Bacterial Diversity Flashcards
1
Q
3 branches of phylogenetic tree
A
Bacteria
Archaea
Eukarya
2
Q
How is grouping into branches of phylogenetic tree determined?
A
Small subunit ribosomal RNA (SSU rRNA)
3
Q
Type of small subunit ribosomal RNA that bacteria and archaea have: name and function
A
16S rRNA
In translation, aligns Shine-Dalgarno sequence with ribosome
4
Q
Type of small subunit ribosomal RNA that eukaryotes have
A
18S rRNA
5
Q
Name of system used to name microbes and two components that comprise a microbe’s name
A
Binomial system (genus and species)
6
Q
Taxonomical order
A
Domain, phylum, class, order, family, genus, species
7
Q
Phylum
A
Group sharing a common ancestor
8
Q
Genus
A
Well defined group of one or more strains
9
Q
Thermus aquaticus: what phylum?
A
Deinococcus-Thermus
10
Q
Thermus aquaticus: what type of extremophile is it? What is its growth temperature?
A
Thermophile
Grows at 70-75 degrees Celsius
11
Q
Thermus aquaticus provides what reagent for PCR?
A
Taq polymerase
12
Q
Deinococcus radiodurans: what phylum?
A
Deinococcus-Thermus
13
Q
Deinococcus radiodurans: is it a thermophile? Is it resistant to anything? What is its speed of DNA repair?
A
Not a thermophile
Extremely resistant to radiation and dessication
Rapid DNA repair
14
Q
Shape of Deinococcus radiodurans
A
Tetrad (4 cocci in a 2x2 square)
15
Q
What phylum includes many photosynthetic bacteria?
A
Cyanobacteria
16
Q
Cyanobacteria are _____ ______ in many ecosystems, meaning that they produce carbohydrates for heterotrophs.
A
Primary producers
17
Q
Cyanobacteria: photosynthetic? If so, what type of photosynthesis?
A
Photosynthetic, oxygenic
18
Q
How many photosystems do Cyanobacteria use?
A
2 photosystems: PSI and PSII
19
Q
What does an oxygenic photosynthesizer use as an electron donor, and what does it produce?
A
Electron donor: water
Produces O2
20
Q
Cyanobacteria generate _____ and ______ through oxygenic photosynthesis that are used in ______ _____ to fix ____.
A
ATP
NADPH
Calvin cycle
CO2
21
Q
Cyanobacteria have what 2 subcellular structures?
A
Thylakoids
Carboxysomes
22
Q
Thylakoids: what pigment used in which photosynthetic reactions?
A
Chlorophyll
Light reactions
23
Q
Carboxysomes: what enzyme used in what cycle?
A
RubisCO
Calvin cycle
24
Q
2 example genera of Cyanobacteria
A
Prochlorococcus
Anabaena
25
Prochlorococcus lives where? What is its concentration there?
Tropical oceans
| Over 100,000 cells/mL
26
Prochlorococcus: relative size compared to other photosynthetic organisms, actual size
Smallest known photosynthetic organism
| 1 micrometer
27
Prochlorococcus carries out which type of photosynthesis? What light gathering pigment does it use?
Oxygenic
| Chlorophyll
28
What do thylakoids look like in Prochlorococcus?
Rings
29
What is the relative and actual size of the Prochlorococcus genome?
Small genome
| About 2000 genes
30
Anabaena: Gram positive or negative? Environment?
Gram negative
| Aquatic
31
What 2 processes does Anabaena carry out?
Oxygenic photosynthesis
| Nitrogen fixation
32
Nitrogen fixation: what is reduced to what?
Atmospheric nitrogen (N2) is reduced to ammonia (NH3)
33
One problem that Anabaena face in nitrogen fixation and how it solves that problem
Problem: enzyme nitrogenase used in nitrogen fixation is sensitive to oxygen
Solution: vegetative cells are differentiated into heterocysts, which are devoid of oxygen and can fix nitrogen
34
Ammonia inside Anabaena heterocysts is incorporated into what amino acid?
Glutamate
35
Vegetative cells of Anabaena carry out what process?
Photosynthesis
36
2 way feeding of Anabaena vegetative cells and heterocysts
Vegetative cells carry out photosynthesis, converting CO2 into carbohydrate
Carbohydrate is brought into heterocysts and is used as a carbon and electron source
Glutamate from the heterocysts is converted into carbohydrate to feed vegetative cells
37
Which phylum includes many obligate intracellular pathogenic bacteria?
Chlamydiae
38
Example genus of Chlamydiae
Chlamydia
39
Chlamydia: Gram positive or negative? What is its relationship with other cells?
Gram negative
| Obligate intracellular bacteria (requires other cells to replicate)
40
2 examples of Chlamydia that are pathogenic and the diseases that they cause
C. pneumoniae (respiratory infections)
| C. trachomatis (STD)
41
2 cell types of Chlamydia
Elementary body
| Reticulate body
42
Elementary body of Chlamydia: can it replicate? Is it infectious? Does it exist inside or outside of host cell?
Dormant (cannot replicate)
Infectious
Extracellular
43
What elementary body of Chlamydia does (3 steps)
Attaches to cell
Enters cell
Develops into reticulate body
44
Reticulate body of Chlamydia: can it replicate? Is it infectious? Does it exist inside or outside of host cell?
Reproductive
Non-infectious
Intracellular
45
What reticulate body of Chlamydia does (2 steps)
Develops back into elementary body
| Elementary body is released from cell
46
Which phylum contains flexible, helical shaped bacteria?
Spirochaetes
47
Where are the flagella located within Spriochaetes? What is the term for this type of flagella?
Located within periplasm
| Axial filament
48
How much of the Spirochaetes cell is turned when its flagella rotate?
The whole cell
49
2 pathogenic strains of Spirochaetes and the diseases they cause
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Treponema pallidum (syphilis)
Borrelia burgdorferi (Lyme disease)
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50
Borrelia burgdorferi causes what type of rash? What is the formal name for this type of rash?
Bulls eye rash
| Erythema Migrans
51
What phylum of bacteria includes many bacteria found in the intestinal tract?
Bacteroidetes
52
Example genus of Bacteroidetes
Bacteroides
53
Bacteroides have what relationship with oxygen?
Obligate anaerobes: oxygen is toxic
54
Bacteroides are important bacteria of what human organ system?
Intestinal tract
55
About what percent of bacteria cultured from human feces are Bacteroides?
30%
56
Bacteroides degrade what structures?
Complex, dietary polysaccharides
57
What phylum comprises the largest group of bacteria?
Proteobacteria
58
Proteobacteria: Gram positive or negative?
Gram negative
59
5 major classes of Proteobacteria
Alpha, beta, gamma, delta, epsilon
60
Proteobacteria can include what type of carbon users?
Heterotrophs (reduced organic compounds as carbon sources)
61
Proteobacteria can include what type of energy users?
Phototrophs
62
Proteobacteria can include what type of electron users?
Lithotrophs (inorganic compounds as electron donors)
63
Alpha Proteobacteria: some are what type of carbon and energy users?
Photoheterotrophs
64
Alpha Proteobacteria: photosynthesis? If so, what type and what does that mean for its source of electrons?
Anoxygenic photosynthesis (cannot split water as source of electrons, so no O2 produced)
65
Alpha Proteobacteria use what type of light harvesting pigment?
Bacteriochlorophyll
66
Some Alpha Proteobacteria are _______, so they live off of other organisms.
Endosymbionts
67
Examples of endosymbiotic Alpha Proteobacteria and what they do
Rhizobium (fixes N2 in root nodules)
Argobacterium (T DNA causes plant tumors/galls)
Rickettsia (obligate intracellular bacteria that causes Rocky Mountain Spotted Fever carried by ticks)
68
Example genus of Alpha Proteobacteria that has two distinct cell types
Caulobacter
69
Caulobacter: Gram positive or negative? Environment?
Gram negative
| Aquatic
70
Caulobacter are dimorphic. What does that mean?
They differentiate between two cell types created by cell division
71
Cell division of Caulobacter generates what 2 types of cells? Which is motile and which is non-motile?
Motile swarmer cells
| Non-motile stalked cells
72
How is the stalk of stalked Caulobacter cells created?
Pushing out of cell membrane
73
The tip of the Caulobacter stalk is called what and is made up of what?
Holdfast
| Made of sticky polysaccharides
74
2 functions of Caulobacter's stalk
Enables microbial attachment via holdfast
| Increases surface area for nutrient uptake (stalk grows longer in nutrient limiting conditions)
75
What is the difference between swarmer and stalked cells of Caulobacter in terms of DNA replication?
Swarmer cells cannot replicate their DNA, but stalked cells can
76
3 steps of Caulobacter life cycle
1. Swarmer cell sheds its flagellum
2. Cell grows stalk where flagellum once was
3. Stalked cell divides and gives rise to both a swarmer cell and a stalked cell
77
Beta Proteobacteria: some are what type of energy and electron users?
Chemolithotrophs
78
Beta Proteobacteria oxidize what 3 compounds?
Nitrate
Sulfur
Iron
79
Example genus of Beta Proteobacteria that completes the first step of nitrification where ____ is oxidized to ____
Nitrosomonas
| Ammonia is oxidized to nitrite
80
3 examples of Beta Proteobacteria that are human pathogens
Neisseria meningitidis
Gonorrhoeae
Burkholderia cepacia
81
In addition to humans, Burkholderia cepacia also functions as a pathogen in what type of organism? What disease does it cause?
Plants
| Onion rot
82
Gamma Proteobacteria includes "enterics." These bacteria have what relationship with oxygen and live where?
```
Facultative anaerobes (prefer oxygen, but can grow in its absence)
Live in intestinal tract
```
83
3 examples of enteric Gamma Proteobacteria and diseases they can cause
Escherichia coli (normally non-pathogenic, but O157:H7 is one strain amongst others that is pathogenic)
Salmonella (food poisoning)
Proteus (urinary tract infections)
84
3 examples of non-enteric Gamma Proteobacteria and what they do
```
Pseudomonas aeruginosa (pathogen in cystic fibrosis and burn wound patients; produces pyoverdin pigment that acts as siderophore)
Vibrio cholerae (cholera)
Shewanella (non-pathogenic bacteria that lives in aquatic and soil environments; extracellular electron transport)
```
85
Example genus of Delta Proteobacteria that is a social bacteria
Myxococcus
86
Myxococcus: Gram negative or positive? Environment?
Gram negative
| Soil
87
How do Myxococcus interact with bacteria of other species?
Attack them
88
Do Myxococcus have flagella? If not, what kind of motility to they demonstrate?
No flagella
| Gliding motility
89
Fruiting bodies of Myxococcus: when are they created? What specialized cell type do they contain?
Created in nutrient limiting conditions
| Myxospores (dormant)
90
Genus of Delta Proteobacteria that parasitizes other bacteria
Bdellovibrio
91
Bdellovibrio parasitization: where does it grow in its bacterial prey? What does it do to the host organism?
Grows in periplasm of prey
| Lyses host
92
Myxococcus fruiting body formation: steps (5)
1. Stress and starvation signal aggregation of vegetative cells
2. Gliding motility through extension and retraction of type IV pili moves cells together
3. Formation of fruiting body along with formation of myxospores at top of fruiting body
4. Myxospores are released
5. Myxospores germinate and give rise to vegetative cells
93
What is the relative time it takes for Mxyococcus to form fruiting bodies?
Hours to days (takes a while)
94
Which has a better chance of survival in Mxyococcus fruiting bodies: myxospores at top or cells on bottom?
Myxospores on top
95
Epsilon proteobacteria: what 2 genera cause disease in humans?
Campylobacter
| Helicobacter
96
Campylobacter causes what 2 diseases?
Guillain-Barre syndrome (flaccid paralysis)
| Gastroenteritis (inflammation of stomach, diarrhea)
97
Helicobacter causes what 3 diseases?
Gastritis, peptic ulcer disease, gastric cancer (all H. pylori)
98
What phylum includes pathogens, "good" bacteria, and spore formers?
Firmicutes
99
Firmicutes: high or low cytosine and guanine concentration in DNA? Gram positive or negative?
Low cytosine and guanine in DNA
| Gram positive
100
Firmicutes pathogens: 2 genera
Staphylococcus
| Streptococcus
101
Firmicutes "good" bacteria: 2 genera, what they produce through what pathway, what they are used to make
Lactobacillus
Lactococcus
Produce lactic acid through fermentation
Probiotics, cheese, yogurt
102
Firmicutes spore formers: what are the spores resistant to, what 2 genera
Spores are heat-resistant
| Clostridium, Bacillus
103
3 species of Clostridium and what diseases they cause
C. tetani (tetanus)
C. botulinum (botulism, produces neurotoxin used in Botox)
C. difficile (colitis- inflammation of colon)
104
3 species of Bacillus and features of these bacteria
B. subtilis (non-pathogen)
B. anthracis (anthrax)
B. thuringiensis (insecticidal toxin)
105
Thuricide insecticide: genus and species, parts of bacteria used, mechanism of action
Bacillus thuringiensis
Spores and toxin
Upon ingestion, forms holes in caterpillar gut
106
Bacillus sporulation: adaptive response to what?
Starvation
107
How long does it take to make Bacillus spore?
8-10 hours
108
Bacillus sporulation results in the formation of what 2 cells? What is the purpose of each?
Mother cell and forespore
Mother cell lyses, releasing spore
Forespore is dormant and stress-resistant and can germinate, becoming an actively growing cell
109
3 steps in Bacillus sporulation
1. Septum forms asymmetrically
2. Mother cell engulfs forespore with second membrane
3. Mother cell adds cortex of peptidoglycan and coat of protein to forespore and then lyses
110
4 layers of Bacillus spore
Innermost (1): chromosome and cytoplasm
2: Inner membrane
3: Outer membrane
Outermost (4): protein coat
111
What system does Bacillus use to sense stress and initiate sporulation?
Two-component system
112
What phylum includes acid-fast and soil-dwelling bacteria?
Actinobacteria
113
Actinobacteria: high or low cytosine and guanine composition of DNA? Gram positive or negative?
High cytosine and guanine
| Gram positive
114
Genus of Actinobacteria that is acid-fast
Mycobacterium
115
Mycobacterium includes what 2 pathogenic species?
Tuberculosis
| Leprae
116
What component of Mycobacterium cell walls makes them acid-fast? What commonly used lab procedure does this component prevent?
Waxy lipids
| Gram staining
117
Genus of Actinobacteria that is soil-dwelling
Streptomyces
118
3 features of Streptomyces: responsible for the ____ of most soil, forms what structures similar to those of fungi, source of many _____
Responsible for odor of most soil
Form hyphae and mycelia
Source of many antibiotics
