Biol 107

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mct
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149057
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Biol 107
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2012-04-25 11:56:44
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Part Two
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Cell Energetics & Energy Sources
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  1. Metabolism
    The totality of an organism's chemical reactions, consisting of catabolic and anabolic pathways, which manage the material and energy resources of the organism
  2. 1st law of Thermodynamics
    Conservation of Energy: no system can consume more energy than it takes up. Energy can be converted from one form to another but it can neither be created nor destroyed.
  3. 2nd Law of Thermodynamics
    If possible an ordered system (ie something with potential or free energy - G) will become less ordered or more relaxed.
  4. Entropy
    A measure of disorder, or randomness
  5. Exergonic
    A spontaneous chemical reaction, in which there is a net release of free energy
  6. Endergonic
    A non-spontaneous chemical reaction, in which free energy is absorbed from the surroundings
  7. Metabolism couples endergonic & exergonic reactions
    Example, exergonic conversion of sugar to energy to drive endergonic contracion of muscle fibers.
  8. ADP
    Adenosine Di-Phosphate
  9. Energy coupling
    In cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction. With ATP often uses phosphate transfer
  10. Energy of Activation
    The 'kick start' to get reactions over the intial bump. The energy needed to destabilize the bonds of the reactants so they are ready to break (in transition state)
  11. Enzyme
    • A macromolecule serving as a catalyst, a chemical agent that increases the the rate of a reaction without being consumed by the reaction. Most enzymes are proteins. Words ending in "ase" are enzymes of some sort.
    • Mechanisms: orientation, micro-environment, intermediates and bonding breaking
  12. Allosteric regulation
    • The binding of a regulatory molecule to a protien at one site that affects the function of he protien at a different site.
    • Allo- other, steric-shape. These are like on and off switches
  13. Thylakoid
    A flattened, membranous sac inside a chloroplast. Thylakoids are exist in stacks called grana that are interconnected; their membranes contain molecular "machinery" used to convert light energy to chemical energy.
  14. Reaction center complex
    A complex of proteins associated with a special pair of chlorophyll a molecules and a primary electron acceptor. Located centrally in a photosystem, this complex triggers the light reaction of photosynthesis. Excited by light energy, the pair of chlorophylls donates an electron to the primary electron acceptor, which passes an electron to an electron transport chain.
  15. Photosystem Reaction Centers
    A light-capturing unit located in the thylakoid membrane of the chloroplast or in the membrane of some prokaryotes, consisting of a reaction center complex surrounded by numerous light-harvesting complexes. There are two types of photosystems, I and II; they absorb light best at different wavelengths.
  16. Photosystem I (PS I)
    A light-capturing unit in a chloroplast`s thylakoid membrane or in the membrane of some prokaryotes; it has two molecules of P700 chlorophyll a at its reaction center
  17. Photosystem II (PS II)
    One of two light-capturing units in a chloroplast`s thylakoid membrane or in the membrane of some prokaryotes; it has two molecules of P680 chlorophyll a at its reaction center.
  18. OIL
    Oxidation Is Loss of electrons
  19. RIG
    Reduction Is Gain of electrons
  20. Non-cyclic photo-phosphorylation
    As electrons `fall` down transport chain, energy is harnessed as ATP
  21. ATP Sythase
    A complex of several membrane proteins that functions in chemiosmosis with adjacent electron transport chains, using the energy of a hydrogen ion (proton) concentration gradient to make ATP. ATP synthases are found in the inner mitochodrial membranes of eukaryotic cells and in the plasma membranes of prokaryotes.
  22. ATP (adenosine triphosphate)
    An adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyed. This energy is used to drive endergonic reactions in cells.
  23. Cyclic electron flow
    A route of electron flow during the light reactions of photosynthesis that involves only photosystem I and that produces ATP but not NADPH or 02
  24. Glyceraldehyde 3-phosphate (G3P)
    A three-carbon carbohydrate that is the direct product of the Calvin cycle, it is also an intermediate in glycolysis.
  25. Calvin cycle
    • The second of two major stages in photosynthesis (following the light reactions), involving fixation of atmospheric CO2 and reduction of the fixed carbon into carbohydrate. It has three phases:
    • Carbon fixation
    • Reduction of 3-phosphoglycerate to Glyceraldehyde 3-phosphate
    • Regeneration of CO2 acceptor (RuBP)
  26. C3 Plants
    A plant that uses the Calvin Cycle for the initial steps that incorportate CO2 into organic material, forming a three-carbon compound as the first stable intermediate.
  27. Photorespiration
    A metabolic pathway that consumes oxygen and ATP, releases carbon dioxide, and decreases photosynthetic output. Photorespiration generally occurs on hot, dry, bright days, when stomata close and the 02/CO2 ratio in the leaf icreases, favoring the binding of O2 rather than CO2 by rubisco
  28. C4 Plant
    A plant in which the Calvin cycle is preceded by reactions that incorporate CO2 into a four-carbon compound, the end product of which supplies CO2 for the Calvin cycle.
  29. CAM Plant
    A plant that uses crassulacean acid metabolism, an adaptation for photosynthesis in arid conditions. In this process, carbon dioxide entering open stomata during the night is converted to organic acids, which release CO2 for the Calvin cycle during the day, when stomata are closed.
  30. Energy Investment Phase
    The first of two phases in glycolysis energy balance
  31. Energy Payoff Phase
    The second phase in glycolysis
  32. Kinases
    Enzymes that transfer a phosphate from one molecule to another. Often the phosphate donor is ATP
  33. Isomerates
    Enzymes that make molecules with same formula but different organization of atoms
  34. Phosphofructokinase
    enxzyme that reulates glycolysis. An allosteric enxyme that regulates cellular respiration. Excess ATP and citrate inhibit this, while AMP stimulates it.
  35. Citric Acid Cycle (Krebs cycle)
    A chemical cycle involving eight steps that completes the metabolic breakdown of glucose molecules begun in glycolysis by oxidizing acetyl CoA (derived from pyruvate) to carbon dioxide; occurs within the mitochondrion in eukaryotic cells and in the cytosol of prokaryotes; together with pyruvate oxidation, the second major stage in cellular respiration.
  36. Cytosol
    The semifluid portion of the cytoplasm
  37. Pyruvate
    An important intermediate compound in metabolism, being produces during glycolysis and converted to acetyl coenzyme A, required for the Krebs cycle. Under anaerobic conditions pyruvate is converted to lactate or ethanol.
  38. Glycolysis
    A series of reactions that ultimately splits glucose into pyruvate. Glycolysis occurs in almost all living cells, serving as the starting point for fermentation or cellular respiration.
  39. Acetyl CoA
    • Acetyl coenzyme A; the entry compound for the citric acid cycle in cellular respiration, formed from a fragment of pyruvate attached to a coenzyme.
    • Production requires a pyruvate from glycolysis, loss of CO2, NAD+ removing hydrogen, and coenzyme A attaching.
  40. Co-enzymes
    Are non-protein helper molecules that bind to and facilitate the catalytic ability of the enzyme; many are what we call vitamins; many are made from nucleic acid
  41. Krebs cycle (citric acid cycle; tricarboxylic acid cycle; TCA cycle)
    • A cyclical series of biochemical reactions that is fundamental to the metabolism of aerobic organisms. The enzymes of the Krebs cycle are ocated in the mitochondria and are in close association with the components of the electron transport chain. The two-carbon acetyl coenzyme A (acetyl CoA) reacts with the four-carbon oxaloacetate to form the six-carbon citrate. In a series of seven reactions, this is reconverted to oxaloacetate and produces two molecules of carbon dioxide. Most importantly, the cycle generates one molecule of guanosine triphosphate (GTP- equivalent to 1 ATP) and reduces three molecules of the coenzyme NAD to NADH and one molecule of the coenzyme FAD to FADH2. NADH and FADH2 are then oxidized by the electron transport chain the generate three and two molecules of ATP per molecule of acetyl CoA.
    • Acetyl CoA can be derived from carbohydrates (via glycolysis), fats, or certain amino acids. Thus, the Krebs cycle is the central `crossroads` in the complex system of metabolic pathways and is involved not only in degradation and energy production but also in the synthesis of biomolecules. It is named after its principle discoverer, Sir Hans Adolf Krebs (1900-81)
  42. Citrate
    The 6-carbon molecule formed in the Kreb's cycle after oxaloacetate combines with CoA
  43. Oxaloacetate
    The four-carbon molecule that reacts with CoA to create citrate. The cycle continues with 7 steps to again create oxaloacetate.
  44. FAD (flavin adenine dinucleotide)
    is derived from vitamin B2 (riboflavin) & ADP; it's an electron carrier (FAD is the oxidized form)
    A coenzyme important in various biochemical reactions. It comprises a phosphorylated vitamin B2 (riboflavin) molecule linked to the nucleotide adenine monophosphate (AMP). FAD is usually tightly bound to the enzyme forming a flavoprotein. It functions as a hydrogen acceptor in dehydrogenation reactions, being reduced to FADH2. This in turn is oxidized to FAD by the electron transport chain, thereby generating ATP (two molecules of ATP per molecule of FADH2).
  45. Citric cycle energy output
    • 8 NADH
    • 2 FADH2
    • 2ATP
    • 6 CO2
    • One glucose produce 2 pyruvates, the pyruvate to Acetyl CoA produces 1 NADH and 1 CO2 each
  46. Oxidative Phosphorylation
    • A reaction occuring during the final stages of aerobic respiration, in which ATP is formed from ADP and phosphate coupled to electron transport in the electron transport chain. The reaction occurs in the mitochondria.
    • This can produce between 26-28 ATP. The max per glucose is 30-32.
  47. Chemiosmosis
    An energy-coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across a membrane to drive cullular work, such as the synthesis of ATP. Under aerobic conditions, most ATP synthesis in cells occurs by chemiosmosis.
  48. Electron Transport Chain (ETC)
    A sequence of electron carrier molecules (membrane proteins) that shuttle electrons down a series of redox reactions that release energy used to make ATP. O2 picks up four electrons from ETC and 4 H+ to become 2 H2O
  49. Cristea
    An infolding of the inner membrane of a mitochodrion. The inner membrane houses electron transport chains and molecules of the enzyme catalyzing the synthesis of ATP (ATP synthase)
  50. Deamination
    • can make a component of Citric Acid cycle from amino acid, strips off the amino group.
    • The removal of an amino group (-NH2) from a compound. Enzymatic deamination occurs in the liver and is important in the amino-acid metabolism, especially in their degradation and subsequent oxidation. The amino group is removed as a ammonia and excreted, either unchanged or as urea or uric acid
  51. Beta-oxidation
    • A metabolic sequence that breaks fatty acids down to two-carbon fragments that enter the citric acid cycle as acetyl CoA.
    • Catabolism of one glucose generates 2 Acetyl CoA, catabolism of one fat molecule generates 24 Acetyl CoA: 12 times as much ATP from fat! 12 times as much exercise to burn it...
  52. Metabolic diversity in Prokaryotes
    Very diverse means of getting energy. Each species of bacteria has a distinctive metabolic 'fingerprint'.
  53. Conditions for chemiosmosis
    • A source of excited electrons
    • Electron carriers
    • A place for electrons to go after the ETC (electron acceptor)
  54. Anaerobic
    use electron donors that do not gerenate O2 as a by product; not water! Maybe H2 H2S, simple organic acids, etc.
  55. Chemoautrophs
    Energy from oxidation of inorganic electron donors. H2, H2S, Fe++, S0, NO2-
  56. Bioremediation
    The use of organisms to detoxify and restore polluted and degraded ecosystems
  57. Binary Fussion
    A method of asexual reproduction by "division in half". In prokaryotes, binary fission does not involve mitosis, but in single-celled eukaryotes that undergo binary fission, mitosis is part of the process.
  58. Bacterial cell growth
    • Chromosome replication begins. Soon thereafter one copy of the origin moves rapidly to the other end of the cell.
    • Replication continues
    • Replication finishes, the plasma membrane grows inward, and new cell wall is deposited.
    • Two daughter cells result.
  59. Generation times for bacteria
    • Most are 1-3 hrs per generation
    • range from ~20 min to >24 hrs
  60. Lag Phase
    Transition from dormant to starting to divide, after the cell obtains some signal that conditions are good; this phase can last 1 hr to several days
  61. Quorum sensing
    All bacteria in a region are generating signals that generally represent metabolic success. When these signals reach a critical concentration - sends bacteria into the beginning of exponential growth
  62. Exponential or Log Phase
    Period of maximum growth & shortest generation times; most metabolically active phase
  63. Stationary Phase
    Conditions for growth deteriorate; rate of growth equals rate of death
  64. Death Phase
    Death rate increases exponentially, growth may go to zero, there may or may not be survivors.

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