Chapter 19-2

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Chapter 19-2
2014-04-27 22:22:18
chapter 19-2
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  1. Fo:
    The respiratory chain – integral membrane protein (oligomycin-sensitive, “o” in Fo). Isolated from mitochondrial membranes (ATP synthase) using detergent treatment. It contains a passive proton pore. The proton pump is made of C-subunits. C(sub)11 means that there are 11 binding sites for H+. The C-subunits are all helices.
  2. F1:
    ATP synthesis- F-type ATPase. Peripheral membrane protein (first oxidative factor  identified, 1 in F1 = first). F1 can be purified away from Fo, isolated F1 can catalyze ATP synthesis.  F1 contains 5 different subunits. 3 alpha and 3 beta are alternating, the beta subunits have the catalytic site. realize that the F1 is inside the matrix of the mitochondria. Gamma subunits only bind one beta subunit at a time, it is the central "pole" looking component. The beta subunits are all in different conformations, each one binds different things on a cyclic basis: one subunit doesn't bind anything, another subunits binds ADP, and another subunit binds ATP.
  3. Rotational catalysis:
    (H+ binds to once C unit, then conformational change and caused conformational change in a different C unit, releasing H+ to other side) C-subunits of Fo rotate in the plan of the membrane - due to passive proton transport. Movement of protons causes association of gamma subunit ("pole") with one of the 3 beta subunits. One rotation forces all 3 beta subunits though all 3 conformations. one rotation = synthesis of 3 ATP. One rotation requires 12 H+. ROTATION DICTATES ATP USE - one direction for ATP synthesis, opposite direction for ATP hydrolysis.
  4. Adenine Nucleotide
    (An Antiport) Exchanges ADP3- for ATP4+ in the intermemrane space. A charge difference: one more negative charge is transported out than in - protons flowing down gradient. The proton motive force drives ATP/ADP exchange, ATP is coming from mainly ATP synthase and the gradient comes from the ETC.
  5. Phosphate translocase:
    (A Symport) Moves 1 H+ and 1 H2PO4- into the matrix. This proton decreases the electrochemical gradient.
  6. Malate-Aspartate Shuttle:
    Think malate-alpha-ketoglutarate transporter (antiport) and glutamate-aspartate transporter (antiport). The purpose is to get NADH where it is needed by moving reducing equivalents through mitochondrial membranes. (1) reducing equivalents of NADH are transferred to oxaloacetate, producing malate (via cytosolic malate dehydrogenase) (2) Malate moves though inner mitochondrial membrane cia the malate-alpha-ketoglutarate transporter (an antiport) (3) reducing equivalents are passed from malate to NAD+ in the matrix (via matrix malate dehydrogenase) 2 pools of same enzyme (4) oxaloacetate and NADH are regenerated.
  7. Photophosphorylation:
    the process by which sunlight drives electron transfers, powering ATP synthesis. Involves oxidation of H2O to O2 --> NADP+ is the final electron acceptor. It absolutely requires light!
  8. Photophosphorylation Overview and Review:
    H2O is not a good donor like NADH, so sunlight assists in creating a good electron donor. Electrons flow though a series of membrane-associated electron carriers. Protons are pumped across a membrane to create an electrochemical gradient (potential) --> similar to complex II of oxidative phosphorylation. The electrochemical potential drives ATP synthesis, the ATP Synthase complex catalyzes the phosphorylation.
  9. Photosynthesis has two phases :
    light-dependent and carbon assimilation/carbon fixation.

    light-dependent: energy from light is absorbed by chlorophyll and other pigments. energy is eventually conserved as NADPH and ATP. O2 is produced.

    carbon assimilation/carbon fixation (not Dark): Driven by the products of light reactions. NADPH and ATP reduce CO2. "New" carbon + existing carbon is coupled to production of starch, triose phosphates, and carbohydrates.
  10. Chloroplasts reduce
    electron...Hill reagent:
    • Chloroplasts reduce electron acceptors in the presence of light.. 2H2O + @A --> 2AH2 + O2 (A is the electron acceptor - Hill reagent). Water is the electron donor and the final electron acceptor (A) in chloroplasts is NADP+ .. 2H2O2 + 2NADP+
    • --> 2NADPH + O2
  11. Chlorophylls (photosynthetic pigment) (primary pigments):
    Green pigments in the thylakoid membranes. Contain polycyclic but planar rings resembling heme + phytol side chains - Mg2+ (not iron) is at the center of the ring. Strongly absorb light in the visible spectrum due to alternating single-double bond ring structure.
  12. Cytochrome b6f complex:
    The proton pump. protons moce from stromal compartment to the thylakoid lumen. 4 net H+ move per pair of electrons, develops an electrochemical gradient. The volume of the space in chloroplasts is small - moving a small number of protons has a large effect --> result: 3 unit pH difference = 1000-fold difference in [H+]. change and concentration differences drive ATP synthesis -The electrochemical gradient. Second link between PSII and PSI. there are 3 components: (1) cytochrome b (2) iron-sulfur protein (3) cytochrome f. There is a Q cycle (as in mitochondria).
  13. Chromophores:
    light-absorbing molecules with different energy states.

    • -Absorbing light energy: Absorbing a photon of light raised the chromophore to the next 
    • energy level. Photon absorption requires exactly enough energy to raise the energy
    • state (an electronic transition state) - molecule now is in an excited state and relatively unstable.

    -Releasing the energy: Chromophore returns to the ground state when energy is released as heat, light, or biological work. emitted light (fluoresence) is longer wavelength (less energy) than that which was absorbed photon energy of light is greater at shorter wavelengths).
  14. ATP synthesis in plants:
    The mechanism for ATP synthesis is analogous to that in mitochondria. ATP synthesis is catalyzed by CF1/CFo complexes in the outer surface of the thylakoid membranes. ATP is produced by rotational catalysis.  The ATP is being made in the stroma, where the CF1 is located. The H+ is stored in the lumen to create the gradient
  15. Pheophytin:
    It is a chlorophyll without central Mg2+ ion. Electrons pass though the pheophytin in the purple bacteria photochemical reaction centers (pheophytin-quinone reaction centers - type II)
  16. Pheophytin-quinone reaction center in purple bacteria (type II):
    It contains 3 molecules: (1) one reaction center P870 (2) cytochrome bc1 electron transfer complex (similar to mitochondrial complex III) (3) ATP synthase. The mechanism is: light --> electron transfer to pheophytin --> electron transfer to a quinone OR semiquinone intermediate (like mitochondria) --> electron transfer to a quinone. Product is Q(sub B)H2. Quinone passes electrons to cytochrome bc1 complex. Electrons flow back to the reaction center = cyclic pathways - ready to start another round.
  17. Iron-sulfur Reaction Centers (type I):
    Found in green sulfur bacteria. Electron transfer is similar to type II. the result is ATP synthesis. The reaction cenet's lost electrons are replaced by oxidation of H2S.
  18. Type I mechanistic differences from type II:
    Some electrons can pass from the reaction center to ferredoxin (iron-sulfur protein). Ferridoxin passes electrons to a ferridoxin-NAD reductase - produces NADH. Iron sulfur complex contains H2S --> oxidized to HSO4 (2-) , this reaction is characteristic of these bacteria.
  19. Thermodynamics of Bacterial
    Reaction Centers:
    electron transfer is very carefully controlled by precise structural arrangements of interacting molecules. Little energy is lost as heat as a result of structural control. Heat is produced, but not from inefficiency. Reactions proceed with extreme speed -  essential no energy is stored in intermediates. The overall energy yeild is ~30% and the rest is lost as heat, kinetics indicate these reactions are nearly irreversible.
  20. How the function of photosystem I and photosystem II depends on their arrangements in the thylakoid membrane:
    Photosystems I and II occur in plants with higher reaction centers in the thylakoids (they resemble the two bacterial systems).
  21. Arrangements in the thylakoid membrane:
    PSI and PSII are physically separated. PSII is in grana stacks and PSI and the STP synthase are in unstacked stromal thylakoid. The separation prevents "electron larceny". Association of PSI and PSII is regulated by sunlight and protein phorphorylation. They both have access to the stroma (i.e. NADP+, AND, Pi, water, etc). The second link between PSII and PSI is the cytochrome b6f complex and the Q cycle.
  22. Oxygen-Evolving Complex of
    it is the final piece of the model - splitting of water. Water is the source of the electrons that end up in NADPH. Bacteria use acetate, succinate, malate, and sulfide as alternative electron donors. 4 photons of light are required to split 2 water. 2H2O = 4H+ + 4e- + O2.
  23. How oxygen-evolving complex works:
    electrons pass from water to P680 one at a time from the oxygen-evolving complex. Four Mn2+ ions become more oxidized with each of the 4 electrons passed. They function as a cluster - removing one H+ at a time in the lumen. ADD FIGURE 19.64a. Mn2+ complex takes 4e- from 2H2O - this releases 4H+ and one oxygen radical. The 4H+ are released into the thylakoid lumen (i.e. the proton pump is driven by e- transfer). lumen: site of high [H+].
  24. What is produced from oxygen-evolving complex:
    2H2O = 4H+ + 4e- + O2. The water provides the electrons that end up in NADPH, that is its most important function.
  25. What metal ion is important for oxygen-evolvings function:
    Mn2+ ions
  26. Synthesis of Malonyl-CoA:
    Acetyl-CoA (2 carbons) + bicarbonate (1 carbon) à Malonyl-CoA (3 carbons). It is catalyzed by Acetyl-CoA Carboxylase, biotin is a prosthetic group (covalently attached to Lys). COO- is transferred to biotin (requires ATP) and then to Acetyl-CoA.
  27. Composition of FA synthase:
    Ketoacyl synthase (KS) and Acyl Carrier Protein (ACP)
  28. Charging of KS and ACP:
    Both thiols KS and ACP must be bound with the correct groups. (1) Acetyl group (of acetyl-CoA) is transferred to the Cys of KS (2) Malonyl group (of Malonyl-CoA) is transferred to the –SH of ACP.