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ENZYMOLOGY
REACTIONS
Endergonic and Exergonic
Energy releasing processes, ones that "generate" energy, are termed exergonic
reactions. Reactions that require energy are known as endergonic reactions. All
natural processes tend to proceed in such a direction that the disorder or
randomness of the universe increases (the second law of thermodynamics).
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookEnzym.html
KINETICS vs. THERMODYNAMICS
Reaction rate is determined by the principles of kinetics; direction of
reaction, by principles of thermodynamics. For example, the conversion
of graphite to diamond is thermodynamically favorable, but kinetically
unfavorable. So, graphite (in pencils) spontaneously converts to
diamond, but the process is so slow that it is not observed in everyday
life.
Enzymes: Organic Catalysts
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 of reactions. By bringing the reactants closer together,
chemical bonds may be weakened and reactions will proceed faster than
without the catalyst.
* Enzymes are typically proteins (exception: ribozymes, which are RNA).
The use of enzymes can lower the activation energy of a reaction (E a). Image
from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates
(www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.
http://www.cartage.org.lb/en/themes/Sciences/LifeScience/GeneralBiology/Biochemistry/En
zymes/OrganicCatalysts/OrganicCatalysts.htm
♦AN ENZYME ALTERS THE MECHANISM. THE
ENZYME-CATALYZED MECHANISM HAS A
LOWER ACTIVATION ENERGY THAN THE
REACTION
MECHANISM
WITHOUT
THE
ENZYME.
MODELS OF ENZYME ACTION
Lock and Key Hypothesis
The "Lock and Key hypothesis" was proposed by
Emil Fischer in 1890. It suggested that there is an
exact fit between the substrate and the active site
of the enzyme, in the same way that a key fits into
a lock very precisely. The two molecules form a
temporary structure called the enzyme-substrate
complex. Products have a different shape from
the substrate and so, once formed, they are
released from the active site, leaving it free to
become attached to another substrate.
The Induced Fit Hypothesis
The "Induced Fit Hypothesis": was proposed in
1959 by Daniel Koshland. It suggested that the
active site may not necessarily be exactly of the
same shape as the substrate. But the enzyme can
have an active site that attracts the substrate.
When a substrate combines with an enzyme, it
induces a change in the enzyme structure. The
amino acids which constitute the active site are
then moulded into a precise conformation,
bringing the chemical groups of the active site
into positions which enable the enzyme to
perform its catalytic function most effectively. The
new configuration of the active site is catalytically
active, which in turn affects the shape of the
substrate, stretching critical bonds or bring
substrates in close proximity thus lowering its
activation energy. This hypothesis can also
explain group specificity, unlike the Lock and Key
hypothesis. The enzyme is flexible and moulds to
fit the substrate molecule in the same way that
clothing is flexible and can mould itself to fit the
shape of the wearer.
http://resources.ed.gov.hk/biology/english/virtual_lab/enzyme.html
While the induced-fit hypothesis was proposed
after the lock-and-key hypothesis and represents
the better model of enzymatic action, particular
enzymes usually catalyze a very limited range of
reactions. This is called enzyme specificity.
APOENZYME, COFACTORS, COENZYMES, AND HOLOENZYME
An apoenzyme is an enzyme without its cofactor(s) and/or coenzyme(s), and is
catalytically inactive.
cofactor: any accessory nonprotein substance, commonly of low molecular mass,
that is necessary for the activity of an enzyme, e.g. metal ion
coenzyme: any of various non protein organic co-factors that are required, in
addition to an enzyme and a substrate, for enzyme activity.
Apoenzyme + Cofactor(s) and/or Coenzyme(s) -> Holoenzyme
inactive
active
A holoenzyme is a complete enzyme with its cofactor(s) and/or coenzyme(s), and is
catalytically active.
ENZYME TAXONOMY
1. OXIDOREDUCTASES – CATALYZE OXIDATIONREDUCTION REACTIONS
2. TRANSFERASES – CATALYZE REACTIONS THAT
INVOLVE THE TRANSFER OF GROUPS FROM ONE
MOLECULE TO ANOTHER
3. HYDROLASES – CATALYZE REACTIONS IN WHICH
THE CLEVAGE OF BONDS IS ACCOMPLISHED BY
ADDING WATER (e.g., trypsin, chymotrypsin)
4. LYASES – CATALYZE REACTIONS IN WHICH
GROUPS ARE REMOVED TO FORM A DOUBLE BOND
OR ARE ADDED TO A DOUBLE BOND
5. ISOMERASES – CATALYZE INTRAMOLECULAR
REARRANGEMENTS (e.g., alanine racemase)
6. LIGASES – CATALYZE BOND FORMATION BETWEEN
TWO SUBSTRATE MOLECULES