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College Biology & Ecology II > EEMB 3: Microbial Biology > Flashcards

EEMB 3: Microbial Biology Flashcards

1
Q

What is mineralizing

A

conversion of organic matter to inorganic substiuents

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2
Q

What performs minerlization

A

microbes

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3
Q

T/F: The body consists of as many microbes as human cells

A

FALSE a lot more microbes

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4
Q

T/F: Microbes help perform bodily fucntions

A

True

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5
Q

“the invisible presence”

A

microbes

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6
Q

the life force of the planet

A

microbes

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7
Q

The origins of life are based on

A

First principles

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8
Q

Name the hypothesis of water

A

degassing-condensation

comets and asteroids bringing ice

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9
Q

The first microfossils appeared when

A

3.5-3.8 bya

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10
Q

6 essential characteristics of life

A
  • membrane
  • aqueous
  • catalysts
  • energy flow/storage
  • anabolic pathways (polymerizing molecules)
  • RNA/DNA
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11
Q

describe the membrane characteristic

A

layer separating outer environment and inner

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12
Q

describe aqueous

A

water-based organism

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13
Q

describe catalysts

A

speed up reactions

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14
Q

describe energy flow/storage

A

metabolism (ATP -> ADP Pi)

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15
Q

describe anabolic pathways

A

monomers -> macromolecules

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16
Q

describe RNA/DNA

A

info carriers/storage + translation apparatus

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17
Q

Name the 3 Theories of life

A

Gaia Hypothesis
Vital Force View
Mechanistic View

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18
Q

What is the Gaia Hypothesis

A

earth is a living entity - its biosphere maintains its homeostasis

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19
Q

What is the Vital Force View

A

science cannot explain life forces (not testable) and does not include physics and chemistry

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20
Q

What is the Mechanistic View

A

Life is chemically based with same chemicals from environment, just in a particular and unique arrangement

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21
Q

Can some forms of life form from inanimate matter?

A

Nopes

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22
Q

Which two guys disproved spontaneous generation

A

Redi and Pasteur

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23
Q

Redi’s exp

A

flies and rotten meat in a jar

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24
Q

Pasteurs exp

A

Broth and swan-neck flask

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25
Origins Hypothesis I is
panspermia
26
What is panspermia
extra terrestrial life was brought here in the form of germs/spores
27
Origins Hypothesis II is
Chemical Evolution (life is unique to Earth)
28
Stages of Chemical Evolution
1) Nucleotide/Amino Acid formation 2) Polymerization 3) Polymers in membranes 4) Living
29
Explain the 3 ways of nucelotide/amino acid formation
E.T. input -> water and organic material delivered by comets and asteroids Reducing atmosphere air contained CH4 NH3 CO2 H2S, H2, NOO2 Hydrothermal Vents: Chemicals interact with energy from heat (CH4 NH3)
30
Explain the stage of polymerization
[difficult with no enzymes present] Energy for polymerization could be possible from: 1) pyrite 2) hydrothermal vents 3) hot pools
31
What is pyrite
sillicate in clay that condense to catalyze
32
what is a hydrothermal vent
vent that consists of metas, iron and nickel, that could catalyze
33
What are hot pools
places where water evaporates and leaves more concentration of materials to interact with each other
34
Explain the stage of polymers in membranes
Membranes form around the polymers and the result is a protobiont
35
What is a protobiont?
aggregate of organic molecules that perform metabolism
36
Catabolism
breaking down materials
37
Anabolism
synthesizing materials
38
What are coacervates
specific protobionts that have lots of sugars and proteins
39
What is the coacervates relationship to the environment?
its internal chemistry is sginificantly different than the surrounding environment
40
The catalyst that allowed protobionts to become living
RNA ribosyme (ribosome)
41
Information carriers in the living microbe
RNA and (Hydrogen bonds)
42
T/F: Ribozyme is an enzyme
FALSE it is only made of nucleotides (amino acids) not proteins
43
Catabolism
breaking down materials
44
Anabolism
synthesizing materials
45
What are coacervates
specific protobionts that have lots of sugars and proteins
46
What is the coacervates relationship to the environment?
its internal chemistry is sginificantly different than the surrounding environment
47
The catalyst that allowed protobionts to become living
RNA ribosyme (ribosome)
48
Information carriers in the living microbe
RNA and DNA
49
T/F: Ribozyme is an enzyme
FALSE it is only made of nucleotides (amino acids) not proteins
50
Other things that allowed microbes to be classified as living
RNA/DNA (hydrogen bonds) (translation/transcription apparatus)
51
Two forms of dating
relative and absolute
52
Relative dating
straiographic layers (sediment layers and fossils)
53
Absolute dating
Half-life (radioactive isotopes)
54
Linnaen Classification
Kingdom - Phylum - Class - Order - Family - Genus - Species (most specific) KPCOFGS
55
Characteristics conserved over all 3 domains
``` RNA/DNA Translation/Transcription apparatus Glycolysis Ribosomes Semi-conserved DNA Replication Plasma Membranes ```
56
Which of the 3 domains is most different from the others
bacteria (archaea and eukarya most similar)
57
Evolutionary Distance
different base pairs/ total base pairs (presented in %)
58
What are all prokaryotes?
Microbes
59
What is the size range of prokaryotes?
100 nm to 100 micrometers
60
What portion of Eukaryotes are microbes? Examples?
1/3 | Protists and fungi
61
What is the advantage prokaryotes have over multi-cellular eukaryotes?
Individual cells can survive by themselves (while other cells need to communicate)
62
Advantages to being small
less competition for space smaller surface area/volume to move nutrients, excrete waste less nutrients needed to maintain
63
Phytoplankton is what percent of the earths biomass? What % of the Earths oxygen do they produce?
0.2% biomass | 45-5-% oxygen
64
What type of organism is phytoplankton?
photoautorophs
65
What type of organism is bacterial plankton?
heterotroph
66
2 other names for autotrophs, derived from what?
chemo-autotrophs chemo lithotrophs derived from converting inorganic materials and CO2 --> organic and oxygen
67
What are ribozymes?
selt-catalyzing strands of RNA that also carry information
68
Proteins become specific to
control reactions
69
RNA folding leads to
stabilization of H-bonds in 3D form
70
What is a reducing atmosphere?
Atmosphere created by desne gasses (volcanic out-gassing) | H2O, ClH2, CH4, H2S, NH3, CO2
71
Miller-Urey experiment? Did it work?
Emulated conditions of early Earth (reducing atmosphere) to try and create organic compounds. Produced nucleotides and AAS
72
Nucleotides and AAs are precursors for
DNA and proteins/enzymes
73
Hydrothermal vents created first organic compounds through (specific terminology)
Thermal gradients and "plume chemistry"
74
Some factors for extinction and evolution
continental drift, climate change, volcanic activiy, unidirectional change in O2, external events.
75
Taxonomy
Theory and practice of classifying organisms
76
Phylogeny
classifying organism based on evolutionary history
77
Systematics
the science of studying diversity of organisms and reconstructing phylogeny
78
2 ways changes in living organisms happen
Genetic exchange | Environmental change
79
Properties of rRNA that help construct phylogenies
its a structural gene highly conserved sufficient variability
80
T/F: Not all prokaryotes are microbes
FALSE
81
How many entire domains are microbes?
2 (bacteria and archaea)
82
Domains are set based on which rRNA gene sequences?
16s and 18s
83
Characteristics of Microbes
sing cell or cluster stand alone organisms capable of living independent of tissue (growth, energy generation, reproduction)
84
Traits that set microoganisms
metabolism, reproduction, differentiation, communication, movement, evolution
85
Common features all microbes share
live in water food for higher trophic levels small
86
T/F: Microbes are not the most abundant organisms in the biosphere
FALSE they are bro
87
T/F: Microbes have a vast physiological diversity (functions)
True
88
2 physiologies of Macrobes
photosynthesis (chloroplasts) | heterotroph (mitochondria)
89
2 basic metabolic strategies
photosynthesis | respiration
90
Another name for photosynthesis and formula. Example?
photoautotrophy CO2 + nutrients --> organic matter + O2 Phytoplankton
91
Another name for respiration and formula. Example
Heterotrophy organic matter + O2 -> CO2 + nutrients Bacterioplankton
92
What is the base of the food web at Hydrothermal vents?
Sulfur oxidizing bacteria H2S + 2O2 --> SO4 + 2H
93
The element most associated with mircobes
nitrogen
94
Macro nutrients
C,H,O,N,P,S
95
T/F: Cells are at equilibrium
FALSE, they are non-equilibrium systems
96
5 Huge impacts of microbes
``` Majority of earths biomass Various functionality Biogeochemical agents Control human history Industry ```
97
Advances in microbiology come from
technological develoments
98
Most early microbe work focused on aspects related to
humans
99
How old of a science is microbiology?
young science
100
Who created the first microscope
Leeuwenhoek
101
What did he call the first observed bacteria
animicules
102
What is a major technological development in the microbiology world?
optics
103
2 terms of microscopy?
magnification | resolution
104
Magnification does what?
increase the viewing size ONLY
105
Resolution does what
distance between two points, used to gain information
106
Disproved spontaneous generation
Pasteur and Redi
107
Got microbes into culture
Pasteur
108
Worked on vaccination
Pasteur
109
proved microbes were responsible for degradation.
Pasteur
110
showed different microbes made different products
Pasteur
111
Guy who started medical microbiology
Koch
112
Who developed pure culture technique
Koch
113
Who was an environmental micobiologist
Winogradsky, Beijernick
114
What is chemolithotrophy
obtaining energy from the oxidation of inorganic compounds (CO2 as carbon source)
115
Organisms who use chemolithotrophy are
autotrophs
116
Who developed the idea of chemolithotrophy
Winograsky
117
Who developed enrichment cultures
beijernick
118
whats enrichment culturing
eh?
119
Who used rRNA genes to construct phylogenies
Woese
120
Who created PCR (polymerase chain reaction)
Mullis
121
What polymerase is used in PCR
Taq polymerase
122
Attributes of Taq Polymerase
thermally stable
123
Who discovered Taq Polymerase? From where?
Brock and Freeze | Isolated from hot springs
124
Cultivation independent techniques formed by who?
Pace
125
How to ID an organism via rRNA genes
1) isolate plasmids 2) Sequence 3) Assess variability 4) construct phylogeny
126
What is genome?
entire genetic make-up (sequence) of an organism
127
Metagenome is?
study of genomic material from a mixed population
128
Steps of Random Shotgun Sequencing Approach
1) library construction 2 DNA sequencing 3) Assemble fragments
129
Main attributes of prokaryotes (3 things)
cell walls no organelles (no microtubules) nucleoid and free ribosomes (ciruclar DNA)
130
Main attributes of eukaryotes (3 things)
organelles cytoskeleton-microtubules can digest material internally pretty much opposite of prokaryotes
131
What is lateral gene DNA transfer?
the gene of one species incorporated into another
132
3 mechanisms for prokaryotic gene recombination
Transformation Conjugation Transduction
133
DNA transfer for eukaryotes and prokaryotes
eukaryotes - sexual | prokaryotes - asexual
134
3 main shapes of prokaryotes
Cocci - sphere Bacilli - rod Spirochetes - spiral
135
Describe Bacteria cell membrane. What type of linkage?
``` phospholipid bilayer (glycerol, fatty acid, membrane protein) Ester Linkage ```
136
Describe archaea cell membrane. What type of linkage?
phospholipid mono- or bilayer, NO fatty acids | ether linkage
137
2 types of bacteria
Gram + | Gram -
138
What process is used to separate bacteria into 2 groups? What group retains what color?
Gram staining Gram+ = violet Gram- = pink/red
139
Properties of Gram +
simple thick cell wall less phsiologically diverse exotoxins
140
Properties of Gream -
more complex lipopolysaccharides (LPS) attached endotoxins
141
Bacteria cell wall is made of
peptidoglycan
142
what is peptidoglycan cell wall made of?
muramic acid
143
T/F: Archaea also have organisms with peptidoglycan walls
FALSE
144
How to differentiate bacteria from archaea?
Use a strong base and see reaction (reacts with acid wall in bacteria and bubbles)
145
Nutritional requirements for anabolism
Energy and carbon
146
If an organism uses CO2 it is an _____ if it uses organic C it is a ____
autotroph | heterotroph
147
T/F: All organisms generate ATP
True
148
What is fermentation
substrate level phsophorylation | no electron acceptor
149
What is Oxidative/Electron Transport Level Phosphorylation (ETLP) ( 2 types)
Anerobic - use non O2 elements as e- receptor | Aerobic - uses O2 as e- acceptor
150
The ETLP uses what two forces to create ATP
electron transport system | proton motive force
151
What is photophosphorilation?
light energy generates a proton gradient and proton motive force
152
What force drives photophosphorilation
proton motive force
153
What is the proton motive force?
electron carriers are oriented in the membrane that separate protons from e-
154
Bacteriorhodopsin?
a protein used (by archae) in synthesis of ATP withouth chlorophyll pigment
155
Primitive photophosphorlyation?
pretty much photosynthesis
156
What bacteria are phototrophs?
purple and green bacteria
157
Phototropic properties of purple and green bacteria
anaerobic, photosystem I anoxygenic
158
What are purple sulfur bacteria? (in terms of trophic level)
photoAUTOtophs bacteria that use CO2 to split H2S and H2 instead of water
159
What are purple non sulfur bacteria? (in terms of trophic level)
photoHETEROtrophs use light and organic carbon
160
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)
161
What attacks bonds of organic matter?
oxygen
162
Obligate aerobe
Organic C + O2 --> CO2 + water
163
Microaerophiles
aerobic respiration
164
Facultative Anaerobe
Respiration with O2 | Fermentation with out it
165
Obligate anerobe
Anerobic respiration | sulfate oxidation/fermentation
166
Examples of Chemoautotrophs
Sulfur oxidizers (microbial miners)
167
conversion formula for sulfur oxidizers and where are they found
H2S + 2O2 -> SO4 + 2H | hydrothermal communities
168
A majority of prokaryotes are what?
chemoheterotrophs
169
Examples of chemoheterotrophs
Saprobes | Parasites
170
What to saprobes feed on?
dead organic matter
171
Type of microbes in relation to increasing temperature
psychophiles <0-20 mseophiles 20-48 thermophiles 42-68 hyperthermophile 65-110
172
3 Main domains
Bacteria, Archaea, Eukarya
173
How many branches of bacteria are there and what are they?
``` 5 Proteobacteria Cyanobacteria Firmicutes Spirochetes Chlamydias ``` CCFPS
174
How many branches of Archaea and what are they?
2 branches Crenarchaeota Euryarchaeota
175
Sub-categories of proteobacteria
purple bacteria rhizobium enteric bacteria
176
Firmicutes are what type of bacteria and what do they consist of?
Low gram positive (GC) | endospores
177
Spirochetes and Chlamydias are what type of bacteria?
Gram negative
178
Crenarchaeota properties
hyperthermophiles | acidophiles
179
Euryarchaeota properties
methanogens (produce methane) | halophiles
180
History wise, what are protists?
ancient eukaryotes
181
Difference between prokaryotes and eukaryotes
``` organizedd nucleus ribosome studded internal membrane cytoskeleton digestive vesicles organelle formation ```
182
What environment are most protists?
aquatic environments
183
T/F: Protists only have one source of nutrition
FALSE they got nutritional diversity
184
Protozoas are similar to ____ and algae to ____
animal like | plant like
185
Locomotion for protists
pseudopod cilia flagella
186
Method of ingestion of protozoa and its subcategories
Endocytosis - pinocytosis (dissolving) - phagocytosis (englufing whole)
187
The contractile vacuole of the protists does what?
assist in osmoregulation
188
T/F: Most protists have similar cell surfaces
FALSE, they are diverse
189
What are endosymbionts? and do protists fall under the category?
organisms that live within other organisms | yes protists are included
190
Sarcodines are a class of
amoeba (pseudopods)
191
Examples of Endosymbionts
forminifera radiolarians acantharia
192
What is the reproduction process of protists? Is it sexual?
Asexual | It is sexual but NOT a "sexual" process
193
Genetic recombination of protists is called
conjugation
194
T/F: protist life cycles don't have an alternation of generations
False!
195
2 types of alternation of generations and what do they do?
heteromorphic - haploid and diplod are different | isomorphic - haploid and diploid are the same
196
Describe Diplomonads and parabasalids
lack mitochondria | obligate parasites
197
Describe Euglenids
no cell wall | heterotrophic and photoautotrophic
198
What is bacteriorhodopsin
synthesis of ATP without chlorophyll pigment using light
199
Bacteriorrhodopsin use ____ phosphorliation, What is that?
Primitive absorb light and pump protons out for a gradient to make ATP
200
What groups are closely related to dinoflagellates?
Ciliates and apicomplexans (Plasmodium)
201
Describe dinoflagellates
``` 2 flagella of different sizes bioluminescent red tides endosymbionts auto, mixo, and heterotrophs ```
202
What type of eukaryote causes malaria?
Apicomplexans
203
In the Theory of Endosymbiosis aquisition of what leads to protozoa/animals and algae/plants
proteobacteria and cyanobacteria
204
What type of protist has two types of nuclei?
Ciliates
205
Conugation is what type of protists way of genetic recombination?
paramecia
206
Alveolates include which protists?
Dinoflagellates and apicomplexas
207
Phytoplankton is what type of protist?
dinoflagellates
208
Paicomplexans are ___ of animals which use ___ for reproduction
parasites | spores
209
the defining structures of the apicomplexas is the ____ use to ___
apical complex that is used to burrow into host tissue or cells
210
T/F: Apicomplexas have a simple life cycle
FALSE, its intricate
211
Two types of stramenopila
diatoms, brown algae
212
Properties of diatoms
cartenoids, yellow/brown, silica shells, important marine phytoplankton, asexual/sexual reproduction, harmful algal blooms
213
Properties of brown algae
photoautotrophs fucoxanthin pigment multicellular (seaweed)
214
Describe Coccolithophorids (haptophytes)
foudn in calcium carbonate plates ) coccoliths auotorophic ocean acidification will have major effect
215
Eukaryote group plantae is the ____ to all plants
precursor
216
Ancestral trait of plantae
endosymbiosis of cyanobacteria to make chloroplasts
217
Another name for green algae
chlorophytes
218
The red algae, and the key pigment that makes it red
rhodophyta | phycoerythrin
219
Do rhodophyta have flagellated stages? Are the multi or unicellular or both? What chemical do they secrete
NO all multicellular calcium carbonate
220
Properties of excavates and what groups of protists do they include?
``` -mostly heterotrophs include: -kinetoplastids -diplomonads -euglenids ```
221
Properties of Rhizaria
marine most heterotrophic -ameoboids with complex shell-skeletons include: forminifera and radiolarins
222
What are the radiolaria and forminifera shell-skeletons made out of?
raidolaria - silica | forminifera - Calcium carbonate
223
Two groups of unikonts
ameobozoa | choanoflagellida
224
Describe ameobozoa
move by pseudopods heterotrophic - phagocytosis Ex: plasmodial slime molds
225
Describe choanoflagellida
closest relative to animals | similar to sponges (colonial)
226
Fugi are ____trophic. And in which domain?
heterotrophic/chemoorganotrophic Ekaryotes (unikonts) can be unicelluar or multi
227
Relationships of fungi to other organisms
saprobic parasitic mutualistic
228
Fungi have ____ in cell walls
Chitin
229
What do fungi produce for reproduction?
spores
230
T/F: Fungi have tolerance to hypertonic environments as well as low and high temperatures
True!
231
Fungi are good ____ and produce _____ chemical byproducts
degraders and produce secondary chemical byproducts
232
T/F: Fungi can alternate between uni- and multicellular form and unicellular members are present in all fungal groups
True
233
How do fungi alternate between uni- and multicellular forms?
alternation of generations
234
What is the mycelium?
the body of a multicellular fungus
235
What is mycorrhizae?
associations between vascular plant roots and fungal mycelia
236
Different characteristics of hyphae
spetate- incomplete cross walls (pores) Coenocytic - no septa Haustroia- push into cells - parasite
237
Fungi multiply by ____ and ____
reporduction and sporulation
238
Dikaryote stage is seen in ____ fungi
higher "crown"
239
Fruiting bodies are called
sporangia
240
Hyphae are what part of the fungi
the "roots"
241
Fungi are good ____ and produce _____ chemical byproducts
degraders and produce secondary chemical byproducts
242
T/F: Fungi can alternate between uni- and multicellular form and unicellular members are present in all fungal groups
True
243
How do fungi alternate between uni- and multicellular forms?
alternation of generations
244
What is the mycelium?
the body of a multicellular fungus
245
What is mycorrhizae?
associations between vascular plant roots and fungal mycelia
246
Different characteristics of hyphae
spetate- incomplete cross walls (pores) Coenocytic - no septa Haustroia- push into cells - parasite
247
Fungi are tolerant to ____-tonic environments and high/low ____
hypertonic high and low temperatures
248
the prime terrestrial remineralizers
Fungi
249
T/F: Not all fungi are heterotrophs
False - they all are
250
Fungi reproduce asexually in _____ conditions while sexual in ____ conditions
asexual - favorable sexual - unfavorable
251
T/F: Mating for fungi are based one male and female
False- mating TYPES
252
Instead of a diploid phase (2n) fungi have a _____ phase (n + n)
Dikaryon
253
The symbiotic relationship between fungi and algae/cyanobactiera
Lichen
254
The "pioneer" organism
Lichen
255
Name the main groups of fungi (5)
``` Chytrids Zygomycota Glomeromycota Ascomycota Basidiomycota ```
256
The type of fungi under glmoeromycota
mycorrihzae
257
The fungi with flagella, and no dikaryotic stage
Chytrids
258
Which group of fungi is the most important step to colonization of land?
Glomeromycota : mycorrhizae
259
The fungi that have rapid spreading growth (mold)
zygomycota
260
``` Sac fungi (fruiting bodies), include plant pathogens and have septate hyphae Make penicillin ```
Ascomycota
261
The typical mushroom falls under what class fungi
Basidiomycota
262
Animals originated from the acquisition of
proteobacteria
263
Describe Koch's Postulates (medicinal microbio)
1) suspected pathogen should be present in the infected and absent from the healthy 2) the pathogen should be isolated and grown in pure culture 3) this culture should cause the disease in the healthy organims 4) when reisolated, the pathogen should be identical to the orignal

College Biology & Ecology II (21 decks)

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