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EXAM 1, CELLS, PROTON MOTIVE FORCE, organisms that can use external energy…

- - - - Early thermophiles gave way to cooler environments
        
        Photosynthesis limited by temperature.
    - - Relevant to study the origin of photosynthesis
        
        Layers of photosynthetic bacteria/cyanobacteria
        
        Secrete mucilage
        
        Bands of sediment and dead bacteria, growing similar to reef
    - - Oldest known fossilized organism
        
        close to LUCA
        
        fossils similar to present day species cell structure
        
        2-methylhopane almost exclusive in cyanobacteria cell walls
    - - took time to build up photsynthesizers
        
        iron is plentiful on Earth
        
        little free oxygen
        
        Iron depleted and then oxygen began to build up in atmosphere
    - - iron formantions dissapeared
        
        iron-rich oceans were gone
        
        iron loving microbes dropped out of fossil record
        
        oxygen enriched oceans precipitated iron
  - - - 2 stages
        
        thylakoid reactions
        
        light reactions
        
        thylakoid reactions involve dozens of pigments
        
        stromal reactions
        
        dark reactions
        
        Calvin-Benson- Bassham Cycle
    - - Early atmosphere without oxygen, so without the protective ozone layer
        
        Cyanobacteria with scytonemin in sheath, pigment that protects them for UV radiation
        
        Chlorophyll similar to hemoglobin
    - - molecules that absorb particular wavelengths of light energy and reflect others
        
        properties of light
        
        reflection
        
        why plants are green
        
        transmission
        
        absorption
        
        ABSORBED LIGHT ENERGY
        
        makes electrons to become excited
        
        electron bumps to the next orbital
        
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        ABSORBANCE SPECTRUM
        
        energy absorbed depends on the pigment
        
        electromagnetic spectrum holds much energy that cannot be used
        
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    - - Chlorophyll a
        
        Most abundant
        
        Peak absorbance
        
        430 nm
        
        660 nm
      - Chlorophyll b
        
        Second most abundant
        
        Peak absorbance
        
        450 nm
        
        650 nm
      - ACTION SPECTRUM
        
        indicates that Chl a & b not only pigments
        
        should have accessory pigments
        
        Carotenoids
        
        Beta carotene
        
        Help broaden absorption spectrum
        
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    - - occurs in organized complexes of pigments & proteins called photosystems
        
        absorbed energy is moved around via resonance energy
  - - - made of
        
        Accessory pigments
        
        Chlorophyll pigments
        
        Reaction center
        
        in thylakoid membrane
        
        Antennal complex
    - - P700
        
        Absorb longer wavelengths
        
        Chl a>>Chl b
    - - P680
        
        Absorb shorter wavelengths
        
        Chl b >> Chl a
        
        Hydrolysis
    - - energy of excited electrons released in a stepwise controlled manner
        
        have evolved as a way to dissipate excess energy
    - - electron passed from PSII to PSI
        
        excited PSII electron grabbed by pheophytin
        
        passed to plastoquinone
        
        passed to cytochrome b6f complex
        
        passed to plastocyanin
        
        passed to PSI
        
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  - - - electrons does not directly create ATP
        
        electron flow coupled with flow of protons
        
        electron energy drops when flow through cytochrome complex
        (Drag protons across membrane)
        
        electrons return to chlorophyll
        
        Protons trapped in special internal chamber, thylakoids
    - - e- from PSII to NADPH
        
        NADP+
        
        build proton motive force
    - - light energy to split water
        
        Oxygen evolving complex of PSII
        
        Oxygen and protons released
        
        Oxygen diffuses out of stomata
        
        Protons left behind
    - - Plastoquinone & Cytochrome b6f
        
        work in concert to bring protons from stroma to lumen
        
        creates lake of protons
        
        in both cyclic and noncyclic photophosphorylation
      - ATP SYNTHASE
        
        Use the proton motive force
        
        Run the molecular machine
        
        Pi onto ADP to form ATP
  - - - Ribulose 1,5-bisphosphate carboxylase oxygenase
      - Fixes CO2 into organic carbon
        
        in most autotrophs
        
        50% total soluble protein in plant leaf or microbe
    - - CO2 bound to RuBP (C5)
        
        breaks into 2 C3
      - 2.REDUCTION
        
        Energy from ATP stored into C3 molecule
        
        Energetic electrons reduce C3 molecule
        
        Ends in a pool of G3P (C3)
        
        3.REGENERATION
        
        Carbon shuffling
        
        Get the RuBP back (C5)
        
        Takes more ATP
    - - RuBisCO binds to 2 molecules
        
        CO2 & O2
        
        at low CO2, binds to O2
        
        Disadvantages
        
        Not as efficient
        
        toxic by-product
        
        sometimes advantageous
        
        High light tolerance
        
        Reduce photo-inhibition
        
        Provides metabolites for other processes, including stress protection proteins
        
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    - - production of glucose
        
        builds from smaller molecules
        
        happens in
        
        amyloplasts
        
        cytosol
        
        chloroplasts
  - - - herbaceous forms
        
        dry regions where fire is common
        
        primarily in monocotyledons
        
        418 genera
        
        Dicotyledons
        
        86 genera
      - PHOTSYNTHESIS
        
        RuBisCO
        
        isolated in cells next to vascular bundle
        
        Excluded from mesophyll cells
        
        Carbonic anhydrase
        
        Water + CO2→ bicarbonate
        
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        ADVANTEGEOUS
        
        Under low atmospheric CO2
        
        Under high temperatures
        
        When C3 photosynthesis undergoing high photorespiration
      - ORIGINS
        
        Evolved independently multiple times
        
        Water availability declined
        
        Selective pressure to reduce photorespiration
        
        dominant
        
        8Mya in North America, South America & China
        
        10Mya in East Africa & South Asia
    - - more numerous than C4
        
        30 families
        
        intensively cultivated crops
      - Crassulacean Acid Metabolism
        
        Separates PEP carboxylase and RuBisCO temporally
        
        Open stomata at night
        
        Cooler
        
        Less water is lost
        
        PEP carboxylase: CO2 + PEP → oxaloacetate
        
        Oxaloacetate reduced to malate
        
        Malate stored in vacuoles for night
        
        at day
        
        Malate moves out of vacuole & decarboxylated
        
        Some can use C3 during day
      - ADVANTEGOUS
        
        Similar selective pressure to C4
        
        Under high light conditions
        
        Under arid conditions
        
        Under high temperature conditions
        
        CO2 diffusion is limiting
        
        More tortuous routes
        
        Higher leaf thickness
- - - - metabolism may have predated biological macromolecules
      - Hydrogen sulfide react with iron monosulfide to form pyrite
        
        Yield chemical reducing power (hydrogen)
        
        Yield energy
      - fixation of carbon dioxide to form organic compounds
    - - Early Earth different from today
      - Chemosynthesis and heterotrophy metabolisms in lower clades
      - Photosynthesis only found on upper branches of bacterial limb
      - eneergy from inorganic minerals drive metabolism
      - often found in extreme conditions
    - - Hyperthermophilic prokaryotes
      - Do not use oxygens in metabolism
      - Most die in presence of oxygen
    - - Nicotinamide adenine dinucleotide
      - Electron carrier
      - helps with
        
        Move electrons around in cell
        
        Oxidation-reduction
      - reducing agent
    - - Adenosine diphosphate
      - Primary energy courier in all living cells
      - photophosphorylation
  - - - into pyruvate
    - - energy is stored (two ATP per glucose)
      - reducing equivalents are formed (two NADH per glucose).
    - - uses up to 2 ATP
      - produces 4 ATP
      - begins with glucose as C6 and ends as pyruvate as C3
    - - Pyruvate final product that then enters
        
        FERMENTATION
        
        NADH recycled to NAD+
        
        leads to
        
        Lactic acid
        
        Ethanol
        
        Aerobic respiration
    - - ~2.7 bya cyanobacteria used H2O as electron donor
      - Oxygen remained low for 2 billion years
      - Carbon burial
      - Eukaryotes arose ~1.8bya so ~1.3 billion years in anaerobic conditions
  - - - reductive citric acid cycle
      - some bacteria use to synthesize C compounds
      - Precursor to stromal reactions of photosynthesis in plants
    - - Energy required to drive creation of sugars
      - Chemosynthesizers use oxidation of energy-rich inorganic molecules
      - Plants use sunlight
    - - basic sugar used for energy
      - C6H12O6
      - GLUCOSE ISOMERS
        
        same formula C6H12O6
        
        Alpha: energy storage
        
        Beta: structure
        
        STARCH
        
        Amylose
        
        Alpha 1,4 bonds
        
        angular
- - - - Last Universal Common Ancestor (LUCA)
      - Evolution to modern day extant taxa
      - Prebiotic Earth?
      - Evidence of organic microbial mats
      - Stromatolite like structures
      - Isotopic signature suggests photosynthesis
    - - Seed plants ~350mya
      - First land plants before 600mya
      - First identifiable algae ~1.6bya
      - Flowering plants ~150mya
    - - New forms appear suddenly
      - Many reasons: intermediate forms dit not fossilize and very few fossils with limited distribution.
    - - Multicellular photosynthetic organisms that live on land (normally).
      - Some of their features emerged millions years ago
        
        Origin of photosynthesis
        
        Plant cell
        
        Diversity
        
        Transition to land
    - - Common core of molecular features
        
        ATP = life's principal energy currency
        
        Common genetic code: DNA and RNA
        
        Molecular machinery for transcribing DNA to RNA
        
        Machinery to translate RNA messages to proteins: structure and regulation
    - - Evolutionary divergence from common ancestors under natural selection
    - - Based on similiraty of ribosomes
      - History of life microbial
    - - Give clues as to descent
      - Fossils
      - Biological molecules
      - Environmental isotopes
        
        Evidence for photosynthesis
    - - C12: living organisms are enriched from it, compared to nevironment
      - C13: discriminated against by photosynthesis
      - C14: not generally used to time
  - - - It was thought that ammonia and methane were most abundant
      - Chemical reactions could have made live possible
    - - Stanley Miller 1953
        
        Gases thought to be relevant to early atmosphere
        
        experiments showed that reducing atmosphere necessary (4H:1C) & absence of oxygen
    - - Self-replicating
      - Direct synthesis of other compounds
      - Synthesize molecules needed for growth
      - Tapping chemical/solar energy to fuel working
    - - Early conditions not quite right to leap right into RNA
      - PNA can direct formation of RNA complement
      - RNA could have replaced it as a precursor
    - - RNA information rich molecule
      - Form by self-organization
      - DNA provided more stable library
      - Proteins took over most catalytic reactions
    - - Simple beginnings = naturally occurring molecules
      - biosynthetic pathways evolved
      - Complex biochemistry shaped by
        
        Natural selection
        
        Gene duplication
        
        Lateral transfer
- - - - More specialized enzymes
        
        Compartmentalization
  - - - Uses the mitochondria
        
        Continue to strip energy from pyruvate from glycolysis
        
        major steps
        
        CITRIC ACID CYCLE
        
        Acetyl CoA (C2) joins to C4 → Citrate (C6)
        
        Strip off electrons and provide to NAD+→NADH
        
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        PYRUVATE OXIDATION
        
        Electrons taken from pyruvate and given to NAD+
        
        CO2 broken, C3 → C2
        
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        OXIDATIVE PHOSPHORYLATION
        
        NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD)
        
        NAD+ oxidizing agent, accepting electrons
        
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        FLAVIN ADENINE DINUCLEOTIDE (FAD)
        
        oxidizing agent
        
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        CHEMIOSMOTIC, ELECTROCHEMICAL GRADIENT
        
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        ATP SYNTHASE
        
        Catalyzes ATP from ADP + Pi
        
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        ELECTRON TRANSPORT CHAIN
        
        creates proton motive force
        
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        THE PROCESS
        
        1.Electrons dropped off by NADH & FADH2
        
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        GLYCOLISIS
        
        Start with glucose (C6)
        
        Ends with pyruvate (C3)
        
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- - - - share genomes & metabolic abilities
  - - - Dry and wet cycles
        
        DNA + lipids
        
        Sandwich to lipid vesicle with DNA inside
        
        Suggest spontaneously formed
  - - - facilitate metabolism
      - Receptors for functions
        
        self identify
  - - - selection pressure
        
        Favored cells are able to
        
        Those less dependent on exogenous sources of nutrients
        
        Origin basic metabolic pathways
        
        Synthesizing limited molecules
- - - - Endoplasmic reticulum
      - Golgi body
      - Plasma membrane
      - Nuclear envelope
  - - - More permanent, fix things in place
      - Dimers→ tetramers
    - - vesicle movement near membrane
      - Actin
  - - - structure
        
        Outer membrane
        
        Inner membrane
        
        Folded areas are cristae
        
        where oxidative phosphorylation occurs
        
        Matrix
        
        Internal solution
        
        where the citric acid cycle occurs
    - - CHLOROPLASTS
        
        typically green plastids used for photosynthesis.
      - ETIOPLASTS
        
        precursors for 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
  - - - inner membrane
        
        grana
        
        stack of thylakoids
        
        Thylakoid reactions with proteins embedded in thylakoid
        
        Stromal reactions within aqueous stroma
- - - - 70s ribosomes
  - - - chromosomes
        
        80s ribosomes
  - - - cytoskeleton
- - - - the symbiosis becomes interdependence
        
        Mitochondrial containing eukaryote eats a photosynthetic cyanobacterium
        
        later became independent
        
        exchanges DNA
  - - - similar size to bacteria
        
        binary fission
        
        only made from pre-existing ones
        
        ribosomes similar in size to bacteria
        
        double membrane
- - - - Create turgor pressure
        
        Composed primarily of
        
        Hemicellulose
        
        Pectin
        
        Cellulose→𝛃-glucose
        
        CELLULOSE MICROFIBRILS
        
        Made of glucose monomers
        
        𝛃1,4-glucose bonds
        
        dehydration synthesis
        
        Hydrogen bonds make cellulose extremely strong
        
        not many organisms can break/digest cellulose
        
        Fiber in our diets
        
        CELLULOSE SIMILARITIES
        
        CHITIN
        
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        KERATIN
        
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        flexible to permit growth
  - - - Change in hydroxyl group at C1
        
        Distinguishes from 𝜶-glucose
        
        Important for biological activity
      - Major building block of cellulose
- - - - Oxidation is a loss
      - Reduction is a gain