Ch 17 Krebs Cycle 2

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Ch 17 Krebs Cycle 2
2014-11-23 22:00:26
Test four
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  1. ·         Conversion of pyruvate into acetyl CoA by __ is the link between __ and __ because __ is the fuel for the CAC; all fuels are metabolized to __ or components of the CAC
    ·         The CAC begins with the __--> __ and __are the products
    • pyruvate dehydrogenase complex
    • glycolysis and cellular respiration
    • acetyl CoA
    • acetyl CoA

    condensation of a four-carbon unit, oxaloacetate, and a two-carbon unit, the acetyl group of acetyl CoA

    citrate and CoA
  2. o   Citrate synthase catalyzes this __ followed by __
    §  Oxaloacetate first condenses with acetyl coA to form __, a molecule that is energy rich because it contains the __ that originated in acetyl CoA
    ·         Hydrolysis of __to __ and __ drives the overall reaction far in the direction of the synthesis of citrate
    o   The hydrolysis of the __powers the synthesis of a new molecule from two precursors
    • aldol condensation followed by hydrolysis
    • citryl CoA
    • thioester bond
    • citryl CoA thioester 
    • citrate and CoA
    • thioester
  3. ·         Citrate synthase prevents __
    o   Each active site of citrate synthse (a dimer) is located in a __between the large and small domains of a subunit, adjacent to the subunit interface
    o   The enzyme undergoes __ in the course of catalysis
    §  Citrate synthase exhibits __; __binds first, followed by __
    wasteful hydrolysis of acetyl CoA


    large conformational changes

    sequential, ordered kinetics


    acetyl CoA
  4. ·         Oxaloacetate induces a major structural rearrangement leading to the __
    o   The binding of oxaloacetate does what?
    §  In each subunit, the small domains do what?
    Movements as large as __ are produced by the __ elicited by quite small shifts of the __
    o These structural changes create a __
    • creation of a binding site for acetyl CoA
    • converts the open form of the enzyme into a closed form
    • rotates 19 degrees relaive to the large domain
    • 15 angstroms
    • rotation of alpha helices
    • side chains around bound oxaloacetate

    binding site for acetyl CoA
  5. ·         Citrate synthase catalyzes the __ by doing what?
    o   The __ and __ of __ transforms acetyl CoA into an __, which goes on to __. 
    §  The newly formed __ induces more structural changes in the enzyme,c ausing the active site to become __. The enzyme cleaves the __ by __. __leaves the enzyme, followed by __, and the enzyme returns to the initial open conformation. 
    • condensation reaction
    • bringing the substrates into close proximity, orienting them, and polarizing certain bonds
    • donation and removal of protons

    • enol intermediate
    • attack oxaloacetate
    • citryl CoA
    • completely enclosed
    • citryl CoA thioester
    • hydrolysis
    • CoA 
    • citrte
  6. ·         Essentially, citrate synthase can hydrolyze __ but not __. It discriminates against the two because, first, __; and, second, __. This is __ again
    • citryl CoA
    • acetyl CoA
    • acetyl CoA does not bind to the enzyme until oxaloacetate is bound and ready for condensation
    • the catalytic residues crucial for the hydrolysis of the thioester linkage are not appropriately positioned until citryl CoA is formed
    • induced fit
  7. ·         Because the hydroxyl group is not in a right place, citrate is __into __to enable the six-carbon unit to undergo __
    o   The __ is accomplished by a __ followed by a __. The result is the interchange of an H and an OH
    §  The enzyme catalyzing both steps is called __, which is an __ protein that contains iron not bound to heme
    • isomerized 
    • isocitrate 
    • oxidative decarboxylation
    • isomerization of citrate
    • dehydration step
    • hydration step
    • aconitase
    • iron-sulfur
  8. ·         Its four iron atoms are bound to __ and __, leaving one __ available to bind citrate through one of its COO- groups and an OH group.
    o   This __ participates in __ and __ the bound substrate 
    • four inorganic sulfides
    • three cysteine sulfur atom
    • iron atom
    • Fe-S cluster
    • dehydrating and rehydrating
  9. ·         The first of four oxidation-reduction reactions in the CAC is catalyzed by __; it is the __ of __. Int his reaction, __is lost and __ is formed.
    o   This first oxidation generates the first __
    • isocitrate dehydrogenase
    • oxidative decarboxylation
    • isocitrate
    • CO2 
    • alpha-ketoglutarate
    • high-transfer- potential electron carrier, NADH
  10. ·         The second __ is the second step, the formation of __ from __, which is catalyzed by __, an organized assembly of three kinds of enzyme that has a similar mechanism to the pyruvate dehydrogenase complex
    o   Both reactions include the __of an __ and the subsequent formation of a __ with __that has a __. 
    • oxidative decarboxylation
    • succinyl CoA
    • alpha-ketoglutarate
    • alpha-ketoglutarate dehydrogenase complex
    • decarboxylation 
    • alpha-ketoacid
    • thioester linkage
    • CoA 
    • high transfer potential
  11. ·         __ is an energy rich thioester compound. In the __ reaction, the cleavage of the __ powers the synthesis of the __ from the __ and the __
    o   The cleavage of the __ is coupled to the __
    §  This reaction is readily reversible and is catalyzed by __
    • Succinyl CoA
    • citrate synthase
    • thioester bond
    • six-carbon citrate
    • four-carbon oxaloacetate and the two-carbon fragment
    • thioester bond of succinyl CoA
    • phosphorylation of a purine nucleoside diphosphate, usually ADP
    • succinyl CoA synthetase
  12. ·         This reaction is the only step in the CAC that yields a compound with __
    o   In mammals, there are two __ of the enzyme, one for __ and one for __
    §  __ have the GTP one; __have the ATP form
    ·         The GDP requiring enzyme works in the __; used to power __
    • high phosphoryl-transfer potential
    • isozymic forms
    • ADP and one for GTP
    • Anabolic tissues
    • tissues that respire a lot 
    • reverse of the TCA cycle
    • synthesis of succinyl CoA
  13. ·         The enzyme __ catalyzes the reaction: GTP+ ADPßà GDP + ATP
    ·         The mechanism of __ has energy in the __; and, this energy is transformed into __
    o   Step one: __ by __, which generates __
    §  A histidine acts as a __that does what?
    • nucleoside diphosphokinase
    • succinyl Coenzyme A synthase
    • thioester molecule
    • phosphoryl-group transfer potential
    • displacement of CoA
    • orthophosphate
    • enery rich succinyl phosphate
    • moving arm 
    • detaches the phosphoryl group, swings over to the bound nucleoside diphosphate, and transfers the group to form the NTP
  14. ·         __ is an __; a phosphoryl group is transferred first to __ bound in the __ and then to an __ in the __
    o   Each subunit has two domains
    §  The amino-terminal domains have different structures
    ·         Alpha forms a __, binding __ of succinyl CoA synthetase
    ·         Beta  is an __, which binds and activates ADP
    • Sucinyl CoA synthetase
    • a2B2 heterodimer
    • succinyl CoA
    • alpha subunit
    • NDP bound
    • beta subunit
    • Rossmann
    • ADp
    • ATP-grasp domain
  15. ·         Reactions of four-carbon compounds is the final stage: __
    o   A __ is converted into a carbonyl group in three steps: __
    §  __is regenerated and more enery is extracted as __ and __
    • reneration of oxaloacetate
    • methylene group
    • oxidation, hydration, and second oxidation
    • Oxaloacetate 
    • FADH2 and NADH
  16. ·         Succinate is oxidized to __by __, passing electrons to __because the free-energy change is insufficient to reduce NAD+.
    o   FAD is always the electron acceptor in oxidations that remove __ from a substrate
    §  In __, the isoalloxazine ring of FAD is covalently attached to a histidine side chain of the enzyme
    • fumarate 
    • succinate dehydrogenase
    • FAD 
    • two hydrogen atoms
    • succinate dehydrogenase
  17. o   Succinate dehydrogenase is an __ proteins ahd have __
    §  It is in the __ and directly associated with the __, the link between the CAC and ATP formation
    ·         __produced by oxidation of succinate like NADH in other reactions; instead, __ are transferred from __directly to __of the enzyme, which passes the electrons to __, which passes them to xygen
    • iron-sulfur
    • 3 different iron-suulfur clusters
    • inner mitochondrial membrane
    • eTC
    • FADH2
    • two electrons
    • FADH2 
    • iron-sulfur clusters 
    • CoQ
  18. ·         The next step is the __.
    o   __catalyzes the __ addition of H+ and OH-. The OH- group adds to only one side of the double bond of fumarate. So, only the __ is formed
    ·         Finally, __is oxidized to __by __and __ is the hydrogen acceptor
    • hydration of fumarate to form L-malate
    • Fumarase 
    • stereospecific trans
    • L isomer
    • malate 
    • oxaloacetate 
    • malate dehydrogenase 
    • NAD+
  19. ·         The net reaction of the CAC is:
    o   Acetyl CoA + 3 NAD+ + FAD + ADP + Pi + 2 H2O à 2 CO2 + 3 NADH + FADH2 + ATP + 2 H+ + CoA
  20. Summary 
    Two carbon atoms enter the cycle and condense with __. Two carbon atoms leave the cycle in the form of __int eh successive __ catalyzed by __ and __

    o   __ leave the cycle in four oxidation reactions. Two __molecules are reduced in the oxidative decarboxylations of __, one __molecule is reduced in the __, and one __ is reduced in the oxidation of __
    • oxaloacetate
    • CO2 
    • decarboxylations
    • isocitrate dehydrogenase
    • alpha-ketoglutarate dehydrogenase
    • Four pairs of hydrogen atoms
    • NAD+ 
    • isocitrate and alpha-ketoglutarate
    • FAD 
    • oxidation of succinate
    • NAD+
    • malate

  21. o   One compound with __, usually ATP, is generated from the cleavage of the __
    o   Two __ are consumed: one in the __ and the other in the __
    • high phosphoryl-transfer potential
    • thioester linkage in succinyl CoA
    • water molecules
    • synthesis of citrate by the hydrolysis of citryl CoA
    • hydration of fumarate
  22. ·         __ revealed that the two carbon atoms that enter each cycle are not what, but what?; they remain __
    o   The two carbons that enter the cycle will be released as __in subsequent trips through the cycle
    • Isotope-labeling studies
    • not the ones that leave, but instead are retained during the initial two decarboxylation reactions
    • incorporated in the four-carbon acids of the cycle
    • CO2
  23. Evidence shows that the enzymes of the CAC are __, enhancing the efficiency of the CAC due to __; the structure is called a __
    physically associated with one another

    substrate channeling

  24. ·         The ETC oxidizes the __ and __ formed in the CAC. The transfer of electrons from the carriers to oxygen leads to the __ across the __; the __ powers the generation of ATP
    o   2.5 ATP per NADH; 1.5 ATP per FADH2
    • NADH and FADH2
    • proton gradient
    • inner mitochondrial membrane
    • proton-motive force
  25. §  __ are generated when the ETC oxidizes __ and __, and one high-transfer potential phosphoryl group is directly formed in one round of the CAC
    ·         Thus, one __ generates approximately 10 molecules of ATP
    Nine high-transfer potential phosphoryl groups

    three NADH molecules and 1 FADH2 molecule

    acetyl unit
  26. ·         The CAC cycles only under aerobic conditions because __ can be regenerated in the mitochondrion only by the __
    o   Glycolysis has both an aerobic and anaerobic mode, whereas the CAC is strictly __
    • NAD+ and FAD
    • transfer of electrons to molecula roxygen
    • aerobic