biomi2900 quiz 4

Phototrophy

Photosynthesis: using light energy to support biosynthesis
Phototrophs: organisms that use light as an energy source

Photophosphorylation: Light mediated ATP synthesis

Photoautotrophs: use ATP to assimilate C from CO2
Photoheterotrophs: use ATP to assimilate C from organic C

Oxygenic phototrophs: make O2 as waste product
Anoxygenic phototrophs: do not make O2 as a waste product

Photosynthetic pigments

Photosynthesis requires light sensitive photopigments:
Chlorophyll (plants and cyanobacteria)
bacteriochlorophyll (anoxygenic phototrophs)

Accessory pigments absorb light and funnel energy to the reaction center (satellite dish) → diverse pigments!
Reaction centers: contribute to e- transfer reactions → use light to excite e- from low to high redox potential (antenna)
Two types of RC: Type I - Fe-S (stronger), Type II - Quinone type,
all RC are homologous → photosynthesis likely arose once and diversified via gene duplications and HGT

Oxygenic photosynthesis

Oxygenic phototrophs use light E to remove an e- from H2O → generate O2, H2O is the e- donor (its pretty hard to use though because its low on the redox tower, that’s why it evolved much later than anoxygenic)

Reaction centers: both photosystem I and II → forms the z scheme
Generates PMF and NADPH

NADPH used to reduce CO2 for biosynthesis → CO2 is C source and terminal e- acceptor

Like cyanobacteria!

Oxygenic photosynthesis process

H2O → donates 2e- to photosystem II → light excites the e- to higher redox potential (Q-type RC) → Q cycle (alt b/w things that accept e- and H+ and those that only accept e-) → photosystem I → light excites the e- again (FeS type RC) → e- move downhill to reduce NAD+ and make NADPH

noncyclic e- flow generates PMF → drain e- out for growth
Cyclic e- flow can also generate pmf → cycles it back to Q cycle to generate infinite PMF

Anoxygenic photosynthesis

Anoxygenic phototrophs use light E to remove an e- from an e- donor like H2S, S⁰, H2, organic acids, amino acids, Fe2+ → diverse e- donors
Live in habitats that have light but lack O2, have adapted to use diffferent wavelengths of light

Obligate anaerobes typically do not generate O2

Evolved before oxygenic anaerobes

Reaction centers: EITHER photosystem I or II, never both

Cyclic e- flow generates PMF, e- donors need to reduce CO2 for biosynthesis → CO2 often terminal e- acceptor

Sulfur Cycling

1. Sulfate assimilation: nearly all Bacteria and Archaea can assimilate SO₄^2- as a S source

   • SO4^2- → HS in protein

2. Desulfurylation: from breakdown or protein

   • HS in protein → H2S

3. Aerobic H2S/S Oxidation: Chemolithotrophy of H2S/S

   • H2S → S⁰ → SO4^2- (Oxic)

4. Anaerobic S oxidation: Chemolithotrophy of H2S/S, Anoxygenic Phototrophs using H2S/S

   • H2S → S⁰ → SO4^2- (Anoxic)

5. Sulfate Reduction: Anaerobic respiration of SO4²

   • SO4^2- → H2S (Anoxic)

Sulfur facts

S is common in minerals like gypsum and pyrite

NaSO4 is abundant in salt water (28mM)

S is found in proteins (cysteine, methionine)

H2S and S0 is produced by volcanoes

H2S is highly toxic to plants/animals → rotten egg smell + is reacts rapidly with O2 to make H2SO4

From most reduced to most oxidized (lowest to highest oxidation state):
HS in protein, H2S (HS-), FeS (-2) → S⁰ → SO4^2- (+6)

Sulfate reducing bacteria

Chemolithoautotrophs and chemoorganoheterotrophs
Obligate anaerobes that reduce sulfate (SO4^2-) to sulfide (H2S)

e- donor: H2 (Litho); Lactate or acetate (organo)
e- acceptor: SO4^2- → anaerobic respiration
Carbon source: CO2 (autotroph) or organic C (heterotroph)
Habitat: anoxic environments that have SO4^2-

Sulfide Oxidizing bacteria

Chemolithoautotrophs → facultative anaerobes that oxidize H2S or S0

e- donor: H2S, S0, FeS, other reduced forms of S
e- acceptor: O2, NO3- (aerobic or anaerobic respiration)
C source: CO2
Habitat: anywhere reduced forms of S and O2 mix → like overlaying sulfidic marine sediments or S-containing minerals exposed to O2

Also responsible for bioleaching of minerals, acid mine drainage, corrosion → by converting H2S + 2O2 → H2SO4, important in mining to convert minerals into soluble form and then collect the leachate

Metal respiration

Microbes can respire using metals as e- donors or acceptors

If they are insoluble in their oxidized form, they will be soluble in their reduced form, and vice versa

e- donors can be H2, or organic C
e- acceptors can be O2, or NO3- for Fe

Iron reducing bacteria

phylogenetically diverse
Chemoorganoheterotrophs
Obligate or facultative anaerobes that reduce Fe3+ to Fe2+

e- donor: organic compounds, H2
e- acceptors: Fe-oxides, Mn-oxides, other metal oxides
C sources: organic carbon
Habitat: anoxic habitats containing reduced metals → sediments, subsurface, groundwater

Metal reducing bacteria often use nanowires: electrically conductive protein filaments (pili or fimbrae) that conduct e- to e- acceptors outside the cell → reduces iron oxide minerals outside of the cell

Iron oxidizing bacteria

phylogenetically diverse
Chemolithoautotrophs or heterotrophs, typically
can be aerobic or anaerobic

e- donor: reduced Fe
e- acceptor: O2 or NO3-
C source: CO2 or organic C
Habitat: seeps and sediments where reduced Fe is present along with O2 or NO3-

Must oxidize the metal outside the cell and avoid becoming entrapped → often make sheaths made of metal → produce slimy goop

General characteristics of biosynthetic reactions

Require E in the form of ATP

Require reducing power → NADH/NADPH, Ferredoxin (Fd), etc.

Catabolic reactions are often reversible at the expense of E

Pathways are modular

Many pathways use universal precursors from glycolysis, Citrica acid cycle, or pentose phosphate pathway → core building blocks every organism must produce to synthesize amino acids, nucleotides, lipids, and sugars necessary for life

Anabolic reactions are highly conserved but not universal

Carbon assimilation differs between organisms

Heterotrophs: Get C for anabolic rxns from organic molecules
Autotrophs: Get C for anabolic reactions from CO2 Fixation → anabolic process, needs ATP and reducing power, but some microbes can use it as both a C source and e- acceptor

Nitrogen assimilation

N can be assimilated in several different forms with organisms using the N source that requires the least expenditure of E

Inorganic N: NH4+, NO3- → plants, most Bacteria and Archaea
Organic N: protein → animals, many bacteria and archaea
Atmospheric N: N2 fixation → many bacteria and archaea

Autotrophic pathways

Autotrophs can get C for biosynthesis from CO2 in air by fixing it:
There are 6 pathways, but the ones we care about are the Calvin cycle, Reverse Citric Acid Cycle, and Reductive Acetyl-coenzyme A pathway

Calvin cycle

used by most photolithoautotrophs and chemolithoautotrophs to fix CO2 for biosynthesis, most tolerant pathway to O2

3ATP + 2NADH required per CO2 reduced → requires the most E
6 molecules of CO2 are required to make 1 molecule of glucose

Key enzyme = RuBisCO → ribulose biphosphate carboxylase

Reverse Citric Acid Cycle

Used by diverse anaerobes, microaerophiles, and anoxygenic phototrophs to fix CO2 for biosynthesis → anaerobic autotrophs

Uses ATP and NADH/NADPH to run citric acid cycle and glycolysis backwards → 1.66 ATP + 1.33 Fd_red + 1.33 NAD(P)H per CO2 reduced

Most enzymes in citric acid cycle and glycolysis are reversible, but 3 are replaced → succinate dehydrogenase, alpha-ketoglutarate dehydrogenase, citrate synthase

Requires Ferredoxin for reducing power (Fd_red) → intolerant to O2, so this is inhibited by O2

Reductive Acetyl-CoA pathway

Used by strict anaerobes like methanogens and acetogens that are able to metabolize C1 compounds and use H2 and CO2 to fix CO2 for biosynthesis

Requires the least E → 1.33 ATP + Fd_red + 1NAD(P)H

Key enzyme: Carbon monoxide Dehydrogenase → intolerant to O2, so this pathway is inhibited by O2

Was likely present in the first cells

Only CO2 fixation pathway that can also be used in catabolism, with H2 as e- donor

Nitrogen N2 fixation

Nitrogen fixing organisms like diazotrophs get N for biosynthesis from N2 in the air by fixing it

Uses the key enzyme Nitrogenase, which is inhibited by O2, and repressed by NH4+ → an ancient enzyme, HGT common, found in diverse microbes

An assimilatory reaction that requires a lot of energy and reducing power (e-) → 16ATP per N2
Process Under tight regulation

Prior to Haber-Bosch this was the main source of ‘fixed N’ in the biosphere, today provides about ½ the worlds N-budget

Nitrogen uptake

Nearly all miroorganisms can assimilate ammonia (NH3)/ammonium NH4+

NH3 is incorporated by glutamate dehydrogenase or glutamine synthetase

Biosynthesis of amino acids

Carbon skeletons for amino acids come from intermediates of glycolysis or the citric acid cycle. The amino group will then be transferred from glutamate or aspartate

Essential amino acids
Plants and most microbes can synthesize all amino acids
But some microbes and most animals (like us) cannot synthesize them all → humans can’t make 9 essential amino acids → it is important to get a varied diet, we can get all essential AA from meat usually

Features of biogeochemical cycles

each step is mediated by a set of organisms

Cycling replenishes reactants over time

Cycling couples the oxidation and reduction of reactants, and this typically requires coupling of aerobic and anaerobic processes

Steps can be driven by assimilatory or dissimilatory processes
Assimilatory: molecule is assimilated into biomass → anabolic reactions
Dissimilatory: molecule is transformed but not assimilated → catabolic

Nitrogen oxidation states

Oxidized
Nitrate: NO₃^- (+5)
Nitrite: NO₂^- (+3)
Nitrous Oxide: N2O (+1)
Dinitrogen: N2 (0)
Ammonia/Ammonium: NH3/NH4+ (-3)
Reduced

Plants and animals in the nitrogen cycle

Have limited roles
Animals:
Organic N (protein) → organic N (protein, urea), NH4+
Assimilation, ammonification

Plants:
NO₃^- or NH4+ → Organic N (protein)
assimilation

Microbes also do these processes

Rhizobia

Aerobic chemoorganoheterotophs
N2 fixing symbionts of legumes
Microbes provide N to plant
Plant provides: C and E source, a home, leghemoglobin (contains iron to regulate O2, gives just enough O2 to the bacteria)

Nitrification

NH3 → NO₂^- → NO₃^-
one by Bacterial phyla: proteobacteria, nitrospira
Archaeal Phyla: thaumarchaeota

Metabolism: chemolithoautotrophs, obligate aerobes
Key enzyme: ammonia monooxygenase (AmoA) → replaces complex 1 in e- transport chain
e- donor: NH4+ or NO₂^-
e- acceptor: O2
C source: CO2 (autotrophic)
Habitat: widespread in oxic soil and aquatic habitats
Uses reverse e- transport to make NADH for assimilation and anabolic

Ammonia oxidizers:
2NH3 + 3O2 → 2NO₂^- + 2H2O + 2H+
Overall: NH3 → NO2

Nitrite oxidizers:
2NO₂^- + O2 → 2NO₃^-

Denitrification

Reductive pathway: NO₃^- → NO₂^- → NO, N2O → N2
done by phylogenetically diverse microbes

Metabolism: chemoorganoheterotrophs, facultative anaerobes (typically)
e- donors: organic C typically → NADH formed using e- from e- donor
e- acceptors: NO₃^-, NO₂^-
C source: organic C
Habitat: widespread anoxic soil and anoxic habitats
Return N to the atmosphere as N2 or N2O gas

Fish tank nitrogen cycle

organic C (food) → FISH or decomposing matter→ ammonium (NH4+) → microbes make Nitrites NO₂^- → Nitrates NO₃^- → Water changes

first ammonium fixing microbes increase, then nitrite, then nitrate → and then you basically only measure nitrate cause after a long time the process will be faster

Agriculture N-cycle

Haber Bosch process: chemical fixation of N2 into NH3 → used to make fertilizer, requires lots of natural gas for E
Increased human input of NH3 into biosphere to support growing pop with food

N in fertilizer is mostly NH4+
Nitrifiers convert NH4+ to NO₃^- → NO₃^- moves with H2O in runoff → eutrophication
Denitrifiers convert NO₃^- into N₂O and N2 gasses → N2O a powerful GHG, more powerful than CO2 + promotes acid rain (BOOOO)

Eutrophication: lots of nutrients (N or P runoff) → algae bloom → they die and decay → O2 is used up → anoxic dead zone, fish dead

Carbon cycle

Oxic:
CO2 fixation (reductive): CO2 → (CH2O)n/organic matter via oxygenic photosynthesis or chemolithotrophy
Decomposition (oxidative): (CH2O)n/organic matter → CO2 via aerobic respiration

Anoxic:
CO2 fixation (reductive): CO2 → (CH2O)n/organic matter via chemolithotrophy, acetogenesis, anoxygenic photosynthesis
Decomposition (oxidative): (CH2O)n/organic matter via anaerobic respiration and fermentation

Generally earth balances fixation with decomposition, but there is nothing to balance our human input

Decomposition

breakdown of dead biomass (organic carbon, (CH2O)n)
Organic C is oxidized to CO2
Releases nutrients (N, P, S, etc)
Mediated by chemo organo heterotrophs through aerobic respiration, anaerobic respiration, fermentation
Anaerobic respiration couples the C-cycle to other biogeochemical cycles

Human CO2 measurements

Mauna Loa: continuous CO2 measurement → fluctuation = coupling
More land in N hemisphere → in winter C increases, when plant blooms C decreases

Keeling curve

Ice core data: big fluctuations of CO2 when glaciers come and go

Composting

aerating plant matter to promote decomposition → turns waste to resource (nutrients)

Helps alleviate C cycle and excess C

Made in piles, to produce convection (circulation of heat) → hot air goes up, brings in cold O2, maximizes growth

Dont want the pile too heavy, wet, or big
Turn pile to mix so all microbes get the food

Wastewater treatment

Aerate (bubble O2) the waste to promote decomposition in water
Very important to prevent H2O borne diseases

Goals: eliminate pathogens, reduce biological oxygen demand (reduce organic C content, measured by how quickly O2 decreases), remove nutrients and contaminants

Stages:
Primary treatment (physical) - screens, sedimentation
Secondary treatment (biological) - activated sludge (aeration), anaerobic digestion
→ Anaerobic digestion: anaerobic respiration, fermentation, denitrification, methanogenesis
→ aeration: aerobic respiration, nitrification
Tertiary treatment (chemical) - chlorination, UV, chemical flocculation

Anoxic habitats

Found anywhere there is stagnant water and microbial O2 consumption
Even 100 microns of water is enough to produce one

Ex: anaerobic digestion, gut communities, wet soil, wetlands and sediments

Anaerobic food webs

Complex polymers (cellulose, proteins, lipids, nucleic acids) → monomers (sugars, amino acids, fatty acids) via fermentation and respiration → Volatile fatty acids (propionate, butyrate, succinate), H2 + CO2, or acetate by fermentation

Volatile fatty acids can be made into H2 + CO2 or acetate via syntrophs
H2 + CO2 can be made into acetate be acetogens

Methanogens convert H2 + CO2 to CH4 or acetate to CH4 + CO2

Syntrophs

Volatile fatty acids → H2 + CO2
Volatile fatty acids → acetate

Carry out fermentation reactions → energetically unfavorable under standard conditions
Reactions are made favorable by consumption of H2 or acetate by other organisms → rely on methanogens → they gotta eat together!!

Methanogens

4H2 + CO2 → CH4 + 2H2O
Acetate → CH4 + CO2
Basically turn H2 or acetate into methane

Chemo litho autotrophs or chemo organo heterotrophs, ogblicate anaerobes

e- donor: H2 and/or acetate
C source: CO2 and/or acetate
Habitats: wetlands, sediments, gut

Methane budget

Sources:
Mostly from methanogens in (most to least) man made rice paddies, natural wetlands, animal agriculture (cow burps)
Fossil fuels
Geological sources

Net Methane sinks (most to least)
Atmospheric reactions, methanotrophs, yearly buildup in atmosphere

Aerobic methanotrophs

consume methane and turn it into CO2
CH4 + 2O2 → CO2 + 2H2O

Chemo organo heterotrophs, obligate aerobes

e- donor: CH4
e- acceptor: O2
C source: CH4
Habitats: anoxic/oxic interface of freshwater habitats and soils

We got a methane feedback loops where if global warming melts norhtern permafrosts, they will become wetlands that emit lots of CH4 → exacerbates warming

Enceladus

one of saturns moons that has all of the essential things for life

Plume contains:

silicate, H2, N, CH4, CO2,

organics (up to 200 MW)

Silicate minerals indicate:

-liquid water, pH 8.5 – 10.5

-salinity 0.5% - 4%

-hydrothermal activity

-conditions compatible with

serpentinization reactions

(can yield H2, Fe3+ and Mn4+)

How do we know about the origin of life?

Direct evidence available from rocks, minerals, and fossils
→ Isotopic ratios of O and C in minerals (<4.4 bya)
→ Isotopic ratios and mineral composition of rocks (<4.0 bya)
→ Fossil evidence (3.5 - 4.28 bya)

Inference from experimentation and comparative biology
→ experiments that demonstrate abiotic formation of organic moleules
→ comparison of structure and sequences from living organisms

Early earth and solar system

Big bang 13.8 bya → solar system and earth forms 4.6 bya

Early earth is anoxic, boiling hot, and sterile → since anoxic, minerals on early earth are reduced

Earth lacks ozone layer → UV light sterilizes Earth’s surface

As Earth cools, water vapor becomes liquid, O isotopic ratios in ancient zircon minerals indicate oceans are present ~4.3 bya

Oceans full of reduced iron (Fe²⁺) and H2S
Very little organic carbon, most N is in form of N2 → first cells would be chemolithoautotrophs that used H2 and CO2

H2 and H2S from volcanism

Prebiotic chemistry

Life started in hydrothermal vents → pores strongly concentrated chemicals/minerals → form awaruite (nickle-iron mineral) at vents → allows H2 + CO2 to react to form organics like acetate that form the building blocks for life (amino acids, nucleosides, sugars)

These reactions form the reductive acetyl-CoA pathway → CO dehydrogenase requires Ni, which was used by first cells

How did cells form

Prebiotic chemistry → precellular life → Early cellular life → LUCA → evolutionary diversification

Precellular life

From earliest to latest:

RNA World: catalytic RNA that carry out reactions, self replicating RNA

Protein synthesis: RNA-templated translation

DNA: replication, transcription allows for regulation

DNA replication, transcription, and translation are conserved in all cells

Early cellular life + LUCA

Early cell life: Lipid bilayers form → leads to cellular compartmentalization, early cells like had high HGT rates
Phospholipid bilayers, ion motive force, ATP synthetase conserved in all cells

LUCA: last universal common ancestor of all cellular life
Was an acetogen, anaerobic, used reductive acetyle CoA pathway, can be fermentative or respiratory, can use either H2 + CO2 or organics
Common within tree of life
H2 + CO2 → acetate
4.3 - 3.8 bya

Evolutionary diversification

Divergence of bacteria and Archaea:
Components of DNA replication, transcription, and translation all in place
Diverged from LUCA, a prokaryote
Archaea eventually split off into eukarya

After LUCA

LUCA → anoxygenic photosynthesis → early stromatolites → oxygenic photosynthesis → great oxidation event → early multicellular eukaryotes → ozone shield → O2 at current levels, cambrian explosion (now we can support multicellular organisms real good) → plants → dinosaurs → mammals

before oxidation

Anoxygenic photosynthesis originally occurred in the deep dark ocean → E came from infrared light to excite e- in H2S

Stromatolites → microbes grow on surfaces, results in layered rocks

after oxidation

Oxygenic photosynthesis: O2 production causes O2 to increase over time and minerals are oxidized

Causes great oxidation event
Iron oxidizing bacteria form banded iron formations → rust from iron ox bacteria

Origin of Eukarya

Eukarya are genetic chimera derived from archaea and bacteria

DNA replication, transcription, translation related to archaea

Fatty acid lipids, central metabolism, mitochondria and chloroplasts related to or derived from bacteria

Endosymbiosis theory

Endosymbiosis theory: Chloroplasts and mitochondria derived from ancient prokaryotic cells that were engulfed by ancestors of modern eukaryotic cells
→ we know this because mitochondria and chloroplasts have their own DNA and genomes and their sequences are bacterial

Eukaryotic nuclei also have genes derived from bacteria

Darwinian Evolution

Variations between organisms arise naturally and resources are limited (finite carrying capacity) → the most successful individuals have more offspring, are more fit = natural selection

Over time, individuals will evolve to have greater fitness in a given environment, resulting in a hierarchical pattern of groups within groups → an evolutionary tree!

Evolution and genetic variation

A change in gene (or allele) frequency in a population over time resulting in descent with modification

Genetic variation caused by mutations and recombination (gene rearrangements or HGT)
HGT is a special case of recombination where the DNA comes from another organism

Changes in gene/allele frequency is caused by selection (fitter individuals make more babies, which contribute to more of their genes) and genetic drift (random, not selection, like a natural disaster)

Phylogeny

Evolutionary history, like the origins of phyla
Phylogenetic trees allow us to make predictions about relationships between organisms

Similarity = shared characterisitcs
Homology = genes that come from a shared ancestor
Orthologous = homologous genes with shared function
Paralogous = homologous genes with different functions, resulting from gene duplication

Molecular phylogeny relies on examination of orthologous genes

Problems of microbial phylogeny

No fossil record, few morphological differences, most bacteria are difficult to grow and characterize
Due to HGT and convergent evolution, morphology and physiology are poor predictors of phylogeny

So we rely on molecular sequences (proposed by Zuckerkandl and Pauling) → because morphology is misleading, sequences provide lots of data, and we are able to compare dissimilar organisms as long as they share genes

Molecular sequences record evolution by showing us the random accumulation of mutations over time

Making a phylogenetic tree

Align sequences you are studying → make a distance matrix by calculating the number of sequence differences between each sequence → make tree, add nodes to join lineages that have the fewest differences (1 node = the part that splits = 1 difference)

Unrooted trees: show similarities and relationships between current lineages that are still alive
Rooted trees: demonstrate deep ancestral roots, indicates a shared common ancestor between the lineages (the root)

What do we use to infer phylogeny and why?

Woese discovered archaea by analyzing rRNA → proved molecular phylogeny is real!! a universal tree of life is reconstructed

16s rRNA is used because it is found in all cellular life, it has a very slow rate of evolution, conserved function (orthologous), low probability of HGT

The steps before making the tree

Extract DNA from environmental sample → make copies of rRNA genes by PCR (Mullis) → isolate individual DNA molecules from DNA mixture, make copies of each, sequence copies (Sanger!) → Analyze sequence → generate tree

Pace: developed approach using rRNA genes to study microbial diversity

Why traits of organisms do not match phylogeny predicted by 16S rRNA genes?

Gene loss → deletion → if the ancestors are dead then we no longer can see their connection, hard to compare the different branches now because they are no longer similar

Convergent evolution: non-homologous genes that evolved multiple times independently, resulting in species that lack a common ancestor having similar traits

HGT → one gene may pass to other guys, very complicated stuff
Genes may have different evolutionary histories and trees than the cell itself
80 universally conserved orthologous genes present in all cells → support rRNA tree of life

Microbial genomes

Core genome: those genes shared by nearly all strains of a species (size varies but typically 20-60% of a genome belongs to the core)

Pan genome: the set of all genes found in all strains of a species

Auxiliary genome: non-essential genes shared by some subset of strains (also called the Accessory genome or Dispensable genome) = pan genome - core genome