5887255 ap bio chapter six an introduction to metabolism
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1UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
METABOLISM, ENERGY, AND LIFE
MetabolismMetabolismMetabolismMetabolism 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. Catabol ic pathwaysCatabolic pathwaysCatabolic pathwaysCatabolic 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 pathwaysAnabolic pathwaysAnabolic pathwaysAnabolic 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 bioenergeticsbioenergeticsbioenergeticsbioenergetics, the study
of how organisms manage their energy resources.
Organisms Transform Energy
EnergyEnergyEnergyEnergy is the capacity to do work. Cells must be able to transform energy from one type into another.
Anything that moves has kinetic energykinetic energykinetic energykinetic 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 energypotential energypotential energypotential energy, the energy matter
possesses because of its location or structure. Chemical energyChemical energyChemical energyChemical energy is a form ofpotential 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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2UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
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
ThermodynamicsThermodynamicsThermodynamicsThermodynamics is the study of the energy transformations that occur in a collection of matter. The
term systemis used to refer to matter being studied, while everything outside the system is referred to
as surroundings. A closed systemis 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 ofThe first law ofThe first law ofThe first law of thermodynamicsthermodynamicsthermodynamicsthermodynamics 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 thermodynamicsthe second law of thermodynamicsthe second law of thermodynamicsthe second law of thermodynamics is that every
energy transfer or transformation makes the universe more disordered.
EntropyEntropyEntropyEntropy 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 quantityof energy in the universe is constant, the qualityof
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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UNIT ONE: THE CHEMISTRY OChChChChapter Six: An Introductionapter Six: An Introductionapter Six: An Introductionapter Six: An Introduction(Text from Biology, 6th Edition,
Energy flows into an ecosystem
entropy of their surroundings.
Additionally, while the entropy
universeincreases.
Organisms Live at the Expense
A spontaneous process is a cha
harnessed to perform work. For
generate power. Nonspontane
example, cells must expend en
The stability of a system increa
change in a way that they beco
than the same water at sea lev
reservoir wall is removed). A st
Free Energy: A Criterion for Spo
Free energyFree energyFree energyFree energy is the portion of a
throughout the system. It is te
LIFEo Metabolismo Metabolismo Metabolismo Metabolismy Campbell and Reece)
as light, and then leaves as heat. Living syste
of a particular system can decrease, the total e
f Free Energy
ge that can occur without outside assistance.
example, the downhill flow of water can be us
us processes will only occur if energy is added t
rgy to create a protein about amino acids.
es when a spontaneous process occurs. Unsta
e stable. For example, a body of water in a re
l. The water will fall in order move toward grea
ndard for spontaneous process is free energy.
taneous Chang
ystems energy that can perform work when te
med free because it is available for work.
G
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5UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
Free Energy and Metabolism
Exergonic and EndExergonic and EndExergonic and EndExergonic and Endergonic Reactions in Metabolismergonic Reactions in Metabolismergonic Reactions in Metabolismergonic Reactions in Metabolism
Chemical reactions can be classified as either exergonic (energy outward) or endergonic (energy
inward). An exergonic reactionexergonic reactionexergonic reactionexergonic reaction proceeds with a net release of free energy. Since the mixture loses
free energy, G is negative. (Remember free energy (G) moves outoutoutout from the reactants, so G is
negative). Exergonic reactions are those that occur spontaneously. The magnitude ofG is the
maximum amount of work the
reaction can perform.
An endergonic reactionendergonic reactionendergonic reactionendergonic 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 intointointointo the products,
so there is a positive G). These
reactions are nonspontaneous,
and the magnitude ofG is the
quantity of energy required to
power the reaction.
Metabolic DisequilibriumMetabolic DisequilibriumMetabolic DisequilibriumMetabolic 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 couplingenergy couplingenergy couplingenergy coupling is the use of an exergonic process to drive an endergonic one.
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UNIT ONE: THE CHEMISTRY OChChChChapter Six: An Introductionapter Six: An Introductionapter Six: An Introductionapter Six: An Introduction(Text from Biology, 6th Edition,
ATP Powers Cellular Work by C
A cell does:
1. Mechanical work, such2. Transport work, pumpin
movement
3. Chemical work, the pusas synthesizing polymer
ATP is usually the source of ene
The Structure and Hydrolysis o
ATP (adenosine triphosphate)ATP (adenosine triphosphate)ATP (adenosine triphosphate)ATP (adenosine triphosphate)
to one type of nucleotide found
ATP has the nitrogenous base a
ribose. It is very similar to an a
in RNA.
The bonds between the phosph
can be broken by hydrolysis. W
phosphate bond is broken, a mo
phosphate leaves the ATP, whic
ADP (adenosine disphosphate).
exergonic reaction that release
per mole of ATP hydrolyzed.
However, that was the free-en
G is about -13 kcal/mole, whi
conditions. Since the hydrolysi
referred to as high-energy phos
bonds are unusually strong h
fact, the bonds are relatively wbroken. The ADP and phosphat
energy is being released to crea
Since the phosphate groups are
instability of the bonds. This is
LIFEo Metabolismo Metabolismo Metabolismo Metabolismy Campbell and Reece)
upling Exergonic Reactions to Endergonic Reac
as the contraction of muscle cells or the beatin
g substances across membranes against the dir
hing of endergonic reactions that would not occ
s from monomers
rgy powering cellular work.
ATP
is closely related
in nucleic acids.
denine bonded to
enine nucleotide
te groups in ATP
hen the end
lecule of inorganic
h now becomes
This is an
7.3 kcal of energy
rgy change measured in laboratory conditions.
h is 78% greater than the energy released in th
of the phosphate bonds release energy, the bo
hate bonds. Be careful to not see high-energ
igh-energy in this case means that the hydroly
ak and unstable, which allows for the energy ree are more stable than the ATP. Thus, the chan
e stability.
all negatively charged, being bonded together s
comparable to a loaded spring.
6
ions
of cilia
ction of spontaneous
ur spontaneously, such
In the cell, the actual
standard laboratory
ds are sometimes
and think that the
sis yields energy. In
leased when they aree is exergonic free
o closely results in
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8UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
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 activationfree energy of activationfree energy of activationfree energy of activation, also known
as activation energyactivation energyactivation energyactivation 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 ofthe 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 cells 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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9UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
Enzymes are Substrate Specific
The reactant an enzyme acts on is referred to as its substratesubstratesubstratesubstrate. 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 siteactive siteactive siteactive 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 enzymes 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 f itinduced fitinduced fitinduced fit brings chemical groups
of the active site into positions that help the enzyme catalyze the chemical reaction.
The Active Site is the Enzymes 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 aminoacids 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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10UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
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 ofreaction. 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 bebusy 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 Cells Physical and Chemical Environment Affects Enzyme Activity
Effects of Temperature and pH
As a protein, an enzyme has conditions in which it worksoptimally, 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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11UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(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 theacceptable range for the hypothetical enzyme.
Cofactors
Many enzymes require nonprotein helpers for catalytic activity. These adjuncts, called cofactorscofactorscofactorscofactors, 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 coenzymecoenzymecoenzymecoenzyme. 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 inhibitorscompetitive inhibitorscompetitive inhibitorscompetitive 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 inhibitorsNoncompetitive inhibitorsNoncompetitive inhibitorsNoncompetitive 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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12UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
THE CONTROL OF METABOLISM
All a cells 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 enzymes shape and function by binding weakly to an
Allosteric siteAllosteric siteAllosteric siteAllosteric site, a specific receptor site on some part of the enzyme molecule away from the active site.
It can either inhibit or stimulate the enzymes 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 theenzyme. 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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13UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)
Feedback Inhibition
Feedback inhibitionFeedback inhibitionFeedback inhibitionFeedback 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 enzymes 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 cooperaticooperaticooperaticooperativityvityvityvity, 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.