CHEM 351 CH 13

CHAPTER 13 Bioenergetics and Reactions

– Thermodynamics applies to biochemistry, too – Organic chemistry principles are still valid – Some biomolecules are “high energy” with respect

to their hydrolysis and group transfers – Energy stored in reduced organic compounds can be

used to reduce cofactors such as NAD+ and FAD, which serve as universal electron carriers

Key topics:

Life needs energy

• Recall that living organisms are built of complex structures

• Building complex structures that are low in entropy is only possible when energy is spent in the process

• The ultimate source of this energy on Earth is the sunlight

Metabolism is the sum of all chemical reactions in the cell

• Series of related reactions form metabolic pathways• Some pathways are primarily energy-producing

– This is catabolism

• Some pathways are primarily using energy to build complex structures– This is anabolism or biosynthesis

Laws of thermodynamics apply to living organisms

• Living organisms cannot create energy from nothing• Living organisms cannot destroy energy into nothing• Living organism may transform energy from one form to another

• In the process of transforming energy, living organisms must increase the entropy of the universe

• In order to maintain organization within themselves, living systems must be able to extract useable energy from their surroundings, and release useless energy (heat) back to their surroundings

Free energy, or the equilibrium constant, measure the direction of processes

G = H - TS

Gibbs free energy (G): amount of energy capable of doing work during a reaction at a constant temperature and (absolute) temperature.

Exergonic: G is negative Endergonic: G is positive

G must be negative (energetically favorable) for a process to be spontaneous.

Exergonic: G is negativeEndergonic: G is positive

H: change in enthalpy (heat content of the system). Reflects the number and kinds of chemical bonds in the reactants and products.

Exothermic: H is negativeEndothermic: H is positive

Free energy, or the equilibrium constant, measure the direction of processes

G = H - TS

Exergonic: G is negativeEndergonic: G is positive

Exothermic: H is negativeEndothermic: H is positive

S is the entropy (disorder) in a system. When S is positive, the entropy of the system has increased.

Free energy, or the equilibrium constant, measure the direction of processes

G = H - TS

Free energy, or the equilibrium constant, measure the direction of processes

G = H - TS

S is negative S is positive

H is negative ? G is negative

H is positive G is positive ?

Free energy, or the equilibrium constant, measure the direction of processes

G = H - TS

G can be related to Keq by:

G’˚ = -RT ln K’eq

Standard conditions: 298 K (25˚C) and 101.3 kPa (1 atm)

Free energy, or the equilibrium constant, measure the direction of processes

Energetics of Some Chemical Reactions• Hydrolysis reactions tend to be strongly favorable

(spontaneous)• Isomerization reactions have smaller free-energy

changes – Isomerization between enantiomers: G = 0

• Complete oxidation of reduced compounds is strongly favorable – This is how chemotrophs obtain most of their energy– In biochemistry the oxidation of reduced fuels with O2 is

stepwise and controlled– Recall that being thermodynamically favorable is not the

same as being kinetically rapid

Energetics within the cell are not standard• The actual free-energy change of a reaction in the

cell depends on:– The standard change in free energy– Actual concentrations of products and reactants– For the reaction aA + bB cC + dD:

• Standard free-energy changes are additive: (1) A B ΔG’1

(2) B C ΔG’2

Sum: A C ΔG’1 + ΔG’2

ba

dc

BA

DCRTGG

][][

][][ln'

Lesson in Quantum Chemistry• Most organic molecules, including the reduced fuels, are in

the singlet spin state– All electrons are paired into electron pairs

• Molecular oxygen is in the triplet spin state– Two electrons are unpaired

• Direct electron transfer from a singlet reduced species to a triplet oxidizing species is quantum-mechanically forbidden

• This is why direct oxidation (spontaneous combustion) of biomolecules does not occur readily

• Few cofactors, such as transition metal ions, and flavin adenine dinucleotide are able to catalyze consecutive single-electron transfers needed for utilization of O2

Review of Organic Chemistry

• Most reactions in biochemistry are thermal heterolytic processes

• Nucleophiles react with electrophiles • Heterolytic bond breakage often gives rise to

transferable groups, such as protons• Oxidation of reduced fuels often occurs via transfer of

electrons and protons to a dedicated redox cofactor

Chemical Reactivity

Most reactions fall within few categories: •Cleavage and formation of C–C bonds

•Cleavage and formation of polar bonds

‒ Nucleophilic substitution mechanism

‒ Addition–elimination mechanism

• Hydrolysis and condensation reactions

•Internal rearrangements

•Eliminations (without cleavage)

•Group transfers (H+, CH3+, PO3

2–)

•Oxidations-reductions (e– transfers)

Chemistry at Carbon

• Covalent bonds can be broken in two ways• Homolytic cleavage is very rare • Heterolytic cleavage is common, but the products

are highly unstable and this dictates the chemistry that occurs

Homolytic vs. Heterolytic Cleavage

Nucleophiles and Electrophiles in Biochemistry

Examples of Nucleophilic Carbon-Carbon Bond Formation Reactions

Isomerizations and Eliminations:No Change in Oxidation State

Addition–Elimination Reactions

• Substitution from sp3 carbon proceeds normally via the nucleophilic substitution (SN1 or SN2) mechanism

• Substitution from the sp2 carbon proceeds normally via the nucleophilic addition–elimination mechanism– Nucleophile adds to the sp2 center giving a

tetrahedral intermediate – Leaving group eliminates from the tetrahedral

intermediate– Leaving group may pick up a proton

Addition–Elimination Reactions

Group Transfer Reactions

• Proton transfer, very common• Methyl transfer, various biosyntheses• Acyl transfer, biosynthesis of fatty acids• Glycosyl transfer, attachment of sugars • Phosphoryl transfer, to activate metabolites

‒ also important in signal transduction

Nucleophilic Displacement

• Substitution from sp3 phosphorous proceeds via the nucleophilic substitution (usually associative, SN2-like) mechanism– Nucleophile forms a partial bond to the

phosphorous center giving a pentacovalent intermediate or a pentacoordinated transition state

Nucleophilic Displacement

Phosphoryl Transfer from ATPATP is frequently the donor of the phosphate in the biosynthesis of phosphate esters.

Hydrolysis of ATP is highly favorableunder standard conditions

• Better charge separation in products

• Better solvation of products

• More favorable resonance stabilization of products

Actual G of ATP hydrolysis differs from G’

• The actual free-energy change in a process depends on:

– The standard free energy

– The actual concentrations of reactants and products

• The free-energy change is more favorable if the reactant’s concentration exceeds its equilibrium concentration

• True reactant and the product are Mg-ATP and Mg-ADP, respectively

G also Mg++ dependent]MgATP[

]P[]MgADP[ln'

2i

RTGG

G of ATP hydrolysis is Mg++ dependent

Cellular ATP concentration is usually far above the equilibrium concentration, making ATP a very potent source of chemical energy.

Several phosphorylated compounds have large G’ for hydrolysis

• Again, electrostatic repulsion within the reactant molecule is relieved

• The products are stabilized via resonance, or by more favorable solvation

• The product undergoes further tautomerization

Phosphates: Ranking by the Standard Free Energy of Hydrolysis

Reactions such as

PEP + ADP => Pyruvate + ATP

are favorable, and can be used to synthesize ATP.

Phosphate can be transferred from compounds with higher ΔG’ to those with lower ΔG’.

Hydrolysis of Thioesters

• Hydrolysis of thioesters is strongly favorable– such as acetyl-CoA

• Acetyl-CoA is an important donor of acyl groups– Feeding two-carbon units into metabolic pathways

– Synthesis of fatty acids

• In acyl transfers, molecules other than water accept the acyl group

Hydrolysis of Thioesters

Molecular Basis for Thioester ReactivityThe orbital overlap between the carbonyl group and sulfur is not as good as the resonance overlap between oxygen and the carbonyl group in esters.

Oxidation-Reduction ReactionsReduced organic compounds serve as fuels from which electrons can be stripped off during oxidation.

Reversible Oxidation of a Secondary Alcohol to a Ketone

• Many biochemical oxidation-reduction reactions involve transfer of two electrons

• In order to keep charges in balance, proton transfer often accompanies electron transfer

• In many dehydrogenases, the reaction proceeds by a stepwise transfers of proton (H+) and hydride (:H–)

Reduction Potential• Reduction potential (E)

– Affinity for electrons; higher E, higher affinity– Electrons transferred from lower to higher E

E’ = -(RT/nF)ln (Keq) = G’/nF

∆E’ = E’(e- acceptor) – E’(e- donor)

∆G’ = –nF∆E’For negative G need positive E

E(acceptor) > E(donor)

NAD and NADP are common redox cofactors

• These are commonly called pyridine nucleotides• They can dissociate from the enzyme after the

reaction• In a typical biological oxidation reaction, hydride

from an alcohol is transferred to NAD+ giving NADH

NAD and NADP are common redox cofactors

Formation of NADH can be monitored by UV-spectrophotometry

• Measure the change of absorbance at 340 nm• Very useful signal when studying the kinetics of

NAD-dependent dehydrogenases

Flavin cofactors allow single electron transfers

• Permits the use of molecular oxygen as an ultimate electron acceptor– flavin-dependent oxidases

• Flavin cofactors are tightly bound to proteins

Chapter 13: Summary

• The rules of thermodynamics and organic chemistry still apply to living systems

• Reactions are favorable when the free energy of products is much lower than the free energy of reactants

• Biochemical phosphoryl transfer reactions are favorable when:– The phosphate donors are destabilized by electrostatic repulsion, – and the reaction products are often stabilized by resonance

• Unfavorable reactions can be made possible by chemically coupling a highly favorable reaction to the unfavorable reaction

• Oxidation-reduction reactions commonly involve transfer of electrons from reduced organic compounds to specialized redox cofactors

– Reduced cofactors can be used in biosynthesis, or may serve as a source of energy for ATP synthesis

In this chapter, we learned: