An Introduction to
AP Biology Chapter 6
• Metabolism is the sum total of all chemical
reactions involved in maintaining the living
state of the cells, and thus the organism.
• In general metabolism may be divided into
– catabolism or the break down of molecules to
– anabolism or the synthesis of all compounds
needed by the cells.
• Bioenergetics is a term which describes
the biochemical or metabolic pathways by
which the cell ultimately obtains energy.
• Nutrition is a science that deals with the
relation of food substance to living things.
• Energy is the ability to bring about change
or to do work.
• Energy exists in many forms, such as
heat, light, chemical energy, and electrical
• Thermodynamics is the study of energy.
• First Law of Thermodynamics: Energy
can be changed from one form to another,
but it cannot be created or destroyed.
• The total amount of energy and matter in
the Universe remains constant, merely
changing from one form to another.
• The First Law of Thermodynamics
(Conservation) states that energy is
always conserved. In essence,
energy can be converted from one
form into another.
• The Second Law of Thermodynamics
states that "in all energy exchanges, if no
energy enters or leaves the system, the
potential energy of the state will always be
less than that of the initial state." This is
also commonly referred to as entropy.
• Entropy is a measure of
• Cells are NOT disordered and
so have low entropy.
• The flow of energy maintains
order and life. Entropy wins
when organisms cease to take
in energy and die.
• Potential energy,
as the name
implies, is energy
that has not yet
been used, thus
the term potential.
• This is the
• Chemical energy is a
form of potential energy.
• In biological systems, it
is stored in molecules
as a result of the
arrangement of the
atoms in those
• Potential energy is stored in the
chemical bonds of molecules.
• Carbon-carbon and carbon-hydrogen
bonds are relatively rich in energy.
• This energy is released when the
chemical bond is broken.
• Some compounds contain high energy
• Notable among theses is adenosine
triphosphate [ATP] with its high-energy
• The high-energy bond is the one between
the last two phosphate groups.
• Energy releasing
energy, are termed
• Example: cellular
• Reactions that
require energy to
initiate the reaction
are known as
• Some reactions are spontaneous because
they give off energy in the form of heat.
• Others are spontaneous because they
lead to an increase in the disorder of the
• Free energy is the portion of a system’s
energy that can do work at a uniform
• A spontaneous process is one that
occurs without outside help.
• When a spontaneous process
occurs in a system, the stability of
the system increases.
• A system moves toward greater
stability when nothing prevents a
• How do we know which changes
lead to greater stability or are
• Free Energy is free because it is available,
not because it is without cost to the
• Organisms can only live at the expense of
• Systems that are rich in energy are
unstable, they tend to change
spontaneously to a more stable state, to
low entropy or both.
• For a reaction to occur spontaneously, the
system must give up energy, order, or
• Nature runs downhill (so there is a loss of
• In any spontaneous process, the free
energy of a system decreases.
Free Energy and
• Maximum stability = equilibrium.
• Most reactions proceed until the forward
and backwards reactions occur at the
same rate- this is chemical equilibrium.
• As a reaction proceeds toward chemical
equilibrium, the free energy of the mixture
of reactants and products decreases.
• A chemical reaction or physical process at
equilibrium performs NO work.
• Reactions in a closed system eventually
reach equilibrium and thus no work can be
• Metabolic reactions are reversible and
would reach equilibrium in a closed
system. (equilibrium = no work = death)
Metabolic Disequilibrium II
• Metabolic Disequilibrium is a defining
feature of living things.
• A cell is an open-system, thus there is a
constant flow of materials in and out.
• This maintains disequilibrium.
• A key feature of bioenergetics is energy
• This is the use of an exergonic process to
drive an endergonic process.
• ATP mediates these energy couplings.
Cells do 3 kinds of work
1. Mechanical work
• muscle cell contractions
2. Transport work
• pumping substances across the cell
3. Chemical work
• synthesis of proteins
• ATP, the energy currency or coin of the
cell, transfers energy from chemical bonds
to endergonic (energy absorbing)
reactions within the cell.
• Structurally, ATP
consists of the
adenine base, and
PO4-2) plus two
• Energy is stored in the covalent bonds
between phosphates, with the greatest
amount of energy (approximately 7
kcal/mole) in the bond between the
second and third phosphate groups.
• This covalent bond is known as a
• When energy is needed, ATP is
hydrolyzed, the terminal phosphate (at the
pyrophosphate bond) is transferred to
another molecule (which is said to be
• This results in a release of energy.
• The resulting ATP molecule is transformed
consists of the
• An analogy between ATP and
rechargeable batteries is appropriate.
• The batteries are used, giving up their
potential energy until it has all been
converted into kinetic energy and
• Recharged batteries (into which energy
has been put) can be used only after the
input of additional energy.
• Thus, ATP is the higher energy form
(the recharged battery) while ADP is
33 the lower energy form (the used
• When the terminal (third) phosphate is
cut loose, ATP becomes ADP, and the
stored energy is released for some
biological process to utilize.
• The input of additional energy (plus a
phosphate group) "recharges" ADP
into ATP (as in this analogy the spent
batteries are recharged by the input of
• Two processes convert ADP into ATP
1. Substrate-level phosphorylation
• Substrate-level phosphorylation occurs in
the cytoplasm when an enzyme attaches
a third phosphate to the ADP (both ADP
and the phosphates are the substrates
on which the enzyme acts).
• Chemiosmosis involves more than the
single enzyme of substrate-level
• Enzymes in chemiosmotic synthesis are
arranged in an electron transport chain
that is embedded in a membrane
• Enzymes allow many chemical reactions
to occur within the homeostasis
constraints of a living system.
• Enzymes function as organic catalysts.
• A catalyst is a chemical involved in, but
not changed by, a chemical reaction.
• Many enzymes function by lowering the
activation energy (The minimum amount
of energy required for a given reaction to
occur) of reactions.
• By bringing the reactants closer together,
chemical bonds may be weakened and
reactions will proceed faster than without
40 Speed up Reactions
• Enzymes can act rapidly, as in the case of
carbonic anhydrase, which causes the
chemicals to react 107 times faster than
without the enzyme present.
• Carbonic anhydrase speeds up the
transfer of carbon dioxide from cells to the
• There are over 2000 known enzymes,
each of which is involved with one specific
• Enzymes are substrate specific.
• The enzyme peptidase (which breaks
peptide bonds in proteins) will not work on
starch (which is broken down by human-
produced amylase in the mouth).
• Enzymes are proteins. The functioning of
the enzyme is determined by the shape of
• The arrangement of molecules on the
enzyme produces an area known as the
active site within which the specific
substrate(s) will "fit".
• In this hypothesis, the substrate does
not simply bind with the active site.
• It has to bring about changes to the
shape of the active site to activate the
enzyme and make the reaction
• The hypothesis suggests that
46 when the enzyme's active site
comes into contact with the right
substrate, the active site slightly
changes or molds itself around
the substrate for an effective fit.
• This shape adjustment triggers
catalysis and helps to explain
why enzymes only catalyze
• On the surface of an enzyme is usually a
small crevice that functions as an active
site or catalytic site to which one or two
specific substrates are able to bind.
(Anything that an enzyme normally
combines with is called a substrate)
The Catalytic Cycle
51 on Enzyme Activity
• The conformation of an enzyme is
maintained by interactions between
the various amino acids that
• This conformation is sensitive to
changes in the enzyme's
52 Factors Affecting
1. the concentration of the enzyme
2. the concentration of the substrate
3. the temperature
4. the pH
• Assuming a sufficient
concentration of substrate is
available, increasing enzyme
concentration will increase the
enzyme reaction rate.
• If enough enzyme is present, then as the
substrate concentration increases, the
enzyme reaction rate increases.
• However, at very high substrate
concentrations, the enzymes become
saturated with substrate and a higher
concentration of substrate does not
increase the reaction rate.
• Chemical reactions speed up as
temperature is increased, so, in general,
catalysis will increase at higher
• However, each enzyme has a
temperature optimum, and beyond this
point the enzyme's functional shape is lost.
• Boiling temperatures will denature most
• Each enzyme functions best within a
certain pH range.
• For example, the enzyme pepsin, which
works in your stomach, functions best in a
strongly acidic environment.
• When the pH changes, the active site
progressively distorts and affects enzyme
• Enzyme inhibitors are
molecules that interact in
some way with the enzyme to
prevent it from working in the
60 Competitive Inhibitor
• A competitive inhibitor is any compound
which closely resembles the substrate.
• The inhibitor competes for the same active
site as the substrate molecule.
• The inhibitor is "stuck" on the enzyme and
prevents any substrate molecules from
reacting with the enzyme.
• However, competitive inhibition is usually
reversible if sufficient substrate molecules
are available to ultimately displace the
• A noncompetitive inhibitor is a substance that
forms strong covalent bonds with an enzyme
and may not be displaced by the addition of
• Therefore, noncompetitive inhibition is
• A noncompetitive inhibitor may be bonded at,
near, or remote from the active site.
• The basic structure of the enzyme is modified to
the degree that it ceases to work.
Cofactors and Coenzymes
• Many enzymes require a non-protein cofactor to
assist them in their reaction. In this case, the
protein portion of the enzyme, called an
apoenzyme, combines with the cofactor to form
the whole enzyme or haloenzyme.
• Some cofactors are ions such as Ca++, Mg++,
• Other cofactors are organic molecules called
coenzymes which serve as carriers for chemical
groups or electrons. NAD+ and FAD are examples
• In order to control the rate of the
catalyzed reaction, the cell must have a
way to turn the enzyme on and off.
• This can either be accomplished by
1. blocking the active site directly, or
2. by inducing a change in the enzyme's
shape (called a conformation change)
that alters the shape of the active site.
• Allosteric regulation is a major mechanism by
which enzymes are controlled in cells.
• Enzymes that undergo shape changes are
called allosteric proteins, and the substances
that induce them are known as allosteric
• Allosteric means "other site," and refers to the
fact that the regulator is not binding at the active
site, but at another site on the surface of the
– Allosteric inhibitors are noncompetitive
inhibitors that are capable of inhibiting the
proper functioning of the active sites of
– For example, assume that an enzyme
consists of otherwise identical subunits A, B,
C, and D; an allosteric inhibitor may bind to
A and that binding is sufficient to inhibit the
activity of not just A but of B, C, and D as
• Feedback regulation is the mechanism by
which biosynthetic and catabolic pathways
• The term feedback inhibition refers to a
situation in which the substances at the
end of a long series of reactions inhibits a
reaction at the beginning of the series of
• These pathways have evolved self-
regulation such that, if too much of
the end product is around, it, or a
byproduct, acts as an inhibitor of an
• Generally, the end product acts as
a noncompetitive inhibitor of the
first step in the pathway.
The end product (inhibitor) of a pathway binds to the active site of the first
enzyme in the pathway. As a result, the enzyme can no longer bind to the
starting substrate of the pathway.
• Cooperativity is when an enzyme with
multiple subunits, the binding of one
substrate molecule to its active site can
cause the other active sites (on the other
subunits) to become active.
• One substrate molecule primes an
enzyme to accept additional substrate
molecules more readily.
• The cell is not just a bag of chemicals
with enzymes floating around randomly.
• Structures within cells help organize
1. Multienzyme complexes
• Multienzyme complexes produce key
chemical reactions necessary for life.
• The complexes are referred to as
multienzyme because they are made up of
multiple enzyme units.
• The product of the first reaction becomes
the substrate for the adjacent enzyme in
the complex, and so on.
• Lysosomes contain hydrolytic enzymes
necessary for intracellular digestion.
• Peroxisomes are responsible for
protecting the cell from its own
production of toxic hydrogen peroxide.
The oxidative enzymes in peroxisomes
break down the hydrogen peroxide into
water and oxygen.