Download Enzymes: Principles of Catalysis

Chapter 6.1 and 6.2:
Introduction to Enzymes
CHEM 7784
Biochemistry
Professor Bensley
CHAPTER 6.1 and 6.2
Introduction to Enzymes and How
Enzymes Work
Today’s Objectives: (To learn and understand the)
– Physiological significance of enzymes
– Origin of catalytic power of enzymes
– Chemical mechanisms of catalysis
What are Enzymes?
• Enzymes are catalytically active
biological macromolecules
• Most enzymes are globular proteins,
however some RNA (ribozymes, and ribosomal
RNA) also catalyze reactions
• Study of enzymatic processes is the oldest
field of biochemistry, dating back to late
1700s
Why Biocatalysis?
•
•
•
•
Higher reaction rates
Greater reaction specificity
Milder reaction conditions
Capacity for regulation
COO
-
COO
NH2
O
OH
COO
OH
COO
Chorismate
mutase
COO
OOC
O
NH2
-
-
O
COO
COO
• Metabolites have
many potential
pathways of
decomposition
OH
-
• Enzymes make the
desired one most
favorable
Quiz Question 29
In order to function properly, some
enzymes require the presence of an
additional chemical component such
as inorganic ions (Zn2+ or Fe2+).
These inorganic ions are known as
for enzymes.
Quiz Question 30
Chymotrypsin is an enzyme that cleaves
peptide bonds. It most likely, therefore,
belongs to which class of enzymes?
a) Transferases
b) Ligases
c) Isomerases
d) Hydrolases
Classes of enzymes
1.
Oxidoreductases = catalyze oxidation-reduction
reactions (Transfer of electrons) (NADH)
2.
Transferases = catalyze transfer of functional groups
from one molecule to another.
3.
Hydrolases = catalyze hydrolytic cleavage (transfer of
functional groups to water)
4.
Lyases = catalyze removal of a group from or addition of
a group to a double bond, or other cleavages involving
electron rearrangement.
5.
Isomerases = catalyze intermolecular rearrangement.
6.
Ligases = catalyze reactions in which two molecules are
joined.
Enzymes named for the substrates and type of reaction
E
E S
+ S
E+S
k1
k-1
ES
E
k2
k-2
E+P
+
P
Rate Acceleration
• The enzyme lowers the activation barrier compared
to the uncatalyzed aqueous reaction
• In theory, the enzyme may also facilitate the tunneling
through the barrier. This may be important for
electrons.
How to Lower G?
1.
Enzymes organize
reactive groups into
proximity
2.
Enzymes bind transition
states best (Largely a
‡
H effect)
Support for the Proximity Model
• The rate of
anhydride
formation from
esters and
carboxylates
shows a strong
dependence on
proximity of two
reactive groups
Support for TS Stabilization
• Structure-activity correlations in chymotrypsin
substrates
Illustration of TS Stabilization Idea:
Imaginary Stickase
How is TS Stabilization
Achieved?
acid-base catalysis: give and take protons
covalent catalysis: change reaction paths
metal ion catalysis: use redox cofactors, pKa
shifters
electrostatic catalysis: preferential
interactions with TS
Acid-base Catalysis:
Chemical Example
Consider ester hydrolysis:
O
O
+
R
O CH3
H-OH
R
O
OH
O
+ H
+
+
R
CH3OH
OH
CH3
Water is a poor nucleophile, and methanol is a
poor leaving group
Aqueous hydrolysis can be catalyzed either by
acids or by bases
Enzymes can do acid and base catalysis
simultaneously
Amino Acids in General
Acid-Base catalysis
Covalent Catalysis: Chemical Example
O
O
CH3
O
H3C
O
H2O
slow
O
O
H3C
+
-
-
+
+
2 H
O
O
O
CH3
O
H3C
fast
O
+
N
CH3
..
N
..
H
O
O
..
N
O
H3C
O
+
H3C
O
+
N
+
H
H
CH3
OH
+
H3C
O
-
• The anhydride hydrolysis
reaction is catalyzed by
pyridine, a better
nucleophile than water
(pKa=5.5).
• Hydrolysis is accelerated
because of charge loss in
the transition state
makes pyridine a good
leaving group.
Covalent Catalysis: In Enzymes
• Proteases and peptidases
– chymotrypsin, elastase, subtilisin
– reactive serine nucleophile
• Some aldehyde dehydrogenase
– glyceraldehyde-3-phosphate dehydrogenase
– reactive thiolate nucleophile
• Aldolases and decarboxylases
– amine nucleophile
• Dehalogenases
– carboxylate nucleophile
NH
2
-
HO
O
S
-
O
N
O
N
O
N
O
N
O