Evolution of microbial life Flashcards
what are the 3 types of primary nutritional categories?
- photo-organo-autrotroph
- photo-litho-heterotroph
- chemo-organo-autotroph
Why is the calvin cycle common in aerobes?
- common in aerobic autotrophs despite RuBiscCO being sensitive to O2
- requires 12 NADPH and 18ATP to reduce 6 CO2 to 1 glucose: LOT’S OF ENERGY
what type of microbes use the calvin cycle?
organisms that have a high energy yield from chemo- or photo-lithotrophy
best energy yield for chemolithotroph?
using what as TEA/pathway
using O2 as terminal electron acceptor
best energy yield for photolithotroph
using what pathway?
oxygenic Z pathway
Explain the earth’s early history:
-atmosphere
- what kind of trophes would we see rn?
- where would the living world be
- Atmosphere had no oxygen
- The exact composition is up for debate
- Most gases are coming from volcanic and geothermal activity.
- There is an abundance of metals, acting as an abundance of metals.
- There was no ozone (no oxygen), therefore no protection to UV.
○ Life probably would not be on the surface of the planet, therefore there was subsurface organisms that were not exposed to the light§ Likely an autotroph.
what is the Miller-Urey experiment?
when energy is added, organic compounds can be formed.
- if you keep cycling the gasses around and give constant energy to primordial soup , organic compounds can be formed (prebiotics). `
How do we take the prebiotic molecules (organic molecules) and condensing them in one place where a cell would be?
- Early organic molecules would be floating freely when primordial soup gets zapped with energy
- Macro-macromolecule interactions are more favourable than macromolecule-water interactions,
○ Under the right conditions, macromolecules will prefer to associate with one another than with water
§ Leads to liquid-liquid phase separation
○ You’ll get clumps of macromolecules separate from the water.
Under microscope, kind of looks like cells.
- Macro-macromolecule interactions are more favourable than macromolecule-water interactions,
How are coacervates built and broken down?
- If you add more nutrients, the coacervates get bigger.
- When you apply a shear stress (movement of water, tides, in the ocean)…
○ The coacervates divide into smaller bits
○ You add nutrients and they get big again, they shear into small bits again, etc. - Based on physical processes only, we can see growth and division of coacervates.
- When you apply a shear stress (movement of water, tides, in the ocean)…
why would metabolism evolve?
- When you think about early earth and prebiotic soup, there was probably a limited supply of spontaneously formed molecules.
- The protocell figured out how it can make more of these molecules by itself so that it can have an advantage compared to other things in the environment, because if you need something and it is limited in the environment, if you make it yourself then you will no longer run out and you can keep living.
what is LUCA
LUCA: the last common ancestor among bacteria and eukaryota/archaea
What are the 2 criteria for including proteins in LUCA?
- Present in at least two higher taxa of bacteria and archaea
- Its tree must recover bacterial and archaeal monophyly
What is LUCA like then?
- LUCA has a membrane
- It will acquire carbon from Wood-Ljungdahl pathway for a source of carbon
- With our understanding of the carbon source… we know that LUCA has enzymes (CoA and Acetyl-Coa) for the Wood-Ljungdahl pathway.
- Took nitrogen gas for biosynthesis
- LUCA had DNA.
- Cofactors are there to help store the oxygen
- Energy: acetyl-phosphate (like ATP) that came from membrane bound ATP synthase.
LUCA is run on s
Evidence that hydrothermal vents are a good source for life
Spontaneous thioester synthesis (common bond in biological molecules)
- H2 is abundant (for the Wood-Ljundhal pathway)
- Environment is acidic, so natural PMF
- Salt water (so you get this sodium proton system)
○ Get energy from bringing Na+ in, and then you send sodium out and proton in
§ Forming a natural PMF.
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criteria for including proteins in LUCA (2)
- Present in at least two higher taxa of bacteria and archaea respectively
- Its tree must recover bacterial and archaea monophyly
Why is there no evidence for metabolic pathways in LUCA?
- The Wood Ljungdahl pathway produces acetyl-CoA, so we don’t really need catabolic pathways to break down larger carbon molecules
- What we think of today as catabolic pathways likely evolved in reverse
- LUCA would synthesize acetyl-CoA and the cell eventually had to find a way to store the acetyl-CoA as a carbon storage (which is modernly known as catabolic pathways to build up thinks like glucose, sugars, etc.).
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Which three of the metabolic pathways might have evolved first?
- Start with little energy
Lower energy options for catabolism is: ED
What are the three true catabolic pathways:
EMP, ED, PPP
What is a problem with genome-based reconstruction?
- Horizontal gene transfer
- It is more likely that rather than one super cell that we all came from, LUCA as we think about it was likely a community of cells exchanging ATP, metabolites, etc and this community essentially evolved into life as we know it.
Not one super cell!
- It is more likely that rather than one super cell that we all came from, LUCA as we think about it was likely a community of cells exchanging ATP, metabolites, etc and this community essentially evolved into life as we know it.
LUCA might be the last universal ancestor of all organisms, but because of HGT
It is not the last ancestor of all genes.
At some point, the early community of cells needed to separate into archaea and bacteria domains.
How were bacteria and archaea hypothesized to differentiate into two domains?
- Wood-Ljungdahl pathway produces acetate, but a small change will cause it to produce methane rather than acetate.
- If you just swap a few enzymes, methane can be made from the WL pathway
- So some community of cells made acetyl-CoA and some made methane (Archaea)
- Therefore, we have distinguished archaea and bacteria
How are stromatolites formed?
- cyanobacteria grow in a mat or biofilm, creating a layer of cells
- sediments deposit on top of the biofilm (biofilms are sticky) and/or cells cause minerals to precipitate, creating a layer of sediment
- cells migrate to the surface of the sediments for better access to sunlight, creating a new layer of cells
- the process continues indefinitely…
Explain banded iron formations:
- Increase in iron, decrease in iron, cycling
- Dark bands form from iron deposition
- The light bands’ form from non-iron mineral deposition
Oxygenic photosynthesis evolved before cells evolved mechanisms for oxygen tolerance.
What does banded iron formations tell us?
That oxygenic photosynthesis evolved before cells evolved mechanisms for oxygen tolerance.
Do stromatolites still roam the earth?
They still form in a select few places but are very uncommon.
Do banded iron formations still roam the earth?
No because we have an oxygen rich environment and iron is not rich in the ocean to produce enough solid layers of rock.
but there are still some stromatolites.
What is the great oxidation event?
- When the atmosphere went from very little oxygen to lot’s of oxygen
- This was 2.2 billion years ago
- Oxygen slowly accumulated and was neutralized by iron in the ocean for 1 billion years
But life evolved to use it once it became available.
Where did eukaryotes come from?
- Endosymbiosis theory
- Eukaryotes arose when a pre-eukaryote engulfed a bacterial endosymbiont, which became the mitochondrion.
- Driven by bioenergetics and survival necessity : O2 concentrations were increasing globally, a heterotrophic anaerobe engulfed an aerobic bacterium.
One lineage of eukarotes later engulfed a cyanobacteria, which became the chloroplast.
what archaeon swallowed the bacteria? and why?
asgard archaea
carry many eukaryotic signature proteins (ESPs)
Why is the eukaryotic cell line metabolically limited?
- Because eukaryotes arose from one archaeal group that engulfed ONE bacterial group (or two for chloroplasts)
Therefore, their metabolism is limited
