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BIOL-M 250 > Exam 4 > Flashcards

Exam 4 Flashcards

1
Q

How are large deletions repaired

A

Bring in fresh copy of genetic sequence with all missing info
Recombination and gene replacement
DNA comes from external source and once its inside it can be either destroyed by restriction (defense) or recombined into chromosome

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2
Q

What is recombination

A

If incoming DNA strand is similar to chromosome, it may replace old sequence. Sequence must base pair over some of their length for replacement

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3
Q

What protein facilitates homologous recombination

A

RecA

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4
Q

Vertical Transfer

A

Requires Cell division

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5
Q

Horizontal transfer

A

requires 2 cells

`

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6
Q

What is Transformation

A

Uptake of free DNA directly from the environment (“com” machinery)

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7
Q

What are the proteins involved with transformation?

A

com machinery

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8
Q

What are the steps of transformation?

A

1) dsDNA binding
2) digested to single strand
3) single strand uptake by com system
4) recombination

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9
Q

What are the possible benefits of transformation?

A

1) sample genetic environment for beneficial genes
2) repair damaged DNA gene sequences
3) eating DNA

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10
Q

What is conjugation

A

cell interaction facilitated by sex pilus

Donor cells have fertility factor (F Factor)

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11
Q

What is the F Factor

A

plasmid encoded with sex pilus, tra machinery (for DNA transfer) and independent origin of replication (oriT)

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12
Q

What are the steps involved with conjugation

A

1) pilus extends
2) recognizes and binds to a receptor on surface of recipient
3) pilus retracts to bring cells into contact
4) plasmid replication begins at oriT via rolling circle mechanism and transferred through Tra machinery
5) recipient gains copy of F factor plasmid and can now be a donor for other bacteria

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13
Q

What is the type of replication required for plamids

A

Rolling circle: one replication complex, unidirectional migration, synthesizes continuous strand, makes many copies, indefinite

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14
Q

What is transduction

A

phage accidentally packages bacterial chromosomal DNA and transfers DNA to another bacterium

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15
Q

What are the two types of transduction

A

Generalized: mispackaged bacterial DNA can come from any location on the bacterial chromosome

Specialized: mispackaged DNA can only come from part of bacterial chromosome adjacent to prophage integration site (att site)

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16
Q

What are bacteriophages

A

tiny viruses that infect bacteria
phages use host to make copies of themselves
Lack ribosomes and cannot make their own energy
Parasites

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17
Q

How does generalized transduction occur

A

Phage mispackages random fragment of bacterial DNA instead of phage DNa

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18
Q

What is lysogeny

A

Phage DNA is stably integrated into host chromosome and remains dormant as a prophage

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19
Q

How does specialized transduction occur

A

phage will package adjacent bacterial DNa in all particles from that cell
only genes near the att site

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20
Q

OOTW: Agrobacterium tumefaciens

A

Plant pathogen
creates tumors (galls)
transfers Ti plasmid to plant by conjugation
Ti plasmid directs production of 1) growth hormone 2) octopine synthesis
genetic engineering of plants

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21
Q

Is blocking attachment similar to innate or adaptive immunity

A

Innate

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22
Q

How do bacteria block phage attachment?

A

Capsules/slime layers: blocks phage from attaching by masking phage receptors

Phase variation: altering protein expression to evade immune system

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23
Q

Is blocking DNA entry innate or adaptive

A

innate

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24
Q

What is a mechanism for blocking DNA entry

A

Phage exclusion: prophages block similar related phages from infecting DNA into same cells

Superinfection immunity

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25
Q

What is a prophage

A

when a phage gets integrated into the DNA of the host

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26
Q

Is replication modification innate or adaptive

A

innate

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27
Q

What are restriction enzymes

A

Recognize patterns of dsDNA and cut incoming DNA into pieces
Defense agains foreign DNA

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28
Q

How is the bacterial chromosome protected from restriction enzymes

A

DNA methyltransferase methylates old strand so it can be identified

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29
Q

Is abortive infection similar to innate or adaptive

A

innate

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30
Q

How does abortive infection protect from phage infection

A

bacterial cell sacrifices itself to protect surrounding clonal bacterial cells

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31
Q

Is CRISPR-Cas adaptive or innate

A

adaptive

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32
Q

What does CRISPR-Cas stand for

A 
Clustered
Regularly
Interspaced
Short 
Palindromic 
Repeats
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33
Q

What is Cas

A

endonuclease that recognizes foreign DNA using spacers and cut DNA

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34
Q

What are the 3 stages for CRISPR-Cas based immunity?

A

Adaption

crRNA biogenesis

Interference

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35
Q

What is swimming

A

Individual movement powered by rotating flagella that takes place in liquid

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36
Q

How are Flagella organized

A

monotrichous: single flagella
lophotrichous: multiple flagella at one pole
amphitrichous: multiple flagella at both poles
petritrichous: multiple flagella along cell body

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37
Q

How is flagellum built

A

from the inside out

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38
Q

How is a flagellum powered

A

PMF

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39
Q

What is swarming

A

surface motility, social/ group behavior, requires flagella and surfactant to reduce surface tension, cells become hyperflagellate (requires more energy and creates more flagella on their bodies)

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40
Q

How is swarming different from swimming

A

social group behavior

moves on surface

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41
Q

How is swarming similar to swimming

A

requires flagella

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42
Q

What is twitching motility

A

surface motility, pilus extends and attaches to surface, pilus retracts and pulls cell along, jerky movement over surfaces

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43
Q

What structure is required for twitching

A

type IV pilus

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44
Q

What is gliding?

A

requires slime/ surfactant, no visible surface structures, trail following, very slow

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45
Q

How does the cell move

A

Focal adhesion complexes: bind surfaces
Internal helical track moves relative to adhesion complex
moves like a tank

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46
Q

What is floating

A

gas vesicles inflate to rise, deflate to shrink

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47
Q

What structure is required to float

A

gas vesicles

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48
Q

OOTW: Borrelia burgdorferi

A

Causative agent of Lime disease, spirochete, endoflagellum, rotates cell body to push through viscous environment, requires no iron, has linear chromosome

49
Q

What is chemotaxis

A

Directed movement with respect to a chemical gradient. Gradient is essential

50
Q

How do you measure chemotaxis

A

Plate assay and the use of chemo attractants and repellents to observe movement and response

51
Q

What are chemo-attractants and cheme-repellents

A

Chemo-attractant: migration up a chemical gradient (Food sources)
Chemo-repellent: migration down a chemical gradient (toxic compounds)

52
Q

What is random walk

A

only 2 behaviors: run and tumble
With each new tumble a new random direction is required
Statistically no net displacement

53
Q

What is biased random walk

A

directed movement with respect to chemical gradient
tumbles discouraged as long as concentration of attractant increases
increasing attractants indirectly favors runs
Direction still completely random

54
Q

How do bacteria sense a chemical gradient

A

TIME not space. They sample the enviroment every 4 seconds

55
Q

What is adaption with respect to chemotaxis

A

Inhibition of behavioral response in presence of constant stimulus
essential for all sensory systems

56
Q

What proteins are involved in sensing and signaling to the flagella? How?

A

CheA phosphorylates CheY response regulator
Ground state: MCP partially inhibits CheA so that CheY is partially phosphorylated
Excitation: MCP fully inhibits CheA to make cell run. CheY is unphosphorylated

57
Q

What is a chemoreceptor and where are they located

A

located on the skin and help mediate movement and direction

58
Q

what are the 3 stages of biofilm development

A

attachment, growth and detachment

59
Q

how is the switch between motility and biofilm formation modulated

A

cyclic-di-GMP

2GTP get converted to c-di-GMP and then suppress motility and express EPS (biofilm) development

GGDEF makes c-di-GMP

60
Q

What is the role of EPS in biofilm formation

A

helps stick ells to each other and other surfaces

61
Q

How do bacteria control gene expression in biofilms

A

different levels of biofilm express different genes

62
Q

What are the advantages of biofilms

A

1) concentrate digestive enzymes. Many bacteria eating as one
2) Persist in favorable environment: prevent cells from being flushed out of environment
3) Aids collaborative metabolism between different species
4) EPS provides for chemical diffusion barrier to antibiotics and engulfment defense
5) maintains high cell density to facilitate a variety of processes; quorum sensing

63
Q

Some examples of good biofilms

A

rhizosphere (growth on plant roots)
cyanobacterial mats/blooms (“pond scum”)
marine snow
normal body flora

64
Q

Some examples of bad biofilms

A 
"bathtub scum"
on the hulls of ships
biocorrosion 
plaque and dental carries
contaminate medical supplies
virulence and pathogenesi
65
Q

OOTW: Myxococcus xanthus

A 
mistaken for eukaryote due to complex multicellular behavior
gliding motility: mobile biofilm
only eats AA
predator of other bacteria
multicellular fruiting bodies
sporulation
makes antibodies and anti-cancer drugs
66
Q

Why were biofilms only recently discovered

A

we selected against biofilm production in lab strains

Domestication

67
Q

What is the role of autoinducers in quorum sensing

A

extracellular signaling molecule that cells can directly sense and group

68
Q

How are autoinducers synthesized

A

LuxI => autoinducer synthase (enzyme)

69
Q

How are autoinducers detected by LuxR proteins

A

high concentrations of autoinducer

LuxR binding site

70
Q

What role does quorum sensing play in vibrio fischeri

A

Regulates luciferase production

71
Q

How does quorum sensing control gene expression with regard to population density

A

at critical cell density the concentration of autoinducer reaches threshold to activate gene expression

72
Q

Compare and contrast intraspecies and interspecies autoinducers

A

Inter: between cell species
Intra: within cell species

LitR activates LuxR

73
Q

What is the interspecies autoinducer? Why is this unique?

A

AI-2

passive diffusion

74
Q

What are the two signaling systems used by vibrio fisheri

A

LuxPQ LuxO

75
Q

OOTW: Vibrio Cholerae

A

Causes cholerae
7 historic pandemics
Lives in brackish water
mode of infection: ingestion of contaminated water
Life cycle: pathogenic at low population densities
Form biofilm after binding and growing then release and resume motility
cycle continues

76
Q

What is pathogenesis

A

nutritional strategy to take nutrients away from other cells

77
Q

Compare and contrast mutualism, commensalism and parasitism

A

mutualism: both partners benefit
commensalism: one benefits, one is unharmed
parasitism: one benefits, one is unharmed

78
Q

Colonization

A

persistence of a microbe in a specific site within the host body

79
Q

infection

A

colonization of host body by pathogen

80
Q

pathogen

A

mircoorganism or agent able to cause disease

81
Q

Disease

A

defect in body function caused by infection

82
Q

Pathogenicity or virulence

A

ability to cause disease

83
Q

Virulence factors

A

bacterial products that contribute to pathogenicity

84
Q

What are Koch’s postulates

A

1) Isolate organism from infected individual
2) culture in lab
3) re-infect new individual and reproduce disease
4) re-isolate organism

85
Q

Problems with Koch’s postulates

A

not all infectious diseases are culturable
not all agents can be deliberately re-introduced into host
not all hosts react the same way to an agent
Not all diseases are caused by only one organism

86
Q

How do we measure pathogenicty

A

ID50 and LD50

87
Q

ID50

A

number of bacteria that results in infections in 50% of hosts

88
Q

LD50

A

number of bacteria that results in leathality in 50% of hosts

89
Q

What are the human defenses against pathogens

A

Dry environment: resistant to infection (skin, lungs, stomach)
Flushing: tears, mucus, urine
Enzyme: lysosyme in tears destroys peptidoglycan and saliva and stomach acid have suites of digestive enzymes
Native Microbial Flora: harmless bacteria cover outside surfaces
Iron sequestration: body starves invaders of iron
Macrophages: WBC that protects body
Antibodies: proteins made by immune system that bind to antigens

90
Q

Virulence Factors: Motility

A

aids in migration to target tissues

91
Q

Virulence Factors: Adhesion, Pili

A

attachment at site of infection, resists flushing

92
Q

Virulence Factors: Capsules

A

Also attach at site of infection, resist flushing and also protect from H2O2, block engulfment by macrophages, shield surface antigens from antibodies and form biofilms

93
Q

Virulence Factors: Siderophores

A

switch between versions of antigens

94
Q

Exotoxins

A

secreted enzymes that disrupt host cell structure or processes

95
Q

hemolysins

A

protein secreted by bacteria that creates holes in host cell membranes. Host cells burst

96
Q

phospholipases

A

lest bacteria escape from endolytic vesicle and breaks phospholipid bilayer

97
Q

Proteases

A

degrades antibodies and prevents them from targeting bacteria

98
Q

A/B toxins

A

Self injecting secreted toxin complex
A= toxin
B=Delivery vesicle

99
Q

Endotoxins

A

structures released from dead bacteria that hyperstimulate immune system

100
Q

OOTW: Streptococcus pneumonia

A

infects the lungs
makes com machinery
antigenic variation: 90 different capsules to evade immune system
mimicry: some capsules look like host cell sugars

101
Q

OOTW: Yersinia pestis

A

causes bubonic plague
carried bn rodents and people by fleas
wide variety of virulence factors encoded on plasmids (pMT1: encodes pili, pPCP1: encodes proteases, pCD1: encodes toxins and type 3 secretion machine)
Injects toxins directly

102
Q

What did the Avery and Griffith experiments demonstrate

A

capsule genes (virulent) transferred to avirulent strain during co-infection by natural competence (transformation)

103
Q

Penicillin

A

Fungus, inhibited the growth of a bacterium

antibiotic dose decreases as it gets farther away

104
Q

Static

A

suspend growth while antibiotic is present

105
Q

cidal

A

actually kill bacteria

106
Q

assay

A

lawn of bacteria

107
Q

What is Minimal inhibitory concentration (MIC)

A

lowest concentration of antibiotic required to inhibit an organism
different fore each combination of antibiotic and organism
less antibiotic does not kill less, just less needed to kill

108
Q

What are ideal (general) targets for antibiotics

A

Target systems bacteria require to grow
Target pathways humans do not use
Target enzymes for which humans have similar but substantially different variation
Complex multistep processes provide many targets

109
Q

OOTW: Streptomyces coelicolor

A 
mistaken for eukaryotic fungus
linear chromosome
hyphal growth, cell division is rare
multiple chromosomes per cell
developmental cycle, sporulation, polyketide antibiotics (produces naturally)
110
Q

Examples of antibiotics produced by streptomyces coelicolor

A

erythromycin
globomycin
vancomycin

111
Q

Where does antibiotic resistance come from

A

Bacteria make antibiotics to kill other bacteria
antibiotic produces contain genes that encode resistance to their own antibodies
Antibiotic resistance genes get passed to other bacteria by genetic transfer mechanisms
Resistance genes often found on plasmids

112
Q

What antibiotic resistance strategies exist

A

Exclusion: a) prevent antibiotic from entering, passive b) actively pump; antibiotic out. transporter genes
Inactivation: a) enzymatically destroy antibiotic. enzyme genes b) enzymatically modify antibiotic
Immunity: modify cellular target. spontaneous mutations in target

113
Q

How do we prevent resistance

A

Make new antibiotics
only take antibiotics for bacterial infections
when sick take your full prescription of antibiotics
Take a combination of antibiotics
stop using antibiotics on farm animals
hiatus on particular antibiotics

114
Q

DNA polymerase III proofreading

A

DNAPIII backs up one base and excises the mismatch and then proceeds with replication

115
Q

Which proteins are involved in methyl-directed mismatch repair, how do they function?

A

MutS: recognizes and binds to DNA distortion
MutL: “Linker protein” recruits MutH to MutS
MutH: endonuclease, nicks DNA near damaged base
DNAPI: repair polymerase

Damaged DNA is excised and repair DNAP1 loads and fills the gap

116
Q

How does the cell know which base is the right and the wrong one to get rid of

A

older, original DNA strand is modified by methylation and newer strand lacks methyl groups

117
Q

What protiens are involved in SOS repair

A

RecA: binds to damaged base and becomes activated RecA*
LexA: transcriptional repressor DNA binding protein that inhibits SOS genes (RecA* causes cleavage of LexA and expresses SOS genes)

118
Q

What genes are under SOS control? how do they function?

A

SulA: inhibitor of FtsZ (blocks Zring formation undil DNA damage has been resolved)
UvrABC: DNA excision repair (detects chemically damaged base)
Pol IV: error prone polymerase (fills in gap)

BIOL-M 250 (11 decks)

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