material after exam 2 Flashcards
describe the basis of a phylogenetic tree
length of branch is proportional to differences between sequence
node is the branch point
root is the node of a branch group
list the major well studied bacterial phyla and defining features of each
cyanobacteria - only prokaryotes to use z pathway -found in all habitats firmicutes -thick cell wall spore formers
actinobacteria - acid fast - spore forming -
non mycelial: irregular shape and short chain organism
deep branching gram - most anaerobes
spirochetes - hetrotrophic form coiled spiral irregular cells
cyanobacteria
- only prokaryotes to use z pathway -found in all habitats
firmicutes
- Thick cell wall and spore formers\
- Low GC
- Bacicillales
- Rod shaped vegetative cells are easily stained
- Spores can be used as insecticide
- Clostridiales
- Found soil water and Digestive tract
- Drum stick spores
- Lactobacillales
- Lactic acid
- Obligate fermenters
- Streptococcus
- Hemolysis
actinobacteria
- Acid-fast
- High GC
- Spore formers
- Non Mycelial: irregular shape and short chain organism
-
Actinomycetales
- Acid fast
- Filamentous spore formers
-
Streptomyces
- Multicellular filaments dispersible spores( by wind)
- Obligate aerobes
- Large genome
- Produce antibiotics
-
Mycobacterium
- Slow growth
- Thick envelope containing mycolic acid
-
Corynebacterium
- Irregularly shaped
- Diphtheria lung disease
-
Mycoplasma
- Parasites
- Lack cell wall
- Smallest genomes
- Proteobacteria
- Most diverse metabolism
- Broken into alpha beta gamma delta and epsilon classes
-
Methylotrophy
- Ability to oxidize single carbon compounds such as methanol and methane
-
Bataproteobacteria
- Nitrifiers
- Oxidize ammonia to nitrate
- Pathogens
- Nitrifiers
-
Gammaproteobacteria
- Sulfur oxidizing genus beggiatoa
- Oxidize H2S to sulfur
- Enterobacteriacea
- E. coli
- Ferment sugars
- Pseudomonadacea
- Obligate respires (O2 or NO3
- Can infect plants
- Biofilm producers
-
Acidithobacillus
- Oxidize iron or sulfur
-
Phototrophs
- Uilize sulfise and produce sulfur
-
Deltaproteobacteria
- Lithotrophs multicellular communities
- Sulfur iron reducers
- Myxobacteria
- Spore producing multicellular fruiting bodies spore disperser
- Bdellovibrio
- Attack proteobacteria host such as e.coli by invading periplasm +
-
Epsilonproteobacteria
- Microarophilic
- Helical pathogens
- Sulfur oxidizers
- Found in marine habitats
- Campulobactor and helicobacter
- Casutive agent of gastritis and stomach ulcers
- Microarophilic
deep branching gram
- Most anaerobes
-
Acidobacteria
- Abundant in soil and extreme conditions
-
Chlorobi
- Green sulfur bacteria
- Photolithotrophs
-
Bacteroidetes
- Grow anerobically
- Feed other gut bacteria
- Remove chanes from bile acids
-
Fusobacteria
- Dental plaque
spirochetes
- Heterotrophic that form coiled spiral
- Aerobic and anoerobic
- Cause disease
- Treponema-syphilis
- Borrelia
- Lyme
- Relapsing fever
irregular cells
no cell wall or diminished
- Differentiate between bacillales and clostridiales endospores
- Bacicillales
- Rod shaped vegetative cells are easily stained
- Spores can be used as insecticide
- Clostridiales
- Found soil water and Digestive tract
- Drum stick spores
- Identify both spore forming and non spore forming firmicutes
- Spore forming - bacillales and clostridiales
- Non spore forming –bacillaeles staphylococcus lactobacillales, streptococcus, mycoplasma
name three major phyla of archaeal domain
crenarchaeota thaumarchaeota euryachaeota
creanarchaeota
hyper thermophiles: hotspings geysers hydrothermal vents extreme acidic environments mesophilic, psychrophilic
- Anaerobic, low ph environment, steep temperature, reduce sulfur
thaumarchaeota
live on human skin
- Aerobically oxidize ammonia to nitrite, ammonia-oxidizing archaea (AOA)
- Symbiotic
lokiarchaeota
- recently chatacterized deep sea archae
- shares traits with euraryotes
- genes associated with actin cytoskeleton and phagocytocis
euryarchaeota
grow in soil animal digestive trracts and marine floor sediments
- Produce methane
- Extreme anaerobes
- Diverse cell forms
- Blance osmotic presure by high internal [KCl]
explain why archael phylogeny is challanging to peice together
wide range of size and form can be multi or unicellular
recall the features of hotsprings and geysers that impact the growth of micriobes
- reduced minerals
- low oxygen content
- steep temp gradient
- acidity
describe technologies used to collect samples from black smoker habitats and how scientist study barophiles
submersible devices with arms and use deep aquarium deep sea extractions ( mini lab)
differentiate among protozoa algae and protist
- protist: single or colonial euk. other than fungi
- amoebozoa
- rhizaria
- parasitic protozoa
- typanosomes
- metamonads
- protozoa: protist that are heterotrophs
- algae:
- primary- closely related to green plants
- secondary heterotrophic protist that incorporated algae
-
bacillariophycea
- diatoms
- coccolithophores
- phaeophycea
- brown algae
*
- brown algae
outline steps required to obtain metagenomic DNA
- seperate cells from surrounding.
- filter fractionating sample
- isolate DNA
- with a universally used kit or
- multiple DNA extractions ( best chance for extracting and maximizing coverage)
- PCR amplification i
- sequencing
- functional annotation to recognize gene encoding functional products
- FISH
- flourophore labled oligonucleotide probe
- need to know what youre looking for
define niche
set of conditions habitat resource where an organism grows
assimilation vs dissimilation
- assimiliation -acquiring an element to build into cells
- primary producers -organisms that produce biomass from inorganic carbon
- dissimilation - process of breaking down organic nutrients into inorganic material
- CO2 and NO2
evaluate the roles decomposer in food web
decomposers return carbon and minerals back into the environment
distinguish different levels of consumers
grazers feed on producers predators feed on grazers
mutualism
- both benefit and cant grow independently
- lichen symbiosos between fungus and alga
synergism
- both benefit but can grow independently
- human colonic bacteria produce fermentation products
commensialism
one befits while the other is unaffected
amemsalism
- one benefits the other one is harmed
- actinomycete production of antimicrobial peptides that kill surounding bacterial
parasitism
- obligatory for parasite but host is lost
- vibrio cholerae human pathogen is mutialist of copepods
biogeochemistry
is the interaction of microbes and their ecosystem
biogeochemistry source
is what is making the elements available
biogeochemistry sink
is to which the element returns
compare and contrast carbon reservoirs
ocean absorbs co2 from atmosphere atmosphere smaller than the ocean earth crust is largest reservoir but least accessible
summarize the factors contibuting to atmospheric CO2 levels
marine terrestrial - aerobic: phototrophs produce O2 litotrophs reduce CO2 and respiration returns CO2 - anearobic: fossil fuel, fermentation and lithotropic respiration
•Differentiate the three sides of the nitrogen triangle and describe what happens in each
- atmospheric N2 gets fixed to reduced nitrogen (NH3 or NH4) which goes trhough nitrification to produce oxidizeded nitrogen ( NO2, NO3) then denitrification takes you back to atmospheric nitrogen N2
- Atmospheric N2: N2–>NH3–>NH4+, catalyzed by nitrogenase • Reduced Nitrogen: NH4+–>NO2–>NO3- • Excess Ammonia affect water supplies and fish can die • Oxidized Nitrogen: NO3–>NO2–>NO–>N2O–>N2 • NO3 has 200x the effect of CO2
•Recall the anammox reaction
- • This reaction is the major source of N2 •
- NH4+ + NO2–>N2 + 2H2O
- accounts for majorety of the N2 retured to atmosphere
*
Distinguish between assimilatory and dissimilatory nitrate reduction
- • nirite assimilation to biomass is called assimilatory nitrate reduction
- casues nitrate runoff
- dangerous to water and fish
- nitrate and ditrite reduction is called dissimilatory nitrate reduction
- excessive fertilization
- green house gas
- Oxidized nitrogen is dissimilatory • Reduced nitrogen is assimilatory
Outline the sulfur cycle
• H2S + O2—>SO2—>SO4^2- • Sulfate is an electron acceptor and can oxidize sulfur
•State the hygiene hypothesis
- • Due to our restricted access to microbes our microbiota appears less diverse than our ancestors
- can contribute to inflamatory diseases
•Recall the benefits and risks of the microbiome
- • Benefits: digest food, make vitamins, promote tissue development Risks: infection
- beneficial gut microbiota
- akkermansia
- promotes host tissue differntiation by degrading protective mucin layer
- bacteroides
- breaks down complex cabohydrates into products that can be absorbs by the body
- akkermansia
•Describe the Gordon lab’s experiment that connects microbiota and obesity t
• Scientist transplanted microbiomes from an obese and fit twins to mice • The mice who had the obese microbiome became obese • When microbiome from lean mouse was transfer to obese, it gained less weigh
•Differentiate between innate and adaptive immunity
- • Innate: barriers (skin) nonspecific, since birth
- • Adaptive: specific, recognizes, faster response
- reacts to antigens when exposed
•List the types of white blood cells and how they combat microbes
- • Polymorphonuclear leukocytes
- neutrophils -majority or WBC
- engulf and destro microbes
- neutrophil extracellular traps (NET)
- baaophils ans eosinophils
- realese toxins
- stain
- monocytes
- single nucleus
- phagocytosis
- can migrate
- Lymphocytes • T cell have specific response
- B cells
- produce antigens binding antibodies
- • Natural kills cells •
- Destroy host cells •
- Detects changes in cell surface •
- Secretes perforin proteins
- neutrophils -majority or WBC
Phagocytosis, neutrophil extracellular traps (NET), release toxins, stain with basic or acidic dye • monocytes • Phagocytosis, can migrate to various tissues, make first contact • Lymphocytes • T cell have specific response • B cells produce antigens binding antibodies • Natural kills cells • Destroy host cells • Detects changes in cell surface • Secretes perforin proteins
•Describe physical and chemical defenses
- Physical: skin oil, mucous, AND LUNGS
- Chemical: Acidic pH (stomach), lysozyme (tears) antimicrobial peptides (DEFENSINS)
Describe the acute inflammatory response
- A way for phagocytes to leave bloodstream and access infection
- Capillary cell express selections
- Macrophages then attack bacteria
- Damage tissue release histamine which opens vessels
- Prostaglandin is released and causes itching and pan
Recall what part of the bacterial cell the alternative complement pathway recognizes and the impact of MAC
• C3 recognizes gram neg microbes • This causes the formation of membrane attack complex (MAC) which makes a destructive pore
•Differentiate between humoral immunity and cell-mediated immunity
Both are adaptive • Humoral: Attack invading pathogens in body fluids • Cell-mediated: Attack infected host cells
•Describe the general structure of antibodies
- 4 polypeptide chain, 2 heavy and 2 light hold by disulfide bonds
- Binding site are amino terminal ends
- Both bind identical antigens
•Explain the role of B cells in humoral immunity
- humeral immunity type of lymphocyte made in bone marrow
- Each B cell expresses one antibody recognizes one antigen
- Epitope: is the part of the pathogen that being to B cell
- memory cells allows for quick initiation of immune respone
- plasma/effector cells
- factories to make antibodies 2000/s
•Recall three consequences of antibody binding to a pathogen
- Neutralization: antibody prevent adhesion
- Opsonization: antibody promotes phagocytosis
- Complement activation: enhances opsonization and lysis bacteria
•Differentiate between helper and cytotoxic T cells
- • Helper:
- Display the surface antigen CD4, Assist activation of B cells and other T cells
- recognize and bind to antigen/ MHC2
- specific binding interaction
- • Cytotoxic:
- Display the surface antigen CD8, Destroy bacteria and infected host cells
- recognize and bind to antigen/ MHC 1
- activated by cytokines
*
explain the diffrence between MHC 1 and MHC 2 proteins
- mhc class 1 presents intracellular antigens
- microbial proteins made in host cytoplasm are degraded presented on MHC 1 molecules
- MHC class 2 presents extracellullar antigen
- microbial proteins made outside cell are endocytosed in an endosome
- then degraded and presented on MHC 2 molecules
•Explain The Concept Of Selective toxicity
- • Antibiotic must affect the target organism not humans
- *
•Define broad spectrum, narrow spectrum, bactericidal, and bacteriostatic antibiotics
- Broad: effective against many species
- Narrow: effective against few or a single species
- Bactericidal: antibiotics kill target organisms
- Bacteriostatic: Antibiotics Prevent Growth Of Organisms
•Describe methods to determine minimal inhibitory concentration
- lowest concentration of the drug that will prevent growth of an organism
- varies for difertnt bacteria
- test by diluting antibiotic
- lowest concentration with no growth =MIC
- does not indicagte wether drug is bactericidal or bacteriostatic
- strip test ( Etest)
- strip contains a gradient of antibiotic
- place on plate dreshly seeded with lawn
- MIC is the point at which the elliptical zone of inhibition intersects with the strip
•Recall the mechanism of action of penicillin
• Beta-lactam ring chemically resembles the D-ala piece of peptidoglycan • Allows the drug to bind to penicillin binding proteins o Inhibits traspeptidase mediated cross linking between adjacent peptidoclycan chains
Describe therapeutic strategies to combat resistance
- ESKAPE pathogens cause 2/3 if us infections
- targeted species specific theraputics
- dummy target compoinds
- compounds that inactivate resistance enzyme
- clavulanic acid -blocks beta lactamase from cleaving penicillin
- compounds that inactivate resistance enzyme
- linking antibiotics
- develope compunds to interfere with activation of resistance genes
*
•Provide Examples Of Edible microbes
• Red alga (algae) • Fungi: mushrooms
•Explain Why Most Bacteria Cannot be eaten
• Nucleic acids can be converted to uric acid
•Recall The Functions Of Food fermentation
• Preserves food, limit microbial growth •
Improve digestibility: breaks fibers
• Add nutrients and flavor
•Name the major classes of fermentation reactions and their products
- Homolactic acid: pyruvate to lactic acid
- Propionic acid: lactic acid to propionic acid
- Heterolactic acid: pyrutvate—> lactic acid + EtOH + CO2
- Alkaline: proteolysis + amino acid—>NH4+
•Outline The Steps In Cocoa Bean fermentation
- Yeast: acidifies and degrade pectin in pulp. sugar—-> citrate + EtOH + CO2 + acetate
- Lactic acid bacteria: grows when citric acid is gone and converts sugars to lactate and acetate
- Acetic Acid bacteria: when introduced to O2, EtOH and acids are oxidized to CO2
Compare And Contrast Food Spoilage And Food contamination
• Food spoilage: microbial change renders product unfit
- • Food contamination: presence of human pathogens
- dairy products sourued by excessive ferminatation or made bitter by bacterial proteolysis
- meat and poultry are putrefied by decarboxylating bacteria
- seafood spoils rapidly because their unsaturated fatty acids rapidlly oxidize
- plant foods spoil by excess bacterial or mold growth
- pathogens destroy food crops before harvest
•Recall Challenges for commercial success of industrial microbial products
- • Identifying product, isolating microbe, scaling production, business plan, safety, Effective marketing
- microbual products must be competitive with alternitve technologies
explain the general categories of antibiotic resistance
- reduce intracellular concentrations of antibiotics
- reduce intake or pump out
- Multidrug resistance efflux pups
- reduce intake or pump out
- modify the target
- mutations in the ribosomal proteins penicillin binding protiens or gyrases ect
- add modifyg group that inactivate antibiotics
- destroy antibotic before it gets into cell
- beta-lactamase destroys beta actam ring of penicillins
*
- beta-lactamase destroys beta actam ring of penicillins
