Ch 18.3

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Ch 18.3
2014-11-29 23:05:09
Test Four
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  1. ·         Electrons are transferred from __ to O2 through a chain of three large protien complexes called __(3)__
    o   Electron flow within these transmembrane complexes leads to the __
    ·         A fourth large protein complex, called __, contains the __ that generates FADH2 in the CAC
    • NADH
    • NADH-Q oxidoreductase, Q-cytochrome c oxidoreductase, and cytochrome c oxidase
    • transport of protons across the inner mitochondrial membrane
    • succinate-Q reductase
    • succinate dehydrogenase
  2. o   Electrons from this FADH2 enter the ETC at __
    §  __, in contrast with the other complexes, does not pump protons
    §  __(4)__  are also called Complex I, II, III, and IV
    ·         Complexes I, II, and III are associated in a __, which facilitate the __ and prevent the __
    • Q-cytochrome oxidoreductase
    • Succinate Q reductase
    • NADH-Q oxidoreductase, succinate Q-reductase, Q- cytochrome c oxidoreductase, and cytochrome c oxidase
    • supramolecular complex termed the respirasome
    • rapid transfer of substrate
    • release of reaction intermediates
  3. ·         Two special electron carriers ferry the electrons from one complex to the next
    o   The first is __, aka __because it is a ubiquitous quinone in biological systems
    §  It is a __ that __ within the inner mitochondrial membrane
    o   Electrons are carried from __ to __, the second complex of the chain, by the __. Electrons from the FADH2 generated by the CAC are transferred first to __and then to the __
    • coenzyme Q
    • ubiquinone 
    • hydrophobic quinone
    • diffuses rapidly
    • NADH-Q oxidoreductase to Q-cytochrome c oxidoreductase
    • reduced form of CoQ
    • ubiquinone 
    • Q-cytochrome c oxidoreductase complex
  4. ·         Coenzyme Q is a __ with a long tail consisting of __ that account for its hydrophobic nature
    o   The number of __ units in the tail depends on the species
    §  The most common mammalian form contains 10 isoprene units
    • quinone derivative
    • five carbon isoprene units
    • isoprene
  5. ·         Quinones can exist in three oxidation states
    o   In the fully oxidized state (Q), coenzyme Q has __
    §  The addition of one electron and one proton results in the __
    ·         The __can lose a proton to form a __.
    • two keto groups
    • semiquinone form (QH•)
    • semiquinone 
    • semiquinone radical anion (Q•-)
  6. o   The addition of a second electron and proton to the semiquinone generates __, the fully reduced form of coenzyme Q, which holds its protons more tightly.
    §  Thus, for quinones, __ are coupled to __, a property that is key to __
    ·         Because ubiquinone is soluble in the membrane, a pool of __ and __—the __—is thought to exist in the __
    • ubiquinol (QH2)
    • electron-transfer reactions
    • proton binding and release
    • transmembrane proton transport
    • Q and QH2
    • Q pool
    • inner mitochondrial membrane
  7. ·         In contrast with Q, the second special electron carrier is a protein
    o   __, a small soluble protein, shuttles electrons from __ to __, the final component in the chain and the one that catalyzes the reduction of O2
    • Cytochrome c
    • Q-cytochrome c oxidoreductase to cytochrome c oxidase
  8. ·         The electrons of NADH enter the chain at __, an enormous enzyme consisting of about 46 polypeptide chains
    o   This proton pump, like that of the other two in the respiratory chain, is encoded by genes residing in both the mitochondria and the nucleus
    §  __ is __, with a horizontal arm lying __ and a vertical arm that __
    • NADH-Q oxidoreductase (also called Complex I and NADH dehydrogenase)
    • NADH-Q oxidoreductase
    • L-shaped
    • in the membrane
    • projects into the matrix
  9. o   The initial step is the __ and the __
    §  The electron acceptor of __, the isoalloxazine ring, is identical with that of FAD
    • bidning of NADH
    • transfer of its two high-potential electrons tot eh flavin mononucleotide (FMN) prosthetic group of this complex to give the reduced form, FMNH2
    • FMN
  10. ·         Electrons are then transferred from __to a series of __, the second type of prosthetic group in NADH-Q oxidoreductase
    o   __ in __ play a critical role in a wide range of __reactions in biological systems
    §  Several types of __ are known
    ·         Simplest: __
    ·         Another: __

    §  Iron ions in these Fe-S complexes cycle between__ and __ states
    ·         Iron-sulfur clusters generally undrgo __ without __ or __
    • FMNH2 
    • iron-sulfur clusters
    • Fe-S clusters in iron-sulfur prteins
    • reduction 
    • Fe-S clusters
    • one iron coordinated to sulfydryl groups of four cysteines
    • 2Fe-2Sà two irons, two sulfides, four cysteine residues
    •  Fe2+ (reduced) and Fe3+ (oxidized)
    • redox reactions
    • releasing or binding protons
  11. ·         All of the redox reactions take place in the __
    o   NADH binds to a site in the __ and transfers its two electrons to FMN
    §  These electrons flow through a series of __ and then to __
    ·         The flow of two electrons from NADH to CoQ through NADH-Q oxidoreductase leads to the __. In accepting two electrons, Q does what as it is reduced to QH2, which leaves the enzyme for the __ of the membrane
    §  __ is a source of NADH for the ETC
    • extramembranous part of NADH-Q oxidoreductase
    • extramembranous domain
    • Fe-S centers
    • CoQ
    • pumping of four hydrogen ions out of the matrix of the mitochondrion
    • takes up two protons from the matrix
    • hydrophobic interior
    • Fatty acid oxidation
  12. ·         FADH2 enters the ETC at the __; and, it is formed in the CAC, in the __
    o   __, a CAC enzyme, is part of the __, an integral membrane protein of the inner mitochondrial membrane
    o   FADH­2 does not leave the complex
    §  Its electrons are transferred to __ and then finally to __ to form __, which then is ready to transfer electrons further down the ETC
    • second protein complex of the chain
    • oxidation of succinate to fumarate by succinate dehydrogenase
    • Succinate dehydrogenase
    • succinate-Q reductase complex (Complex II)
    • Fe-S centers
    • Q
    •  QH­2
  13. ·         The succinate-Q reductase complex, in contrast with NADH-Q oxidoreductase, does not what?
    o   Consequently, less ATP is formed from FADH2 oxidation than from NADH
    pump protons from one side of the membrane to the other
  14. o   Two other enzyems, __ and __, transfer thir high-ptential electrons from FADH2 to Q to form __, the reduced state of ubiquinone
    §  These enzymes oxidize __ and __, respectively, providing electrons for oxidative phosphorylation; they do not __
    • glycerol phosphate dehyedrogenase and fatty acyl CoA dehydrogenase
    • ubiquiol
    • glycerol and fats
    • pump protons
  15. ·         The electrons from __are passed on to __by the second of the three proton pumps in the respiratory chain, __
    o   The function of __ is to __, a water-soluble protein, and concomitantly __
    §  The flow of a pair of electrons through this complex leads to the __, half the yield obtained with NADH-Q reductase because of a smaller thermodynamic driving force
    • QH2 
    • cytochrome c 
    • Q-cytochrome c oxidoreductase (Compex III)
    • Q-cytochrome c oxidoreductase
    • catalyze the transfer of electrons from QH2 to oxidized cytochrome c
    • pump protons out of the mitochondrial matrix
    • effective net transport of 2 H+ to the cytoplasmic side
  16. ·        __ itself contains two types of cytochromes, named __ and __
    o    A cytochrome is an __
    §  The iron ion of a cytochrome alternates between a __ and an during electron transport
    ·         The two cytochrome subunits of __, termed __, and one heme within __
    • Q-cytochrome c oxidoreductase
    • b and c1
    • electron-transferring protein that contains a heme protsthetic group
    • reduced ferrous (+2) state and an oxidized ferric (+3) state
    • Q-cytochrome b
    • heme bL (L for low affinity) and heme bH (H for high affinity)
    • cytochrome c1
  17. o   The heme prosthetic group in cytochromes b, c1, and c is __, the same heme present in myoglobin and hemoglobin
    §  These identical hemes have different electron affinities because they are __
    • iron-protoporphyrin IX
    • in different polypeptide environments
  18. o   In addition to the hemes, the enzyme contains an __, termed the __, which is unusual in that one of the iron ions is coordinated by two __residues rather than two __ residues
    §  This coordination does what?
    • iron sulfur protein with a 2Fe-2S center
    • Rieske center
    • histidine 
    • cysteine
    • stabilizes the center in its reduced form, raising its reduction potential so that it can readily accept electrons from QH2
  19. ·         QH2 passes two electrons to __, but the acceptor of electrons in this complex, __, can only __
    ·         How does the switch from the two electron carrier ubiquinol to the one electron carrier cytochrome c take place?
    o   The mechanism for the coupling of electron transfer from Q to cytochrome c to transmembrane proton transport is the __. Explain it. 

    • Q-cytochrome c oxioreductase,
    • cytochrome c
    • accept one electron
    • Q cycle
    • §  Two QH2 molecules bind to the complex consecutively, each giving up two electrons and two H+.
  20. §  These protons are released to the __ of the membrane.
    ·         The first __ to exit the Q pool binds to the first __ and its two electrons travel through the complex to different destinations
    o   One electron flows first to the __; then, to __; and, finally, to a molecule of oxidized __, converting it into its __. The __molecule is free to diffuse away from the enzyme to continue down the respiratory chain
    • cytoplasmic side
    • QH2
    • Q binding site (Q0)
    • Rieske 2Fe 2S cluster
    • cytochrome c1
    • cytochrome c
    • reduced form
    • reduced cytochrome c
  21. o   The second electron passes through __to an oxidized __in a __
    §  The Q in the second binding site is reduced to a __ by the electron from the __.
    ·         The now fully oxidized Q leaves the first Q site, free to reenter the Q pool
    • two heme groups of cytochrome b 
    • ubiquinone 
    • second Q biding site (Qi)
    • semiquinone radical anion (Q•-)
    • first QH2
  22. ·         A second molecule of __ binds to the __ and reacts in the same way as the first
    o   One of the electrons is transferred to __.
    o   The second electron passes through the __to partly reduced __bound in the __
    §  On the addition of the electron from the second QH2 molecule, this __ takes up two protons from the matrix side from QH2
    ·         The removal of these two protons from the matrix contributes to the formation of the proton gradient
    • QH2
    • Q0 site of Q-cytochrome c oxidoreductase
    • cytochrome c
    • two heme groups of cytochrome b 
    • ubiquinone 
    • Qi binding site
    • quinone radical anion
  23. §  In sum, __ are released on the cytoplasmic side, and __ are removed from the mitochondrial matrix
    ·         In one Q cycle, two __ molecules are oxidized to form __, and then one __ is reduced to __
    o   The problem of how to efficiently funnel electrons from a __ to a __ is solved by the __
    §  The __ is in essence a recycling device that enables both electrons of QH2 to be used effectively
    • four protons
    • two protons
    • QH2 
    • two Q molecules
    • Q molecule
    • QH2
    • two-electron carrier (QH2)
    • one-electron carrier (cytochrome c)
    • Q cycle
    • cytochrome b component of the reductase
  24. ·         The last of the three proton-pumping assemblies of the respitaory chain is __
    o   __ catalyzes the transfer of electrons from the __ to __ 
    • cytochrome c oxidase (Complex IV)
    • Cytochrome c oxidase
    • reduced form of cytochrome c to molecular oxygen, the final acceptor
  25. ·         The requirement of oxygen makes aerobic organisms aerobic
    o   __ are funneled to O2 to completely reduce it to __, and, concomitantly, protons are pumped from the __ to the __
    §  The reaction is thermodynamically favorable
    ·         As much of this free energy as possible must be captured int eh form of a __ for subsequent use in __
    • Four elecrons
    • H2O
    • matrix to the cytoplasmic side of the inner mitochondrial membrane
    • proton gradient
    • ATP synthesis
  26. ·         Structure (as told b bovine cytochrome c oxidase)
    o   __
    o   additional
    §  One center __ contains two copper ions linked by two bridging cysteine resiues
    13 subunits, 3 of which are encoded by the mitochondrion’s own genome

    Two heme A groups and three copper ions, arranged as two copper centers, designated A and B

  27. ·         This center does what?
    o   The remaining copper ion, __, is coordinated by __ residues, one of which is modified by __
    §  The copper centers alternate between the __ and __ as they accept and donate electrons
    • accepts electrons from reduced cytochrome c
    • CuB
    • three histidine
    • covalent linkage to a tyrosine residue
    • reduced Cu+ form and the oxidized Cu2+ form
  28. o   There are two __, called __ and _, in cytochrome c oxidase
    §  Heme A differs from the heme in cytochrome c and c1 in three ways:
    __ (3)__
    • heme A molecules
    • heme a and heme a3

    • · A formyl group replaces a methyl group·
    • A C17 hydrocarbon chain replaces one of the vinyl groups
    • The heme is not covalently attached to the protein
  29. §  Heme a and heme a3 have distinct __ because they are located in different environments within __
    ·         An electron flows from cytochrome c to __, __, and __
    o   Heme __ and __ are directly adjacent
    §  Together, __ and __ form the active center at which O2 is reduced to H2O
    • redox potentials
    • cytochrome c oxidase
    • CuA/CuA, to heme a to heme a3 to CuB, and finally to O2
    • a3 and CuB
    • heme a3 and CuB­
  30. o   Four molecules of __ bind consecutively to the enzyme and __
    §  Electrons from two molecules of reduced __flow down an electron-transfer pathway within __, one stopping at __ and the other at __. With both centers in the reduced state, they together can now bind an oxygen molecule
    §  As molecular oxygen binds, it does what to do what?
    • cytochrome c
    • transfer an electron to reduce one molecule of O2 to H2O
    • cytochrome c 
    • cytochrome c oxidase
    • CuB
    • heme a3
    • abstracts an electron from each of the nearby ions in the active center
    • form a peroxide bridge between them
  31. §  Two more molecules of __bind and release electrons that travel to the __. The addition of an electron as well as H+ to each oxygen atom reduces the two ion-oxygen groups to __ and __ 
    §  Reaction with two more H+ ions allows the release of two molecules of H2O and resets the enzyme to its initial, fully oxidized form
    o   The four protons in this reaction come exclusively from the __. Thus, the consumption of these four protons contributes directly to the __
    • cytochrome c 
    • active center
    • CuB2+--OH and Fe3+--OH
    • matrix
    • proton gradient
  32. ·         Cytochrome c oxidase uses the __ to do what in the course of each reaction cycle for a total of __ removed from the matrix
    o   Two effects contribute to the mechanism
    §  First, __
    ·         Thus, the addition of an electron to a site inside a protein tends to favor the binding of H+ to a nearby site
    • lost energy
    • pump four additional protons from the matrix to the cytoplasmic side of the membrane

    eight protons

    charge neutrality tends to be maintained in the interior of proteins
  33. §  Second, __
    ·         Presumably, in one conformation, protons may do what, whereas, in another, they may do what? 
    • conformational changes take place, particularly around the heme a3-CuB center, in the course of the reaction cycle
    • enter the protein exclusively from the matrix side
    • exit exclusively to the cytoplasmic side.
  34. ·         The flow of electrons from NADH and FADH2 through the respiratory chain: the series of __ is coupled to the __
    ·         When O2 is reduced partially, __ come about. In particular, the transfer of a single electron to O2 forms __, whereas the transfer of two electrons yields __
    o   To prevent this, the catalyst does not __; cytochrome c oxidase holds O2 tightly between Fe and Cu ions
    • exergonic reactions
    • pumping of protons from the matri
    • hazardous compounds
    • superoxide anion
    • peroxide
    • release partly reduced intermediates
  35. ·         __ scavenges superoxide radicals by catalyzing the conversion of two of these radicals into hydrogen peroxide and molecular oxygen
    o   Eukaryortes have two forms of this enzyme: a __ version located in mitochondria and a __ cytoplasmic form
    • Superoxide dismutase
    • manganese-containing
    • copper- and zinc- dependent
  36. §  These enzymes perform the __by a similar mechanism
    ·         The oxidized form of the enzyme is reduced by __to form oxygen
    ·         The reduced form of the enzyme, formed in this reaction, then reacts with a __ to form __, which takes up two protons along the reaction path to yield __
    The hydrogen peroxide formed is scavenged by __. __ also plays a role in scavenging H2O2
    • dismutation reaction 
    • superoxide 
    • second superoxide ion
    • peroxide
    • hydrogen peroxide
    • catalase
    • Glutathione peroxidase
  37. ·         Electrons can move through space, but the rate of electon transfer through space falls off rapidly as what? 
    o   The protein environment provides more efficient pathways for electron conduction: typicaly, the rate of electron transfer decreases by a factor of 10 every 1.7 angstroms
    o   For groups in contact, __ can be fast
    • the electron donor and electron acceptor move apart from each other, deceasing by a factor of 10 for each increase in separation of 0.8 angstroms
    • electron-transfer reactions
  38. o   Within proteins in the electron-transport chain, electron carrying groups are separated by 15 angstroms beyond their __
    §  Without the mediation of the protein, an __ over this distance would take a day
    o   A series of hydrophobic interactions bring the __ to within 4.5 angstroms of each other, with the iron atoms separated by 17.4 angstroms
    • van der Waals contact distance
    • electron transfer
    • heme groups of cytochrome c and c1
  39. ·         __ is present in all organisms having mitochondrial respiratory chains
    o   Its function has been conserved
    §  __ of any eukaryotic species reacts in vitro with the cytochrome c oxidase of any other species tested thus far
    o   The similarity extends to the amino acid sequence
    • Cytochrome c
    • Cytochrome c