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172 Cards in this Set

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psychrophile
grows optimally at cold temperatures
mesophile
grows optimally at medium temperatures
koch's postulates
1. bacteria should be found in all diseased animals, but not healthy animals
2. bacteria should be grown and isolated in pure culture
3. bacteria from culture should cause disease in a healthy animal
4. same bacteria should be re-isolated from diseased animal
thermophile
grows optimally at high termperatures
hyperthemophile
grows optimally at really high temperatures
nonhalophile
cannot tolerate high osmolarity
halotolerant
can tolerant high salt conditions
halophile
grows optimally at high salt concentrations
extreme halophile
grows optimally at really high salt concentrations
obligate aerobes
require oxygen for growth
facultative aerobes
do not require oxygen for growth but grow better with it
microaerophillic
likes a little bit of oxygen and requires reduced oxygen conditions
obligate anaerobes
little to no tolerance for oxygen
aerotolerant anaerobes
do not use oxygen for respiration and do not require it for growth
complex broth
made from extracts of yeast and tissues (cell extracts); rich in nutrients, can grow many kinds of bacteria
minimal media
specific and defined nutrients, nutrient poor compared to complex broth, only works for some bacterial species and not others
fastidious organisms
require special addition to media such as blood or another component
prototroph
bacterial strain with no unusual nutritional requirements
auxotroph
Strain that carries a mutation that causes a nutritional requirement

Ex. e. coli mutant requiring certain amino acids (leucine - ) would need leucine for growth; Can be less virulent than parental, prototrophic strain
formula for ideal exponential growth in culture
N = N(0)2^(n)
generation time
t/n
lag phase
adjustment to new culture conditions
log phase
period of exponential growth
stationary phase
phase where cell number is relatively constant over time
death phase
bacteria run out of nutrients in culture and can't survive
acidophiles
grow optimally under acidic conditions
akaliophiles
grow optimally under basic conditions
acid tolerant
tolerates acidic conditions
complement
group of proteins in blood that bind to pathogens and promote inflammation
pathogen
a microoganism capable of producing pathology (disease) in a percentage of normal (non immune individuals)
oppotunistic pathogen
a microorganism that does not cause disease in a healthy host but only in individuals whose normal defense mechanisms have been compromised
nosocomial infections
secondary infections that are a result of treatment in a hospital
virulence
quantitative measure of pathogenesis
LD 50
lethal dose 50; the number of microorganisms required to kill 50% of the test animals
ID 50
infectious dose 50 is the number of organisms (or amount of a toxin) required to produce an infection in 50% of the test animals
stages in pathogenesis
1. encounter
2. entry
3. colonization
4. multiplication
5. invasion
6. evasion of host immunity
7. transmission
virulence factor
components of the pathogen responsible for its ability to cause an infection
obligate pathogen
cannot be found anywhere but in association with its host
facultative pathogen
one that can grow/survive in environment or in its host
stealth strategy
pathogens try to avoid being recognized (capsules)
offensive strategies
pathogens try to kill immune cells or interfere with cellular communication
infiltrate
pathogens live inside immune cells
effector molecules of pathogenesis
proteins that specifically interact with the host
coccus
round shaped
rod
rod shaped
spirillum
spiral shaped
gram positive
stains purple in gram staining
gram negative
stains red
molecular phylogenetic classification
use differences in sequences of genes in bacteria to see evolutionary relationships between species of bacteria (ex. 16s rRNA sequences) and construct a phylogentic tree based on those relationships
classification of bacteria
done by cell shape, gram positive vs. gram negative, molecular phylogenetic classification, and whether it is spore forming or not
cytoplasmic membrane
encloses the cytoplasm; composed of lipids and alphanoids; represents a permeability barrier to hydrophyllic molecules
bacterial cell wall
bacterial cell wall is composed of peptidoglycan; functions to provide support and prevent osmotic lysis
glycan tetrapeptide
building block of peptidoglycan
what cleaves peptidoglycan?
autolysins and lysozyme
LPS Structure
Consists of three parts:
1. Lipid A: fatty acid + N-acetylglucosamine phosphate
2. core polysaccharide: KDO (2-keto deoxyoctanoic acid), heptoses, other sugars
3. O-antigen: some unusual sugars, heterogenous
what linkage does lysozyme cleave on peptidoglycan?
the Beta 1,4 glycosidic linkage
Components in gram positive cell surface
about 25 layers of peptidoglycan, teichoic acid, lipoteichoic acid (LTA)
Components in gram negative cell surface
outer membrane composition: composed of lipopolysaccharide (LPS), lipid A, core polysaccharide, O-antigen
lipid A
toxin that affects eukaryotes (called endotoxin)
core polysaccharide
composed of unusual sugars
O-antigen
composed of unusual sugars; can be heterogeneous between species or even between a variety of same species; can be recognized by immune system
capsule
coat of polysaccharide; functions for protection and fooling white blood cells, helps bacteria to stick
flagellin
protein that is in flagella of bacteria
peritrichous flagella
flagella around entire surface of bacterium
polar flagella
flagella centered at one "pole" of bacterium
gene expression
pathogen response to environment
protein secretion
pathogen influence over environment
RNA polymerase
core enzyme; carries out polymerization of RNA
sigma factor
initiates transcription; bacteria can have a few to 50 sigma factors
promoter
site where the initiation of transcription occurs
intrinsic terminators
sequence that promotes termination of transcription
stem loop in RNA
binds to polymerase and knocks RNA polymerase off DNA and causes transcription termination
operon
found only in prokaryotes; complete unit of transcription
regulon
co-regulated operons in response to environmental changes
polar effect
genetic phenomenon that arises when a mutation in an upstream gene in an operon can stop transcription or can stop transcription/translation of downstream genes
global control systems
regulate many operons all at the same time
phosphotransfer
phosphate group transferred is an Asp group (response regulator)
accessory secretory pathways
possessed only by gram negative bacteria
Type III secretion pathway
contact dependent pathway; injectisome
bactericidal
antibiotic kills bacteria (bug doesn't lyse)
bacteriostatic
antibiotic doesn't kill pathogen but prevents growth
bacteriolytic
antibiotic causes the bacteria to die and lyse
MIC
minimal inhibitory concentration; the amount need of an antibiotic to stop bacterial growth
MBC
minimal bactericidal concentration; the amount needed of an antibiotic to cause bacteria to die (concentration that kills bacteria)
antibiotic antagonism
together, two antibiotics work worse
antibiotic synergism
together, two antibiotics work better
broad spectrum antibiotics
hit lots of bacterial targets
narrow spectrum antibiotics
hit few or one type of bacterial targets
selective toxicity
relative toxicity to the bacteria compared to the host
targets of antibiotics
antibiotics target essential bacterial machines of macromolecular biosynthesis such as: cell wall synthesis, protein synthesis (majority of antibiotics), nucleic acid biosynthesis, folic acid metabolism
Beta lactam antibiotics
Includes penicillins, ampicillin, cephalosporins; name derived from the 4 member beta lactam ring they all have in common; bacteriocidal (kill only growing bacteria); only negative aspect is development of allergic reactions; structural analogs of D-alanyl-D-alanine. Act by binding to enzymes involved in peptidoglycan biosynthesis which blocks transpeptidation and promotes activity of autolysins and lysis
vancomycin
glycopeptide that inhibits peptidoglycan synthesis; binds D-ala-D-ala; extremely important in treatment of gram positive bacteria and is the last line of defense against them
aminoglycosides
protein synthesis inhibitor; target the 30s subunit resulting in misreading of mRNA and are cidal. Examples are streptomycin, kanamycin, and gentamycin; don't penetrate membranes
erythromycin
macrolide that targets the 50s subunit. Can be cidal or static
Tetracycline
targets the 30s subunit and is static. Use of tetracycline and beta-lactam antibiotic together can result in antagonism. Beta lactam and aminoglycoside is synergistic; wonderful pharmacology, drawbacks include resistance and side effects on the developing teeth of children
ciprofloxicin
nucleic acid synthesis inhibitor; quinolone antibiotic and drug of choice for treatment of anthrax
trimethoprim
inhibitor of folic acid metabolism, folate analogue blocks another step in the tetrahydrofolic acid pathway, this time dihydrofolate reductase
sulfonamides
structurally similiar to paraaminobenzoic acid, a substrate for the first enzyme in the tetrahydrofolic acid pathway; inhibitor of folic acid metabolism
chloramphenicol
antibiotic that is a protein synthesis inhibitor
mechanisms of antibiotic resistance
endogenous, multi-drug transport, spontaneous, inactivating enzymes, target
Satellites
bugs that aren't resistant to a certain antibiotic in a plate but grow because they are in a non-antibiotic area due to the presence of a bug that is antibiotic resistant
non-phagocytic cells
don't normally eat bacteria in the environment
phaogocytes
eat bacteria; neutrophiles, macrophages, dendritic cells
Phagocytosis
process for cellular eating, specialized to eat bacteria
chemotaxis
directed movement that is controlled by a gradient of chemical attractant
chemokines
call other cells to infected/wounded areas
why is the permeability of LPS/L bilayer of OM so low?
Bridging by divalent cations, of anionic groups in LPS
spontaneous acquired resistance
when a bacterium suddenly acquires resistance to a antibiotic; may have arisen due to the following explanations:
1. Some particularly robust cells in the population might adjust to the harsh environment
2. exposure to the toxic conditions might produce rare resistant mutations in the population of bacteria (i.e. induced mutations)
3. spontaneous mutants might have occurred in the bacterial population prior to exposure to the toxic conditions yielding resistant progeny cells
4. single point mutations to drug resistance that arise at normal mutation frequency (10^(-6) to 10^(-9)
why is spontaneous resistance not clinically significant for most pathogens?
this is because a spontaneous resistance usually results in the reduced virulence of the pathogen
antibiotic resistance acquired by genetic exchange
plasmids and transposons may encode one or more different antibiotic resistances and thus selection for one antibiotic can lead to resistance to other antibiotics
how does erythromycin resistance work?
erythromycin resistance is mediated by methylation of an adenine on the 23 rRNA
how does vancomycin resistance work?
mediated by changing the terminal D-ala-D-ala to D-ala-D-lactate or D-ala-D-serine
approximately how many pounds of antibiotics are used each year?
50 million pounds
polarization step
controlled by Cdc42
protrusion step
controlled by Rac
Adhesion
controlled by Rho
Translocation
controlled by Rho
what drives protrusion?
polymerization
adenylate cyclase
converts ATP to cAMP
fMLP
formylmethionine- unique to bacteria
complement
C5a complement component
chemoattractants
attract cells that are sensitive to the attract
heterotrimeric GTP binding proteins
GTPases
actin cytoskeleton
made up of actin protein
stages of conversion from G-actin to F-actin
1. nucleation
2. elongation
3. depolymerization
Zipper mechanism of induced phagocytosis in non-phagocytic cells
actin polymerizes only immediately around bacterium
trigger (splash) mechanism
induced by type III secretion effectors. Actin polymerizes in broad area around bacterium
opsinized
coated
plasmids
extrachromosomal DNa that can vary in size; most bacteria from wild have one or more plasmids; not rare but cryptic
plasmid encoded properties
1. replication functions
2. fertility
3. antibiotic resistance
4. heavy metal resistance
5. virulence genes
6. bacteriocims- protein made by 1 bacterium that kill other bacteria
7. alternative Fe acquisition
characteristics of plasmids
1 kB to 300 kb in size (1 gene to 3000 genes); host range is either narrow or broad; copy number can range from one per chromosome equivalent to high copy number
curing
loss of a plasmid
conjugation
mediated by transfer (tra) proteins that encode pili.
F-pilus
complex retractable organelle that mediates bacterium-bacterium interaction
mobilization
piggy-back transfer mediated by mob and an Origin of transfer (ori)
Rec A
signature gene involved recombination and is a major part of natural transformation
Rec-dependent recombination
general or homologous recombination results from the genetic exchange between homologous DNA from two different sources. Rec A is an enzyme necessary for this process
competence (competent bacteria)
state of readiness to accept naked DNA
electroporation
method for introduction of plasmid DNA into many different bacterial species simply by inducing holes in the cell membrane via electronic pulses
unnatural transformation of plasmid DNA
calcium and cold-shocked induced; works great for e. coli but not in most
Transposons
jumping genes and are important in the evolution of multiple antibiotic resistance
General properties of transposons
ubiquitous in nature, found on chromosome, plasmids, and phage; Rec-independent, transposons hop at a frequency of 10^(-3) to 10^(-7), encode transposase, have inverted terminal repeats at their ends, minimal target sequence specifically bordering on random, often confer antibiotic resistance, regulated (controlled by transposase and repressor), generate polar mutations due to presence of transcriptional terminators
conservative transposon
copy number doesn't increase upon transposition but can result in two copies per chromosome
replicative transposon
Tn is copied upon transposition resulting in two copies
conjugative
transposon encodes plasmid-like tra functions: excises, transfers by conjugation to another host and re-inserts
transformation (genetic exchange)
DNase-sensitive DNA uptake. RecA-dependent for chromosomal markers, not plasmids
conjuation (genetic exchange)
DNase-insensitive, contact dependent, RecA-independent
Transposition
DNase-insensitive, recA-independent, contact independent within bacterium, but dependent between bacteria
Transduction (genetic exchange)
filterable, RecA-dependent
pathogenicity islands
often have different G+C content than chromosomal DNA and usually have virulence genes on them
transposon mutagenesis
transposable elements that can be introduced into the genome of bacteria where they insert somewhat randomly causing insertion mutations
transposon library
collection of bacteria that contains multiple individuals each with a single transposon insertion
reporter
used in biological systems to quantitate gene or protein expression. usually an enzyme with easy properties to measure
transcriptional fusions
rely on the promoter of a target gene but contain own ribosome binding site and start codon.
translational fusions
in-frams fusions between two proteins so that the promoter, ribosome binding site, start codon and some or all of the coding sequence are fused in frame with another protein
Tnlac
transcriptional or translational fusions
TnPhoA
Translational fusions to identicy genes encoding proteins with signal sequences
forward genetics
use transposon library; select for mutatnts affecting phenotype, identify site of insertion
reverse genetics (biased)
start with a genomic sequence, identify gene based on homology that you hypothesize has important phenotype
introduce mutation: insertion, deletion or point
score phenotype
Transposon site hybridization
to identify genes that are expressed under one condition relative to another
cytokines
are a category of signaling molecules that, like hormones and neurotransmitters, are used extensively in cellular communication. They are proteins, peptides or glycoproteins. The term cytokine encompasses a large and diverse family of polypeptide regulators that are produced widely throughout the body by cells of diverse embryological origin.[1]
chemokines
subset of cytokines that make cells move towards them
PAMP's
pathogen associated molecular patterns
Prr's
pattern recognition receptors
NLR's
nod-like receptors
Nalips, Naips, Ipat
activate inflammasome
inflammasome
activates protease called caspase one that cleaves pro-IL-1 to IL-1
complement
group of proteins in blood, bind pathogen and promote inflammation; C1 to C9
antigen
any molecule that can be recognized by the immune system; some small piece of protein, cell wall, etc. that will be recognized by a receptor on a B or T cell
IgM
good at activating complement
IgA
easy to secrete across epithelial barriers and mucosal surfaces
IgG
promotes phagocytosis