Chapter 11: Enzymatic Catalysis Flashcards
Enzymes differ from ordinary chemical catalysts in several important respects
Higher reaction rates
Milder reaction conditions
Greater reaction specificity
Capacity for regulation
catalyzes the oxidation of alcohols by
removing hydrogen
alcohol dehydrogenase
catalyzes the
hydrolysis of urea
urease
Enzymes are commonly named by what?
appending the suffix-ase to the name of the enzyme’s substrate or to a phrase describing the enzyme’s catalytic action
oxidation-reduction reactions
oxidoreductases
transfer of functional groups
Transferases
hydrolysis reactions
hydrolases
group elimination to form double bonds
lyases
isomerization
isomerases
bond formation coupled with atp hydrolysis
ligases
vary considerably in their degree of geometric specificity
Enzymes
Although enzymes catalyze such reactions, they can do so only in
association with small
cofactors
what are types of cofactors
metal
coenzymes
organic molecules
coenzymes
types of coenzymes
cosubstrates
prosthetic groups
Permanently associated cofactors like
heme in cytochrome c.
prosthetic groups
A catalytically active enzyme–cofactor complex is called
holoenzyme.
The holoenzyme without the cofactor
apoenzyme
If the activation energy of the 2nd step is greater than that of the
1st step, then the 2nd step is “bottleneck” or the
rate-determining step
act by providing a reaction pathway with a transition state whose free energy is lower than that in the original reaction.
Catalysts
The types of catalytic mechanisms that enzymes employ have been classified as
- Acid–base catalysis
- Covalent catalysis
- Metal ion catalysis
- Proximity and orientation effects
- Preferential binding of the transition state complex
a process in which proton transfer from an acid lowers the
free energy of a reaction’s transition state.
General acid catalysis
the ability of enzymes to arrange several catalytic groups around their substrates makes concerted acid–base catalysis what
enzymatic mechanism
the inflection points of the curve
observed pK
often provide valuable clues to the
identities of the amino acid residues essential for enzymatic activity
observed pK’s
pH effects on an enzymatic rate may reflect what
denaturation
is a more reliable approach to
identifying residues that are required for substrate binding or catalysis.
The replacement of a particular residue by site-directed mutagenesis or comparisons of enzyme variants generated by evolution
is a digestive enzyme that is secreted by the pancreas into the small intestine, where it hydrolyzes RNA to its component nucleotides.
Bovine pancreatic RNase A
acting as a general base,
abstracts a proton from an RNA 2′
-OH group, thereby promoting its nucleophilic attack on the adjacent phosphorus atom
His 12
acting as a general acid, promotes bond scission by protonating the leaving group.
His 119
accelerates reaction rates through the transient formation of a catalyst–substrate covalent bond
Covalent catalysis
Usually, this covalent bond is formed by the reaction of a nucleophilic group on the catalyst with an electrophilic group on the
substrate, and hence this form of catalysis is often also called
nucleophilic catalysis
function in association with their apoenzymes as covalent catalysts
pyridoxal phosphate
enzymes require metal ions for catalytic activity
metalloenzymes
which often play a structural rather than a catalytic role in enzymes.
Na+
K+
Ca2+
Mg2+
Zn2+
contain tightly bound metal ion cofactors, most commonly
transition metal ions such as
Fe2+
Fe3+
Cu2+
Mn2+
Co2+
metalloenzymes
Metal ions participate in the catalytic process in 3 major ways
- By binding to substrates to orient them properly for reaction.
- By mediating redox reactions through reversible changes in the metal ion’s oxidation state.
- By electrostatically stabilizing or shielding negative charges.
By simply binding their substrates, enzymes facilitate their catalyzed reactions in 4 ways
- Enzymes bring substrates into contact with their catalytic groups and, in reactions with more than
one substrate, with each other to enhance reaction rates by a factor of ~5. - Enzymes bind their substrates in the proper orientations for reaction. It is estimated that properly
orienting substrates can increase reaction rates by a factor of up to ~100. - Charged groups may help stabilize the transition state of the reaction, a phenomenon termed
electrostatic - Enzymes freeze out the relative translational and rotational motions of their substrates and catalytic
groups. This is an important aspect of catalysis because, in the transition state, the reacting groups
have little relative motion. Indeed, experiments with model compounds suggest that this effect can
promote rate enhancements of up to ~107
Enzymes Catalyze Reactions by Preferentially what the Transition State
Binding
An enzyme may bind the transition state of the reaction it catalyzes with what?
greater affinity than its substrates or products.
stable molecules that geometrically and electronically resemble the transition state
analogs
If an enzyme preferentially binds its transition state, then it can be expected that transition state what?
analogs
is an enzyme that destroys bacterial cell walls.
Lysozyme
include digestive enzymes from prokaryotes and eukaryotes, as well as more specialized proteins that participate in development, blood coagulation (clotting), inflammation, and numerous other processes.
Serine proteases
The best studied serine proteases are
chymotrypsin, trypsin, and elastase
what are serine proteases synthesized by
pancreas and secreted into the small intestine
what do serine proteases catalyze
hydrolysis of peptide (amide) bonds but with different specificities
is specific for a bulky hydrophobic residue (Phe, Trp, or T yr )
Chymotrypsin
specific for a positively charged residue (Arg and Lys)
trypsin
is specific for a small neutral residue (Ala, Gly , and Val).
elastase
reacts only with Ser 195 of chymotrypsin, thereby demonstrating that this residue is the enzyme’s active site Ser.
Diisopropylphosphofluoridate (DIPF)
are so toxic to
humans (death occurs through the inability to breathe) that it
has been used militarily as a nerve gas
Diisopropylphosphofluoridate (DIPF)
DIPF inactivates what?
acetylcholinesterase
is responsible for much of the catalytic efficiency of serine proteases
preferential binding of the transition state over the enzyme-substrate complex
such an effective inhibitor of serine
proteases because its tetrahedral phosphate group makes this compound a transition state analog.
DIPF
