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Chapter 13

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Department
Chemistry
Course
CHY 205
Professor
Mario Estable
Semester
Winter

Description
Chapter 13: Bioenergetics & Biochemical Reaction Types -Metabolism means obtaining chemical energy, converting nutrients into cells’ own molecules, polymerizing precursors into macromolecules, synthesizing & degrading specialized biomolecules, involves hundreds of enzyme-catalyzed rxns, conserves central metabolic pathways and is highly coordinated. -Anabolism & catabolism are not catalyzed by the same enzymes in reversed b/c of regulation, ie. Turning on one pathway while turning off the other, thus if there’s an excess, one pathway can be turned off w/o affecting subsequent steps. -Cycle between autotrophs and heterotrophs is the Biosphere C & O cycle: Autotrophs get C from a sole source (atmospheric CO2), some get N from sole source (atm N2), many obtain E from sunlight, photosynthesis and all of them can generate O2. Heterotrophs get C from complex organic molecules, obtain E from degradation of organic nutrients, they can consume & generate O2. 4x10^11 metric tons of C are turned over annually. In the Biosphere C & O cycle, there is a unidirectional flow of energy starting from the sun to autotrophs to heterotrophs, etc. -Sources of N (N2(g) is 80% of our atm): The Biosphere N cycle=N and its sources are req for synthesis of aa, nucleotides & other compounds. Plants & bacteria use NH4+ or nitrate; animals req aa; cyano bacteria & soil bacteria can fix N2; nitrifying bacteria oxidize NH4+ to nitrites and nitrates; denitrifying bacteria & fungi convert NO3- back to N2; anammox bacteria convert NH4+ and NO2- to N2. -Metabolism: is the sum of chemical rxns in the cell. A series of interrelated rxns form metabolic pathways which can be linear, branched or cyclic, convergent/divergent and regulated or comparmentalized. Catabolism involve pathways that are energy-producing, ie. when organic nutrients are converted into smaller products (degradation); energy is transduced into ATP and reduced electron carriers; convergent process. Anabolism involve pathways that are primarily using energy to build complex structures, ie. the biosynthesis of macromolecules from precursors; energy input comes from ATP and reduced electron carriers; divergent process. Introduction -Modern organisms carry out various energy transductions, conversions of one energy form to another, they use chemical energy in fuels to bring about the synthesis of complex, highly ordered macromolecules from simple precursors. -Antoine Lavoisier recognized that animals somehow transform chemical fuels (foods) into heat & this respiration process is essential to life, ie. Animals that respire are true combustible bodies that burn and consume themselves. -Life needs energy: living organisms are built of complex structures. Building ordered complex structures are only possible when energy is spent in the process. The ultimate source of energy on Earth is the sun & life uses energy by transducing it, ie. Converting one form of energy to another. -Laws of thermodynamics apply to living organism: 1) Living organism can’t create energy from nothing, 2) Living organisms can’t destroy energy into nothing, 3) Living organisms may transform energy from one form to another. In the process of transforming energy, living organisms must inc the entropy of the universe which means disorder/randomness in the system. In order to maintain organization w/in themselves, living systems must be able to extract useable energy from the surrounding & release useless energy, eg. heat back to the surroundings. Living organisms are open systems, exchanging energy & matter w/ the environment. They are never at equilibrium w/ their surroundings. -Complete oxidation of reduced compounds is strongly favourable in catabolism which is how chemotrophs obtain most of their energy. In biochem, the oxidation of reduced fuels w/ O2 is stepwise & controlled. Note: being thermodynamically favourable is not the same as being kinetically rapid. 13.1 Bioenergetics & thermodynamics -Bioenergetics is the quantitative study of energy transductions. -Biochemical energy transformations obey the laws of thermodynamics: 1 law is the principle of the conservation of energy (for any physical/chemical change, the total amt of energy in the universe remains constant, ie. Energy can’t be created or destroyed but can be transduced), the 2 law says that the universe always tends toward inc disorder (in all natural processes, the entropy of the universe inc). The reacting system is the collection of matter that is undergoing a particular chemical/physical process. The reacting system+surroundings constitute the universe. ∆G = ∆H - T∆S ∆G & ∆H are expressed in J/mole or cal/mole *(1 cal=4.184 J), ∆S as J/molxK. At absolute temp: *25°C=298K, at 25°, RT=2.478 kJ/mol (0.592 kcal/mol) -Gibbs free energy (G) expresses the amt capable of doing work during a rxn at constant temp & pressure; when ∆G is -, system releases free energy, ie. System contains less free energy, ie. Rxn is exergonic vs. when ∆G is +, system gains free energy, ie. Rxn is endergonic. -Enthalpy (H) is the heat content of the reacting system reflecting the # of chemical bonds in reactants & products; rxn can be exothermic (heat content of products is less than reactants; neg) or endothermic (reacting systems take up heat from surroundings; pos). -Entropy (S) is the quantitative expression for the randomness/disorder in a system; if products of rxn are less complex & more disordered than reactants, rxn proceeds w/ gain of entropy. *if ∆S is + & ∆H is -, typical of energetically favourable processes tend to make ∆G -, ie. Spontaneous rxn. Living organisms preserve their internal order by taking from surroundings free energy in the form of nutrients/sunlight & returning to their surroundings an equal amt of energy as heat or entropy. -Cells req sources of free energy: cells are isothermal systems, ie. They function essentially at constant temp & pressure. Cells do use heat as source of energy b/c it can only do work as it passes to a zone/object at a low temp, instead they use G which predicts direction of chemical rxn, their exact equilibrium posn & amt of work they can perform at constant temp & pressure. -Std free energy change is directly related to the Keq: aA+bB  cC+dD Keq= [C]^c[D]^d / [A]^a[B]^b -The [ ] of reactants & products at equilibrium define the equilibrium constant, Keq. When a reacting system is not at equilibrium, the tendency to move toward equilibrium represents a driving force represented by ∆G. ∆G°, the std free energy change is defined at conditions of 298K (25°C), 1 M initial [ ] or 101.3 kpa or 1 atm for gases, ie. [H+] would be 1 M or pH=0. This is not appropriate for biochemistry b/c most biochemical rxns occur in well- buffered aq sol near pH 7. Thus, ∆G’°, the biochemical std free energy change is defined at conditions 298 K (25°C) but at pH 7.0 and [H2O] of 55.5M; for rxns that involve Mg2+ which include those w/ ATP as a reactant, [Mg2+] in soln is commonly constant at 1 mM. (Note: K’eq incorporate [ ] of H2O, H+ & Mg2+ but not incl in equations, eg. Keq) ∆G’° = --RT lnK’eq (*R=8.315 l/molK) *-When K’eq for a rxn is 1.0, ∆G’° is 0, ie rxn is at equilibrium vs. when K’eq>1.0, ∆G’° is neg, ie. Rxn proceeds forward vs. when K’eq<1.0, ∆G’° is pos, ie. Rxn proceeds in reverse. Note that this only applies for 1 M initial [ ] for all components. B/c the relationship b/w K’eq & ∆G’° is exponential, relatively small changes in ∆G’° correspond to large changes in K’eq. All chemical rxns tend to go in the direction that results in a dec in free energy change of the system. -(Table 13-4): Hydrolysis for simple esters, amides, peptides & glycosides as well as rearrangements & eliminations proceed w/ relatively small std free energy changes vs. hydrolysis of acid anhydrides (eg. ATP + H2OADP + Pi, ∆G’°= -30.5kJ/mol) is assoc’d w/ large dec in std free energy change. The complete oxi of organic compounds, (eg. Glucose + 6O2  6CO2 + 6 H2O, ∆G’°= -2840 kJ/mol) results in very large dec in std free energy b/c they req many steps; they are highly favourable & exergonic. -Actual free-energy changes depend on reactant & product [ ]: Std ∆G’° vs. Actual ∆G are not the same. ∆G’° tells us the direction & how far a given rxn must go to reach equilibrium when the initial [ ] of each compound is 1 M, pH 7, temp of 25°C and pressure of 101.3kpa/1 atm, ie. ∆G’° is a constant. Actual ∆G is a function of the reactant & product [ ] & of the temp prevailing during the rxn, not necessarily matching std conditions, ie. ∆G determines the spontaneity of a rxn. ∆G = ∆G’° + RT ln ([C][D] / [A][B]) or simply ∆G = ∆G’° + RT ln ([products]/[reactants]) -The criterion for the spontaneity of a rxn is the value of ∆G, not ∆G’°; a rxn with a +∆G’° can go in the forward direction if ∆G is neg. The amt of work done by the rxn at constant temp & pressure is always less than the theoretical amt b/c some energy is always loss to entropy during the process. Some thermodynamically favourable rxns (rxns which have a large ∆G’° & negative) do not occur at measurable rates. In living cells, rxns that would be extremely slow if uncatalyzed are caused to proceed not by supplying additional heat but by lowering a.e. via enzymes. The ∆G for a rxn is independent of the pathway at which the rxn occurs, it depends only on the nature & [ ] of the initial reactants & products. Enzymes can’t change equilibrium constants but they can & do inc the rate at which the rxn proceeds in the direction dictated by thermodynamics. -Std free energy changes are additive sequentially: (1) AB ∆G’°1 (2) BC ∆G’°2 (Sum) AC ∆G’°1+∆G’°2 (∆G’°total) -This is significant b/c it explains how a thermodynamically unfavourable (endergonic) rxn can be driven in the forward direction by coupling it to a highly exergonic rxn via common intermediates. Eg. (1) Glucose + Pi  Glc-6-P + H2O ∆G’°= 13.8kJ/mol (2) ATP + H2O  ADP + Pi ∆G’°= -30.5kJ/mol Glucose + ATP  ADP + Glc-6-P ∆G’°total = -16.7kJ/mol (1) K’eq = [glc-6-P] / [glc][Pi] = 3.9 x 10^-3M^-1 *H2O is not incl in the expression, as its [ ] of 55.5mM is assumed to remain unchanged (2) K’eq = [ADP][Pi] / [ATP] = 2.0 x 10^5 M K’eqtotal= [glc-6-P][ADP] / [glc][ATP] = 7.8x10^2 *In thermodynamic calc, all that matters is the state of the system at the beginning of the process & at the end, the route b/w is immaterial. The K’eq calc is important b/c it shows that for sequential rxns w/ a common intermediate, K’eq are multiplicative & ∆G’° are additive. This common-intermediate strategy is employed by all living cells in the synthesis of metabolic intermediates & cellular components. Summary: -Cells require energy to do work. Bioenergetics is the quantitative study of energy relationships & energy conversions in biological systems. All chemical rxns are influenced by 2 forces, tendency to achieve the most stable bonding state & to achieve the highest degree of entropy; the net driving force in a rxn is ∆G. ∆G’° is the std transformed free energy change, a physical constant that is characteristic for any rxn (∆G’° = --RT lnK’eq). ∆G is the actual free energy change, a variable that depends on ∆G’° & on [ ] of reactants & products (∆G = ∆G’° + RT ln ([products]/[reactants]). When ∆G is large & neg, rxn tends to move forward; when ∆G is large & pos, rxn tends to go in reverse; when ∆G=0, system is at equilibrium. 13.2 Chemical logic & common biochemical rxns -Which rxns take place in biological systems & which don’t are determined by their relevance to that particular metabolic system & their rates. A relevant rxn is one that makes use of an available susbtrate & converts it into a useful product but even pot relevant rxns don’t occur b/c of their high a.e. even w/ the aid of powerful enzyme catalysts. Most cells have the capacity to carry out thousands of specific, enzyme-catalyzed rxns, eg. transformation of glc to aa, nucleotides/lipids, extraction of energy from fuels via oxidation & polymerization of monomeric subunits into macromolecules. -5 major categories of biochemical reactions: 1. Cleavage or formation of C-C bonds: Heterolytic cleavage of a C—C bond yields a carbanion & carbocation; they are generally so unstable that their formation of rxn intermediates can be energetically inaccessible even w/ enzyme catalysts, ie. Impossible rxns unless chemical assistance is provided via func groups containing O & N which can alter the electronic structure of adj C atoms to stabilize & help formation of carbanion & carbocation intermediates. Carbonyl groups are particularly important in the chemical transformations of metabolic pathways; the C of a carbonyl group has a S+ charge due to the e- withdrawing property of the carbonyl O & thus is an electrophilic C, ie. Carbonyl group can help form a carbanion on adj C by delocalizing the carbanion’s neg charge. Imines have a similar function & both can be enhanced by a general acid catalyst/ metal ion, eg. Mg2+. -3 major classes of rxns are aldol condensations (the aldolase rxn which converts 6C compound to 2 3C compounds in glycolysis, is an aldol condensation in reverse; carbanion Nu reacts w/ carbonyl C electrophuile), Claisen ester condensations (carbanion is stabilized by adj carbonyl thioester, eg. synthesis of citrate in CAC; carbanion Nu reacts w/ carbonyl C electrophile) & decarboxylations (carbanion Nu formed, stabilized by adj carbonyl & reacts w/ H+ electrophile as CO2 leaves; eg. formation of ketone bodies during FA catabolism). Elimination of a very good LG (eg. PPi) helps form intermediate carbocation that is stabilized by resonance w/ adj C=C before condensation. 2. Internal rearrangements, isomerizations & eliminations: intramolecular rearrangement is the redistribution of e-s resulting in alterations of many diff types w/o a change in the overall oxidation state of the molec, eg. cis-trans rearrangement, oxi-red rxns, transposition of a C=C. An ex of an isomeration involving oxi-red is the formation of frc-6-P from glc-6-P in glycolysis, C1 is reduced from an aldehyde to alcohol & C2 is oxidized from alcohol to ketone. An ex of elimination is loss of H2O from an alcohol to form C=C. 3. Free-radical reactions: once thought to be rare, the homolytic cleavage of covalent bonds to generate free radicals has been found in various biochemical processes, eg. isomerizations that use vitB12, biosynthesis of heme in E.coli 4. Group transfers (H+. CH3+, PO32-): the transfer of acyl, glycosyl & phsphoryl groups from a Nu to another. Acyl group transfer generally involves the add of a Nu to the carbonyl C of the group to form a tetrahedral intermediate and eliminating the LG steps (Y: attached, X removed). Phosphoryl group transfer play a special role in metabolic pathways. A general theme in metabolism is the attachement of a good LG to a metabolic intermediate to activate the intermediate for subsequent steps, eg. inorganic orthophosphate (Pi, the ionized form of H3PO4 at neutral pH, a mix of H2PO4- & HPO42-) & inorganic pyrophosphate (PPi, P2O74-). Because O is more EN than P, the sharing of e-s is unequal, ie. The central P bears a S+ charge & thus can act as an electrophile which is why PO32- is frequently transferred via kinases, eg. from ATP to alcohol. When a Nu attacks the electrophilic P atom in ATP, a relatively stable pentacovalent intermediate forms; w/ the departure of LG, ADP, the transfer of the phosphoryl group is complete. Kinases are a large family of enzymes that catalyzed phosphoryl group transfers w/ ATP as a donor 5. Oxidation-reduction (e- transfers): C atoms can exist in 5 oxidation states depending on the elements w/ which they share e-s. In many biological oxidations, a compound loses 2e- or 2 H+, ie. 2 H which are commonly called dehydrogenations & enzymes that catalyze them are called dehydrogenases. On some, a C atom becomes covalently bonded to an O & the enzymes that catalyze these oxidations are oxidases or oxygenases if the O is derived from O2. Oxidation rxns (loss of e-s) usually release energy; most cells obtain energy by oxidizing metabolic fuels, eg. CHO or fat. Reduction rxns involve the gain of e-s. The high affinity of O2 for e-s makes the overall e- transfer process highly exergonic which provides the energy that drives ATP synthesis—the central goal of catabolism. -Many of the rxns w/in these 5 classes are facilitated by cofactors in the form of coenzymes & metals; cofactors bind to enzymes sometimes reversibly/irreversibly & changes their chemistry. -Some chemical principles: More E.N. atons “own e-s in a covalent bond. A covalent bond consists of a shared pair of e-s & the bond can be broken in 2 general ways: homolytic cleavage (each atom leaves the bond as a radical, carrying 1 unpaired e-; generates carbon radicals which are not very stable) or heterolytic cleavage (one atom retains both bonding e- s; generates carbanions, carbocations & hydride ions which are highly unstable & it is that instability that shapes their chemistry). Many biochemical rxns involve interactions b/w nucleophiles (func groups rich in & capable of donating e-s, eg. neg charged ions or ions w/ lone pairs) and electrophiles (e- deficient func groups that seek e-s). Nucleophiles combine w/ & give up e-s to electrophiles. Bonds & functional groups surrounding a C atom, allow it to function as an electrophile or nucleophile, eg. a carbonyl group C can act as an electrophile vs. a C bonded to adj carbonyl group C can act as a nucleophile. -Nonpoplar covalent bonds have ∆EN<0.5, polar covalent bonds have 0.52.0 -Biochemical & chemical equans are not identical: Biochemical equans are simplified. The K’eq of the ATP rxn depends on the pH & [free Mg2+] thus a biochemical equan doesn’t necessarily balance H,Mg or charge but does so for other elements involved in the rxn. Biochemical equans are used to determine in which direction a rxn will proceed spontaneously, given a specified pH & [Mg2+] or to calculate K’eq of such rxn. Summary -There are thousands of cellular enzyme-catalyzed rxns which are aided by cofactors, eg. coenzymes & metals. There are 5 major categories of biochemical rxns. Carbonyl groups play a special role in cleavage/formation of C—C bonds; carbanions are common & stabilized by adj carbonyl groups or less often by imines & certain cofactors. A redistribution of e-s can produce internal rearrangements, isomerizations & eliminations incl. intramolecular oxi-red, change in cis-trans arrangement at a = and transposition of =. Homolytic cleavage of covalent bonds to generate free radicals occur in some pathways, eg. isomerizations, decarboxylations, reductase & rearrangement rxns. Phophoryl group transfers are an especially important type of group transfer in cells req for the activation of molec for rxns that would otherwise be highly unfavourable. Oxi-red rxns involve the loss/gain of e-s: one reactant gains e-s & is reduced while the other loses e-s & is oxidized; oxi rxns generally release energy & important in catabolism. 13.3 Phosphoryl group transfers & ATP -ATP is the energy currency that links catabolism & anabolism. Heterotrophic cells obtain free energy in a chemical form by the catabolism of nutrient molec & they use that energy to make ATP from ADP & Pi; ATP then donates some of its chemical energy to endergonic processes via covalent participation of ATP, eg. synthesis of metabolic intermediates, macromolecules from smaller precursors, transport of substances across membranes against [ ] gradients & mechanical motion. Energy donation by ATP mostly involves group transfers, not the simple hydrolysis of ATP. -The Free energy change for ATP hydrolysis is large & neg: The chemical basis for this is 1) charge separation of the 3 neg charged phosphates that results from hydrolysis relieves some of the electrostatic repulsion, 2) Pi released is stabilized by the formation of resonance forms not possible in ATP, 3) ADP2- immediately ionizes releasing H+ into a medium w/ low [H+] (~10^-7M) & 4) the greater salvation/hydration of the products Pi & ADP relative to ATP further stabilizes products relative to the reactants. B/c [ ] of the direct products of ATP hydrolysis are, in the cell, far below the [ ] at equilibrium, mass action favours the hydrolysis rxn in the cell. ∆G’°= -30.5kJ/mol for ATP hydrolysis under std conditions but ∆G in living cells are very diff b/c the cellular [ ] of ATP, ADP & Pi are not identical & much lower than 1 M of std conditions (ie. ∆Gp differs among cells). Also, Mg2+ in the cytosol binds ATP & ADP & for most enzymatic rxns that involve ATP as the donor, MgATP2- is the true substrate. The ∆G of ATP hydrolysis under intracellular conditions is often called its phosphorylation pot, ∆Gp. ∆Gp = ∆G’° + RT ln ([ADP][Pi] / [ATP]) : ∆Gp can vary depending on metabolic conditions & how they affect [ ] of ATP, ADP, Pi & H+ (pH). The total [ ] of ATP, ADP, Pi & H+ in a cell may be substantially higher than free [ ] which are thermodynamically relevant values; the diff is b/c of tight binding of ATP, ADP & Pi to cellular pro. In vivo, the energy released by ATP hydrolysis is greater than the ∆G’°. What makes ATP such a suitable energy currency is also b/c in the course of evolution, there has been very strong selective pressure for regulatory mechanisms that hold cellular [ATP] far above equilibrium [ ] for the hydrolysis rxn. When ATP level drops, the amt of fuel dec but the fuel itself also loses potency, ∆Gp for its hydrolysis is diminished. -Other phosphorylated compounds & thioesters also have large ∆G’° of hydrolysis: PEP (- 61.9kJ/mol), 1.3-BPG (-49.3 kJ/mol) & PCr (-43kJ/mol). Phosphoenolypyruvate (PEP) contains a phosphate ester bond which hydrolyzes to yield the enol form of pyruvate which can immediately tautomerize to the more stable keto form; it has a large ∆G’° b/c PEP has only one form while pyruvate has 2 forms which makes the product more stabilized than the reactant. 1,3-bisphosphoglycerate (1,3-BPG) contains an anhydride bond b/w C1 carboxyl group & phosphoric acid; hydrolysis of the acyl phosphate yields stabilized products. The direct product of hydrolysis is 3-phosphoglyceric acid w/ an undissociated –COOH but dis
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