Bioenergetics: Free Energy, ATP, and Oxidation of Carbon Fuels

INTRODUCTION

Bioenergetics -> quantitative study of 1) energy transductions (= conversion of one form of energy into another) taking place in living cells and of 2) chemical processes featuring these transductions

• quantitative observations concerning the changes of different energy forms led to the development of thermodynamics, as well as to the formulation of its laws -> thermodynamic quantities describing energy changes during chemical reactions were defined.
• Enthalpy (H) = heat content of a reacting system, keeping constant pressure -> during a chemical reaction, heat is released (exothermic process) when the heat content of the products is less than that of the reactants, being enthalpy change a negative value (AH<0) # reacting systems absorbing heat from the surroundings are defined as endothermic and are associated to AH>0 Entropy (S) = measure of system disorder/randomness -> reaction yielding products that are less complex and more disordered compared with the reactants proceed with an entropy gain (AS>0).
• Free energy (G) (from J. Willard Gibbs) = amount of energy capable of doing work, associated with a reaction conducted at constant T and P -> reactions proceeding with free energy release are defined exergonic, thus displaying a negative (< 0) AG value # in endergonic reactions, the reacting system gains free energy and AG > 0.

FREE ENERGY

Free energy change/variation (AG) is related with reactions/processes occurring within closed systems (those one exchanging heat, but not matter, with surroundings) at fixed temperature and pressure -> these conditions co-exist within biological systems AG value associated with chemical reactions occurring within cells allows the prediction of 1) their direction + 2) the equilibrium position + 3) the amount of the theoretical performed work.

... + 1M starting concentrations of all components aA + bB=cC + dD [C] &q[D]e Keq = [A] & [B]eq Under standard conditions `(P = 1atm + T = 273K and marked with """) and upon reaching the point of equilibrium, it is possible to relate the equilibrium constant Ked with the free energy change eg (AG) AGº = - RTIn K AG Keq = e AG = AH - T . AS AG = Gibbs free energy AH = Change in enthalpy AS = Change in entropy T = Temperature in K

FREE ENERGY RELATIONSHIPS

The standard free-energy change (AGO) of a chemical reaction simply represents an alternative mathematical way of expressing its equilibrium constant (Keg) there is a relationship between this 2 quantities

Since there is an exponential relationship between AGO and Keg, relatively small changes in AGº correspond to large changes in Keg AGº = - RTIn Ke G Keq = @

FREE ENERGY AND REACTION SPONTANEITY

AG (or AGº) = the difference between G content of the products and G content of the reactants -> AG < 0 is referred to products containing less free energy than the reactants and the reaction will proceed spontaneously # AG < 0 means that the reaction products contain more free energy than the reactants. EXERGONIC REACTION: AG < O ENDERGONIC REACTION: AG > O Reaction is spontaneous Reaction is not spontaneous

Gibbs Free Energy Release

Energy is released reactants AG < 0 products Time

Gibbs Free Energy Added

Energy is added products AG> 0 reactants Time

BIOCHEMICAL REACTIONS

Within cell, thousands of relevant (when an available substrate is converted to a useful product) + specific + enzyme-catalyzed reactions are carried out -> transformation of nutrients into amino acids, nucleotides or lipids + energy extraction from fuels (glucose or fatty acids) by oxidation + polymerization of monomeric subunits (monosaccharides, amino acids or nucleotides) into macromolecules (polysaccharides, proteins and nucleic acids).

• internal rearrangements, isomerizations, and eliminations
• group transfer reactions
• reactions that make or break C-C bonds
• free-radical reactions
• oxidation- reductions

BIOCHEMICAL REACTION MECHANISMS

Covalent Bond Cleavage

Covalent bonds (= shared electron pairs) can be broken by generating a homolytic cleavage, (unpaired electron = radical formation + less common) or a heterolytic cleavage (retention of both bonding electrons = ions formation + more common).

• Homolytic cleavage -C-H =- C + H - Carbon radical 1 -C-C- -C + ℃- 1 - Carbon radicals
• Heterolytic cleavage -C-H I 1 -C:" 1 + H+ Carbanion Proton -C-H I 1 -C+ 1 + H :- Carbocation Hydride - - -C-C- 1L -C:" 1 + + C- Carbanion Carbocation

Nucleophile and Electrophile Interactions

Biochemical reactions include interactions between nucleophile and electrophile species → functional groups rich in electrons and capable of donating them + electron-deficient functional groups that seek negative charged or polarized centers.

BIOCHEMICAL GROUP TRANSFER REACTIONS

group transfer reactions

O 5+ P-O- δ- O Enzymes catalyzing phosphoryl group transfers, using ATP as donor, are called kinases (i.e. hexokinase, moving a phosphoryl group from ATP to glucose)

O O O= Adenosine HO-P-O-P-O-P-O- HÖ-R - I Glucose 0 O ATP O Adenosine -0-P-O-P-O" + "O-P-O-R 1 1 ADP I -O 0 Glucose 6-phosphate, a phosphate ester Metabolic pathways are often characterized by phosphoryl group (-PO22-) transfers -> it represents a good leaving group that, once attached to a metabolic substrate, is able to activate the intermediate for subsequent reaction -> among the better leaving groups, it participate to hundreds of metabolic reactions. Oxygen (O) is more electronegative than phosphorus (P) -> unbalanced electron sharing = P bears a partial positive charge (o+), acting as an electrophile species -> in many metabolic reactions, a phosphoryl group is transferred from ATP to an alcohol or to a carboxylic acid, thus forming a phosphate ester or a mixed anhydride, respectively.

BIOCHEMICAL REDOX REACTIONS

redox reactions In biochemical molecules, carbon atoms can display five different oxidation states and transitions between these states occur during oxidation-reduction (redox) reactions featuring metabolism -> biological oxidations = e- and H+ loss = dehydrogenation reactions catalyzed by dehydrogenase enzyme.

• CH2 -CH3 Alkane
• CH2-CH2OH Alcohol
• O -CH2-C Aldehyde (ketone) H(R)
• O -CH2-C Carboxylic acid OH
• O=C=0 Carbon dioxide

the oxidation of an electron donor is always associated with the reduction of an electron acceptor -> oxidation reactions generally release energy and living cells obtain the needed energy by oxidizing metabolic fuels such as carbohydrates or fat -> during these (catabolic) energy-yielding processes, electrons are transferred from fuel molecules to oxygen (O2), by using a series of electron carriers. Oxygen display a great electron affinity -> electron- transfer process is highly exergonic, thus providing the energy for ATP synthesis = the central goal of catabolism

OH 2H+ + 2e O O I - CH3-CH-C CH3-C-C 1 1 2H+ + 2e- Lactate lactate dehydrogenase Pyruvate

THE ROLE OF ATP

Within biological reactions (metabolism), ATP plays a fundamental role as the energy currency that links catabolismo and anabolism -> cells of heterotrophic organisms obtain "chemical" energy through catabolic reactions (usually exergonic) of nutrient (complex) molecules.

-O-P-O-P-O-P-O- Adenosine - H-0: O 0- O ATP4- H 0 O 0 1 HO-P-O-P-O- Adenosine -O-P-OH hydrolysis, with relief of charge repulsion O 0- ADP2- 0- P 2 resonance stabilization 8- 3- 0 8-0- P - 0 8- H+ O / ATP4- + H20 - ADP3- + HPO2- + H+ AG'º = - 30.5 KJ/mol This energy is used to synthetize ATP (ADP + Pi) that, in turn, undergoes hydrolysis (accompanied with a wide free energy release) to provide chemical energy to allow cell to carry on endergonic processes featuring 1) anabolism (= synthesis of metabolic O H+ + "O-P-O-P-O- I 1 0- 0 Adenosine ADP3- ionization = intermediates and macromolecules starting from smaller precursors) + 2) transport of substances across membranes against concentration gradients + 3) mechanical motion.

THE ROLE OF ATP IN METABOLISM

Within biological reactions (metabolism), ATP plays a fundamental role as the energy currency that links catabolismoand anabolism -> cells of heterotrophic organisms obtain "chemical" energy through catabolic reactions (usually exergonic) of nutrient (complex) molecules.

O C O -O-P-O-P-O-P-O- Adenosine - H-0: O O ATP4- ー エ O O O 1 HO-P-O-P-O- Adenosine -O-P-OH hydrolysis, with relief of charge repulsion O 0- ADP2- 0- ionization 2 resonance stabilization O O 8- 3- 0 H+ + "O-P-O-P-O- Adenosine 1 0 ADP3- ATP4- + H20 -> ADP3- + HPO2 + H+ AG'º = - 30.5 KJ/mol Chemical basis for the relatively large and negative standard free energy of ATP hydrolysis = cleavage of the terminal (one out of three) negatively charged phosphoryl grou p bond to the rest of the molecule relieves some of the internal electrostatic repulsion + released P can be stabilized by the formation of several resonance forms 8-0- P - 0 8- H+ O=2-0 P -C

THE ROLE OF ATP + OTHER PHOSPHORYLATED COMPOUNDS

In the cytosol, Mg2+ ions usually binds to both ATP and ADP molecules, in order to stabilize negative charges of phophoryl groups -> in most enzymatically catalyzed reactions involving ATP as phosphoryl group donor molecule, the substrate is not ATP but MgATP2 -.

O O O= TO-P-O-P-O-P-O- Adenosine O O MgATP2- Mg 2+ O C -O-P-O-P-O- Adenosine O O- MgADP- g2+ Mg- In addition to ATP, significantly large, negative free energy values are reported for the hydrolysis of a wide variety of biologically important phosphorylated compounds -> this is due to the several resonance forms available to phosphoryl group (Pi), stabilizing this product that is generated following the associated phosphate-releasing reactions -> i.e. glycolysis intermediates + other important substrates.