Microbes and Metabolism Flashcards
Describe main features of prokaryotes
- Bacteria are prokaryotes
- Do not have a nucleus
- But some have organelles
What is the idea of endosymbiosis
- Mitochondria is an ancestor from bacteria
What is the main way bacteria are categorised
- Gram positive and Gram negative cells based on cell wall structure
How are prokaryotes diverse
- Catabolic diversity of prokaryotes greatly exceeds that in eukaryotes (although, arguably, fungi rival them)
- Diversity of substrates utilised
- Diversity of metabolic pathways
What are the two divisions of how the energy source is acquired
- Photo: Light energy excites e- to higher-energy state
2. Chemo: Chemical e- donors are oxidised
What are the two divisions based on electron source
- Organo: Organic molecules donate e-
2. Litho: Inorganic molecules donate e-
What are the two divisions based on carbon source of biomass
- Auto: CO2 is fixed and assembled into organic molecules
2. Hetero: Preformed organic molecules are acquired from outside and assembled
Give an example of a chemolithoautotroph
- Tube worms are packed of chemolithoautotrophs which eat inorganic molecules from geothermal vents
- Fix CO2 from water and turn it into themselves – organic structure- worm eats itself
- Can have ecosystems not based primarily on light
What is energy needed for
- Energy needed for anabolism and growth e.g.
- Growth and reproduction
- Maintenance – biosynthesis, transport, motility, etc.
How is energy converted to a usable form
- Redox- e- “float” from one compound to another
- Oxidation – loose e-
- Reduction – gain e-
- Energy conserved as energy-rich chemical bond or used directly for work
Describe the types of reaction relating to gibbs energy
Exergonic reaction 1. ΔG is negative 2. Free energy leaves the system 3. Free energy is energy that can do work (available energy) Endergonic reaction 1. ΔG is positive 2. Free energy is gained by the system
What does delta G depend on
- ΔG of reaction varies depending on concentrations, temperature and pressure
What are the main features of the electron transport chain
- The membrane is a boundary between the cytoplasm and the surroundings-semipermeable which allows an electrochemical gradient
- e- donor and e- acceptor (terminal)
- Acceptor from surroundings
- Respiration
Describe conditions with and without oxygen
- Aerobic – presence of O2 (aerobic conditions)
- Anaerobic – absence of O2 (anoxic conditions)
- O2 is the terminal e- acceptor in aerobic respiration
- Atmosphere ~21% O2
- Solubility is low in water
Where does the energy for Chemoorganotrophy come from
- Energy from organic compounds
Where does the energy for Chemilithotrophy come from
- Energy from inorganic compounds
Give examples of Chemolithotrophic e- donors
- Hydrogen (H2) e.g., Pseudomonas hydrogenovara
- Sulphur compounds (H2S, S0, thiosulfate (S2O32-)) e.g., Thiobacillus spp., Beggiatoa spp.
- Ammonia (NH3) e.g., Nitrosomonas europaea
- Nitrite (NO2-) e.g., Nitrobacter winogradskyi
- Iron (Ferrous iron (Fe2+)) e.g. iron pyrite FeS2 e.g., Thiobacillus spp.
- Arsenite (H3AsO3) e.g., Pseudomonas arsenitoxidans
Describe examples of electron acceptors in anaerobic respiration
- Anaerobic respiration use other molecules as terminal e- acceptor
- Facultative anaerobes- can use oxygen but don’t need it
- Often use nitrate (NO3-) or nitrite (NO2-)
- Obligate anaerobes- must live with no oxygen around
- Often use sulfate (SO42-)
- CO2 as terminal e- acceptor for methanogens
- CO2 + 4H2 CH4 + 2H2O
What do chemolithotrophs still need
- Chemolithotrophs still need ATP and NAD(P)H
How do chemolithotrophs generate NAD(P)H
- Most inorganic e- donors have redox potentials higher than NAD(P)+ and NAD(P)H
- So e- are transferred to coenzyme Q or a cytochrome and then;
- Some generate a proton motive force when passed to a terminal e- acceptor- Forward e- transport
- Some are passed to NAD(P)+ to make NAD(P)H but uses the proton motive force- Reverse e- transport
- This takes 5x forward pathway to power 1x reverse pathway
What do Acidiothiobacillus ferrooxidans do
- Eat rock – FeS2 using H2O
- Have protein that makes FE2+ go to Fe3+ put electrons into transport chain
- Only works because external pH is acidic
Describe the carbon sources of chemolithotrophs
- Most chemolithotrophs are autotrophs (chemolithoautotrophy)
- Most use the Calvin cycle
- Alternatives are reverse TCA cycle, acetyl-CoA pathway, and 3-hydroxypropionate cycle
- Some chemolithotrophs use organic carbon sources (chemolithoheterotrophs or mixotrophs)
Describe Campylobacter jejuni
- Common cause of gastroenteritis
- Microaerophilic
- A chemoorganotroph with diverse metabolic pathways
- Can’t use glucose
- Can also use H2 and sulphite (SO32-) as an e- donor
- Has chemolithotrophic capability- not sure why as live in organic compound
- Sulphite released by neutrophils as part of immunity
Give examples of anaerobic environments
- water,
- soil,
- food,
- plant and animal tissues,
- GI tract
What are 3 methods of anaerobic metabolism
- anaerobic phototropy
- Anaerobic respiration
- fermentation
Describe anaerobic respiration
- An e- transport chain delivers e- to a non-O2 e- acceptor
2. Electron transport phosphorylation generated ATP
Describe fermentation
- In environments where no e- acceptor for e- transport chain
- Used instead of respiration
- Some bacteria have fermentation only (obligate fermenters)
- Limited to chemoorganotrophs
- Fermentation of inorganic compounds not possible- so little energy from inorganic electron donors and so little from fermentations so not enough energy
Describe the redox processes in fermentation
- Oxidation of a substrate- Substrate only partially oxidised
- Reduction of e- carriers (NAD(P)+ or FAD)
- NAD(P)H or FADH is then oxidised (recycled)
- Reduction of a derivative of the starting substrate (typically) or an independent substrate (amino acid fermentation, electron is given to different amino acid than is taken from)
- Typically the e- acceptor is organic and “internally” supplied
- Reduced product has to be excreted as a fermentation product
What is the delta G for fermentation
- An exergonic reaction
- A large substrate turns into two or more simpler molecules
- Therefore, entropy increase so ΔG goes down
How is ATP produced in fermentation
- ATP produced mainly by substrate-level phosphorylation
- Typically during the 1st oxidation step(s)
- Direct transfer of P group from an organic P to ADP
- Significantly less ATP produced than in phototrophy or e- transport based respiration
- Some instances of ATP production by alternative methods
Compare amount of ATP produced from lactate fermentation and respiration
- Far less energy from fermentation
2. e.g., 2 ATP from lactate fermentation vs. 38 ATP from respiration of lactate
Describe different features of coenzymes
- NAD, NADP, FAD and FMN
a) Water-soluble coenzymes (cofactors)
b) Carry e- from oxidation reactions and donate them to wide variety of reduction reactions - NAD and NADP
a) Free moving from one enzyme to another - FAD and FMN
a) Tightly bound to enzymes (flavoproteins)
What are coenzymes
- Small organic molecules
2. Interact with apoenzyme to form active holoenzyme
What are the different types of fermentation pathway
- Linear- glycolysis etc
2. Branched/split- Multiple products but Everything needs to be redox balanced
Describe basics of glycolysis
- Glycolysis is fermentation
- Pyruvate is reduced to fermentation products
- Balances redox
- Regenerates NAD+
- Substrate level phosphorylation
How is it ensured
- Some fermentation pathways are endergonic- ΔG is positive
- But when concentration of reaction products are kept low, the reactions become exergonic
- Concentrations can be kept low if products either diffuse away or are consumed by another organism
- Syntrophy- a way to keep concentrations low
What is syntrophy
- One species lives off the products of another species
2. Dependent organism is a syntrophic organism
Give an example of syntrophy
- Interspecies hydrogen transfer
- Methanogens
- Hydrogen gas is eaten by methanogen so syntrophic organism can ferment ethanol and produce acetate
Describe the range of substrates that can be fermented
- Relatively large no. of substrates can be fermented
- Therefore, large no. of fermentation products
- One organism may use/produce more than one substrate/product using the Same or different pathways
- Sugars (hexoses, pentoses, tetroses), polyalcohols, organic acids, amino acids, purines and pyrimidines
- Acetylene, citrate, glyoxylate, succinate, oxalate and malonate
- Some bacteria can ferment xenobiotic compounds- man made compounds - Anthropogenic compounds unknown in natural ecosystems
- e.g., polychlorinated biphenyls (PCBs)- bi product of many industrial processes
What is the name if there is one fermentation product and give example
- One fermentation product
- Homofermentative
- e.g., lactate produced by Lactobacillus spp.
What is the name if there are two fermentation products and give example
- Heterofermentative
2. e.g., lactate, acetate and ethanol produced by Bifidobacterium spp.
How are pathways named and give examples
- Pathways are named by main product
- E.g. yeast fermentation to produce ethanol is ethanol fermentation
- Lactococus fermentation produces only lactate- homolactic acid fermentation
- Leuconostoc fermentation produced lactate + ethanol + CO2- heterolactic acid fermentation
What is the difference between primary and secondary fermenters
- Sequential fermentation pathways
- Primary- ferment normal molecules
- Secondary – ferment the products of the primary
How can Fermentation produce energy without substrate-level phosphorylation
- Use ion pumps to produce a potential difference
E.g. - Decarboxylation driven ion transport
- Ion-coupled end-product efflux via a symport
Describe how energy can be produced by Ion-coupled end-product efflux via a symport
- Use sodium motive force- atpase runs of sodium gradients
- Or some Generate potential difference with sodium to flow back down the concentration gradient to pump out hydrogen ions to generate second ion gradient and use this to produce ATP
Describe how energy can be produced by Decarboxylation driven ion transport
- Single molecule can decarboxylate to produce 2 molecules- exergonic
- Dicarboxylic acids- remove one carboxylate group
How can a proton motive force be generated if not used to produce ATP
- Fermentation can produce ATP without creating a proton motive force
- Some processes require a proton motive force
- e.g., flagella rotation
- Some strict fermentative bacteria use ATP to run the ATPase in reverse!
What is the basics of photosynthesis
- A process converting light E into biological E which in turn is consumed to fix CO2 into organic compounds
What are the basics of fermentation
- A process converting chemical E into biological E without the use of an external e- acceptor
What are the basics of respiration
- A process converting chemical E into biological E by oxidising organic or inorganic e- donors coupled with the reduction of externally supplied e- acceptors
