Exam 4 Flashcards
How are large deletions repaired
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
What is recombination
If incoming DNA strand is similar to chromosome, it may replace old sequence. Sequence must base pair over some of their length for replacement
What protein facilitates homologous recombination
RecA
Vertical Transfer
Requires Cell division
Horizontal transfer
requires 2 cells
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What is Transformation
Uptake of free DNA directly from the environment (“com” machinery)
What are the proteins involved with transformation?
com machinery
What are the steps of transformation?
1) dsDNA binding
2) digested to single strand
3) single strand uptake by com system
4) recombination
What are the possible benefits of transformation?
1) sample genetic environment for beneficial genes
2) repair damaged DNA gene sequences
3) eating DNA
What is conjugation
cell interaction facilitated by sex pilus
Donor cells have fertility factor (F Factor)
What is the F Factor
plasmid encoded with sex pilus, tra machinery (for DNA transfer) and independent origin of replication (oriT)
What are the steps involved with conjugation
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
What is the type of replication required for plamids
Rolling circle: one replication complex, unidirectional migration, synthesizes continuous strand, makes many copies, indefinite
What is transduction
phage accidentally packages bacterial chromosomal DNA and transfers DNA to another bacterium
What are the two types of transduction
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)
What are bacteriophages
tiny viruses that infect bacteria
phages use host to make copies of themselves
Lack ribosomes and cannot make their own energy
Parasites
How does generalized transduction occur
Phage mispackages random fragment of bacterial DNA instead of phage DNa
What is lysogeny
Phage DNA is stably integrated into host chromosome and remains dormant as a prophage
How does specialized transduction occur
phage will package adjacent bacterial DNa in all particles from that cell
only genes near the att site
OOTW: Agrobacterium tumefaciens
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
Is blocking attachment similar to innate or adaptive immunity
Innate
How do bacteria block phage attachment?
Capsules/slime layers: blocks phage from attaching by masking phage receptors
Phase variation: altering protein expression to evade immune system
Is blocking DNA entry innate or adaptive
innate
What is a mechanism for blocking DNA entry
Phage exclusion: prophages block similar related phages from infecting DNA into same cells
Superinfection immunity
What is a prophage
when a phage gets integrated into the DNA of the host
Is replication modification innate or adaptive
innate
What are restriction enzymes
Recognize patterns of dsDNA and cut incoming DNA into pieces
Defense agains foreign DNA
How is the bacterial chromosome protected from restriction enzymes
DNA methyltransferase methylates old strand so it can be identified
Is abortive infection similar to innate or adaptive
innate
How does abortive infection protect from phage infection
bacterial cell sacrifices itself to protect surrounding clonal bacterial cells
Is CRISPR-Cas adaptive or innate
adaptive
What does CRISPR-Cas stand for
Clustered Regularly Interspaced Short Palindromic Repeats
What is Cas
endonuclease that recognizes foreign DNA using spacers and cut DNA
What are the 3 stages for CRISPR-Cas based immunity?
Adaption
crRNA biogenesis
Interference
What is swimming
Individual movement powered by rotating flagella that takes place in liquid
How are Flagella organized
monotrichous: single flagella
lophotrichous: multiple flagella at one pole
amphitrichous: multiple flagella at both poles
petritrichous: multiple flagella along cell body
How is flagellum built
from the inside out
How is a flagellum powered
PMF
What is swarming
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)
How is swarming different from swimming
social group behavior
moves on surface
How is swarming similar to swimming
requires flagella
What is twitching motility
surface motility, pilus extends and attaches to surface, pilus retracts and pulls cell along, jerky movement over surfaces
What structure is required for twitching
type IV pilus
What is gliding?
requires slime/ surfactant, no visible surface structures, trail following, very slow
How does the cell move
Focal adhesion complexes: bind surfaces
Internal helical track moves relative to adhesion complex
moves like a tank
What is floating
gas vesicles inflate to rise, deflate to shrink
What structure is required to float
gas vesicles
OOTW: Borrelia burgdorferi
Causative agent of Lime disease, spirochete, endoflagellum, rotates cell body to push through viscous environment, requires no iron, has linear chromosome
What is chemotaxis
Directed movement with respect to a chemical gradient. Gradient is essential
How do you measure chemotaxis
Plate assay and the use of chemo attractants and repellents to observe movement and response
What are chemo-attractants and cheme-repellents
Chemo-attractant: migration up a chemical gradient (Food sources)
Chemo-repellent: migration down a chemical gradient (toxic compounds)
What is random walk
only 2 behaviors: run and tumble
With each new tumble a new random direction is required
Statistically no net displacement
What is biased random walk
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
How do bacteria sense a chemical gradient
TIME not space. They sample the enviroment every 4 seconds
What is adaption with respect to chemotaxis
Inhibition of behavioral response in presence of constant stimulus
essential for all sensory systems
What proteins are involved in sensing and signaling to the flagella? How?
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
What is a chemoreceptor and where are they located
located on the skin and help mediate movement and direction
what are the 3 stages of biofilm development
attachment, growth and detachment
how is the switch between motility and biofilm formation modulated
cyclic-di-GMP
2GTP get converted to c-di-GMP and then suppress motility and express EPS (biofilm) development
GGDEF makes c-di-GMP
What is the role of EPS in biofilm formation
helps stick ells to each other and other surfaces
How do bacteria control gene expression in biofilms
different levels of biofilm express different genes
What are the advantages of biofilms
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
Some examples of good biofilms
rhizosphere (growth on plant roots)
cyanobacterial mats/blooms (“pond scum”)
marine snow
normal body flora
Some examples of bad biofilms
"bathtub scum" on the hulls of ships biocorrosion plaque and dental carries contaminate medical supplies virulence and pathogenesi
OOTW: Myxococcus xanthus
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
Why were biofilms only recently discovered
we selected against biofilm production in lab strains
Domestication
What is the role of autoinducers in quorum sensing
extracellular signaling molecule that cells can directly sense and group
How are autoinducers synthesized
LuxI => autoinducer synthase (enzyme)
How are autoinducers detected by LuxR proteins
high concentrations of autoinducer
LuxR binding site
What role does quorum sensing play in vibrio fischeri
Regulates luciferase production
How does quorum sensing control gene expression with regard to population density
at critical cell density the concentration of autoinducer reaches threshold to activate gene expression
Compare and contrast intraspecies and interspecies autoinducers
Inter: between cell species
Intra: within cell species
LitR activates LuxR
What is the interspecies autoinducer? Why is this unique?
AI-2
passive diffusion
What are the two signaling systems used by vibrio fisheri
LuxPQ LuxO
OOTW: Vibrio Cholerae
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
What is pathogenesis
nutritional strategy to take nutrients away from other cells
Compare and contrast mutualism, commensalism and parasitism
mutualism: both partners benefit
commensalism: one benefits, one is unharmed
parasitism: one benefits, one is unharmed
Colonization
persistence of a microbe in a specific site within the host body
infection
colonization of host body by pathogen
pathogen
mircoorganism or agent able to cause disease
Disease
defect in body function caused by infection
Pathogenicity or virulence
ability to cause disease
Virulence factors
bacterial products that contribute to pathogenicity
What are Koch’s postulates
1) Isolate organism from infected individual
2) culture in lab
3) re-infect new individual and reproduce disease
4) re-isolate organism
Problems with Koch’s postulates
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
How do we measure pathogenicty
ID50 and LD50
ID50
number of bacteria that results in infections in 50% of hosts
LD50
number of bacteria that results in leathality in 50% of hosts
What are the human defenses against pathogens
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
Virulence Factors: Motility
aids in migration to target tissues
Virulence Factors: Adhesion, Pili
attachment at site of infection, resists flushing
Virulence Factors: Capsules
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
Virulence Factors: Siderophores
switch between versions of antigens
Exotoxins
secreted enzymes that disrupt host cell structure or processes
hemolysins
protein secreted by bacteria that creates holes in host cell membranes. Host cells burst
phospholipases
lest bacteria escape from endolytic vesicle and breaks phospholipid bilayer
Proteases
degrades antibodies and prevents them from targeting bacteria
A/B toxins
Self injecting secreted toxin complex
A= toxin
B=Delivery vesicle
Endotoxins
structures released from dead bacteria that hyperstimulate immune system
OOTW: Streptococcus pneumonia
infects the lungs
makes com machinery
antigenic variation: 90 different capsules to evade immune system
mimicry: some capsules look like host cell sugars
OOTW: Yersinia pestis
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
What did the Avery and Griffith experiments demonstrate
capsule genes (virulent) transferred to avirulent strain during co-infection by natural competence (transformation)
Penicillin
Fungus, inhibited the growth of a bacterium
antibiotic dose decreases as it gets farther away
Static
suspend growth while antibiotic is present
cidal
actually kill bacteria
assay
lawn of bacteria
What is Minimal inhibitory concentration (MIC)
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
What are ideal (general) targets for antibiotics
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
OOTW: Streptomyces coelicolor
mistaken for eukaryotic fungus linear chromosome hyphal growth, cell division is rare multiple chromosomes per cell developmental cycle, sporulation, polyketide antibiotics (produces naturally)
Examples of antibiotics produced by streptomyces coelicolor
erythromycin
globomycin
vancomycin
Where does antibiotic resistance come from
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
What antibiotic resistance strategies exist
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
How do we prevent resistance
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
DNA polymerase III proofreading
DNAPIII backs up one base and excises the mismatch and then proceeds with replication
Which proteins are involved in methyl-directed mismatch repair, how do they function?
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
How does the cell know which base is the right and the wrong one to get rid of
older, original DNA strand is modified by methylation and newer strand lacks methyl groups
What protiens are involved in SOS repair
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)
What genes are under SOS control? how do they function?
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)
