Chapter 13 Principles of Bioenergetics

Transcription

1 Chapter 13 Principles f Bienergetics Read Intr t part II n yur wn 13.1 Bienergetics and Thermdynamics A. Bilgical Transfrmatins bey Laws f thermdynamics st 1 law, - in any physical r chemical change ttal amunt f E in universe is cnstant (E nt created r destryed) 2nd law entrpy f universe (S) is always increasing Backgrund - what is entrpy use 3 quantities t describe the energy f chemical prcesses Enthalpy (ÄH j/ml) heat cntent f the system, is negative if heat released Entrpy (ÄS J/ml K) randmness f the system, is psitive if gets mre randm Free Energy (ÄG j/ml) energy available fr ding wrk is - fr spntaneus reactins Review f Gen Chem terms Internal Energy -E -Sum f kinetic and ptential energy f all particles in a system Enthalpy -H- heat cntent f a reactin Entrpy -S- a measurement f randmness in a system Gibbs Free Energy -G- Amunt f energy available t d wrk In bilgical systems, P, T cnstant ÄG = ÄH -TÄS Since ÄH is a measure f heat released t surrunding yu can think f as randmness f surrundings ÄS is randmness f system itself S ÄG is a measure f verall randmness f universe and as lng as that is negative, the randmness f universe has increased and the reactin can be spntaneus B. Cells Require Surces f Free Energy Mst cells are in isthermal and isbaric envirnment (Cnstant T and P) Since cnstant T, cannt use heat flw as energy surce S Gibb Free energy is nly frm f energy available

2 2 C. Free energy related t K eq aa + bb cc + dd c d a b K eq = [C] [D] / [A] [B] ÄG= -RT lnk eq If nt at equilibrium will try t mve in that directin ÄG is a measure f hw far frm equilibrium yu are when everything is []=1M T=298 P=1atm [gas]=1 atm Nt a great def fr bichemists + 1M H = ph 0 [H O]=55.5M and essentially a cnstant 2 ÄG used in Bichem fr ph=7, [H2O]=55.5M and essentially a cnstant ÄG = -RT lnk eq Nte 1: -ÄG, K eq>1, reactin g tward prducts +ÄG, K eq<1, reactin g tward reactants can use t cnvert frm ÄG t K eq 2+ Nte 2: This bk state that [Mg ] is als treated as a cnstant. I have nt seen that befre Prblem 2(b) frm end f chapter Calculate ÄG fr the reactin: Dihydrxyacetne phsphate glyceraldehyde 3-phsphate Given that the K fr the reactin is eq ÄG = -RT ln K eq = J/K ml 298K ln(.0475) = J/ml = 7.55 kj/ml D. Actual free-energy changes depend n reactant and prduct cncentratins ÄG the energy change when [] start at 1M ÄG the energy change that ccurs fr a reactin under a particular set f cnditins Nte these are different. Lts f tables arund that tabulate ÄG fr varius bichemical reactins

3 3 And this is ften used t determine if a reactin will be spntaneus in a cell hwever [] are never 1M, s may nt apply Example 2. Cntinue n with previus example f Dihydrxyacetne phsphate glyceraldehyde 3-phsphate ÄG = 7.55 kj/ml pretty highly unfavrable. Say we had ther prcesses in the cell that kept the cncentratin f the reactant high, say 1M, but kept the cncentratin f the prduct lw, say.01m. What des this d t ur ÄG? ÄG=ÄG +RT lnq = 7, (298) ln([prducts]/[reactants]) = 7, (298) ln(.01/1) =7, (298) ln(.01) = 7,500-11,400 J = J = -3.9 kj In this case ur cellular cnditins have made a reactin that we thught was unfavrable with a + ÄG int ne that is favrable with a - ÄG. Thus always have t put in cellular cncentratins t find ut if really spntaneus in cell Other pints ÄG and ÄG are measures f the maximum amunt f free energy that an reactin can theretically deliver under ideal cnditins... actual results may be less and usually are. Remember, just because ÄG <0 des nt mean will ccur. Just that it can ccur. Kinetics and high activatin energy may prevent reactin frm ccurring withut a catalyst When yu use a catalyst, nly changes the rate des nt change the energy E. Free energy changes are additive A B ÄG =5 kj/ml B C ÄG =-6 kj/ml A C ÄG = ÄG A + ÄG B = 5-6 = -1kJ/ml

4 4 K eq = Keq1 Keq2 Try with cncrete example Glucse + Pi Glucse-6-phsphate + H2O ÄG =13.8 kj.ml, K eq = 3.9x10 5 ATP + H O ADP + P ÄG = kj/ml K =2x i eq What is ÄG and K eq fr Glucse + ATP Glucse-6-phsphate+ ADP? Nte t get this we simply add the equatins tgether Glucse + Pi Glucse-6-phsphate + H2O ATP + H2O ADP + P i Glucse + P i + ATP + H2O Glucse-6-phsphate + H2O + ADP + P i And the Pi and H2O fall ut f bth sides f the equatin t give us the equatin we want if yu add the equatins yu add the ÄG s S ÄG = (-30.5) = kj/ml if yu add the equatins yu multiply the K eq x10 x 2x10 = 7.8x10 If yu had t subtract the secnd equatin what wuld yu have dne? (Subtract the ÄG, divide the K ) 13.2 Chemical lgic and cmmn Bichemical reactins Cells can t d all the different chemical reactin yu learned in rganic class S this sectin emphasizes the types f chemistry seen in cells 5 main categries Make r break C-C bnds internal rearrangements Ismerizatins Eliminatins Free-radical reactins Grup transfers xidatin/reductin Tw ther principles When breaking a cvalent chemical bnd, where d the electrns g? Figure 13-1 Hmlytic cleave - each atm in bnd get an electrn s each is a radical Heterlytic Cleavage(mre cmmn) 1 atm retains bth electrns, ther atm ges withut eq

5 5 Many bichemical (and rganic reactins) invlve interactins between: Electrphiles = electrn seeking = electrn deficient= electrn acceptr = Lewis Acid Nuclephiles = + charge seeking = electrn rich = electrn dnr = Lewis Base Figure 13-2 Reactins that make r break C bnds Heterlytic cleavage f a C-C bnd yields carbcatin and carbanin. Reverse is Frmatin f a C-C bnd usually invlves a nuclephilic carbanin (L.B.) And a electrphillic carbcatin (L.A.) Carbanins and carbcatins are s unstable that d nt ccur in Bichemistry, s neither reactin can take place bichemicallywhen nly C is invlved. Can nly ccur if adjacent functinal grups cntain electrnegative atms like N r O s electrnic structure f adjacent t C atm helps stabilize in in a Bichemical Reactin Figure 13-3 Lk fr reactin that ccur adjacent t Carbnyls (Figure 13-4) Rearrangments, ismerizatins and eliminatins redistributin f electrns arund a mlecule Can be simple as water eliminatin (right clumn page 514) Or cmplicated internal xidatin/reductin Figure 13-6 Free Radical Reactins Once thught t be rare (free radicals are very reactive and dangerus t cells) Nw has been bserved in may reactins See Figure 13-7 Grup Transfers the transfer f acyl, glyssyl and phsphryl grups frm ne nuclephile t anther is cmmn left clumn page 515 Gd ld SN1r SN2 type reactins Will see a lt with PO grup (next sectin) 4 Oxidatin/Reductin C can be in 5 xidatin states (Figure 13-9) Reactin where cmpund lses 2 electrns and 2 prtns - dehydrgenatins When C becme bund t an xygen - xidases

6 6 Unless O cmes directly frm O 2 then - xygenase Oxidatin requires a reductin Oxidatins release energy Invlved in release f E fr cell energy Mst f abve reactin require cfactrs Bichemical and Chemical Equatins are nt equivalent Bichemical reactins are usually simplificatins Fr instance ATP + H2O ADP + Pi - Different frms f ATP,ADP and P depending n ph 2+ Als Mg is part f reactin S a whle lt f things are swept under the table 2+ PH7, 1mM Mg are part f ÄG 13.3 Phsphryl Grup Transfers and ATP Yu already knw that ATP is the majr energy currency in cell will use this E fr virtually every thing frm active transprt t synthesis f a new prtein let s examine the energy f this prcess in mre detail A. Free E change fr ATP hydrlysis is large and negative Figure n bard Lts f E released kj/ml Why is this energetically favred prcess? 1. ATP had a -4 charge Releasing Pi allws sme f the charges t separate thus lwering E f system 2. Pi itself, resnance stabilized s likes t be in that frm As shwn ADP-H will inize t ADP releasing anther H T lw [H ] f slutin (10 H ) 4. G frm 2 mlecules t 3 mlecules... entrpy increases Als remember earlier nte ÄG is at 1M cnc. What abut real cnc in cell (See wrked example 13-2 fr full analysis) ATP and ADP usually assciated with Mg 2+ see table 13-5 fr example cncentratins [ATP]= 2,25x10-3 [ADP] = 2.5x10-4 [Pi]=1.65x10-3 Final answer kj/ml!!!

7 7 (That als means it takes that much E t make ATP) Say phsphrylatin ptential is -50 t -65 kj/ml B. Other Phsphrylated cmpunds and Thiesters There are several phsphrylated cmpunds that have a higher dephsphrylatin energy than ATP, and these cmpunds can be used t make ATP 1,3-Biphsphglycerate (figure 13-14) Phsphenlpyruvate, PEP Figure Phsphcreatine Figure In all cases can see that the prduct has sme resnance stabilizatin that help t drive the reactin tward the prduct Will see 1,3 Bisphsphglycerate and PEP as intermediates in glyclysis (breakdwn f sugar t make E withut xygen) Phsphcreatine is used t stre E in muscles S far have lked at phph- anhydrides...thiesters are anther set f high e cmpunds Thiesters have a higher E than plain ld esters because regular esters have sme degree f resnance stabilizatin relative t thiesters, s have a lwer starting E (see figure 13-17) Thiesters aren t used s much fr energy, but as a high energy intermediate that helps t dnate acetate grups t ther cmpunds One f the biggies is Acetyl-CA. Will see a lt f this guy in xidative phsphrylatin and in fatty acid synthesis because lves t dnate the acetate grup. (N structure at this pint) C. ATP prvides E by grup transfer, nt simple hydrlysis Figure ften yu will see ATP driving reactin written as 1 step reactins This implies that ATP is simply hydrlyzed fr the reactin t ccur This is versimplificatin. If ATP simply hydrlyzed, then E is released as heat, and nt useful

8 8 Usually is a 2 step prcess P i r PPi r AMP is cvalently attached either t substrate r t enzyme This frms a High E intermediate This grup then cmes ff in a secnd step where the prduct is frmed Thus ATP is usually part f cvalent catalysis I said usually abve because there are sme prcess where ATP (r GTP) is bund, and its hydrlysis is used t tggle prtein cnfrmatins Used in mechanical mtin Used in transprt? Phsphate cmpund usually divided arbitrarily int High E (>-25 kj/mle) Lw E (<-25 kj.mle ATP an the likes are high E Glu-6-P lw Watch ut fr tem High Energy Phsphate bnd Its nt that the bnd has lts f E, but, as seen abve, its that the prducts have a much lwer E than the cmbined cmpund. Often due t resnance frms that ccur in the prducts that weren t there in the parent. One final pint abut why ATP is a gd E strage cmpund 1. Releases large amunt f E 2. Actually is kinetically very stable Requires large activatin energy ( kJ/mle) Thus des nt spntaneusly hydrlyze D. ATP Dnate mre than just P i ATP reactin usually SN2 Nuclephillic reactins (figure 13-20) As such 3 different places t attack (á, â, ã) Actually see three in bilgical systems hydrlysis f âã linkage releases 31 kj hydrlysis f áâ linkage releases 46 kj s mre E Further push is PPi t 2Pi give additinal 19 kj use this linkage when need mre E

9 9 E. Assembly f Infrmatin mlecules requires E - nthing special use ATP r NTP r dntp F. ATP Energy fr active transprt and muscle cntractin Saw sme transprts g thugh phsphrylated intermediate Other didn t Wn t study muscle cntractin here, but think that cnfrmatinal tggling Between ATP and ADP + Pi frms s n direct phsphrylated intermediate S simple hydrlysis G. Transphsphrylatins between nucletides ccur in all cell types Fcused n ATP But GTP, UTP CTP, datp, dgtp, dttp and dctp are all energetically equivalent all cells have nucleside diphsphphate kinases ATP + NDP NTP + ADP In presence f Mg 2+ Delta G abut 0, s K abut 1 But bug excess f ATP drives frward Let s skip Adenylate kinase, creatine kinase H. Skip Inrganic Phsphate 13.3 Bilgical Redx Reactins transfer f phsphate grups is ne way t mve E in metablism, but there is a secnd way transfer f electrns in redx reactins The math t understanding this is linked t redx reactin and redx ptentials. Sme f yu had redx ptentials in Analytical sme f yu haven t s let s explre this fr a bit Nte: Nt taking bk methd A. A reminder f Oxidatin math & cncepts In any redx reactin there is always ne species underging xidatin, and ne underging reductin. That is why we call it a re-dx reactin Fr instance Fe + Cu Fe + Cu

10 10 Has the tw half reactins Fe Fe + e Electrns n right - xidatin r psitive charge increased -xidatin Cu + e Cu Electrn n left reductin, r Psitive charge reduced - reductin Yu might want t brush up n hw t balance redx reactins, I wn t g int it here If yu never saw this reactin befre. Hw wuld yu knw that the reactin ges as written, and nt in the reverse directin?? B. Reductin ptentials This is tied t a quantity called the reductin ptential Reductin ptential is a number that is used t tell the tendency f a reactin t ccur as a reductin reactin. When yu cmbine tw reactin the reactin with the large reductin ptential will ccur as a reductin, while the ½ reactin with the smaller reductin ptential will g in the ppsite directin and becme an xidatin. Fr instance n page 531 yu have a table 13-7 that says that the reactin + - ½ O + 2H +2e H O has a E f.816 V 2 2 E the ptential when everything is a t 1M cncentratin, ph 7, the usual bilgical assumptins The chemical reactin + - Acetaldehyde + 2H + 2e ethanl has an E f CH COH CH CH OH Based n these tw E yu wuld predict that the 1st reactin shuld g as written, as reductin that requires electrns, and that it can reverser reactin 2 d it will g as an xidatin t supply the electrns thus the reactin will be

11 11 CH CH OH + 1/2O + 2H +2e H O + 2H + CH COH + 2e Remving cmmn terms CH CH OH + 1/2O H O + CH COH Thus yu have predicted that ethanl can be xidized t acetaldehyde Reductin ptentials are established by measuring each ½ reactin + - against the reactin H + e ½ H as shwn in figure This reactin has been chsen as ur 0 pint and is given the ptential 0.00 V (That explains why sme ptential listed in table are + and sme are -) C. Reductin ptentials and ÄG Just like the ÄG and ÄG we ut table is established using 1M cncentratins (ÄG ), but yu can find the E f any given reactin by using an equatin that adjusts fr cncentratin terms. This equatin is: 0 E = E + RT/nF ln [prduct]/[reactants] Where prduct and reactant refer t the reductin reactin equatin If T is 25 C, RT/N is a cnstant, s yu will see the equatin 0 E = E +.026V/n ln[prduct]/[reactants] Where n is the number f electrns in the reactin There is a direct te between ÄG and E ÄG=-nfE Or, at standard state ÄG = -nfe Where F is Faraday s cnstant = 96.5 kj/v ml If yu had Analytical yu knw there is a lt mre calculatin than we can d here. But fr Bichem we will stp here. 0 Remember that yu can cnvert between E and ÄG 0 And that the reactin with the mre psitive E ges frward, while the 0 ne with the less psitive E gets reversed.

12 D. Bilgical xidatins Nte figure in text xidatin state f C cmpunds. Get much different numbers than the methds taught in General Chem may want t pint this ut When C is in the CH 4 fr it is the mst reduced, that is Assign H = +1 Then C = -4 CH3OH methanl H=+1. O= -2 C= -2 CH2O frmaldehyde H=+1, O= -2, C=0 HCOOH Frmic acid H = +1, O= -2, C = +2 When C is in CO 2 it is in its mst xidized frm Assign O =-2 Then C = +4 As C is attached t mre O it gets mre and mre xidized Since ur bichemistry is based n getting E frm xidizing things, the mre reduced and saturated a C is the mre energy it can give yu. This is why fats, -CH2- stre mre energy than sugars -CHOH- because the alchlic C are already partially xidized Thus ne way t xidized C is t simply add mre O C are als mre xidized when they have multiple bnds t ther C CH3-CH3 H=+1, C = -3 CH2-CH2 H=+1, C = -2 HCCH H=+1, C= -1 Thus a secnd way t xidize C is t remve H frm it in a dehydrgenatin reactin (dne by a dehydrgenase enzyme) 12 Nt all bilgical redx reactin invlve C, thus let s generalize just a bit mre

13 13 All redx reactins invlve the transfer f electrns. Base n hw these electrns are transferred we grup bilgical redx reactin take 4 different frms 1. Direct electrn transfers Fe + Cu Fe + Cu + 2. Transfers invlving H r H atms - + AH 2 A +2e + 2H 2 ntes here This is NOT and Acid reactin 2- - We did nt end up with A but A + 2e this can be disguised in net reactins - + AH 2 A +2e + 2H - + B +2e + 2H BH 2 Net: AH 2 + B BH 2 + A Transfers invlving the hydride in (H ) (:H) Will see mre f this in a bit 4. Direct cmbinatins f C with Oxygen R-CH + ½ O RCH OH etc All 4 happen in cells Will talk abut reducing equivalents, r the number f electrns transferred in a reactin, and may ignre the details f what ther atms were mved r transfrmed E. Oxidatin f glucse t CO 2 will invlve the release f lts f energy. Only a few f the steps will invlve direct phsphrylatin intermediates, and direct synthesis f ATP. There are many ther steps where xidatin and reductin are perfrmed and tw majr carriers f electrns in these reactin are + + NAD /NADP and FAD r FMN The bk spends sme time talking abut these, but I think I will skip until we are further alng. We will cme back t these imprtant cfactrs when we have them in actual reactins.