ENZYMES
➢ Holoenzyme – biochemically active
conjugated enzyme
➢ Coenzyme – a small organic
molecule that acts as a cofactor in a
conjugated enzyme
➢ Inorganic Ions – include Zn2+, Mg2+,
Mn2+, and Fe2+. An important source
of this is dietary minerals
Greek words – “en” and “zyme” which means
in and yeast, respectively
GENERAL CHARACTERISTICS
-
-
Most remarkable and highly specialized
protein and has a high degree of specificity
for their substances
“central” to every biochemical process
Acts as catalysts for biochemical reactions
lowers the activation energy for a chemical
reaction
less energy is needed to convert reactant
molecules to products
Most are globular proteins
Not all enzymes are proteins – some are
ribonucleic acids (1980s)
SUBSTRATE - is the substance upon which the
enzyme “acts.”
NOMENCLATURE
-
Named based on function, the catalyzed
reaction, and substrate identity as focal
points.
1) Suffix -ase identifies a substance as an
enzyme. Suffixes -in are used to name
digestive enzymes.
2) Prefix indicates the type of catalyzed
reaction – (hydrolase (hydrolysis), and oxidase
(oxidation))
3) identity of the substrate is often noted in
addition to the type of reaction (glucose
oxidase, pyruvate carboxylase)
General Structure Classes
1. Simple Enzymes – composed only of
proteins
2. Conjugated Enzymes – has protein and nonprotein part
➢ Apoenzyme – protein part
➢ Cofactor
–
non-protein
part.
Generally, either a small organic
molecule or an inorganic ion
APOENZYME + COFACTOR = HOLOENZYME
Why do apoenzymes need cofactors?
Cofactors provide additional chemically
reactive functional groups besides those present in
amino acid side chains of apoenzymes.
Classes Based on Type of
Reactions
1. Oxireductase - catalyzes an oxidationreduction reaction (linked process)
- requires a coenzyme that is oxidized or
reduced as the substrate is reduced or
oxidized.
Example:
Lactate
dehydrogenase
is
an
oxidoreductase that removes hydrogen
atoms from a molecule.
2. Transferase - catalyzes the transfer of a
functional group from one molecule to
another
Major subtypes:
1) Transaminase – catalyzes the
transfer of an amino group from
one molecule to another.
2) Kinases – play a major role in
metabolic
energy-production
reactions that catalyze the transfer
of a phosphate group from ATP to
give ADP and phosphorylated
product
3. Hydrolase - catalyzes a hydrolysis reaction
(center to the process of digestion) in which
the addition of a water molecule to a bond
causes the bond to break.
•
Carbohydrase
breaking
of
glycosidic
bonds in oligo- and polysaccharides
• Proteases – the breaking of peptide
linkages in proteins
• Lipases – the breaking of ester
linkages in triacylglycerols
4. Lyase - catalyzes the addition of a group to
a double bond or the removal of a group to
form a double bond in a manner that does
not involve hydrolysis or oxidation.
• Dehydrase - removal of the components
of water from a double bond
• Hydratase - effects the addition of the
components of water to a double bond.
5. Isomerase - catalyzes a substrate's
isomerization (rearrangement of atoms) in a
reaction, converting it into a molecule
isomeric with itself.
6. Ligase - catalyzes the bonding together of
two molecules into one with the
participation of ATP.
2
Mechanisms:
1) Lock and Key Theory – the active site is
rigid, thus providing a rigid, pre-shaped
template fitting with the size and shape of
the substrate molecule.
2) Induced Fit Theory or Koshland theory –
the active site is flexible. The substrate
during its binding induces conformational
changes in the active site to attain the final
catalytic shape and form.
Models of Enzyme Action
2 Important Concepts:
1) Active site
2) Enzyme-Substrate Complex
Enzyme Specificity – determined by the active
site
-
Some
accommodate
only
one
compound
while
others
can
accommodate a family of closely related
compounds.
Absolute Specificity – enzyme will catalyze a
particular reaction for only one substrate
Active Site – a relatively small part of an enzyme’s
structure that is involved in catalysis.
- Usually the “crevice–like” location
Enzyme-Substrate Complex – intermediate
reaction species formed when a substrate binds to
the active site
-
Most restrictive of all specificities, NOT
COMMON.
Example: Urease
Stereochemical Specificity – enzyme can
distinguish between isomers. Chirality is
inherent at active site since amino acids are
chiral.
-
Example: L-amino acid oxidase
Group Specificity – involves structurally
similar compounds with the same functional
groups
-
Example: Carboxypeptidase
Linkage Specificity – involves a particular
type of bond irrespective of the structural
features in the vicinity of the bond.
-
MOST GENERAL
Example: Phosphatases
Enzyme Activity
-
Measure of the rate at which an enzyme
converts substrate to in a biochemical
reaction.
Factors Affecting Enzyme Activity
1. Temperature – reaction rate increases
with temperature until the point at
which the protein is denatured (above
50 degrees Celsius) and activity drops
sharply.
- Optimum temperature is around 37
degrees Celsius
2. pH – maximum enzymatic activity is
possible only within a narrow pH range
(5-9); outside this range, the protein is
denatured
- Optimum pH is 7.0-7.5
3. Concentration of Substrate – reaction
rate
increases
with
substrate
concentration until full saturation
occurs
4. Concentration of Enzyme – reaction
rate increases with increasing enzyme
concentration,
assuming
enzyme
concentration is lower than that of
substrate.
Enzyme Inhibition
➢ Negative regulator – decreases
enzyme activity (noncompetitive
inhibitor)
Regulation of Enzyme Activity
-
Minimize the process of energy-wasting
Several “turn off” and “turn on”
mechanisms to regulate
Regulation Mechanism
1. Feedback Control – associated with
allosteric enzymes
- process in which activation/inhibition
of the first reaction sequence is
controlled by the product of the
reaction sequence
2. Proteolytic Enzymes and Zymogens
Proteolytic enzymes – catalyzes the
breaking of peptide bonds that maintain the
primary structure of protein.
-
Allosteric Enzymes – has two or more protein
chains (quaternary structure) and two kinds of the
active site (substrate & regulator)
Regulator – molecules that
regulatory sites
➢ Positive regulator –
enzyme activity
bind on
increases
Generated in an inactive form but
converts back to active form if needed.
Zymogens – inactive form of proteolytic
enzyme (proenzyme)
-
Names of zymogens can be recognized
by the suffix -ogen or the prefix pre- or
pro-.
Table 1.1 Main Classes and Subclasses of
Enzymes
Main Classes
3. Covalent Modification – a process
where enzyme activity is altered by
covalently modifying the structure of an
enzyme thru attachment of a chemical
group or removal of a chemical group
from a particular amino acid within
enzyme structure
- Most encountered type are
➢ Phosphorylation – addition of
phosphate group to an enzyme
➢ Dephosphorylation – removal of
phosphate group
Selected
Subclasses
Type of
Reaction
Catalyzed
oxidases
oxidation of
a substrate
reductases
reduction of
a substrate
introduction
of
double
bond
Oxidoreductase
(oxidation)
s
by
formal
dehydrogenase removal of
s
two H atoms
from
substrate, the
H
being
accepted by a
coenzyme
transaminases
transfer of an
amino group
between
substrate
kinases
transfer of a
phosphate
group
between
substrates
lipases
hydrolysis of
ester
linkages in
lipids
proteases
hydrolysis of
amide
linkages in
proteins
nucleases
hydrolysis of
sugar–
phosphate
ester bonds
Transferases
Hydrolases
in
nucleic
acids
carbohydrases
hydrolysis of
glycosidic
bonds
in
carbohydrate
s
phosphatases
hydrolysis of
phosphate–
ester bonds
dehydratases
removal of
H2O from a
substrate
deaminases
removal of
NH3 from a
substrate
hydratases
addition of
H2O to a
substrate
decarboxylase
s
removal of
CO2 from a
substrate
racemases
conversion
of D isomer
to L isomer,
or vice versa
mutases
transfer of a
functional
group from
one position
to another in
the
same
molecule
synthases
formation of
new
bond
between two
substrates,
with
participation
of ATP
carboxylases
formation of
new
bond
between
a
Lyases
Isomerases
Ligases
substrate and
CO2, with
participation
of ATP