Final Flashcards
(51 cards)
1
Q
Chemotrophs
A
energy derived form redox rxns involving organic or inorganic compounds
2
Q
Organotrophs
A
organic compounds are the source of electrons
3
Q
Lithotrophs
A
Inorganic compounds are source of electrons
4
Q
Autotrophs
A
carbon source is CO2 or HCO3-
5
Q
Heterotrophs
A
carbon source is reduced organic compounds
6
Q
O2 vs NO3 respiration in E.coli(facultative anaerobes)
A
- aerobic(O2) respiration a total of 6 H+ are transports; more ATP production
- anaerobic(NO3) respiration total of 4 H+ transported out; less ATP production
- genes encoding enzymes for anaerobic respiration are repressed by O2 and activated by presence of the electron acceptor(NO3)
7
Q
oxygenic phototrophs
A
- evolve O2
- 2 photosystems
- calvin-benson cycle(CO2 fixation)
8
Q
anaerobic anoxygenic phototrophs
A
- 1 photosystem
- reverse TCA cycle hydroxyproprionate pathway(CO2 fixation)
9
Q
Fermentation
A
- does not require a proton motive force for ATP generation
- the substrate fermented is both the e- donor and the e- acceptor
- is energetically weak
- many substrates can be fermented
10
Q
Anoxic Decomposition
A
-one bugs waste is anothers meal
11
Q
Oxygenic Photolithoautotrophy
A
- contains chlorophyll
- H2O(e- donor) oxidized to O2
- has 2 photosystems
- non cyclic phosphorylation
- light required for reducing power and energy conservation
12
Q
Anoxic Photolithoautotrophy
A
- contains bacteriochlorophyll
- various e- donors(H2S, S, H2, Fe2+)
- 1 photosystem
- cyclic phosphorylation
- light required for energy conservation alone(ATP syn)
13
Q
Chlorophyll a
A
- oxygenic phototrophs
- principle molecule in green plants, algae and cyanobacteria
14
Q
Bacteriochlorophyll a
A
- Anoxygenic phototrophs
- tremendous chemical diveristy; chemical diversity alters aborbtion spectrum for light harvesting
15
Q
Carotenoids
A
carotenes and xanthophylls
- function in photo-protection
- prevent oxidative damage
- isoprenoid chains
- responsible for cool colors of phototrophic species
- mostly absorb blue light
16
Q
Phycobiliproteins
A
- found in cyanobacteria
- 3 primary pigment types
- phycobilisome content increases when light intensity decreases
17
Q
Anoxygenic Photosynthesis
A
- poor e- donor(p870) is converted to a strong e- donor(p870*) due to light activation
- cyclic photophosphorylation; no terminal e- acceptor
- light energy responsible for generation of PMF(ATP syn) but not reducing power
18
Q
Oxygenic Photosynthesis
A
- 2 photosystems(p700 and p680)
- e- from H2O generate PMF and NADPH reducing power
- p700 required for NADPH synthesis; required for anabolic synthesis
- non cyclic phosphorylation
19
Q
Phototrophs
A
energy souce is light
20
Q
Unified Species Concept
A
- 16S rRNA gene sequence homology; 97% identity
- DNA-DNA hybridization; 70% hybridization genome wide
- multi-locus sequence typing(MLST); sequence similarity among housekeeping genes
21
Q
Geneological Species Concept
A
-species is a group of strains that cluster together phylogenetically and are distinct from other cohesive groups of strains
22
Q
Nanowires
A
- can be several times longer than cells themselves
- they are pilus-like appendages
- they are proteinacous and also electrically conducive
- e- transport long the length of bacterial nanowires
23
Q
Stromatolites
A
- fossilized microbial mats
- evidence for early microbial life
- likely formed by ancient anoxygenic phototrophic microbes such as chloroflexins
24
Q
Banded Iron Formations
A
- evidence of atmospheric oxygenation
- dark bands contain oxidized iron
- once abundant Fe2+ was oxidized, O2 was free to accumulate in atmosphere
25
Species Richness
total number of species present
26
Species Eveness
proportion of each species in the system
27
Species Eveness
proportion of each species in the system
28
mtrc gene
Decaheme C-Type Cytochrome; electrically conductive nanowires
29
GSPD gene
translocation of cytochromes to membrane; nanowires are electrically conductive
30
Impact of Burning Fossil Fuels
- increased CO2 in the atmosphere
- increased photosynthesis and productivity of some plants and microorganisms
- C-fixation removes atmospheric CO2 thus helping abate the negative consequences of accumulated green house agents
31
Factors that limit primary productivity in aquatic ecosystems
-Nitrogen, Iron, and Phosphorus are common limiting nutrients in many environments
32
Health affects of mercury exposure
- disrupt thiol groups in protein
- nervous system deterioration
- involuntary muscle contractions
- skin and mucosal surface corrosion
- neurological birth defects
33
Methylmercury
the chemical form that initiates concentration through the food web
34
Oxidative dechlorination of PCBs
- polychlorinated biphenyls(PCBs)
- sources of carbon for microbes
- their hydrolysis is catalyzed by complex oxidase enzymes
- reductive dechlorination of highly halogenated PCBs complements this process; use of PCBs as electron acceptors
35
PhyloChip
- DNA microarray for rapid profiling of microbial populations based on 16s rRNA homology
- contains tens of thousands of 16s rRNA probes for diverse microbial groups
- Hybridization of envir DNA to phylochip tells you what species are present
36
GeoChip
- DNA microarray for rapid profiling of functional genes based on sequence homology
- containis tens of thousands of gene probes for diverse metabolic functions
- hybridization of envir DNA to the geochip tell you what genes are present
37
Metagenomics
- communities are organized species and strains whose aggregate properties exceed the sum of their constituent members
- metagenomic analysis can provide a window into community interactions and processes
38
In Situ
- Field based sampling and data collection
- knowing the ecosystem; environment and organisms
- correlate microbial genotypes and metabolisms with prevailing environmental conditions
39
Ex Vivo
- Lab based sample processing and DNA sequencing
- determining species richness and evenness of environmental samples
- genome coverage is proportional to abundance in the library
- genomic library construction
- paired end DNA sequencing
40
In Silico
- Read based vs Assembly driven
- phylogenetic binning
- annotation of genomic fragments
41
Read based sequence analysis
- gene prediction
- functional annotation
- analysis provides an inventory of functional capabilities within a community
42
Assembly Driven Analysis
- comparison against other sequenced genomes
| - comparison against other populations in the same community
43
Phylogenetic Binning
-assigning DNA fragments to bins corresponding to the pprobable species of origin
44
Phylogenetic Binning Metrics
Nucleotide composition, homology to sequenced genomes, depth of coverage
45
Annotation of Genomic Fragments
- assignment of functional info to predicted genes
| - each gene is linked to an organism telling you something about it
46
Mutualism
A symbiotic relationship wherein both species benefit from the interaction
47
Commensalism
A symbiotic relationship wherein one species benefits while the other partner neither benefits nor is harmed by the interaction
48
Parasitism
A relationship wherein one member is harmed in the interaction
49
Biofertilizers
micro inoculants containing living cells of either nitrogen fixing or phosphate solubilizing bacteria
50
Azotobacter
- free living diazotrophs(N2-fixers)
| - Azolla and its nitrogen fixing partner, Anabaeria, have been used as green manure
51
Intercropping
co-cultivation of mixed species for the purpose of improving crop production and minimizing fertilizer use
