Biology

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Biology
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2012-04-03 21:31:29
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  1. Photons
    Discreet units of light energy
  2. Wavelegth
    measured as the distance between two consecutive wave crests/throughs
  3. Photo Autotrophs
    use light energy to perform carbon fixation
  4. Chemo Autotrophs
    use energy from the oxidation of inorganic molecules to perform carbon fixation
  5. Photo Heterotrophs
    use light energy to produce some atp but cannot perform carbon fixation
  6. Chemo Heterotrophes
    cannot use light and cannot perfom carbon fixation
  7. Photosynthesis
    an endergonic metabolic pathway that converts light energy into chemical bond energy through the process of carbon fixation
  8. Carbon Fixation
    an energonic metabolic pathway that converts inorganic carbon (CO2) into organic carbon (carbohydrate)
  9. Carboxylation
    addition of a carboxyl group
  10. Decarboxylation
    removal of a carboxyl group
  11. Phosphorylation
    addition/transfer of a phosphate group
  12. Dehydrogenation
    removal of hydrogens

    catalyzed by an enxyme called "Dehydrogenase" which removes two electrons and two hydrogens from some substrate molecule and then trasfers both electrons and either one or both hydrogens to a coenzyme
  13. Photosynthesis

    (Coenzymes)
    NADP+ (oxidized form) --> NADPH (reduced form)
  14. Cellular Respiration
    • NAD+ (oxidized form) --> NADH (reduced form)
    • FAD (oxideized form) --> FADH2 (reduced form)
  15. Photosynthesis Pigments
    • Chlorophyll-a
    • Chlorophyll-b
    • Xanthrophyll
    • Carotens

    The photosynthetic pigments are located embedded in the phospholipic bilayer of the thylakoid membranes and are organized into clusters called photosystems.
  16. Photosystem
    a complex of light-gathering "antemae" molecules and a "reaction center" which is a special chlorophyll-a molecule located in close proximit to a "primary electron acceptor" molecule.

    There are two photosystems (1 and 2).
  17. Photosystem-1 (PS-1)
    Has a reaction center chlorophyll-a molecule called P700.
  18. Photosystem-2 (PS-2)
    Has a reaction center chlorophyll-a molecule called P680.
  19. Photooxidation of Chlorophyll
    When the energy from a photon of light is absorbed by the reaction center chlorophyll-a molcule, it makes it possible for an electron to go from its normal "ground state" to a higher energy "excited state" orbital.

    Before the electron can give off the energy and return it to its more stable lower-energy ground state, the elctron is stolen by the primary electron acceptor an entered into an electron trasport chain.
  20. Electron Transport Chain (ETC)
    a series of membrane protens, each one being more electronegative than the previous one.

    as electrons are pulled exergonically down the ETC the energy is used to actively pump hydrogen ions (H+) from the stroma into the Thylakoid space to establish a proton gradient.

    The potention energy of the proton gradient is converted to kinetic energy as the H+ spill back into the stroma through membrane protein cores called ATP-Synthase.
  21. ATP Synthase
    uses the kinetic energy from the flow of H+ to phosphorylate ADP and from ATP.
  22. Cyclic e- flow
    • Involves only photosystem-1 (PS1)and P700
    • Photooxidation of PS1 (P700) electrons into an ETC that terminates with P700
    • The exergonic form of e- from P700 back to P700 is used to generate ATP
    • NADPH is formed
    • No O2 is formed
  23. Noncyclic e- flow
    • Involves both PS-1 (P700) and PS-2 (P680)
    • Photooxidation of PS-1 (P700) sends e- into an ETC that terminates with NADP+ reducing it to NADPH
    • Photooxidation of PS-2 (P680) sends e- into an ETC that terminates with P700 and generates ATP in the process
    • Through a process known as "Photolysis" , a photon of light is used to split a water molecule into 2H+, 2e-, and oxygen.
    • The 2H+ are released into the stroma, the 2e- are given to P680 to replace the electrons lost to P700, and the oxygen atom combines with another oxygen atom to form O2 which is realsed as waste
  24. Dark Reactions
    Stroma
    • The dark reactions begin when Ribulose Biphosphate Cazboxylase (or "rubP carboxylase" or "Rubisco") picksup a molecule of CO2 from the leaf air spaces and fixes (attatches) it to a 5-carbon compound already in the calvin cycle called ribulose biphosphate (or "RuBP")
    • The resukting 6-carbon molecule is unstable and immediately spilts into two stable 3-carbon molecules called 3-Phosphoglycerate
    • Atp is used to phosphorylate each 3-Phosphoglycerate to Glyceraldehyde-3 Phosphate (or "G3P") which is the actual product of the calvin cycle
    • At this point, one molecule of G3P leaves the calvin cycle as a product and additional ATP is udes to convert any remaining G3P molecules back into RuBP to complete the cycle
  25. Photorespiration
    an ineffective metabolic pathway that consumes O2 and ATP, evolves CO2, does not produce any carbohydrate and robs the calvin cycle
  26. Photorespiration
    • It occurs because Rubisco's active site will accept either O2 or CO2 with equal affinity.
    • When Rubisco picks up O2 and attatches it to RuBp, the resulting unstable 5-carbon compound splits into a 3-carbon molecule called 3-phosphoglycerate and 2-carbon compound called glycolate.
    • 3-phosphoglycerate remains in the calvin cycle but glycolate exits the cycle and goes to a peroxisome and then to a mitochondrion where it completely oxidized to two molecules of CO2.
    • C4 and CAM photosynthesis both evolved as a way to by-pass photorespiration
    • Photorespiration typically occurs under dry conditions when plants are forced to close their leaf stromata (openings) prematurely.
    • When this occurs, the O2 concentration in the leaf air spaces increases while the CO2 concentration decreases, favoring rubisco picking up O2
  27. C4 and CAM Photosyntheiss
    • Both evolved to by-pass/ avoid/ reduce photorespiration
    • Both use two carbon fixation episodes instead of one
  28. Primary/Initial Carbon Fixation
    fixes CO2 into an organic acid
  29. Secondary/ Final Carbon Fixation
    fixes CO2 into a carbohydrate and is the calvin cycle
  30. C4 Photosynthesis
    Uses a "spartial" separation of primary and secondary carbon fixation episodes
  31. 1o Carbon Fixation
    • Occurs only in the mesophyll cells and uses pepcarbolase instead of Rubisco.
    • Pep-Carboxylase (phosphoenyl carboxylase) picks up a molecule of CO2 it attatches it to a 3-carbon molecule called phosphoenyl pyruvate (pep) which forms a stable 4-carbon intermediate called oxaloacatate.
    • Oxaloacetate is then converted to another 4-carbon oraganic acid called malate which is shuttled from a mesophyll cell and into a bundle sheath cell via a plasmodesma.
    • Once inside the bundle sheath cell, t he malate is broken down into a 3-carbon molecule called pyruvate and a 1-carbon molecule CO2
    • The CO2 is picked up by Rubisco and fixed a second time into carbohydrates via the calvin cycle
    • The pyruvate molecule is shuttled back into the bundle sheath cell where ATP is used to phosphorylate it into pep to complete the cycle
  32. CAM Photosyntheiss "Crassulacean Acid Metabolism"
    CAM plants use a "temporal" separtion of primary and secondary carbon fixation events
  33. Primary Carbon Fixation
    • fixes CO2 unto organic acids like malate, occurs at night when the stomata are open
    • The malate is stored in the central vacuole.
  34. Secondary Carbon Fixation
    occurs in the datytime via the calvin cycle when the stored malate is broken down into pyruvate and CO2 while the stomata are closed.
  35. Substrate Level Phosphorylation (SLP)
    Phosphorylation (Cellular Respiration)
    involves the direct transfer of a phosphate group from some molecule to ADP
  36. Oxidative Phosphorylatin/ETC (OP/ETC)
    Phosphorylation (Cellular Respiration)
    involves using the kinetic energy from the exergonic flow of electrons down the ETC to pump H+ against their concentration gradient and then converting the potential energy of the H+ to phosphorylate ADP to form ATP.
  37. 4-Phases of Cellular (Aerobic) Respiartion
    • Glycolysis
    • Oxidation of Pyruvate to Acetyl Coenzume-A (Acetyl CoA)
    • Kreb's Cycle
    • OP/ETC
  38. Glycolysis
    • Occurs in the cytoplasm (cytosol) whether O2 is present or absent.
    • One 6-carbon glucose molecule is oxidized and split into 3-carbon pyruvate molecules
    • 2 ATP are consumed
    • 4 ATP are produced by SLP (2 net gain/yeild)
    • 2 NAD+ are reduced to 2 NADH (each one is worth 2 ATP by OP/ETC)
    • No FADH2 are produced
    • No CO2 are formed/evolved released
  39. Fate of Pyruvate
    • Depends on the presence/ absence of O2
    • If O2 is absent (an aerobic) pyruvate remains in the cytosol and is reduced to either ethanol/locate through a metabolic process known as fermentation.
    • If O2 is present (Aerobic) pyruvate enters the mitochondrial matrix and is oxidized to Acetyl CoA. (2-C)
  40. Oxidation of Pyruvate to Acetyl CoA
    • Occurs in the mitochondrial matrix only f O2 is present
    • Each 3-carbon pyruvate is oxidized to a two carbon molecule called acetyl CoA
    • One molecule of CO2 is formed/evolved
    • One molecule of NAD+ is reduced to NADH and is worth 3 ATP through OP/ETC
    • No ATP is produced by SLP
    • No FADH2 is formed
  41. Kreb's Cycle
    • Occurs in the mitochondrial matrix if O2 is present.
    • For every 2 carbon acetly CoA that enters the cycle:
    • -2 CO2 are formed/evolved
    • -1 ATP is formed by SLP
    • -1 FADH2 is formed (worth 2 ATP throguh OP/ETC)
    • -3 NAPH are formed (each one is worth 3 ATP each through OP/ETC)
  42. OP/ETC
    • Located embedded in the inner mitochondiral membrane (cristae)
    • Occurs only if O2 is present (aerobic)
    • electrons are entered into the chain, from the matrix side, by both FADH2 and NADH
    • The exergonic flow of e- down the ETC is used to pump H+ gradient in the intermembrane space is converted to kinetic energy as the H+ spill back into the matrix through membrane protein channels called ATP synthase
    • The kinetic energy from the exergonic flow of H+ through ATP synthase is used to phosphorylate ADP to for ATP
    • Since NADH enters its electrons into the beginning of the chain, enough H+ are pumped into the intermembrane space to perform 3 phosphorylation reactions (each NADH is worth 3 ATP)
    • Since FADH2 enters its electrons further down the chain, its electrons into the intermembrane space to perfom 2 phosphorylation reactions (each FADH2 is worth 2 ATP)
    • Exception:
    • The NADH fromed during glycolysis are each worth only 2 ATP (because the inner mitochondrial membrane is impermeable to NADH, so NADH sends its electrons across the inner membrane and itno the matrix where they are picked up by FAD, reducing it to FADH2, which enters the electrons into the ETC).
  43. Fermentation
    • If O2 is absent, glycolysis sitll occurs and splits glucose into two molecules of pyruvate
    • Instead of entering the mitochondrion and being oxidized to acytyl CoA, pyruvate remains in the cytosol and is reduced to either ehtanol or lactate as a way of regenerating NAD+ from NADH.
    • The process is known as fermentation and the NADH formed during glycolysis serves as the reducing agent while pyruvate serves as the oxidizing agent
    • No ATP are consumed/produced during the process and no NADH or FADH2 are formed
    • 2 carbon ethanol, no CO2 is evolved if pyruvate is reduced to 3 carbon lactate/ lactic acid

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