1. Chemistry 501 Handout 6 Enzymes Chapter 6
Dep. of Chemistry & Biochemistry
Prof. Indig
Chemistry Handout 6 Enzymes Chapter 6
Lehninger. Principles of Biochemistry.
by Nelson and Cox, 5th Edition; W.H. Freeman and Company

2. Complete, catalytically active enzyme: holoenzyme
With exception of a small group of catalytic RNA molecules, all enzymes are proteins
Largest class of proteins. More than 3000 enzymes known. Enzymes are biological catalysts that accelerate reactions. Enzymes are generally highly specific and react with only one substrate to form one product and can enhance reaction rates by as much as 1017.
Some enzymes require cofactors / coenzymes for activity
Coenzymes act as transient carriers of specific functional groups
A cofactor or coenzymes that is very tightly or even covalently bound to the enzyme protein is called a prosthetic group.
Complete, catalytically active enzyme: holoenzyme
Only protein part (without cofactor and/or coenzyme): apoenzyme or apoprotein

3. Enzymes are classified by the reactions they catalyze
International Classification System (nomenclature):
(Four-part classification number and a systematic name)
Systematic name: ATP:glucose phosphotransferase
Classification number:
2. --> Transferase (class)
7. --> phosphotransferase (subclass)
1. --> phosphotransferase with a hydroxyl group as acceptor
1. --> D-glucose as the phosphoryl group acceptor
ATP + D-glucose --> ADP + D-glucose-6-phospate
Hexokinase

4. Binding of a substrate to an enzyme at the active site
Representation of a simple
enzymatic reaction
Enzymes affect reaction rates,
not equilibria
E + S  ES  EP  E + P
Reaction coordinate diagram for a chemical reaction
Reaction coordinate diagram comparing enzyme-catalyzed
and uncatalyzed reactions

5. S  P S → P Equilibrium Reaction Reaction rate = V = k [S]
If the rate depends only on the
concentration of S (first-order)
From the Transition-State Theory:

6. Weak interactions between enzyme and substrate are optimized in the transition state
The energy derived from enzyme-substrate
interaction is called binding energy, DGB
Enzyme active sites are complementary not
to the substrate per se, but to the transition
state through which substrates pass as they
are converted into products during an
enzymatic reaction
Complementary shapes of a substrate and its binding site on the enzyme
Role of binding energy in catalysis
An imaginary enzyme (sticase) designed to catalyze breakage of a metal stick

7. How a catalyst circumvents unfavorable charge
development during cleavage of a amide
Rate enhancements by entropy reduction
Specific
acid-base
catalysis
General
acid-base
catalysis
Hydrolysis of an amide bond - same reaction as
that catalyzed by chymotrypsin and other proteases

8. formation of covalent bonds with substrates
Amino acids in general acid-base catalysis
Covalent and general acid-base catalysis
First step of the reaction
His57
His57
Amino acid side chains and the functional groups of some cofactors can serve as nucleophiles in the
formation of covalent bonds with substrates

9. Enzyme Kinetics Michaelis-Menten kinetics initial rate measurements
Effect of substrate concentration on the initial velocity
of an enzyme-catalyzed reaction
Michaelis-Menten kinetics
initial rate measurements
[S] >> [E]
[ES] ~ constant
V0 = K2 [ES]
Michaelis constant

10. When km > > [S] When [S] > > km
Dependence of initial velocity on substrate concentration
When km > > [S]
When [S] > > km

11. A double-reciprocal or Lineweaver-Burk plot
Lineweaver-Burk equation

13. Kcat describes the limiting rate of any enzyme-catalyzed reaction at saturation

15. Many enzymes catalyze reactions with two or more substrates
Common mechanisms for enzyme-catalyzed bisubstrate reactions

16. Pre-steady state kinetics can provide evidence for specific reaction steps
Ternary complex is formed
in the reaction
(as indicated by the intersecting lines)
Ping-Pong (double displacement)
reaction

17. Enzymes are subject to reversible and irreversible inhibition

20. Enzymes are subject to reversible and irreversible inhibition

22. Irreversible inhibition
Reaction of chymotrypsin with
diisopropylfluorophosphate
irreversibly inhibits the enzyme
Suicide inactivators or
mechanism-based inactivators

23. Three polypeptide chains linked
Examples of Enzymatic Reactions
Chymotrypsin is a protease specific for peptide bonds adjacent to aromatic amino acids
(Trp, Tyr, Phe)
Key active-site amino acid
residues Ser195, His57, and
Asp102
Aromatic amino
acid side chain
Pocket in which the amino
acid side chain of the
substrate is bound
Three polypeptide chains linked
by disulfide bonds

24. The chymotrypsin mechanism involves acylation and
deacylation of a Ser residue

25. Regulatory Enzymes
Allosteric enzymes undergo conformational changes in response to modulator binding
Conformational change
Subunit interactions in an
allosteric enzyme, and
interactions with inhibitors
and activators

26. Two views of the regulatory enzyme aspartate transcarbamoylase
This allosteric regulatory enzyme has two stacked catalytic clusters, each with three
catalytic polypeptide chains (in shades of blue and purple) and three regulatory clusters, each with two regulatory peptide chains (in red and yellow).
Modulator binding produces large changes in enzyme conformation and activity

27. In many pathways a regulatory step is catalyzed by an
Feedback inhibition
Buildup of the end product ultimately
slows the entire pathway
In many pathways a regulatory
step is catalyzed by an
allosteric enzyme
Example of heterotropic
allosteric inhibition

28. Phosphoryl groups affect the structure and catalytic activity of enzymes
Regulation of muscle glycogen phosphorylase activity by multiple mechanisms

29. Activation of zymogens by
Some enzymes and other proteins are regulated by proteolytic cleavage of a precursor
Activation of zymogens by
proteolytic cleavage