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:zap: THE ENERGY :zap: (ENERGY FROM CARBON (EVOLUTION (timeline (2.7 bya -…

- - - - ANABOLIC
        
        synthesis of organic compounds
      - CATABOLIC
        
        breaking down of organic compounds
      - facultative microbes can use many modes of energy source
    - - physical requirements
        
        temperature
        
        pH
        
        osmotic pressure
      - chemical requirements
        
        important chemical carbon, nitrogen, sulfur, phosphorous
        
        trace elements
        
        oxygen
        
        tree biomass comes from the air :wind_blowing_face:
        
        human biomass comes from diet :bento:
    - - CHEMICAL
        
        chemotrophy
        
        organic molecules
        
        glucose
        
        acetate
        
        chemoorganotrophs :apple:
        
        inorganic molecules
        
        H2, H2S, Fe2+, NH4+
        
        chemolithotrophs :leaves:
      - LIGHT
        
        phototrophy
        
        phototrophs :sunny:
  - - - get carbon from CO2
      - get energy from H2
    - - 2.7 bya - cyanobacteria developed photosystem - use H2O instead of H2S :arrow_right: make O2
      - 2.4 bya - O2 rise :arrow_right: Great oxidation event
      - many organisms evolved to live in presence of O2
  - - - O2 reduced by electrons
        
        cons - form toxic and reactive products
        electrons leaked out of ETC
        
        superoxide radicals
        
        hydrogen peroxide
        
        solution - detoxify oxygen species
        
        remove superoxide radicals
        
        superoxide dismutase -
        
        remove hydrogen peroxide
        
        catalase
        
        peroxidase
        
        organisms live with O2 produce all or some of these enzymes
      - pro - best electron acceptor in respiration
        (or any pathway uses an electron transport chain)
  - - - DESCRIPTION
        
        MECHANISM for ATP synthesis
        
        proton move through ATP synthase into cytoplasm
        
        gamma and epsilon subunit rotate :arrow_right: change active site conformation
        
        this adds Pi to ADP to form ATP
        
        MECHANISMS for ATP hydrolysis
        
        ATP synthase is reversible
        
        hydrolysis of ATP cause gamma epsilon subunit to rotate in the opposite direction
        
        H+ is pumped from cytoplasm into the space
        
        NOTE: bacteria that only does fermentation have ATP synthase only spins 1 direction
      - SIGNIFICANCE
        
        some bacteria might have all the components of the ETC, some might not have all the components
        
        ROLES
        
        produce ATP
        
        spin flagella
        
        assist in nutrient transport :fried_shrimp:
        
        aka. the proton motor force
        
        ETC works by pumping protons across the membrane
        
        enzyme to produce ATP
    - - performed by Hehermann
      - Bacteroides plebeius
        
        make porphyranase
        
        poryphan found many in read algae porphyra
        
        cleave porphyran
        
        population
        
        bacteria isolated from Japanese people
        
        but not found in US or European
        
        bacteria got gene from where
        
        acquire genes from Zobellia galactanivorans (marine bacteria) thru HGT
        
        seaweed/ nori, derived from porphyra - possible vector :sushi:
    - - COMPARE
        
        produce ethanol
        
        facultative anaerobes
      - CONTRAST
        
        sccahromyces cerevisiae
        
        unicellular fungus
        
        alternate haploid/ diploid stage
        
        produce :bread: :beer_mugs: :wine_glass:
        
        baker's yeast
        
        can also form biofilms
  - - - AEROBIC
        
        Electron transport chain
        
        4 complexes of carrier :black_square_for_stop:
        
        quinone reductase
        
        succinate dehydrogenase
        
        cytochrom bc I
        
        cytochromes a & a3
        
        each of the carriers transports electrons part of the way to O2 :question:
        
        connect the complexes
        
        Coenzyme Q / Quinones
        
        cytochrome c
        
        locate in plasma membrane
        
        can be branched, may contain different cytochromes and use electron acceptors other than O2
        
        E.coli
        
        aerobic respiration
        
        anaerobic - nitrate reduction (look for pictures in lecture slide)
        
        total of 38 ATP produced / glucose
        
        3 ATP/ NADH
        
        2 ATP / FADH2
        
        Krebs cycle :recycle:
        
        complete oxidation
        
        degradation of glucose and other molecules to CO2
        
        amphibolic - meaning both catabolism and anabolism
        
        produce
        
        2 CO2
        
        3 NADH
        
        1 FADH2
        
        1 GTP
        
        oxidation succinyl CoA to succinic acid
        
        final electron acceptor in the ETC is O2
      - ANAEROBIC
        
        glycolysis
        
        oxidation of glucose to pyruvic acid
        
        produce
        
        2 NADH
        
        2 ATP
        
        must maintain high NAD+ to maintain glycolysis
        
        preparatory step
        
        formation of acetyle CoA
        
        produce 2 NADA
        
        final electrons acceptor in the ETC is nitrate, sulfate, or carbonate
        
        yield less energy than aerobic
        
        anaerobic bacteria habitat
        
        soil sediments :deciduous_tree:
        
        swamps :leaves::
        
        intestinal tracts
        
        SHIGELLA live in the tracts
        
        facultative anaerobes
        
        with O2
        
        or without O2
        
        intestinal pathogen
        
        virulent factor T3SS
        
        molecular syringe
        
        after activation, T3SS triggers invasion of Shigella inside epithelial cells
        
        T3SS elongation - anaerobic lumen
        
        secretion - villi where there's O2
        
        T3SS activated by switch between O2/ no O2
        
        lumen
        
        intestinal lumen is anaerobic
        
        there is a zone that relatively oxygenated adjacent to gastrointestinal tract mucosa
        
        due to capillaries in intestinal villi
        
        facultative anaerobes reposbilities
        
        grow by utilizing O2
        
        keep O2 level low in the lumen
        
        MICROBES MAIN ROLE
        
        first line of defense
        
        educator of immune system
        
        metabolism
    - - TYPES
        
        homolactic fermenter
        
        end product: 1 product: lactate
        
        produce yogurt :glass_of_milk:
        
        ex: lactic acid bacteria, streptococcus thermophilus
        
        mechanism - lactate dehydrogenase: pyruvate + NADH :arrow_right: lactate + NAD+
        
        involve in tooth decay :lips:
        
        dental cavities
        
        streptococcus mutants
        
        cause demineralization from glucose
        
        pathway: glycolysis
        enzyme: aldolase
        
        alcoholic fermentation
        
        end product: ethanol
        
        produce :wine_glass: :bread:
        
        mechanism
        
        pyruvate decarboxylase: pyruvate :left_right_arrow: acetaldehyde + CO2
        
        alcohol dehydrogenase: acetaldehyde + NADH :arrow_right: ethanol + NAD+
        
        ex: yeast (saccharomyces cerevisiae)
        
        heterolactic fermentation
        
        end products: MORE products lactate, ethanol, CO2
        
        produce: sauerkraut, silage, kefir, kimchi
        
        pathway
        
        pentose phosphate pathway
        enzyme: phosphoketolase
        
        operates with glycolysis/ can be at the same time
        
        catabolic and anabolic functions
        
        aerobic and anaerobic
        
        produce
        
        carbon skeleton
        
        2 more items...
        
        NADPH - biosynthesis
        
        ribose-5P - nucleotide synthesis
        
        reaction: glucose :arrow_right:1 lactate + 1 ethanol + CO2 + ATP
      - DESCRIPTION
        
        fermentation maintain NAD+ for glycolysis
        
        organism types
        chemoorganotrophes
        
        propionibacterium
        
        CO2
        propionic acid
        
        swiss cheese :cheese_wedge:
        
        asergillus
        lactobacillus
        streptococcus
        
        lactic acid
        
        cheddar cheese :cheese_wedge:, yogurt :glass_of_milk:, soy sauce
        
        saccharomyces
        
        CO2
        ethanol
        
        :wine_glass: :beer:
        
        clostridium
        
        acetone
        isopropanol :champagne:
        
        nail polis remover :nail_care:
        rubbing alcohol :face_with_head_bandage:
        
        mixed acid fermentation - INDUSTRY
        
        several bacteria and fungi produce a miture of fermentation products
        
        adapted for commercial purposes
        
        acetone production
        
        butanol production
        
        the yeast and the pulque enzyme
        saccharomyces and zymosomething :question:
        
        pasteur effect
        
        you have to prevent O2 from accessing sacchromyces cause they prefer aerobic respiration
    - - replace glycolysis in some bacteria
      - combine step of pentose phosphate pathway + glycolytic pathway
      - produce
        
        ATP
        
        NADPH
        
        NADH
      - Ex
        
        pseudomonas
        
        rhizobium
        
        agrobacterium
        
        zymomonas
        
        (used for pulque production)
      - enzyme: 2-keto-3 deoxy-6-phosphogluconate aldolase (KDPG aldolase)
- - - - OVERVIEW
        
        3.5 bya, when O2 wasn't even on the planet
        nitrogen fixation - ancient process
        
        2.5 bya nitrogen fixation evolved when O2 began to rise
        
        obligate anaerobes - no adaptability required for
        
        aerobes - evolved strategies to have nitrogenase function
        
        AMINO ACID ANABOLISM
        
        N2 :arrow_right: NH3 :arrow_right: glutamine
        
        microbes that can fix nitrogen can live without amino acid
      - types of bacteria
        
        alpha - & beta - rhizobia
        
        symbionts that fix N2
        
        determine nodules of lotus and bean
        
        rhizobium
        
        gram (-)
        
        nitrogen fixing
        
        soil bacterium
        
        form nodules on the roots of host legume
        
        live in nodule cells as bacteroids
        
        no flagella cause it doesn't need to move anymore
        
        symbiosis
        
        rhizobia - give fixed nitrogen to host
        
        legume
        
        produce leghemoglobin - to bind to O2, make sure that there's enough O2 for respiration but not too much free O2 to inhibit nitrogenase
        
        give photosynthases (from photosynthesis)
        
        infection thread step - read Rachael slide
        
        plant has flavonoids
        rhizobium has nod protein
        
        flavonoids bind to nod protein, attract bacteria
        
        rhizobium bind to root hair
        
        root hair is induced to curl and engulf rhizobium
        
        plant cell envelope opens tube inward as infection thread
        
        rhizobium bacteria travel down the infection threads
        plant nucleus travels ahead
        
        rhizobium reach the cortical cells of plant
        
        bacteria enter cortical cell and differentiate to bacteroids
        
        legume symbiosis - most important symbiotic association in terms of nitrogen fixation
        
        CYANOBACTERIA
        
        2.7 bya - developed photosystem uses water to produce O2
        
        2.4 bya - great oxidation event , O2 level rises
        
        ANABAENA
        
        METABOLISM
        
        fix N2 when nitrogen source is not readily available
        
        photosynthesis
        
        aerobic respiration
        
        STRUCTURE
        
        gram (-)
        
        filamentous contain
        (big filament)
        
        vegetative cells
        
        2 more items...
        
        "specialized" cells
        
        2 more items...
        
        thick carbohydrate-rich glycocalix - 3 layers outside the outermembrane that closely ressemble
        sheat, capsule, slime
    - - HABER-BOSCH PROCESS
        
        cost
        
        natural gas - 946 kJ of energy to break the triple bond
        
        1 % of the world energy is for this project
        
        hidden environmental costs
        
        N2 leaching in soils
        
        pollution of lake & waterway
        
        greenhouse gas
        
        generate ammonia for fertilizer
      - lightning and photochemical conversion
      - fossil fuel combustion