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Metabolism Ch. 8 (Photosynthesis (Dark Cycle (Phase 1: the Calvin Cycle…

- - - - chloroplast
        
        mesophyll
        
        the tissue in the interior of the leaf
        
        stomata
        
        the microscopic pores on the leaf that allows carbon dioxide to enter into the plant
        
        stoma is singular, meaning mouth
        
        Stroma
        
        a dense fluid surrounded by two membranes
        
        Chlorophyll
        
        the green pigment that gives the leaves their color
        
        Chlorophyll a
        
        the key light-capturing pigment that participates directly in the light reaction
        
        Chlorophyll b
        
        accessory pigment
        
        Thylakoid
        
        sacs suspended within the stroma and is known as the third membrane of the system
        
        stacks in the thylakoid are called grana
      - light and water are taken in
        
        the water is broken down into hydrogen ions, electrons , and oxygen
        
        the oxygen is excreted out of the thylakoid as a waste product
        
        the hydrogen ions stays inside of the thylakoid
        
        the electrons are transported to photosynthesis II and all other proteins that allows molecules to pump in and out of the thylakoid
        
        electrons are passed on from Photosystem II into cytochrome complex
        
        the cytochrome complex pumps hydrogen ions from the stroma into the thylakoid.
        
        electrons get passed on to other proteins such as Photosystem I
        
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        photosysten II is known as P680 because the pigment is best at absorbing light having wavelength of 680 nm
        
        Linear electron Flow
        
        energy transformation is a flow of electrons through photo systems and other molecular components built into the thylakoid membrane
        
        Photosystem II gets the energy they need from the sun in order to break down water molecules
        
        These is an example of a catabolic and exergonic reaction because energy is realsed and product is being broken down
        
        exergonic
        
        the electron and hydrogen ions are transferred from water to an electron acceptor called NADP+
        
        the light reaction uses the solar energy to reduce NADP+ to NADPH by adding a pair of electrons along with an hydrogen ion
        
        the solar energy also generates ATP using chemiosmosis to power the addition of a phosphate group to ADP
        
        Phosphorylation
        
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        the light is absorbed through the chlorophyll
  - - - Carbon Fixation
        
        initial corporation of carbon into organic compounds
        
        the calvin cycle reduces the fixed carbon to carbohydrate by the addition of electrons
        
        this power is provided by NADPH that acquired its electrons in the light reaction
        
        to convert Carbon dioxide the Calvin cycle requires energy chemical energy in the form of ATP
        
        this allows the calvin cycle to make sugar but only with the help of NADPH and ATP being produced from the light reaction
        
        C3 plants
        
        the first organic product of carbon fixation is a three-carbon compound
        
        produce less sugar because the declining level of carbon dioxide in the leaf starves the Calvin Cycle
        
        when carbon dioxide becomes scarce, oxygen could build up in the leaves and used in the place of carbon dioxide
        
        photorespiration
        
        peroxisomes and mitochondria within the plant cell rearrange and split this compound, releasing carbon dioxide
        
        uses ATP rather than generating it this decreases photosynthetic output by siphoning organic material from the Calvin Cycle and release carbon dioxide that would otherwise be fixed
        
        C4 plants
        
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        CAM
        
        Crassulacean Acid metabolism
        
        a CAM plant stores the organic acids they make during the night in their vacuoles
        
        when the light reaction occurs, ATP and NADPH are supplied to realsed carbon dioxide from the organic acids made the night before to become incorporated into sugar in the chloroplasts
    - - the enzyme that catalyzes this first step is known as rubisco
      - Product: a six- carbon intermediate that is short-lived because it is energetically unstabled and it splits in half forming two molecules of 3- phosphoglycerate
      - Phase 2: Reduction. each molecule of 3-phosphoglycerate receives an additional phosphate group from ATP, becomin 1, 3- bisphoglycerate
        
        a pair of electrons donated from NADPH reduces 1, 3-bisphosphoglycerate, which loses a phosphate group becoming glyceraldehyde 3- phosphate (G3P)
        
        G3P is a sugar- the same three-carbon sugar formed in glycolysis by the splitting of glucose
        
        for every three molecules of Carbon Dioxide, there are six molecules molecules of G3P formed but only one molecule of this three-carbon sugar can be counted as a net gain of carbohydrates because the rest are required to complete the cycle
  - - - the reactants in photosynthesis are water and carbondioxide
      - the products of photosynthesis are oxygen and glucose
    - - objects that have fixed quantity of energy
      - Step 1: strikes one of the pigment molecules in a light-harvesting complex, boosting one of its electrons to a higher energy level.
        
        Step 2: This electron is transferred from the excited P680 to the primary electron acceptor.
        
        Step 3 : an enzyme catalyzes the splitting of a water molecule into two electrons, two hydrogen ions and an oxygen atom. The electrons are supplied one by one to the P680 pair , each electron replacing one transferred to the primary electron acceptor
        
        Step 4:each photoexcited electron passes from the primary electron acceptor of PII to PI via an electron transport chain
        
        the electron transport chain is made up of the electron carrier plastoquinone and a protein called plastocyanin
        
        Step 5 the potential energy stored in the proton gradient is used to make ATP in a process called chemiosmosis
        
        Step 6 P700 can now act as an electron acceptor, accepting an electron that reaches the bottom of the electron transport chain from PS II.
        
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        chemiosmosis is an electron transport chain that pumps hydrogen ions across a membrane as electrons are passed through a series of carrierrs that are progressively more electronegative
- - - - Each pyruvate contains three carbons and one carbon from each of the pyruvates are broken off
        
        the one carbon that was broken off from the 3-carbon pyruvate binds to an oxygen and an electron
        
        As a product, Carbon Dioxide is produced and released by the organism during respiration
        
        The two carbons that remain from each of the pyruvates binds with an Acetyl COA
        
        Anabolic reaction occurs
        
        Product: Acetyl COA is produced
        
        Exergonic Reaction
        
        energy is released after the carbons separate
        
        As a result, 2 NAD+ are yielded
        
        2 NAD+ is then reduced to form produce 2 NADH
        
        NADH is an electron carrier
        
        This is an endergonic reaction
      - The pyruvates form from a catabolic reaction of glucose being split
  - - - Makes citric acid containing 6 carbons
        
        the citric acid is then broken down into 2 Carbon Dioxide molecules and a 4 carbon oxaloacetic acid to restart the second repetition
        
        End products
        
        2 ATPS
        
        6 NADH
        
        2 FADH2
        
        The Carbon Dioxide molecules are then lost from the cycle in respiration
      - is an endergonic reaction
      - Is an anabolic reaction because the molecules bind to form citric acid
  - - - These molecules help pump hydrogen ions through the inner membrane
        
        the high concentration of hydrogen ions then bind to oxygen to make water
        
        water is the waste product of cellular respiration
      - the electron carriers alternate between reduced and oxidized states as they accept and donate electrons
        
        oxidative agent
        
        the molecule that receives the electron from the other molecule , therefore giving the molecule a higher charge
        
        Reductive agent
        
        the molecule that donates the electron, giving the other molecule a more negative charge
    - - converts ADP into ATP
        
        Is an anabolic relationship and an endergonic reaction
      - The ATP Synthase is powered by the pumping of hydrogen ions that moves through the inter membrane of the mitochondria
        
        Chemiosmosis
        
        is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work
        
        proton-motive force
        
        the hydrogen ion gradient that is resulted
      - 3ADPs turns into ATP
      - 1 FADH2 phosphoralate 2 ATP
    - - Prosthetic Groups
        
        tightly bound to these proteins
        
        nonprotein components such as cofactors and coenzymes essential for the catalytic functions of certain enzymes
  - - - glucose
        
        a six-carbon sugar that is split into two three-carbon sugars
        
        these smaller sugars are then oxidized and their remaining atoms are rearranged to form two molecules of pyruvate
        
        Pyruvate
        
        the ionized form of pyruvate acid
        
        the pyruvate in the eukaryotic cell where the oxidation of glucose is completed
        
        No carbon is released as CO2 during glycolysis
    - - the cell spends ATP
        
        ATP is produced by the substrate-level phosphorylation
        
        4 ATPs are produced
        
        NAD+ is reduced to NADH by electrons released from oxidation of glucose
        
        2 NADH are produced
    - - 4 ADPs form 4 ATPs
      - 2 NAD+ yields 2 NADH and 2 hydrogen ions
- - - - Delta
        
        Delta refers to the change in
        
        Delta H
        
        symbolizes the change in the system's enthalpy ( which is equivalent to the total energy)
        
        Enthalpy
        
        if the enthalpy in a system increases then the Available energy increases while the entropy decreases
        
        measures order in a system
        
        If the enthalpy decease then the available energy will decrease while the entropy will increase
        
        Delta S
        
        symbolizes the change in a system's entropy
        
        Delta G
        
        the value of Delta G is dependent upon pH, temperature, and concentration of reactants and products
        
        Negative Delta G
        
        are spontaneous reactions
        
        decrease the system's free energy
        
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        T (Delta) S must be positive, meaning the system gives up order and S increases
        
        Delta H must be negative where the system gives up enthalpy and H decreases
        
        (Delta G < 0)
        
        Delta G is negative when the process involves a loss of energy during change from initial state to final state
        
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        difference between the free energy of the final state and the free energy of the initial state
      - T: symbolizes the absolute temperature in Kelvin (K) units
        
        K= C degrees celsius+ 273
  - - - an unstable system that tends to turn into a more stabled system
        
        (lower G )
        
        Example:
        
        States of maximum stability refers to Equilibrium
        
        when the forward and backwards reaction occur at the same rate
        
        therefore there is no further change in the concentration between reactants and products
        
        free energy of the mixture of reactants and products decreases
        
        G is at the lowest possible value in a system that reaches equilibrium
        
        a process is spontaneous and can perform work only when it is moving toward equilibrium
  - - - is one that absorbs free energy from its surrounding
        
        Delta G increases because because free energy is stored in molecules
        
        Such reactions are Non spontaneous reaction
      - Example: E- , H+, NADP , in the NADPH synthase
- - - - begins with a specific molecule that is altered through a series of defined steps
      - some metabolic pathways release energy by breaking down complex molecules to simpler compounds
        
        This is known as Catabolic Pathways
        
        Example: Sucrose is broken down into fructose and glucose
        
        A degradative process where organic fuels are broken down in the presence of oxygen
        
        Cellular Respiration
        
        can be referred to as the "downhill" avenue of the metabolic landscape
      - Anabolic Pathway
        
        the exact opposite of a catabolic pathway
        
        consumes energy to build complicated molecules from simpler ones
        
        can be referred to as the "uphill" avenue of the metabolic landscape
        
        also known as Bio synthetic pathways because they are synthesizing new molecules
        
        Example: synthesis of amino acids from simpler molecules and synthesizes of proteins from amino acids
      - Energy is fundamental to all metabolic pathways
        
        energy released from the catabolic pathway can be stored and used to drive the reaction of the anabolic pathway
        
        Energy is the capacity to cause change and is used to do work
        
        Energy is the ability to rearrange matter
        
        Example: energy is expended when turning pages of a book
        
        Kinetic Energy
        
        relative motion of an object
        
        Thermal Energy
        
        associated with the random movement of atoms or molecules and can be transferred from one object to another
        
        This process is known as heat
        
        heat is the total movement of all the molecules
        
        Potential Energy
        
        energy that matter possess because of its location or its structure
        
        For example: Water behind a dam posses potential energy because it is high above sea level
        
        Molecules posses energy because of the arrangement of electrons in their bonds
        
        Chemical Energy
        
        potential energy available for release in a chemical reaction
        
        for example: catabolic reactions release energy during the breakdown of products
        
        derived from light energy absorbed by plants during photosynthesis. Organisms are energy transformers
        
        The Laws of Energy Transformation
        
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- - - - cell is comparmentalized
      - enzymes assemble in a mutlienzyme complex
        
        the product from the first enzyme becomes the substrate for the next enzyme and so on
        
        For example : the enzyme for the second and third stages of cellular respiration reside in specific locations within the mitochondria
  - - - the binding of an activator to a regulatory site stabilizes the shape that has functional active sites
      - substrate molecule binding to one active site changes the shape in all subunits
        
        increases catalytic activity at the other active sites called cooperativity
    - - stabilizes the inactive form of the enzyme
      - Feedback Inhibition
        
        a metabolic pathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the early pathway
        
        prevents the cell from making too much of one thing
        
        can mainly occur in anabolic pathways
        
        Example: as isoleucine accumulates, it slows down its own synthesis by allosterically inhibitng the enzymes in the first step
- - - - Chemical Work
        
        pushing of endergonic reactions that would not occur spontaneously
        
        Example: synthesis of polymers from monomers
        
        ATP hydrolysis drives chemical work
        
        Endergonic reaction
        
        if delta G of an endergonic reaction is less than the amount of energy released by ATP hydrolysis, then the two reactions can be coupled so that the coupling reaction is exergonic
        
        Phosphorylation
        
        the transfer of a phosphate group from ATP to some other molecule (the reactant)
        
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      - Transport Work
        
        the pumping of substances across membranes against the direction of spontaneous movement
        
        directly , carries out active transport of a solute
        
        indirectly, noncovalent binding of TP and its hydrolytic products
      - Mechanical Work
        
        the contraction of muscle cells , and the movement of chromosomes during cellular reproduction
        
        Example: beating of cilia
        
        ATP is bound noncovalently to the motor proteins,
        
        ATP is hydrolyzed, releasing ADP and Phosphorus
        
        Another ATP molecule can then bind
        
        then bind to the cytoskeleton resulting in movement of the protein along the cytoskeletal track
    - - the use of exergonic process to drive and endergonic one
      - ATP is the immediate source of energy that powers cellular work
        
        Adenosine Triphosphate
        
        contains the sugar ribose, a nitrogenous base adenine and a chain of three phosphate groups
        
        bonds between the phosphate groups can be broken by hydrolysis
        
        when a bond id broken, a molecule from the inorganic phosphate leaves the ATP and becomes Adenosine Diphosphate (ADP)
        
        Exergonic reaction because it releases energy and is breaking down a structure
        
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        the release of free energy merely heats the surrounding
        
        Example: the process of shivering uses ATP hydrolysis during muscle contraction to warm the body
        
        a nucleoside triphosphate that is used to make RNA
        
        a renewable resource that can be regenerate by the addition of phosphate to ADP
        
        the free energy required to phosphorylate ADP comes from exergonic breakdown reactions
        
        also known as a Catabolism reaction
        
        The ATP Cycle
        
        couples the cell's energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones.
        
        is a non spontaneous reaction, free energy must be spent to make it occur
- - - - a chemical agent that speeds up a reaction without being consumed by the reaction
        
        enables the reactant molecules to absorb enough energy to reach transition state even at moderate temperatures
        
        the activity of an enzyme is affected by the temperature and pH
        
        Temperature
        
        as temperature increases the enzymatic reaction increases as well
        
        disrupts the hydrogen bonds, ionic bonds, and other weak attractions that stabilizes the active shape
        
        Denaturing
        
        pH
    - - each enzyme is specific for what reaction they catalyze
        
        they pair with subtrates, making an enzyme-substrate complex
        
        substrates
        
        the reactant an enzyme acts on
        
        the catalytic action of the enzyme converts the substrate to the product of the reaction
        
        Example: Enzyme+ Substrate(s) <=> Enzyme - substrate complex <=> Enzyme + Product (s)
        
        Active Site
        
        a pocket or groove on the surface of the enzyme where catalysis occurs
        
        a restricted region of the enzyme molecule actually binds to the substrate
        
        formed by the enzyme's amino acids
        
        when substrate enters the active site , the enzyme hanges shape due to the interactions between the substract's chemical groups and chemical groups on the side chains of the amino acid
        
        induced fit
        
        the tightening of the binding after initial contact
        
        most enzyme names end in -ase
        
        Example.: Sucrase breaks down sucrose
        
        Lipase breaks down lipids
        
        Carbohydrase breaks down carbohydrates
        
        Protease breaks down proteins
    - - Chemical Reaction
        
        involves bond breaking and bond forming between molecules
        
        Example: hydrolysis of sucrose involves breaking the bond between glucose and fructose and one of the bonds of a water molecule
        
        contortion occurs
        
        the bending of a shape into a certain form
        
        Example: bending of a metal key ring when you pry it open to add a key
        
        before the reaction occurs, the molecule is highly unstabled
        
        reactant molecules must absorb energy from their surrounding to form new bonds
        
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        activation energy
        
        the initial investment of energy for starting a reaction
        
        the energy required to contort the reactant molecules so the bond can break
        
        supplied by heat in forms of thermal energy that the reactant molecules absorb from the surrounding
        
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      - the more substrate molecules, the more frequently they access the active sites of molecules
        
        there is a limit to how fast a reaction can be pushed by adding more substrate to a fixed concentration of enzymes
        
        saturated
        
        when enzyme population is saturated, adding more enzymes will increase the rate of product formation
    - - non protein helpers for catalytic activity
      - can be bound tightly to the enzyme as a permanent resident
      - can be bound loosely and reversibly along with substrate
      - inorganic
        
        zinc
        
        iron
        
        copper
      - if cofactor is said to be organic
        
        it is a coenzyme
        
        Example: Vitamins
    - - Competitive Inhibitors
        
        reduce the productivity of enzymes , blocking substrates from entering active sites
        
        this can be overcame be increasing the concentration of substrates so active sites become more available
      - Noncompetitive Inhibitors
        
        do not directly compete with the substrate to bind to the enzyme at the active site
        
        impede enzymatic reactions by binding to another part of the enzyme
        
        causes the enzyme to change its shape making the active site less effective for substrates