respiration/photosynthesis

• Metabolic reactions:

  Glycolysis is the first step. It happens in the cytoplasm. All the other reactions occur in mitochondria. 

  Glycolysis is generally split into two steps:

  \_ The energy investing step occurs first where ATP is invested to convert the glucose into 2 carbon 3 molecules

  \_ The energy harvesting step where the C3 gets oxidized and ATP is harvested
• First step of glycolysis

  1. Invest an ATP

  2. Enzyme called hexokinase catalyses the reaction

  3. Generation of an energy rich phosphate bond

  4. Generation of a negatively charged molecule

  5. Trapping the molecule in the cell

  6. Removal of glucose

  7. Allowing more glucose to enter the cell

  8. Isomerization of glucose to fructose

  9. Addition of a second phosphate

  10. Splitting the molecule in the middle

  11. Formation of two Glyceraldehyde 3-phosphate (G3P)
• End products of glycolysis

  • Two pyruvate molecules
• Pyruvate oxidation:

  The reaction is coupled with the half reaction of NAD+ to NADH. When they are coupled they release a lot of free energy (high negative ΔG value, very spontaneous). Part of this energy can be captured by generating novel covalent bonds to coenzyme A. 

  At the end of pyruvate oxidation the molecule acetyl-coA is formed.
• Then the energy harvesting step comes. It’s the first oxidation step. The CH bond becomes oxidized and is coupled to NAD+ reduction (very favorable coupling). These phosphates are transferred to ADP to generate ATP → it’s called substrate level phosphorylation. 

  Since there are two C3 molecules and two phosphate rich bonds in each of C3 molecules you generate 4 ATPs in total even though you invested two ATPs at the beginning. 

  The end result is two pyruvate molecules.
• Citric acid cycle

  1. Two Acetyl-CoA come into the citric acid cycle

  2. It happens in the mitochondrial matrix

  3. They are covalently bound to the first molecule to form citrate

  4. As the cycle progresses, the two carbon compounds are completely oxidized

  5. It leads to the release of two CO2 molecules

  6. All the enzymes that catalyze these redox reactions are called dehydrogenases

  7. In most cases the redox reactions (oxidation) are coupled with the half reactions of NAD+ to NADH (reduction)
• Reduced electron carriers

  NADH and FADH
• End products of the citric acid cycle

  • 3 NADH + H+
  • One FADH
• Electron transport chain

  1. Step after pyruvate glycolysis where reduced electron carriers are converted to ATPs

  2. Electrons have to be transferred from NADH to the terminal electron acceptor: Oxygen

  3. The electron transport chain occurs in the membrane invaginations that are called cristae, invagination of the inner membrane of the mitochondria. There are big protein complexes that sit and gradually catalyze in a series of redox reactions, the transfer of NADH to oxygen to eventually form water (final product)

  4. In complex 1, NADH binds to and gives up its electron. A cofactor bound tightly to the enzyme complex. The NADH gets oxidized and the cofactor gets reduced. This redox reaction releases enough energy so that some of it can be coupled to a conformation change of the complex 1 that results in the transport of the proton across the inner mitochondrial membrane

  5. Some of the energy is harvested to transport protons across the membrane and against the concentration gradient

  6. The electron gets transferred to a ubiquinone, a small hydrophobic carrier molecule. It shuttles the electron from complex 1 to complex 3. First, this complex gets oxidized, the ubiquinone gets reduced by taking up that electron and taking up a proton at the same time. It diffuses across the membrane and can only bind complex 3 on the other side. When ubiquinone gets oxidized and passes on its electron, a proton is transported across the membrane to make the concentration gradient steeper by transporting more protons. The binding site for ubiquinone is on the inside of complex 1 and on the outside of complex 3

  7. FADH2 carries less energy and has to give up its electron to a unique protein complex. The redox reduction can transport one proton less. It kind of enters halfway done to redox reaction

  8. From complex 3 to complex 4, there is a very small protein called cytochrome C. It’s a hydrophobic protein that diffuses laterally in the membrane. Cytochrome C becomes reduced, that’s how the electron moves. The electron enters complex 4, which is a proton transporter. Oxygen is tightly bound to a cofactor. Oxygen becomes reduced to form water
• Cyanide is a very poisonous toxin that binds irreversibly to the heme bound and prevents any further binding of oxygen. 

  \_ unnatural competitive inhibitor.
• ATP synthase


  A multiprotein complex that makes ATPs through the chemiosmotic mechanism
• Chemiosmotic mechanism

  Diffusion of protons across the membrane that leads to the chemical reaction of ADPs + inorganic phosphates to make ATPs
• ATP synthase

  • Has a rotating part
  • Has a static part
  • Has a channel through which protons can flow in
  • Releases a lot of free energy
  • Drives the rotation of the complex
  • ADP binds in the static part
  • Comes into close contact with the inorganic phosphate so that ATPs can be formed
  • About three protons make one ATP (depends on proton gradient)
• Light harvesting complex


  A complex of about 100 chlorophyll molecules sitting next to each other
• Solar energy is very low energy
• A photon hits an individual chlorophyll molecule

  Very rare
• A photon hits a chlorophyll molecule

  Initiates the excited state and is transferred by resonance energy transfer
• Resonance energy transfer

  The transfer of energy from one molecule to another without the transfer of an electron
• All the resonance energy transfers have to end up at the longest lowest energy chlorophyll called the reaction center
• Excited electron

  1. Grabs one from water

  2. Splitting of water

  3. Electron transport chain
• Electron transport chain

  In plants, the excited electron is used to reduce pheophytin
• There’s a molecule called plastoquinone that is very similar to ubiquinone, they are protons pumps that eventually make ATPS.  

  You have huge protein complexes, because the reaction of splitting water contributes massively to the generation of the proton gradient. 

  The plastoquinone takes one proton from the outside when it gets reduced and gives it up when it gets oxidized.

  The regular ATP synthase makes ATP in the process called photophosphorylation.
• You have a non cyclic electron transport called the Z scheme.

  During photosystem 2 the water gets split and eventually the protons get on photosystem 1. The proton gets excited and initiates another series of redox chemical reactions where eventually they will make reduced electron carriers by ending up on NADP+ to make NADH.

  2 systems are required because the energy of 1 photon is not enough to make both ATP and NADPH.
• The Calvin cycle is composed of three steps. The first one is the fixation of carbon dioxide to make 3 phosphoglycerate. The second step is where the reduction takes place. You have to reduce this molecule to glyceraldehyde 3 phosphate (same molecule than in glycolysis just before the oxidation). To make that molecule you use up all the NADPH for the reduction step and the ATP. Step 3 is the regeneration, this glycer LDI 3 phosphate. 

  This cycle has to run a couple of times 
• In plants leaves you have stomata where oxygen and carbon diffuse in and out of the leaf, they can be regulated. Water evaporates through these stomata. In order for plants to not lose too much water, they have to close their stomata on a hot day for instance. But when they do that the oxygen accumulates inside the leaves and the carbon dioxide reduces and that causes a problem called photorespiration.