EEMB 3: Microbial Biology Flashcards
(263 cards)
2
Q
What is mineralizing
A
conversion of organic matter to inorganic substiuents
3
Q
What performs minerlization
A
microbes
4
Q
T/F: The body consists of as many microbes as human cells
A
FALSE a lot more microbes
5
Q
T/F: Microbes help perform bodily fucntions
A
True
6
Q
“the invisible presence”
A
microbes
7
Q
the life force of the planet
A
microbes
8
Q
The origins of life are based on
A
First principles
9
Q
Name the hypothesis of water
A
degassing-condensationcomets and asteroids bringing ice
10
Q
The first microfossils appeared when
A
3.5-3.8 bya
11
Q
6 essential characteristics of life
A
-membrane-aqueous-catalysts-energy flow/storage-anabolic pathways (polymerizing molecules)-RNA/DNA
12
Q
describe the membrane characteristic
A
layer separating outer environment and inner
13
Q
describe aqueous
A
water-based organism
14
Q
describe catalysts
A
speed up reactions
15
Q
describe energy flow/storage
A
metabolism (ATP -> ADP Pi)
16
Q
describe anabolic pathways
A
monomers -> macromolecules
17
Q
describe RNA/DNA
A
info carriers/storage + translation apparatus
18
Q
Name the 3 Theories of life
A
Gaia HypothesisVital Force ViewMechanistic View
19
Q
What is the Gaia Hypothesis
A
earth is a living entity - its biosphere maintains its homeostasis
20
Q
What is the Vital Force View
A
science cannot explain life forces (not testable) and does not include physics and chemistry
21
Q
What is the Mechanistic View
A
Life is chemically based with same chemicals from environment, just in a particular and unique arrangement
22
Q
Can some forms of life form from inanimate matter?
A
Nopes
23
Q
Which two guys disproved spontaneous generation
A
Redi and Pasteur
24
Q
Redi’s exp
A
flies and rotten meat in a jar
25
Q
Pasteurs exp
A
Broth and swan-neck flask
26
Origins Hypothesis I is
panspermia
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What is panspermia
extra terrestrial life was brought here in the form of germs/spores
28
Origins Hypothesis II is
Chemical Evolution (life is unique to Earth)
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Stages of Chemical Evolution
1) Nucleotide/Amino Acid formation2) Polymerization3) Polymers in membranes4) Living
30
Explain the 3 ways of nucelotide/amino acid formation
E.T. input -\> water and organic material delivered by comets and asteroidsReducing atmosphere air contained CH4 NH3 CO2 H2S, H2, NOO2Hydrothermal Vents: Chemicals interact with energy from heat (CH4 NH3)
31
Explain the stage of polymerization
[difficult with no enzymes present]Energy for polymerization could be possible from:1) pyrite2) hydrothermal vents3) hot pools
32
What is pyrite
sillicate in clay that condense to catalyze
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what is a hydrothermal vent
vent that consists of metas, iron and nickel, that could catalyze
34
What are hot pools
places where water evaporates and leaves more concentration of materials to interact with each other
35
Explain the stage of polymers in membranes
Membranes form around the polymers and the result is a protobiont
36
What is a protobiont?
aggregate of organic molecules that perform metabolism
37
Catabolism
breaking down materials
38
Anabolism
synthesizing materials
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What are coacervates
specific protobionts that have lots of sugars and proteins
40
What is the coacervates relationship to the environment?
its internal chemistry is sginificantly different than the surrounding environment
41
The catalyst that allowed protobionts to become living
RNA ribosyme (ribosome)
42
Information carriers in the living microbe
RNA and (Hydrogen bonds)
43
T/F: Ribozyme is an enzyme
FALSE it is only made of nucleotides (amino acids) not proteins
44
Catabolism
breaking down materials
45
Anabolism
synthesizing materials
46
What are coacervates
specific protobionts that have lots of sugars and proteins
47
What is the coacervates relationship to the environment?
its internal chemistry is sginificantly different than the surrounding environment
48
The catalyst that allowed protobionts to become living
RNA ribosyme (ribosome)
49
Information carriers in the living microbe
RNA and DNA
50
T/F: Ribozyme is an enzyme
FALSE it is only made of nucleotides (amino acids) not proteins
51
Other things that allowed microbes to be classified as living
RNA/DNA (hydrogen bonds) (translation/transcription apparatus)
52
Two forms of dating
relative and absolute
53
Relative dating
straiographic layers (sediment layers and fossils)
54
Absolute dating
Half-life (radioactive isotopes)
55
Linnaen Classification
Kingdom - Phylum - Class - Order - Family - Genus - Species (most specific)KPCOFGS
56
Characteristics conserved over all 3 domains
RNA/DNATranslation/Transcription apparatusGlycolysisRibosomesSemi-conserved DNA ReplicationPlasma Membranes
57
Which of the 3 domains is most different from the others
bacteria (archaea and eukarya most similar)
58
Evolutionary Distance
different base pairs/ total base pairs (presented in %)
59
What are all prokaryotes?
Microbes
60
What is the size range of prokaryotes?
100 nm to 100 micrometers
61
What portion of Eukaryotes are microbes? Examples?
1/3Protists and fungi
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What is the advantage prokaryotes have over multi-cellular eukaryotes?
Individual cells can survive by themselves (while other cells need to communicate)
63
Advantages to being small
less competition for spacesmaller surface area/volume to move nutrients, excrete wasteless nutrients needed to maintain
64
Phytoplankton is what percent of the earths biomass? What % of the Earths oxygen do they produce?
0.2% biomass45-5-% oxygen
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What type of organism is phytoplankton?
photoautorophs
66
What type of organism is bacterial plankton?
heterotroph
67
2 other names for autotrophs, derived from what?
chemo-autotrophschemo lithotrophsderived from converting inorganic materials and CO2 --\> organic and oxygen
68
What are ribozymes?
selt-catalyzing strands of RNA that also carry information
69
Proteins become specific to
control reactions
70
RNA folding leads to
stabilization of H-bonds in 3D form
71
What is a reducing atmosphere?
Atmosphere created by desne gasses (volcanic out-gassing) H2O, ClH2, CH4, H2S, NH3, CO2
72
Miller-Urey experiment? Did it work?
Emulated conditions of early Earth (reducing atmosphere) to try and create organic compounds. Produced nucleotides and AAS
73
Nucleotides and AAs are precursors for
DNA and proteins/enzymes
74
Hydrothermal vents created first organic compounds through (specific terminology)
Thermal gradients and "plume chemistry"
75
Some factors for extinction and evolution
continental drift, climate change, volcanic activiy, unidirectional change in O2, external events.
76
Taxonomy
Theory and practice of classifying organisms
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Phylogeny
classifying organism based on evolutionary history
78
Systematics
the science of studying diversity of organisms and reconstructing phylogeny
79
2 ways changes in living organisms happen
Genetic exchangeEnvironmental change
80
Properties of rRNA that help construct phylogenies
its a structural genehighly conservedsufficient variability
81
T/F: Not all prokaryotes are microbes
FALSE
82
How many entire domains are microbes?
2 (bacteria and archaea)
83
Domains are set based on which rRNA gene sequences?
16s and 18s
84
Characteristics of Microbes
sing cell or clusterstand alone organismscapable of living independent of tissue (growth, energy generation, reproduction)
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Traits that set microoganisms
metabolism, reproduction, differentiation, communication, movement, evolution
86
Common features all microbes share
live in waterfood for higher trophic levelssmall
87
T/F: Microbes are not the most abundant organisms in the biosphere
FALSE they are bro
88
T/F: Microbes have a vast physiological diversity (functions)
True
89
2 physiologies of Macrobes
photosynthesis (chloroplasts)heterotroph (mitochondria)
90
2 basic metabolic strategies
photosynthesisrespiration
91
Another name for photosynthesis and formula. Example?
photoautotrophyCO2 + nutrients --\> organic matter + O2Phytoplankton
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Another name for respiration and formula. Example
Heterotrophyorganic matter + O2 -\> CO2 + nutrientsBacterioplankton
93
What is the base of the food web at Hydrothermal vents?
Sulfur oxidizing bacteriaH2S + 2O2 --\> SO4 + 2H
94
The element most associated with mircobes
nitrogen
95
Macro nutrients
C,H,O,N,P,S
96
T/F: Cells are at equilibrium
FALSE, they are non-equilibrium systems
97
5 Huge impacts of microbes
Majority of earths biomassVarious functionalityBiogeochemical agentsControl human historyIndustry
98
Advances in microbiology come from
technological develoments
99
Most early microbe work focused on aspects related to
humans
100
How old of a science is microbiology?
young science
101
Who created the first microscope
Leeuwenhoek
102
What did he call the first observed bacteria
animicules
103
What is a major technological development in the microbiology world?
optics
104
2 terms of microscopy?
magnificationresolution
105
Magnification does what?
increase the viewing size ONLY
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Resolution does what
distance between two points, used to gain information
107
Disproved spontaneous generation
Pasteur and Redi
108
Got microbes into culture
Pasteur
109
Worked on vaccination
Pasteur
110
proved microbes were responsible for degradation.
Pasteur
111
showed different microbes made different products
Pasteur
112
Guy who started medical microbiology
Koch
113
Who developed pure culture technique
Koch
114
Who was an environmental micobiologist
Winogradsky, Beijernick
115
What is chemolithotrophy
obtaining energy from the oxidation of inorganic compounds (CO2 as carbon source)
116
Organisms who use chemolithotrophy are
autotrophs
117
Who developed the idea of chemolithotrophy
Winograsky
118
Who developed enrichment cultures
beijernick
119
whats enrichment culturing
eh?
120
Who used rRNA genes to construct phylogenies
Woese
121
Who created PCR (polymerase chain reaction)
Mullis
122
What polymerase is used in PCR
Taq polymerase
123
Attributes of Taq Polymerase
thermally stable
124
Who discovered Taq Polymerase? From where?
Brock and FreezeIsolated from hot springs
125
Cultivation independent techniques formed by who?
Pace
126
How to ID an organism via rRNA genes
1) isolate plasmids2) Sequence3) Assess variability4) construct phylogeny
127
What is genome?
entire genetic make-up (sequence) of an organism
128
Metagenome is?
study of genomic material from a mixed population
129
Steps of Random Shotgun Sequencing Approach
1) library construction2 DNA sequencing3) Assemble fragments
130
Main attributes of prokaryotes (3 things)
cell wallsno organelles (no microtubules)nucleoid and free ribosomes (ciruclar DNA)
131
Main attributes of eukaryotes (3 things)
organellescytoskeleton-microtubulescan digest material internallypretty much opposite of prokaryotes
132
What is lateral gene DNA transfer?
the gene of one species incorporated into another
133
3 mechanisms for prokaryotic gene recombination
TransformationConjugationTransduction
134
DNA transfer for eukaryotes and prokaryotes
eukaryotes - sexualprokaryotes - asexual
135
3 main shapes of prokaryotes
Cocci - sphereBacilli - rod Spirochetes - spiral
136
Describe Bacteria cell membrane. What type of linkage?
phospholipid bilayer (glycerol, fatty acid, membrane protein)Ester Linkage
137
Describe archaea cell membrane. What type of linkage?
phospholipid mono- or bilayer, NO fatty acidsether linkage
138
2 types of bacteria
Gram +Gram -
139
What process is used to separate bacteria into 2 groups? What group retains what color?
Gram stainingGram+ = violetGram- = pink/red
140
Properties of Gram +
simple thick cell wallless phsiologically diverseexotoxins
141
Properties of Gream -
more complexlipopolysaccharides (LPS) attachedendotoxins
142
Bacteria cell wall is made of
peptidoglycan
143
what is peptidoglycan cell wall made of?
muramic acid
144
T/F: Archaea also have organisms with peptidoglycan walls
FALSE
145
How to differentiate bacteria from archaea?
Use a strong base and see reaction (reacts with acid wall in bacteria and bubbles)
146
Nutritional requirements for anabolism
Energy and carbon
147
If an organism uses CO2 it is an _____ if it uses organic C it is a \_\_\_\_
autotrophheterotroph
148
T/F: All organisms generate ATP
True
149
What is fermentation
substrate level phsophorylationno electron acceptor
150
What is Oxidative/Electron Transport Level Phosphorylation (ETLP) ( 2 types)
Anerobic - use non O2 elements as e- receptorAerobic - uses O2 as e- acceptor
151
The ETLP uses what two forces to create ATP
electron transport systemproton motive force
152
What is photophosphorilation?
light energy generates a proton gradient and proton motive force
153
What force drives photophosphorilation
proton motive force
154
What is the proton motive force?
electron carriers are oriented in the membrane that separate protons from e-
155
Bacteriorhodopsin?
a protein used (by archae) in synthesis of ATP withouth chlorophyll pigment
156
Primitive photophosphorlyation?
pretty much photosynthesis
157
What bacteria are phototrophs?
purple and green bacteria
158
Phototropic properties of purple and green bacteria
anaerobic, photosystem I anoxygenic
159
What are purple sulfur bacteria? (in terms of trophic level)
photoAUTOtophsbacteria that use CO2 to split H2S and H2 instead of water
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What are purple non sulfur bacteria? (in terms of trophic level)
photoHETEROtrophsuse light and organic carbon
161
What are cyanobacteria?
bacterial that go through photosynthesis(obligate photoautotrophs)(a huge source of O2 on earth, one of the first to largely produce O2)
162
What attacks bonds of organic matter?
oxygen
163
Obligate aerobe
Organic C + O2 --\> CO2 + water
164
Microaerophiles
aerobic respiration
165
Facultative Anaerobe
Respiration with O2Fermentation with out it
166
Obligate anerobe
Anerobic respirationsulfate oxidation/fermentation
167
Examples of Chemoautotrophs
Sulfur oxidizers (microbial miners)
168
conversion formula for sulfur oxidizers and where are they found
H2S + 2O2 -\> SO4 + 2Hhydrothermal communities
169
A majority of prokaryotes are what?
chemoheterotrophs
170
Examples of chemoheterotrophs
SaprobesParasites
171
What to saprobes feed on?
dead organic matter
172
Type of microbes in relation to increasing temperature
psychophiles \<0-20mseophiles 20-48thermophiles 42-68hyperthermophile 65-110
173
3 Main domains
Bacteria, Archaea, Eukarya
174
How many branches of bacteria are there and what are they?
5ProteobacteriaCyanobacteriaFirmicutesSpirochetesChlamydiasCCFPS
175
How many branches of Archaea and what are they?
2 branchesCrenarchaeotaEuryarchaeota
176
Sub-categories of proteobacteria
purple bacteriarhizobiumenteric bacteria
177
Firmicutes are what type of bacteria and what do they consist of?
Low gram positive (GC) endospores
178
Spirochetes and Chlamydias are what type of bacteria?
Gram negative
179
Crenarchaeota properties
hyperthermophilesacidophiles
180
Euryarchaeota properties
methanogens (produce methane)halophiles
181
History wise, what are protists?
ancient eukaryotes
182
Difference between prokaryotes and eukaryotes
organizedd nucleusribosome studded internal membranecytoskeletondigestive vesiclesorganelle formation
183
What environment are most protists?
aquatic environments
184
T/F: Protists only have one source of nutrition
FALSE they got nutritional diversity
185
Protozoas are similar to ____ and algae to \_\_\_\_
animal likeplant like
186
Locomotion for protists
pseudopodciliaflagella
187
Method of ingestion of protozoa and its subcategories
Endocytosis-pinocytosis (dissolving)-phagocytosis (englufing whole)
188
The contractile vacuole of the protists does what?
assist in osmoregulation
189
T/F: Most protists have similar cell surfaces
FALSE, they are diverse
190
What are endosymbionts? and do protists fall under the category?
organisms that live within other organismsyes protists are included
191
Sarcodines are a class of
amoeba (pseudopods)
192
Examples of Endosymbionts
forminiferaradiolariansacantharia
193
What is the reproduction process of protists? Is it sexual?
AsexualIt is sexual but NOT a "sexual" process
194
Genetic recombination of protists is called
conjugation
195
T/F: protist life cycles don't have an alternation of generations
False!
196
2 types of alternation of generations and what do they do?
heteromorphic - haploid and diplod are differentisomorphic - haploid and diploid are the same
197
Describe Diplomonads and parabasalids
lack mitochondriaobligate parasites
198
Describe Euglenids
no cell wallheterotrophic and photoautotrophic
199
What is bacteriorhodopsin
synthesis of ATP without chlorophyll pigment using light
200
Bacteriorrhodopsin use ____ phosphorliation, What is that?
Primitiveabsorb light and pump protons out for a gradient to make ATP
201
What groups are closely related to dinoflagellates?
Ciliates and apicomplexans (Plasmodium)
202
Describe dinoflagellates
2 flagella of different sizesbioluminescentred tidesendosymbiontsauto, mixo, and heterotrophs
203
What type of eukaryote causes malaria?
Apicomplexans
204
In the Theory of Endosymbiosis aquisition of what leads to protozoa/animals and algae/plants
proteobacteria and cyanobacteria
205
What type of protist has two types of nuclei?
Ciliates
206
Conugation is what type of protists way of genetic recombination?
paramecia
207
Alveolates include which protists?
Dinoflagellates and apicomplexas
208
Phytoplankton is what type of protist?
dinoflagellates
209
Paicomplexans are ___ of animals which use ___ for reproduction
parasitesspores
210
the defining structures of the apicomplexas is the ____ use to \_\_\_
apical complex that is used to burrow into host tissue or cells
211
T/F: Apicomplexas have a simple life cycle
FALSE, its intricate
212
Two types of stramenopila
diatoms, brown algae
213
Properties of diatoms
cartenoids, yellow/brown, silica shells, important marine phytoplankton, asexual/sexual reproduction, harmful algal blooms
214
Properties of brown algae
photoautotrophsfucoxanthin pigmentmulticellular (seaweed)
215
Describe Coccolithophorids (haptophytes)
foudn in calcium carbonate plates ) coccolithsauotorophicocean acidification will have major effect
216
Eukaryote group plantae is the ____ to all plants
precursor
217
Ancestral trait of plantae
endosymbiosis of cyanobacteria to make chloroplasts
218
Another name for green algae
chlorophytes
219
The red algae, and the key pigment that makes it red
rhodophytaphycoerythrin
220
Do rhodophyta have flagellated stages? Are the multi or unicellular or both? What chemical do they secrete
NOall multicellularcalcium carbonate
221
Properties of excavates and what groups of protists do they include?
-mostly heterotrophsinclude:-kinetoplastids-diplomonads-euglenids
222
Properties of Rhizaria
marinemost heterotrophic-ameoboids with complex shell-skeletonsinclude: forminifera and radiolarins
223
What are the radiolaria and forminifera shell-skeletons made out of?
raidolaria - silicaforminifera - Calcium carbonate
224
Two groups of unikonts
ameobozoachoanoflagellida
225
Describe ameobozoa
move by pseudopodsheterotrophic - phagocytosis Ex: plasmodial slime molds
226
Describe choanoflagellida
closest relative to animals similar to sponges (colonial)
227
Fugi are \_\_\_\_trophic. And in which domain?
heterotrophic/chemoorganotrophicEkaryotes (unikonts)can be unicelluar or multi
228
Relationships of fungi to other organisms
saprobicparasiticmutualistic
229
Fungi have ____ in cell walls
Chitin
230
What do fungi produce for reproduction?
spores
231
T/F: Fungi have tolerance to hypertonic environments as well as low and high temperatures
True!
232
Fungi are good ____ and produce _____ chemical byproducts
degraders and produce secondary chemical byproducts
233
T/F: Fungi can alternate between uni- and multicellular form and unicellular members are present in all fungal groups
True
234
How do fungi alternate between uni- and multicellular forms?
alternation of generations
235
What is the mycelium?
the body of a multicellular fungus
236
What is mycorrhizae?
associations between vascular plant roots and fungal mycelia
237
Different characteristics of hyphae
spetate- incomplete cross walls (pores)Coenocytic - no septaHaustroia- push into cells - parasite
238
Fungi multiply by ____ and \_\_\_\_
reporduction and sporulation
239
Dikaryote stage is seen in ____ fungi
higher "crown"
240
Fruiting bodies are called
sporangia
241
Hyphae are what part of the fungi
the "roots"
242
Fungi are good ____ and produce _____ chemical byproducts
degraders and produce secondary chemical byproducts
243
T/F: Fungi can alternate between uni- and multicellular form and unicellular members are present in all fungal groups
True
244
How do fungi alternate between uni- and multicellular forms?
alternation of generations
245
What is the mycelium?
the body of a multicellular fungus
246
What is mycorrhizae?
associations between vascular plant roots and fungal mycelia
247
Different characteristics of hyphae
spetate- incomplete cross walls (pores)Coenocytic - no septaHaustroia- push into cells - parasite
248
Fungi are tolerant to \_\_\_\_-tonic environments and high/low \_\_\_\_
hypertonichigh and low temperatures
249
the prime terrestrial remineralizers
Fungi
250
T/F: Not all fungi are heterotrophs
False - they all are
251
Fungi reproduce asexually in _____ conditions while sexual in ____ conditions
asexual - favorablesexual - unfavorable
252
T/F: Mating for fungi are based one male and female
False- mating TYPES
253
Instead of a diploid phase (2n) fungi have a _____ phase (n + n)
Dikaryon
254
The symbiotic relationship between fungi and algae/cyanobactiera
Lichen
255
The "pioneer" organism
Lichen
256
Name the main groups of fungi (5)
ChytridsZygomycotaGlomeromycotaAscomycotaBasidiomycota
257
The type of fungi under glmoeromycota
mycorrihzae
258
The fungi with flagella, and no dikaryotic stage
Chytrids
259
Which group of fungi is the most important step to colonization of land?
Glomeromycota : mycorrhizae
260
The fungi that have rapid spreading growth (mold)
zygomycota
261
Sac fungi (fruiting bodies), include plant pathogens and have septate hyphaeMake penicillin
Ascomycota
262
The typical mushroom falls under what class fungi
Basidiomycota
263
Animals originated from the acquisition of
proteobacteria
264
Describe Koch's Postulates (medicinal microbio)
1) suspected pathogen should be present in the infected and absent from the healthy2) the pathogen should be isolated and grown in pure culture3) this culture should cause the disease in the healthy organims4) when reisolated, the pathogen should be identical to the orignal
