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Micro 450 > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

gut microbiota contributes to:

A

gut development
immune maturation
biosynthetic activities
outcome of pathogenic diseases

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2
Q

intestinal microbiota has:

A 
150 species/person
glycoside hydrolases (not found in human genome)
variability depending on human diet
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3
Q

microbiota digests:

A

polysaccharides into SCFAs

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4
Q

SCFAs

A

10% caloric intake
modulate intestinal motility, insulin sensitivity, and blood pressure
protect against diet-induced obesity

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5
Q

Most commom phyla in human gut

A

bacteroidetes

firmicutes

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6
Q

UniFrac

A

method to calculate a distance between organismal communities using phylogenetic information

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7
Q

steps to make UniFrac

A
  1. build a master phylogenetic tree
  2. label species by community
  3. label branches by community
  4. calculate number of unique branches per community
  5. create a distance matrix
    * see slides in color to make sense of this
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8
Q

Analysis UniFrac

A

higher value difference=more evolutionary distance/more different

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9
Q

metagenomics

A

all DNA extracted is sequenced

can discover function instead of phylogeny and diversity as is the case with 16s rRNA

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10
Q

Age-Associated Differences in microbiota

A

adult microbiota acquired by age 3
genes for vitamin B12 enzymes increased with age
folate-forming genes highest in babies, decreased with age

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11
Q

gnotobiotics

A

known life

descriptor of mice living in germ-free environments

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12
Q

microbes and energy harvest

A

germ-free mice eat more but have a lower % body fat

microbes assist in energy harvest

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13
Q

obesity and microbes

A

higher amount of firmicutes, lower amount of bacteroidetes in obese
leaner test subjects has high SCFA production that obese counterparts

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14
Q

sizes of virueses

A

poxvirus: largest

average size: 10^-7 to 10^-8 m

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15
Q

general characteristics of viruses

A

infectious obligate intracellular parasites
virion/virus particle: nucleic acid genome surrounded by capsid and maybe a lipid envelope
RNA or DNA (single, double, or partial double stranded; circular, linear, or segmented)

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16
Q

infection cycle of virus

A
  1. attachment
  2. entry of particle
  3. decoding of genome information
  4. translation of viral mRNA by host ribosomes
  5. genome replication
  6. assembly of new viruses
  7. release of particles
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17
Q

Challenges of virus evolution

A

don’t survive in historical samples
polymerases have no proofreading activity and the high rate of replication skews evolutionary time
segmented genomes leads to shuffling
no genetic equivalent to rRNA in 3 domains

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18
Q

Progressive hypothesis of viral origins

A

result of mobile genetic elements

explains retroviruses as they use integrase and reverse transcriptase to insert their genome into hosts

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19
Q

Regressive hypothesis of viral origin

A

viruses are remnants of more complex cellular organisms that lost many genes and became parasitic
supported by presence of Mimivirus as it has some translationally-related genes

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20
Q

virus-first hypothesis

A

viruses existed before cellular life. self-replicating units may have gained ability to form membranes and cell walls leading to three domains of life.
viruses then continued to evolve with their hosts

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21
Q

define life

A 
homeostasis
energy metabolism
response to stimuli
reproduction
growth via cellular division (not assembly)
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22
Q

naming viruses

A

based on disease they cause, type of disease, geographic location, their discoverers, combination of previous

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23
Q

Baltimore classification system

A
  1. dsDNA
  2. ssDNA
  3. dsRNA
  4. (+) sense ssRNA
  5. (-) sense ssRNA
  6. RNA reverse transcribing viruses (retroviruses)
  7. DNA reverse transcribing viruses
    * *classiication dictates treatment**
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24
Q

dsDNA viruses

A 
class 1
uses host DNAP/RNAP-limiting factor
translation via host machinery
some encode their own DNA polymerase
some force host into replication stage-causes cancer 
ex: HPV
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25
Q

ssDNA viruses

A

class 2
be ssDNA can not be transcribed, must first become dsDNA using host DNAP
ex: canine and feline parvo viruses

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26
Q

dsRNA viruses

A

class 3
10 distinct dsRNAs in genome
one encodes RNAP to transcribe dsRNA into (+)ssRNA
(+)RNA=mRNA that can be translated into protein or made into dsRNA
ex: Rotavirus

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27
Q

ss(+)RNA viruses

A 
class 4
genome functions as mRNA
(-)sense RNA formed form (+)sense RNA
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28
Q

ss(-)RNA viruses

A

class 5
largest group
contains RNA-dependent RNA polymerase and (-)ssRNA in capsid
inside cell, viral polymerase makes 2 types of (+)ssRNA: some for translation of viral proteins and some for replication

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29
Q

RNA reverse transcribing viruses

A 
class 6
(+)RNA not associated with ribosomes-used to make DNA copy of viral genome done by viral reverse transcriptase
synthesized dsDNA goes into nucleus, inserted and linked to host DNA
now can be transcribed by host into (+)RNA
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30
Q

DNA reverse transcribing viruses

A 
class 7 
replications occurs in cytoplasm and in nucleus of host
though they enter as dsDNA, not true dsDNA viruses because must go through RNA intermediate first. 
Do not require integration into host genome so they do not code for an integrase
DNA enters-->RNA intermediate-->DNA product
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31
Q

Classifications of Viruses

A

most classifications can only go as far as family because few/no similarities exist beyond here

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32
Q

Structural classification of viruses

A

icosahedral symmetry
helical symmetry
non-enveloped (naked)
enveloped

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33
Q

helical symmetry

A

identical helical subunites (protomers) create helical array surrounding viral nucleic acid
form elongated rods or flexible filaments

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34
Q

Bacteriophages

A

dsDNA, ssDNA and RNA

bacteria is host

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35
Q

Problems with Prokaryotes

A

characterization of what they lack (nucleus, membrane bound organelles)
paraphyletic group
eukaryotes did not originate from prokaryotes as names imply

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36
Q

origins of Eukaryotes

A

explained by endosymbiont theory

mitochondria, chloroplasts, other organelles result of bacteria taking up permanent residence inside others.

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37
Q

evidence in favor of endosymbiont theory

A

mitochondria and chloroplast size of average bacterium
they replicate by fission and independent of host nuclear fission
have own ribosomes and proteins
cyanobacteria similar structure to chloroplasts, contain same chlorophyll
sequencing show that hey evolved with proteobacteria and cyanobacteria, respectively

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38
Q

Archaea: general characterisitcs

A 
0.1-15um in diameter
can form long agregates or filaments
variety of cell walls but no peptidoglycan-have S-layer and pseudomurein instead
single circular chromosome
can have plasmids
asexual reproductions
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39
Q

archaeal cell membrane

A

L-glycerol instead of D-glycerol
side chains bound by ether linkages
side chains in bilayer isoprene
cytoplasmic membrane only-no outer membrane

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40
Q

archaeal similarities to bacteria

A 
no nucleus
no membrane bound organelles
DNA in a single loop
genes grouped in operons
genes in metabolism are similar
overall size
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41
Q

archaeal similarities to eurkaryotes

A

similar RNAP
methionine initiates protein synthesis (fMet in bacteria)
histones

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42
Q

methanogens

A

polyphyletic group (more than one common ancestor)
total anaerobes
produce methane from various carbon sources
wetlands, rice paddies, landfills, rumen

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43
Q

hydrogen-consuming methanogens

A

remove excess H2 produced by other species
helps other organisms to more effectively oxidize pyruvate by forming acetate instead of succinate. Process requires low concentration of H2

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44
Q

Halophiles

A

salt-loving
polyphyletic-also occurs in bacteria
some capable of light-driven ATP synthesis
survive by increasing salt level inside cell to match environment/selective influx of potassium
can survive in up to 25% salt solutions

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45
Q

Extreme Thermophiles

A

45-122 degrees C
enzymes must function at high temperatures, makes them not functional at lower temperatures because they are too stable
ferredoxins used-more heat stable
chaperonins refold partially unfolded proteins
DNA contains polyamines to stabilize and has archaeal histones to compact it

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46
Q

Archaea phyla (4)

A

Euryarchaeota
Crenarchaeota
Karoarchaeota
Nanoarcheota

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47
Q

Euryarchaeota

A

largest phyla
dominated by methanogens
diverse habitats
some extreme thermophiles-aerobic and anaerobic

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48
Q

Crenarchaeota

A

often irregularly shaped
make crenarchaeol-a tetraether lipid
more cyclepentane rings in lipid=more stability=ability to withstand higher temperatures
abundant in marine systems
most lack histones (despite high temperatures)
stain gram negative
Sulfolobales: oxidize sulfur to sulfuric acid

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49
Q

Karoarchaeota

A

known only by sequences

found in extremely hot environments

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50
Q

Nanoarchaeota

A

small, parasitic

lack genes for all core molecular processes-depend on host for cellular needs

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51
Q

Protists Generalizations

A 
eukaryotes not like animals, plants, or fungi "junk drawer"
single or multicellular
nucleated microbes
asexual and/or sexual reproduction
not a monophyletic group
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52
Q

Problems with protist classification

A

some protists are not closely related

they share qualities with the three other kingdoms but do not match characterisitics

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53
Q

Rhodophyta, the red algae

A

most multicellular
found in deep tropical waters
red caused by phycoerythrin
important in reef building

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54
Q

phycoerythrin

A

causes red pigment of red algae

absorbs blue wavelengths which can penetrate deep into water

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55
Q

Chromista

A

most are photosynthetic
have chlorophyll c which is not found in plants
includes diatoms, giant kelps, plant pathogens (potato famine)

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56
Q

Diatoms

A

part of chromista phylum
cells surrounded by frustules-hard, porous cell wall made of silica
sexual reproduction; spend most of life as diploid
unicellular and filamentous
40% of ocean CO2 fixation done by them

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57
Q

Diatomaceous earth

A

rock product made entirely by diatom fossils

used as abrasives, insecticides, filters

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58
Q

Diatom cell division

A

frustules split and new half build inside of old.
result if new cells are always smaller than parent
Meiosis is triggered by small cell size; large cell formed by sexual reproduction

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59
Q

Green Algae

A 
unicellular and multicellular
closely related to plants
paraphyletic group
model system for evolution of multicellularity
photosynthetic
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60
Q

Alveolates

A

includes Dinoflagellates, ciliata, Apicomplexa, Formaninifera
All have sacs under cell membrane called alveoli

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61
Q

Dinoflagellates

A 
member of Alveolates phyla
marine and freshwater
photosynthetic
unicellular
plated theca (walls) made of cellulose
cause of red tides
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62
Q

Zooanthellae

A

class of Dinoflagellates
symbionts of coral, sponges, and other protists by providing host with photosynthetically-derived nutrients
coral bleaching is a result of their loss

63
Q

Ciliates

A 
an Alveolate
found in all liquid water
feed on bacteria, algae, yeasts
have 2 nuclei: one for reproduction and one for all other cellular functions-both contain same DNA 
ex: Paramecium (genus)
64
Q

Apicomplexa

A 
an Alveolate
obligate parasites of animals
complex life cycles
possess apical complex for penetrating host
Plasmodium, Toxoplasma, Cryptosporidium
65
Q

Toxoplasma

A 
Alveolate, Apicomplexa
infects cats
transmitted through infected meat, feces
not fatal but may alter behavior of host
promotes risk taking behavior
66
Q

Plasmodium

A

genus of Apicomplexa
parasite of vertebrates
needs mosquito vector
causes malaria

67
Q

Parabasalids

A 
only found associated with animals
no mitochondria
anaerobic
help termites degrade cellulose
Ex: Trichomonas vaginalis
68
Q

Kinetoplastids

A

have mitochondria
flagella
Ex: Trypanosoma
transmitted by biting insects

69
Q

Trypanosomes

A

causes African Sleeping Sickness (T. brucei), Chagas’ disease, and Leishmaniasis

70
Q

T. brucei

A

African sleeping sickness
transmitted by Tsetse fly
can cross blood-brain barrier
100% fatal if untreated

71
Q

Diplomonads

A 
no mitochondria (used to have one) or Golgi
have mitosome-mitochondrial remnants
heterotrophic, anaerobic
found mostly in animal intestines
Ex: Giardia
72
Q

T. cruzi

A

Chagas’ disease

accumulates in muscle tissues (heart) and break it

73
Q

Slime Molds

A 
1. Plasmodial slime molds
form swarms-enormous single cells, thousands of nuclei
2. dictyostelids (cellular slime molds)
ameoboid single cellular stage, 
form swarms
74
Q

Phylum Firmicutes

A

“strong skin”/low C+G gram positive bacteria
most have gram-positive cell wall, some lack walls, some have pseudo-outer membrane that stain gram negative
form endospores

75
Q

Classes of Firmicutes

A

Bacilli
Clostridia
Erysipelotrichia
Mollicutes

76
Q

Firmicutes metabolism, morphology, habitat

A 
heterotrophic
usually anaerobic
energy via fermentation and substrate level phosphorylation
wide range of energy, C, and fermentation products
rods or cocci
can form chains
endospores common
skin, soil, mucous membranes, gut
77
Q

Class Clostridia

A 
phylum Firmicutes
anaerobic, endospores
C. botulinum: botulism
C. tetani: tetanus
C. thermocellum: used in bioenergy
78
Q

Class Mollucutes

A

phylum Firmicutes
lack cell walls-stain gram negative
live inside host
genome size reduced, making them obligate parasites
UGA sequence used for tryp, codon instead of stop

79
Q

Class Bacilli, order Bacillales

A 
phylum Firmicutes
rod shaped
B. anthracis: anthrax
B. subtillis: gram positive model species
S. aureus: MRSA
80
Q

Class Bacilli, order Lactobacillales

A

phylum Firmicutes
lactic acid bacteria
S. pneumoniae: pneumoni, memingitis
Lactococcus lactis: WI state microbe

81
Q

Phylum Bacteroidetes

A

degrade complex polysaccharides
rod shaped
soil, seawater, animal symbionts, sediments

82
Q

evolution

A

descent with modification

changes in gene/allele frequency over time

83
Q

phylogeny

A

evolutionary history of a group of organisms

goal is to determine branching lineages.

84
Q

lineage

A

set of individuals descended from a common ancestor

85
Q

ancestral character

A

features that are shared by the group being considered and the ancestors of that group

86
Q

Derived character

A

features that distinguish an organism or species from its immediate ancestor

87
Q

symplesiomorphies

A

shared ancestral traits
shared from a common ancestor
not useful in determining evolutionary relationships

88
Q

Autapomorphies

A

unique derived traits

not useful in determining evolutionary history because only one organism/group has the trait.

89
Q

Synapomorphies

A

shared derived traits
shared traits derived from a common ancestor
reveals evolutionary relationships

90
Q

node

A

point where recent common ancestor found

91
Q

Ingroup

A

group of taxa whose phylogeny is being reconstructed

92
Q

outgroup

A

taxon not part of the ingroup, included to provide information about root of the ingroup and to distinguish apolmorphies and plesiomorphies

93
Q

polytomy

A

unresolved branch point

94
Q

monophyletic group

A

group whose members all share a common evolutionary history/ancestor and all of its descendants

95
Q

paraphyletic group

A

set of species that includes a recent common ancestor and some but not all of the descendants.

96
Q

homology

A

character that is shared by inheritance from a common ancestor
synapomorphies are these

97
Q

homoplasy

A

similar traits independently evolved in two or more lineages/
shared characteristics that are not homologous
result of convergent evolution

98
Q

parsimony

A

preference is simplest explanation

tree with the least amount of evolutionary events

99
Q

classes of phylum Bacteroidetes

A

Bacteroidia
Flavobacteria
Sphingibacteria

100
Q

order Flavobacteriales

A

aerobic rods
cause disease in fish
Phylum Bacteroidetes, class flavobacteria

101
Q

order Sphingobacteriales

A

little known
synthesize sphingolipids for membranes which are usually found in eukaryotic membranes
phylum bacteroidetes, class sphingobacteria

102
Q

order Bacteroidales

A 
phylum bacteroidetes, class bacteroidia
most abundant gram negative organism in human gut
103
Q

Phylum Actinobacteria

A 
called actinomycetes
gram positive with high G+C content
form filaments
many antibiotics/anti-cancer drugs from this phylum
very diverse; found in soils
104
Q

Geosmin

A

earthy smell

produced by actinobacteria

105
Q

Genus Frankia

A

phylum actinobacteria
plant mutualists
fix nitrogen

106
Q

genus streptomyces

A

phylum actinobacteria

important in antibiotic production

107
Q

Mycobacterium tuberculosis

A

phylum actinobacteria

forms TB

108
Q

Phylum Cyanobacteria

A 
kyano=blue
blue-green algae
oxygenic photosynthesis
morphologically diverse, physiologically similar
25% carbon fixation
fix nitrogen
may be a skin irritant for some.
109
Q

Genus Prochlorococcus

A

phylum cyanobacteria, order Prochlorales
most abundant ocean organism
low light and high light varieties

110
Q

Stromatolite

A

rock-like deposition of carbonantes and trapped sediments

formed by cyanobacteria and diatoms

111
Q

Heterocyst

A

nitrogen fixing cells of cyanobacteria chains.

special mechanism to protect nitrogenase form oxygen

112
Q

Antibiotics from?

A

phylum actinobacteria

genus streptomyces

113
Q

phylum spirochaete

A 
Class spirochataes
order spirochaetales
gram negative
aquatic environments and animals
helical coiled cells
internal polar flagella that entends entire cell, used for motion
114
Q

Genus Borrelia

A

phylum spirochaetes
lyme disease
can survive without iron, uses manganese instead

115
Q

Treponema pallidum

A

phylum spirochaetes
causes syphilis
microaerophile

116
Q

Leptospira spp.

A

phylum Spirochaetes
can cause leptospirosis
obligate aerobes
contaminated drinking water spreads them

117
Q

phylum proteobacteria

A

includes E. coli
lots of pathogens
gram negative
great metabolic diversity; most facultative or obligate anaerobes

118
Q

classes of phylum proteobacteria

A 
alpha
beta
gamma
delta
epsilon

phylum proteobacteria not a monophyletic group

119
Q

class alphaproteobacteria

A

orders Rhizobiales, Ricketsiales, Rhodobacterales

120
Q

Order Ricketsiales

A 
class alphaproteobacteria, phylum proteobacteria
endosymbiont of insects
Wolbachia: modifies host reproduction
121
Q

order rhodobacteriales

A

class alphaproteobacteria, phylum proteobacteria
anoxygenic photosynthesis
in presence of O2, grow heterotrophically
purple bacteria

122
Q

Order Rhizobiales

A

class alphaproteobacteria, phylum proteobacteria
symbionts of plants
nitrogen fixing mutualists

123
Q

Class Betaproteobacteria

A

phylum proteobacteria
mostly aerobic or facltative anaerobes
neisseria gonorrhaea
Burkholderia cepacia: cystic fibrosis infection

124
Q

Class Deltaproteobacteria

A

phylum proteobacteria
includes myxobacteria: multicellular, social bacteria, forms spores
includes sulfate/sulfur reducing bacteria (Desulfovibrio and Desulfobacter genera) where H2S is end product

125
Q

Genus Geobacter

A

class deltaproteobacteria
phylum proteobacteria
consume oil-based pollutants

126
Q

class epsilonproteobacteria

A

phylum proteobacteria
GI tract of animals, symbionts–some pathogens
Heliobacter pylori-ulcers and cancer

127
Q

class gammaproteobacteria

A

lots of pathogens

orders: Enterobacteriales, Legionellales, Pseudomonadales, Vibrionales

128
Q

order enterobacteriales

A 
class gammaproteobacteria
phylum proteobacteria
rod shaped, facultative anaerobes
flagella
E. coli
129
Q

order vibrionales

A 
class gammaproteobacteria
phylum proteobacteria
have flagella 
facultative anaerobes
fresh and salt water
Vibrio cholera
130
Q

Order Pseudomonadales

A 
class gammaproteobacteria
phylum proteobacteria
gram negative bacilli
polar flagella
plant pathogens, mutulaists
P. aeruginosa
131
Q

Phylum Chlamydia

A

infect eukaryotic cells
obligate intracellular pathogens
poor metabolic capacity
difficult to study and very small

132
Q

Infection cycle of Chlamydia

A

Elementary body: rigid cell wall, non-growing, infectious. Found in secretions
Reticulate body: fragile cell wall, growing, non-infectious. Found inside host cell

133
Q

Phylum Acidobacteria

A 
discovered 1997
acidophilic
abundant in soils
monophyletic
contaminant of DNA extraction kits
134
Q

Division/phylum ending Fungi

A

-mycota

135
Q

Class ending bacteria and fungi

A
  • ia

- mycetes

136
Q

Order ending

A

-ales

137
Q

family ending

A

-aceae

138
Q

characteristics fungi

A 
eukaryotic
non-vascular
heterotrophic: digest then ingest
diffuse, branched, tubular bodies
reproduce through spores
cell walls of chitin
nonmotile
store carbohydrates as glycogen not starch
139
Q

somatic

A

vegetative

140
Q

hyphae

A

web
body of fungus
microscopic/threadlike

141
Q

mycelium

A

cellective structure that makes up the body of the fungus

small to acres in size

142
Q

septa

A

cross walls in hyphae

143
Q

fungi growing conditions

A

consume organic substrates
readily form symbiotic associations (lichens=fungi and cyanobacteria)
require free water for diffusion of nutrients
optimal growth temperature 25-30C

144
Q

plasmogamy

A

stage of sexual reproduction
cytoplasm of two parent cells from the mycelia fuse
nuclei do not fuse

145
Q

karyogamy

A

fusion of nuclei

146
Q

anamorph

A

asexual stage of fungal life cycle

spore–>germination—>mycelium–>spore

147
Q

teleomorph

A

sexual stage of fungal life cycle

plasmogamy–>heterokaryotic–>karyogamy–>meiosis–>spores–>plasmogamy

148
Q

fungi importance

A

ecological: decomposers, mycorrhizae assist plants in nutrient uptake, plant pathogens
source of chemicals: antibiotics, vitamins, horomones
industrial and food fermentations
biological control agents

149
Q

phylum Chytridiomycota

A

simplest fungi
have single flagellum
linked to global amphibian decline

150
Q

zygomycota phylum

A

when parent cells fuse, there are more than 2 nuclei present
have deploy method for spores?

151
Q

phylum ascomycota

A

sac fungi
sexual reproduction via ascospores in ascus
molds and yeasts

152
Q

ascomycota life cycle

A

after plasmogamy, ascocarp forms–>karygamy–>spores deployed as diploid from ascus

153
Q

ascomycota and humans

A

yeasts
Penicillium
ring work and athletes foot

154
Q

Phylum Basidiomycota

A

club fungus
sexual reproduction via basidiospores on basidium
mushrooms, puff balls, bracket fungi
plant pathogens

Micro 450 (3 decks)

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