AP Biology:
Notes:  Dark Reaction

Light Reactions Review:
     noncyclic electron flow:
        The photosystems of the thylakoid membrane transform light energy to the
        chemical energy stored in NADPH and ATP. This process:
        *Pushes low energy-state electrons from water to NADPH, where they are 
         stored at a higher state of potential energy.  NADPH, in turn, is the electron 
         donor used to reduce carbon dioxide sugar (Calvin cycle).
        *Produces ATP from this light driven electron current
        *Produces oxygen as a by-product
      cyclic electron flow:
        electron ejected from P700 reach ferredoxin and flow back to P700.  This process:
        *Produces ATP
        *Unlike noncyclic electron flow, does not produce NADPH or O₂

Dark Reaction?calvin cycle uses ATP and NADPH to convert CO₂ to sugar: 
      * The Calvin cycle is similar to the Krebs cycle in that the starting material is regenerated 
         by the end of the cycle
       * Carbon enters the Calvin cycle as CO₂ and leaves as sugar
       *ATP is the energy source, while NADPH is the reducing agent that adds high energy 
         electrons from sugar
       * The calving cycle actually produces a three-carbon sugar glyceraldheyde 3-phospate 
          (G3P)

Phase 1:  Carbon Fixation The Calvin cycle begins when each molecule of CO₂ 
                is attached to a five-carbon sugar, ribulose biphospate (RuBP)
                   * This reaction is catalyzed by the enzyme RuBP carboxylase (rubisco)--one of 
                      the most abundant proteins on Earth.
                   * The produce of this reaction is an unstable six-carbon intermediate that 
                      immediately splits into two molecules of 3-phosphoglycerate
                   * For every three  CO₂ molecules that enter the Calving cycle via rubisco, 
                      three RuBP molecules are carboxylated forming six molecules of 
                      3-phosphoglycerate.
Phase 2:  Reduction  This endergonic reduction phase is a two-step 
                process that couples:

                 ATP hydrolysis with the reduction of 3-phosphoglycerate to glyceraldehyde 
                 phosphate.
                       *An enzyme phosporylates 3-phosphoglycerate by transferring a phosphate group 
                         from ATP.  This reaction:
                       * Produces 1, 3-biosphosphoglycerate
                       * Uses six ATP molecules to produce six molecules of 1, 3 biosphosphoglycerate.
                          Primes 1, 3-bisphosphoglycerate for the addition of high-energy electrons 
                          from NADPH.
                Electrons from NADPH reduce the carboxyl group of 1,30bisphosphoglycerate 
                to the aldehyde group of glyceraldehyde 3-phosphate (G3P)
                        * This cycle begins with three five-carbon RuBP molecules--a total of 15 
                           carbons
                        * The six G3P molecules produce contain 18 carbons, a net gain of three 
                           carbons from  CO₂
                        * One G3P molecule exits the cycle; the other five are recycled to regenerate 
                           three molecules of RuBP.

Phase 3:  Regeneration of  CO₂ acceptor (RuBP).  A complex series of reactions 
rearranges the carbon skeletons of five G3P molecules into three RuBP molecules.
        *These reactions require three ATP molecules
        *RuBP is thus regenerated to begin the cycle again.

For the net synthesis of one G3P molecule, the Calvin cycle uses the products of the 
light reactions:
        9 ATP molecules
        6 NADPH molecules
G3P produced by the Calvin cycle is the raw material used to synthesize glucose and 
other carbohydrate.
        The Calvin cycle uses 18 ATP and 12 NADPH molecules to produce one 
        glucose molecule.

Alternative mechanisms in plants
A metabolic pathway called photorespiration reduces the yield of photosynthesis.
Photorespiration: In plants, a metabolic pathway that consumes oxygen, 
evolves carbon dioxide, produces no ATP and decreases photosynthetic output.
        *Occurs because the active site of rubisco can accept  O₂ as well as  CO₂.
        * Produces no ATP molecules
        * Decreases photosynthetic output by reducing organic molecules used 
           in the Calvin cycle
When  O₂ concentration in the leaf's air spaces is higher than  CO₂ concentration, 
rubisco accepts  O₂ and transfers it to RuBP.  (The "photo" in photorespiration 
refers to the fact that this pathway usually occurs in light when photosynthesis 
reduces  CO₂ and raises  O₂ in the leaf spaces)

        It is know that some crop plants (e.g. soybeans) lose as much as 50% 
        of the carbon fixed by the Calvin cycle to photorespiration
        If photorespiration could be reduced in some agricultural plants, crop 
        yields and food supplies would increase.
        Under these conditions, plants close their stomata to prevent dehydration 
        by reducing water loss from the leaf.
        Photosynthesis than depletes available carbon dioxide and increases oxygen 
        within the leaf air spaces.  This condition favors photorespiration

C₄ plants
The Calvin cycle occurs in most plants and produces 3-phosphoglycerate, a three-
carbon compound as the first stable intermediate.
        *These plants are called C₃ plants because the first stable intermediate has 
        three carbons
        *Agriculturally important C₃ plants include rice, wheat, and soybeans

Many plant species preface the Calvin cycle with reactions that incorporate 
carbon dioxide into four-carbon compounds
        *These plants are called C₄ plants
        *The C₄ pathway is used by several thousands species in at least 19 families 
           include corn and sugarcane, important agricultural grasses.
        *This pathway is adaptive, because it enhances carbon fixation under conditions 
          that favor photorespiration, such as hot, arid environments.

Step 1:  
            *CO₂ is added to phosphoenolpyruvate (PEP) to form oxaloacetate, a four
              carbon product.
           * PEP carboxylase is an enzyme that adds  CO₂ to PEP.  Compared to rubisco, 
              it has much greater affinity for  CO₂ and has no affinity for  O₂.
           * Thus PEP carboxylase can fix  CO₂ efficiently when rubisco cannot--under hot,
             dry conditions that cause stomata to close,  CO₂ concentrations to drop and  
             O₂ concentrations to rise.
Step 2:  After  CO₂ has been fixed by mesophyll cells, the convert oxaloacetate to 
              another four-carbon compound (usually malate).

Step 3:  Mesophyll cells than export the four-carbon produces (e.g. malate) 
              through plasmodesmata to bundle-sheath cells
               In the bundle-sheath cells the four carbon compounds release  CO₂ 
                   which is then fixed by rubisco in the Calvin cycle.
              Mesophyll cells thus pump  CO₂ into bundle-sheath cells, minimizing
               photorespiration and enhancing sugar production by maintaining a  
               CO₂ concentration sufficient for rubisco to accept  CO₂ rather than 
                oxygen.

CAM plants
A second photosynthetic adaptation exists in succulent plants adapted to 
very arid conditions.  These plants open their stomata primarily at night and 
close them during the day (opposite of most plants).
        *This conserves water during the day, but prevents  CO₂ from entering 
        the leaves.
When stomata are open at night,  CO₂ is taken up and incorporated into a 
variety of organic acids.  This mode of carbon fixation is called crassulacean 
acid metabolism (CAM).
       * The organic acids made at night are stored in vacuoles as mesophyll cells
         until morning, when the stomata close.
        *During daytime, light reactions supply ATP and NADPH for the Calvin 
         cycle.  At this time  CO₂ is released from the organic acids made the
         previous night and is incorporated into sugar in the chloroplasts.