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Botanical: Origins, Early Metabolism, Cellular Structures, and Respiration…

- - - - Earliest:
        
        Last Universal Common Ancestor (LUCA)
        
        ~3.5-3.6 Billion Years Ago
      - Evolution Model:
        
        Punctuated Equilibrium:
        
        The hypothesis that evolutionary development is marked by isolated episodes of rapid speciation between long periods of little or no change.
        
        Major new forms seems to appear suddenly
        
        Various reasons:
        
        Intermediate forms did not fossilize
        
        Very few fossils with limited distribution
        
        CONTRASTED BY:
        
        Phyletic Gradualism:
        
        Theorizes that most speciation is slow, uniform and gradual
        
        When evolution occurs in this mode, it is usually by the steady transformation of a whole species into a new one
      - Chronogram for Plant Evolution:
      - Descent with Modification:
        
        Nested design give rise to taxonomic groupings
        
        Evolutionary divergence from common ancestors under the influence of natural selection
      - Tree of Life:
        
        Based on similarity of ribosomes (RNA + proteins)
        
        History of life microbial
        
        Depiction of the genealogical relationships of living organisms
      - Geological strata:
        
        Give clues as to descent
        
        Fossils
        
        Biological molecules
        
        Environmental Isotopes
        
        Evidence for photosynthesis
        
        Carbon Isotopes:
        
        Carbon atoms come in three varieties, distinguished by molecular weight
        
        C14 decays so not generally used to time
        
        C13 discriminated against by photosynthesis
        
        C12 enriched in organisms compared to environment
        
        Earliest Evidence:
        
        ~3.5bya
        
        Evidence of organic microbial mats
        
        Stromatolite like structures
        
        Isotopic signature suggests photosynthesis
        
        North Pole rocks preserve some of our earliest evidence of life and environments on the young Earth.
    - - Early:
        
        Chemical reactions could have made life possible
        
        Early scientists thought that ammonia and methane were most abundant
      - Chemosynthetic Hypothesis:
        
        Gases thought to be relevant to early atmosphere
        
        Later experiments showed that reducing atmosphere necessary (4H:1C) & absence of oxygen
      - RNA WORLD?:
        
        Sophisticated molecular machines:
        
        Simple enough to form by physical processes
        
        Sufficiently complicated to lay evolutionary groundwork for living cells
        
        Peptide Nucleic Acid
        
        HYPOTHESIS:
        
        Early conditions not quite right to leap right into RNA
        
        1 more item...
        
        Self-replicating
        
        Direct synthesis of other compounds
        
        Trajectory eventually independent of physical processes
        
        Synthesize molecules needed for growth
        
        Tapping chemical/solar energy to fuel workings
        
        As life matured, Evolution introduced division of labor:
        
        Proteins took over most catalytic functions
        
        DNA provided more stable library
- - - - Energy from inorganic minerals used to drive metabolism,
        
        Synthesis of ATP
        
        ATP
        
        Primary energy courier in all living cells
        
        Light-driven electron flow linked to existing machinery for making ATP
        
        Photophosphorylation
        
        Adding phosphate group to ADP, Creates high-energy bond
        
        Generation: Electron Transport Chain:
        
        Proton motive force
        
        Protons are pumped from the mitochondrial matrix to the intermembrane space, and oxygen is reduced to form water
        
        Series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen
        
        Mitochondrial ETC consists of 4 large protein complexes
        
        1 more item...
        
        Circulation of electrons
        
        Circulation of protons
      - Often found in extreme environments
      - Chemosynthetic organisms use the energy released by chemical reactions to make sugars, or food.
    - - Some suggest that metabolism may have predated biological macromolecules
      - Hydrogen sulfide react with iron monosulfide to form pyrite
        
        Yield energy
        
        Yield chemical reducing power: HYDROGEN
        
        Powering fixation of carbon dioxide to form organic compounds on pyrite surface
        
        Deep-sea hydrothermal
        vents:
        
        hydrogen sulfide emitted from vents can
        react with iron monosulfide to form pyrite
        
        Hydrothermal vent bacteria oxidizes: hydrogen sulfide (H2S) + carbon dioxide (CO2) + oxygen (O2) > produce sugar (CH2O), sulfur (S), and water (H2O)
        
        Carbon fixation:
        
        Likely began with chemosynthesizers
        Living around ancient volcanic vents
        
        biochemical pathways in chemosynthetic communities still under study
      - Earliest organisms:
        
        Hyperthermophilic Prokaryotes
        
        They are found on the
        earliest branches of both the archaeal and bacterial limbs
        
        Do not use oxygen during metabolism
        
        Most die in presence of oxygen
      - Eukaryotes evolved under low oxygen
        
        ~2.7 bya Cyanobacteria used H2O as electron donor
        
        Monophyletic origin of land plants:
        
        boosted O2 accumulation to modern levels through massive carbon burial
        
        Eukaryotes arose ~1.8bya so ~1.3 billion years in anaerobic conditions
        
        The Great Oxidation event and an Overview of the changes in Earth's biochemistry and the rise and diversification of major groups with respect to oxygen concentration
        
        Geologically stable biomarker made predominantly by Eukaryotes
        
        Steranes
        
        Cholesterol
    - - most ancient
      - Does NOT require oxygen
      - Minimal output of 2 net ATP
      - component steps of glycolysis were provided by the non-cellular fermentation experiments
      - Embden-Meyerhof-Parn Pathway:
        
        widespread metabolic pathway that produces PYRUVATE
      - MAJOR STEPS:
        
        Begins with Glucose (C6) as the substrate (reactant)
        
        Uses: 2 ATP
        
        Produces: 4 ATP
        
        Ends with Pyruvate (C3) as the product then can enter:
        
        Fermentation:
        
        Formation of lactic acid or ethanol in the cytosol
        
        Aerobic Respiration(cyclic)
        
        shuttling of the reducing equivalents to the mitochondrial respiratory electron transport chain
        
        increased ATP yield
        
        Uses the mitochondria to complete process
        
        Major steps:
        
        Glycolysis
        
        Pyruvate oxidation
        
        Oxidative phosphorylation
        
        Citric acid cycle
        
        To keep the pathway going, NADH needs to be recycled to NAD+: 2 OPTIONS:
      - OCCURS IN CYTOPLASM
    - - Electron movement provides impetus for energy production
      - NADH
        
        Nicotinamide adenine dinucleotide
        
        NAD+ oxidizing agent, accepting electrons
        
        Electron carrier through:
        
        Oxidation-Reduction Reactions
        
        Stronger proton motive force that FADH2
    - - Reverse TCA:
        
        Reductive citric acid cycle
        
        Possible candidate for prebiotic early-earth condition
        
        Some bacteria use to synthesize C compounds:
        
        sometimes using hydrogen, sulfide, or thiosulfate as electron donors
        
        Some steps can be catalyzed by minerals through photochemistry
        
        Precursor to stromal reactions of photosynthesis in plants
      - Activation Energy:
        
        Energy required to drive the creation of sugars
        
        Chemosynthesizers use oxidation of energy-rich inorganic molecules
        
        Plants use sunlight
        
        Glycolysis requires 2 ATP to get the reaction going
      - Glucose Monomer:
        
        Basic sugar that many organisms use for energy
        
        Different models for the same molecule
      - Glucose Isomers:
        
        Same formula:
        C6H12O6
        
        Different biological roles:
        
        Alpha: energy storage
        
        OH: Down
        
        Beta: structure
        
        OH: up
        
        Major building block of cellulose
        
        Change in hydroxyl (OH) group at C1
      - Starch:
        
        Amylose:
        
        Alpha 1,4 bonds
        
        Angular
        
        Amylopectin:
        
        Alpha 1,6 bonds
        
        Linear
- - - - Bubble World:
        
        The first living systems probably did stem directly from the primordial soup and evolved relatively fast up to a common ancestor, usually referred to as Last Universal Common Ancestor (LUCA),
        
        Possibly, the linkage of metabolism and replication began
        with the packaging of RNA (or protein and RNA) molecules inside primitive membranes
        
        Experimental evidence:
        
        Dry and wet cycles
        DNA + lipids
        
        Sandwich to lipid vesicle with DNA inside
        
        Simple experiment suggests:
        
        that the structural association of lipids, proteins, and nucleic acids could have arisen spontaneously on the early Earth
        
        Selection for complexity:
        
        Increasing number of early cells thriving on primordial soup would have led to the depletion of essential nutrients
        
        Imposed selective pressure:
        
        Favored cells capable of:
        
        Synthesizing limited molecules
        
        Origin basic metabolic pathways
        
        Those less dependent on exogenous sources of nutrients
      - Containing information molecule
      - Perform limited # of metabolic reactions
      - Able to:
        
        Divide
        
        Interact
        
        Fuse & share genomes & metabolic abilities
      - Plasma Membrane:
        
        Covered with protective wall in some organisms
        
        Embedded Proteins:
        
        Facilitate metabolism
        
        Receptors for functions such as self identify
    - - Endomembrane System:
        
        Continuous connected membrane
        
        Forming multiple organelles:
        
        Golgi Apparatus
        
        Endoplasmic Reticulum
        
        Nuclear Envelope
      - Vs. Prokaryote
        
        Both organelles lack histones and introns like bacteria.
      - Mitochondria and Chloroplast DNA exists in closed circular form as it does in a prokaryotic cell
    - - Microfilaments:
        
        Important for vesicle movement near membrane
        
        Actin
      - Intermediate filaments:
        
        More permanent, fix things in place
        
        Dimers→ tetramers
      - Microtubules:
        
        trackway for long-range movement of transport vesicles
        
        Tubulin
        
        2 subunits
    - - Evidence:
        
        The electron transport chain
        
        Mitochondria and chloroplast are the same in size as bacteria.
        
        Mitochondria and chloroplasts are surrounded by two or more membranes like bacteria.
      - The Theory:
    - - Mitochondrial Structure:
        
        Outer membrane
        
        Porins
        
        Inner membrane:
        
        Folded areas are cristae
        
        Location of oxidative phosphorylation
        
        Matrix:
        
        Internal solution
        
        Location of the citric acid cycle
      - Plant Plastids:
        
        Chloroplasts: typically green plastids used for photosynthesis.
        
        Thylakoid reactions with proteins embedded in thylakoid
        
        Stromal reactions within aqueous stroma
        
        Etioplasts: are the precursors of chloroplasts
        
        Chromoplasts: coloured plastids for pigment synthesis and storage
        
        Leucoplasts: colourless plastids for monoterpene synthesis;
        
        Amyloplasts: for starch storage
        Elaioplasts: for storing fat
        
        Proteinoplasts: for storing and modifying protein
    - - Primary cell wall:
        
        Function:
        
        Layer of additional protection
        
        Create turgor pressure along with large central vacuole
        
        Composed primarily of:
        
        Hemicellulose
        
        Pectin
        
        Cellulose >> Beta Glucose
        
        Cellulose Microfibrils:
        
        made of:
        
        glucose monomers
        
        beta glucose bonds
        
        Through dehydration synthesis
        
        Hydrogen bonds make cellulose extremely strong
        
        Very few organisms have the capacity to break/digest cellulose
        
        Fiber in our diets
        
        Cellulose Similarities:
        
        Chitin: Insect exoskeleton
        
        Keratin: Hair, Fingernails
        
        Remains somewhat flexible to permit growth
- - - - Substrate level phosphorylation
      - https://youtu.be/hIAnuG2r8WI
        7min
    - - Pyruvate oxidation:
        
        pyruvate is attached to CoA releases a carbon dioxide molecule and forms NADH
        
        Electrons stripped from pyruvate and given to NAD+
        
        Carbon dioxide broken off, C3 → C2
        
        Acetyl Coenzyme A
    - - Flavin adenine dinucleotide (FAD):
        
        Strong oxidizing agent
        
        FAD is reduced to FADH2
        
        Weaker proton motive force compared to NADH
      - THE PROCESS OF THE PLAYERS:
        
        1) Electrons dropped off by NADH & FADH2
        
        2) ^ Electrons pass through ETC
        
        4)
        
        3)
    - - Proton motive force
        
        Trapped protons creates a battery
      - Only way down concentration gradient is through special protein complex
      - ATP Synthase:
        
        Catalyzes formation of ATP from ADP + Pi
      - Drive synthesis of ATP across membranes:
        
        Mitochondrial cristae
        
        Prokaryotic cell membranes
        
        Plant thylakoid membranes