AP Bio Chapter Six An Introduction To Metabolism

1
UNIT ONE: THE CHEMISTRY OF LIFE

Chapter
Chapter Six: An Introduction To Metabolism
(Text from Biology, 6th Edition, by Campbell and Reece)

METABOLISM, ENERGY, AND LIFE
Metabolism is the sum total of all chemical reactions in an organism.
The Chemistry of Life is Organized Into Metabolic Pathways
The thousands of chemical reactions in the cell are arranged in

intricate metabolic pathways that alter molecules in a step-by-step
fashion. Metabolism manages the material and energy resources of
the cell. Catabolic pathways release energy by breaking down
complex molecules to simpler compounds. An example of such
pathway is cellular respiration, in which glucose and other fuels are
broken down into carbon dioxide and water. Anabolic pathways
consume energy to build complicated molecules from simpler ones.
An example is the building of a protein from amino acids.
Catabolic and anabolic pathways transfer energy – the energy

produced by catabolism is used to power anabolism. This transfer is
called energy coupling.
The concepts in this chapter are central to bioenergetics,

bioenergetics the study
of how organisms manage their energy resources.
Organisms Transform Energy
Energy is the capacity to do work. Cells must be able to transform energy from one type into another.
Anything that moves has kinetic energy,

energy the energy of motion. Moving objects perform work through
imparting motion to other matter. Light is also a type of kinetic energy – light can power
photosynthesis. Heat is kinetic energy that results from the random movement of molecules.
Resting objects have stored energy, or potential energy,

energy the energy matter
possesses because of its location or structure. Chemical energy is a form of
potential energy stored in molecules because of the arrangement of atoms in those
molecules.
An example of potential energy being transformed into kinetic energy can be seen
by a ball being thrown into the air – when the ball is highest, there is the most
potential energy. This becomes kinetic energy as the ball moves toward the
ground. When chemical reactions rearrange the atoms of molecules in such a way
that potential energy in the molecules is converted into kinetic, chemical energy
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can be used. Cellular respiration and other catabolic pathways can release stored energy in molecules
and make it available to the cell.
The Energy Transformations of Life Are Subject To Two Laws of Thermodynamics
Thermodynamics is the study of the energy transformations that occur in a collection of matter. The
term system is used to refer to matter being studied, while everything outside the system is referred to
as surroundings. A closed system is isolated from its surroundings. In an open system, energy and
matter can be transferred between the system and its surroundings. Organisms are considered open
systems, since they can absorb energy (light or chemical) and release waste products to the
surroundings. Two laws of thermodynamics are central in energy transformations in organisms as well
as all matter.
The First Law of Thermodynamics
The first law of thermodynamics states that the energy of the universe is constant: energy can be
transferred and transformed, but it cannot be created or destroyed. This law is also known as the
principle of conservation of energy.
The Second Law of Thermodynamics
The main idea behind the second law of thermodynamics is that every
energy transfer or transformation makes the universe more disordered.
Entropy is a measure of disorder and randomness. The greater entropy a
collection of matter has, the more disorganized it is. Thus, the second law
can also be written as: every energy transfer increases the entropy of the
universe.
Increasing entropy can be easy to observe in cases of physical

disintegration – think of an old building crumbling to the ground.
Increasing heat is also increasing entropy, since heat is the energy of
random molecular motion. In most energy transformations, ordered forms
of energy are at least partly converted into heat.
Although forms of energy have been converted to heat, the first law of thermodynamics is still upheld,
since heat is a form of energy. While the quantity of energy in the universe is constant, the quality of
the energy is not. Heat can be put to work only when there is a temperature difference that results in
heat moving from a warmer location to a cooler one – as a result, it can be seen as the “lowest grade”
of energy.
While cells created ordered structures from less organized starting materials, organisms also take in
organized forms of matter and break them down into less ordered forms. For example, animals take in
starch, proteins, and complex molecules, then break them down, releasing carbon dioxide and water.
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Chapter
Energy flows into an ecosystem as light, and then leaves as heat. Living systems ultimately increase
entropy of their surroundings.
Additionally, while the entropy of a particular system can decrease,

decrease, the total entropy of the entire
universe increases.
Organisms Live at the Expense of Free Energy
A spontaneous process is a change that can occur without outside assistance. Such changes can be
harnessed to perform work. For example, the downhil
downhilll flow of water can be used to turn a windmill to
generate power. Nonspontaneous processes will only occur if energy is added to the system. For
example, cells must expend energy to create a protein about amino acids.
The stability of a system increases when a spontaneous process occurs. Unstable systems tend to
change in a way that they become stable. For example, a body of water in a reservoir is less stable
than the same water at sea level. The water will fall in order move toward greater stability (once the
reservoir wall is removed). A standard for spontaneous process is free energy.
Free Energy: A Criterion for Spontaneous Change
Free energy is the portion of a system’s energy that can perform work when temperature is uniform
throughout the system. It is termed “free” because it is available for work.
  

    
G<0)
    
    
 

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A system’s quantity of free energy is symbolized by G. The two components of G are the system’s total
energy (H) and its entropy (S).
G = H – TS, where T is absolute temperature in Kelvin.
Since temperature measures the intensity of heat (random molecular motion), it is important to the
equation. Not all energy stored in a system (H) is available for work. The entropy factor (disorder) is
subtracted from the total energy to determine the maximum capacity of useful work the system can
perform. Free energy is then less than the system’s total energy.
Free energy G is a measure of how unstable a system is. Systems rich in energy or highly organized
systems are unstable and want to change to a more stable state. In other words, these systems have
high energy, low entropy, or both – they are more likely to change spontaneously into a more stable
state. In any spontaneous process, the free energy of a system decreases.
G = H – TS
For a process to occur spontaneously, the system must either give up energy (decrease H), give up
order (an increase in S), or both. Once these changes occur, G must have a negative value (G < 0).
The greater the decrease in free energy, the greater the maximum amount of work the spontaneous
process can perform.
Free Energy and Equilibrium
Maximum stability is equilibrium, where G = 0. As a reaction proceeds toward equilibrium, the free
energy of the mixture of reactants and products decreases. Free energy increases when a reaction is
pushed away from equilibrium. When G = 0, there is no net change in the system and equilibrium has
been reached. A chemical reaction at equilibrium performs no work. A process is spontaneous and can
perform work when sliding toward equilibrium. Movement away from equilibrium is nonspontaneous
and can only occur with the help of an outside energy source.
Equilibrium is an energy valley:
Spontaneous Nonspontaneous
Process: Process:
Does not require Requires an outside

input of energy energy source
Example: water Example: machine

Equilibrium (G = 0) pumps water up against
flowing downhill
gravity
Exergonic Reaction
Endergonic Reaction
-G
+G
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Chapter
Free Energy and Metabolism
Exergonic and Endergonic

Endergonic Reactions in Metabolism
Chemical reactions can be classified as either exergonic (“energy outward”) or endergonic (“energy
inward”). An exergonic reaction proceeds with a net release of free energy. Since the mixture loses
free energy, G is negative. (Remember – free energy (G) moves out from the reactants, so G is
negative). Exergonic reactions are those that occur spontaneously. The magnitude of G is the
maximum amount of work the
reaction can perform.
An endergonic reaction is one

that absorbs free energy from its
surroundings. This takes free
energy from the surroundings and
stores it in molecules, which
makes G positive. (Free energy
(G) is moving into the products,
so there is a positive G). These
reactions are nonspontaneous,
and the magnitude of G is the
quantity of energy required to
power the reaction.
Metabolic Disequilibrium
In a closed system, reactions will reach equilibrium and be unable to do work. A cell that reaches
metabolic disequilibrium is dead – no work is being performed. Thus, metabolic disequilibrium is
extremely important for life.
Since a cell is an open system, it can maintain disequilibrium. The constant transfer of materials in and
out of the cell prevents the metabolic pathways from reaching equilibrium. A catabolic pathway in a
cell releases free energy in a serious of reactions. The product of one reaction never continually
accumulates: instead, it becomes the reactant in the next step. The overall sequence of reactions is
powered by the large free-energy difference between glucose and the carbon dioxide and water (waste
products) at the end.
Free energy is transmitted to an ecosystem through sunlight – animals and nonphotosynthetic

organisms depend on free-energy transfusions in the form of the products of photosynthesis.
Remember that energy coupling is the use of an exergonic process to drive an endergonic one.
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Chapter
ATP Powers Cellular Work by Coupling Exergonic Reactions to Endergonic Reactions
A cell does:
1. Mechanical work, such as the contraction

contraction of muscle cells or the beating of cilia
2. Transport work, pumping substances across membranes against the direction of spontaneous
movement
3. Chemical work, the pushing of endergonic reactions that would not occur spontaneously, such
as synthesizing polymers
lymers from monomers
ATP is usually the source of energy powering cellular work.
The Structure and Hydrolysis of ATP
ATP (adenosine triphosphate) is closely related

to one type of nucleotide found in nucleic acids.
ATP has the nitrogenous base adenine bonded
b to
ribose. It is very similar to an adenine nucleotide
in RNA.
The bonds between the phosphate groups in ATP

can be broken by hydrolysis. When the end
phosphate bond is broken, a molecule of inorganic
phosphate leaves the ATP, which now becomes
ADP (adenosine disphosphate). This is an
exergonic reaction that releases 7.3 kcal of energy
per mole of ATP hydrolyzed.
However, that was the free-energy

energy change measured in laboratory conditions. In the cell, the actual
G is about -13
13 kcal/mole, which is 78% greater than the energy released in the standard laboratory
conditions. Since the hydrolysis of the phosphate bonds release energy, the bonds are sometimes
referred to as high-energy
energy phosphate bonds. Be careful to not see “high-energy”
energy” and think that the
bonds are unusually strong – “high-energy”
“high energy” in this case means that the hydrolysis yields energy. In
fact, the bonds are relatively weak and unstable, which allows for the energy released when they are
broken. The ADP and phosphate are more stable than the ATP. Thus, the change is exergonic – free
energy is being released to create stability.
Since the phosphate groups are all negatively charged, being bonded together so closely results in
instability of the bonds.
s. This is comparable to a loaded spring.
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Chapter
How ATP Performs Work
A cell can couple the energy of ATP hydrolysis directly to

endergonic processes by transferring a phosphate group
from ATP to some other molecule. The molecule that
receives the phosphate group is said to have been
phosphorylated.
phosphorylated Once a molecule is phosphorylated, it
becomes more reactive than the original, which helps
create a spontaneous reaction.
The diagram at right illustrates how phosphorylation can

induce spontaneous reactions.
(a) Normally, the formation of glutamine is

nonspontaneous and requires 3.4 kcal/mol.
(b) With ATP present, glutamic acid becomes

phosphorylated, making it more reactive. Thus, it will
spontaneously join with ammonia.
(c) The originally endergonic process became exergonic with the help of ATP.
The Regeneration of ATP
An organism at work constantly uses ATP, but ATP is a renewable resource. When a phosphate group
is added to ADP, ATP can be created. The free energy required to phosphorylate ADP comes from
catabolism in the cell. The ATP cycle is a coupling of the cell’s energy-yielding processes to the
energy-producing ones. This cycle moves extremely quickly: a working muscle cell can recycle its
entire supply of ATP about once each minute.
The regeneration of ATP from ADP is endergonic – it is an example of anabolism in the cell. Catabolic
pathways, especially cellular respiration, provide energy for the endergonic process of making ATP.
ENZYMES
Enzymes Speed up Metabolic Reactions by Lowering Energy Barriers
A catalyst is a chemical agent that changes the rate of a reaction without being consumed by the
reaction; an enzyme is a catalytic protein (ribozymes, made up of RNA, are also enzymes).
The Activation Energy Barrier
Every chemical reaction between molecules involves both bond breaking and bond forming. For
example, hydrolyzing a sucrose molecule involves breaking the bonds between glucose and fructose,
then bonding the hydrogen and hydroxyl group to make water. Whenever a reaction rearranges the
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Chapter
atoms of molecules, existing bonds must be broken and new bonds of the product must be formed.
The reactant molecules absorb energy from their surroundings (free energy) to break, and then release
the energy when the new bonds of the product molecules are formed.
The energy required to start a reaction (break the bonds) is the free energy of activation,
activation also known
as activation energy (EA). It is usually provided through heat the molecules absorb. When the
molecules absorb enough energy to become unstable, the bonds will break. Remember, systems rich in
free energy become unstable, and seek to become stable (breaking bonds). The speed of the reactant
molecules is increased as they absorb more heat, which makes the molecules collide more often and
more forcefully. When the molecules settle into a new, more stable
bonding arrangement, energy is released into the surroundings. If
the reaction was exergonic, EA will be repaid, since the formation of
the new bonds will give off more energy than was invested in the
activation energy.
In the graph of a reaction, the free energy of activation is

represented as the energy needed to push the reactants over a hill,
where the “downhill” portion is where the reaction actually takes
place. The graph at right shows hypothetical molecules being
rearranged in a chemical reaction. This is an exergonic reaction,
since the products have less free energy than the reactants.
Enzymes and Activation Energy
Proteins, DNA, and other complex molecules are rich in free

energy and have the potential to break down spontaneously.
They exist only because only a few molecules have sufficient
activation energy at a cell’s temperature to break them apart.
Occasionally, the barrier for certain reactions must be lowered,
or else metabolism could not take place. While heat speeds a
reaction, too much heat will kill cells. Thus, organisms use
catalysts.
Through lowering the AE barrier, the transition stage is

accessible even at moderate temperatures. An enzyme does
not change the G for a reaction. It only speeds up reactions that would eventually occur. Since
enzymes are so selective about which reactions they catalyze, they determine which chemical
processes will be occurring in the cell.
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Chapter
Enzymes are Substrate Specific
The reactant an enzyme acts on is referred to as its substrate.

substrate The enzyme binds to its substrate (or
substrates). When the two are joined, the catalytic action of the enzyme changes the substrate to the
product of the reaction.
An enzyme can distinguish its substrate from even closely related compounds, such as isomers, so that
each type of enzyme catalyzes a particular reaction. For instance, sucrose will only accept sucrose.
Enzymes, as proteins, have a unique three-dimensional shape that allows them to recognize their
substrates.
A restricted region of the enzyme molecule binds to the substrate – this region is the active site,
site and
is typically a pocket or groove on the surface of the protein. While the active site is formed by only a
few of the enzyme’s amino acids, the R groups play a large part in reinforcing the shape of the active
site. When the substrate enters the active site, it induces the enzyme to change in its shape slightly
so the active site fits even more snugly around the substrate. This induced fit brings chemical groups
of the active site into positions that help the enzyme catalyze the chemical reaction.
The Active Site is the Enzyme’s Catalytic Center
In an enzymatic reaction, the substrate binds to

the active site to form an enzyme-substrate
complex. The substrate is usually held in the
active site with weak bonds, such as hydrogen or
ionic bonds. Side chains of a few of the amino
acids in the active site catalyze the conversion of
substrate to product, and the product departs
from the active site. The enzyme can then take
another substrate molecule into its active site.
The entire cycle happens quickly, and a single
enzyme molecule can act on a thousand
substrate molecules per second.
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Chapter
An enzyme can catalyze both the forward and reverse reactions of reversible metabolic reactions.
Enzymes catalyze in the direction of equilibrium: if there is more A than B, enzymes will transform B to
A and vice versa.
There are different ways enzymes can lower activation energy and speed up a reaction. In reactions
involving two or more reactants, the active site provides a template for the substrates to come
together in the proper position for a reaction to occur. As the active site folds around the substrates,
the enzyme may stress the substrate molecules in order to stretch and bend critical chemical bonds
that need to broken. EA involves the energy needed to break bonds, thus, distorting the substrate
reduces the amount of heat energy needed to reach the transition state.
The active site could also provide a small environment that is conducive to a particular type of
reaction. For example, if the active site has amino acids with acidic side chains, the active site could
be a pocket of low pH in an otherwise neutral cell. The active site could move H+ into the substrate as
a key step in catalyzing the reaction.
Another mechanism involves brief covalent bonding between the substrate and a side chain of an
amino acid of the enzyme. Of course, the reaction will always restore the side chains to their original
state in order to keep the active site the same as before.
The rate at which a certain amount of enzyme converts substrate to product is partly a function of the
initial concentration of the substrate. The more substrate molecules there are, the more frequently
they can access the active sites of enzyme molecules. However, at a certain point, all enzymes will be
busy converting substrates and adding more substrate will not speed up the reaction. The enzyme is
said to be saturated at the point when enzymes are constantly converting substrates. The rate of the
reaction can then be determined by the speed at which the active site can convert substrate to
product. When an enzyme population is saturated, the only way to increase productivity is to add
more enzymes.
A Cell’s Physical and Chemical Environment Affects Enzyme Activity 
Effects of Temperature and pH


As a protein, an enzyme has conditions in which it works

optimally, because that environment favors the most active
conformation for the enzyme molecule.
Up to a point, the velocity of an enzymatic reaction will increase

with increasing temperature, partly because substrates will
collide with active sites more frequently when moving quickly.
Beyond a certain point, the speed will drop sharply, since too
much heat will denature the enzyme, which after all, is a protein. 
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Chapter
(Text from Biology, 6th Edition, by Campbell and Reece) 
The temperature to the left of the optimal temperature-mark

(dotted line) is perfectly fine for the enzyme. Although it may be
too cold to catalyze a reaction, the enzyme will still be in its
original form. After the optimal temperature, right of the dotted
line, the enzyme will be denatured.
Just as an enzyme has an optimal temperature, it also has a pH

at which it is most active. Most enzymes work best from pH 6-
8, but there are exceptions. Unlike temperature, enzymes
cannot fall too far down either side, or they will denature. If they 
become either too acidic or too basic, they denature. In the
diagram to the right, the area within the dotted line denotes the
acceptable range for the hypothetical enzyme.
Cofactors
Many enzymes require nonprotein helpers for catalytic activity. These adjuncts, called cofactors,
cofactors may
be bound tightly to the active site as permanent residents, or they could bind loosely and reversibly
along with the substrate. Some cofactors are inorganic, such as zinc, iron, and copper ions. If the
cofactor is an organic molecule, it is called a coenzyme.
coenzyme Most vitamins are coenzymes or raw
materials from which coenzymes are made.
Enzyme Inhibitors
Certain chemicals selectively prevent the action of specific

enzymes. If the inhibitor attaches to the enzyme with covalent
bonds, inhibition is usually permanent. However, reversible
inhibition occurs when the inhibitor binds with weak bonds.
Some reversible inhibitors are competitive inhibitors,

inhibitors
resembling the normal substrate and competing for entrance
into the active site. They can reduce the productivity of
enzymes by physically blocking the substrate from entering the
active site. This kind of inhibition can be overcome by
increasing substrate content where more substrate molecules
than inhibitor molecules are available to enter the sites.
Noncompetitive inhibitors do not directly compete with the

substrate. Instead, they bind to another part of the enzyme,
which causes the active site to change shape and either
become unreceptive to substrate or less effective at catalyzing
conversion of substrate to product.
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Chapter
THE CONTROL OF METABOLISM
All a cell’s metabolic pathways are not open at the same time. A cell carefully regulates when and
where various enzymes are active by either switching on and off the genes that encode specific
enzymes or regulating the activity of enzymes.
Metabolic Control Often Depends on Allosteric Regulation
In many cases, molecules that naturally regulate enzyme activity in the cell behave like reversible
noncompetitive inhibitors. They change an enzyme’s shape and function by binding weakly to an
Allosteric site,
site a specific receptor site on some part of the enzyme molecule away from the active site.
It can either inhibit or stimulate the enzyme’s activity through binding to it.
Allosteric Regulation
Most allosterically regulated enzymes are constructed from

two or more polypeptide subunits. Each subunit has its own
active site, and allosteric sites are often located where two
subunits are joined. The entire complex switches between
the two conformational states, of which one is active and
one is inactive. The binding of an activator to an allosteric
site stabilizes the shape with a functional active site, while
the binding of an inhibitor stabilizes the inactive form of the
enzyme. The areas of contact between the subunits of an
allosteric enzyme fit in such a way that a conformation
change in one subunit is transmitted to all others. Thus, a
single activator or inhibitor molecule binding to one allosteric
site will affect the active sites of all subunits.
Sometimes, an inhibitor and an activator are similar enough

in shape to compete for the same allosteric site. For
example, some enzymes of catabolic pathways may have an
allosteric site fitting both AMP (adenosine monophosphate) and ATP, being activated by AMP and
inhibited by ATP. This makes sense because a purpose of catabolism is to make ATP: if there are too
many AMP, it will stimulate key enzymes to speed up catabolism and make more ATP. If there is a
large supply of ATP, the ATP will compete for allosteric sites and slow down the catabolism.
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Chapter
Feedback Inhibition
Feedback inhibition is the switching off of a

metabolic pathway by its end product, which acts as
an inhibitor of an enzyme within the pathway. Once
the end product accumulates in enough numbers, it
will allosterically inhibit the enzyme for the first step
of the pathway. This prevents the cell from wasting
chemical resources to synthesize more of a product
than necessary.
Cooperativity
Similar to allosteric activation, substrate molecules may

stimulate the catalytic powers of an enzyme. Recall that the
binding of a substrate to an enzyme can induce a favorable
change in the shape of the enzyme’s active site. If an
enzyme has two or more subunits, an interaction with one
substrate molecule can trigger the same conformational
change in all other subunits. Called cooperativity
cooperativity,
vity this
mechanism amplifies the response of enzymes to substrates:
one substrate molecule primes an enzyme to accept
additional substrate molecules more readily.
The Localization of Enzymes Within a Cell Helps Order Metabolism
Structures within the cell help bring order to metabolic pathways. In some cases, enzymes for several
steps of a metabolic pathway are arranged together as a multienzyme complex. The arrangement helps
control the sequence of reactions. Some enzymes and enzyme complexes have fixed locations in the
cell as structural components. Others are in solution with specific membrane-enclosed eukaryotic
organelles, each with its own internal chemical environment. For example, enzymes used in cellular
respiration are kept within mitochondria.

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1

UNIT ONE: THE CHEMISTRY OF LIFE

Metabolism is the sum total of all chemical reactions in an organism.

The Chemistry of Life is Organized Into Metabolic Pathways

The thousands of chemical reactions in the cell are arranged in

Catabolic and anabolic pathways transfer energy – the energy

The concepts in this chapter are central to bioenergetics,

Organisms Transform Energy

Anything that moves has kinetic energy,

Resting objects have stored energy, or potential energy,

The Energy Transformations of Life Are Subject To Two Laws of Thermodynamics

The First Law of Thermodynamics

The Second Law of Thermodynamics

Increasing entropy can be easy to observe in cases of physical

Additionally, while the entropy of a particular system can decrease,

Organisms Live at the Expense of Free Energy

Free Energy: A Criterion for Spontaneous Change

  

G = H – TS, where T is absolute temperature in Kelvin.

Free Energy and Equilibrium

Equilibrium is an energy valley:

Does not require Requires an outside

Example: water Example: machine

Free Energy and Metabolism

Exergonic and Endergonic

An endergonic reaction is one

Free energy is transmitted to an ecosystem through sunlight – animals and nonphotosynthetic

ATP Powers Cellular Work by Coupling Exergonic Reactions to Endergonic Reactions

1. Mechanical work, such as the contraction

ATP is usually the source of energy powering cellular work.

The Structure and Hydrolysis of ATP

ATP (adenosine triphosphate) is closely related

The bonds between the phosphate groups in ATP

However, that was the free-energy

How ATP Performs Work

A cell can couple the energy of ATP hydrolysis directly to

The diagram at right illustrates how phosphorylation can

(a) Normally, the formation of glutamine is

(b) With ATP present, glutamic acid becomes

The Regeneration of ATP

Enzymes Speed up Metabolic Reactions by Lowering Energy Barriers

The Activation Energy Barrier

In the graph of a reaction, the free energy of activation is

Enzymes and Activation Energy

Proteins, DNA, and other complex molecules are rich in free

Through lowering the AE barrier, the transition stage is

Enzymes are Substrate Specific

The reactant an enzyme acts on is referred to as its substrate.

The Active Site is the Enzyme’s Catalytic Center

In an enzymatic reaction, the substrate binds to

A Cell’s Physical and Chemical Environment Affects Enzyme Activity 

Effects of Temperature and pH

As a protein, an enzyme has conditions in which it works

Up to a point, the velocity of an enzymatic reaction will increase

The temperature to the left of the optimal temperature-mark

Just as an enzyme has an optimal temperature, it also has a pH

Certain chemicals selectively prevent the action of specific

Some reversible inhibitors are competitive inhibitors,

Noncompetitive inhibitors do not directly compete with the

THE CONTROL OF METABOLISM

Metabolic Control Often Depends on Allosteric Regulation

Most allosterically regulated enzymes are constructed from