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Micro Bio 315 CSUN > material after exam 2 > Flashcards

material after exam 2 Flashcards

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Biology 101 flashcards
1
Q

describe the basis of a phylogenetic tree

A

length of branch is proportional to differences between sequence

node is the branch point

root is the node of a branch group

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2
Q

list the major well studied bacterial phyla and defining features of each

A

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

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3
Q

cyanobacteria

A
  • only prokaryotes to use z pathway -found in all habitats
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4
Q

firmicutes

A
  • 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
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5
Q

actinobacteria

A
  • 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
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6
Q
  • Proteobacteria
A
  • 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
  • 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
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7
Q

deep branching gram

A
  • 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
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8
Q

spirochetes

A
  • Heterotrophic that form coiled spiral
  • Aerobic and anoerobic
  • Cause disease
    • Treponema-syphilis
    • Borrelia
      • Lyme
      • Relapsing fever
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9
Q

irregular cells

A

no cell wall or diminished

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10
Q
  • Differentiate between bacillales and clostridiales endospores
A
  • Bacicillales
    • Rod shaped vegetative cells are easily stained
    • Spores can be used as insecticide
  • Clostridiales
    • Found soil water and Digestive tract
    • Drum stick spores
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11
Q
  • Identify both spore forming and non spore forming firmicutes
A
  • Spore forming - bacillales and clostridiales
  • Non spore forming –bacillaeles staphylococcus lactobacillales, streptococcus, mycoplasma
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12
Q

name three major phyla of archaeal domain

A

crenarchaeota thaumarchaeota euryachaeota

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13
Q

creanarchaeota

A

hyper thermophiles: hotspings geysers hydrothermal vents extreme acidic environments mesophilic, psychrophilic

  • Anaerobic, low ph environment, steep temperature, reduce sulfur
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14
Q

thaumarchaeota

A

live on human skin

  • Aerobically oxidize ammonia to nitrite, ammonia-oxidizing archaea (AOA)
  • Symbiotic
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15
Q

lokiarchaeota

A
  • recently chatacterized deep sea archae
  • shares traits with euraryotes
    • genes associated with actin cytoskeleton and phagocytocis
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16
Q

euryarchaeota

A

grow in soil animal digestive trracts and marine floor sediments

  • Produce methane
  • Extreme anaerobes
  • Diverse cell forms
  • Blance osmotic presure by high internal [KCl]
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17
Q

explain why archael phylogeny is challanging to peice together

A

wide range of size and form can be multi or unicellular

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18
Q

recall the features of hotsprings and geysers that impact the growth of micriobes

A
  • reduced minerals
  • low oxygen content
  • steep temp gradient
  • acidity
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19
Q

describe technologies used to collect samples from black smoker habitats and how scientist study barophiles

A

submersible devices with arms and use deep aquarium deep sea extractions ( mini lab)

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20
Q

differentiate among protozoa algae and protist

A
  • 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
        *
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21
Q

outline steps required to obtain metagenomic DNA

A
  • 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
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22
Q

define niche

A

set of conditions habitat resource where an organism grows

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23
Q

assimilation vs dissimilation

A
  • 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
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24
Q

evaluate the roles decomposer in food web

A

decomposers return carbon and minerals back into the environment

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25
Q

distinguish different levels of consumers

A

grazers feed on producers predators feed on grazers

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26
Q

mutualism

A
  • both benefit and cant grow independently
    • lichen symbiosos between fungus and alga
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27
Q

synergism

A
  • both benefit but can grow independently
    • human colonic bacteria produce fermentation products
28
Q

commensialism

A

one befits while the other is unaffected

29
Q

amemsalism

A
  • one benefits the other one is harmed
    • actinomycete production of antimicrobial peptides that kill surounding bacterial
30
Q

parasitism

A
  • obligatory for parasite but host is lost
    • vibrio cholerae human pathogen is mutialist of copepods
31
Q

biogeochemistry

A

is the interaction of microbes and their ecosystem

32
Q

biogeochemistry source

A

is what is making the elements available

33
Q

biogeochemistry sink

A

is to which the element returns

34
Q

compare and contrast carbon reservoirs

A

ocean absorbs co2 from atmosphere atmosphere smaller than the ocean earth crust is largest reservoir but least accessible

35
Q

summarize the factors contibuting to atmospheric CO2 levels

A

marine terrestrial - aerobic: phototrophs produce O2 litotrophs reduce CO2 and respiration returns CO2 - anearobic: fossil fuel, fermentation and lithotropic respiration

36
Q

•Differentiate the three sides of the nitrogen triangle and describe what happens in each

A
  • 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
37
Q

•Recall the anammox reaction

A
  • • This reaction is the major source of N2 •
  • NH4+ + NO2–>N2 + 2H2O
  • accounts for majorety of the N2 retured to atmosphere
    *
38
Q

Distinguish between assimilatory and dissimilatory nitrate reduction

A
  • • 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
39
Q

Outline the sulfur cycle

A

• H2S + O2—>SO2—>SO4^2- • Sulfate is an electron acceptor and can oxidize sulfur

40
Q

•State the hygiene hypothesis

A
  • • Due to our restricted access to microbes our microbiota appears less diverse than our ancestors
  • can contribute to inflamatory diseases
41
Q

•Recall the benefits and risks of the microbiome

A
  • • 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
42
Q

•Describe the Gordon lab’s experiment that connects microbiota and obesity t

A

• 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

43
Q

•Differentiate between innate and adaptive immunity

A
  • • Innate: barriers (skin) nonspecific, since birth
  • • Adaptive: specific, recognizes, faster response
    • reacts to antigens when exposed
44
Q

•List the types of white blood cells and how they combat microbes

A
  • • 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

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

45
Q

•Describe physical and chemical defenses

A
  • Physical: skin oil, mucous, AND LUNGS
  • Chemical: Acidic pH (stomach), lysozyme (tears) antimicrobial peptides (DEFENSINS)
46
Q

Describe the acute inflammatory response

A
  • 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
47
Q

Recall what part of the bacterial cell the alternative complement pathway recognizes and the impact of MAC

A

• C3 recognizes gram neg microbes • This causes the formation of membrane attack complex (MAC) which makes a destructive pore

48
Q

•Differentiate between humoral immunity and cell-mediated immunity

A

Both are adaptive • Humoral: Attack invading pathogens in body fluids • Cell-mediated: Attack infected host cells

49
Q

•Describe the general structure of antibodies

A
  • 4 polypeptide chain, 2 heavy and 2 light hold by disulfide bonds
  • Binding site are amino terminal ends
  • Both bind identical antigens
50
Q

•Explain the role of B cells in humoral immunity

A
  • 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
51
Q

•Recall three consequences of antibody binding to a pathogen

A
  • Neutralization: antibody prevent adhesion
  • Opsonization: antibody promotes phagocytosis
  • Complement activation: enhances opsonization and lysis bacteria
52
Q

•Differentiate between helper and cytotoxic T cells

A
  • • 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
      *
53
Q

explain the diffrence between MHC 1 and MHC 2 proteins

A
  • 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
54
Q

•Explain The Concept Of Selective toxicity

A
  • • Antibiotic must affect the target organism not humans
  • *
55
Q

•Define broad spectrum, narrow spectrum, bactericidal, and bacteriostatic antibiotics

A
  • Broad: effective against many species
  • Narrow: effective against few or a single species
  • Bactericidal: antibiotics kill target organisms
  • Bacteriostatic: Antibiotics Prevent Growth Of Organisms
56
Q

•Describe methods to determine minimal inhibitory concentration

A
  • 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
57
Q

•Recall the mechanism of action of penicillin

A

• 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

58
Q

Describe therapeutic strategies to combat resistance

A
  • 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
  • linking antibiotics
  • develope compunds to interfere with activation of resistance genes
    *
59
Q

•Provide Examples Of Edible microbes

A

• Red alga (algae) • Fungi: mushrooms

60
Q

•Explain Why Most Bacteria Cannot be eaten

A

• Nucleic acids can be converted to uric acid

61
Q

•Recall The Functions Of Food fermentation

A

• Preserves food, limit microbial growth •

Improve digestibility: breaks fibers

• Add nutrients and flavor

62
Q

•Name the major classes of fermentation reactions and their products

A
  • 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+
63
Q

•Outline The Steps In Cocoa Bean fermentation

A
  • 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
64
Q

Compare And Contrast Food Spoilage And Food contamination

A

• 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
65
Q

•Recall Challenges for commercial success of industrial microbial products

A
  • • Identifying product, isolating microbe, scaling production, business plan, safety, Effective marketing
  • microbual products must be competitive with alternitve technologies
66
Q

explain the general categories of antibiotic resistance

A
  • reduce intracellular concentrations of antibiotics
    • reduce intake or pump out
      • Multidrug resistance efflux pups
  • 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
      *
67
Q
A

Micro Bio 315 CSUN (2 decks)

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