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248 Cards in this Set
- Front
- Back
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1st golden age of microbio
|
1879 - 1910
French and German scientists race to identify bacterial causes of major diseases |
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hx of microbio
|
mem years, p. 327
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2nd golden age of microbio
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1910 - 1960s
widespread development and use of antibiotics and vaccines |
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dates of 3rd golden age of microbio
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mem - p. 329
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only infectious disease that has been eradicated to date
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small pox
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nucleus differences: pro- vs. eukaryotes
|
prokaryotes - NO neuclear membrane or nucleoli
eukaryotes - true nucleus |
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differences in chromosome arrangement:
pro- vs. eukaryotes |
prokaryotes - single circular chromosomes; lacks histones
eukaryotes - multiple linear chromosomes complexed w/ histones: haploid, diploid, multiploid |
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differences in cell division:
pro- vs. eukaryotic |
prokaryotes - binary fission
eukaryotes - mitosis (microtubule spindle) |
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differences in sexual reproduction:
pro- vs. eukaryotic |
prokaryotic - unidirectional transfer of DNA fragments: no meiosis
eukaryotic - meiosis: reassortment of chromosome complement |
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differences in introns:
pro- vs. eukaryotic |
prokaryotic - rare
eukaryotic - common |
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differences in extrachromosomal DNA:
pro- vs. eukaryotic |
prokaryotes - extrachromasomal DNA often in plasmids
eukaryotes - extrachromasomal DNA in organelles |
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differences in PLASMA MEMBRANES:
pro- vs. eukaryotic |
prokaryotes - no carbohydrates, usually lacks sterols
eukaryotes - sterols and carbs |
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differences in INTERNAL MEMBRANES:
pro - vs. eukaryotes |
prokaryotes - simples, limited
eukaryotes - complex: ER and Golgi |
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differences in RIBOSOMES:
pro- vs. eukaryotic |
prokaryotes - smaller size (70S)
eukaryotes - 80S (70S in organelles) |
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differences in MEMBRANE-BOUND ORGANELLES:
pro- vs. eukaryotic |
prokaryotes - none
eukaryotes - mitochondria, Golgi, lysosomes, chloroplasts, etc. |
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differences in RESPIRATORY SYSTEM:
pro- vs. eukaryotes |
prokaryotes - part of plasma membrane
eukaryotes - in mitochondria |
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differences in CELL WALLS:
pro- vs. eukaryotes |
prokaryotes - usually present, rigid, peptidoglycan and D-amino acids
eukaryotes - when present, chemically simple, usu. polysaccharides |
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differences in FLAGELLA:
pro- vs. eukaryotes |
prokaryotes - submicroscopic, composed of one fiber of protein
eukaryotes - microscopic, complex, multiple microtubules in characteristic pattern |
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differences in CYTOPLASM:
pro- vs. eukaryotes |
prokaryotes - no cytoskeleton
eukaryotes - cytoskeleton w/ microtubules |
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bacterial species =
|
clusters of strains/clones with a high degree of phenotypic similarity and with significant differences from other groups
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serovars or biovars
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= variants within bacterial species
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taxonomic heirarchy
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kingdom
phylum SUBPHYLUM class order SUBORDER family genus species |
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5 major criteria for grouping bacteria
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cell structure and arrangement
differential staining based on cell wall structure oxygen requirements endospore formation motility |
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a differential stain based on chemical differences in cell wall structure, particularly on thickness of peptidoglycan layer and presence of outer membrane
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Gram stain
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Gram stain:
primary stain - mordant - decolorizer - counterstain - |
Gram stain:
primary stain - crystal violet mordant - iodine decolorizer - alcohol or alcohol-acetone counterstain - safranin |
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differential stain the binds strongly to bacteria that have a WAXY MATERIAL in their CELL WALLS
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acid fast stain
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acid fast stain is used especially to identify which species?
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mycobacterium
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acid fast stain
primary stain - decolorizer - counterstain - |
acid fast stain
primary stain - hot carbolfuschin decolorizer - acid alcohol counterstain - methylene blue |
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appearance of acid fast stain
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acid-fast bacteria stain red
all others stain blue |
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biochemical tests to differentiate bacteria
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fermentation or oxidation of carbohydrate substrates
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differentiation of bacteria via production of enzymes:
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catalase, oxidase, coagulase
urease, hemolysins, etc |
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4 aspects of genotypic classification of bacteria
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GC content
DNA hybridization molecular probes 16S rDNA sequencing |
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serotyping =
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using highly specific Ab-Ag interactions to classify bacteria
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2 genus of gram positive cocci
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Micrococcae
Streptococcae |
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describe Micrococcae
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gram positive cocci in pairs and clusters
catalase-positive |
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describe Streptococcae
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gram positive cocci in pairs and chains
catalase-negative |
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describe Neisseria
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gram-negative cocci
oxidase-positive |
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2 types endospore-forming, gram-positive rods
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bacillus
clostridium |
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describe Bacillus
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gram-positive aerobic, spore-forming rods
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desribe Clostridium
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gram-positive anaerobic spore-forming rods
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2 types of non-spore-forming, gram-positive rods
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regular in shape (Listeria moncytogenes)
irregular in shape - pleiomorphic (corynebacterium diphtheriae) |
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5 types gram-negative, aerobic rods
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pseudomonada
legionella bordatella fransicella brucella |
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facultatively anaerobic, gram-negative rods
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enterobacteria
vibrionaceae pasteurella |
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describe enterobacteria
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gram-negative rods
glucose fermenters oxidase-negative |
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describe vibriona
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curved gram-negative rods
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describe Pasteurella
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gram negative coccbacilli
often pleiomorphic |
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2 aerobic, helical, gram-negative rods
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Campylobacter jejuni
Helicobacter pylori |
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Campylobacter jejuni causes ____
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gastroenteritis
|
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Helicobacter pylori is associated with _____
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gastric ulcers
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Spirochetes
definition 2 types |
gram-negative helical bacteria
spirochaeta leptospira |
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anaerobic, gram-negative rods
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bacteroida
|
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2 types gram-negative, obligate intracellular pathogens
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rickettsia
chlamydia |
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cell wall-less bacteria
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mycoplasmata - contain no peptidoglycan cell wall
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acid-fast rods
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mycobacteria
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specific species from lecture 1
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memorize?
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3 things prokaryotic cells don't have
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no nucleus
no organelles no internal membranes |
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4 things in prokaryotic cytoplasm
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most metabolic reactions
ribosomes and protein synthesis machinery nucleoid plasmids |
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hydrophilic layer around the cell, outside outermost layer of the cell wall & membranes
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capsule
|
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capsule is usually (type of macromolecule)
(relationship to immune system) (important virulence factor) |
usually polysaccharide
usually antigenic anti-phagocytic |
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part of prokaryote to be involved in adherence and/or invasion
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capsule
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4 characteristics of cell wall
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rigid, gives cell shape
prevents osmotic rupture acts as course molecular seive basis of Gram stain |
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peptidoglycan, aka:
|
murein/mucoprotein
|
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polymer found only in prokaryotes
|
petpidoglycan
|
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describe backbone of peptidoglycan
|
backbone = linear chain of 2 alternating sugars:
NAG: N-acetylglucosamine NAM: N-acetylmuramic acid |
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what compound is found only in peptidoglycan
|
muramic acid
|
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in peptidoglycan, attached to each muramic acid residue is a _____
|
peptide side chain
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linear glycan chains are crosslinked via ___ ____ ___ to form very strong scaffold structure
|
peptide side chains
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lysozyme degrades peptidoglycan by hydrolyzing the ______
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glycan chain
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3 places where peptidoglycan biosynthesis takes place, in order:
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cytoplasm
cell membrane cell surface |
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what step of peptidoglycan biosynthesis occurs in the cytoplasm
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synthesis of muramic acid - pentapeptide
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what step of peptidoglycan synthesis occurs in the cell membrane
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addition of NAG &
formation of full disaccharide pentapeptide predursor |
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what step of peptidoglycan syntehsis occurs on cell surface?
|
addition of precursor to growing glycan chain
& crosslinking to other glycan chains |
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Gram-positive staining
|
retains crystal violet dye during decolorization --> purple
|
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Gram-negative staining
|
loses crystal violet stain during decolorization, must be counterstained (safranin) to be seen --> pink
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describe gram-positive cell wall
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thick 3-D layer of cross-linked peptidoglycan
anchored to the cytoplasmic membrane by lipoteichoic aicd |
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2 major components
|
peptidoglycan
teichoic acid |
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compound unique to gram-positive cells
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teichoic acid
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gram-negative cell envelope
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thin layer of peptidoglycan within periplasmic space between cell/inner membrane and outer membrane
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peptidoglycan linked by ____ to outer membrane
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lipoprotein
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outer membrane has
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lipopolysaccharide (LPS)
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where is periplasmic space located?
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between cell/inner membrane and outer membrane of gram-negative cell
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major permeability barrier for gram negative cell
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outer membrane of cell envelope
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composition of outer membrane of gram negative cell envelope
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asymmetric phospholipoprotein bilayer
inner leaflet - phospholiupids outer leaflet - lipopolysaccharide |
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______ links outermembrane to peptidoglycan layer
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Braun's lipoprotein
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where are porins found?
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outer membrane
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LPS is an _____
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endotoxin
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major virulence factor in Gram-negative bacteremia (sepsis)
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LPS/endotoxin
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is LPS found in gram-positive bacteria?
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no
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is LPS found in all gram-negative bacteria?
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yes
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3 consituents of LPS
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Lipid A
core polysaccharide O antigen |
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phosphorylated glucosamine disaccharide to which fatty acids are attached
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Lipid A
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O antigen is found on what type of LPS
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smooth
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rough LPS is characterized by _____
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no O-antigen
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flagella are called what kind of antigens in enterics?
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H antigens
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some bacteria can switch from production of one antigenic type of _____ to another
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flagella
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phase variation
mechanism purpose |
changing from one type antigenic flagella to another
to avoid elimination by host immune response |
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2 types variation of surface antigen expression
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phase variation
antigenic variation |
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phase variation =
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on/off switch
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antigenic variation =
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expression of different antigenic types
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pili or fimbriae
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hair-like protein projections on the bacterial cell surface
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sex pili are involved in _____
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the exchange of genetic material
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what can pili inhibit
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phagocytosis
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type IV pili/fimbriae associated with _____
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twitching motility
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types of adhesin pili
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type I :mannose-sensitive
mannose-resisitant, P pili, colonization factor antigens, type IV, etc. |
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are phase variation and antigenic variation mutually exclusive?
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no
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repeat found in pili gene
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Sma-Cla repeat
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pilin antigenic variation occurs via ...
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inter - and intra-genic recombination
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why are piliated strains of Neisseria gonorrhoeae more virulent than strains that do not have pili?
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pili as adhesins
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why is it unlikely that a pilus vaccine against N. gonorrhoeae would be effective?
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pili undergo antigenic variation
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2 medially important spore-formers
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Bacillus
Clostridium |
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4 characteristics of endospores
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specialized structures that are highly resisitant to adverse conditions
produced under nutrient limitation or other stress sporulation germination |
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endospores are extremely resistant to ____ & _____
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heat and drying
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are endospores metabolically active?
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NO
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are endospores viable?
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yes
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6 things bacteria need to grow
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energy source
carbon source nitrogen source inorganic ions essential metabolites water |
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energy sources for bacteria
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light
oxidation of inorganic compounds oxidation of organic compounds |
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carbon sources
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carbon dioxide
any complex carbon containign compound from glucose to wood |
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most important inorganic substrate for bacteria
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iron
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4 iron-dependent processes
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electron transport and energy metabolism
protect from O2 toxicity amino acid biosynthesis DNA synthesis |
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siderophores
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iron chelators w/ high affinity for iron
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2 bacterial mechanisms for solubilizing iron from mammalian iron complexes
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siderophores
iron-regulatable outer membrane proteins |
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gene encoding proteins for iron aquisition are often regulated by ____
|
iron
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ability of a bacterium to compete successfully for host iron is a _____
|
major virulence factor
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means of bypassing iron dependence
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few/no Fe-S center proteins - don't need if they can ferment
use Mn instead of Fe as enzyme co-factors |
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Barrelia burgdorferi as example of iron abstinence
|
no cytochromes in CM preps
genome shows metallo-enzymes with homology to Mn-containing rather than Fe-containing homologs |
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most pathogens prefer what kind of pH
|
neutral to slightly alkaline
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most pathogens prefer what temperature range?
|
mesophilic (20-40*C)
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3 types of bacteria, based on O2 requirements
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strict aerobe
strict anaerobe facultative anaerobe |
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O2 requirements for strict aerobes
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require O2 - cannot ferment
possess catalase and SOD |
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O2 requirements for strict anaerobes
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grow only in ABSENCE of O2
vary in sensitivity to exposure to O2 energy by fermentation do not usu. possess catalase or SOD |
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O2 requirements for facultative anaerobes
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respire in presence of O2 & ferment in absence
usually have both catalase & SOD |
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4 mechs of nutrient entry into bacteria cells
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simple diffusion
facilitated diffusion active transport group translocation |
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group translocation is utilized to transport ____ across _____ with the use of _____ found in the _____
|
group translocation is utilized to transport GLUCOSE across BACTERIAL MEMBRANES with the use of ENZYMES found in the CM
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Embden-Meyerhof pathway, aka:
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glycolysis
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additional central fueling reactions (ie. respiration or fermentation) may occur, depending on:
|
atmosphere (O2)
enzyme pathways present functional ETC appropriate terminal electron acceptor |
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5 possible terminal electron acceptors
|
O2
fumarate succinate NO2 NO3 |
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goal of phosphorylation
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generate energy in form of ATP
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fermentation
|
mode of energy-yielding metabolism
organic substrate & its derivatives serve as primary electron donor and terminal electron acceptor |
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converts glucose into various sugars via transketolases and transaldolases
|
pentose-phosphate shunt
|
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pentose-phosphate shunt, aka:
|
hexose-monophosphate shunt
|
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3 polymerization reactions
|
DNA polymerization: replication
RNA synthesis: transcription protein synthesis: translation |
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DNA replication is catalyzed by
|
DNA polymerase
|
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directionality of DNA replication
|
bidirectional
|
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where does DNA replication initiate?
|
replication origin
|
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2 processes to which DNA replication is coupled
|
growth
cell division |
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transcription is catalyzed by
|
RNA polymerase
|
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polyA cap on RNA?
|
no
|
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is transport through nuclear membrane required?
|
no
|
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transcrips are usually ____cistronic
|
polycistronic
|
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size of prokaryotic ribsome large subunit
|
50S
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size of prokaryotic ribosome small subunit
|
30S
|
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size of prokaryotic ribosome
|
70S
|
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initiation of prokaryotic protein synthesis requires
|
initiation factors IF1, IF2, IF3
20S and 50S ribosomal subunits mRNA fmet-tRNA |
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step 1 of prokaryotic protein synth initiation
|
mRNA binds to 30S subunit (requires RBS on the mRNA)
|
|
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step 2 - initiation protein synthesis
|
initiator fmet-tRNA binds to this complex
|
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step 3 - initiation protein synthesis
|
50S subunit associates with mRNA-30S-tRNA complex
|
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Initiation complex =
|
2 ribosomal subunits
mRNA fmet-tRNA |
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elongation
|
repetitive addition of amino acids to growing peptide chains
|
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_____ ____ are the key to fidelity to the genetic code
|
aminoacyl tRNAs
|
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termination of protein synthesis requires
|
release factors RF1, RF2, or RF3 (depends on stop codon used)
|
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what two processes are coupled in bacteria?
|
transcription and translation
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general secretion pathway targets protein to ...
|
CM and beyond
|
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export apparatus for GSP includes multiple ___ proteins
|
Sec proteins
|
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proteins secreted from GSP have ____ _____ sequence
|
N-terminal signal sequence
|
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Signal recognition particle (SRP) targets proteins to ...
|
CM
|
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export apparatus for SRP includes
|
2 proteins + 1 RNA
|
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two pathways that use CM SecYEG translocon
|
GSP & SRP
|
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differences in fate of N-terminal signal sequence between GSP and SRP
|
GSP - sequence cleaved by periplasmic signal peptidase (Lep)
SRP - not cleaved by Lep |
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SRP export is __ - translational
|
co-translational
|
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GSP export is ___-translational
|
post-translational
|
|
|
diagrams of SRP and GSP
|
CP p. 384
|
|
|
Type I protein secretion systems of Gram neg bacteria
|
ABC transporters
C-terminal signal sequence 4-5 genes involved E. coli hemolysin |
|
|
Type II protein secretion systems of Gram neg bacteria
|
two step secretion
N-terminus signal sequence 12-14 + Sec system Klebsiella pul, Cholera toxin |
|
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Type III protein secretion systems of Gram neg bacteria
|
contact dependent
mRNA signal 12-14 genes involved Shigella, Yersinia |
|
|
Type IV protein secretion systems of Gram neg bacteria
|
conjugal transfer system
unknown signal 12 genes involved Agrobacterium T-DNA Bordetalla pertussis toxin |
|
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Type V protein secretion systems of Gram neg bacteria
|
autotransporters
N-terminus signal sequence 1 gene involved Neisseria IgA protease |
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Type VI protein secretion systems of Gram neg bacteria
|
name?
unknown signal V cholerae |
|
|
ABC transporters =
|
ATP-binding cassette
|
|
|
Type I secretion crosses membranes how?
|
both membranes simultaneously
no periplasmic phase |
|
|
2 steps of type II secretion
|
step 1: cross cytoplasmic membrane
step 2: cross outer membrane |
|
|
step 1 of type II secretion
|
signal sequence required
Sec (BSP) system used once in periplasm, protein may be processed, folded peptidases and chaperones may be required |
|
|
type II secretion is structurally related to
|
type IV pili
|
|
|
type II secreted proteins
|
Klebsiella oxytoca Pul system
Pseudomonas aeruginosa Xcp system Vibrio eps system (cholera toxin) |
|
|
type III secretion
|
secretion of proteins directly from bacterial cytoplasm into host cell cytoplasm
|
|
|
Type III secretion activated by
|
contact with host cell
|
|
|
type III secretion mechanism of transport
|
one or more of secreted proteins forms a pore in the host cell membrane through which other secreted proteins may enter
|
|
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type III secretion is independent of...
|
Sec independent
no signal sequence required |
|
|
type II secretion is often encoded on...
|
pathogenicity islands
|
|
|
type III secreted proteins
|
shigella flexneri Ipa protins
Yersinia YOPs Salmonella Inv/Spa proteins Pseudomonas syringae Erwinia sp |
|
|
type IV secretion, aka:
|
conjugal transfer
|
|
|
type IV secretion is an apparent adaptation of...
|
bacterial plasmid conjugal transfer systems (F-plasmids)
|
|
|
transport mechanism of type IV secretion
|
components form a pilus-like apparatus through which proteins (and DNA) can pass
|
|
|
where is 12 protein complex found during conjugal transfer?
|
spans entire cell envelope
|
|
|
describe conjugal transfer as used by Agrobacterium system
|
Sec-independent
pertussis toxin uses Sec to get to periplasm, then type IV to get across OM |
|
|
type IV secreted proteins
|
Bordetella pertussis toxin
Agrobacterium tumefaciens T-DNA Legionella Dot/Icm Heliobacter pylori cag Neisseria DNA Rickettsia Actinobacillus |
|
|
type of secretion that encodes everything necessary for secretion on a single gene product
|
Type V (autotransporters)
|
|
|
what triggers Type V secretion
|
N-terminal signal sequence
by Sec/BSP targeting system |
|
|
what cleaves signal sequence in Type V secretion
|
leader peptidase
|
|
|
what encodes proteolytic enzyme in type V secretion
|
structural gene
|
|
|
mechanism of Type V secretion
|
C-terminal domain forms secretion pore in outer membrane
protein is secreted through this pore mature protein releases itself into the supernatant by autoproteolysis |
|
|
type V secreted proteins
|
Neisseria IgA1 protease
Haemophilus influenzae IgA protease Serratia marcescens serine protease Helicobacter pylori VacA |
|
|
Type VI secretion system is reminiscent of what proteins on what virus
|
E coli bacteriophage T4 tail proteins
|
|
|
type VI secretion proteins
|
vibrio cholerae
pseudomonas aeruginosa, Burkholderia mallei Francisella tularensis Y. pestis E. coli Salmonella enterica |
|
|
types of genetic mutation
|
base substitution
small deletions/insertions large deletions/insertions inversions |
|
|
3 types of mutagens
|
chemicals
radiation viruses |
|
|
3 types of chemical mutagens
|
nucleotide analogs
frameshift mutagens DNA-reactive chemicals |
|
|
5 types of DNA repair
|
direct DNA repair
excision repair post-replication repair SOS response error-prone repair |
|
|
3 major forms genetic exchange in bacteria
|
transformation
transduction conjugation |
|
|
uptake of naked donor DNA from the environment
|
transformation
|
|
|
transformation requires...
|
competent recipient cell
|
|
|
3 steps to transformation
|
1. binding of exogenous DNA to cell surface
2. uptake of donor DNA into cells 3. recombination with the recipient cell genome |
|
|
transfer of DNA from donor to recipient cell via bacteriophage
|
transduction
|
|
|
process of transdution governed by whose genes
|
phage's
|
|
|
generalized transduction is mediated by ____ phages
|
lytic
|
|
|
specific transduction is mediated by _____ phages
|
lysogenic
|
|
|
plasmid mediated transfer of DNA from donor to recipient cell by direct contact
|
conjugation
|
|
|
conjugation governed by whose genes?
|
plasmid's
|
|
|
function of F(fertility) plasmid
|
encodes proteins to form sex pilus, which allows capture of F- cell and transfer of DNA through F pilus into recipient cell
|
|
|
standard conjugation occurs btw what 2 types of cells
|
F+ and F-
|
|
|
rolling circle replication, aka:
|
replicative transfer of DNA
|
|
|
mechanism of rolling circle replication
|
one strand directs synthesis of its complement w/in the male cell
the other is transferred to the female cell where its complementary strand is synthesized |
|
|
standard conjugation results in high frequency transfer of ____, but NOT of ______
|
standard conjugation results in high frequency transfer of PLASMID, but NOT of HOST CHROMOSOMAL GENES
|
|
|
recipient cell of standard conjugation becomes..
|
F+
|
|
|
donor cell of standard conjugation is F(___) at the end of the process
|
F-
|
|
|
Hfr
|
high frequency recombination
|
|
|
In an Hfr strain, the F plasmid is ....
|
integrated into host chromosome
|
|
|
incomplete transfer of F plasmid sequences leaves recipient cell _____; donor remains _____
|
incomplete transfer of F plasmid sequences leaves recipient cell FEMALE; donor remainsHfr
|
|
|
mechanism of conjugation involving Hfr donor
|
transfers part of plasmid and part of bac chromosome in linear fasion, by replicative transfer
length of contact btw cell deterimines amount of donor chromosome transfered |
|
|
3 possible fates of transferred DNA
|
degradation by nucleases
stabilization by circularization integration into host chromosome (or plasmid) |
|
|
if transferred DNA is degraded, what mediates it?
|
restriction-modification systems
|
|
|
what stabilizes transferred DNA by circularization?
|
plasmid
|
|
|
integration into host chromosome occurs by ____
and requires ____ |
homologous recombination
requires specific genes (i.e.: recA) |
|
|
3 major characteristics of plasmids
|
autonomous extrachromosomal elements
have separate origins of replication some are conjugative |
|
|
properties encoded by plasmids
|
fertility
production of toxins production of pili and other adhesins resistance to toxic chemicals production of siderophores |
|
|
R plasmids =
|
resistance plasmids
|
|
|
homologous recombination requires (2 things)
|
recA
significant homology btw donor and recipient DNA fragments |
|
|
is site-specific recombination recA dependent?
|
no
|
|
|
site specific recombination is involved in ....
|
integration of phage and transposable elements
|
|
|
transposable elements - 2 types
|
IS or insertion elements
transposons |
|
|
4 characteristics of insertion elements
|
simplest transposable elements
encode enzymes for site-specific recombination can mediate own insertion and duplication when element moves, leaves original copy behind = replicative recombination |
|
|
2 characteristics of transposons
|
larger segments of DNA bounded by IS sequences
have all characteristics of IS elements, plus addition genes, ie.: for ABS resistance |
|
|
3 uses of horizontal gene transfer
|
phase/antigenic variation
acquisition of ABS resistance acquisition of new characteristics |
|
|
pathogenicity islands are found in...
|
pathogenic strains
|
|
|
pathogenicity islands have different _____ content than host bacterium
|
G + C content
|
|
|
pathogenicity islands are often flanked by...
|
direct repeats, insertion element sequences or tRNA genes
|
|
|
pathogenicity islands often have...
|
degenerate/non-functional "mobility" genes, such as transposases and/or phage remnants
|
|
|
Gram positive bacteria (5)
|
Micrococcae
Streptococcae Bacillus Clostridium Listeria Corynebacteria |
|
|
Gram negative bacteria (8)
|
Neisseria
Pseudomonas Bordetella Fransicella Brucella Enterobacteria Vibriona Pasteurella |
