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Unit 1 Flashcards

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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
ssDNA viruses
class 2 be ssDNA can not be transcribed, must first become dsDNA using host DNAP ex: canine and feline parvo viruses
26
dsRNA viruses
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
27
ss(+)RNA viruses
``` class 4 genome functions as mRNA (-)sense RNA formed form (+)sense RNA ```
28
ss(-)RNA viruses
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
29
RNA reverse transcribing viruses
``` 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 ```
30
DNA reverse transcribing viruses
``` 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 ```
31
Classifications of Viruses
most classifications can only go as far as family because few/no similarities exist beyond here
32
Structural classification of viruses
icosahedral symmetry helical symmetry non-enveloped (naked) enveloped
33
helical symmetry
identical helical subunites (protomers) create helical array surrounding viral nucleic acid form elongated rods or flexible filaments
34
Bacteriophages
dsDNA, ssDNA and RNA | bacteria is host
35
Problems with Prokaryotes
characterization of what they lack (nucleus, membrane bound organelles) paraphyletic group eukaryotes did not originate from prokaryotes as names imply
36
origins of Eukaryotes
explained by endosymbiont theory | mitochondria, chloroplasts, other organelles result of bacteria taking up permanent residence inside others.
37
evidence in favor of endosymbiont theory
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
38
Archaea: general characterisitcs
``` 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 ```
39
archaeal cell membrane
L-glycerol instead of D-glycerol side chains bound by ether linkages side chains in bilayer isoprene cytoplasmic membrane only-no outer membrane
40
archaeal similarities to bacteria
``` no nucleus no membrane bound organelles DNA in a single loop genes grouped in operons genes in metabolism are similar overall size ```
41
archaeal similarities to eurkaryotes
similar RNAP methionine initiates protein synthesis (fMet in bacteria) histones
42
methanogens
polyphyletic group (more than one common ancestor) total anaerobes produce methane from various carbon sources wetlands, rice paddies, landfills, rumen
43
hydrogen-consuming methanogens
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
44
Halophiles
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
45
Extreme Thermophiles
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
46
Archaea phyla (4)
Euryarchaeota Crenarchaeota Karoarchaeota Nanoarcheota
47
Euryarchaeota
largest phyla dominated by methanogens diverse habitats some extreme thermophiles-aerobic and anaerobic
48
Crenarchaeota
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
49
Karoarchaeota
known only by sequences | found in extremely hot environments
50
Nanoarchaeota
small, parasitic | lack genes for all core molecular processes-depend on host for cellular needs
51
Protists Generalizations
``` eukaryotes not like animals, plants, or fungi "junk drawer" single or multicellular nucleated microbes asexual and/or sexual reproduction not a monophyletic group ```
52
Problems with protist classification
some protists are not closely related | they share qualities with the three other kingdoms but do not match characterisitics
53
Rhodophyta, the red algae
most multicellular found in deep tropical waters red caused by phycoerythrin important in reef building
54
phycoerythrin
causes red pigment of red algae | absorbs blue wavelengths which can penetrate deep into water
55
Chromista
most are photosynthetic have chlorophyll c which is not found in plants includes diatoms, giant kelps, plant pathogens (potato famine)
56
Diatoms
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
57
Diatomaceous earth
rock product made entirely by diatom fossils | used as abrasives, insecticides, filters
58
Diatom cell division
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
59
Green Algae
``` unicellular and multicellular closely related to plants paraphyletic group model system for evolution of multicellularity photosynthetic ```
60
Alveolates
includes Dinoflagellates, ciliata, Apicomplexa, Formaninifera All have sacs under cell membrane called alveoli
61
Dinoflagellates
``` member of Alveolates phyla marine and freshwater photosynthetic unicellular plated theca (walls) made of cellulose cause of red tides ```
62
Zooanthellae
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
Ciliates
``` 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
Apicomplexa
``` an Alveolate obligate parasites of animals complex life cycles possess apical complex for penetrating host Plasmodium, Toxoplasma, Cryptosporidium ```
65
Toxoplasma
``` Alveolate, Apicomplexa infects cats transmitted through infected meat, feces not fatal but may alter behavior of host promotes risk taking behavior ```
66
Plasmodium
genus of Apicomplexa parasite of vertebrates needs mosquito vector causes malaria
67
Parabasalids
``` only found associated with animals no mitochondria anaerobic help termites degrade cellulose Ex: Trichomonas vaginalis ```
68
Kinetoplastids
have mitochondria flagella Ex: Trypanosoma transmitted by biting insects
69
Trypanosomes
causes African Sleeping Sickness (T. brucei), Chagas' disease, and Leishmaniasis
70
T. brucei
African sleeping sickness transmitted by Tsetse fly can cross blood-brain barrier 100% fatal if untreated
71
Diplomonads
``` no mitochondria (used to have one) or Golgi have mitosome-mitochondrial remnants heterotrophic, anaerobic found mostly in animal intestines Ex: Giardia ```
72
T. cruzi
Chagas' disease | accumulates in muscle tissues (heart) and break it
73
Slime Molds
``` 1. Plasmodial slime molds form swarms-enormous single cells, thousands of nuclei 2. dictyostelids (cellular slime molds) ameoboid single cellular stage, form swarms ```
74
Phylum Firmicutes
"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
Classes of Firmicutes
Bacilli Clostridia Erysipelotrichia Mollicutes
76
Firmicutes metabolism, morphology, habitat
``` 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
Class Clostridia
``` phylum Firmicutes anaerobic, endospores C. botulinum: botulism C. tetani: tetanus C. thermocellum: used in bioenergy ```
78
Class Mollucutes
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
Class Bacilli, order Bacillales
``` phylum Firmicutes rod shaped B. anthracis: anthrax B. subtillis: gram positive model species S. aureus: MRSA ```
80
Class Bacilli, order Lactobacillales
phylum Firmicutes lactic acid bacteria S. pneumoniae: pneumoni, memingitis Lactococcus lactis: WI state microbe
81
Phylum Bacteroidetes
degrade complex polysaccharides rod shaped soil, seawater, animal symbionts, sediments
82
evolution
descent with modification | changes in gene/allele frequency over time
83
phylogeny
evolutionary history of a group of organisms | goal is to determine branching lineages.
84
lineage
set of individuals descended from a common ancestor
85
ancestral character
features that are shared by the group being considered and the ancestors of that group
86
Derived character
features that distinguish an organism or species from its immediate ancestor
87
symplesiomorphies
shared ancestral traits shared from a common ancestor not useful in determining evolutionary relationships
88
Autapomorphies
unique derived traits | not useful in determining evolutionary history because only one organism/group has the trait.
89
Synapomorphies
shared derived traits shared traits derived from a common ancestor reveals evolutionary relationships
90
node
point where recent common ancestor found
91
Ingroup
group of taxa whose phylogeny is being reconstructed
92
outgroup
taxon not part of the ingroup, included to provide information about root of the ingroup and to distinguish apolmorphies and plesiomorphies
93
polytomy
unresolved branch point
94
monophyletic group
group whose members all share a common evolutionary history/ancestor and all of its descendants
95
paraphyletic group
set of species that includes a recent common ancestor and some but not all of the descendants.
96
homology
character that is shared by inheritance from a common ancestor synapomorphies are these
97
homoplasy
similar traits independently evolved in two or more lineages/ shared characteristics that are not homologous result of convergent evolution
98
parsimony
preference is simplest explanation | tree with the least amount of evolutionary events
99
classes of phylum Bacteroidetes
Bacteroidia Flavobacteria Sphingibacteria
100
order Flavobacteriales
aerobic rods cause disease in fish Phylum Bacteroidetes, class flavobacteria
101
order Sphingobacteriales
little known synthesize sphingolipids for membranes which are usually found in eukaryotic membranes phylum bacteroidetes, class sphingobacteria
102
order Bacteroidales
``` phylum bacteroidetes, class bacteroidia most abundant gram negative organism in human gut ```
103
Phylum Actinobacteria
``` 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
Geosmin
earthy smell | produced by actinobacteria
105
Genus Frankia
phylum actinobacteria plant mutualists fix nitrogen
106
genus streptomyces
phylum actinobacteria | important in antibiotic production
107
Mycobacterium tuberculosis
phylum actinobacteria | forms TB
108
Phylum Cyanobacteria
``` kyano=blue blue-green algae oxygenic photosynthesis morphologically diverse, physiologically similar 25% carbon fixation fix nitrogen may be a skin irritant for some. ```
109
Genus Prochlorococcus
phylum cyanobacteria, order Prochlorales most abundant ocean organism low light and high light varieties
110
Stromatolite
rock-like deposition of carbonantes and trapped sediments | formed by cyanobacteria and diatoms
111
Heterocyst
nitrogen fixing cells of cyanobacteria chains. | special mechanism to protect nitrogenase form oxygen
112
Antibiotics from?
phylum actinobacteria | genus streptomyces
113
phylum spirochaete
``` Class spirochataes order spirochaetales gram negative aquatic environments and animals helical coiled cells internal polar flagella that entends entire cell, used for motion ```
114
Genus Borrelia
phylum spirochaetes lyme disease can survive without iron, uses manganese instead
115
Treponema pallidum
phylum spirochaetes causes syphilis microaerophile
116
Leptospira spp.
phylum Spirochaetes can cause leptospirosis obligate aerobes contaminated drinking water spreads them
117
phylum proteobacteria
includes E. coli lots of pathogens gram negative great metabolic diversity; most facultative or obligate anaerobes
118
classes of phylum proteobacteria
``` alpha beta gamma delta epsilon ``` **phylum proteobacteria not a monophyletic group**
119
class alphaproteobacteria
orders Rhizobiales, Ricketsiales, Rhodobacterales
120
Order Ricketsiales
``` class alphaproteobacteria, phylum proteobacteria endosymbiont of insects Wolbachia: modifies host reproduction ```
121
order rhodobacteriales
class alphaproteobacteria, phylum proteobacteria anoxygenic photosynthesis in presence of O2, grow heterotrophically purple bacteria
122
Order Rhizobiales
class alphaproteobacteria, phylum proteobacteria symbionts of plants nitrogen fixing mutualists
123
Class Betaproteobacteria
phylum proteobacteria mostly aerobic or facltative anaerobes neisseria gonorrhaea Burkholderia cepacia: cystic fibrosis infection
124
Class Deltaproteobacteria
phylum proteobacteria includes myxobacteria: multicellular, social bacteria, forms spores includes sulfate/sulfur reducing bacteria (Desulfovibrio and Desulfobacter genera) where H2S is end product
125
Genus Geobacter
class deltaproteobacteria phylum proteobacteria consume oil-based pollutants
126
class epsilonproteobacteria
phylum proteobacteria GI tract of animals, symbionts--some pathogens Heliobacter pylori-ulcers and cancer
127
class gammaproteobacteria
lots of pathogens | orders: Enterobacteriales, Legionellales, Pseudomonadales, Vibrionales
128
order enterobacteriales
``` class gammaproteobacteria phylum proteobacteria rod shaped, facultative anaerobes flagella E. coli ```
129
order vibrionales
``` class gammaproteobacteria phylum proteobacteria have flagella facultative anaerobes fresh and salt water Vibrio cholera ```
130
Order Pseudomonadales
``` class gammaproteobacteria phylum proteobacteria gram negative bacilli polar flagella plant pathogens, mutulaists P. aeruginosa ```
131
Phylum Chlamydia
infect eukaryotic cells obligate intracellular pathogens poor metabolic capacity difficult to study and very small
132
Infection cycle of Chlamydia
Elementary body: rigid cell wall, non-growing, infectious. Found in secretions Reticulate body: fragile cell wall, growing, non-infectious. Found inside host cell
133
Phylum Acidobacteria
``` discovered 1997 acidophilic abundant in soils monophyletic contaminant of DNA extraction kits ```
134
Division/phylum ending Fungi
-mycota
135
Class ending bacteria and fungi
- ia | - mycetes
136
Order ending
-ales
137
family ending
-aceae
138
characteristics fungi
``` 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
somatic
vegetative
140
hyphae
web body of fungus microscopic/threadlike
141
mycelium
cellective structure that makes up the body of the fungus | small to acres in size
142
septa
cross walls in hyphae
143
fungi growing conditions
consume organic substrates readily form symbiotic associations (lichens=fungi and cyanobacteria) require free water for diffusion of nutrients optimal growth temperature 25-30C
144
plasmogamy
stage of sexual reproduction cytoplasm of two parent cells from the mycelia fuse nuclei do not fuse
145
karyogamy
fusion of nuclei
146
anamorph
asexual stage of fungal life cycle | spore-->germination--->mycelium-->spore
147
teleomorph
sexual stage of fungal life cycle | plasmogamy-->heterokaryotic-->karyogamy-->meiosis-->spores-->plasmogamy
148
fungi importance
ecological: decomposers, mycorrhizae assist plants in nutrient uptake, plant pathogens source of chemicals: antibiotics, vitamins, horomones industrial and food fermentations biological control agents
149
phylum Chytridiomycota
simplest fungi have single flagellum linked to global amphibian decline
150
zygomycota phylum
when parent cells fuse, there are more than 2 nuclei present have deploy method for spores?
151
phylum ascomycota
sac fungi sexual reproduction via ascospores in ascus molds and yeasts
152
ascomycota life cycle
after plasmogamy, ascocarp forms-->karygamy-->spores deployed as diploid from ascus
153
ascomycota and humans
yeasts Penicillium ring work and athletes foot
154
Phylum Basidiomycota
club fungus sexual reproduction via basidiospores on basidium mushrooms, puff balls, bracket fungi plant pathogens

Micro 450 (3 decks)

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