2. Enzymes
Ribbon diagram of cytochromecoxidase, the
enzyme that directly uses oxygen during
respiration.
3. 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.
5. 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.
7. Classification of Enzymes
4. Lyase:
COO CH2
C-COOCH
+ H2O
Aconitase
COOCH2
C-COOHO C-H
-
COO-
COO
cis-Aconitate
Isocitrate
5. Isomerase:
CH2 OPO3 2Phosphohexose
O
isomerase
OH
OH
HO
OH
a-D- Glucose-6-phosphate
6. Ligase:
ATP + L-tyrosine + t-RNA
CH2 OPO3 2O
H HO
H
H
HO
CH2 OH
OH
a-D-Fructose-6-phosphate
Tyrosine-tRNA
synthetase
L-tyrosyl-tRNA + AMP + PPi
8. 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.
9. Schematic of an Active Site
Schematic diagram of
the active site of an
enzyme and the
participating
components.
10. 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.
11. Enzyme Activity
Enzyme activity: A measure of how much a
reaction rate is increased.
We examine how the rate of an enzymecatalyzed reaction is affected by:
– Enzyme concentration.
– Substrate concentration.
– Temperature.
– pH.
12. The effect of enzyme concentration on the rate
Substrate concentration, temperature, and pH are constant.
13. The effect of substrate concentration on the rate
Enzyme concentration, temperature, and pH are constant.
14. The effect of temperature on the rate
Substrate and enzyme concentrations and pH are constant.
15. The effect of pH on the rate
Substrate and enzyme concentrations and temperature are
constant.
16. Lock-and-key model
- The enzyme is a rigid three-dimensional body.
– The enzyme surface contains the active site.
19. 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.
21. 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).
22. Catalytic Power
• 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.
23. Enzyme Regulation
Feedback control: An enzyme-regulation process
where the product of a series of enzymecatalyzed reactions inhibits an earlier reaction in
the sequence.
– The inhibition may be competitive or
noncompetitive.
24. 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.
25. 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.
26. Enzyme Regulation
• The allosteric
effect. Binding of
the regulator to a
site other than
the active site
changes the
shape of the
active site.
27. Enzyme Regulation
Effects of binding activators and inhibitors to allosteric
enzymes. The enzyme has an equilibrium between
the T form and the R form.
28. 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: Pyruvatekinase (PK) is the active form of the
enzyme; it is inactivated by phosphorylation to
pyruvatekinase phosphate (PKP).
29. 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.
30. Enzyme Regulation
The isozymes of lactate dehydrogenase (LDH). The
electrophoresis gel depicts the relative isozyme
types found in different tissues.
32. Transition-State Analogs
• Transition state analog: A molecule whose
shape mimics the transition state of a
substrate.
• Figure 23.17 The prolineracemase reaction.
Pyrrole-2-carboxylate mimics the planar
transition state of the reaction (next screen).
34. Transition-State Analogs
• 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. (b) The abzyme is then
used to catalyze the reaction on the next screen.
