Chapter 8 An Introduction to Metabolism

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KEY CONCEPTS
An organisms metabolism transforms matter and energy, subject to the laws of thermodynamics
The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously
ATP powers cellular work by coupling exergonic reactions to endergonic reactions
Enzymes speed up metabolic reactions by lowering energy barriers
Regulation of enzyme activity helps control metabolism

SECTION 8.1
THE ENERGY OF LIFE
Sugars -> Amino Acids -> Proteins
o Sugars can be converted to amino acids that are linked together into proteins
o Proteins are dismantled into amino acids that can be converted to sugars when food is
digested
Cellular Respiration
o Responsible for the cellular economy
o Extracts energy stored in sugars and other fuels
Cells apply this energy to do various works
o Process of oxidizing food molecules, like glucose, to carbon dioxide and water
o C6H12O6 + 6O2 + 6H2O 12H2O + 6CO2
Bioluminescence (and other metabolic activities) is coordinated and controlled
o Bioluminescence is the production and emission of light by a living organism
Bioenergetics the study of how energy flows through living organisms

METABOLISM TRANSFORMS MATTER & ENERGY Laws of Thermodynamics
Metabolism the totality of an organisms chemical reactions; road map of thousands of chemical
reactions that occur
Metabolic Pathway begins with a specific molecule, which is then altered in a series of defined
steps, resulting in a certain product
o Pathways can have more than one starting molecule
o Each step of the pathway is catalyzed by a specific enzyme
o
o Catabolic & anabolic pathways are the downhill and uphill avenues of the metabolic
map
Energy released from the downhill reactions of catabolic pathways can be stored
and then used to drive the uphill reactions of anabolic pathways
o Metabolism manages the material and energy resources of the cell
o Catabolic pathways (breakdown pathways) release energy by breaking down complex
molecules to simpler compounds
Cellular Respiration sugar glucose and other organic fuels are broken down in the
presence of oxygen, carbon dioxide, and water.
o Anabolic Pathways (biosynthetic pathways) consume energy to build complicated
molecules from simpler ones
Ex: synthesis of a protein from amino acids

FORMS OF ENERGY
Energy the capacity to cause change
o Can be used to do work
o Ability to rearrange a collection of matter
o Kinetic Energy energy can be associated with the relative motion of objects
Heat/Thermal Energy kinetic energy associated with the random movement of
atoms or molecules
o Light (do not forget) is also a type of energy that can be used to perform work, such as
powering photosynthesis in plants
o Potential Energy energy that matter possesses because of its location or structure
Ex: Water behind a dam possesses energy b/c of its altitude above sea level
Molecules have energy b/c of its arrangement of atoms
Chemical Energy potential energy available for release in a chemical reaction
Catabolic pathways release energy by breaking down complex molecules,
which are high in chemical energy
o During a catabolic reaction, atoms are rearranged and energy is
released, resulting in lower-energy breakdown products
o Ex: Engine of a Car hydrocarbons of gasoline react violently with
oxygen, releasing energy that pushes pistons and produces exhaust
EXAMPLE: Transformations between potential & kinetic energy in divers
o

LAWS OF ENERGY TRANSFORMATION
Thermodynamics the study of the energy transformations that occur in a collection of matter
o System denotes the matter under study
Isolated System unable to exchange either energy or matter with its surroundings
Ex: liquid in a thermos bottle
Open System energy and matter can be transferred between the system and its
surroundings
Ex: Organisms b/c they absorb energy and release heat and metabolic waste
to the surroundings
o Surrounding(s) everything outside the system (universe)
First Law of Thermodynamics (the Principle of Conservation of Energy) energy can be
transferred and transformed, but it cannot be create or destroyed
o The energy of the universe is constant
Ex: Electric companies do not make energy, but convert it to a form that is
convenient for use
Ex: Plants convert sunlight to chemical energy, but does not produce sunlight for it
to create chemical energy
Ex: Consumers convert chemical energy of organic molecules in food to kinetic (and
other forms of energy as it carries out biologic processes)
Second Law of Thermodynamics every energy transfer or transformation increases the disorder
(entropy) of the universe; for a process to occur spontaneously, it must increase the entropy of the
universe
o During every energy transfer/transformation, some energy becomes unusable energy,
unavailable to do work
o More usable forms of energy are at least partly converted to heat (energy associated with
the random motion of atoms/molecules)
o Ex: Consumption of Food
A small fraction of the chemical energy from food is transformed into usable energy
Most of the chemical energy is lost as heat
o Systems can put heat to work when there are temperature differences that result in heat
flowing from warmer to cooler locations
Temperature is uniform (as it is in a living cell) heat energy during chemical
reactions warm a body of matter, such as the organism
EXAMPLE: A cheetah eating a deer
o First Law of Thermodynamics energy can be transferred or transformed but not created
nor destroyed
The chemical (potential) energy in food will be converted to the kinetic energy of
the cheetahs movement
o Second Law of Thermodynamics every energy transfer/transformation increases the
disorder (entropy) of the universe
Disorder is added to the cheetahs surroundings in the form of heat and the small
molecules that are the by-products of metabolism, such as carbon dioxide
Entropy measurement of disorder or randomness
o The more randomly arranged a collection of matter is, the greater its entropy
o Increased entropy is evident in the physical disintegration of a systems organized
structure
Ex: Gradual decay of an unmaintained building
o For a process to occur on its own, without outside help (an input of energy), it must
increase the entropy of the universe
o Spontaneous a process that can occur without an input of energy (the process could occur
instantaneously or slowly)
o Nonspontaneous a process that cannot occur on its own and can only occur if energy is
added to the system
o Ex: Water flows downhill spontaneously, but moves uphill only with an input of energy

BIOLOGICAL ORDER & DISORDER
Cells create ordered structures from less organized starting materials
o Ex: Amino acids are ordered into the specific sequences of polypeptide chains
Organisms also takes in organized forms of matter and energy from the surroundings and replaces
them with less ordered forms
o Ex: Animal obtains starch, proteins, and other complex molecules from the food it eats. As
catabolic pathways break these molecules down, the animal releases CO2 and O2 (molecules
that possess less chemical energy than the food eaten)
Energy flows into an ecosystem in the form of light and exists in the form of heat
The entropy of a particular system (such as an organism) may decrease as long as the total
entropy of the universe increases

CONCEPT CHECK 8.1
1. How does the second law of thermodynamics help explain the diffusion of a substance across a
membrane?
a. When a substance diffuses across a membrane, it goes from a high concentration to a low
concentration, or high entropy to low entropy. Since this action releases energy, this helps
to increase the entropy of the universe. Diffusion of a substance to a region where it is
initially less concentrated increases entropy, making it an energetically favorable
(spontaneous) process as described by the second law.
2. Describe the forms of energy found in an apple as it grows on a tree, then falls, and is digested by
someone who eats it.
a. As an apple forms and grows, it has chemical energy and as it hangs from the tree, it has
potential energy. If it falls onto the ground, it has kinetic energy. After it is eaten, its
molecules are broken down, and some of its chemical energy is used to do work through
kinetic energy, saved as potential energy, and lost as thermal energy.
3. What if you place a teaspoon of sugar in the bottom of a glass of water, it will dissolve completely
over time. Left longer, eventually the water will disappear and the sugar crystals will reappear.
Explain these observations in terms of entropy.
a. The sugar crystals become less ordered (entropy increases) as they dissolve and become
randomly spread out in the water. Over time, the water evaporates, and the crystals form
again because the water volume is insufficient to keep them in solution. While the
reappearance of sugar crystals may represent a spontaneous increase in order (decrease
in entropy), it is balanced by the decrease in order (increase of entropy) of the water
molecules, which changed from a relatively compact arrangement as liquid water to much
more dispersed/disordered form as water vapor.



SECTION 8.2 FREE ENERGY CHANGE OF REACTIONS DETERMINE SPONTANEITY
Universe is equivalent to the system plus the surroundings.

FREE-ENERGY CHANGE, G
1878 J. Willard Gibbs
o Free-Energy denoted by the letter G, is the portion of a systems energy that can
perform work when temperature and pressure are uniform throughout the system (Ex.
Living Cell)
o The change in free-energy, denoted by G, can be calculated for a chemical reaction with
the formula:
G = H T S
H = the change in the systems enthalpy (equivalent to total energy)
S = the change in the systems entropy
T = the absolute temperature in Kelvin (K) units (K = C + 273)
change in free energy = change in enthalpy (absolute temp.)*(change in entropy)
o Knowing G will help predict whether the process will be spontaneous (whether it will
occur without an input of an outside energy source)
Negative G are spontaneous
o Spontaneous Processes system must either:
Give up enthalpy (H must decrease)
Give up order (TS must increase)
Or both, give up enthalpy and give up order
o When H and TS are tallied, G must have a negative value (G < 0) for a spontaneous
reaction to occur
o Every spontaneous process decreases the systems free energy
Processes with a positive or zero G are never spontaneous

FREE ENERGY, STABILITY, & EQUILIBRIUM
G represents the difference between the free energy of the final state and the free energy of the
initial state:
G = G final state G initial state
G can be negative only when process involves a loss of free energy during the change from initial
state to final state.
o With less free energy, the system in its final state is less likely to change and is more stable
than before.
Free energy measure of a systems instability, its tendency to change to a more stable state.
o Unstable Systems (higher G) tend to change so that they become more stable (lower G)
Ex. Diver on top of a platform is less stable (more likely to fall) than when floating in
the water system moves towards greater stability (diver falls)
Ex. A drop of concentrated dye is less stable (more likely to disperse) than when the
dye is spread randomly through the liquid system moves towards greater stability
(solution becomes uniformly colored)
Ex. Sugar molecule is less stable (more likely to break down) than the simpler
molecules into which is can be split system moves towards greater stability (sugar
molecule breaks down)
Equilibrium describes a state of maximum stability
o Note: chemical reactions are reversible and proceed to a point at which the forward and
backward reactions occur at the same rate; said to be at chemical equilibrium, and there is
no further net change in the relative concentration of products & reactants
o Free energy (of the mixture of reactions & products) decrease when a reaction tends
toward equilibrium
Free energy decreases as reactions tend towards equilibrium
o Free energy (of the mixture of reactions & products) increases when a reaction is moves
away from equilibrium
Free energy increases as reactions move away from equilibrium
o For a system at equilibrium, G (free energy) is at its lowest possible value in that system
Any change from the equilibrium position will have a positive G and will not be
spontaneous
Process is spontaneous and can perform work only when it is moving toward
equilibrium
The relationship of free energy to stability, work capacity, and spontaneous change:

Unstable systems (top row) are rich in free energy and have a tendency to change
spontaneously to a more stable state (bottom row)
Able to harness this downhill change to perform work

FREE ENERGY & METABOLISM
Exergonic (energy outward) & Endergonic (energy inward) Reactions in Metabolism
o Exergonic Reaction proceeds with a net release of free energy
The lost of free energy (G decreases), G is negative for an exergonic reaction
Exergonic Reaction = -G
Exergonic reactions occur spontaneously
Represents the amount of work the reaction can perform
The greater the decrease in free energy, the greater the amount of work that
can be done
More G = More Work


Ex: Cellular Respiration


Each mole (180 g) of glucose broken down by cellular respiration under
standard conditions (1 M of each reaction and product, at 25C and pH 7),
686 kcal (2,870 kJ) of energy are made available for work
o Conservation of energy dictates that chemical products (in cell. resp.)
store 686 kcal less free energy per mole than the reactants
The products are the spent exhaust of a process that tapped the free energy
stored in the sugar molecules.
o Endergonic Reaction absorbs free energy from its surroundings and stores free energy in
molecules (G increases)
Positive G
Endergonic Reaction = +G
Nonspontaneous
Magnitude of G is the quantity of energy required to drive the reaction(s)
If a chemical process is exergonic (downhill), releasing energy in one direction then
the reverse process must be endergonic (uphill), using energy
Reversible processes cannot be downhill in both directions
Ex: Cellular Respiration
If G = -686 kcal/mol., then the reverse process (the conversion of carbon
dioxide and water to sugar and oxygen) must be strongly endergonic, with
G = +686 kcal/mol.
Such a reaction would never happen by itself
Plants, on the other hand, require energy from the environment by
capturing light and converting its energy to chemical energy

Equilibrium and Metabolism
o Reactions in isolated systems eventual reach equilibrium and can then do no work
o Systems are equilibrium are at a minimum of G and can do no more work (cell has reached
metabolic equilibrium and is dead)
Living cells are never in equilibrium b/c there is a constant flow of materials in and
out of the cell
Ex: Cellular Respiration
Glucose is broken down in a series of exergonic reactions that power the
work of the cell
The product of each of these reactions become the reactants for the next
reaction
Therefore, no reaction reaches equilibrium
The overall sequence of reactions is continuous by the huge free-energy
difference between glucose and oxygen at the top of the energy hill and
carbon dioxide and water at the downhill end.
CONCEPT CHECK 8.2
1. Cellular respiration uses glucose and oxygen, which have high levels of free energy, and releases
carbon dioxide and water, which have low levels of free energy. Is respiration spontaneous or not?
Is it exergonic or endergonic? What happens to the energy released from glucose?
a. Cellular respiration is a spontaneous exergonic process and the energy released from
glucose is used to either do work in the cell or is lost as heat.
2. A key process in metabolism is the transport of hydrogen ions (H+) across a membrane to create a
concentration gradient. Other processes can result in an equal concentration of hydrogen ions on
each side. Which arrangement of hydrogen ions allows the H+ to perform work in this system?
a. When the H+ concentrations are the same, the system is at equilibrium and can do no work.
H+ can perform work only if their concentrations on each side of a membrane are different
(when a gradient is present). The energy input (provided by ATP hydrolysis) is required to
establish the concentration gradient (the H+ gradient) that can in turn perform work.
3. At nightly celebrations, revelers can sometimes be seen wearing glow-in-the-dark necklaces. They
start glowing once they are activated, in a way that allows two chemicals to react and emit light
in the form of chemiluminescence. Is this exergonic or endergonic?
a. The reaction is exergonic because it releases energy in the form of light.


SECTION 8.3
ATP POWERS CELLULAR WORK BY COUPLING EXERGONIC REACTIONS TO ENDERGONIC REACTIONS
A cell has three main kinds of jobs:
o Chemical Work the pushing of endergonic reactions, which would not occur
spontaneously, such as the synthesis of polymers from monomers.
o Transport Work the pumping of substances across membranes against the direction of
spontaneous movement
o Mechanical Work such as the beating of cilia, the contraction of muscle cells, and the
movement of chromosomes during cellular reproduction
Energy coupling the use of an exergonic process to drive an endergonic process
o ATP is responsible for mediating most energy coupling in cells
o ATP acts as the immediate source of energy that powers cellular work

Structure and Hydrolysis of ATP
Adenosine triphosphate (ATP) contains the sugar ribose, with the nitrogenous adenine base, and
a chain of three phosphate groups bonded to it
o
o Note: Aside from its role in energy coupling, ATP is also one of the nucleoside
triphosphates used to make ribonucleic acid (RNA)
o Bonds between the phosphate groups in ATP can be broken by hydrolysis
When a terminal phosphate bond is broken, a molecule of inorganic phosphate
leaves the ATP and becomes adenosine diphosphate (ADP)
Reaction is exergonic and releases 7.3 kcal of energy per mole of ATP hydrolyzed

Above is the free-energy change measured under standard conditions
In the cell, conditions do not conform to standard conditions b/c reaction
and product concentrations differ from 1 M.
Since hydrolysis releases energy, the phosphate bonds of ATP are sometimes
referred to as high-energy phosphate bonds (but the bonds are not unusually strong
bonds)
The reactants (ATP and water) have high energy relative to the energy of the
products (ADP and the inorganic phosphate (P))
o Hydrolysis of ATP the reaction of ATP and water yields inorganic phosphate, ADP, and
energy

The release of energy comes from the chemical change to a state of lower free
energy, not from the phosphate bonds
o ATP is useful b/c the energy it releases on losing a phosphate group is somewhat greater
than the energy most other molecules could deliver
o Hydrolysis releases so much energy
All three phosphate groups in the ATP molecule are negatively charged
Negatively charges crowd together and their mutual repulsion contributes to the
instability of this region of the ATP molecule

How ATP Performs Work
Shivering in humans uses ATP hydrolysis
during muscle contraction to generate heat
and warm the body
In most cases in the cell, the generation of
heat alone would be an inefficient (and
potentially dangerous) use of a valuable
energy resource
o Instead, cells proteins use the energy
released during ATP hydrolysis in
several ways to perform chemical,
transport, and mechanical works.
Ex: Energy coupling using ATP hydrolysis
(right)
o The exergonic process of ATP
hydrolysis is used to drive an
endergonic process
Cellular synthesis of the amino
acid glutamine from glutamic
acid and ammonia
Cells can use the energy released by ATP
hydrolysis (with the help of specific
enzymes) to drive chemical reactions that, by
themselves, are endergonic
o If G of an endergonic reaction is less
than the amount of energy released by
ATP hydrolysis, then the two reactions
can be coupled so that the coupled
reactions are exergonic.
Involves the transfer of a
phosphate group from ATP to
some other molecule (reactant)
Phosphorylated recipient of the phosphate group
Key to coupling exergonic and endergonic reactions is the formation of this
phosphorylated intermediate, which is more reactive and less stable than the
original unphosphorylated molecule
Transport & Mechanical works in the cell are powered by the hydrolysis of ATP
o ATP hydrolysis leads to a change in a proteins shape and often its ability to bind another
molecule (sometimes occurs through a phosphorylated intermediated)
o Mechanical work involving motor proteins walking along cytoskeletal elements
ATP is first bound noncovalently to the motor protein
ATP is then hydrolyzed, releasing ADP and inorganic phosphate
Another ATP molecule can then bind
At each stage, the motor protein changes its shape and ability to bind the
cytoskeleton, resulting in movement of the protein along the cytoskeletal track
o Quick Summary:
ATP hydrolysis causes changes in the shapes & binding affinities of proteins, which
can occur either:
(A) DIRECTLY by phosphorylation, as shown for the membrane proteins
involved in active transport of solutes
(B) INDIRECTLY by noncovalent binding of ATP and its hydrolytic
products, as is the case for motor proteins that move vesicles (and
organelles) along cytoskeletal tracks in the cell



The Regeneration of ATP
ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP
o The free energy required to add a phosphate group to ADP comes from exergonic
breakdown reactions (catabolism) in the cell, called the ATP cycle
o ATP cycle couples the cells energy-yielding (exergonic) process to the energy-consuming
(endergonic) ones
ATP-Cycle

o Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate
ADP, regenerating ATP.
o Chemical potential energy stored in ATP drives most cellular work
o Both directions of a reversible process cannot go downhill, the regeneration of ATP from
ADP and (P) is endergonic

o ATP from ADP and (P) is not spontaneous
Free energy must be spent to make ATP-Cycle work
Catabolic (exergonic) pathways provide the energy for the endergonic process of
making ATP
Plants use light energy to produce ATP
o ATP-Cycle is a turnstile through which energy passes during its transfer from catabolic to
anabolic pathways.
Note: Catabolic & anabolic pathways are the downhill and uphill avenues of the
metabolic map
Energy released from the downhill reactions of catabolic pathways can be stored
and then used to drive the uphill reactions of anabolic pathways
CONCEPT CHECK 8.3
1. In most cases, how does ATP transfer energy from exergonic to endergonic reactions in the cell?
a. ATP usually transfers energy to endergonic processes by phosphorylating (adding
phosphate groups to) other molecules. Exergonic processes phosphorylate ADP in order to
regenerate ATP.
2. Which of the following combinations has more free energy:
a. glutamic acid + ammonia + ATP
b. glutamine + ADP + (P)
c. A set of coupled reactions can transform the first combination into the second. Since this is
an exergonic process overall, G is negative and the first combination must have more free
energy.