Metablism: Oxidative Phsphrylatin Hand-ut fr the CBT versin April 2012 1. On average, hw much ATP is needed each day by ur bdy? 2. Which f the fllwing ccurs during cellular respiratin? Bisynthesis f glycgen in the liver and muscles Cnversin f an electrn-mtive frce int a prtn-mtive frce Frmatin f cmpunds with high electrn transfer ptential 3. The size f human cells lies between apprximately 10-100 µm. A. What is the typical size (length) f a mitchndrin? B. The reactins f which metablic prcesses are fund in the matrix f a mitchndrin? C. Which f the fllwing is true fr the inner membrane f a mitchndrin? It has pres and is readily permeable t mst small metablites. It is highly flded int cristae Its surface is the equivalent f 3 American ftball fields 4. A. Are mitchndria fund in all kingdms f life? B. Are mitchndria autnmus rganelles? C. Hw has a mitchndrin likely cme int existence?
5. The reductin ptential is als called redx ptential, r xidatin-reductin ptential. A. Is the redx ptential related t the free energy f the reactin? B. What des the redx ptential fr a reactin predict? Whether a given cmpund can reduce anther Whether a given xidatin will prvide sufficient energy fr the frmatin f ATP frm ADP and P i The rate f O 2 uptake upn the xidatin f a given substance 6. Cytchrme a is part f cytchrme c xidase and believed t be the acceptr f electrns frm cytchrme c. The equatin fr the reductin f cytchrme a by cytchrme c is: Cyt a (+3) + Cyt c (+2) Cyt a (+2) + Cyt c (+3) Where Cyt a (+3) + e- Cyt a (+2) E 0 = + 0.27 V Cyt c (+3) + e- Cyt c (+2) E 0 = + 0.22 V A. Hw many electrns are transferred in this reactin? B. Des this reactin prceed spntaneusly under standard cnditins? ([prducts]=[reactants]=[1m] and ph=7) C. Hw much energy des this reactin yield? D. Des this reactin yield sufficient energy fr ATP synthesis? E. Des this reactin alter the absrptin spectra f the cytchrmes?
7. Cnsider the reactin succinate + FAD fumarate + FADH 2. Table 18.1 n page 547 gives the E 0 and n fr the reactins invlved. What is the Gº fr this reactin? 8. The parameters Gº and E 0 can be used t predict the directin f chemical reactins in standard cnditins. On the ther hand, G can be used fr any cncentratin f reactants and prducts t predict in what directin a chemical reactin will prceed. Using the expressins G = G 0 + RT ln (prducts] / [reactants] Gº = -F E 0 Derive an expressin fr E. 9. Cnsider the reactin succinate + FAD fumarate + FADH 2. Table 18.1 n page 547 gives the E 0 and n fr the reactins invlved. In Questin 7 yu have calculated Gº fr this reactin. The cncentratins f all cmpunds is: Succinate: 2 10-3 M Fumarate: 0.5 10-3 M FAD: 2 10-3 M FADH 2 : 0.2 10-3 M The temperature is 37ºC. The value f gas cnstant R = 8.314 10-3 kj/ml. K The value f Faraday cnstant F = 96.48 kj/ml.v A. What is the G fr this reactin? Answer: kj/ml B. What is the E f this reactin?
10. Prtns are transprted ut f the matrix acrss the inner membrane and int the inner membrane space f a mitchndrin. Hw much free-energy ptential is generally generated acrss the inner membrane by each prtn? 11. A. Place the respiratry-chain cmpnents in their prper sequence. B. Mark the cmpnents that are mbile carriers f electrns. 12. Succinate reductase is anther cmplex, which has the ability t accept electrns and dnate them t a cmpnent in this chain. These grups belw are part f the redx chain. In which cmplex f the respiratry chain d they take part? heme a heme a 3 heme b l heme b H heme c 1 FAD FMN irn-sulfur cmplexes Cu A and Cu B
13. The fllwing questins are abut the enzyme cmplexes f the electrn transprt system. A. Are all cmplexes lcated in the mitchndrial matrix? B. Can they be separated frm ne anther in functinal frm? C. D the enzyme cmplexes that include heme r flavin prsthetic gups have very similar light absrptin spectra? D. Are the integral membrane prteins f the enzyme cmplexes lcated in the inner mitchndrial membrane? E. D the enzyme cmplexes transfer electrns t ne anther by means f mbile electrn carriers? 14. The fllwing questins are abut ubiquinl. A. Ubiquinl is the mbile electrn carrier between which cmpnents? B. Ubiquinne is.. C. Where is ubiquinl situated in the mitchndrin? D. Hw is it xidized t ubiquinne?
15. Several cytchrmes have a prtprphyrin IX heme, much alike that in myglbin and haemglbin. In which cytchrme is the heme nt cvalently bund t prtein? 16. The Q-cytchrme c xidreductase cmplex accepts electrns frm ubiquinne, and transfers them t cytchrme c. This requires a special prcess, as ubiquinne dnates tw electrns, and cytchrme c can nly accept ne electrn. The cmplex has tw binding sites fr Q: Q fr Q and Q i fr QH 2. A. Hw is this prcess called? B. Ubiquinne is represented by the letter Q. Give the first reactin that ccurs in this cycle. C. What is the destinatin f the prtns? D. What is the destinatin f the electrns? E. What happens next? F. What is the destinatin f the prtns? G. What is the destinatin f the electrns? H. What is the reactin that happens in Q i? I. What is the net reactin that has taken place?
17. In the reductin f O 2 t H 2 O by cytchrme xidase, fur electrns and fur prtns are used. Hw can this happen when a single electrn at a time is transferred by cytchrme c? 18. The fllwing questins deal with the structure and prperties f cytchrme c. A. Cytchrme c is a very small prtein. Des cytchrme c cntain an α-helix r β- pleated sheet secndary structure? B. Des cytchrme c have a heme? C. Is it cytchrme c that has retained a highly cnserved cnfrmatin thrughut evlutin? D. Is cytchrme c sluble in water? 19. The fllwing questins deal with reactive xygen species (ROS). A. Which f the fllwing are ROS? OH H 2 O 2 O 2 2- O 2 O 2 - H 2 O B. Where d ROS cme frm? C. Hw is the danger frm ROS avided?
20. FADH 2 is generated by the succinate-q dehydrgenase cmplex, but is nt free t diffuse frm the enzyme cmplex. A. Hw can it participate in electrn transprt? B. Des the xidatin f succinate transprt prtns? 21. The fllwing questins deal with an aerated preparatin f mitchndria which are still functinal and fr which the reduced substrate is succinate. A. Which cmpnents f the electrn-transprt chain will be reduced? B. Hw many prtns will the succinate dehydrgenase cmplex pump acrss the inner membrane? C. Hw many ATP mlecules will apprximately be frmed per succinate xidized t fumarate? D. Hw many ATP mlecules will apprximately be frmed per succinate xidized t fumarate when CN - (cyanide) is added? 22. The chemismtic mdel f xidative phsphrylatin is supprted by several experimental bservatins. Which f the fllwing bservatins prvide evidence fr this mdel? A clsed membrane r vesicle cmpartment is required fr xidative phsphrylatin. A system f bacterirhdpsin and ATPase can prduce ATP in synthetic vesicles when light causes prtn pumping. A prtn gradient is generated acrss the inner membrane f mitchndria during electrn-transprt. ATP is synthesized when a prtn gradient is impsed n mitchndria.
23. The redx ptentials f the electrn-transprt chain cmpnents are knwn. This way the free energy charge can be calculated fr each step. Can yu therefre precisely predict the site where the cupling f xidatin t phsphrylatin ccurs? 24. The fllwing questins all deal with the mitchndrial ATP-synthesizing cmplex. A. Hw many subunits des it cntain? B. Where is the cmplex situated? C. What des it translcate? D. By what substance Is ATP synthase inhibited? 25. Belw are sme cmpnents and functins f the majr units f ATP synthase. Match these cmpnents and functins t the crrect majr unit. is mstly in the matrix cntains the catalytic sites fr ATP synthesis NTP-ase family members cntains α, β, γ, δ, and ε subunits cntains sequences hmlgus t P-lp cntains a prtn channel spans the inner mitchndrial membrane
26. The next questins all deal with the prpsed mechanism fr ATP synthesis. A. The prtn mtive frce results in cnfrmatinal changes f the ATP synthase and is necessary because B. Hw many active sites has ATP synthase per cmplex? C. Are the three active sites f ATP synthase functinally equivalent at a given time? 27. ATP synthase can frm ATP in the absence f a prtn gradient when it is mixed with ADP and P i. Hw can this happen when the frmatin f ATP frm ADP and P i requires 30.6 kj/ml f free energy? 28. There are sme similarities between the mechanisms f G prteins and ATP synthase. Which f the fllwing are similarities? They bind nucletides based n interactin with prteins. They can bind the duble phsphrylated frm as well as the triple phsphrylated frm They release the nucletides triggered by an effectr prtein 29. The inner mitchndrial membrane cntains translcases (specific transprt prteins). One f them is ATP-ADP translcase. Fr which pairs f substances are these als present? 30. In the inner mitchndrial membrane exists a malate-aspartate shuttle. Which pairs f mlecules are transprted in ppsitin t each ther acrss the membrane by this shuttle?
31. This is a drawing f five f the mitchndrial transprters. The ATP-ADP translcase transprts ADP int the matrix and ATP ut f it. Match the ther fur mitchndrial transprters likewise with the mlecules they transprt. 32. When the ATP-ADP translcase functins in the presence f a prtn gradient, the rate f inversin (NL: verwisseling) f the binding site frm the matrix t the cytslic side is mre rapid fr ATP than fr ADP. Why is this? Circle the crrect answers. The membrane is mre psitively charged at the inner membrane space / matrix side than at the inner membrane space / matrix side therefre ATP is mre / less attracted. 33. Fr each extra-mitchndrial NADH that is xidized t NAD + by O 2 via the electrn transprt chain a certain number f ATP is frmed. Assuming that the glycerl phsphate shuttle is perating, apprximately hw many ATP are frmed? 34. Assume that the glycerl phsphate shuttle is perating. Hw many ATP mlecules are generated during the cmplete xidative generatin f each f the fllwing t CO 2 and H 2 O? A. Acetyl CA: B. Phsphenlpyruvate: C. Glyceraldehyde 3-phsphate:
35. By respiratry cntrl the rate f xidative phsphrylatin is regulated. Hw is this dne? 36. Uncuplers, such as dinitrphenl (DNP) r thermgenin, uncuple electrn transprt and phsphrylatin. Hw d they achieve this? 37. Which f the fllwing are the prducts f the reactin f superxide dismutase? H 3 O + H 2 O 2 H 2 O O 2 O 2-38. There are several inhibitrs f the xidative phsphrylatin, listed belw. Give fr each inhibitr its primary effect. azide atractylside rtenne dinitrphenl carbn mnxide ligmycin 39. In apptsis a cascade f prtelytic enzymes is activated, in which each enzyme destrys a particular target. Which f the fllwing mlecules are directly invlved in apptsis? Caspase Caspase-activated DNase Nuclear RNase RNA plymerase II Cytchrme c Cytchrme xidase