enzymes Flashcards
enymes
In 1878, Kuhne coined the term enzyme from the greek enzumos , which refers to the leavening of bread by yeast.
However, the modern term refers to:
The biological catalysts in the form of globular proteins that facilitate chemical reactions in the cell of living organisms.
The vast majority of all known enzymes are globular proteins.
Ribozymes are enzymes made of ribonucleic acids.
catalytic effecincy
Enzymes are true catalysts that speed chemical reactions by lowering activation energies and allowing reactions to achieve equilibrium more rapidly.
They increase reaction rates by anywhere from 109 to 1020 times.
characteristics of enzymes
Enzymes are well suited to their essential roles in living organisms in three major ways:
They have enormous catalytic power,
They are highly specific in the reactions they catalyze, and
Their activity as catalysts can be regulated.
enzyme nomenclatue
Some of the earliest discovered enzymes were given names ending with -in to indicate their protein composition.
For example, three of the digestive enzymes that catalyze protein hydrolysis are named pepsin, trypsin, and chymotrypsin.
However, these names provide no information regarding enzyme function or the substrate on which enzyme is acting.
For this purpose, the International Union of Biochemistry (IUB) adopted a systematic nomenclature of enzymes that was prepared by its Enzyme Commission (EC).
specifity
Enzymes, unlike other catalysts, are often quite specific in the type of reaction they catalyze and even the particular substance that will be involved in the reaction.
For example, strong acids catalyze the hydrolysis of any amide, the dehydration of any alcohol, and a variety of other processes.
However, the enzyme urease catalyzes only the hydrolysis of a single amide, urea. (Absolute specificity)
Other enzymes display relative specificity by catalyzing the reaction of structurally related substances.
For example, the lipases catalyze the hydrolysis of any triglycerides.
The specificity of enzymes also extends to stereochemical specificity.
For example, the enzyme arginase hydrolyzes the amino acid L-arginine but has no effect on its enantiomer, D-arginine.
regulation
A third significant property of enzymes is that their catalytic behavior can be regulated.
Even though each living cell contains thousands of different molecules that could react with each other in an almost unlimited number of ways, only a relatively small number of these possible reactions take place because of the enzymes present.
The cell controls the rates of these reactions and the amount of any given product formed by regulating the action of the enzymes.
EC system
In the EC system, each enzyme has an unambiguous (and often long) systematic name that Specifies:
-The substrate (substance acted on),
-The functional group acted on, and
-the type of reaction catalyzed.
All EC names end in -ase.
The hydrolysis of urea provides a typical example:
EC Name: urea amidohydrolase
Substrate: urea
Functional Group: amide
Type of Reaction: hydrolysis
classifiation of enzymes based on the IUB system
According to IUB system of enzyme classification, enzymes are grouped into six major classes on the basis of the reaction catalyzed.
NO.
GROUP NAME
TYPE OF REACTION CATALYZED
oxidoreductase: oxidation-reduction reaction
transferases- transfer of functional groups
hydolases- hydrolysis reaction
lyases- addition t doube bonds or the reverse of that reaction
isomerases- isomerazation reaction
ligases- formation of bonds with ATP cleavage
example of oxidoreductase
lactate dehydrogenase
ex of transferases
Aspartate aminotransferase or Aspartate transaminase
ex of Hydrolases
Acetylcholinesterase
ex of lyases
aconitase
ex of isomerases
phosphohexose isomerase
ex of ligases
Tyrosine-tRNA synthetase
prosthetic groups
If nonprotein components are tightly bound to and form an integral part of the enzyme structure, they are true prosthetic groups.
cofactor
A cofactor is a non-protein molecule that supports a biochemical reaction. Cofactors can take the form of metal ions, organic substances or other molecules with beneficial characteristics not typically present in amino acids.
coenzyme
When the cofactor is an organic substance, it is called a coenzyme.
apoenzyme
The protein portion of enzymes requiring a cofactor is called the apoenzyme.
enzyme–substrate (ES) complex.
About 100 years ago, Arrhenius suggested that catalysts speed up reactions by combining with the substrate to form some kind of intermediate compound.
In an enzyme-catalyzed reaction, this intermediate is called the enzyme–substrate (ES) complex.
The ES complex is formed when a substrate molecule binds to the active site of an enzyme.
This binding occurs through hydrophobic interactions, hydrogen binding, and/or ionic binding.
Once this complex is formed, the conversion of substrate (S) to product (P) may take place:
active ezyme
the combination of an apoenzyme and a cofactor produces an active enzyme:
model
The chemical transformation of the substrate occurs at the active site, usually aided by enzyme functional groups that participate directly in the making and breaking of chemical bonds.
After chemical conversion has occurred, the product is released from the active site, and the enzyme is free for another round of catalysis.
To account for the high substrate specificity of most enzyme-catalyzed reactions, a number of models have been proposed.
Lock-and-Key Model
Induced-Fit Model
lock and key model
According to the lock-and-key theory, enzyme surfaces will accommodate only those substrates having specific shapes and sizes.
Thus, only specific substrates “fit” a given enzyme and can form complexes with it, just as only the proper key can fit exactly into a lock and turn it open.
A limitation of the lock-and-key theory is the implication that enzyme conformations are fixed or rigid.
induced fit model
Induced-fit model was introduced by an American biochemist, Daniel Koshland.
Induced-fit model proposes that enzymes have somewhat flexible conformations to accommodate incoming substrates.
The active site has a shape that becomes complementary to that of the substrate only after the substrate is bound.
enzyme acitivity
Enzyme activity refers in general to the catalytic ability of an enzyme to increase the rate of a reaction.
turnover number
Enzyme activity is measured by turnover number, which is defined as:
“The number of substrate molecules converted into product per unit time, when the enzyme is fully saturated with substrate.”
For most enzymes, the turnover numbers fall between 1 to 104 per second.
The turnover number of 600,000/sec for carbonic anhydrase is one of the largest known.
factors affecting enzyme
Several factors affect the rate of enzyme-catalyzed reactions.
The most important factors are:
Enzyme concentration,
Substrate concentration,
Temperature, and
pH.
enzyme concentration
In an enzyme-catalyzed reaction, the concentration of enzyme is normally very low compared with the concentration of substrate.
When the enzyme concentration is increased, the concentration of ES also increases in compliance with reaction rate theory:
Thus, If we keep the concentration of substrate constant and increase the concentration of enzyme, the rate increases linearly.
That is, if the enzyme concentration doubles, the rate of conversion of substrate to product doubles as well.
substrate concentration
Conversely, if we keep the concentration of enzyme constant and increase the concentration of substrate, we get a saturation curve.
In this case, the rate does not increase continuously.
Instead, a point is reached after which the rate stays the same even if we increase the substrate concentration further.
This happens because at the saturation point, substrate molecules are bound to all available active sites of the enzymes and the reaction is proceeding at its maximum rate (symbolized by Vmax).
Increasing the substrate concentration can no longer increase the rate because the excess substrate cannot find any active sites to which to bind.
temperature
Enzyme-catalyzed reactions, like all chemical reactions, have rates that increase with temperature.
However, because enzymes are proteins, there is a temperature limit beyond which the enzyme becomes vulnerable to denaturation
Thus, every enzyme catalyzed reaction has an optimum temperature, usually in the range 25°C–40°C.
Above or below that value, the reaction rate will be lower
effect of pH
As the pH of its environment changes the conformation of a protein, we would expect pH-related effects to resemble those observed when the temperature changes.
Each enzyme operates best at a certain optimum pH.
Many enzymes have an optimum pH near 7, the pH of most biological fluids.
As the pH of its environment changes the conformation of a protein, we would expect pH-related effects to resemble those observed when the temperature changes.
Each enzyme operates best at a certain optimum pH.
Many enzymes have an optimum pH near 7, the pH of most biological fluids.
Michaelis Menten Approach to Enzyme Kinetics
A particularly useful model for the kinetics of enzyme-catalyzed reactions was devised in 1913 by Leonor Michaelis and Maud Menten.
It helps to describe many enzymatic reactions under the following assumptions:
The reaction has only one substrate
The substrate concentration is much higher than that of the enzyme in the system
Only the initial rate of enzyme activity is measured.
A typical reaction might be the conversion of some substrate, S, to a product, P.
The stoichiometric equation for the reaction is:
E -> S
enzye inhibition
An enzyme inhibitor is any substance that can decrease the rate of an enzyme-catalyzed reaction.
Such a process is known as enzyme inhibition.
Enzyme inhibitors are classified into two categories on the basis of how they behave at the molecular level.
Reversible Inhibitors
Irreversible Inhibitors
overall rxn Michaelis Menten Approach to Enzyme Kinetics
The overall reaction can be written as:
In this reaction, an enzyme (E) combines with the substrate (S) to form ES complex with a rate constant k1.
The ES complex formed can dissociate back to E and S with a rate constant k-1, or it can give rise to a product (P) and regenerated enzyme with a rate constant k2 .
irreverible inhibitors
An irreversible inhibitor forms a covalent bond with a specific functional group of the enzyme and as a result renders the enzyme inactive.
In fact, an irreversible inhibitor dissociates very slowly from its target enzyme because it becomes very tightly bound to its active site, thus inactivating the enzyme molecule.
A number of very deadly poisons act as irreversible inhibitors.
The cyanide ion (CN2) is an example of an irreversible enzyme inhibitor.
It is extremely toxic and acts very rapidly. The cyanide ion interferes with the operation of an iron-containing enzyme called cytochrome oxidase.
The ability of cells to use oxygen depends on the action of cytochrome oxidase.
When the cyanide ion reacts with the iron of this enzyme, it forms a very stable complex and the enzyme can no longer function properly.
As a result, cell respiration stops, causing death in a matter of minutes
reversible
A reversible inhibitor (in contrast to one that is irreversible) reversibly binds to an enzyme.
A reversible inhibitor dissociates very rapidly from its target enzyme because it becomes very loosely bound with the enzyme.
There are two types of reversible inhibitors:
Competitive and
Non-competitive.
competitive inhibitor
A competitive inhibitor binds to the active site of an enzyme and thus “competes” with substrate molecules for the active site.
Competitive inhibitors often have molecular structures that are similar to the normal substrate of the enzyme.
The nature of competitive inhibition is represented in Figure.
There is competition between the substrate and the inhibitor for the active site.
Once the inhibitor combines with the enzyme, the active site is blocked, preventing further catalytic action.
example of competitive inhibitor
The competitive inhibition of succinate dehydrogenase by malonate is a classic example.
Succinate dehydrogenase catalyzes the oxidation of the substrate succinate to form fumarate by transferring two hydrogens to the coenzyme FAD:
Malonate, having a structure similar to succinate, competes for the active site of succinate dehydrogenase and thus inhibits the enzyme.
The enzyme can be also inhibited by oxalate and glutarate because of the similarity of this substance with succinate.
The action of sulfa drugs on bacteria is another example of competitive enzyme inhibition.
Folic acid, a substance needed for growth by some disease-causing bacteria, is normally synthesized within the bacteria by a chemical process that requires p-aminobenzoic acid (PABA).
Sulfanilamide and other sulfa drugs are structural analogues of PABA.
Because sulfanilamide, the first sulfa drug, resembles p-aminobenzoic acid and competes with it for the active site of the bacterial enzyme involved, it can prevent bacterial growth.
This is possible because the enzyme binds readily to either of these molecules.
Therefore, the introduction of large quantities of sulfanilamide into a patient’s body causes most of the active sites to be bound to the wrong (from the bacterial viewpoint) substrate.
Thus, the synthesis of folic acid is stopped or slowed, and the bacteria are prevented from multiplying.
Human beings also require folic acid, but they get it from their diet.
Consequently, sulfa drugs exert no toxic effect on humans.
non competitive inhibition
noncompetitive inhibitor bears no resemblance to the normal enzyme substrate and binds reversibly to the surface of an enzyme at a site other than the catalytically active site.
The interaction between the enzyme and the noncompetitive inhibitor causes the three-dimensional shape of the enzyme and its active site to change.
The enzyme no longer binds the normal substrate, or the substrate is improperly bound in a way that prevents the catalytic groups of the active site from participating in catalyzing the reaction.
Unlike competitive inhibition, noncompetitive inhibition cannot be reversed by the addition of more substrate because additional substrate has no effect on the enzyme bound inhibitor.
Various heavy metals ions (Ag+, Hg2+, Pb2+ ) inhibit the activity of a variety of enzymes.
Urease, for example, is highly sensitive to any of these ions in traces.
Heavy metals form mercaptides with sulfhydryl (-SH) groups of enzymes :
Enz—SH + Ag+ ⇄ Enz—SH—Ag + H+
how are enzymes regulated
Enzymes work together in an organized yet complicated way to facilitate all the biochemical reactions needed by a living organism.
For an organism to respond to changing conditions and cellular needs, very sensitive controls over enzyme activity are required.
Three mechanisms by which this is accomplished are:
Activation of zymogens,
Allosteric regulation, and
Genetic control.
activation of zygomes
Some enzymes are manufactured by the body in an inactive form.
To make them active, a small part of their polypeptide chain must be removed.
These inactive forms of enzymes are called proenzymes or zymogens.
After the excess polypeptide chain is removed, the enzyme becomes active.
For example, trypsin is manufactured in the pancreas as the inactive
molecule trypsinogen (a zymogen).
allosteric regulation
A second method of enzyme regulation involves the combination of the enzyme with some other compound such that the three-dimensional conformation of the enzyme is altered and its catalytic activity is changed.
Compounds that alter enzymes this way are called modulators of the activity.
Modulator may affect the enzyme in either of two ways:
It may inhibit enzyme action; inhibitors (negative modulation) or
It may stimulate enzyme action; activators (positive modulation).
Enzymes that have a quaternary protein structure with distinctive binding sites for modulators are referred to as allosteric enzymes.
The site to which a modulator attaches is called a regulatory site.
Specific modulators can bind reversibly to the regulatory sites.
For example, the enzyme depicted in Figure is an allosteric enzyme.
example of allostric regualation
An excellent example of allosteric regulation—the control of an allosteric enzyme—is the five-step synthesis of the amino acid isoleucine.
Threonine deaminase, the enzyme that catalyzes the first step in the conversion of threonine to isoleucine, is subject to inhibition by the final product, isoleucine.
Isoleucine exerts an inhibiting effect on the enzyme activity.
This type of allosteric regulation in which the enzyme that catalyzes the first step of a series of reactions is inhibited by the final product is called feedback inhibition.
genetic control
One way to increase production from an enzyme-catalyzed reaction, given a sufficient supply of substrate, is for a cell to increase the number of enzyme molecules present.
The synthesis of all proteins, including enzymes, is under genetic control by nucleic acids.
An example of the genetic control of enzyme activity involves enzyme induction, the synthesis of enzymes in response to a temporary need of the cell.
