80
BG McGraw-Hill: Gilbert, Basic Concepts in Biochemistry, JN 5036
•
C H A P T E R
•
7
•
ENZYME MECHANISM
•
Active Site
Transition State
Catalysis
Lock and Key
Induced Fit
Nonproductive Binding
Entropy
Strain and Distortion
Transition-State Stabilization
Transition-State Analogs
Chemical Catalysis
•
•
•
•
•
•
•
•
•
•
•
•
Enzymes do two important things: they recognize very specific sub-
strates, and they perform specific chemical reactions on them at fantas-
tic speeds. The way they accomplish all this can be described by a
number of different models, each one of which accounts for some of the
behavior that enzymes exhibit. Most enzymes make use of all these dif-
ferent mechanisms of specificity and/or catalysis. In the real world, some
or all of these factors go into making a given enzyme work with exqui-
site specificity and blinding speed.
7 Enzyme Mechanism
• 81 •
BG McGraw-Hill: Gilbert, Basic Concepts in Biochemistry, JN 5036
The active site of an enzyme is generally a pocket or cleft that is
specialized to recognize specific substrates and catalyze chemical trans-
formations. It is formed in the three-dimensional structure by a col-
lection of different amino acids (active-site residues) that may or may
not be adjacent in the primary sequence. The interactions between the
active site and the substrate occur via the same forces that stabilize pro-
tein structure: hydrophobic interactions, electrostatic
interactions
(charge–charge), hydrogen bonding, and van der Waals interactions.
Enzyme active sites do not simply bind substrates; they also provide cat-
alytic groups to facilitate the chemistry and provide specific interactions
that stabilize the formation of the transition state for the chemical reac-
tion.
During a chemical reaction, the structure of the substrate changes
into the structure of the product. Somewhere in between, some bonds are
partly broken; others are partly formed. The transition state is the high-
est-energy arrangement of atoms that is intermediate in structure between
t