Geochemie

Zusammenleben von Organismen

Keine wesentliche Effekte

für beide Beteiligten vorteilhafte Beziehung zwischen zwei Arten

für eine oder mehrere Organismen schädliche Beziehung

• Mycorrhiza: Pflanzen liefern Pilzpartner mit fotosynthetischen Produkten & Fungi hilft Phosphor aus Boden zu extrahieren

• Menschliches Mikrobiom: Grösster Teil im Magen-Darm-Trakt (~ 10 billion mikrobiellen Zellen), die durch die Verdaaung von Ballaststoffen Nährstoffe und Vitamine produzieren

• Fluoreszierende bakterien liefern Schutz für Tintenfisch

Interaktion zwischen Organismen und deren Umwelt

Beziehung zwischen zwei Arten zum Nutzen der einen Art und zu Lasten der anderen

Masse Kohlenstoff (550 billionen Tonnen)

• 82% Pflanzen

• 13% Bakterien

• 5% Andere Organismen (Tiere, Fungi,…)

  Terrestrial grösste Biomasse

1. Energy conversion

2. Information storage and replication

3. Ability to evolve

• Age Earth: 457 billion years

  -> planet believed to have formed out of dust particles & hydrogen gas => made up a disk-shaped solar nebula swirling aroung its center (prot-Sun)

  -> Eventually formed larger bodies through accretion (collision andmerging)

• First life forms:

  -> single cells without compartments (-> exlusively prokariotic)

  -> during these times all kinds of meatbolic capabilities were evolved to harness energy

  -> Oxygenic Photosynthesis led over millions of years to accumulation of =2 in atmosphere => starting revolution in atmospheric chemistry

• GREAT OXIDATION EVENT: 2.4 billion years ago

  -> completely changed appearance of our planet: Atmospheric O2 reacted to yield ozone shield & oritext surface form radioactive cosmic rays

• First Eukaryotic Life forms: ~ 2 billions years ago

• Complex multicellular eukaryotes: ~ 0.5 billion years ago (=500 million)

• Modern humans: 100’000 years ago

• Viel O2 im Ozon gelöst

• Viel Eisen, welches zuerst oxidiert wurde

Bakterien und Archae (3.8 b. years ago)

• unseen majority => 10^30 -> most numerous organisms

(Viruses outnumber biomass of bacteria BUT are not considere living organisms)

The total energy in an isolated system remains constant.

-> ex. Physical exercise: chemical energy (food) -> mechanical energy (motion) + heat energy (you feel warmer)

System naturally move towards more disorder (higher entropy)

-> ex. tidy room rends to get messy over time

BUT:

unlike isolated system, living organisms stay ordered by taking in energy from their environsment. If they can’t get or use this energy they become disordered and die (ex. plant dies without sunlight)

• Energy coupling: Living organisms link energy-release (exergonic) reaction with energy requiring (endergonic) one to maintain oder and stay alive

Require energy and move towards more order

ex. burning wood: reacts with oxagen releasing energy in form of heat and light

Require energy to create order

ex. photosyntehsis: Plants require energy (sunlight) to make glucose and oxygen

1. metabolism, RNA, DNA, replication, protein synthesis

2. Oxygenic -> O2 release as byproduct & anoxygenic

3. Complex cells

4. new mechanisms of reproduction; one organism out of two cells

5. Cellular specialization, new trophic levels in food chain

=> Incomplete understanding of major transisions and key events (like origin of life or genesis of eukariotic cell)

1. Land plants, animals, humans

• Antoni van Leeuwenhoek (1632-1723): Invented microscopes -> “father of microbiology” & observed protists (and bacteria)

• Robert Koch (1843-1920): Pure culture of microorganisms

• Martinus Beijerinck (1851-1931): Enrichment cultures: Bacteria isolation from (selective) natural samples by manipuating nutrient & incubation conditions

  -> revealed the presence of Archaea & Bacteria as distinct beings!

• Carl Linneaus (1736):

  -> 2 Kingdoms (plants and animals

  formalised binomial nomenclature (still used)

  believed that living beings were unchangeable => NO EVOLUTION

-> Evolutionary Theory with Means of natural selection

• *Major drivers of evolution

  • Mutation

  • Horizontal gene transfer / recombination (meiosis)

    => genetic variation

  • Natural selection (treibende Kraft, nicht zufällig)

  • Genetic (*bottle necks) drift (random loss of sequence)

    => sorting genetic variation

Darwin

1. Descent with modification

2. common descent

3. graduation

4. multiplication of species

5. natural Selection

1. Genome is structured like mosaic: Bacteria and Archaea frequently exhange genes in process called horizontal gene transer!

2. Eukarya are more closely related to Archaea but also clearly related to Bacteria: Eukarya are chimeric (= composed of 2 different organisms)

Woes tree (1990):

• 3 domains (bacteria, Archaea, Eukarya)

• Logic: Assumption that mutations rate is constant, so divergence between sequences of shared gene in vairous can be used as molecular clock.

  • ex. more differences in rRNA sequences -> diverged longer ago

    Woese used genetic sequences of ribosomal RNA (rRNA) as phylogenetic marker to reconstruct molecular tree of life

    -> Why rRNA?:

    • existed in LUCA -> univerally distributed

    • fulfill essential functions -> highly conserved

    
    

Endosymbiotic origin of eukaryotes (1967)

-> (1) mitochondria descend from aerobic respiring bacteri which were incorporated into an archaeon

-> (2) Chloroplast are result of incorporation of canobacterium into eucaryotic cell

! Endosymbiosis solves contradictions how enkaryotes are of chimeric nature (with different genes most closely related to either bacteria or archaea) but still have monophyletic (one common ancestor and all descendent) origin. !

Theory of Symbiogenesis (1910)

=> Eukaryotic cell result of sybmbiotic relationships

• 80% Water

• 20% Dry Weight

  • 55% Protein

  • 20% RNA

  • 9% Lipids

• Before was thought tha life arrives from non-living matter

SWAN-FLASK-EXPERIMENT:

1. Swan-flask filled with broth (nonsterile)

2. sterilzed with heat

3. waited to cool down

   a) shape of flask allows air to enter but NO DUST AND MICROORGANISM:

   => no formation of bacteria; Liquid remains sterile

   b) Flask is gently tipped

   => Liquid produes smell / different color

=> ALL LIFE IS FROM LIFE!

Additions:

• Sterilization by heat (Pasteurisation)

• Discovery that living beings could discrimination between optical isomeres => Importance of molecular shapes ind biological interactions

• Discovery that fermentation was a biological (not just chemical) process

• Development of vaccines for anthrax, cholera and rabies

  -> Discovery of when germs (bacteria, viruses) were weakened before injected into animals they would get sick but not die. When again infected with strong germs they stayed healthy!

  =>DESIGN VACCINES BY WEAKENING GERMS IN LAB

1. Start: One DNA molecule

2. DNA Replciation starts: cell begins to copy DNA at origin

3. DNA Replication ends: cells ends copying DNA before it divides

4. Cell Division: One DNA copy goes into each daughter cell

Results: 1 DNA molecule in cell

1. Start: One DNA molecule

2. DNA Replication begins: cell begins to copy DNA at origin

3. Before finishing first copy: cell starts again to copy DNA at the same origin

   • two replication forks at the same time

     -> one still finishing one copy

     -> the other starting a new copy

Results:

2 DNA molecules per cell (one nearly finished; the other starting)

=> FASTER

1. Phyisical compartmentation: Barriers separating environsments with different levels of entropy

   • ex. Membranes

2. Source of Energy: preventing thermodynic equilibrium (Equilibrium = death) -> source of energy to drive reactions

   • ex. lightning/volcaninc heat (like Miller-Urey-Experimetn) or Hydrothermal vents (alkaline vents like “lost city”)

3. Antibiotic polymerisation of monomeric units: Building block (amino acids, nucleotides) must link into chains (Proteins, RNA)

   • ex. Hydrothermal vents: Heat and pressure promote polymerization (e.g., fatty acids → membranes)

4. Cazalyzers: promotisch abiotic synthessi of small organic molecules (speed up process without enzymes)

   • ZnS (zincsulfide): helps form sugar from formaldehyde under UV-light

5. Accumulation of organic molecules (high concentration) to establish metabolic networks (enabling reactions)

   • ex. Hydrothermal Vents: Tiny pores in vent minerals trap and concentrate organics, allowing polymers to form and interact.

6. Continues disposal of waste by-products, for pre-biotoic (=before emergence of life) system to not reach equilibrium

   • ex. Geothermal Cycling: Heat breaks down waste polymeres, freeing monomeres for reuse

1. Phase 1 (molecule Formation)

   • Volcanic gases (CO2, H2, NH3) react in icy meltwater, forming amino acids an nucleotides

   • UV light and metal ions drive further synthesis

2. Phase 2 (Polymerization & Compartmentation)

   • Freze-thaw cycles concetrate and polymerize molecules into RNA and peptides

   • Lipid membranes form around these polymers, creating protocells

3. Pahse 3 (metabolic Network)

   • RNA strands begin selp-replciating inside protocells

   • SImple petide enyzmes assist in energy harvestint (e.g.m proton gradients)

4. Phase 4 (Early Life)

   • Protocell with self-replicating RNA and peptide catalysts becomes the first “living” system

   • Natural selection favors more efficient replicators

=> Metabolism-First and RNA-World Hypothesis

• Bottom up: Studying geochemical processes and deriving scenarios contributing to the formation of more and more comples systems

  • ex. “lost city” -> begins abiotic geology/chemistry and builds towards biology

• Top down: comparing todays diversity and trying to find their common roots

  • ex. LUCA -> begins with existing life and traces back to minimal ancestors

• inorganic molecules in anoxic atmosphere (CO2, NH3, H2,…)

• reacted with each other (by slow process of molecule evolution)

• created more and more complex organic molecules which accumulated in the primitive oceans

• simulation of natural lightnigh in reducing atmosphere (CH4, NH3, H2, H2O) transformed to organic molecules like amino acids

  -> Confirming “Primordial Soup” Hypothesis

PROBLEMS:

1. Earth’s atmosphere less reducing and contain different mixture of gases (CO2, N2, H2o and only traces of H2) than used in experiment

2. Amino acids formed were 50/50 left- and right-handed molecules, living beings all live on homochiral molecules (exclusively left-handed aminos acids)

3. Electric lightnigh can’t serve as source of energy to keep pre-biotic system far from thermodynamic equilibrium

• Hypothesis where pre-biotic chemistry already produced large amounts of organic molecules which had starte to form more complex structures (like polymeres)

• First form of pre-biotoic self-replicating structure composed of auto-catalytic RNA molecules

  • able to store information

  • able to catalyze checmical reactions (like their own synthesis)

  -> Proteins eventually replaced RNA as catalysts

  -> DNA became genome and template

• Viruses may have evolved from RNA genome-like structure

Key Evidence:

• Ribozymes: RNA molecules that can catalyze reactions

• RNA’s Dual Role: RNA can do both, store information and perform catalysis

• Prebiotic Chemistry: RNA nucleotides can form under plausible early Earth conditions (though controversial)

Challenges:

• Prebiotic Synthesis: RNA is complex and unstable -> how could have formed spontaniously

• Limited Catalytic Range: Rybozymes (RNA enzymes) are less versatile than protein enzymes -> how could have supported a full metabolic network

• Error-Prone Replication: Early RNA replication would have been inneficient -> high mutation rates and potential collapse of genetic information

!WHERE DID RNA COME FROM?

metabolic networks (self-sustaining chemical cycles) emerged before genetic replication => Life began with autocalytic cycles that could grow and evolve

• IRON SULFUR WORLD HYPOTHESIS (at black smokers)

  • life began with autocatalytic metabolic cycles on mineral surfaces

    -> Iron sulfide (FeS) reacts with CO producing organic molecules and releasing (small amounts) of free energy (that theoretically could promote further biochemical reactions (=early form of metabolism)

PROS:

• long lasting steady flow of energy

• because of the chimney like structure of the vents, the organic molecules produced can accumulate locally (and do not have to fill up the entire ocean as assumed by primordial soup hypothesis)

PROBLEMS:

• Water coming out of the black smokers reaches temperature of 300°C -> would destroy organic molecules

• IRON SULFUR WORLD HYPOTHESIS (at white smokers)

  (compatible with Top-Down Approach, siehe unten)

  • Alkaline Vents (ex. “lost city”) have

    -> moderate temperatures (70-90°) ideal for organic molecule stability

    -> Due to serpentinization (=> sea water reacts with mineral olvine (contained in Earthcrust) formating serpentine and H2) => High pH (9-11)

  • Natural Proton Gradient: Minerals in white smokers form compartments due to the amotsphere rich in CO2(which partially dissolved in oceans and acidifieds it) leading to compartments with different concentrations

    • Vent fluid: pH 9-11 (highly alkaline, low H+ concentration)

    • Seawater: pH ~6 (more acidic, higher H+ concentration)

      -> difference creates a proton gradient

      => natural protonmotive force (same force that drives ATP Syntehsis!)

      -> inorganic compartments = precursos of cell walls & membranes found in free-living prokaryotes

  • Iron-sulfur minerals at surface of bubbles have catalytic properties & can convert H2 and CO2 to simple organic molecules like methane or acetate.

Connection to Top-Down Approach:

• LUCA as anaerobic and thermophilic organism that inhabitated a geochemically-active environment

• LUCA’s Biochemistry: replete with FeS.clusters (transition metal enzymes) that enabnle to live of H2 and fix CO2 and N2

  • Prokaryotic groups identified at base of tree of life (phylogenetic analysis)

    • methanogenic Archaea

    • acetogenic Bacteria

CHALANGES:

• Link to genetics: doesn’t explain how heredity (e.g. RNA/DNA) emerged from puerly metabolic systems

• Limited Evolvability: Experiments show that purely metabolic networks struggle to undergo evolution

• Some reactions (e.g. peptide formation) occur at very low efficiencies

• Did life start with genetic(RNA) or chemistry (metabolism)?

• Could a “messy” mixture of molcules lead to life, rather than a pure RNA or metabolic system?

• How did the genetic code emerged from either Scenario?