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photosynthesis and the processes of life, leading up to it., first cells,…

- - - - punctuated equilibrium
        
        major new forms in evolution seem to appear out of nowhere. why?
        
        intermediate forms are hard to access.
        
        We probably haven't found a lot of intermediate forms yet.
        
        highly debated.
        
        Is it gradual?
        
        Is evolution abrupt?
        
        There is no way to know right now.
      - Living cells tend to be uniform.
        
        Common 'core' molecular features.
        
        DNA and RNA
        
        Common genetic code
        
        ATP #
        
        used universally to shuttle energy around.
      - Darwin
        
        Supported the ideas of phyletic gradualism. #
        
        dissent with modification
        
        Nested design gives rise to taxonomic groupings.
        
        pictured as a tree. "tree of life".
        
        based on similarities of ribosomes.
        
        historical record of life
        
        First life forms likely to be bacteria, based on tree of life.
        
        Geological strata
        
        biological molecules and fossils
        
        Gives clues to dissent.
        
        isotopes
        
        Atoms of the same element
        
        diff number of neutrons.
        
        Carbon dating
        
        99% C12.
        
        1 more item...
        
        Why not C14 and C13?
        
        2 more items...
      - Endosymbiotic theory (evidence) #
        
        Mitochondria and chloroplasts have their own DNA, similar to bacterial DNA.
        
        self-replicate binary fission (Without nucleus)
        
        ONLY made from pre-existing ones. (Cells can't generate their own.)
        
        Ribosomes similar to bacteria (70s)
        
        DOUBLE MEMBRANE.
    - - atmosphere
        
        Heavy ammonia and methane
        
        What I would have said if I existed in early earth
      - Chemosynthetic hypothesis
        
        Stanley Miller's experiment, 1953
        
        Energy source put in
        
        Mimicked lightning storms of early earth.
        
        gases thought to be relevant to early earth atmosphere
        
        Put in a flask together
        
        Experiment ran several days
        
        Organic material found in flask after a span of day.
        
        The outcome of these basic conditions replicated in the flask showed it was possible for environmental conditions in atmosphere to cause life. #
      - sophisticated molecular machines
        
        Complicated enough to lay evolutionary groundwork for living cells.
        
        able to self replicate
        
        Internal processes needed to fuel everything happening in cell.
        
        what comes to mind?
        
        RNA!!! :smiley:
        
        This is a little TOO complicated though.
        
        1 more item...
        
        Simple enough to form by physical processes
    - - Suggestions that metabolism predated biological macromolecules
      - Hydrogen sulfides react with iron monosulfide
        
        form pyrite
        
        make energy
        
        make chemical producing power (H)
      - Chemosythesis
        
        was the norm for early earth.
        
        The early organisms who use chemosynthesis are very old and found in extreme environments.
        
        extent species still use chemosynthesis today.
        
        Most of the fellas who use it will actually die when exposed to oxygen, implying that photosynthesis evolved far later than chemosynthesis.
      - Glycolysis is the most ancient.
    - - Evidence of eukaryotic cells ~2.7 billion years ago.
      - geologically stable biomarker made mostly by eukaryotes. example: cholesterol.
      - Animals and plants are in this category since they are multicellular organisms.
      - Endomembrane system
        
        Continuous connected membrane.
        
        forms multiple organelles!
        
        golgi body
        
        plasma membrane #
        
        Endoplasmic reticulum
        
        nuclear envelope
        
        Cytoskeleton
        
        Microfilaments
        
        important for vesicle movement near membrane
        
        Actin
        
        intermediate filaments
        
        More permanent. fixes things in place.
        
        dimers :arrow_right: tetramers
        
        For structure.
        
        Microtubules
        
        trackway for long-range movement of transport vesicles, like a motor protein for example.
        
        Alpha and Beta Tubulin
      - prokaryotic vs eukaryotic?
        
        Eukaryotic
        
        cytoskeleton differences.
        
        ribosomes are bigger.
        
        Prokaryotic
        
        Membrane-bound genetic material (Chromosomes)
        
        lower number of genes.
        
        Use pilli and flagella
        
        there are SO many more differences but I just wanted to highlight some.
    - - "Ancestral prokaryote"
        
        eats but doesn't digest aerobic bacterium.
        
        Over time, symbiosis happens. mutual benefit.
        
        Symbiosis becomes interdependence.
        
        Mitochondrial containing a eukaryote eats photosynthetic cyanobacteria the same way.
        
        also forms interdependence, then exchanges DNA.
        
        Photosynthetic bacteria becomes chloroplasts.
        
        Natural selection favored cells with endosymbiotic relationships. If you ignore the below two branches and allowed things to persist, you would have animal cells eventually.
        
        Aerobic bacteria evolves into mitochondria
- - - - Does not use glucose as a starting point
        
        derives energy from inorganic materials for metabolic processes.
      - iron bacteria, sulfur bacteria, etc. are examples of animals that use chemosynthesis.
      - Reducing power needed for energy production process of chemosynthesis.
        
        redox reactions are needed for chemosynthesis.
        
        OIL RIG
        
        Oxidation is loss, reduction is a gain.
        
        used to move electrons around.
        
        Electron movement makes an impetus for energy production.
        
        strong reducing agents?
        
        NADH.
        
        also called nicotinamide adenine dinucleotide.
        
        electron carrier.
        
        able to pick up electrons, become reduced
        
        drop off electrons, become oxidized.
        
        safe way to shuttle electrons around the cell in an organism.
        
        electron transport chain is used for this.
        
        moves back and forth
        
        redox
        
        move electrons around in cell
      - Ultimarte goal is the synthesis of ATP.
        
        ATP - Adenosine triphosphate.
        
        All organisms use ATP to generate energy.
    - - Major steps
        
        Glycolysis (1)
        
        The process
        
        starts with C6
        
        uses 2 ATP,
        
        Then produces 4, with a final gain of 2 ATP molecules.
        
        Puts enough energy in to get the reaction going.
        
        Ends with pyruvate (C3) as a product.
        
        Process is very widespread.
        
        Pathway produces pyruvate
        
        AKA Embden Meyerhof-Pam pathway
        
        Doesn't happen inside the mitochondria.
        
        Citric acid cycle (2)
        
        Acetyle CoA enters the CAC, joins with a C4 molecule #
        
        Produces C6 molecule
        
        Strip off electrons and provide NAD+, making NADH.
        
        coupled to break off CO2
        
        Substrate level phosphorylation occurs
        
        2 more items...
        
        Happens in the matrix.
        
        oxidative phosphorylation (4)
        
        Major steps
        
        Electrons pass through ETC
        
        Protons are pumped across
        
        Chemiosmotic electrochemical gradient runs ATP synthase
        
        Oxygen is final electron acceptor
        
        Electrons dropped off by NADH & FADH2
        
        Driving production of ATP
        
        Chemiosmosis (happens in the ATP synthase) involves forcing a lot of phosphate into ADP to create a surplus of ATP.
        
        you can see vaguely that a lot of electrons are being released throughout the process.
        
        pyruvate oxidation (2)
        
        electrons stripped from pyruvate and given to NAD+.
        
        CO2 broken off, C3 :arrow_right: C2
        
        Two carbon molecules are joined by coenzyme A
        
        Makes Acetyl coenzyme A
        
        happens twice.
      - uses mitochondria to complete this process.
      - continues to strip energy from pyruvate from glycolysis
    - - Salvage pathway.
      - Occurs when oxygen is lacking.
        
        NADH recycled into NAD+.
        
        plants use ethanol pathway.
        
        Ethanol is toxic to plants and will kill them if they are forced to keep using fermentation for too long.
      - NOT ideal, meant for short term, emergency use.
  - - - probably began with chemo-synthesizers
        Living around ancient volcanic vents.
      - Variation in bacteria on how sugars are synthesized
      - Organisms can only use this if they are able to use external energy can make their own carbohydrate fuel.
      - Standardized in later lineages!
        
        Calvin-Benson- Bassham cycle describes this.
        
        it's a form used by pllants.
    - - Aka reductive citric acid cycle
      - Some bacteria use this to synthesize carbon compounds.
      - Precursor to stromal reactions.
      - Some steps can be catalyzed by minerals through photochemistry!
- - - - Different models can be used for the same molecule.
      - Represented by the chemical formula, C6H12O6.
      - Basic sugar that many forms of life use for energy.
    - - Same formula!!! #
      - DIFFERENT biological roles.
        
        Alpha - Energy storage.
        
        Also the one WE eat. :cake:
        
        Beta - Structure.
        
        MAJOR building block of cellulose!
      - Beta OH at C1 sticks UP.
        
        Alpha OH at C1 sticks DOWN.
    - - Amylopectin
        
        Alpha 1,6 bonds
        
        linear
      - Amylose
        
        Alpha 1,4 bonds
        
        angular
      - Made of glucose monomers bound by 1,4 bonds.
  - - - Outer membrane
      - inner membrane
        
        Cristae are folded areas
        
        location of oxidative phosphorylation
      - Matrix
        
        Internal solution that exists within the 'empty' space
        
        Citric acid cycle happens here!
  - - - (usually) green plastids used for photosynthesis.
      - Ethioplasts are the precursors to this
    - - Starch storage
    - - Colored, for pigment synthesis and storage.
      - develop for display
      - or as sunblock sometimes.
    - - colorless, used to synthesize monoterpine
    - - fat storage
    - - storing and modifying protein.
  - - - Nicotinamide adenine dinucleotide
      - NAD+ oxidizing agent, accepts electrons.
      - NADH is the reduced form and can give up electrons.
      - stronger proton motive force than FADH2
      - Can be converted to NADP.
      - Niacin vitamin helps build.
      - Numerous redox reactions occur in these changing processes.
    - - Flavin adenine dinucleotide
      - Vitamin B2, riboflavin base for construction.
      - weaker proton motive force compared to NADH.
      - FAD is reduced to FADH2
      - Strong oxidizing agent.
    - - Proton motive force
      - Trapped protons create battery
      - Only way down concentration gradient is through special protein complex
        
        ATP synthase
        
        little mini turbine.
        
        Pretty good example of a molecular machine.
        
        Driven by energy from chemiosmotic, electrochemical gradient across the membranes
        
        can build up in?
        
        Prokaryotic cell membranes
        
        Plant thylakoid membranes
        
        Mitochondrial cristae
        
        Catalyzes formation of ATP from ADP + Pi
        
        drive the synthesis of ATP.
- - - - Respiration does the opposite of this.
  - - - "Dark reactions"
    - - "Light reactions"
      - Thylakoid reactions involve dozens of pigments, specialized electron-handling complexes
  - - - "Molecules that absorb particular wavelengths of light energy and reflect others"
      - Plants appear green because they reflect green light back and absorb other colors.
      - absorbed light energy
        
        Electron bumps to the next orbital
        
        Fate of electron
        
        passed to electron receptor, if it's nearby
        
        If no electron receptor... all back down to original orbital
        
        Releasing energy
        
        heat
        
        fluorescence
        
        Causes electrons to become excited
        
        Absorbance spectrum
        
        Amount of energy absorbed depends on the pigment
        
        lower energy - red
        
        higher energy - purple
        
        Electromagnetic spectrum holds much energy that cannot be used
        
        visible spectrum used
        
        contains all the colors, but appears to the naked eye as white light.
      - chlorophyll
        
        Chlorophyll a
        
        Peak absorbance
        
        430 nm, 660 nm
        
        Most abundant pigment in plants
        
        Chlorophyll b
        
        Second most abundant pigment
        
        peak absorbance
        
        450 nm, 650 nm
      - photosystems
        
        all the accessory pigments combined, embedded with antennal complex and chlorophyll, into the thylakoid membrane.
        
        2 types of photosystems for plants.
        
        PSI
        
        Absorb longer wavelengths
        
        Chl a>>Chl b
        
        P700
        
        PSII
        
        Absorb shorter wavelengths
        
        Chl b >> Chl a
        
        P680
        
        Hydrolysis
        
        oxygen evolving complex
        
        Electron transport chain
        
        How electrons are passed from PSII to PSI
        
        Excited PSII electron grabbed by pheophytin
        
        Passed to plastoquinone
        
        1 more item...
        
        Electron from PSI to NADP+
        
        controlled energy release
        
        Energy of excited electrons released in a stepwise controlled manner
        
        May have evolved initially as a way to dissipate excess energy
        
        Some of the energy used to make stable, energy-rich molecules that can be used by living cells
        
        all to run ATP synthase!
        
        phosphorylation
        
        cyclic phosphorylation
        
        flow of electrons does not directly make ATP
        
        electron flow coupled with flow of protons
        
        Electron energy drops when flow through cytochrome complex
        
        2 more items...
        
        Plastoquinone
        
        Cytochrome b6f
        
        PSI
        
        Plastocyanin
        
        PSII
        
        photolysis
        
        2 more items...
        
        non-cyclic photophosphorylation
        
        electrons from PSII go to NADPH
        
        NADPH
        
        Without it, there would not be enough pull from photolysis to move the electron the whole way through.
        
        More powerful energy carrier than ATP
        
        beginning of sulfur bacteria
        
        3 more items...
        
        important prior to this non-cyclic phosphorylation.
        
        NADP+
        
        is a great oxidizer
        
        Final electron acceptor
        
        Helps to build proton motive force
        
        proton pump
        
        requires energy from the electrons that come from PSII.
        
        Plastoquinone & Cytochrome b6f
        
        pulls out protons from stroma
        
        plastoquinone picks it up and rips the electrons out
        
        shunts it across membrane
        
        1 more item...
        
        atp synthase #
        
        Run the molecular machine
        
        Force Pi onto ADP to form ATP
        
        Use the proton motive force
    - - Indicates that Chl a & b not only pigments
      - MUST have accessory pigments
        
        example: fall leaf colors
        
        chlorophyll is broken down in the fall, exposing the other accessory pigments.
        
        Carotenoids
        
        also sunscreen, again
        
        beta carotene
        
        they help broaden absorption spectrum
        
        helps with energy absorption.
        
        Energy absorption and excitation occurs in organized complexes of pigments & proteins called photosystems
        
        Absorbed energy is moved around via resonance energy
        
        Funnelled to reaction center
        
        special chlorophyll A
- - - - For fusing, exchanging information, and share genomes/metabolic abilities.
    - - wet + dry cycle experiment
        
        little bubble cells form due to this.
        
        These don't use energy
        
        DNA inside lipid vesicle.
    - - Made up of phospholipid molecules.
        
        In a cell, aqueous solution on inside and outside.
        
        Bilayers of phospholipids. tails inside the layers, heads outside, oriented away from the joined tails.
      - Embedded proteins
        
        Receptors for functionality.
        
        These facilitate metabolism.
        
        allow for deciding and knowing what is entering the cell.
        
        Allows for larger things to be transported, since semi-permeability won't always cut it.
        
        Keeps the membrane together.