CHAPTER 13 Bioenergetics and Reactions

Key topics:
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

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

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 = H - TS

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

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

Exergonic: G is negative Endergonic: G is positive G = H - TS

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 negative Endothermic: H is positive

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

Exergonic: G is negative Endergonic: G is positive
Exothermic: H is negative Endothermic: H is positive S is the entropy (disorder) in a system. When S is positive, the entropy of the system has increased.

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 Keq Standard conditions: 298 K (25C) 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:
[C ]c [ D ]d G G ' RT ln [ A]a [ B ]b

Standard free-energy changes are additive:

(1) A B G1 (2) B C G2 Sum: A C G1 + G2

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 singleelectron 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 CC bonds

Cleavage and formation of polar bonds

Nucleophilic substitution mechanism Additionelimination mechanism Hydrolysis and condensation reactions Internal rearrangements Eliminations (without cleavage) Group transfers (H+, CH3+, PO32) 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

AdditionElimination 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 additionelimination 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

AdditionElimination 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 ATP

ATP is frequently the donor of the phosphate in the biosynthesis of phosphate esters.

Hydrolysis of ATP is highly favorable under 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 reactants concentration exceeds its equilibrium concentration True reactant and the product are Mg-ATP and Mg-ADP, respectively

G also

Mg++

dependent

[MgADP ] [ Pi ] G G ' RT ln [ MgATP 2 ]

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

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

Reactions such as

PEP + ADP => Pyruvate + ATP are favorable, and can be used to synthesize ATP.

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 Reactivity

The 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 Reactions
Reduced 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 = nFE 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

In this chapter, we learned:
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