Download Chapter 15 Enzymes

Chapter 15
Enzymes
Enzymes
Ribbon diagram of cytochrome c oxidase, the enzyme that
directly uses oxygen during respiration.
Enzyme Catalysis
Enzyme: A biological catalyst.
• With the exception of some RNAs that catalyze their own
self-cleavage, all enzymes are proteins.
• Enzymes can increase the rate of a reaction by a factor of 109
to 1020 over an uncatalyzed reaction.
• Some catalyze the reaction of only one compound.
• Others are stereoselective; for example, enzymes that
catalyze the reactions of only L-amino acids.
• Others catalyze reactions of specific types of compounds or
bonds; for example, trypsin catalyzes hydrolysis of peptide
bonds formed by the carboxyl groups of Lys and Arg.
Enzyme Catalysis
Figure 15.1 Trypsin catalyzes the hydrolysis of peptide bonds
formed by the carboxyl group of lysine and arginine.
Classification of Enzymes
Enzymes are commonly named after the reaction or
reactions they catalyze.
• Example: lactate dehydrogenase, acid
phosphatase.
Enzymes are classified into six major groups
according to the type of reaction catalyzed:
• Oxidoreductases: Oxidation-reduction
reactions.
• Transferases: Group transfer reactions.
• Hydrolases: Hydrolysis reactions.
• Lyases: Addition of two groups to a double bond,
or removal of two groups to create a double bond.
• Isomerases: Isomerization reactions.
• Ligases: The joining to two molecules.
Classification of Enzymes
1. Oxidoreductase:
2. Transferase:
Classification of Enzymes
3. Hydrolase:
4. Lyase:
COO CH2
C-COOCH
+ H2O
COO cis-Aconitate
Aconitase
COOCH2
C-COOHO C-H
COOIsocitrate
Classification of Enzymes
5. Isomerase:
CH2 OPO3 2Phosphohexose
O
isomerase
OH
OH
HO
OH
a-D- Glucose-6-phosphate
CH2 OPO3 2O
H HO
H
H
HO
CH2 OH
OH
a-D-Fructose-6-phosphate
6. Ligase:
Tyrosine-tRNA
synthetase L-tyrosyl-tRNA + AMP + PP
ATP + L-tyrosine + t-RNA
i
Enzyme Terminology
Apoenzyme: The protein part of an enzyme.
Cofactor: A nonprotein portion of an enzyme that is
necessary for catalytic function; examples are metallic ions
such as Zn2+ and Mg2+.
Coenzyme: A nonprotein organic molecule, frequently a B
vitamin, that acts as a cofactor.
Substrate: The compound or compounds whose reaction an
enzyme catalyzes.
Active site: The specific portion of the enzyme to which a
substrate binds during reaction.
Schematic of an Active Site
Figure 15.2 Schematic
diagram of the active
site of an enzyme and
the participating
components.
Terms in Enzyme Chemistry
Activation: Any process that initiates or increases the activity
of an enzyme.
Inhibition: Any process that makes an active enzyme less
active or inactive.
Competitive inhibitor: A substance that binds to the active site
of an enzyme thereby preventing binding of substrate.
Noncompetitive inhibitor: Any substance that binds to a
portion of the enzyme other than the active site and thereby
inhibits the activity of the enzyme.
Enzyme Activity
Enzyme activity: A measure of how much a reaction rate is
increased.
We examine how the rate of an enzyme-catalyzed reaction is
affected by:
• Enzyme concentration.
• Substrate concentration.
• Temperature.
• pH.
Enzyme Activity
Figure 15.3 The effect of enzyme concentration on the rate of
an enzyme-catalyzed reaction. Substrate concentration,
temperature, and pH are constant.
Enzyme Activity
Figure 15.4 The effect of substrate concentration on the
rate of an enzyme-catalyzed reaction. Enzyme
concentration, temperature, and pH are constant.
Enzyme Activity
Figure 15.5 The effect of temperature on the rate of an
enzyme-catalyzed reaction. Substrate and enzyme
concentrations and pH are constant.
Enzyme Activity
Figure 15.6 The effect of pH on the rate of an enzymecatalyzed reaction. Substrate and enzyme
concentrations and temperature are constant.
Mechanism of Action
Figure 15.7 Lock-and-key model of enzyme mechanism.
• The enzyme is a rigid three-dimensional body.
• The enzyme surface contains the active site.
Mechanism of Action
Figure 15.8 The Induced-fit model of an enzyme mechanism.
• The active site becomes modified to accommodate the
substrate.
Mechanism of Action
Figure 23.9 The mechanism of competitive inhibition.
When a competitive inhibitor enters the active site, the
substrate cannot enter.
Mechanism of Action
Figure 15.10 Mechanism of noncompetitive inhibition. The
inhibitor binds itself to a site other than the active site
(allosterism), thereby changing the conformation of the active
site. The substrate still binds but there is no catalysis.
Mechanism of Action
Figure 15.11 Enzyme kinetics in the presence and the absence
of inhibitors.
Mechanism of Action
• Both the lock-and-key model and the induced-fit model
emphasize the shape of the active site.
• However, the chemistry of the active site is the most
important.
• Just five amino acids participate in the active site in more
than 65% of the enzymes studied to date.
• These five are His > Cys > Asp > Arg > Glu.
• Four of these amino acids have either acidic or basic side
chains; the fifth has a sulfhydryl group (-SH).
Catalytic Power
•
Figure 15.12 Enzymes provide an alternative pathway for
reaction. (a) The activation energy profile for a typical
reaction. (b) A comparison of the activation energy profiles for
a catalyzed and uncatalyzed reactions.
Enzyme Regulation
Feedback control: An enzyme-regulation process where
the product of a series of enzyme-catalyzed reactions
inhibits an earlier reaction in the sequence.
• The inhibition may be competitive or noncompetitive.
Enzyme Regulation
•
Proenzyme (zymogen): An inactive form of an enzyme that
must have part of its polypeptide chain hydrolyzed and
removed before it becomes active.
• An example is trypsin, a digestive enzyme.
• It is synthesized and stored as trypsinogen, which has no
enzyme activity.
• It becomes active only after a six-amino acid fragment is
hydrolyzed and removed from the N-terminal end of its
chain.
• Removal of this small fragment changes not only the
primary structure but also the tertiary structure, allowing
the molecule to achieve its active form.
Enzyme Regulation
Allosterism: Enzyme regulation based on an event
occurring at a place other than the active site but
that creates a change in the active site.
• An enzyme regulated by this mechanism is called
an allosteric enzyme.
• Allosteric enzymes often have multiple
polypeptide chains.
• Negative modulation: Inhibition of an allosteric
enzyme.
• Positive modulation: Stimulation of an allosteric
enzyme.
• Regulator: A substance that binds to an allosteric
enzyme.
Enzyme Regulation
•
Figure 15.14 The
allosteric effect.
Binding of the
regulator to a site other
than the active site
changes the shape of
the active site.
Enzyme Regulation
Figure 15.15 Effects of binding activators and inhibitors to
allosteric enzymes. The enzyme has an equilibrium between
the T form and the R form.
Enzyme Regulation
Protein modification: The process of affecting enzyme activity
by covalently modifying it.
• The best known examples of protein modification involve
phosphorylation/dephosphorylation.
• Example: Pyruvate kinase (PK) is the active form of the
enzyme; it is inactivated by phosphorylation to pyruvate
kinase phosphate (PKP).
Enzyme Regulation
Isoenzyme (Isozymes): An enzyme that occurs in
multiple forms; each catalyzes the same reaction.
• Example: lactate dehydrogenase (LDH) catalyzes the
oxidation of lactate to pyruvate.
• The enzyme is a tetramer of H and M chains.
• H4 is present predominately in heart muscle.
• M4 is present predominantly in the liver and in
skeletal muscle.
• H3M, H2M2, and HM3 also exist.
• H4 is allosterically inhibited by high levels of pyruvate
while M4 is not.
• H4 in serum correlates with the severity of heart
attack.
Enzyme Regulation
Figure 15.16 The isozymes of lactate dehydrogenase (LDH).
The electrophoresis gel depicts the relative isozyme types found
in different tissues.
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Enzymes Used in Medicine
Table 15.2 – Enzyme Assays useful in Medical Diagnosis
Insert Table 23.2, page 648
Transition-State Analogs
•
•
Transition state analog: A molecule whose shape mimics the
transition state of a substrate.
Abzyme: An antibody that has catalytic activity because it
was created using a transition state analog as an
immunogen. (a) The molecule below is a transition analog for
the reaction of an amino acid with pyridoxal-5’-phosphate.
Transition-State Analogs

The abzyme is
then used as a
catalyst
Catalytic Antibodies Against
Cocaine
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Catalytic Antibodies Against
Cocaine
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