chapter8 Flashcards
A nucleophile
A nucleophile is a chemical that is attracted to regions of positive charge in another molecule. A nucleophile participates in a chemical reaction by donating electrons to another chemical, called the electrophile
covalent catalysis
the active site contains a reactive group, usually a powerful nucleophile that becomes temporarily covalently modified in the course of catalysis.
Covalent catalysis relies on the formation of a covalent bond between the catalyst and substrate to lower the activation energy of the reaction. This type of catalysis involves a direct chemical modification of the substrate by the catalyst.
General Acid–Base Catalysis
In general acid–base catalysis, a molecule other than water plays the role of a proton donor or acceptor.
Metal Ion Catalysis (3)
Metal ions can function catalytically in several ways. For instance, a metal ion may serve as an electrophilic catalyst, stabilizing a negative charge on a reaction intermediate. Alternatively, a metal ion may generate a nucleophile by increasing the acidity of a nearby
molecule such as water. Finally, a metal ion may bind to the substrate, increasing the number of interactions with the enzyme and thus the binding energy. Metal ions are
required cofactors for many of the enzymes we will encounter in our study of biochemistry.
Catalysis by Approximation and Orientation
Many reactions include two distinct substrates. In such cases, the reaction rate may be considerably enhanced by bringing the two substrates into proximity and in the proper orientation on a single binding surface of an enzyme.
Catalysis by approximation and orientation involves bringing reactant molecules into close proximity and correct orientation to enhance the likelihood of a reaction occurring. This type of catalysis is particularly relevant in enzyme-catalyzed reactions, where enzymes position substrates favorably for reaction.
The full complement of binding interactions between an enzyme and a substrate is formed only when ——
the substrate is in the transition state
The pH dependence of enzymes is due to the presence of —–
ionizable R groups
reversible inhibition is characterized by …..
rapid dissociation of the enzyme–inhibitor complex
There are three common types of reversible inhibition:
competitive inhibition, uncompetitive inhibition, and noncompetitive inhibition
competitive inhibition (4)
inhibitor description+ what happens+ how to relieve+diminishes
- the inhibitor resembles the substrate and binds to the active site of the enzyme
- The substrate is thereby prevented from binding to the same active site.
- diminishing the proportion of enzyme molecules that are bound to substrate
- At any given inhibitor concentration, competitive inhibition can be relieved by increasing the substrate concentration. Under these conditions, the substrate “outcompetes” the inhibitor for the active site.
Uncompetitive inhibition (2)
What it is+cannot be…
- The uncompetitive inhibitor’s binding site is created
only when the enzyme binds the substrate (the inhibitor binds only to the enzyme–substrate complex) - cannot be overcome by the addition of more substrate
noncompetitive inhibition (2)
binding site+acts by…
- the inhibitor and substrate can bind simultaneously to an enzyme molecule at different binding sites
- A noncompetitive inhibitor acts by decreasing the overall number of active enzyme molecules
Noncompetitive inhibition, in contrast with competitive inhibition, cannot be overcome by ….
increasing the substrate concentration
In the presence of a competitive inhibitor, an enzyme will have the same —— as in the absence of an inhibitor. The effect of a competitive inhibitor is to increase the apparent value of —— meaning that more substrate is needed to obtain the same reaction rate.
- Vmax
- Km
uncompetitive inhibition Vmax, [s] and Km
- In uncompetitive inhibition, the inhibitor binds only to the ES complex. This enzyme–substrate–inhibitor complex, ESI, does not proceed to form any product. Because some unproductive ESI complex will always be present, Vmax will be lower in the presence of an inhibitor than in its absence
- The uncompetitive inhibitor also lowers the apparent value of Km, because the inhibitor binds to ES to form ESI, depleting ES. A lower concentration of S is required to form half of the maximal concentration of ES, resulting in a reduction of the apparent value of Km
In noncompetitive inhibition Vmax and Km
- a substrate can bind to the enzyme–inhibitor complex as well as to the enzyme alone. In either case, the enzyme inhibitor–substrate complex does not proceed to form product. The value of Vmax is decreased.
- the value of Km is unchanged
Competitive inhibition illustrated on a double-reciprocal plot
Uncompetitive inhibition illustrated on a double-reciprocal plot.
Noncompetitive inhibition illustrated on a double-reciprocal plot
irreversible inhibitor dissociates very —- from its target enzyme because it has become ——
- slowly
- tightly bound to the enzyme, either covalently or non-covalently
least specific
Group-specific reagents (2)
+specific for…
- modify specific R groups of amino acids
- specific for a particular reactive R group, not specific for a particular enzyme
Affinity labels, also called substrate analogs
- molecules that covalently modify active-site residues and are structurally similar to an enzyme’s substrate
- covalently bind to their target causing its inactivation
- Affinity labels are small molecules or compounds that possess structural similarities to a substrate of an enzyme or receptor. They are designed to bind tightly and specifically to the active site of the enzyme or receptor. The key characteristic of affinity labels is their ability to covalently modify the active site or nearby residues upon binding. This modification can disrupt the enzyme’s function or signaling activity, essentially “labeling” or altering the active site irreversibly. Affinity labels are often used in biochemical studies to probe enzyme-substrate interactions and mechanisms.
most specific
Suicide inhibitors, or mechanism-based inhibitors
The inhibitor binds to the enzyme as a substrate and is initially processed by the normal catalytic mechanism. The mechanism of catalysis then generates a chemically reactive intermediate that inactivates the enzyme through covalent modification.
transition state analog
A transition state analog, one exhibiting the same properties such as shape and charge of the original transition molecule, may come in and bind. Although the analog displays similar properties as the original transition molecule, but it has higher affinity for the enzyme than the natural substrate and will ultimately deactivate and inhibit the enzyme and prevent it from binding to a substrate.
suicide vs affinity
Affinity influences the binding strength between molecules, affecting enzymatic activity or signaling.
Suicide inhibition irreversibly modifies the enzyme’s active site, disrupting its function permanently.
Oxidoreductases
These enzymes transfer electrons between molecules. In other words, these enzymes catalyze oxidation–reduction reactions
Transferases
These enzymes transfer functional groups
between molecules
Hydrolyases
A hydrolyase cleaves molecules by the addition of water.
Lyases
A lyase adds atoms or functional groups to a double
bond or removes them to form double bonds.
Isomerases
These enzymes move functional groups within a molecule.
Ligases
join two molecules in a reaction powered
by ATP hydrolysi
Translocases
Catalyze movement of ions or molecules across membranes or their seperation within membranes
Protein breakdown is catalyzed by a large class of enzymes called —– and they —–
- proteolytic enzymes or proteases.
- cleave proteins by a hydrolysis reaction—the addition of a molecule of water to a peptide bond
chymotrypsin, which is secreted by the pancreas in response to a —-
meal
Chymotrypsin cleaves peptide bonds selectively on …..
the carboxyl-terminal side of the large hydrophobic amino acids such as tryptophan, tyrosine, phenylalanine, methionine, and isoleucine
How does chymotrypsin use covalent modification?
The enzyme employs a powerful nucleophile to attack the unreactive carbonyl group of the substrate. This nucleophile becomes covalently attached to the substrate briefly in the course of catalysis.
catalytic triad
The side chain of serine 195 is hydrogenbonded to the imidazole ring of histidine 57. The NH group of this imidazole ring is, in turn, hydrogen-bonded to the carboxylate group of aspartate 102
The catalytic triad, shown on the below,
converts serine 195 into a potent —-
nucleophile
What is the purpose of the oxyanion hole in chymotrypsin?
to stabilise the tetrahedral intermediate anion formed during proteolysis and protects substrate’s negatively charged oxygen from water molecules.
