin genes but not all are expressed it can shuffle the genome so a dif pilin is expressed. multiple antigenically different pilins

Front 23

what is Borrelia recurrentis (spirochete)

Back 23

expresses lot of dif surface AG, genes for some AG are on the plasmid.

anyway it does gene conversion (type of AG switching) that causes relapsing fever, you think you got rid of the bug but then it changes its epitope expression and we are "reinfected"

Front 24

what are the examples of bugs that do gene conversion?

Back 24

1. Nisseria Gonorrhoea-change pilin expression
2. Borrelia recurrentis- relapsing fever
3. Plasmodium falciparum-maleria
4. Trypanosoma brucei- african sleeping sickness

Front 25

what is plasmodium falciparum

Back 25

protozoa that carries maleria
*does gene conversion AG switching

**it generates a variable surface glycoprotein that hides in RBC

Front 26

what does trypanosome brucei do to evade the immune system

Back 26

it also does gene conversion (AG switching) genome is constant but shuffled to expression varies

**african sleeping sickness also makes VSG and hides from immune system (same as maleria- plasmodium falciparum)

Front 27

why is there some trouble with vaccine development for HIV, plasmodium (maleria) and trypanosomal (african sleeping sickness)

Back 27

bc they doent have a constant epitope

**the do gene conversion to constantly be switching their epitope

Front 28

what are some methods of genetic exchange for bugs

Back 28

1. Recombination of DNA
2. Mobile gene Elements- intersion sequence, composite transposon, pathogenicity island
3. Mobile Replicans, Plasmids, bacteriophage

Front 29

what is recombination of DNA

Back 29

its when a bug picks up DNA (from any source) and adds it to its own DNA via homologous or nonhomologous recombination

Front 30

what is it called when a bugs picks up any old DNA and then adds it to its own genome via homologous or non homologous recombination

Back 30

recombinatino of DNA

Front 31

rec proteins are used when

Back 31

in HOMOlogous recombinatino

**the bugs takes up any old DNA and replaces its DNA with the new DNA. in non homologous the new DNA is in addition to the old DNA

Front 32

what do you get an additio of DNA when do you get a replacement (recombinatio)

Back 32

Homologous recombination: replacement via rec protein

Nonhomologous: new DNA in addition to old DNA

Front 33

what are the consequences of DNA replacement in homologous DNA recombinatin?

what are the consequences of NonHomologous addition of DNA

Back 33

1. can be a positive negative or neutral change

2. the new DNA can be added anywhere, it can be right after a promoter, it can disrupt the promotor or coding sequence. random addition and deal with the consequences

Front 34

what is another word for site directed recombination

Back 34

non homologous

**no REC proteins used
**its an addition not a replacememt

Front 35

bacteriophage genomes, plasmids, and mobile genetic elements all integrate into the host chromosome, is this an example of homologous or non homologous recombinatino

Back 35

non homologous

**site directed ADDITION of DNA into the genome

Front 36

what is something that can jump in and out of chromosome called

Back 36

mobile genetic element (MGE)

**insertion sequence (Is)
**composite Transposon (Tn)
**Pathogenicity Island (PAI)

Front 37

whatis a "jumping gene"

Back 37

mobile genetic element

Front 38

do no monile replican MGE's undergo homologous or non homologous recombinatin? what are the 3 MGE that are not mbile replicans

Back 38

1. IS insertion sequence
2. TN composite transposon
3. pathogenicity island

**they all do NON homologous (site specific ADDITION of DNA)

**replicans replicate autonomously

Front 39

what is an insertion sequence

Back 39

its the simplist type of MGE (not mobil replican)

**small
**requires transposase gene to integrage into replican
*has inverted repeats at the end of the melecule
*doenst have additional coding regiosn
**inserts in a specific sequence
**creates direct repeates upon insertion

Front 40

what type of MGE does this describe

small
has transposase gene
enters at a specific space
creates direct repeats upon insertion
has inverted repeates ath the end of the molecule
has no additional genes

Back 40

insertion sequence

Front 41

the insertion sequence MGE...
inserts at
has what at the end of the molecule
creates
has this gene and no others

Back 41

specific area
incerted repeates
direct repeats
transposase

Front 42

direct repeats are a characteristic of what MGE

Back 42

insertion sequence

Front 43

what is a composite transposon

Back 43

non replican MGE that transfers DNA within a cell or to anther cell

**this was the method that gave staph such great resistance
*has an insertion sequence at each end

Front 44

do pro or eukaryotes have transposons? what genes do they have

Back 44

both

**genes for AB resistance and toxins
**have an insertion sequence at each end

Front 45

what do transposons do

Back 45

insert into chromosome or plasmid of the same cell or a dif cell, can be in eukaryotes or pro. often has info for AB resistance or toxins

**has 2 insertion sequences

Front 46

if there is something that jumps into the chromosome via non homologous recombinatin and has 2 insertion sequences and carries genes for transposase and AB resistance/toxin what is it

Back 46

its a cpmposite transposon MGE, non replican

Front 47

what is a great example of a bug using a composite transposon

Back 47

when vancomyosin resistance was horizontally transferred from E. faecalis to S aureus

Front 48

if a molecular genetisist makes a knockout to ID specific genes how can they do this

Back 48

with transposon

Front 49

what is a pathogenicity island

Back 49

its a MGE that is not a replican

**distince genome segments of pathogens that encode virulence factors
*inserts in tRNA and tRNA like genes

**has a dif C/G% than parent DNA

Front 50

where do pathogenicity islnads insert? what do they encode

Back 50

insert at tRNA and tRNA like genes

**encode virulence
*have dif C/G%

Front 51

so IS, TN and PAI all have insertion sequences

Back 51

you bet!

Front 52

what are you thinking if you find one section of a bugs DNA that has a higher or lower % C/G than the rest

Back 52

pathogenicity island

**encodes virulence
**unstable and will eventually be lost

Front 53

are PAI permanent additions to the genome

Back 53

nope, initial change in G/C% but over time its unstable and is lost

Front 54

what creates different pathogens of the same bacterial species, example

Back 54

pathogenicity islands (encodes virulence)

Enterotoxic E coli ETEC
Uropathogenic E coli UPEC

Front 55

what are UPEC and ETEC

Back 55

uropathogenic ecoli, and enterotoxic e coli

**PAI created differnet pathogens of same bacterial species
**recall UPEC can do phase variation with finbrea attachment for colonization

Front 56

what are te 2 types of mobile replican MGE

Back 56

1. Plasmid
2. Bacteriophage

Front 57

what are mobile replicans

Back 57

can be plasmids or bacterophages that have linear or circular DNA, replicate as a unit by using host machinery

Front 58

do mobile replicant replicated independently

Back 58

nope, they rely on host cell machinery

Front 59

do plasmids replicate when chromosomal DNA does? what kind of DNA is plasmid

Back 59

nope

CCC dsDNA, circular

Front 60

other than the chromosome where else do we see CCC dsDNA (covalently closed circle double stranded DNA)

Back 60

in the plasmid

Front 61

what genes are carried in the plasmid

Back 61

not really essential but can give the cell an advantage

*AB resistance
*metal/toxin resistance
*virulence factors
*bacteriocins
*metabolic enzymes

Front 62

whats an R plasmid

Back 62

resistance

**carries 1 or more AB resistance

**RTF- resistance transfer factor, mediated transfer of 1 plasmid from one cell to another (conjugation)

Front 63

wwhat is the RTF (resistance transfer factor)

Back 63

its a think on the R plasmid that helps mediate the transfer of one cell to another

Front 64

what helps teh R plasmid transfer from one cell to another

Back 64

RTF: resistance transfer factor

Front 65

whats an episoome

Back 65

its part of some plasmids that can integrate into the host chromosome. it acts like an insertion sequence or transposon and does non homologous recombination

Front 66

for the most part bugs have circular chromosomes and plasmids, what is an exception

Back 66

borrelia burgdorferi- causes lyme disease. it has both linear and circular plasmids and linear chromosomal DNA

Front 67

whats TET SET ETT

Back 67

its virulence factors that are encoded in plasmids for certain bugs

Tetnus neurotoxin- Clostridium tetani
Exfoliative toxin- Staph aureus
Enterotoxins- E coli

Front 68

what are some examples of plasmids that give virulence factors (toxins) to the bug

Back 68

TET: Tetnus neurotoxin: clostridium tetani

SET: Staph aureus, exfoliative toxin

EET: enterotoxin, e coli

Front 69

what is a bacteriophage

Back 69

its a mobile replican that is a virus that infects bacteria.

**it is species specific
**they use host machinery to replicate their DNA and assemble viral particles

**can by lytic or lysogenic and makes new virions

Front 70

are bacteriophages species specific

Back 70

yep

Front 71

what is a virus that infects bacteria? what else is there about it

Back 71

bacteriophage

**species specific take over of host machineryy to make viral DNA and make new viral particles

**uses lytic or lysogenic

Front 72

are bacteria picky with genetic exchange

Back 72

nope, they will exchange with anyone!!!

**it makes new starins
**can be adventageous bc of virulence and resistance factors

Front 73

DNA that has been transferred to a bug can do what 3 things

Back 73

1. integrate into chromosome
2. be extrachromosomal plasmid or bacteriophage
3. passed to other cells as independently replicating replicon

Front 74

what are the 3 ways genetic exchange can occur in baccteria

Back 74

1. Transformation: get genetic info and incorporate exogenous naked DNA

2. Conjugation: "sex" one bugs donates to recipient bug

3. Transduction: transfer via bacterophage

Front 75

what is the mech of genetic transfer that utalizes a bacteriophage

Back 75

tansduction

**transformation is the incorporatino of naked DNA and conjugation is sex

Front 76

explain transformation

Back 76

its a way for bugs to exchange DNA

**naked DNA is taken up and integrated via HOMOLogous recombination (ec protein used)

**bugs must be competent
**develop log phase growth curve *lag, log, stationary, decline)

Front 77

explain transformation

Back 77

its a way for bugs to exchange DNA

**naked DNA is taken up and integrated via HOMOLogous recombination (ec protein used)

**bugs must be competent
**develop log phase growth curve *lag, log, stationary, decline)

Front 78

if a bug has transformed naked DNA into its genome has is done homo or non homologous recombination

Back 78

HOMOlogous so uses rec protein

Front 79

if a bug has transformed naked DNA into its genome has is done homo or non homologous recombination

Back 79

HOMOlogous so uses rec protein

Front 80

explain transformation

Back 80

its a way for bugs to exchange DNA

**naked DNA is taken up and integrated via HOMOLogous recombination (ec protein used)

**bugs must be competent
**develop log phase growth curve *lag, log, stationary, decline)

Front 81

when does a bug have the highest level of competence, what is this imortant for

Back 81

log phase of growth curve

**important for transformation, competent bug is required

**HOMOLOGOUS recombination integrates the new naked DNA in the genome. uses rec protein

Front 82

when does a bug have the highest level of competence, what is this imortant for

Back 82

log phase of growth curve

**important for transformation, competent bug is required

**HOMOLOGOUS recombination integrates the new naked DNA in the genome. uses rec protein

Front 83

if a bug has transformed naked DNA into its genome has is done homo or non homologous recombination

Back 83

HOMOlogous so uses rec protein

Front 84

what process uss a pilus

Back 84

conjugation

almost ALL eubacteria use this mefhod of DNA exchange

**REQUIRES contact
*one way transfer of info- donor to recipient
**info for cong usually on plasmid-make sex pilus, transfer plasmid, DNA synthesis, AB resistance, bacteriocins

Front 85

what process uss a pilus

Back 85

conjugation

almost ALL eubacteria use this mefhod of DNA exchange

**REQUIRES contact
*one way transfer of info- donor to recipient
**info for cong usually on plasmid-make sex pilus, transfer plasmid, DNA synthesis, AB resistance, bacteriocins

Front 86

what is the method of DNA exchange the resuires contact

Back 86

conjugation

**it uses a sex pilus
**one way transfer of into from donor to recipient

Front 87

what is the method of DNA exchange the resuires contact

Back 87

conjugation

**it uses a sex pilus
**one way transfer of into from donor to recipient

Front 88

when does a bug have the highest level of competence, what is this imortant for

Back 88

log phase of growth curve

**important for transformation, competent bug is required

**HOMOLOGOUS recombination integrates the new naked DNA in the genome. uses rec protein

Front 89

what process uss a pilus

Back 89

conjugation

almost ALL eubacteria use this mefhod of DNA exchange

**REQUIRES contact
*one way transfer of info- donor to recipient
**info for cong usually on plasmid-make sex pilus, transfer plasmid, DNA synthesis, AB resistance, bacteriocins

Front 90

explain transformation

Back 90

its a way for bugs to exchange DNA

**naked DNA is taken up and integrated via HOMOLogous recombination (ec protein used)

**bugs must be competent
**develop log phase growth curve *lag, log, stationary, decline)

Front 91

what is the method of DNA exchange the resuires contact

Back 91

conjugation

**it uses a sex pilus
**one way transfer of into from donor to recipient

Front 92

if a bug has transformed naked DNA into its genome has is done homo or non homologous recombination

Back 92

HOMOlogous so uses rec protein

Front 93

when does a bug have the highest level of competence, what is this imortant for

Back 93

log phase of growth curve

**important for transformation, competent bug is required

**HOMOLOGOUS recombination integrates the new naked DNA in the genome. uses rec protein

Front 94

what process uss a pilus

Back 94

conjugation

almost ALL eubacteria use this mefhod of DNA exchange

**REQUIRES contact
*one way transfer of info- donor to recipient
**info for cong usually on plasmid-make sex pilus, transfer plasmid, DNA synthesis, AB resistance, bacteriocins

Front 95

what is the method of DNA exchange the resuires contact

Back 95

conjugation

**it uses a sex pilus
**one way transfer of into from donor to recipient

Front 96

what type of DNA exchange requires contact

Back 96

conjugation

**it uses a sex pilus
**one way transfer of into from donor to recipient

Front 97

explain transformation

Back 97

its a way for bugs to exchange DNA

**naked DNA is taken up and integrated via HOMOLogous recombination (ec protein used)

**bugs must be competent
**develop log phase growth curve *lag, log, stationary, decline)

Front 98

if a bug has transformed naked DNA into its genome has is done homo or non homologous recombination

Back 98

HOMOlogous so uses rec protein

Front 99

when does a bug have the highest level of competence, what is this imortant for

Back 99

log phase of growth curve

**important for transformation, competent bug is required

**HOMOLOGOUS recombination integrates the new naked DNA in the genome. uses rec protein

Front 100

what process uss a pilus

Back 100

conjugation

almost ALL eubacteria use this mefhod of DNA exchange

**REQUIRES contact
*one way transfer of info- donor to recipient
**info for cong usually on plasmid-make sex pilus, transfer plasmid, DNA synthesis, AB resistance, bacteriocins

Front 101

can you have congugation if there is no plasmid in either bug

Back 101

nope, one needs to have a plasmid to transfer

**once a plasmid is transfered to a recipient the recipient becomes a donor

**sex pilius in gram neg only

Front 102

what is rolling curcle replication

Back 102

the process the creased dsDNA plasmid in the recipient after conjugation

**cleavage at oriT, the nick initiates rolling circular replication, displaced linear strand directed to recipient, transferred ssDNA recircularizes and replicates. complimentary strand synthesized

Front 103

what secretion type is used with conjugation

Back 103

type 4 sscretion carries out the process of DNA transfer in gram negative. similar genes in gram positive bugs

Front 104

whats going on,,,

1. plasmid encoded protein nicks oriT
2. transferred ssDNA is replicated

Back 104

rolling circle replication

**how a plasmid is transferred in conjugation

Front 105

what are the steps for conjugation

Back 105

1. F+ makes pilius and contacts recipient with it
2. oriT is nicked, this activates the process and the sex pilus is ised to bring the recipient really close
3. F plasmid is transferred as ssDNA, the other strand stays in the donor
4. each plasmid makes its own complimentary strand (in the original donor and recipient, once the recipient gets the plasmid its considered a donor now)

Front 106

do gram + and neg do conjugation the same

Back 106

nope, gram neg has a pilus

gram + has adhesion molecules on the surface of the donor. no sex pilus

Front 107

can an F plasmid enter the chromosome

Back 107

yep, when it integrates in the chromosome its called an episome. and does non homologous conj by integrating at the IS or Tn site. Once integrated its called F prime. and the cell is called an Hfr (high f of recombination) cell

Front 108

what is an Hfr cell

Back 108

its a cell who had an F plasmid integrated into its chromosome via non homologous recombination at an IS or Tn site.

**the integrated plasmid is called F prime and gives the chromosome the ability to transfer so its called Hfr. high frequency of recombination

Front 109

who would an Hfr cell mate with and how would the DNA be transferred

Back 109

with an F- cell

**first half of F' is transferred and then the chromosome and then the rest of F'

**unstable for so much info to transfer so usually the recipient is NOT changed to an Hfr cell,

Front 110

whats the likely mating btwn Hfr nad F-

Back 110

usually no conversion to an Hfr cell bc there is incomplete transter of full F' AND chromosomal DNA

**if a full transfer does happen the recipient is not an Hfr cell

**the new DNA is integrated into the chromosome, a new plasmid isnt made

Front 111

what is an Hfr

Back 111

basically its a cell who has an F plasmid integrated into its chromosome and so can now transfer its entire chromosome. usually there is an incomplete transfer bc it is fragile and takes so long

**the recipient had new DNA enter its chromosome, its not made into a plasmid

Front 112

explain transduction

Back 112

bacteriophage transfers DNA

**bacteriophage is a virus that infects bacteria

Front 113

what is the structure of a bacteriophage

Back 113

1. caspid protein shell
2. Tail (w/ or w/o tail fibers)
3. DNA or RNA core

Front 114

explain the lytic phase

Back 114

1. bacterophage attaches/adsorption
2. it injects its info
3. it replicates its DNA or RNA
4. It assembles more phages
5. LYSIS and lots of phages are released

Front 115

_____ cycle is key to generalized ______

Back 115

lytic
transduction

Front 116

are phages picky about who they interact with? do they do homo or non homo recombination

Back 116

actually they are picky, host cell specific

**HOMOLOGOUS recombination

Front 117

tell me more about the assembly phase of the lytic cycle

Back 117

the DNA packaging system isnt particular. it can package bacterial OR viral DNA

*so this means a phage can have bacterial DNA only, no viral DNA so its called a defective phage. when it attaches to its host only bacterial DNA is transferred there is generalized transduction and the host cell does homologous recombination

Front 118

what is a defective phage, how does it interact with a donor cell

Back 118

its a phage that has bacterial DNA and NOT viral DNA (oops, there was a problem with the assembly)

**anyway when the phage gets into a donor the bacterial DNA does homologous recombination with the recipient via generalized transduction

Front 119

describe the lysogenic cycle

Back 119

seen in phages who do transduction

1. attachment/adsorption
2. Injection/penetration
3. Lysogeny: viral DNA non homologously enters the bacterial chromosome
4 replication of both viral adn bacterial DNA passed to daughter cells.
5. at times of stress it enters the lytic phase and the cell eventually lysis

Front 120

what a lysogen

Back 120

a bacteria the was taken over by a phage and now has viral DNA integrated into its chromosome, it will replicate like this for a while so daighter cells have viral/bacterial genes on its chromosome but eventually when it encounters stress the cell will enter the lytic cycle and lyse

Front 121

what is it called when a bacterial has some viral DNA in its chromosome

Back 121

lysogen

**genetid transduction via lysogenic cycle of temperate phage

Front 122

_____ cycle is key to specialized _____

Back 122

lysogenic
transduction

**recall the lytic cycle is key to generalized transduction

Front 123

whats the dif btwn generalized and specialized transduction

Back 123

generalized, lytic cycle

soecialized, lysogenic cycle

Front 124

what a pathogenic lysogen. what are some examples

Back 124

a prophage that has a virulent gene

ex
Vibrio cholerae- cholera toxin
e coli, shiga toxin, hemmoragic diarrhea
diptheria toxin
strep pyogenes, scarlet fever

Front 125

Bacteriophage genomes, plasmids, and mobile genetic elements (MGEs) integrate into a
chromosome through what type of recombination

Back 125

NON homologous

Front 126

what processes use non homologous recombination

Back 126

bacteriophage
plasmid
mge (IS, Tn, PAI)