7.

013 Lecture 4: Biochemistry III:  Energy,

Metabolism and Thermodynamics 2/10/16
Section 13.2 What is the structure of DNA?
• Chargaff’s rule states that the amount of adenine in DNA is equal
to the amount of thymine, and that the amount of guanine is
equal to the amount of cytosine; thus the total abundance of
purines (A + G) equals the total abundance of pyrimidines (T + C).
• X-ray crystallography showed that the DNA molecule is a double
helix. Watson and Crick proposed that the two strands in DNA are
antiparallel.
• Complementary base pairing between A and T and between G
and C accounts for Chargaff’s rule. The bases are held together by
hydrogen bonding.
• Reactive groups are exposed in the paired bases, allowing for
recognition by other molecules such as proteins.

Section 8.1 What physical principles underlie biological energy

transformation?
Two laws of thermodynamics govern energy transformations in biological
systems. A biochemical reaction can release or consume energy, and it may
not run to completion, but instead end up at a point of equilibrium.
• Energy is the capacity to do work. In a biological system, the usable
energy is called free energy (G). The unusable energy is entropy
(S), a measure of the disorder in the system.
• Potential energy is the energy of state or position; it includes the
energy stored in chemical bonds. Kinetic energy is the energy of
motion; it is the type of energy that can do work.
• The laws of thermodynamics apply to living organisms. The first
law states that energy cannot be created or destroyed. The second
law states that energy transformations decrease the amount of
energy available to do work (free energy) and increase disorder.
• The change in free energy (∆G) of a reaction determines its point of
chemical equilibrium, at which the forward and reverse reactions
proceed at the same rate.
• An exergonic reaction releases free energy and has a negative ∆G.
An endergonic reaction consumes or requires free energy and has
a positive ∆G. Endergonic reactions proceed only if free energy is
provided.
 • Metabolism is the sum of all the biochemical (metabolic) reactions
in an organism. Catabolic reactions are associated with the
breakdown of complex molecules and release energy (are
exergonic). Anabolic reactions build complexity in the cell and are
endergonic.

Section 8.2 What is the role of ATP in biochemical energetics?

ATP is the “energy currency” of cells. Some of the free energy released by
exergonic reactions can be captured in the form of ATP. This energy can
then be released by ATP hydrolysis and used to drive endergonic reactions.

• Adenosine triphosphate (ATP) serves as an energy currency in

cells. Its bonds are high energy, not strong. Hydrolysis of ATP to
ADP releases a relatively large amount of free energy.
• The ATP cycle couples exergonic and endergonic reactions,
harvesting free energy from exergonic reactions, and providing free
energy for endergonic reactions.

Section 8.3 What are enzymes?

A chemical reaction requires a “push” over the energy barrier to get started.
An enzyme reduces the activation energy needed to start a reaction by
binding the reactants (substrates). This speeds up the reaction.
• The rate of a chemical reaction is independent of ∆G but is
determined by the energy barrier.
• Enzymes are protein catalysts that affect the rates of biological
reactions by lowering the energy barrier, supplying the activation
energy (Ea) needed to initiate reactions.
• A substrate binds to the enzyme’s active site—the site of
catalysis—forming an enzyme–substrate (ES) complex. Enzymes
are highly specific for their substrates.

Section 8.4 How do enzymes work?

Enzymes orient their substrates to bring together specific atoms so that
bonds can form. An enzyme can participate in the reaction it catalyzes by
temporarily changing shape or destabilizing the enzyme–substrate complex.
Some enzymes require prosthetic groups, inorganic cofactors, or coenzymes
in order to function.
• At the active site, a substrate can be oriented correctly, chemically
modified, or strained. As a result, the substrate readily forms its
transition state, and the reaction proceeds.
• Binding substrate causes many enzymes to change shape, exposing
their active site(s) and allowing catalysis. The change in enzyme
shape caused by substrate binding is known as induced fit.
• Some enzymes require other substances, known as cofactors, to
carry out catalysis. Prosthetic groups are permanently bound to
enzymes; coenzymes are not. A coenzyme can be considered a
substrate, as it is changed by the reaction and then released from
the enzyme.
• Substrate concentration affects the rate of an enzyme-catalyzed
reaction.

Section 8.5 How are enzyme activities regulated?

The rates of most enzyme-catalyzed reactions are affected by interacting
molecules (such as inhibitors and activators) and by environmental factors
(such as temperature and pH). Reversible phosphorylation is another
important mechanism for regulating enzyme activity.
• Metabolism is organized into pathways in which the product of one
reaction is a reactant for the next reaction. Each reaction in the
pathway is catalyzed by a different enzyme.
• Enzyme activity is subject to regulation. Some inhibitors bind
irreversibly to enzymes. Others bind reversibly.
o An uncompetitive inhibitor binds to the enzyme–substrate
complex, preventing the complex from releasing products.
Unlike competitive inhibition, it cannot be overcome by
adding more substrate.
o A competitive inhibitor binds to the active site, preventing
substrate binding.
o A noncompetitive inhibitor binds at a site other than the
active site, changing enzyme structure so that normal
substrate binding cannot occur.
• An allosteric effector binds to a site other than the active site and
stabilizes the active or inactive form of an enzyme. It induces the
 enzyme to change its shape. The change in shape alters the affinity
of the active site for the substrate, and so the rate of the reaction is
changed.
o Commonly a protein
• The end product of a metabolic pathway may inhibit an enzyme
that catalyzes the commitment step of that pathway.
• Reversible phosphorylation is another important mechanism for
regulating enzyme activity.
• Enzymes are sensitive to their environments. Both pH and
temperature affect enzyme activity.
o Change in charge on carboxyl and amino groups is affected
by change in pH and can change the active site of the enzyme
o Heat can change the tertiary shape of proteins, changing the
enzyme
2/10/16 11:53 AM
2/10/16 11:53 AM