1.3 – Physical Foundations
SUMMARY 1.3 Physical Foundations
■ Living cells are open systems, exchanging matter and energy with their surroundings,
extracting and channeling energy to maintain themselves in a dynamic steady state distant
from equilibrium. Energy is obtained from sunlight or chemical fuels by converting the
energy from electron flow into the chemical bonds of ATP.
■ The tendency for a chemical reaction to proceed toward equilibrium can be expressed as
the free-energy change, ∆G, which has two components: enthalpy change, ∆H, and entropy
change, ∆S. These variables are related by the equation ∆G = ∆H − T∆S.
■ When ∆G of a reaction is negative, the reaction is exergonic and tends to go toward
completion; when ∆G is positive, the reaction is endergonic and tends to go in the reverse
direction. When two reactions can be summed to yield a third reaction, the ∆G for this
overall reaction is the sum of the ∆G values for the two separate reactions.
■ The reactions converting ATP to Pi and ADP or to AMP and PPi are highly exergonic (large
negative ∆G). Many endergonic cellular reactions are driven by coupling them, through a
common intermediate, to these highly exergonic reactions.
■ The standard free-energy change for a reaction, ∆G°, is a physical constant that is related
to the equilibrium constant by the equation ∆G° = −RT ln Keq.
■ Most cellular reactions proceed at useful rates only because enzymes are present to
catalyze them. Enzymes act in part by stabilizing the transition state, reducing the activation
‡
energy, ∆G , and increasing the reaction rate by many orders of magnitude. The catalytic
activity of enzymes in cells is regulated.
■ Metabolism is the sum of many interconnected reaction sequences that interconvert
cellular metabolites. Each sequence is regulated to provide what the cell needs at a given
time and to expend energy only when necessary.
Living cells and organisms must perform work to stay alive and to reproduce themselves.
The synthetic reactions that occur within cells, like the synthetic processes in any factory,
require the input of energy. Energy input is also needed in the motion of a bacterium or an
Olympic sprinter, in the flashing of a firefly or the electrical discharge of an eel. And the
storage and expression of information require energy, without which structures rich in
information inevitably become disordered and meaningless.
In the course of evolution, cells have developed highly efficient mechanisms for coupling the
energy obtained from sunlight or chemical fuels to the many energy-requiring processes
, they must carry out. One goal of biochemistry is to understand, in quantitative and chemical
terms, the means by which energy is extracted, stored, and channeled into useful work in
living cells. We can consider cellular energy conversions—like all other energy conversions—
in the context of the laws of thermodynamics.
Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their
Surroundings
The molecules and ions contained within a living organism differ in kind and in concentration
from those in the organism’s surroundings. A paramecium in a pond, a shark in the ocean, a
bacterium in the soil, an apple tree in an orchard—all are different in composition from their
surroundings and, once they have reached maturity, maintain a more or less constant
composition in the face of a constantly changing environment.
Although the characteristic composition of an organism changes little through time, the
population of molecules within the organism is far from static. Small molecules,
macromolecules, and supramolecular complexes are continuously synthesized and broken
down in chemical reactions that involve a constant flux of mass and energy through the
system. The hemoglobin molecules carrying oxygen from your lungs to your brain at this
moment were synthesized within the past month; by next month they will have been
degraded and entirely replaced by new hemoglobin molecules. The glucose you ingested
with your most recent meal is now circulating in your bloodstream; before the day is over
these particular glucose molecules will
have been converted into something else—carbon dioxide or fat, perhaps— and will have
been replaced with a fresh supply of glucose, so that your blood glucose concentration is
more or less constant over the whole day. The amounts of hemoglobin and glucose in the
blood remain nearly constant because the rate of synthesis or intake of each just balances
the rate of its breakdown, consumption, or conversion into some other product. The
constancy of concentration is the result of a dynamic steady state, a steady state that is far
from equilibrium. Maintaining this steady state requires the constant investment of energy;
when a cell can no longer obtain energy, it dies and begins to decay toward equilibrium with
its surroundings. We consider below exactly what is meant by “steady state” and
“equilibrium.”
Organisms Transform Energy and Matter from Their
Surroundings
For chemical reactions occurring in solution, we can define a system as all the constituent
reactants and products, the solvent that contains them, and the immediate atmosphere—in
short, everything within a defined region of space. The system and its surroundings together
constitute the universe. If the system exchanges neither matter nor energy with its
surroundings, it is said to be isolated. If the system exchanges energy but not matter with
its surroundings, it is a closed system; if it exchanges both energy and matter with its
surroundings, it is an open system.
A living organism is an open system; it exchanges both matter and energy with its
surroundings. Organisms obtain energy from their surroundings in two ways: (1) they take
up chemical fuels (such as glucose) from the environment and extract energy by oxidizing
them (see Box 1-3, Case 2); or (2) they absorb energy from sunlight.
SUMMARY 1.3 Physical Foundations
■ Living cells are open systems, exchanging matter and energy with their surroundings,
extracting and channeling energy to maintain themselves in a dynamic steady state distant
from equilibrium. Energy is obtained from sunlight or chemical fuels by converting the
energy from electron flow into the chemical bonds of ATP.
■ The tendency for a chemical reaction to proceed toward equilibrium can be expressed as
the free-energy change, ∆G, which has two components: enthalpy change, ∆H, and entropy
change, ∆S. These variables are related by the equation ∆G = ∆H − T∆S.
■ When ∆G of a reaction is negative, the reaction is exergonic and tends to go toward
completion; when ∆G is positive, the reaction is endergonic and tends to go in the reverse
direction. When two reactions can be summed to yield a third reaction, the ∆G for this
overall reaction is the sum of the ∆G values for the two separate reactions.
■ The reactions converting ATP to Pi and ADP or to AMP and PPi are highly exergonic (large
negative ∆G). Many endergonic cellular reactions are driven by coupling them, through a
common intermediate, to these highly exergonic reactions.
■ The standard free-energy change for a reaction, ∆G°, is a physical constant that is related
to the equilibrium constant by the equation ∆G° = −RT ln Keq.
■ Most cellular reactions proceed at useful rates only because enzymes are present to
catalyze them. Enzymes act in part by stabilizing the transition state, reducing the activation
‡
energy, ∆G , and increasing the reaction rate by many orders of magnitude. The catalytic
activity of enzymes in cells is regulated.
■ Metabolism is the sum of many interconnected reaction sequences that interconvert
cellular metabolites. Each sequence is regulated to provide what the cell needs at a given
time and to expend energy only when necessary.
Living cells and organisms must perform work to stay alive and to reproduce themselves.
The synthetic reactions that occur within cells, like the synthetic processes in any factory,
require the input of energy. Energy input is also needed in the motion of a bacterium or an
Olympic sprinter, in the flashing of a firefly or the electrical discharge of an eel. And the
storage and expression of information require energy, without which structures rich in
information inevitably become disordered and meaningless.
In the course of evolution, cells have developed highly efficient mechanisms for coupling the
energy obtained from sunlight or chemical fuels to the many energy-requiring processes
, they must carry out. One goal of biochemistry is to understand, in quantitative and chemical
terms, the means by which energy is extracted, stored, and channeled into useful work in
living cells. We can consider cellular energy conversions—like all other energy conversions—
in the context of the laws of thermodynamics.
Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their
Surroundings
The molecules and ions contained within a living organism differ in kind and in concentration
from those in the organism’s surroundings. A paramecium in a pond, a shark in the ocean, a
bacterium in the soil, an apple tree in an orchard—all are different in composition from their
surroundings and, once they have reached maturity, maintain a more or less constant
composition in the face of a constantly changing environment.
Although the characteristic composition of an organism changes little through time, the
population of molecules within the organism is far from static. Small molecules,
macromolecules, and supramolecular complexes are continuously synthesized and broken
down in chemical reactions that involve a constant flux of mass and energy through the
system. The hemoglobin molecules carrying oxygen from your lungs to your brain at this
moment were synthesized within the past month; by next month they will have been
degraded and entirely replaced by new hemoglobin molecules. The glucose you ingested
with your most recent meal is now circulating in your bloodstream; before the day is over
these particular glucose molecules will
have been converted into something else—carbon dioxide or fat, perhaps— and will have
been replaced with a fresh supply of glucose, so that your blood glucose concentration is
more or less constant over the whole day. The amounts of hemoglobin and glucose in the
blood remain nearly constant because the rate of synthesis or intake of each just balances
the rate of its breakdown, consumption, or conversion into some other product. The
constancy of concentration is the result of a dynamic steady state, a steady state that is far
from equilibrium. Maintaining this steady state requires the constant investment of energy;
when a cell can no longer obtain energy, it dies and begins to decay toward equilibrium with
its surroundings. We consider below exactly what is meant by “steady state” and
“equilibrium.”
Organisms Transform Energy and Matter from Their
Surroundings
For chemical reactions occurring in solution, we can define a system as all the constituent
reactants and products, the solvent that contains them, and the immediate atmosphere—in
short, everything within a defined region of space. The system and its surroundings together
constitute the universe. If the system exchanges neither matter nor energy with its
surroundings, it is said to be isolated. If the system exchanges energy but not matter with
its surroundings, it is a closed system; if it exchanges both energy and matter with its
surroundings, it is an open system.
A living organism is an open system; it exchanges both matter and energy with its
surroundings. Organisms obtain energy from their surroundings in two ways: (1) they take
up chemical fuels (such as glucose) from the environment and extract energy by oxidizing
them (see Box 1-3, Case 2); or (2) they absorb energy from sunlight.
