Chapter 6 - metabolism

The sum total of an
organism’s chemical
reactions is called
The chemistry of life is
organized into metabolic
pathways. A metabolic
pathway begins with a
specific molecule, which
is then altered in a series
of defined steps to form a
specific product.
A specific enzyme
catalyzes each step of the
pathway. Remember,
enzymes are not changed
or used up during the
reaction they are
Catabolic Pathways = Breaking down molecules; Releases Energy; Utilizes
Hydrolysis; Ex. Cellular Respiration (breaking down sugars to get ATP)
Anabolic Pathways = Building up molecules; Stores Energy (in bonds); Utilizes
Condensation or Dehydration Synthesis; Ex. Protein Synthesis (from amino
Building Molecules –
Anabolic Pathways
Breaking Down Molecules –
Catabolic Pathways
Bioenergetics is the study of how energy flows through
living organisms.
Organisms transform energy  energy can be converted
from one form to another.
Energy is the capacity to cause change.
 Kinetic energy is the energy associated with the relative
motion of objects.
 Thermal energy is kinetic energy associated with the
random movement of atoms or molecules.
 Potential energy is the energy that matter possesses
because of its location or structure.
Chemical energy is a term used by biologists to refer to the
potential energy available for release in a chemical reaction;
stored in bonds
Thermodynamics is the study of energy transformations that occur in a collection of
- An isolated system (or CLOSED system), is unable to exchange either
energy or matter with its surroundings.
- In an OPEN system, energy and matter can be transferred between the
system and its surroundings; ORGANISMS are OPEN systems
In a closed system, eventually it reaches equilibrium and no more work can be
done. If no work can be done, the organism would eventually die. The key to
keeping disequilibrium is for the product of one step to be the reactant of the next
(open systems)
Two laws of
govern energy
transformations in
organisms and all
other collections of
The first law of
states that the
energy of the
universe is constant:
Energy can be
transferred and
transformed, but it
cannot be created or
(“conservation of
Entropy (∆S) is a measure of disorder or randomness; the more
random a collection of matter, the greater its entropy.
The second law of thermodynamics states: Every energy transfer or
transformation increases the entropy of the universe.
Every reaction increase the entropy of the UNIVERSE, even if it
decreases the entropy in that exact system. Much of the increased
entropy of the universe takes the form of INCREASING HEAT,
which is the energy of random molecular motion.
Spontaneous = always going to a more stable position (increasing entropy);
decreasing Free Energy (∆G); can occur WITHOUT the input of energy
Non-Spontaneous = going to a less stable position (decreasing entropy);
increasing Free Energy (∆G ); needs energy input to occur
Unstable = ↑ Free E
Stable = ↓ Free E
Free energy is the portion of a system’s energy that can perform
work when temperature and pressure are uniform throughout the
system, as in a living cell.
The change in free energy, ∆G, can be calculated for any specific
chemical reaction by applying the following equation:
∆G = ∆H – T∆S
In this equation, ∆H symbolizes the change in the system’s
enthalpy (in biological systems, equivalent to total energy or
HEAT); ∆S is the change in the system’s entropy; and T is the
absolute temperature in Kelvin (K) units (K = °C + 273).
∆G is negative when the process involves a LOSS of free energy
during the change from initial state to final state; because it has
less free energy, the system in its final state is less likely to change
and is therefore more stable (+∆S) than it was previously.
∆G is positive when the process involves a GAIN of free energy;
the result is usually less stable (-∆S) than what you started with
A system at equilibrium is at maximum stability. However, at
equilibrium, G = 0, and the system can do no work (so a cell
would die).
Exergonic → releasing energy; reactants have MORE energy than products; ∆G =
Endergonic → absorbing energy from environment; reactants have LESS energy
than products; ∆G = positive
Reactants AB and CD must absorb
enough energy from the
environment to become unstable
enough to overcome the activation
energy (EA) and reach the transition
Bonds then break, and new bonds
form. In the process, energy is
released to the surroundings.
Exergonic = Products have LESS
free energy than Reactants
(because some of it got lost to the
Catabolic (breaking down)
Exergonic (giving off E)
Breaking Down
Breaking Bonds
Release Free Energy
∆G = Negative (Free energy
∆ S = Positive (disorder
(entropy) increases)
Stability Increases
Anabolic (building up)
Endergonic (absorbing E)
Building up
Making Bonds
Storing Free Energy
∆G= Positive (free energy
∆S = Negative (disorder
(entropy) decreases)
Stability Decreases
A cell does three main
kinds of work:
Chemical work, such as the
synthesis of polymers from
Transport work, pumping
substances across
Mechanical work, such as
the beating of cilia,
contraction of muscle cells,
and movement of
chromosomes during
cellular reproduction;
Cells manage their
energy resources to do
this work by energy
coupling, using an
exergonic process to
drive an endergonic one.
To break down
ATP, break off the
3rd phosphate; this
releases about +7.3
kcal/mol of energy
triphosphate (ATP!) is
the energy molecule
for cells. It is
composed of the
sugar ribose, the
nitrogen base adenine,
and three phosphate
The third phosphate
can be broken off and
transferred to another
molecule to transfer
the energy. The ATP
is turned into ADP in
that process.
In the cell, the energy from the hydrolysis of ATP is directly coupled to
endergonic processes by the transfer of the phosphate group to another
molecule. This new phosphorylated molecule now has more energy since it got
the phosphate group.
ATP loses a phosphate to form
ADP, energy, and an inorganic
A working muscle cell recycles
its entire pool of ATP once each
minute. More than 10 million
ATP molecules are consumed
and regenerated per second per
Transferring of a phosphate can transfer energy from one molecule to another.
An enzyme is a protein that acts as a catalyst; which is a molecule
that speeds up a chemical reaction WITHOUT being changed or
consumed during the reaction.
Activation Energy (EA)  the energy needed for a reaction to occur
 Sometimes just the thermal energy at room temperature is
enough to get the reactants to reach the transition state
Enzymes work by LOWERING the amount of activation energy
required for a reaction to occur (they do NOT give energy to the
In most cases, EA is high
enough that the transition
state is rarely reached
and the reaction hardly
proceeds at all. In these
cases, the reaction will
occur at a noticeable rate
only if the reactants are
 Heat would speed up
all reactions, not just
those that are needed.
 Heat also denatures
proteins and kills cells.
The reactant that an enzyme acts
on is the substrate. The enzyme
binds to a substrate, or
substrates, forming an enzymesubstrate complex.
The reaction catalyzed by each
enzyme is very specific.
The active site of an enzyme is
typically a pocket or groove on
the surface of the protein where
catalysis occurs; the spot where
the enzyme reacts with the
Notice: In this process we are breaking
apart sucrose, so we are putting water in
to break the bond – HYDROLYSIS!
The specificity of an enzyme is
due to the fit between the active
site and the substrate.
The Induced Fit Theory says that when the substrate binds with the
enzyme at the active site, the enzyme may change shape slightly to
have more of a “snug” fit.. This shape change brings the chemical
groups of the active site into position to catalyze the reaction.
The R groups of a few amino acids on the
active site catalyze the conversion of
substrate to product.
Enzymes are unaffected by the reaction and
are reusable.
Most metabolic enzymes can catalyze a
reaction in both the forward and reverse
directions; in the direction of equilibrium.
The rate at which a specific number of
enzymes convert substrates to products
depends in part on substrate concentrations;
however, there is a limit to how fast a
reaction can occur.
At high substrate concentrations, the active
sites on all enzymes are engaged.
 The enzyme is saturated, and the rate of
the reaction is determined by the speed at
which the active site can convert substrate
to product.
 The only way to increase productivity at
this point is to add more enzyme
Each enzyme works best at certain
optimal conditions.
Temperature has a major impact on
reaction rate. Higher temp = more
collisions = more reactions…just need
to be careful of DENATURATION!
Most human enzymes have optimal
temperatures of about 35–40°C.
Each enzyme also has an optimal pH .
This optimal pH falls between 6–8 for
most enzymes. However, digestive
enzymes in the stomach are designed to
work best at pH 2, whereas those in the
intestine have an optimal pH of 8.
Many enzymes require non-protein helpers, called
cofactors, (usually minerals) to be activated.
Organic cofactors are called coenzymes (usually
Enzymes can be inhibited either competitively
or non-competitively:
Competitive Inhibition = an inhibitor mimics
the shape of the substrate and gets in the way
of the active site of the enzyme; so it is
competing for the active site; ADDING
SUBSTRATE would overcome competitive
Non-Competitive Inhibition = an inhibitor
binds to an allosteric site (a site on the enzyme
that is NOT the active site) and therefore
changes the shape of the active site on the
enzyme. This prohibits the substrate from
properly connecting with the enzyme and
renders it useless. It is NOT competing for the
active site because it uses an allosteric one.
An allosteric site is a spot on an enzyme away from the active site where an
inhibitor OR activator can bind and affect the function of that enzyme. The binding
of an activator stabilizes the conformation that has functional active sites, whereas
the binding of an inhibitor stabilizes the inactive form of the enzyme
Another Picture on Allosteric Regulation…
When an enzyme is
made up of different
subunits, the binding
of a substrate in the
active site of ONE of
the subunits can force
the other subunits to
stay in the active
conformation. This is
called cooperativity.
This amplifies the
response of enzymes
to substrates, priming
the enzyme to accept
additional substrates.
Feedback Inhibition = The
switching OFF of a
metabolic pathway by one
of its end products. The
end product acts as an
inhibitor of one of the
enzymes in the pathway
(usually allosterically). The
process helps cells regulate
and not waste any
resources by making TOO
MUCH of a certain
The cell is compartmentalized: The
organization of cellular structures including
organelles and membranes helps bring order to
metabolic pathways.
Having the enzymes needed for a specific
process all in the same place helps make the
process more efficient. For example, all the
enzymes needed for photosynthesis are found
in the chloroplast.