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206 Cards in this Set
- Front
- Back
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What is a community |
A collection of populations of two or more species |
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What is a population |
All of the organisms of a single species living in a geographical area |
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What is an ecosystem |
Community + abiotic factors |
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What is the abiotic factors |
Non-living things |
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What is a species richness |
Total number of species in a community
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If there is an increase in different species is there a decrease or increase in richness |
Increase |
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What is the species abundance |
Proportion of each species in a community |
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If there is more of species "B" than "A" microbs then "B" would have a greater or less species abundance? |
Greater |
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What type of interactions are there in the microbial communities |
*Microbe-Environment interactions *Microbe-Microbe interactions |
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What are microbe-environment interactions |
How microbes interact with environment and how do they change the environment they are in
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What are microbe-microbe interactions |
How different spcies interact with each other and sustain a community of microorganisms |
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What are the type of microbe-microbe interaction? |
*Competition (getting some resources) *Cooperation (Helping each other) |
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Do microorganisms provide critical ecosystem services? |
Yes |
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_____ processes by microbes impact ecosysem |
Metabolic |
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What are biogeochemistry |
Transformation of an element catalyzed by biological or chemical agents Description of interactions of the organisms in the environment and how they change the environment |
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What type of reactions allow for biochemistry? |
Redox reactions |
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What is biogeochemistry important for? |
C, N, S and Fe cycling |
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What is the microbes in carbon cycling doing |
*Constant cycle of how the carbon is moving around in the environment *CO2 in the atmosphere fixed by land plants and then it converts it to organic CO2 by animals and humans *Microorganisms in ocean would have very little in atmosphere *CO2 fixers are important in the water *Large scale processes would not be able to have it |
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What are microbes in nitrogen cycling |
*Microbes are improtant in nitrogen cycle *Nitrogen fixing bacteria in atmosphere nitrogen and into ammonia and other things and make into other things that are able to be made into the things *Ammonia --> nitrites --> Nitrates and into things that can be used by microorganisms and then denitifying back into N2 |
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What are microbes in sulfur cycling |
*How assimilation and decomposition *We know that certain bacteria through into hydrogen sulfide and made into sulfur and then we see that there are different microorganisms *Same for iron |
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What are microbes in iron cycling |
*Conversion by microbes by amount of oxygen present *Provide iron in a necessary form |
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Where microbes live determine what |
Metabolic processes are possible |
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Where are microbes living |
Terrestrial, soil Aquatic Host (for another time) |
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What are the two environments |
*Macroenvironment *Microenvrionment |
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_____ determines resource availability |
Diffusion |
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What is a microenvironemtn/habitat |
Where microbes live |
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What is a niche |
The adaptive role of the organism within the system Set of conditions or things that microbes do |
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_______ alter growth rates |
Flux of nutrient levels |
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How can microorganisms change quickly |
due to diffusion |
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What is "feast or famine" |
Nutrients enter the system intermittently Nutrients fluxuate in a whole lot or a little bit (IE in desert will have no rain then suddnely have a lot) |
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Does the flux of nutrient levels have consequences on microbial life and growth |
Yes |
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What is rhizosphere |
Soil around plant roots Richer in nutrients Very rich environment that fosters important microbial growth and where most growth occurs |
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Is life in soil very diverse of microbs |
Yes |
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Since soil is the most diverse ecosystem does it have highest or lowest species richness? |
Highest |
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Explain image |
Rapidly changing envornment you will ahve changes in the lake Changes in temperature and that gives rise to changes in processes in lake which changes oxygen and H2S curve This depends on seasons and temperature changes with how deep the water is |
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How much of microorganisms live in freshwater |
<1% |
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What are the type of bacteria in freshwater |
*Photosynthesis vs respiration *Oxygen generating and oxygen consuming |
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Does pollution in freshwater alter microbial communities |
Yes |
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Marine water has ~ ______ of microorganisms live here |
2.2 |
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Does marine water have much lower or higher nutrient concentrations compared to freshwater |
Lower |
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Marine water fosteres communities of ___ |
Oligotrophs
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What are oligotrophs |
Slow growing, low metabolism, low population density |
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What is the primary productivity of water by _______ |
Prochlorococcus |
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What is prochlorococcus |
Photosynthetic bacteria related to cyanobacteria |
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What account for half of photosynthetic biomass in tropical and subtropical regions |
Prochlorococcus |
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Microbe-microbe interactions influence _____ |
The interactions iwth the environemnt
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Many processes require diversity of ______ |
Microbes with different niches |
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What are the advantages of biofilms |
*Greater access to nutrients *Protection from predation and physiochemical distrubances *Stability (less prone to physical disruption) *Facilitate nutrient and genetic exchange |
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How does biofilm development work |
*Attachment (adhesion of a few cells to a suitable solid surface) *Colonization (intercellular communication, growth and polysaccharide formation) *Development (More growth and polysaccharide) |
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An increase amount of C-Di-GMP does what for biofilm production |
Stops motile state Increase biofilm production |
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What is C-Di-GMP regulated by |
Quorum Signaling |
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What are the goods of biofilms |
Facilitates carbon and nitrogen cycling in the environment |
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What are the bad of biofilms |
Provides means for transmission of pathogens |
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What are the ugly of biofilms
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Increased antibiotic resistance whcih can lead to life threatening infections |
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How does glycolysis work |
*Start with glucose *Produces NADH, pyruvate, ATP |
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How much ATP does glycolysis require
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2 ATP |
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How much ATP does glycolysis generate |
4 ATP |
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What is the net generation of ATP from glycolysis |
2 ATP |
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What sort of electron acceptor does fermentation have? |
Organic |
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What phosphorylation does fermentation use to produce ATP |
Substrate level phosphorylation |
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What does fermentation reduce pyruvate into for alcohol fermentation |
Ethanol and CO2 |
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What is pyruvate reduced to during lactic acid fermentation |
Lactic acid |
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How much ATP per 1 glucose does fermentation yeild? |
2 ATP (But that is just from glycolysis) |
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What kind of electron acceptor is aerobic respiration |
Inorganic (Usually oxygen) |
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What type of phosphorylation produces ATP in aerobic respiration |
Oxidative phosphorylation (And substrate-level) |
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How much ATP does Aerobic respiration yield per 1 glucose |
38 ATP |
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Why does aerobic respiration yield more ATP generation |
Because of complexity |
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How does aerobic respiration produce ATP |
Using energized membrane |
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How does aerobic respiration work in terms of redox reactions |
Electrons are transferred through several intermediates to a final electron acceptor |
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What are the five types of electron carriers |
NADH dehydrogenases Flavoproteins Iron sulfur proteins, cytochromes Quinones |
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For NADH dehydrogenases where are the proteins bound |
Inside the cytoplasmic membrane
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What does the active site of the NADH dehydrogenases do |
Binds NADH and facilitates the oxidization to NAD+ |
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What does flavoproteins contain |
A derivative of the vitamin riboflavin (FMN, FAD) |
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What is the flavin protion of the flavoproteins like |
Starts as reduced (+2 electrons and 2 H+ and then is oxidized (-2 electrons) The flavoproteins takes electrons and protons and then gets reduced but only donates the electrons |
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What are iron-sulfur proteins |
Non heme iron sulfur proteins |
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Do iron-sulfur proteins have heme group?
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No |
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What do cytochromes have |
Heme andi ron |
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How does cytochrome get oxidized and reduced |
Through the transfer of 1 electon (no proton) |
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Are quinones hydorphobic |
Yes |
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Are quinones proteins |
No
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Do quinones move about in the membrane? |
Yes |
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How much does quinones accept |
2 electrons 2 protons |
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How much do quinones donate |
2 electrons |
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What do quinones link between |
iron sulfur Cytochromes |
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What is electron carrier (1) |
NADH dehydrogenase |
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What is electon carrier 2 |
Iron-sulfur proteins |
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What is electron carrier 3 |
Quinonine |
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What is electron carrier 4 |
Flavoproteins |
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What is electron carrier 5 |
Cytochrome |
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For all of the proteins that serve as electorn acceptor and donors what are they doing in terms of gradients |
Going from a differential gradient as more protiens outside than in the cytoplasm and that difference help the oxidation of hte phosphorylation of ATP and is done through the ATP synthase (hydrogens pumped out and produce ATP) |
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ATP synthase uses _______ force to generate ATP |
proton motive |
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The _____ feeds into the electron transport chain |
Citric Acid cycle (CAC) or Krebs cycle |
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What does the CAC generate |
GTP CO2 NADH FADH2 |
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The ______ released from the Krebs feed into what |
The electron transport chain |
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What is phototrophy |
The use of light energy |
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What is photosynthesis
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Conversion of light energy to chemical energy |
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Most phototrophs are ______ |
Autotrophs
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What are phototrophs that use CO2 called |
Photoautotrophs |
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What are phototrophs that use organic carbon called
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Photoheterotrophs
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Are purple bacteria anoxygenic or oxygenic phototrophs |
Anoxygenic |
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Are green bacteria anoxygenic or oxygenic phototrophs |
Anoxygenic |
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Are cyanobacteria oxygenic or anoxygenic bacteria |
Oxygenic |
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Are algae oxygenic or anoxygenic bacteria |
Oxygenic |
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Are green plants oxygenic or anoxygenic bacteria |
Oxygenic |
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What are photosynthetic pigments in anoxygenic phototrophs |
Bacteriochlorohyll |
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What are photosynthetic pigments in oxygenic phototrophs |
Chlorophyll |
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Chlorophyll is structurally similar to ______ |
Cytochrome
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What do chlorophyl do |
Absorb light and allow for energy generation |
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Variances in chloropylls allow for waht |
Absorption of different wavelength of light |
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What does a diversity of chlorophylls allow for |
Coexistence of different phototrophs |
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Photosynthesis components are present in _______ systems |
Membrane
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For eukaryotics what are the photosynthetic component |
Chloroplasts |
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What are the photosynthesis componenets for purple bacteria |
Invagination of the cytoplasmic membrane (Invagination of folds in inner membrane form ER-like structure and so have photosynthesis machinerary there) |
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What photosynthetic comonents do heliobacteria have |
Cytoplasmic membrane |
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What photosynthetic componenets do green bacteria have |
Cytoplasmic membrane and chromosome
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What type of photosynthetic components do cyanobacteria have |
Thylakoid membranes |
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How is chlorophylls arranged within the membrane |
In most systems, the chlorophylls are attached to proteins in the membrane (except in the chlorosome) Organization of meolecules allow for efficient transfer for electrons to the reaction center -Chlorophylls -Accessory pigments (cartenoids, phycobillins) |
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Anoxygenic photosynthesis is seen in what type of bacteria |
*Purple bacteria *Green sulfur bacteria *Green nonsulfur bacteria *Heliobacteria *Acidobacteria |
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What are the common electron donors for anoxygenic photosynthesis |
H2S and H2 |
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What type of membranes does anoxygenic photosynthesis occur in |
Photosynthetic membranes (Chromatophores, lamellae) |
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What does the anoxygenic photosynthetic reaction centers look like |
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What does the cyclic electron flow allow for |
Cyclic phosphorylatin |
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What is the reaction center do |
Passes electrons |
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Which has the greatest reducing power |
Heliobacteria because has the largest change in E0 |
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What are hte photosystems like for oxygenic photosynthesis |
Proceeds through two distinct but interconnected photosystems |
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Where is the reducing power for oxygenic photosynthesis coming from |
Electrons splitting water into oxygen |
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Where does oxygenic photosynthesis occur in eukaryotes |
Chloroplasts |
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Where does oxygenic photosynthesis occur in membranes
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Stacks in cytoplasm in cyanobacteria |
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________ generates proton motive force in photosystem II |
Noncyclic electron flow |
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______ when enough NAD(P)H is present in photosystem I |
Cyclic electron flow |
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What does oxygenic photosysnthesis look like? |
N/Z Scheme |
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How does photosynthesis contribute to the carbon cycles |
The redox cycle begins with photosynthetic CO2 fixation driven by light energy
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The nitrogen redox cycle is essential for what |
Obtaining nitrogen in usable forms |
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What are the componenets of the nitrogen cycle |
*Nitrogen fixation *Ammonification *Nitrification *Denitrification |
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Is anammax in soils? |
No |
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What is the equation for nitrogen fixation |
N2 + 8H --> 2NH3 + H2 |
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What performs nitrogen fixation |
*Cyanobacteria *Purple/green bacteria *ETC |
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Is nitrogen fixation performed by any eukaryotes? |
No |
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What performs nitrogen fixation |
Enzyme nitrogenase |
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The NH3 made from nitrogen fixation can be converted to what |
Made into proteins or into NH4+ for nitrification |
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What is nitrogenase inhibited by
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Oxygen |
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How does nitrogenase rapidly remove oxygen |
By respiration |
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Nitrogenase forms _____ |
Slime layers
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Why does nitrogenase form slime layers
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(Biofilms) So the microbes in the middle of the biofilm will use up everything and therefore be anoxic because little oxygen is likely to get through |
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How does nitrogenase protect |
Conformational protection |
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What is conformational protection
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Protection by complexing with another protein |
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What are special cell types of nitrogenase |
Heterocysts |
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What is the equation for ammonification |
Organic N --> NH4+ |
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Is ammonification performed by many or very little types of organisms |
Man |
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What is the equation of nitrification |
NH4+ --> NO3- |
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How many steps in nitrifcation |
2 |
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What are the two steps of nitrification |
NH4 + --> NO2- NO2- --> NO3 - |
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What performs NH4+ --> NO2- |
Nitrosomas |
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What perfroms NO2- --> NO3- |
Nitrobacter |
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What complex turns NH4+ into NO2- |
Ammonia monooxygenase |
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What compound turns NO2- into NO3- |
Nitrite oxidoreductase |
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What is the formula for denitrification |
NO3- --> N2 |
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What performs denitrification |
Bacillus Paracoccus Pseudomonas |
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Is there a little or a lot of enzyme reductases needed? |
Lot |
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Where do chemolithotrophs obtain energy from? |
Oxidation of inorganic compounds |
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Most chemolithotrophs are _____ |
Autotrophs |
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But some chemolithotrophs are _______ |
Mixotrophs |
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What are mixotrophs?
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Get their carbon from a mix of CO2 and organic carbon |
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ATP and electron transport of chemolithotrophs are similar to _______ |
Organotrophs |
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What is reducing power way for chemolithotrophs
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*Directly from inorganic compounds *Reverse electron flow (common) |
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For reverse electron flow it requries energy from what? |
Proton motive force |
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The reverse electron flow is reversing the activity of what |
Complex 1 in ETC |
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NADH is good for what |
Catabolic reactions |
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NADPH is good for what |
Anabolic reactions (IE CO2 fixation) |
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How does the reducing power of the reverse electron flow |
By having a reverse proton pump that sends protons into the cell and allows the negative charges to generate the gradient again |
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Chemolithotrophs use a variety of _________ electron donors |
Inorganic |
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What is the function of nitrogen cycle in terms of chemolithotrophs |
Balance the nitrogen cycle The pollution contaminates drinking water of well reservoir and when we look at that map it shows us the nitrogen in put of reservorir |
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What kind of protein is ammonia monoxygenase |
Transmembrane protein that can get out of the cell by N2 by hydroxylamine oxidoreductase |
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What are the two compounds used during NH4+ --> NO2- |
ammonia monoxygenase Hydroxylamine oxidoreductaseH |
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How go from SO42- to H2S what is that process called |
Sulfate reduction |
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What are the three significant states of sulfur |
-2 [Sulfhydryl, sulfide] (H2S) 0 (elemental sulfur) +6 (Sulfate) |
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What do H2S, S0 and S2O3 2- could lead to |
SO4 2- |
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Are there similar energy yields for H2S, S0, S2O3 2- |
Yes |
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What is toxic to many plants and animals |
Hydrogen Sulfide (H2S)
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How do you get hydrogen sulfide |
Sulfate reduction |
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Why is hydrogen sulfide toxic to many plants and animals |
Because it combines with iron in cytochromes and will screw up the normal function of cytochrome which messes up the ETC and therefore not able to produce ATP and can't get energy H |
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How does sulfur cycle factor into acid rain |
Sulfur into the air and reacts with water and causes it to rain acid Acidifying soil which damages plants and microbes Ocean acidification which damages corals, micro auto-and heterotrophs and others |
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What is iron reduction |
Fe 3+ is an electron acceptor in anaerobic respiration Common in anoxic sediments |
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Where does iron oxidation occur |
At anoxic/oxic interface |
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What type of iron process is found in waterlogged soils, bogs, anoxic lake sediment |
Ferric iron reduction (3+ --> 2+) |
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What pH does iron oxidation occur |
acidic |
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What iron compound is found in coals |
Pyrite (FeS2) |
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What does it mean to be a obligate aerobe |
Only use oxygen (can't live in anoxic conditions) |
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What does it mean to be an obligate anerobe |
Need oxygen |
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What does it mean to be a faculative aerobe |
Either anaerobic or aerobic depending on the environment but aerobic is dominant |
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Does iron do well in acidic or basic conditions |
Acidic |
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What is methanodgensis |
Production of methane (CH4) |
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Are methanogens anaerobic or aerobic archaea? |
Anaerobic |
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What is the process that is very close to LUCA (evidence of first cellular life) |
Methanogensis The first process to really evolve in life especially in hydrothermal vents because had an abundance of the necessary resources |
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Are there a variety of ways to generate methane? |
Yes |
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What reagents can methanogenesis come from |
CO2 + H2 Methanol Acetate |
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What is another way methanogenesis can occur |
Final step in the carbon cycle Important decay of organic matter |
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What motive force produces ATP in CO2 + H2 for methane
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Sodium motive force |
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What motive force produces ATP to make methane from CH3OH |
Proton motive force |
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What motive force produces ATP to make methane from CH3COO- |
Proton |
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Where are methanogens found? |
*Animals (ruminants) *Underground (anoxic sediments) *Hydrothermal vents (high CO2 and H2) |
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Methanogens are an important contributer to what? |
Global warming |
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What do fermenters make |
CO2 and H2 (after donating extra electrons to protons) |
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What do methanogens use to make methane |
CO2 and H2 |
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What is syntrophy
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Process whereby two or more organisms cooperate to generate energy through degrading a substance neither can degrade alone |
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Where do syntrophs usually work |
Secondary fermenters |
