Chemical Logic of Metabolism

Chapter 12

Catabolism

complex

simple

Anabolism

complex

simple

ADP + Pi

ATP

Metabolism

12.1

- Catabolism: complex substances are degraded into simpler molecules, accomplied by net release of chemical energy.- Anabolism: synthesis of complex organic molecules, requires net input of chemical energy.

12.1

Catabolic and anabolic pathways between a given precursor and product not reverse of each other:

•  committed step - essentially irreversible ➯ makes entire pathway unidirectional

•  pathway taken for catabolism energetically impossible for anabolism

Advantage = independently regulated pathways:

1.  often take place in different compartments of cell

2.  Repression/induction of enzyme synthesis

3.  modulation of enzyme activity - often of enzyme catalyzing committed step:

• feedback inhibition by product

• allosteric regulation

• covalent modification

Bioenergetics and ATP

1.  Living systems obtain most of the energy needed to drive biosynthetic reactions from the oxidation of organic substrates.

2.  ∆G depends only on the difference between free energy of the products and free energy of reactants. It is independent of the pathway taken ➜ ∆G is the same whether occurs in 1 step or many.

∆Go’ for ATP + H2O ! ADP + Pi = -30.5 kJ/mol

-30,500 J/mol = -(8.315 J/mol•°K)(298°K)lnK’eq

lnK’eq = 12.3

K’eq = 2.22 x 105 =

�

[ADP][Pi][ATP]

Calculate K’eq:

�

ΔGo = −RT lnK 'eq (eqn 3.27)

ATP as a Free Energy Currency- ATP serves as immediate donor of free energy, continuously formed and consumed.

Standard free energy changes of chemical rxns are additive in any sequence of consecutive rxns = coupled:

A ! B ∆G°1

B ! C ∆G°2

C ! D ∆G°3

sum of rxns = A ! D

∆G°S = ∆G°1 + ∆G°2 + ∆G°3

3 types of Metabolic stoichiometry: A. Reaction stoichiometry: simple chemical stoichiometry

C6H12O6 + 6O2 ! 6CO2 + 6H2O ∆G°’= -2870 kJ/mol

C6H12O6 + 10NAD+ + 2FAD + 6H2O ! 6CO2 + 10NADH + 10H+ + 2FADH2

10NADH + 10H+ + 2FADH2 + 6O2 ! 10NAD+ + 2FAD + 12H2O

C6H12O6 + 6O2 ! 6CO2 + 6H2O

B. Obligate coupling stoichiometry: e.g. oxidation-reduction processes - biological oxidation of glucose removes 12 e- pairs, creating obligate requirement for 12 e- pair acceptors (NAD, FAD) to transfer e- to oxygen.

glucose combustion

3 types of Metabolic stoichiometry:

C. Evolved coupling stoichiometry: not fixed by chemical necessity, but rather a consequence of evolutionary design or selection.

C6H12O6 + 6O2 + 38 ADP + 38 Pi ! 6CO2 + 38 ATP + 44H2O

Fundamental biological purpose of ATP as an energy-coupling reagent is to drive thermodynamically unfavorable reactions.

coupling coefficient = # moles ATP produced or consumed per mole substrate converted.

glucose + 38 ADP --> 38 ATP + CO2 +38

Coupling ATP hydrolysis to a process changes equilibrium ratio of [reactants]/[products] by a factor of 108!

The energetics of ATP is crucial to solvent capacity of the cell: capacity to keep all essential metabolites and macromolecules at low concentrations. This is important because:

1.  for so many solutes to exist in same solution, individual concentrations must be low

2.  decreases probability of unwanted side reactions:

How does ATP help avoid high metabolite concentrations? Go back to previous example:

Non-enzymatic reaction: A + B ! C (1st order wrt both [A] and [B])

Scenario 1: [A] = [B] = 1 M v = k[A][B]���Scenario 2: [A] = [B] = 10-5 M

The quantity of C produced in 1 sec under Scenario 1 would take ~317 years to produce under Scenario 2

Substrate cycles (opposing pathways):∆Go’ K’eq

fructose-6-P + ATP ! fructose-1,6-bisP + ADPPFK

fructose-1,6-bisP + H2O ! fructose-6-P + PiFBPase

-14.2

-16.3

308

719

Net: ATP + H2O ! ADP + Pi For FBPase rxn, at physiological [Pi] = 1 mM, equilibrium ratio

[F − 6 − P][FBP]

≈ 719,000 [FBP][F − 6 − P]

≈ 0.0000014

i.e. under virtually any cellular condition, FBPase rxn is thermodynamically favorable in direction of F-6-P

For PFK rxn, at physiological conditions of [ATP] = [ADP], equilibrium ratio [FBP]

[F − 6 − P]≈ 308 i.e. rxn is favorable in direction of

FBP until [FBP] > 310 X [F6P]

Why is it so important that both pathways be thermodynamically favorable under all conditions? Regulation can be imposed only on reactions displaced far from equilibrium:

Lake Austin

Lake Travis

vs.

Open floodgates, what happens?p. 495

Although opposing pathways may share a # of steps in common (e.g. glycolysis vs. gluconeogenesis), the overall pathways are unidirectional due to a few unique reactions (e.g. PFK vs. FBPase).

The evolved coupling ATP stoichiometry that produces unidirectional pathways is the most important metabolic role of ATP.

The second most important role of ATP is its role as allosteric effector in the kinetic regulation of these unidirectional pathways.

p. 495

12.10

Gibbs free energy as a function of displacement from equilibrium

∆G = RT ln QK

⎛⎝⎜

⎞⎠⎟ (eqn 3.33)

QK

= e∆GRT

⎛⎝⎜

⎞⎠⎟ = e

−1300 × 103 J/mol8.315 J/moliK( ) 298 K( )

⎛

⎝⎜⎞

⎠⎟ ≈10−228

Oxidation of glucose:

[A] high [B] low, Q/K<1, rxn goes to right[A] low, [B] high, Q/K>1, rnx goes to left

Most regulatory enzymes of energy metabolism are allosterically modulated by adenine nucleotides (ATP, ADP, AMP).

ATP + AMP ! 2 ADP

adenylate kinase

�

[ATP][ADP]+ [AMP]

= energy charge

Role of AMP and pyrophosphate:���in some rxns, 2 terminal phosphate groups enzymatically removed as pyrophosphate (PPi), leaving AMP:

PPi + H2O " 2Pi ∆G°' = -19.2 kJ/mol

ATP + H2O " AMP + PPi ∆G°' = -45.6 kJ/mol

�

ΔG = ΔGo + RT ln [Products][Reactants]

Standard free energy change vs. reversibility in cell:

Q = mass-action ratio

A B

12.3 12.4

GlycolysisOxidativemetabolism

12.5 12.6

Carbohydrateanabolism Photosynthesis

NAD+, NADP+ in catabolism and biosynthesis

12.9