Chapter Six- An Introduction to Metabolism (Test Review Notes)

Caitlin Grapentine

The totality of an organisms chemical reactions is called metabolism.

Metabolism emerges from orderly interactions between molecules
Metabolic Pathway Diagram:

In a metabolic pathway, a specific molecule is specifically altered in a series of

defined steps, resulting in a product
Some metabolic pathways release energy by breaking down complex molecules
into simpler ones. These processes are called catabolic pathways, or breakdown
pathways
A major example of catabolism is cellular respiration (where glucose sugar and
other organic fuels are broken down in the presence of O2, CO2, and H2O.
Catabolic pathways store energy which becomes available for the cell to
use.
Anabolic pathways consume energy to BUILD more complex molecules from simpler
ones. They can also be called biosynthetic pathways
Examples include: amino acid synthesis and the building of a proteins primary
structure through amino acids
Catabolic and anabolic pathways are the uphill and downhill avenues in
metabolism. Energy released from catabolic pathways can be stored and used to
fuel anabolic pathways.
FORMS OF ENERGY
Energy is the capacity to cause change. It exists in various forms. Life depends on
the cells ability to transform energy between forms.
Energy associated with the general (relative) motion of objects is called kinetic
energy
i.e- muscle movement
THERMAL ENERGY is (kinetic energy) associated with the RANDOMNESS in movement
of atoms and molecules. IT IS THE MOST RANDOM FORM OF ENERGY.
The transfer of thermal energy between masses is heat.
Energy that is not kinetic is called potential energy. It is energy that matter possesses
because of its location or structure.
Molecules possess potential energy stored in their bonds between electrons.
Chemical energy is a term used to refer to the potential energy available for release
in a chemical reaction.

THE LAWS OF ENERGY TRANSFORMATION

The study of energy transformations that occur in a collection of matter is referred to

as thermodynamics.
 System: the matter under study at the time
Surroundings: everything outside the system
System + Surroundings= Universe
An isolated (closed) system is a system unable to exchange energy or
resources with its surroundings
An open system is a system that is able to exchange energy or resources with
its surroundings.
Organisms are open systems.
The First Law of Thermodynamics: the energy of the universe is constant. This can
also be referred to as the law of conservation of matter. Energy can be transferred
and transformed but NEVER created or destroyed.
The Second Law of Thermodynamics: During every energy transformation or transfer
that some energy is converted to thermal energy and released as heat, becoming
unavailable to do work.
Every energy transfer or transformation increase the entropy of the system
A logical consequence of the energy lost as heat is that this addition of heat
adds more disorder to the universe.
Entropy is the measure of disorder, or randomness in a universe.
For a process to occur on its own, without outside resources or energy, must increase
the entropy of the universe. A process that can occur without an input of energy is
called a spontaneous process, or is energetically favorable.
For a process to occur spontaneously, it must increase the entropy of the
universe.
The entropy of a particular system, such as an organism in this case, may actually
decrease as long as the total entropy of the universe increases.

FREE ENERGY CHANGE (G), STABILITY AND EQUILIBRIUM

Free energy is the portion of a systems energy that can perform work when
temperature and pressure are uniform throughout the system, as in a living cell.
G represents the difference between free energy of the final state and the free
energy of the initial state
G= G final state - G initial state
Only reactions with a negative G can occur with no additional input of energy, so
G can tell us whether or not a reaction was spontaneous or not.
For a reaction to have a negative G, the system must lose free energy during the
change from the initial and final G values. Because it has less free energy, the
system in its final state is likely to change, thus is more stable.
A term that describes maximum stability is equilibrium. At equilibrium, the forward
and reverse reactions are occurring at the same rate so there is no further change in
the relative concentration of the products and reactants of this reaction.
For a system at equilibrium, G is at its lowest possible value in that system. Any
change from the equilibrium state will have a positive G, will NOT be spontaneous
due to the necessary addition of free energy to activate the reaction. (Systems
NEVER move away from equilibrium spontaneously)
 Because a system at equilibrium cannot spontaneously change, it cannot do work.
A process is spontaneous and can do work only when it is moving TOWARDS
equilibrium.

EXERGONIC AND ENDERGONIC REACTIONS

An exergonic reaction (energy outward) ends up releasing energy. Because the

reaction loses free energy (G decreases) G is negative, thus spontaneous
The magnitude of G is an exergonic reaction represents the maximum amount of
work that reaction can perform (since some of the energy is released as heat and
cannot do work). The greater the decrease in free energy, the more amount of work
can be done.

An endergonic reaction is a reaction that absorbs energy form its surroundings.

Because this reaction type stores free energy in molecules G increases, G is
positive, and these reactions are NOT spontaneous.
Reactions in an isolated system eventually reach equilibrium and then cannot do
work (are considered dead)
The constant flow of materials in and out of the cell keeps the metabolic pathways
from ever reaching equilibrium and the cell continues to constantly do work
throughout its life.

A cell does three kinds of work:

Chemical: the use of endergonic processes that require chemical energy (such
as protein synthesis from amino acids
Transport: movement of substances across membranes against the
concentration gradient
Mechanical: during digestion, or chromosomal movement during meiosis/mitosis
Cells manage their energy resources primarily through energy coupling, where a
exergonic process fuels and endergonic one.

STRUCTURE AND HYDROLYSIS OF ATP

ATP, adenosine triphosphate, contains a ribose sugar, the nitrogenous base of

adenine and a chain of three phosphate groups bonded to it.
 Bonds between phosphates can be broken by hydrolysis. When the terminal
phosphate bond is broken by the addition of water, ATP turns into ADP. This reaction
is exergonic and releases 7.3 kcals of energy per mole of ATP hydrolyzed.
When ATP is converted to ADP in cellular conditions, the actual G is about -13
kcal/mol which is 78% more energy released than in STP outside the cell.
Phosphate bonds are generally referred to as high energy phosphate bonds, but this
term is misleading. The bonds are not unusually strong, they just have more energy
compared to the energy of the products (ADP and an inorganic phosphate group).
The release of energy during the hydrolysis of ATP comes from the chemical change
to a state of lower free energy, not the bonds themselves.
ATP hydrolysis releases so much energy because of how three negatively charged
phosphate groups are being bunched together and their mutual repulsion (since
like charges repel) contributes to the instability of the ATP molecule. You could say
that the chain of three phosphates is spring loaded.

HOW THE HYDROLYSIS OF ATP DOES WORK

 An enzyme is a macromolecule that acts as a catalyst, which speeds up a reaction
without being used up.
Every chemical reaction between molecules involves the formation and breaking of
bonds. To reach a state where bonds have the ability to change, reactant
molecules must absorb energy from their surroundings. When new bonds form,
energy is lost as heat, and the molecules restore their stability with lower energy.
The initial energy needed to start a reaction so that bonds can break, is known as
the free energy of activation, or activation energy.
Activation energy is often supplied as thermal energy that the reactants absorb. The
absorption of thermal energy accelerates the reactant molecules, making them
collide more often and more forcefully. It also agitates the bonds, making breakage
of said bonds, more likely. When the molecules have absorbed enough energy to
have their bonds break, this is known as the transition state.

The reactant an enzyme acts on is the enzymes substrate. The enzyme binds to its
substrate forming an enzyme-substrate complex.
Process Summary

Only a certain site of an enzyme bonds to a substrate. This region is called the active
site. The specificity of an enzyme is attributed to a complementary fit between the
shape of an enzymes active site and the shape of the substrate.
As the substrate enters the active site, the enzyme changes shape slightly due to
interactions between the substrates chemical groups an dchemical R groups of the
amino acids that form the active site. This change is shape makes the active site
more snugly around the substrate- the induced fit.
 The rate at which a particular amount of enzyme converts substrate to product is
partly a function of the initial concentration of the substrate
More substrate molecules available more frequent possible access to enzymes
Saturation when the concentration of substrate is at max for its current
efficiency. You would need to add more enzyme to speed this reaction further.
The rate of reaction of an enzymatic reaction increases with increasing temp.
Above that temp., the speed of enzymatic processes slows sharply. Because
extreme temperature will cause the enzyme to denature. Enzymes have optimal
temperatures at which they are most efficient
Most human enzymes have an optimal temperature of 30-40 degrees Celsius
Enzymes also have an optimal pH value. Human enzymes usually are between the
pH range of 6-8, but has few exceptions such as pepsin, which has an optimal pH of
2.
Cofactors are non-protein helpers for catalytic activity. Some are inorganic (metals-
Zn, Fe, Cu). If the cofactor is organic it is called a coenzyme. (most vitamins are
coenzymes)
ENZYME INHIBITORS
Some enzyme inhibitors resemble the normal substrate molecule and compete for
the active site. These are called competitive inhibitors. Can only be overcome by
adding more substrate molecules.
Noncompetitive inhibitors do not directly compete with the substrate for the active
site. Instead, they bind to other points on the enzyme, changing the enzymes
shape. Toxins and poisons are examples of noncompetitive inhibitors.