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Metabolism (Gibbs Free Energy (change in free energy can be calculated by…

- - - - measure of a systems instability, or its tendency to change to a more stable state.
  - - - ΔS is the change in the systems entropy
        
        T is the absolute temperature in Kelvin(K)
    - - values will depend on conditions(pH, temperature, and concentrations)
  - - - am process is spontaneous and can perform work only when it is moving toward equilibrium
        
        Metabolism is never at equilibrium
  - - - absorbs free energy from its surroundings
        
        stores free energy in molecules, G increases therefore ΔG is positive.
  - - - proceeds with a net release of of free energy, when a chemical mixture loses free energy, ΔG is a negative.
        
        cellular respiration reaction: C6H12O6 --> 6 CO2 + 6 H2O
- - - - used to make RNA
  - - - push of endergonic reactions that would not occur spontaneously (ex. synthesis of polymers and monomers)
    - - pumping substances across membranes against the direction of spontaneous movement
      - powered by the hydrolysis of ATP
        
        changes the proteins shape and its ability to bind to other molecules
        
        proteins move along the cytoskeletal track
    - - contraction of muscle cells and the movement of chromosomes during cellular reproduction.
      - powered by the hydrolysis of ATP
  - - - the recipient molecule with the phosphate group covalently bonded to
      - the formation of this is key to coupling exergonic and endergonic reactions
        
        more reactive-less stable, more free energy than the original unphosphorlyated molecule
  - - - ATP cycle
        
        muscle cells recycle its entire pool of ATP in under a minute.
        
        free energy must be spent to cause ATP formation
- - - - 2. Pyruvate Oxidation(Intermediate Step)( occurs in the mitochondria)
        
        3. Citric Acid Cycle/Krebs Cycle **(occurs in the matrix of the mitochondria)**
        
        4. Oxidative Phosphorlyation. (occurs in the inner membrane of the mitochondrion)
        
        Start with a net gain of 4 ATP, 10 NADH, and 2 FADH2
        
        the coenzymes NADH & FADH2 provide electrons to the electron transport chain, embedded in the cristae
        
        electrons are passed from one enzyme to another. enzymes "pump" hydrogen to the inter-membrane(in between the inner and outer) of the mitochondria
        
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        Acetyl-CoA binds to a 4 carbon molecule called oxaloacetic acid
        
        this forms a 6 carbon molecule called citric acid
        
        this is then broken down. 2 carbons are removed and excreted as waste in the form of CO2 (catabolic reaction) (exergonic reaction)
        
        the remaining 4 carbons bind to another incoming acetyl-CoA
        
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        2 pyruvates are transported to the mitochondrion
        
        one of the 3 carbons are released and bind to oxygen-creating CO2
        
        this CO2 is released as waste by the organism as it respires (exergonic reaction)(catabolic reaction)
        
        the remaining 2 carbons are oxidized = 1 NADH
        
        these 2 carbon molecules are called acetyl-CoA
      - GLU is taken in by the cells-6 carbon molecules. GLU is then broken into two pyruvates (containing 3 carbons each) (catabolic reaction) (exergonic reaction)
        
        Activation energy for this is released in the form of 4 ATPs & 2 NADH coenzymes. (catabolic)(exergonic)
        
        Only 2 of the ATPs are used--there is a net gain of 2 ATPs
        
        if O is not available, NADH will recycle its H ions back onto the pyruvate creating lactic acid
        
        this is called fermentation
        
        in this case only 2 ATP are produced.
  - - - fermentation
        
        cristae
        
        facilitated diffusion
        
        phosphoylate
        
        respires
        
        aerobic respiration
        
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        to exhale; breath
        
        addition of a phosphate to an organic compound
        
        passage of molecules down their concentration gradient; requires no energy
        
        infolding of the inner membrane of the mitochondrion. inner membrane houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP
        
        catabolic process that makes a limited amount of ATP from glucose without an electron transport chain and that produces ethyl alcohol or lactic acid
      - sequence of electron carrier molecules that shuttle electrons down a series of redox actions that release energy used to make ATP.
  - - - cellular respiration is a measure in the change of entropy, or a change in disorder.
        
        when something gains entropy or gains disorder, it loses energy. Which is the process of cellular respiration.
  - - - lactic acid
        
        ATP
        
        pyruvate
        
        NADH
        
        FADH2
        
        ADP
        
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        temporarily stores electrons during cellular respiration
        
        1 glucose molecule forms 2 pyruvates
        
        ATP is produced by lactic acid when oxygen is scarce in the body
      - the enzyme responsible for making ATP from ADP and inorganic phosphate
- - - - 2. Dark Reactions/Calvin Cycle occurs in the stroma
        
        starts with the ATP produced earlier in the light reactions that was left in the stroma of the thylakoid
        
        1 carbon + 5 carbon(RuBisCo), forming a 6 molecule carbon
        
        this then breaks into a 3 carbon molecule (catabolic) (exergonic)
        
        the molecule then gains energy from ATP + NADPH (anabolic) (endergonic)
        
        the molecule is then transformed into G3P
        
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      - water & light enters through the cell wall and into the membrane of the chloroplast (anabolic)(endergonic)
        
        this produces oxygen, NADPH, and ATP
        
        (the energy produced goes into the Calvin cycle later on) where CO2 goes in and glucoses goes out
        
        light and water enter the first membrane protein called photo system 2
        
        light powers the movement of an electron through an electron transport chain--this electron is changed into NADPH
        
        a water molecule is then split, leaving a oxygen molecule that will leave the cell as a waste product(catabolic) (exergonic)
        
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  - - - cytoplasm
        
        chloroplast
        
        stroma
        
        grana
        
        thylakoids
        
        structure of the chloroplast organelle responsible for
        
        stacks of thylakoids embedded in the stroma of a chloroplast
        
        a microscopic pore surrounded by guard cells in the epidermis of leaves and other stems that allows gas exchange between the environment and the interior of the plant
        
        organelle in the plant cell responsible for
        
        the contents of the cell bound by the plasma membrane
      - structure of the plant cell (boarder)
  - - - photosynthesis is a measure in the change of enthalpy, or the change in order in a system.
        
        when enthalpy increases there is more order in a system
  - - - cytochrome complex
        
        photosystem 1
        
        NADP+ reductionase
        
        ATP synthase
        
        complex of several membrane proteins that use energy of a hydrogen ion concentration gradient to make ATP
        
        the oxidized form of nicotinamide adenine dinucleotide phosphate; an electron carrier that can accept electrons becoming NADPH- this temporarily stores energized electrons
        
        a light capturing unit in the chloroplast's thylakoid membrane
        
        iron containing protein that is a component of electron transport chains in the mitochondria and chloroplasts
      - 1 of 2 light-capturing units in a chloroplast's thylakoid membrane
- - - - initial investment of energy, used to start a reaction
        
        transition state
        
        when molecules have absorbed enough energy to for the bonds to break the reactants are in an unstable state
    - - process by which a catalyst selectively speeds up a reaction without without itself being consumed
        
        an enzyme cannot change the ΔG for a reaction; it cannot make an endergonic reaction exergonic.
    - - the reactant an enzyme acts on
        
        high concentration of substrates means the enzyme is saturated
        
        rate of reaction after this can only be increases by adding more enzymes
      - enzyme-substrate complex
        
        the enzyme binds to its substrate
        
        active site
        
        pocket or groove on the surface of the enzyme where catalysis occurs
        
        saturated
        
        induced fit
        
        tightening the binding after initial contact
    - - permanent change in a gene.
  - - - coenzyme
        
        an organic cofactor
        
        enzyme inhibitors
        
        competitive
        
        reduce productivity of enzymes by blocking substrates from entering active sites.
        
        non-competitive
        
        do not directly compete with the substrate to bind to the enzyme at the active site.
        
        allosteric regulation
        
        any case in which a proteins function at one site is affected by the binding of a regulatory molecule to a separate site.
        
        cooperativity
        
        amplifies the response of enzymes to substrates
        
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- - - - Kinetic
        
        energy associated with the relative movement of objects(ex. rollercoaster)
      - Thermal
        
        kinetic energy associated with the random movement of atoms or molecules
        
        heat
        
        thermal energy transferred from one object to another
      - Potential
        
        energy that is not kinetic, or an object that is not presently moving
      - Chemical
        
        potential energy available for release a chemical reaction
  - - - Metabolism is the totality of an organisms chemical reactions
    - - a specific molecule which is then altered in a series of defined steps, resulting in a certain product
    - - release energy by breaking down complex molecules into simpler compounds. (ex. cellular respiration)
    - - consume energy to build complicated molecules from simpler ones.
      - also called biosynthetic pathways
      - ex. the synthesis of amino acids from simpler molecules
- - - - First Law
        
        the energy of the universe is constant
        
        energy can be transferred and transformed but it cannot be created or destroyed
      - Second Law
        
        every energy transfer or transformation increase the entropy of the universe
        
        entropy
        
        a measure of molecular disorder, randomness
        
        spontaneous process
        
        "energetically favorable"
        
        a decrease in entropy is said to be non spontaneous--will happen only if energy is supplied
    - - surroundings
        
        everything outside of the system
      - isolated systems
        
        unable to to exchange either energy or matter with its surroundings
      - open systems
        
        energy an matter can be transferred between the system and its surroundings(ex. organisms)
    - - Order
        
        meaning organized
        
        doesn't violate the second law of thermodynamics
      - Disorder
        
        un organized