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Biology 207 > Exam 3 Terms > Flashcards

Exam 3 Terms Flashcards

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1
Q

biological species concept

A

organisms that create fertile offspring are the same species

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2
Q

phylogical species concept

A

based on shared evolutionary history (DNA)

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3
Q

16S rRNA

A

is a chronometer to measure relatedness, ribosomal genes must be ancient, compared via PCR and alignment (reveals 3 branches of life)

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4
Q

informational genes

A

transcription and translation, generally passed on vertically

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5
Q

operational genes

A

metabolism, pathogenicity, can be traded horizontally

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6
Q

gene sharing

A

more commons between organisms in different environments

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7
Q

pan genome

A

all genes found in any strain

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8
Q

core genome

A

all genes found in all strains

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9
Q

pathogenicity island

A

region of the genome that contains virulence factors (the genetic information transferred into it to make it infect others), may contain skewed GC ratio or codon bias

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10
Q

shigella

A

genus with 4 species, all are pathogenic (S. dysenteriae, S. flexneri, S. sonnel, S. boydii, can cause body flux and kidney failure

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11
Q

how shingella differs from E. coli?

A

non-motile, does not ferment lactose, indole, lysine-decarboxylase negative, more insertion sequences, virulence plasmin, causes similar but more severe disease

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12
Q

how is shigella similar to E. coli

A

the sequencing shows they are very closely related:
- 94% same open reading frames
- causes similar diseases
- PINV plasmid, can invade other species

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13
Q

form species

A

observable characteristics

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14
Q

morphology

A

size and shape

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15
Q

biochemistry

A

composition and metabolism

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16
Q

ecology

A

habitat and tolerances

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17
Q

pathogenicity

A

ability to cause disease

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18
Q

paralog

A

same gene in same species duplicated (happens by HGT or errors in DNA repair)

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19
Q

reduction

A

organism lives in a stable, predictable environment and loses genes to reduce energy (common in nutrient poor environments and symbiosis)

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20
Q

evolution determinants

A

growth rate and strength of selection

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21
Q

MRSA

A
  • treated with two rounds of antibiotic due to weakened immune system, developed small colony variant/multiple drug resistant
  • mutation to S. aureus made ppGpp, normally triggered by stress
  • ppGpp binded to polymerase, creating slow growth of bacteria and recycle instead of growth (shows regulatory mechanisms have large impact)
    takeaway: benefit of being antibiotic resistant was greater than the cost of slow growth
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22
Q

E. coli long term growth experiment

A

takeaways: cultures evolved, every point mutation occurred
-molecular clock: mutations happen at a steady rate
-all populations evolved faster growth rates and larger cells size (rate dramatically increased more early on)
-after 33,000 generations, one culture was notably denser (cit+ mutation)

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23
Q

Cit+ mutation

A

-can use citrate as a C source, Cit- phenotype had gone extinct
-duplication copied citrate anti-porter, making citrate come in and succinate go out (behind a different promoter, CitT is usually not produced in aerobic conditions

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24
Q

why is CitT mutation bad?

A

loss of succinate, only good with gltA mutation

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25
Q

GltA mutation

A

offsets loss of succinate through the Krebs cycle

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26
Q

how was citT further improved?

A
  1. multiple copies of mutated citT
  2. increase in DctA (brings in succinate, making reversions of GltA beneficial)
  3. succinate using cells arose
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27
Q

eukaryotic tree

A

animals and plants are no longer together, although they are both amitochondriate groups (once had mitochondria, then lost it), reordered due to sequencng advancements

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28
Q

asexual reproduction

A

spores, germination (exit from dormancy), mycellium (mitosis), spore-producing structures (mitospores)

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29
Q

sexual reproduction

A

spores, mycellium (mitosis), plasmogamy (fusion of cytoplasm) leads to heterokaryotic stage, karyogamy (fusion of nuclei) leads to zygote (diploid), meiosis, spore producing structures

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30
Q

ascomycetes

A

many live in association with algae, lichens, yeast and hyphal morphology

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31
Q

glomeromycota

A

obligate plant mutualists, form arbuscular mycorrhizae (fungus penetrates cortical root cells and plant hormones regulated formation and they exchange sugar for fungal materials like ammonium and phosphate)

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32
Q

protist

A

not fungi but eukaryotes

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33
Q

protazoa

A

type of protists, heterotrophic single celled

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34
Q

primary algae

A

photosynthetic eukaryotes, not land plants, no roots or vascular tissues; derived from eukaryote that engulfed a cyanobacteria

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35
Q

secondary algae

A

photosynthetic eukaryotes, not land plants, no roots or vascular tissues; derived from a protozoan that engulfed a primary alga

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36
Q

slime molds

A

heterotrophic spore formers

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37
Q

plankton

A

any aquatic organism unable to swim against a current

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38
Q

photoplankton

A

phototrophic aquatic organisms unable to swim against a current

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39
Q

zooplankton

A

aquatic organisms unable to swim against a current that feed on other plankton

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40
Q

cyanobacteria

A

green-blue algae
- only photosynthetic prokaryotes (unicellular)
- organelles sacs contain thylakoids
- adappt to non ideal conditions
- produce external toxins

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41
Q

heterocysts

A

cyanobacteria that can fixate nitrogen

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42
Q

akinetes

A

spore formating cyanobacteria

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43
Q

primary algae

A

green and red
- origin engulfed cyanobacterium, became the chloroplast
- has double membrane (one is from the cyanobacteria, one is from the host)

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44
Q

secondary algae

A

origin by engulfing primary alga, two double membranes
nucleo morph- vestigal nucleus from first host

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45
Q

issues with algae: the plankton paradox

A

limited amount of resources can support algae that need different resources

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46
Q

issues with algae: algal blooms

A
  • increase in nutrient availability cause harmful toxins
  • when they die, they lead to anoxic zones because they serve as food for heterotrophs that deplete O2 from the water (they all gather to feed on it)
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47
Q

issues with algae: red tides

A
  • bloom of dinoflagellates
  • produce neurotoxins
  • dismantle Na+ ion pump
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48
Q

issues with algae: biofuels

A

extract lipids from algae

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49
Q

phylum

A

major branch of tree, distinct group of organisms

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50
Q

candidate phyla

A

new group categorized by DNA isolates

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51
Q

CPR

A

monophyletic group close to the root of the tree (unculturable, analyzed by DNA alone, do not abide by Koch)

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52
Q

ribosomes

A

make organisms seem further apart than they are

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53
Q

phototrophy takeaways

A
  • color not able to be absorbed is reflected and the color that the organism appears as
  • phototrophy differs depending on organism
  • absorption wavelength reduces competition over light
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54
Q

cyanobacteria and procholorphytes

A
  • 80% of ocean photosynthesis
  • significant N fixers
  • can form spores
  • related ancestor of chloroplasts
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55
Q

proteobacteria

A
  • photoautotrophs without O2
  • purple! slay
  • chromatophores produce color, more in low light, no O2
    type: pelagibacteria: rhodopsin based phototrophy, Gr-, from archaea?
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56
Q

green S bacteria

A
  • consortia =mutualistic relations with heterotrophic bacteria, trades food for motility
  • divide in synchrony, coculturing possible
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57
Q

deinococci/thermus

A
  • stain Gr+ but do not have typical Gr+; peptidoglycan layer between inner and outer membrane
  • resistant to radiation and breakdown: has multiple DNA repair enzymes, tightly coiled chromosomes hold fragments
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58
Q

High GC Gr+ species: streptomyces morphology

A
  • complex lifecycle and metabolisms, largest genomes
  • body = hyphae (thinner than fungal), no crossbodies
  • linear chromosomes
  • makes lots of antibiotics
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59
Q

High GC Gr+ species: mycobacteria

A
  • high lipid content; wrinkled colonies, can’t take in stains
  • causes TB
  • detected by acid-fast staining
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60
Q

High GC Gr+ species: corynebacteria

A

includes diphtheria pathogen

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61
Q

proteobacteria: pseuodomonads

A

rods with flagella, organoheterotrophs, aerobes

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62
Q

proteobacteria: neisseria

A

cocci or bacilli, organoheterotrophs, nonmotile, can cause gonorrehea

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63
Q

proteobacteria: enteric

A

rods, organoheterotrophs, GI tract, motile

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64
Q

proteobacteria: vibrios

A

curved rods, aquatic, bioluminescence

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65
Q

proteobacteria: rhizobia

A

N-fixers, endosymbionts of legumes

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66
Q

proteobacteria: rickettsia

A

parasites, causes human diseases transmitted by insects

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67
Q

proteobacteria: spirilla

A

pray on other Gr- bacteria, spiral shaped

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68
Q

Low GC Gr+ species

A

thick cell walls, form biofilms and endospores

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69
Q

Low GC Gr+ species: bacillus thuringinese

A

insecticidal protein, engineered into plans

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70
Q

Low GC Gr+ species: clostridium

A

can cause illness

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71
Q

Low GC Gr+ species: lactobacillus and listeria

A

dairy, fermented foods, food poisoning, invades nerve and epithelial cells

72
Q

Low GC Gr+ species: staphylcoccus

A

boils, impetigo, skin infections, TS

73
Q

Low GC Gr+ species: streptococcus

A

cavities, throat, pneumonia

74
Q

Low GC Gr+ species: mycoplasma

A

no cell wall but match sequencing, have sterols and lipoglycans

75
Q

proteobacteria: sheathed proteobacteria

A

grow within layer of protein, polysacchrides and lipids, elongated capsule

76
Q

proteobacteria: stalked proteobacteria

A

unequal cell division: budding or polar growth, stalk is for attachment, coordinated to cell division

77
Q

proteobacteria: myxobacteria

A

rod shaped, vegetative, aerobes, aggregates with nutrient depletion, grow in soil

78
Q

elementary chlamydia

A

extracellular replication, inert, no cell wall

79
Q

reticulate chlamydia

A

intracellular replication, active

80
Q

verrucomicrobia

A

tubulin genes received via horizontal transfer

81
Q

archaea

A

most ecologically diverse domain:
- more extreme habitats (high temperatures, low pH)
- symbioses with bacteria and eukarya
- central dogma like eukarya
- methanogenesis + rhodopsin phototroph capabilities

82
Q

how can archaea adapt to high temperature?

A
  • proteins have hydrophobic cores, ionic residues on surface, active chaperonins
  • DNA is positively supercoiled
  • tetraether lipid monolayers
  • hot spring/vent habitat
83
Q

euryarchaeotes

A

major group within archaea, have methanogens, extremophiles

84
Q

methanogens

A

aerobes, can oxidize hydrogen, most are mesophiles

85
Q

halophiles

A
  • high salt tolerance: slight, moderate, extreme
  • mesophiles (normal temp),
  • photoheterotrophs
  • usually obligate aerobe
  • some produce bacteriorhodopsin at low O2, creating H+ gradient for ATP synthesis
  • have Na+ powered flagella, gas vesicles
86
Q

adaptations to high salt

A

high GC content, more acidic, K+ in cytoplasm offsets external Na+, S-layer has acidic AA glycoproteins, stable in high Na+

87
Q

ecology

A

interaction of organisms with each other and their environments

88
Q

example of communities interacting with each other

A

phototrophs make O2, aerobes need O2, they take it from the anerobes in anoxxic sediments

89
Q

community

A

organisms in given time and place

90
Q

ecosystems

A

interconnected group of organisms and habitat

91
Q

richness

A

number of different species

92
Q

abundance

A

proportion of species
balance depends on nutrients, physical conditions, ability to use nutrients

93
Q

guild

A

group of species that carry out related metabolic activities

94
Q

pure cultures

A

remove competition, making it hard to understand the organisms
ex: plants for light, heterotrophs for carbon (enzymes tapping into new source eliminates competition)

95
Q

metagenome

A

sum of DNA found in environmental sample (differences show DNA evolved through adaptations)

96
Q

how do we sample microbial communities?

A

fluorescent staining highlighting living cells, 16S rRNA sequencing

97
Q

how do conditions cary in small distances?

A

nutrients fluctuate, feast or famine (bursts of growth), natural growth rate is less than lab, habitat can change, micro colonies and films form in favorable areas, heterogeneous habitat = more niches = greater richness (more nutrients)

98
Q

FISH

A

16S rRNA identities bacteria through fluorescent staining

99
Q

microbial symbioses

A

binary interactions in which both organism are present (not in the real world), intensity increase with population size, third species may strengthen or counteract interaction

100
Q

mutualism

A

obligate, needed to survive

101
Q

synergism

A

can live without the interaction but is beneficial for growth of both organisms

102
Q

syntrophism

A

eat each other

103
Q

lichens

A

fungus and algae (organism is formed by mutualistic relationship)

104
Q

corals

A

coral and algae

105
Q

amensalism

A

one species benefits by harming the other

106
Q

colonization resistance

A

one species dies

107
Q

climate change

A

one consequence of CO2 increase
- positive feedback loop for methane release
- warming accelerates due to water vapor, clouds, ice albedo, soil respiration

108
Q

layers of soil

A

Ogres (organic declines) Munch (mineral content) And (aeration decrease) Hydrate (hydration increases)

109
Q

rhizoplane

A

plant root surface

110
Q

rhizosphere

A

region around plant root that can receive substances from plant (fungi help plants take up minerals)

111
Q

legumes

A

have advantange in unfertilized soil, they can get N from the fungi (needs no O2, leghemoglobin makes red)

112
Q

biofilms attach by…

A

polysacchrides

113
Q

planktonic habitat

A

more volume
- as depth increases, light, oxygen, and temperature decrease
- organic molecules are at the surface, minerals at the floor
- aquatic systems are generally considered oligotrophic (low N, P, Fe)
- pressure may be an issue in oceans

114
Q

eutriphication

A

excessive nutrients leading to too many microbes, depleting water of O2, animals die

115
Q

ruminents

A

cattle, sheep, goats, deer, elk, giraffes, buffalo etc.

115
Q

rumen

A

specialized fore stomach
- contains complicated microbial community
- came from mother after birth

116
Q

animal gut ecology (rumens eat grass…)

A
  1. fibers broken down by fungi
  2. cellulose, starch, and AA broken down by bacteria
  3. glucose converted and absorbed as volatile fatty acids
  4. hydrogen used by methanogens
    eructation (burping methane and CO2, contributes to global warming)
  5. carbon, proteins, and vitamins produced by bacteria in the gut can be used by ruminants
  6. if they eat too much grains and not enough grass, acidosis results (streptococcus bovis overgrowth)
  7. acids from starch fermentation can kill other bacteria (cost)
117
Q

eructation

A

burping methane and CO2, contributes to global warming

118
Q

vents

A

heated water emerges from ocean floor

119
Q

cold seeps

A

pressure is squeezing water through ocean sediment

120
Q

lithoautotrophs

A

basis of local food chain (animals)
- bacteria may also attach to animals present (protection, symbiosis)

121
Q

tube worms + bacteria

A
  • worm supplies H2S and O2
  • bacteria oxidizes H2S and fixes O2 (get a home in the worm away from the vent)
122
Q

termites

A

termites “eat” wood: delivers wood fiber to gut via jaw
- protists in gut breakdown lignin
- bacteria break down cellulose
- termite absorbs fermentation product, typically acetic acid

123
Q

mixotricha paradoxa (protist with 4 symbiotic bacteria)

A

Protist in gut of termites
- spirochete - function as flagella for movement (flagella of its own help with steering)
- anchor bacteria - related to bacterioides
- internal bacteria - take place of mitochondrion which mixo has lost
- bacteria are obtained through HGT, VGT; correlates with diet

124
Q

our gut

A
  • we gain nutrition and protection from pathogens
  • diet and genetics influence gut microbiome
  • fecal transplant may be needed
  • imbalances can lead to disease
125
Q

reserviors

A

pools of element

126
Q

flux

A

movement between pools
- mediated by a process
- measured by chemical and spectroscopic analysis, radioisotope incorporation, isotope ratios

127
Q

ocean (food webs describe movement)

A

phytoplankton, bacteria, archaea, algae (producers) goes 60% to grazers (protists and invertebrates - consumers) and 40% to viruses (decomposers)

128
Q

forest (food webs describe movement)

A

plants (producers) goes 20% to grazers (protists and invertebrates - consumers) and 80% to fire, fungi and bacteria (decomposers)

129
Q

biotic fluxes

A
  • oxygenic PS
  • lithotrophic carbon-fixation
  • aerobic respiration
  • acteogenesis (acetate production) - auto or heterotrophic
  • anoxygenic PS
  • anaerobic respiration
  • fermentation
  • methanogenesis (syntrophy)
  • methanotrophy (oxycline - the zone between oxic and anoxic)
130
Q

abiotic fluxes

A
  • CO2 in/out of oceans
  • sedimentation
  • vulcanism
  • burning of fossil fuels
  • deforestation
131
Q

role of microbes

A
  • prokaryotes perform all known types of metabolism (eukaryotes don’t play key role)
  • bacteria have dominant role in demineralization process, important in oligotrophic (low nutrient) environment
  • bacteria control nutrient available to primary producers
132
Q

reservoirs (where carbon is found)

A

from biggest to smallest:
1. crust/minerals (mostly unavailable)
2. ocean water (dissolved organic C or diss. C) - CO2 dissolves in water, produces carbonates, lowers pH
3. fossil fuels (mostly unavailable)
4. soil (decaying biomass)
5. atmosphere (increasing)
6. terrestrial + freshwater biomass (standing in trees)

133
Q

human sources have accelerated processes

A
  • agriculture (pro is more PS, con is more humans exhale CO2)
  • burning of fossil fuels
  • deforestation
  • methane release from livestock
134
Q

nitrogen cycle reservoirs

A

present as NH2, NH3, NO2, NO3 (N is limiting)
1. atmosphere (limited bioavailability)
- energetically expensive to fix
- industrial fixation significant
2. crust/minerals (unavailable)
3. ocean water (dissolved N2 and also available N)
4. soil
5. terrestrial biomass (grass, insects, fungi)

135
Q

haber-bosch

A

nitrogen is fixed via combination of N + H to make NH3 (industrial process); given to plants in the form of fertilizer

136
Q

downsides to fertilizer

A
  1. pollutes groundwater (excessive algae + plant growth; O2 is used + depleted to break down excessive algae creating dead zone)
  2. oxygen depletion leads to dead zone
  3. formation of N2O (greenhouse gas - leads to O2 depletion)
137
Q

N fixation

A

fixation: N2 to 2 NH3
(consumes 8 e-, 16-24 ATP)
- N2 is not useable for most organisms
- this rxn is carried out by only bacteria + archaea (may be symbiotic with plants)
- key enzymes = dinitrogenase and dinitrogenase reductase; cofactors are iron and molybdenum; only works w/o oxygen, O2 may destroy enzymes
- 20 genes are involved (similar in bacteria + archaea) - transcription is regulated by O2, NH3, fixed N

138
Q

assimilation

A

using NH3 to make aa, n-bases

139
Q

ammonification

A

NH3 from breakdown of aa

140
Q

nitrification

A

NH3 to NO2 (anaerobic) and NO2 to NO3 (aerobic)
- generally aerobic (uses O2 as the e- acceptor)
- use calvin cycle in carboxysomes for CO2 fixation

141
Q

lithotrophy

A

oxidizing NH3 for minimal energy

142
Q

nitrosifyers

A

NH3 to No2

143
Q

nitrofyers

A

NO2 to NO3

144
Q

denitrification

A

N compounds to N2
- N species used as e- acceptor for anaerobic respiration
- removes N from ecosystem - good for wastewater treatment, bad for farmers

145
Q

anammox

A

anaerobic ammonia oxidation
- ammonia is ox, nitrite is the e- acceptor
- dissimilatory, producing N2

146
Q

sulfur cycle reservoirs

A
  • crust/minerals - weathering makes inorganic forms available
  • ocean water - dissolves sulfates, vents spew H2S
  • soil
  • biomass
  • atmosphere - volcanoes and burning of fossil fuels
147
Q

sulfur cycle reservoirs

A
  • S needed for some AA + cofactors
  • reduced S often contaminates oil + coal deposits (when burned, plays a role in acid rain; S ox. bac. can clean coal)
  • S bac. can also destroy concrete pipes
148
Q

sulfur flux

A
  • chemolithotrophy
  • anoxygenic PS
  • calvin cycle
  • organoheterotrophy
  • assimiliatory S rxns for AA
  • inorganic fermentation (for energy, anaerobic)
149
Q

sulfur reduction

A
  • mostly anaerobes
  • used as e- acceptor for anaerobic resp.
  • organoheterotrophs or lithoautotrophs
150
Q

phosphate cycle reservoirs

A
  • insoluble minerals/salts
  • biomass
151
Q

phosphate cycle flux

A
  • P is solubilized by bacteria, fungi, photoplankton
  • passed up the food chain
    *needed for DNA
152
Q

why are humans a favorable environment for microbes

A
  • nutrient dense
  • controlled temp.
  • pH
  • osmotic balance
    (some tissues have more O2 than others)
153
Q

normal flora

A

organisms present in healthy individuals
(human cells ~ microbial cells in human)

154
Q

composition of normal flora depends on

A

age, sex, diet, etc.

155
Q

diversity of normal flora is

A

mostly bacteria, also archaea, fungi, protists

156
Q

transient flora

A

organisms present in passing
(assume interaction is beneficial to microbe)

157
Q

composition of transient flora depends on

A

exposure, disease, etc.

158
Q

colonization

A

growth of microbe in/on body
- if its disease-causing = infection

159
Q

gut-brain axis

A
  • microbiome interacts w/ endocrine, nervous + immune systems
  • affects conditions like allergies, inflammation, autism, depression, metabolism
160
Q

holobiont

A

human = microbiota
- exists on all surfaces exposed to outside world
- starts @ birth
- natural birth vs. c section, source of milk may affect

161
Q

hygiene hypothesis

A

gut microbiome is less diverse than before

162
Q

tissues

A

microbes here = disease

163
Q

skin

A

protective microbes (normal flora)
- skin is tough to penetrate, has tightly packed epithelial cells, keratins are hard to break down
- epidermis, dermis, SC layer
- shedding limits accumulation of microbes

164
Q

hair follicles + sweat glands

A
  • slightly acidic
  • high salt
  • nutrient rich
  • contain antibacterial peptides, enzymes
165
Q

skin flora includes

A
  • mostly Gr+ (Gr- in more moist regions, fungi on scalp + feet)
  • staphylococcus epidermis (harmless)
  • cutibacterium acnes + related cornyebacteria (harmless, can cause odor + acne, breaks down lipids)
  • staphylococcus aureus (can cause impetigo and boils)
166
Q

oral cavity

A

moisture and food make for dense + diverse biodiversity (more than skin)
- antibacterial action of lyzozyme + lactoperoxidase
- acid production, diet high in sucrose causes cavities
- gingivitis + periodontal disease can also occur
- dental procedures may allow these organisms to enter blood + form biofilms in heart

167
Q

shift in species post teething

A

anaerobes colonize crevices between teeth + gums

168
Q

teeth = surface for attachment

A
  • glycoprotein film from saliva covers teeth (streptococcus species can attach and make dental plaque)
  • filamentous bacteria occupy root of teeth
169
Q

upper respiratory tract

A
  • microbes enter inhalation
  • normal microbes prevent harmful microbes, normal flora may include pathogens in carriers
  • defense includes mucus and antibodies (lysozyme)
170
Q

lysozyme

A

enzyme that helps with immune system

171
Q

lower respiratory system

A

not sterile as previously thought - infection from URT, viral, and secondary bac.

172
Q

GI tract

A
  • generally anaerobic
  • strong pH gradient
  • organisms may stay in mucus lining (H. plylori to ulcers)
  • higher pH = more bacteria
  • diet affects composition
  • disruption of community balance can lead to water uptake issues (diarrhea)
  • aerobes may cause disease if introduced to other areas (UTI)
  • organisms consume + make nutrients
  • bottle fed infants get mixed flora sooner
  • organisms are being flushed out of system + replaced by upstream microbes
173
Q

dysbiosis

A

out of balance community
- restored by probiotics + fecal transplant
- linked to obesity

174
Q

exposure/breach in containment

A

organisms go where they shouldn’t

175
Q

microbial virulence factors

A

adherence/invasion, colonization, growth toxins (factors that make microbes more virulent)

176
Q

host risk factors

A

age, stress, diet, disease

Biology 207 (3 decks)

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