2054, Chap. 8, page 1
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1 2054, Chap. 8, page 1 I. Metabolism: Energetics, Enzymes, and Regulation (Chapter 8) A. Energetics and work 1. overview a. energy = ability to do work (1) chemical, transport, mechanical (2) ultimate source = sun (exception = chemolithoautotrophs) (3) photosynthetic organisms convert solar energy into chemical energy b. chemical energy resides in bonds between atoms, specifically in the electrons (1) potential energy = bonds remain unchanged (2) kinetic energy = bond energy freed for cellular work (a) redox reactions = rearrangement of electron distribution (b) can be used for synthesis, growth, movement c. exergonic = reaction releases energy d. endergonic = reaction requires input of energy 2. coupled reactions and the role of ATP a. ATP functions as an energy "storehouse" (1) energy released in exergonic reactions drives phosphorylation of ADP to ATP (2) ATP can release the energy to drive endergonic reactions (3) "metabolic money" - can be earned, banked, saved, spent, exchanged (4) not really "high-energy" bonds, more like "unstable" (a) not a large amount of energy released (b) energy released quickly and easily (kerosene) b. energy extraction in biological systems involves transfer of electrons, termed redox reactions (1) oxidation = loss of electrons (2) reduction = gain of electrons (3) redox reactions always occur in pairs, with an electron donor and an electron acceptor (a) conjugate or redox pair (b) may involve a temporary electron carrier (4) energy released from redox reactions can be coupled to phosphorylation (addition of an inorganic phosphate, P i, to ADP or some other carrier)
2 2054, Chap. 8, page 2 (a) usually refer to electron transfer, but generally occurs as part of atom, like hydrogen (b) hydrogen ions (in addition to electrons) have a role in energetics (c) dehydrogenation = removal of hydrogen during a redox reactions c. electron carriers = coenzymes that shuttle electrons between molecules (1) often transfer both electrons and hydrogens, but can be electrons only (2) NAD is most common carrier (a) 2 electrons, 2 protons (b) actual reduced state = NADH + H +, but often written as NADH or NADH 2 (3) electrons are transferred through a series of redox reactions (carriers) = electron transport chain or respiratory chain (4) other carriers = FAD, NADP, CoA, cytochromes d. substrate level phosphorylation = energy released directly from substrate to phosphorylate ADP (1) no external electron acceptor (2) redox reactions occur between portions of the substrate molecule e. oxidative phosphorylation - ATP formed through a series of redox reactions through a respiratory pathway f. photophosphorylation = ATP formed through sunlight-driven reactions B. Laws of thermodynamics 1. thermodyanamics = analysis of energy changes within a system a. focus on initial and final states of system (1) route is unimportant (2) rate is unimportant b. the change in energy of a system depends only on the initial and final state and not on the path of the transformation 2. 1st law = energy neither created or destroyed a. )E can increase if energy absorbed from surroundings b. cannot predict if reaction is spontaneous 3. explained by 2nd law: process occurs spontaneously only if the sum of the entropies of the system and its surroundings increases: a. ()S system + )S surroundings ) > 0 for a spontaneous reaction
3 2054, Chap. 8, page 3 b. ultimately, all systems + surroundings increase in entropy (tends towards lowest energy state) 4. entropy changes of chemical reactions difficult to measure; starting values difficult to determine a. instead of entropy, use free energy b. by combining the 1st and 2nd laws of thermodynamics: )G = )H -T)S c. )H = )E + P)V, since )V is small, )H )E and )G )E - T)S 5. So, the change in free energy of a reaction depends on changes in internal energy and entropy of the system 6. a reaction can occur spontaneously only if the )G is negative a. the )G of products must be less than the )G of reactants b. )G of a reaction is independent of the path or mechanism of the transformation c. )G is unrelated to the reaction rate 7. for the reaction A + BöC + D a. )G = )G o + RT ln ([C][D]/[A][B]) b. )G o = standard free energy change, at ph 7, use )G o ' c. )G o ' = -RT ln ([C][D]/[A][B]) = -RT K' eq 8. the overall free energy change for a chemically coupled series of reactions is equal to the sum of the free-energy changes of the individual steps 9. a thermodynamically unfavorable reaction can be driven by a thermodynamically favorable reaction that is coupled to it C. energy required for work, active transport, synthesis 1. energy from external source a. chemotrophs use chemical energy b. phototrophs use light energy 2. ATP is the most common energy carrier in biological systems a. considered an energy-rich molecule becase its triphosphate unit contains two phosphoanhydride bonds with )G o ' = -7.3 kcal/mol b. under cell conditions, )G- -12 kcal/mol for breakage of each phosphoanhydride bond c. turnover rate of ATP very high (1) immediate donor of free energy (2) continuously formed and consumed
4 2054, Chap. 8, page 4 3. phosphate group transfer potential = tendency to transfer terminal phosphoryl group 4. structural basis of the high phosphate group-transfer potential of ATP a. electrostatic repulsion (1) at ph 7, triphosphate unit has 4 negative charges, repelling each other (2) repulsion is reduced when ATP is hydrolyzed b. resonance stabilization (1) ADP and P i have greater resonance stability than ATP (more forms) (2) resonance forms with ATP limited and produce unfavorable electrostatic conditions 5. several other biological compounds have high phosphate group transfer potential 6. these are high energy bonds because free energy is released when they are hydrolyzed D. ATP hydrolysis shifts the equilibria of coupled reactions by a factor of reactions that are unfavorable under standard conditions can be made favorable a. increase ratio of reactants to products b. couple reaction to hydrolysis of ATP (sum of reaction equal to sum of its parts) 2. That is, for A º B with )G o ' = +4 kcal a. K' eq = ([B] eq /[A] eq ) = 10 -)Go'/1.36 = 1.15 x 10-3 b. with ATP: A + ATP + H 2 O º B + ADP + P i + H + and )G o ' = -3.3 kcal c. K' eq = ([B]eq/[A]eq)([ADP]eq[Pi]eq/[ATP]eq) = /1.36 = 2.67 x 10 2 d. so at equilibrium, [B]eq/[A]eq = K' eq ([ATP] eq /[ADP] eq [P i ] eq ) e. at a typical ATP/ADP ratio of 500, [B]eq/[A]eq= 2.67 x 10 2 x 500 = 1.34 x 10 5 f. equilibrium ratio has changed by 8 magnitudes 3. To sum, cells use energy from oxidizable substrates or light to maintain high concentrations of ATP. ATP hydrolysis changes the equilibrium ratio of products to reactants by a large factor, generally 8 magnitudes
5 2054, Chap. 8, page 5 a. hydrolysis of n ATP molecules changes the equilibrium ratio by a factor of 10 8n b. an unfavorable reaction can be converted to a favorable one by coupling it to the hydrolysis of a sufficient number of ATP molecules E. Oxidation-reduction reactions and electron carriers 1. oxidation-reduction (redox) reactions are those where electrons are transferred from a donor molecule to an acceptor molecule a. reduction = gain of electrons b. oxidation = loss of electrons c. reactions occur as redox pairs (donor reaction + acceptor reaction) oxidant + ne - º reductant 2. standard reduction potential (E o ) is a measure of the ability for a reducing agent to lose an electron a. more negative = better donor b. more positive = greater affinity to accept electrons 3. electron tower (Table 8.1) show the relationship between better electron donors (top) and better electron acceptors (bottom) a. the greater the difference in standard reduction potentials, the more free energy is made available b. )G o = -nf)e o F. Enzymes 1. protein catalysts with high specificity for the reaction catalyzed and molecules acted upon a. catalyst = increases rate of reaction without being permanently altered itself b. acts on reactants or substrates to form products 2. many enzymes are pure proteins but others have cofactors and are called holoenzymes a. apoenzyme = protein portion b. cofactor = nonprotein component (1) prosthetic group = cofactor firmly attached to apoenzyme (2) coenzyme = loosely bound cofactor (e.g., NAD, many vitamins) 3. general mechanisms a. enzymes effect the rate, but not the energy yield or requirement b. in a reaction, reactants come together an form a transition-state complex that
6 2054, Chap. 8, page 6 resembles both reactants and products (1) activation energy = energy required to bring reacting molecules together in the correct way to reach transition state (2) transition-state complex decomposes to yield products (3) enzymes accelerate reactions by lowering the activation energy c. active site or catalytic site = specific binding site for substrates on enzyme (1) enzyme may bring substrates together at active site (a) in effect, concentrates substrates (b) aligns substrates in correct orientation to form transition-state complex (2) can accelerate reaction rates hundreds of thousand-fold over uncatalyzed reaction rates (a) allows reactions to occur at lower temperatures (b) essential to life processes 4. inhibition and regulation a. enzyme activities strongly influenced by environmental factors (1) temperature can increase rate until protein denatures (2) ph effects charges on amino acids, altering 3-D enzyme structure b. substrate concentrations effect rate of reaction (active site is saturatable) c. competitive inhibition = enzyme reactions inhibited by chemicals that compete with the substrate for the active site (1) does not undergo reaction to form products (2) some can bind irreversibly (3) sulfanilamide, a sulfa drug (analog of PABA) d. noncompetitive inhibition = interact with enzyme but not at active site (1) allosteric inhibition (2) can alter the shape of enzyme active site (3) some inhibitors interact with metal ions, often permanently inactivating enzymes e. end-product inhibition = allosteric inhibition of a key enzyme in a pathway by a product of the pathway (reversible)
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