Bioenergetic Bioenergetics application Endergonic process Exergonic reaction governing Energy - First law G = 2) Second law + TS H total E = KloyD Hydrolysis ↳ - Rates entropies of all participating body increases . constant . of becomes - (-s) order. S Kloy'D = that mean but spontaneousity & is reaction reaction will proceed a G = -30 of reaction speed not highly 5 k5/mol . at . favorable a measurable rate The rate but high at Biological depend will not in system ? activation energy. on speed . controlled Direction Vs (Rutes) enzymes - of the sum KloyD of ATP metabolic are work. entrophy for is Centhalpy) by high degree = negative OG , S large-oG a the , disorder = and is ex) How . . energy unavailable for = : / Life ↳ No transform energy free E (energy able to do work) = K Boltzman's characterized is Does and spontaneous entrophy (5) every process D :. describe energy flow to order in conserved is Law of : in 4 Not . , iS Life system reaction/phenomenon a consuming C = biological to Energy producing Spontaneous - Energy : H S principles thermodynamics Laws of 1) force driving ↳ thermodynamic of : regulation of substrates and availability ) direction product Muss action ratio For the [A] + [B] [C] + [D] reaction Kep where when [AJIBJICJID] ↳ When ↳ · = any - RT one In of Redefine RTInkep equilibrium constant equilibrium concentrations at &G =0 [AJIBJ[C] [D] are the direction to equilibrium concentration of each leading [A] [BI [CS [D] . equilibrium J Q concentration , , not EA]' as equilibrium at are ID kep , concentration , GEO [BJ [C] ; [D]' ↳ actual =E D [AS'[BJ'ICJ'[DJ' when = + product and reactant. condition physiological Since kep 06: Kep Reaction proceeds to under [A] [B] are = reactions net no 48Go [C] [D] = OG , normally relatively maintained at the and Stable level reaction predominates reverse define and Q , the - , the direction in non-spontunesa leadforadreactionpredominatesSpontaneoa when ex) ATP hydrolysis -G kep = - 32 . 2k5/mol = S = mass action ratio as concentration 105 Q ke4] Q :. Q isa orders of magnitude of - is toward equilibrium. reaction hydrolysis strongly favours the forward ATP Q for exceryonic for ATP hydrolysis (32 2k5/mol) &G . ex) phosphorylation of can be reaction Clarge to less coupled DG) , but it exceryonic favourable reaction is the not to drive them case. forward . glucose - Positive G but with coupled reaction , able to be synthesized was Redox Reactions Reduction - Oxidation Redox potential (E) ↳ of measure Redox reaction is Electron transfer Redox potential is are involves measure of the potential require the trunster of electron reaction an . tendency relative to donor electrical spontaneous from related to * = - electron # Faraday's constant (9 65x10"JN mot = difference electron couple with acceptor more accept reaction in redox a negative at an standard electron . condition , urbitarily set to OU couple mid-point potential (Em) to a couple with a potential . mid-point positive more transferred number of rEm and or energy nFEm n= = compound to donate HeE2H ++ he a redox free a . in midpoint potential between redox couple (Em acceptor - Em donor Electron will move from lower potential to higher .. NADH/NAD + hult-cell ↳ potential Negative reading confirms potential NADH/NAD+ , to the on He voltmeter (-320) hult-cell electron donor in this is lower at setup . H2/2H Hult reaction - + candonate electrons to NADH/NAD + under appropriate condition two part of Redox reaction. involves electron transfer . Separate into two reaction ↳ other oxidation and one reduction Membrune potential underlying basis of membrane The chemical potential potential (m) of >= ↳ Uncharged molecule a equivalent to free is driving biological to processes lies energy 10 + RTIn[C] molecule uncharged hydrophilic ↳ could exist at do molecules different = mci at readily not concentration Mc = Moco Mo ci Standart T-P /20 = = /ci + Mco RT InIci] -RTIn[Co] RTIn[] when [Ci]d[Co] Om neutral molecule = W/(w +s) >0 O (water diffuses out) because Xwi(Xwo 00 (water diffuses in ( more mol truc inside in selective permeability of the lipid bilayer . ↳ Ion transport ↳ membrane . charged molecule potential lipid biluyer combination of concentration and charge . a Mc readily cannot , M = ° +RTIn[C] whereMc Y for - - diluted under 04 of ( constant RTIn[C]/2nF condition. = cFYc furnday's = (Mc MO) = . potential charge = F + 2 electrical = 2c cross Mc = ° and M C Yc = -RTIn[c]/2cF Uci-Pro - = In ([(i]/[Co]) RT 2cF "Proton Motive ↳ force both chemical - synthesis of ATP component [H+] pmf = NH 0 and electrical -n590pH + through (unit both photophosporylation and oxidative phosphorylation. component = mr) Three classes of ↳ channels pumps , transport Coupled between Typical plant chloroplast Chloroplast structure by ↳ Thylukoid ↳ enclosed active and passive transporters . (TEM) double membrane Conter membrane contains "The Stromn lumellue and integral contains PSI envelope inner membrane proteins essential while grunn lumillue (stacked TEM imaging of chloroplast. ↳ ↳ stacked grana and lumen of ↳ thylakoid interconnected is essential for proton positively thylakoid charged , gradient formation . membrane. compared to stroma . for photosynthesis. thylukoid) contains PSI , membrane curriers transport proteins I of Arrangement photosystem in membrane. thylakoid PSI PSI in , stacked region (grann ATP synthase unstacked Cytochrombot complexes lamellae region the stroma into protruding facilitating evenly distributed . electron transport between PSI and PSI Electron carriers Plastocyanin Plustoquinone (PC) (PQHa) Chlorophyll-protein Photosynthetic Linear electron Water Transport(PET) transport absorbs red PSI ↳ Electron splitting : Linear the in thylakoid the lumen. membrane complexes optimize energy transfer and minimize pathway cyclic and in (2-scheme) light (P680) PSI in ↳ Electron transferred ↳ PSI absorbs for ↳ Proton gradient formed : - excited electron Produce O2 light (PDOO) drives : more protons and cytochrom b6f through red > - the electron through transport chain . thylukoid lumen in . complex plastocyanin - . + Reduces NADP PSI > - NADPH > - by ATP Synthuse ATP Synthesis . > - · Cyclic ↳ electron Electron transport cycle between PSI and cytochrome b6t ↳ No NADPH formed ↳ Prevents only ATP synthesis NADP + reducing reduction of NADP+ and provides additional ATP for the Calvin Cycle. over The Qcycle of instead enhunces CH + Reduced PQHa transports Q cycle to pump proton electron from PSI into lumen in four protons pumped Two electrons O ③ Then to ① & b6f the lumen per two PQHa molecules oxidized . transferred to PSI 1) binds to cytochrom bot ② One electron to D are into to cytochromb6 + then to 2) to PQ FeSp 3) & Cytf plustocyanin ③ .. two protons ↳ one are released electron advance to into PSI the lumenvia Plastocyanin transfers : other recycled back > PQH2 reenters the plustoquinone pool electron again . -> ready for shuttle fully electron to Cytb (formed earlier reduced in the cycle) plustoquinol waste. So how movement ↳ high e-shuttle do of electron energy Photosystem electrons and not are from PQHa spontaneous - and back driven by transformed to PQ photon reducing Doesn't this violate ? again accepted in PSI to PQH light hurresting LHC-maximize trunster - mmm 2 Chla ma a chib ↳ * Resonance the law of thermodynamics ? energy trunster - energy can Excited of absorption energy efficiently to absorbes : : : reaction blue-violet absorbes Carotenoids light by increasing the blue and light and orange light. broudens absorption Chlorophyll molecule pass center energy and via antenna size photosystem wound . . red against photooxidative damage. protects transfer resonance be transferred between closely associated molecules . , down un gradient. energy · Light excites curotenoid and molecule to higher energy chlorophyll state. > - energy ensuring All absorbed energy is tunneled to the reaction center P680 for photochemical reaction. is lost as efficient heut during excitation transfer to reaction center . transfer excited energy , charge initiating used to separation electron transfer . Balancing lightabsorption with use energy number of component that PSI Overload , Repair than it through heat balance restored are can reactive generates excess number of PSI reaction energy pigment area of PSI process oxygen excitation excess , ? species (ROS) Xanthophyll cycle - energy damaging prevent PSI and nearby structure . photodumage. Producin ATP but not as in heat vin pigment light herresting like curetenoids complex (Regulating in the untenna center Redirects electron from PSI ↳ How .% photons dissipated by dissipation of decrease · sectional cross NADPH , back relieves to cytochrome b 6f complex pressure . on the linear electron transport chain . light size harvesting complex as sink life time of sink Y through Fixed · < n center reaction Excess energy NPQ more : when consequences absorbes E Incident photonHuy functional OpIX] nx[/ = - ↓ ↓ are electron ↑ OPSIX] what consumes acting : turnover rate. Fate for excited Chl four + chlorophyll photon to get back to ways photon 1) Re-emit loss of Complete 3) Energy transfer 4) Photochemistry (charge of charge energy 2) trunster Photochemical state . toanother separated heat as pigment separation from e- Chl + photon - Chl 1) Electron ground fluoresence. as 2) fate * ChI - + chlorophyll + e (PET) recombination quencing (charge constitutive , quenching) . energy · Light ↳ dependent decreases in Light photosynthetic rate ↳ Photodamage PSII more prohibition than PSI Photosynthesis High light ↳ · Light Excess ↳ ↳ ↳ light region - ROS beyond the saturation point lead to photo inhibition plants Fate of dissipates excess or excess energy in use of efficiency , excess damage light energy photons as effectively are used reaches a photosynthesis pluten is , all reaction center saturated . limited by enzymatic processes capacity of the photosynthetic in Calvin cycle the not light. system . Photo-Inhibited Region not contribute to due to the overexcitation light to PSI light intensity . generated , with saturated region Indicates the ↳ linearly availability Rate of ↳ (Low Irradiance) increases Photosynthesis ↳ · region blimited by to sensitive Limited does through photosynthesis. ↳ of reaction center . heat (non-photochemical Photosynthesis Reactive rate Oxygen declines as light excessive Species (ROS) may form , causes photodumage harming chloroplast. quenching ( photosynthesis Excess energy generates ROS dumnying photosynthetic machinery in PSI Plants rely Suppression Mechanism Cheat dissipation) and scuvenying system · , on prevent Repair ↳ and Persistent Cantioxidants) to photodamage. replacement imbulance of the leads to D2 protein are crucial for photoinhibition (impars plant growth muntaining photosynthetic and survival. efficiency. to PSI Fate of charge-separated from e- chlorophyll Light absorption · LMCb1 + 2+ 3 · 4+5 + 6 antenna absorbs photons reaction excitation and Lh(b harvesting light ↳ and and complexes transfers center. energy to PST P680 ↳ chlorophyll that becomes photon absorption . Reaction center upon excited photochemistry for of photon energy ATP/NADPH use Electron transport water split ↳ ) · ↳ · Constitutive Role under Quenching &PH : proton gradient Lea : water - dissipates at + OEC through across excess , Produce 9680 producing 4H +, 02 and e- - energy quenching pool condition of condition as - deals sensor photostasis. the , PQ pool excitation energy thylakoid the Xanthophyll pigment aiding of PQ under stress and b6t complex mechanism Non-Photochemical ↳ transport PSI Pheo-QA- QB- PQ Reduced PQ(PQH2) transfers electrons to the cytochrome ↳ electron oxidation ↳ Electron flow Quenching in driving heat in with heat to prevent as photodumage. membrane. dissipation residual . excess energy that cannot be used for photochemistry or dissipated by NPQ for imbulance PQ becomes pool partially reduced over-reduced - , and e-flow linear election flow is disrupted manages and more the balance between photosystem energy is and energy dissipated through charge consumption . recombination and NPQ cyclic electron flow is induced . The PSI D1 protein Photo inhibition and · DI protein ↳ PSI in from D1 and D2 proteins ↳ DI ↳ Vulnerable to directly is involved dumage in under the reaction center electron trunster core during high light intensity of PSI photosynthetic light reaction due to ROS . Reaction Center ↳ includes ↳ facilitates ↳ ↳ · OEC asplits photo inhibition of DI protein Excess · ROS · · photon include source ROS generate will energy ↳ Singlet oxygen leading , (02) to oxidative damage , , primary Electron Damaged DI De novo synthesis D2 central location ↳ protein degraded is replaced within the PSI occurs PSI in is and repair - water molecule to D1 protein susceptible for damage Photo inhibition decreases Light dependent PSE more sensitive to Photoinhibition : main State Trunsition : site Excess light energy Redistribution . to photodumage. lend photo inhibition than PSI (watersplitting generation , of migration of Photostasis distribution photosynthetic rates in damage is LHCI between of LHC over of LHCI and PSs DI : reactive System PSI in of ROS direct , exposure to center protein and PSI balance. reduced PQ pool ; induced phosphorylation of LHCI subunits induced cycle e-flow ; re-oxidation of PQ pool light. and associated co-factor . reaction . under stress. PQ 23kDa into Electron donation to PSI cycle highly to comprised of synthesized DI for electron flow but also critical - by newly molecule) photochemical transfer Superoxide (02) and (chlorophyll Photon absorption Repur mechanism ↳ · DI D2 4680 , 02 , Proton and 4H * 33kDa proteins (contribute to photon gradient) e-Cused for gradient formation , PSI Electron transport). The Xunthophyll Cycle This is not an e-shunt The photoreactive does not and result of seaxanthin role removal of in from arises excess its e of from PQ pool the lower energy state relative to violuxanthin . Zeaxanthin represents a trunster between pigment reaction ATP synthesis channel ↳ · CF , ↳ membrane through Photon channel · side of CF2 dissipating absorbed contributes to centers. synthesis rotates the rotate and converts riny a of subunits and a the riny c subunit of subunits. to ATP ADD and Pi Photosynthesis balance sheet Synthesis requires 3H Synthesis of NADPH How There many -OEC - two are It requires are : It (and 2H + ) + linear PET ? 2e-through translocation/ generation : 2H + PQtzetIHt > Ze pumped for every H+ sites of PQH2 6 He 420-cOc : PQpool .. + , + < 2e PQHa- + Qcycle = 4H /ze- + PQtZetIHt translocated/generated for each pair of else What e- · Proton Proton release Pumping Proton uptake Proton transport from water by the in NADPH Cytochrome b6t complex formation (PSI) associated with plustoquino (PQHz) energy energy CFo the interface between lies at Proton translocation ↳ LHCI the resonant thylakoid membrane for ATP site , in protein attutched to the stromal active CHC1 acceptor ATP Synthuse via CFo-integral · terminal pH as heat rather than transferring it to force Proton motive · Recall : Since opH pmf My It of ATP Lineur PET of e What · force behind interconnected integrated by , net contribution of He to the OU overall small is photophorylation requires to 2e for GH + yeilds and - each Ht Sufficient 2H + pair for of e- ATP and electron for INADPH. 2 of serve common redox carriers : reaction chemical catalyzed enzme ATP/ADP , NAD(PH/NADCP) ↳ Protein # N amino acd is the involument of Catalysis Comprised of function ↳ brings reactive ↳ Can ter . · amino and enzymes acids to chain that participate & 0- # A amino acid at Physiological pH R groups Amino acting acid as can interact side acid chain or with can proximity energy , with base. reaction primary orientation. correct through transition state substrates. function in immobilize their substrates. groups into reaction the side , acid amino · OH feature of metabolism Lange " of + key ↳ Antony . A · An PET metabolism . is & during 3Ht requires PET the opposite direction to H + in driving translocation of ↳ Each pair · translocated Synthesis of NADPH · · is that provides Synthesize · OYH -4540PH = and facilitate reaction by stubilization. General Acd-Base catalysis Proton ubstruction leads to · - Enzymes Enzyme Basic · facilitate can can Comprised of with Enzymes are substrates. cleavage by acting place a as holder for protons . large Coupled one substrates and transfer it to unother . enzymes acids amino reactive lower Can of retain part properties Brings bond reactive Cutulysis Covulent · more the side chains of which function and groups , to reaction participate in reaction. immobilize their substrates. to proximity activation can , with energy the through correct orientation transition state stabilization. reaction The Q The lurge for ATP hydrolysis strongly favours the forward exeryonic OG for this reaction reaction (-322k5/mol) can be coupled with less favorable reaction to drive them forward . The effect Proximity can be substantial · Larger cyalic unhydride thermodynamically and · Ep in ex) Immobilization of substrates proximity , * Transition state stabilization helps of reacting reduce activation groups and interaction of chemical energy with amino and side chain facilitate reaction . Enzyme Classification EC number classification scheme for is broad level classification Six 1) , based on enzyme overall , based type of on chemical reaction reaction. Oxidoreductase Catalyzes Includes redox reaction dehydrogenase , Requires cofactors and/or · · Often involves metul Oxidases. , peroxidases co-substrate ions. , Oxygenases, reductase they catalyze . the reaction. are more favorable due to reduced riny strain higher stability constant (kep) shows favorability decreasing a strain . drumatic increase 2 . Transferase Group transfer reaction Many Transferred 3 . cofactors require . may group . , , Biotin covalently be , or rely on bound to the acid base , enzyme or catalysis. cofactor during the reaction. Reductase Group transfer reaction 4 PLP TPP in which water the is acceptor of the group being transferred . Lynse Non-hydrolytic Reverse and non-oxidative elimination has addition of a reaction reactions substrate to a or substrate lysis double bond on 5. Isomerase catalyze structural changes within a molecule - isomerization 6. Liguses Catalyze ligation Requires · Reffered input energy to or as joining reactions typically synthefuse vin ATP between two substrates reaction generating double bond another substrate. Enzyme regulation 1) 2) Course scale regulation regulation Fine scale one · all energetically · · · scale manipulation of changes existing . protein. once . can scale of take fluctuation many ↳ Allosteric effectors ↳ Covalent modification - in seconds or minutes. key regulatory forms or enzymes brunch-point enzyme. concentration substrate in Change Protein of the level acts at pH Protein interaction Alteration generally small affect with or co-substrate concentration usually sub-saturation is does [substrate] changes [S] Enzyme . of substrate [substrate] · large enzymes affected at ↳ 4 . Involves minutes. on Involves . the time on Regulation ↳ . Regulation Fine Scale typically days or expensive protein turnover Operates of pathway enzymes Compartmentation · hours on Regulation regulation or timescale timescale - Course Scale down/up - vary some enzyme typical change not in in more more vivo than . typically told during and 2-S < km normal metabolic condition. than other Michaelis-Menten Enzyme Kinetics. substrate concentration has little effect on reaction rate . Enzyme with Cooperative Enzyme Kinetics. same small change insubstrate concentration has larger effect typical M-m enzyme reaction rate than Mass action New ratio Equilibrium Near equilibrium ↳ freely ↳ direction Physiologically unidirectional can affect the regulation of physiologically Irreversible and reaction occurs when substrate enzyme on . activity Reaction and product concentration are near their reaction equilibria reversible reaction depends on small Irreversible reaction reaction. changes occurs in in [substrates] and [Product] vivo when [substrate] and [product] are held far from their reaction equilibria ; these are to control substrate concentration Strategies that rupidly diffuse yuseous products degeneration/utilization Rupid Coupled · (co-substrate reaction Rapid modification of product (phosphorylation ( of macromolecules (sturch oil droplets) Storage · of co-substrate , ATP balance Cenergy charge Tight coupling between reaction successive in pathway a Compartmentation · ↳ active transport of stored Controlled release ↳ metabolites. Result of stress Up-regulation · stored metabolites Controlled release · of of specific enzyme) up-regulation require pathway unused an (may ↳ increased production of substrates ↳ increased for specific reaction. of products "demand for upstream substrates utilization " , Enzyme regulation 1) 2) Course scale Fine scale Change · · · · in regulation regulation - - timescale timescale Photosynthesis and It transporters Cell wall efflux cycle manipulation of changes existing . protein. - molecule non-covulent (reversible) Often and inner vacuoles. substrate not in enzyme in photosynthesis of light energy into chemical energy . access that binds to the cutulytic an enzyme at efficiency of the site other . than active site , and the enzyme binding conformation feed back with pH gradient induced by high light. of the lumen activates violuxanthin de-epoxidase affects change acidity thylakoid : are triggered by allosteric effectors typically can accross in acidification ↳ increased · scale during cell growth and expansion cell wall change local pl cycle pH sensitive carbon assimilation synchronized · Involves large acidification Xanthophyl · . pH gradient in tonoplast membrane Enzyme of Calvin · minutes. on Involves days or function respiration result in active H + " hours pH Affects protein structure and ↳ on - either increase/decrease inhibition and/or cutulytic feed-forward efficiency activation. (activation or inhibition Covulent modification · Reversible Result in two , covulent modification change major of an enzyme enzyme conformation that in types lead to activation can inhibition. or plants in dephosphorylation ↳ phosphorylation ↳ dithiol -disulfide interconversions - . Phosphorylation/Dephosphorylation Serine theonine · , , · Protein phosphatuses tyrosine residue can be cleave the phospho-serine can by phosphorylated linkage to (deactivate Phosphorylation/dephosphorylation changes protein "backbone" ↳ changes lowest energy conformation lowest energy conformation ↳ · Conformational changes Typically · can re-aligh activity involves in conformational change. Change activate amino acids active in sites to enhance or enzyme their function reduce . in enzyme or to typically the redox state within of a a protein. cell . thioredoxins Induced conformational · phosphorylated formation/clearage Reversible formation of disulfide bonds Links enzyme · results the shift towards Disulfide bond · kineuse protein changes have backbone deactivate enzyme the same effects as for protein phosphorylation/dephosphorylation . Protein-Protein interaction Protein-Protein interaction ↳ · release of an can lead to inhibitor (Cu-Calmodulin ↳ association of subunits ↳ Some Can lend ↳ ex) enzyme to fatty change active sites Synthuse 3-D structure which regulated require enzymes . amino alter can and complex (pyruvate dehydrogenase . residues from more into multi-enzyme complexes All Synthuse , activity kinase. into active enzyme association of acid in than or mitochondrial electron transport complex one protein molecule to be active. channels chain complexes (1 11I2 [Val . ,