8.2 Photosynthesis

8.2.1. Chloroplast structure:

The chloroplast is a large complex double membrane organelle that performs the function of photosynthesis within plant cells and also contains a substance called chlorophyll that is essential for photosynthesis. The chlorophyll in addition also produces a sugar from the sun this sugar is made within the cell; this provides food for all the organelles.

Inter membrane:The membrane of the mitochondria that is the site of electron transport and chemiosmosis., where the electron transport chain occurs, Where the electron transport chain of cellular respiration occurs

Outer membrane:Forms a boundary between mitochondrion and cytoplasm; helps define the inner membrane space, smooth membrane in mitochondria

Inner membrane space:Fluid filled space between the inner and outer mitochondrial membranes, the region between the inner membrane and the outer membrane of a mitochondrion or a chloroplast. The main function of the intermembrane space is nucleotide phosphorylation.

Stroma: Gel like substance. Sugars are made in the stroma by the enzymes form the Calvin cycle. Light independent reactions take place here.

Granum: A stacked portion of the thylakoid membrane. The Grana functions in the light reactions of photosynthesis

Thylakoid: The disk shaped organelle. The structure of the thylakoid is the site of the photosynthetic light reactions takes place. These are the reactions that initially excite the electrons so they fall down the electron transport chain and release ATP and continue on to release NADPH.

Lumen: this is the thylakoid membrane bound to the chloroplast compartment.

Lamella: linking a thylakoid within one granum to one in another. They are the sites of photosystem I. Simply put, lamellae may be considered as a pair of membranes containing chlorophyll. It is placed between the two primary cell walls of two plant cells and made up of intracellular matrix. 

8.2.2 STAGES OF PHOTOSYNTHESIS:

 Two stages:

8.2.3 LIGHT DEPENDENT REACTIONS: There are two types of photosystems, Photosystem II and Photosystem I. When a chlorophyll molecule absorbs light, the energy from this light raises an electron within the chlorophyll molecule to a higher energy state. The chlorophyll molecule is then said to be photo activated. Excited electron anywhere within the photosystem are then passed on from one chlorophyll molecule to the next until they reach a special chlorophyll molecule at the reaction center of the photosystem. This special chlorophyll molecule then passes on the excited electron to a chain of electron carriers. 

 Starts within Photosystem II. As this excited electron passes from one carrier to the next it releases energy. This energy is used to pump protons (hydrogen ions) across the thylakoid membrane and into the space within the thylakoids. Then this forms a gradient. Protons travel across the membrane down the concentration gradient, but to do so the must pass through ATP synthase. This is located in the thylakoid membrane. The energy used to move protons down the concentration gradient is used to synthesis ATP from ADP and inorganic phosphate. The synthesis of ATP is called non-cyclic photophosphorylation. Photosystem I then accepts the electrons from the chain of electron carriers. These electrons replace electrons previously lost from Photosystem I. Photosystem I then absorbs light and becomes photo activated. The electrons become excited again as they are raised to a higher energy state. These excited electrons then pass along a short chain of electron carriers and are eventually used to reduce NADP+ in the stroma.  NADP+ accepts two excited electrons from the chain of carriers and one H+ ion from the stroma to form NADPH. In addition to producing NADPH, the light dependent reactions also produce oxygen as a waste product.  

Summery:

·      Light energy is converted into chemical energy.

▪       Chlorophyll molecules are attached to the thylakoid membranes.

▪       They are often associated with accessory pigments and other proteins to form Photosystem.

▪       At the center of all photosystem are forms of chlorophyll a each of which is specialized to absorb a particular wavelength of light.

▪       Electrons within the chlorophyll absorb the energy from photons and this raises them to higher 'excited' states.

Excited electrons are more easily lost from the chlorophyll, which is a form of oxidation

8.2.5 LIGHT INDEPNDENT REACTONS: occurring in the stroma of the chloroplast and involve the conversion of carbon dioxide and other compounds into glucose. The light-independent reactions can be split into three stages; these are carbon fixation, the reduction reactions and finally the regeneration of ribulose bisphosphate. Collectively these stages are known as the Calvin Cycle. 

First stage: carbon fixation- The single carbon in carbon dioxide is first trapped by Ribulose bisphosphate (5C) to form a 2 molecules of Glycerate-3-phosphate (GP).  The product of the reactions is a 6-carbon intermediate, which is unstable and immediately splits in half to form two molecules of 3- phosphoglycerate

Second stage: reduction- each molecule of 3-phisphogycerate recives an additional phosphate group from ATP, becoming 1,3 bisphosphoglycerate. NADPH reduce the carboxyl group. Which store potential energy. G3P is a sugar- the same three-carbon sugar formed by glycolysis. For every three molecules of carbon dioxide there are six molecules of G3P. But only one molecule of this three- carbon sugar can be counted as a net gain of carbohydrate.  One molecule exits the cycle to be used in the plant.

Third stage: regeneration- In a complex series of reactions, the five molecules of G3P are rearranged by the last steps of the Calvin cycle into three molecules of RuBP. For this to happen uses three more molecules of ATP. Now the RuBP is prepared to receive carbon dioxide again then the cycle happens again.

-       The regeneration of RuBP is essential for carbon fixation to continue. Five triose phosphate molecules will undergo a series of reactions requiring energy from ATP, to form three molecules of RuBP. RuBP is therefore consumed and produced during the light-independent reactions and therefore these reactions form a cycle, called the Calvin cycle.

8.2.4 PHOTOPHOSPHORYLATION

• As the electrons (released from chlorophyll) cycle through the electron transport chains located on the thylakoid membrane, they lose energy
• This free energy is used to pump H⁺ ions from the stroma into the thylakoid
• The build up of protons inside the thylakoid creates an electrochemical gradient (or proton motive force)
• The H⁺ ions return to the stroma via the transmembrane enzyme ATP synthase, which uses the potential energy from the proton motive force to convert ADP and an inorganic phosphate (Pi) into ATP
• This process is called chemiosmosis

8.2.6 STRUCTURE AND FUNCTION OF THE CHLOROPLAST 

(for more detail refer to 8.2.1)

-Function- To capture light energy, which is stored in ATP. This is all possible by the

A pigment called chlorophyll; chlorophyll absorbs the energy from sunlight and utilize this energy to synthesize food from carbon dioxide and water. Chloroplast is involved in the photosynthesis process of the plants.

8.2.7 ACTION SPECTRUM AND ABSORPTION SPECTRUM.

-Absorption spectrum: provides us clues to relative effectiveness of different wavelengths for driving photosynthesis, since light can perform work in chloroplast only if it is absorbed.  (Wavelengths are absorbed and to what extent.)

-The three curves show the wavelengths of light best absorbed by three types of pigments extracted from chloroplast. 

-Action spectrum: Shows the relative performance of different wavelengths. An action spectrum illuminates chloroplasts different colors of lights and then plotting wavelengths against some measure of photosynthetic rate such as carbon dioxide consumption or oxygen release.  (Wavelengths of light can actually be used to make photosynthesis work.)

-This graph plots the effectiveness of different wavelengths of light during photosynthesis. The peaks of the action spectrum are broader than the peaks in the absorption spectrum for chlorophyll and the valley is narrower and not as deep. 

8.2.8 LIMITING FACTORS ON THE RATE OF PHOTOSYNTHESIS

-Light: Gradually the rate falls of and at a certain light intensity the rate of photosynthesis stay constant.

-Temperature: The higher the temperature then the rate of photosynthesis goes up. But when temperatures above 40°C the rate slows down. This is because the enzymes involved in the chemical reactions of photosynthesis are temperature sensitive and destroyed at higher temperatures.

-Carbon dioxide: The rate of photosynthesis increases linearly with increasing carbon dioxide concentration. Gradually the rate falls at a certain carbon dioxide concentration the rate of photosynthesis stays constant. 

7.6 Enzymes

Metabolic Pathways

• Chemical changes in living organisms often happen with a number of stages. Each stage has its own specific enzyme.
• Catabolic pathways breakdown molecules.
• Anabolic pathways build up molecules.

 Linear Change Pathways (Example: Glycolysis)

• Enzyme 1 is specific only to substrate 1. It is then converted to product 1.
• Enzyme 2 is specific only to product 1 which becomes the substrate and then converted to product 2.
• Enzyme 3 is specific to product 2 which becomes the substrate and converted to product 3.
• Product is called the 'End product'.

Cyclic Pathways (Example: Krebs Cycle and Calvin Cycle)

• The initial substrate is fed into the cycle.
• Enzyme 1 combines the regenerated 'intermediate 4' with the initial substrate to catalyses the production of intermediate 1. 
• Enzyme 2 is specific to intermediate 1 and converts intermediate 1 to intermediate 2.
• Enzyme 3 is specific to intermediate 2 and catalyses it conversion to product and intermediate 3.
• Enzyme 4 is specific to intermediate 3 and catalyses its conversion to intermediate 4.
• The difference is the regeneration of the intermediate, in this case intermediate 4. 

 Induced Fit Model

•  Enzymes are very specific to certain substrates, like a lock is to a certain key.
• There is 1 enzyme for every substrate.
• The substrate induces change in a active site - the enzyme "adjusts" its structure to accommodate the substrate.

 Activation Energies

Exergonic reactions

 

 

• Enzymes lower the activation energy of the chemical reaction that they catalyse. 
• In the activated complex or transition state energy is put into the substrate to make structure weak. This allows the reaction to occur with a minimal amount of additional energy required. 
• Normal activation energy would cause damage to the proteins of the cell. So reduced activation energy make these reactions possible in a cell.
• After the product is formed, energy is released.
• Exergonic reactions release more energy than the activation energy.

Competitive and Non-Competitive Inhibitors

• Inhibitors - substances that reduce or completely stop the action of an enzyme.
• Inhibition can act on the active site (competitive) or on another region of the enzyme molecule(non-competitive). The competition in the former being for the active site of the enzyme. 

A. Competitive Inhibitors 

• The substrate and inhibitor are chemically very similar in molecular shape.
• The inhibitor can bind to the active site.
• Enzyme-inhibitor complexing blocks substrate from entering the active site. This blockage reduces the rate of reaction. 
• If the substrate concentration is increased it occupies more active sites than the inhibitor. Therefore the substrate out-competes the inhibitor for the active site.
• The rate of reaction will increase again.

Example:Succinate is converted to Fumerate by Succinate dehydrogenase(SDase).
SDase can be inhibited by a later intermediate in the cycle called malonate.

• When a competitive inhibitor is present the rate of reaction is reduced.
• Increasing the concentration of the substrate reduces the effect of the inhibitor.
• At high concentrations the substrate out-competes the inhibitory molecules for the active site. The rate of reaction therefore increases.

 B. Non-competitive Inhibitors

• The substrate and the inhibitor are chemically different in molecular structure.
• The inhibitor cannot bind to the active site, but the inhibitor can bind to another region of the enzyme molecule.
• The bonding of the inhibitor with the enzyme causes structural changes in the enzyme molecule.  
• The active site then changes shape. 
• The substrate cannot bind therefore the rate of reaction decreases.  

Example: Inhibition by metal ions (Ag⁺)
Silver ions inhibiting the formation of sulphide bridges at the amino acid cysteine.
This changes the protein bonding and in turn the active site changes excluding the substrate.

• The presence of an non-competitive inhibitor always significantly reduces the rate of reaction.  
• Increasing the concentration of the enzyme increases the chance of a collision between the substrate and an enzyme that is not inhibited already. Therefore the rate can increase.
• The rate of reaction is always lower when the inhibitor is present.

End Product Inhibition of Enzyme Pathway

• Enzyme pathways can be controlled by concentration of products from the end of the pathway.
• The principle is illustrated by the transamination (change R group) of the amino acid threonine to isoleucine. 

•  Isoleucine the end product, this molecule can inhibit the enzyme Threonine Deaminase.
• The inhibition occurs at an inhibition site on the enzyme but not the active site.
• An excess of end product (Isoleucine) switches off any more production of that product, isoleucine.
• At high concentrations, Isoleucine attaches to the inhibition site of Threonine deaminase.
• This attachment causes the active site of the enzyme to change blocking any further reaction.  
• Isoleucine is used up in cellular processes that require this particular amino acid.
• The isoleucine concentration in the cell falls and so the Isoleucine that is attached to the enzyme detaches. This amino acid is also used up in the various cellular processes.  
• With the inhibitor removed the the active site then becomes active again and the pathway switches back on. 
• The isoleucine is again in production but once high concentrations are reached the pathways is once more inhibited. The process then cycles on in alternating stages of production and inhibition.
• Notice the similarity with non-competitive inhibition.
• This mechanism makes the pathway self-regulating in terms of product manufacture.

Topic 8.1 : Cellular Respiration

Cellular Respiration - controlled release of energy from organic compounds in cells to form ATP
          -Occurs in both plants and animals

2 Pathways of Cellular Respiration:

      

- Both begin with glycolysis

        

        a.) Anaerobic Respiration

            

                 - Oxygen = not available

                       

                        1.) Alcoholic Fermentation - Yeast

                       

                        2.) Lactic Acid Fermentation - Muscles

       

        b.) Aerobic Respiration

                

                 - Most efficient pathway

                 - Oxygen = available

                

                 - Yields large amounts of ATP

                 - Occurs in mitochondria

Glycolysis                                                                                

 -Takes place in cytosol                                            

     - First pathway of cellular respiration

     - Begins with glucose

   

Lactic Acid and Alcoholic Fermentation

Lactic Acid Fermentation

          - Muscle cells, yogurt cheese

          - Produces NAD+ and lactic acid

Alcoholic Fermentation

        - Yeast

        - Produces NAD+ and ethyl alcohol

Aerobic Cellular Respiration

   a.) Glycolysis in cytoplasm

   b.) Krebs Cycle and ETC in Mitochondria

   

2 Types of Chemical Reactions:

    a.) Oxidation 

      - Results in many C-O bonds

      - Results in compounds with lower potential energy

    b.) Reduction

      - Results in many C-H bonds

      - Results in compounds with higher potential energy

          

  

Fe2+à Fe3+ + electron       Oxidation

Fe3+ + electron à Fe2+        Reduction    

Terms:

   -Phosphorylation: addition of phosphate group to compound/molecule

        Ex: Glucose + 2 ATP --> Hexose Bi-phosphate

   - Substrate-Level Phosphorylation: way of producing ATP

        Ex: ADP + Phosphate --> ATP

   - Decarboxylation: removal of carbon atom

   - Oxidative Decarboxylation: removal of hydrogen atom and carbon dioxide

   - Coenzyme: molecule that aids an enzyme in its action by acting as electron donor/acceptor

       Ex: Acetyl CoA

Uses for ATP in Respiration

     a.) Releasing energy

           - Breaking of chemical bonds

           - Loses phosphate

                  - Bond between 2nd and 3rd phosphate group broken

      b.) Substrate Level Phosphorylation

              - Forming ATP

                  - Cells create ATP to store energy

                  - ADP--> grabs Pi --> Energy stored in ATP bond

                  - Breaking down ATP to make ADP to release energy

Glycolysis

     - Splitting of glucose into two pyruvate (3-carbon molecules)

     - One hexose sugar converted into two 3-C atom compounds (pyruvate) with net gain of 2 ATP and 2 NADH + H+

               - Both pathways begin with:

                         - Total of 4 ATP molecules

                         - Requires 2 ATP to start process -- net gain of 2 ATP per glucose molecule

4 Steps to Glycolysis:

Step 1 - Phosphorylation - Energy Investment Phase

      - Phosphates from 2 ATPs are added to glucose to create hexose bi-phosphate molecule

    1.) Hexokinase (enzyme that transfers 1st phosphate to sugar)

         - Product formed called Fructose-6-Phosphate

    2.) Phosphofructokinase (2nd enzyme that transfers 2nd phosphate to sugar) -

         - Product formed called Fructose-1, 6-bi-phosphate (hexose bi-phosphate) 

                -- 6 carbon sugar with 2 phosphates attached

Step 2 - Lysis

      1.) 6-carbon phosphorylated fructose splits by enzyme aldolase into two, 3-carbon sugars with       phosphate attached

          -Product formed: 3-carbon sugars (G3P) - triose phosphate molecules

Step 3 - Oxidation - Energy Payoff Phases begin

      1.) Each G3P undergoes oxidation by enzyme triose phosphate dehydrogenase where it loses 2 atoms of hydrogen by reducing NAD+ into NADH + H+

        2.) While NADH is formed, releases energy enzyme then uses to add phosphate group to both of 3-carbon molecules with one phosphate group

          - Results in a 3-carbon molecule with 2 phosphate groups attached (Phosphogylcerate - PGA)

Step 4 - ATP Formation

      1.) Enzyme removes the 2 phosphate groups

      2.) Enzyme Enolase extracts water molecule, forming phosphoenolpyruvate (PEP)

      3.) Phosphate groups transferred from PEP to ADP (substrate-level phosphorylation_)

      4.) ATP is produced

           - Product: 2, 3-carbon molecules called Pyruvate

Glycolysis Summary

     - 2 ATPs used to start process

     - 4 ATP produced (net gain of 2)

     - 2 NADH molecules produced (NAD+ converted into NADH + H+

     - Includes: phosphorylation, lysis, oxidation, ATP formation

     - Pathway controlled by enzymes

     - In cytoplasm, one glucose (6C) is converted into 2 pyruvate (3C) molecules

Mitochondrial Structure in Relation to its Functions

1. Cristae folds increase surface area for electron transfer system

2. Double membrane creates small space into which H+ can be concentrated

3. Matrix creates isolated space in which Krebs cycle can occur

 

Aerobic Cellular Respiration

1.) Glycolysis (see above)

2.) Link Reaction and Krebs Cycle

     - Occurs in mitochondrial matrix

     - Requires Oxygen

 a.) Link Reaction:

         - Produces 1 CO2 and 1 NADH for every pyruvate

 b.) Krebs Cycle

         - 2 ATP produced for life processes

                 *1 from one Krebs Cycle runs twice

         - 6 Molecules of NADH produced

                 *3 from one Krebs Cycle that runs twice

         - 2 Molecules of FADH2 produced

                 *1 from Krebs Cycle that runs twice

         - 4 Molecules of CO2 produced

                 * 2 from Krebs Cycle that runs twice

3.) Electron Transport Chain

         - Requires oxygen

               a.) Final electron acceptor

         - Where most of ATPs from glucose catabolism produced

         - Occurs in intermembrane space and membranes of cristae

         - Water = waste product

Aerobic Cellular Respiration Step 2 Part A: Link Reaction

   1.) Pyruvate from glycolysis absorbed by mitochondria after glycolysis when oxygen = present

   2.) Pyruvate enters matrix of mitochondria by active transport

   3.) Oxidative decarboxylation

        - Goal = hydrogen and carbon dioxide removed from pyruvate

   4.) Enzymes in matrix of mitochondria remove hydrogen and carbon

   5.) Pyruvate = decarboxylated to form acetyl group (2C)

         - CO2 released

   6.) Pyruvate = oxidized

         - Hydrogen atom accepted by NAD+ to form NADH + H+

     7.) Acetyl group combines with coenzyme (CoA) to form Acetyl CoA

    8.) Acetyl CoA then enters Krebs cycle to continue aerobic respiration process in matrix of mitochondria

Acetyl coenzyme A (Acetyl CoA)

     - Pyruvic Acid from Glycolysis converted to Acetyl CoA - 2C compound

Cellular Respiration using Fatty Acids
    - Fatty acids = source of energy in cellular respiration
CH3(CH2)nCOOH
   ** Glycolysis = not needed; goes straight  to link reaction **
- Fatty acids have long chain of carbon atoms.
- CoA can oxidize this chain and break it down

 - Fatty acids make Acetyl CoA with two carbons and carries them to Krebs Cycle

                      - If odd number of carbons, remaining carbon atom released as CO2

Krebs Cycle

—Acetyl CoA (CH3CO) yields 2 CO2

C2 + C4 = C6 → C5 + CO2 → C4 + CO2

    

Aerobic Cellular Respiration Step 2: Part B: Krebs Cycle
1.) Formation of citrate
      - Acetyl CoA from link reaction combines acetyl group (2C) with oxaloacetate (4C)
           2C + 4C = 6C
      - Results in 6-carbon molecule called citrate/citric acid
2.) Citrate converted to isocitrate by removal of one water molecule and addition of another
3.) Oxidation
      - Isocitrate (6C) goes through oxidative decarboxylation to form a 5C compound (Alpha-ketoglutarate)
             NAD+ is reduced to NADH + H+ (oxidized).
             Carbon dioxide removed decarboxylation process to form waste product
4.) 5C = oxidized and decarboxylated again
      - Coenzyme A added to form 4C compound (succinyl-CoA)
      - CO2 released

      - NAD+ --> NADH + H+ 

      5.) This 4C undergoes various changes to be converted back into oxaloacetate (4C)
            
                   - Phosphate group displaces CoA from succinyl-CoA which produces succinate (4C)
           
          - Substrate-Level Phosphorylation
        
        6.) Succinate is oxidized by molecule FAD (Flavin adenine dinucleotide)
          
              - Creates Fumarate (4C) FAD--->FADH2

        7.) Enzyme adds water to fumarate to form malate (4C)

        8.) Malate oxidized by NAD+ molecule reducing NAD+ to NADH + H+ and regenerating oxaloacetate
             Produces:
              - 2 ATP
              - 6 NADH
              - 2 FADH2
              - Oxaloacetate
              - 4 CO3
        Oxaloacetate will begin cycle again 
             

            

          - Cycle follows one acetyl group
          
          - Each glucose that enters will produce 2 acetyl groups                        

           

      Aerobic Cellular Respiration Step 3- Electron Transport Chain 

      

      - Pathway where most of ATPs from glucose catabolism are produced

     

      - Contains series of electron carriers

                - Carriers will form "chain" to pass electrons and proteins from one another

 -              - As electrons are transported, small amounts energy released

      - NADH and FADH2 from Krebs Cycle will pass electrons to ETC

      

      - Electrons passed as H+ ions to be pumped out of matrix --> cross into inner mitochondrial matrix --> travel into intermembrane space

                   - Proton gradient = produced

                   - Energy = released in process

       ETC Steps

       1.) NADH supplies 2 electrons to first carrier in chain (initially flavoprotein - FMN) and then series of Fe-S proteins

             - Drops off H2 in inner mitochondrial space

             - Turns into NAD+ again

       2.) The 2 electrons pass along chain of carriers because they give up energy each time they pass from one carrier to next

       3.) At 3 points along chain enough energy is given up for ATP to be made by ATP synthase

       4.) Proteins move from inner membrane space to matrix and produce ATP (Oxidative Phosphorylation)  

               - ATP synthase = located in inner mitochondrial membrane         (look on ppt for detailed arrows)

* In the chain, electrons pass from one carrier to another because receiving molecule has a higher electronegativity (stronger attraction of electrons)

- Process accomplishes pumping of four protons across inner mitochondrial membrane to inner membrane    space (used to generate ATPs)

5.) The iron sulfur protein then passes electrons to compound ubiquinone (Q - lipid (only member not a protein)

       - Most of remaining electron carriers between Q and oxygen are proteins - cytochromes (cyt)

       - Cytochromes prosthetic group = heme (iron atom) 

6.) FADH2 enters ETC further along --> sufficient energy released for ATP production by electrons for FADH2

       - FADH2 passes electrons to electron carrier

       - Hydrogen = moved from matrix to intermembrane space

  - Products: Carbon dioxide, water, and ATP

Role of Oxygen

 - Final electron acceptor in ETC

 - Oxygen accepts hydrogen ions to form water

 - If oxygen = not available, electron flow along ETC stops

 - Glycolysis can still occur

Oxidative Phosphorylation in terms of Chemiosmosis
- Process that occurs at inner membrane
- Chemiosmosis involves movement of protons (H2 ions) moving across membrane (down its concentration gradient) to provide energy so that oxidative phosphorylation (ATP synthesis) can occur
    A.) ATP synthase:
          - too many H2 ions are in intermembrane space (high concentration)
          - creates overall positive charge
          - Accumulation of H2 will cause proton force
                    - Allows movement of H2 ions through ATP synthase --> uses energy from H2 flow to couple phosphate with ADP to produce ATP

         - The Production of ATP

               - ATP synthase uses energy from H2 flow to phosphorylate with ADP

                     - ATP = produced

                  * Each NADH pumped 3 pairs of H2 atoms --> produces 3 ATPs

Protons move from inner membrane space to matrix