Assignment: to be submitted next year FIRST MEETING!

Yellow paper. handwritten. 10% of your prelim grade

1. Illustrate the RAAS 2. List some of anti-anemic drugs and their mode of actions 3. How can drug size and shape affect drug action

Enzymes ( /nzamz/) are proteins that catalyze (i.e., increase the rates of) chemical reactions.[1][2] In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.

Like all catalysts, enzymes work by lowering the activation energy (Ea) for a reaction, thus dramatically increasing the rate of the reaction. As a result, products are formed faster and reactions reach their equilibrium state more rapidly. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions. As with all catalysts, enzymes are not consumed by the reactions they catalyze, nor do they alter the equilibrium of these reactions. However, enzymes do differ from most other catalysts in that they are highly specific for their substrates. Enzymes are known to catalyze about 4,000 biochemical reactions.[3] A few RNA molecules called ribozymes also catalyze reactions, with an important example being some parts of the ribosome.[4][5] Synthetic molecules called artificial enzymes also display enzyme-like catalysis.[6]

Enzyme activity can be affected by other molecules. Inhibitors are molecules that decrease enzyme activity; activators are molecules that increase activity. Many drugs and poisons are enzyme inhibitors. Activity is also affected by temperature, chemical environment (e.g., pH), and the concentration of substrate. Some enzymes are used commercially, for example, in the synthesis of antibiotics. In addition, some household products use enzymes to speed up biochemical reactions (e.g., enzymes in biological washing powders break down protein or fat stains on clothes; enzymes in meat tenderizers break down proteins into smaller molecules, making the meat easier to chew).

Temperature - too cold the enzyme will still work but slowly, too hot and the enzyme will become denatured

pH - different types of enzymes work best in different pH environments

enzyme and substrate concentration - how many there is of each. eg. too many enzymes etcetera.

enzyme inhibitors

co-factors

1. Oxidoreductases catalyze a variety of oxidation-reduction reactions. Common names include dehydrogenase, oxidase, reductase and catalase.

2. Transferases catalyze transfers of groups (acetyl, methyl, phosphate, etc.). Common names include acetyltransferase, methylase, protein kinase and polymerase. The first three subclasses play major roles in the regulation of cellular processes. Their chemical reactions are shown in Figure 2-E-1. The polymerase is essential for the synthesis of DNA and RNA.

3. Hydrolases catalyze hydrolysis reactions where a molecule is split into two or more smaller molecules by the addition of water. Common examples are given below.

Proteases splits protein molecules. Examples: HIV protease and caspase. HIV protease is essential for HIV replication. Caspase plays a major role in apoptosis.

Nucleases splits nucleic acids (DNA and RNA). Based on the substrate type, they are divided into RNase and DNase. RNase catalyzes the hydrolysis of RNA and DNase acts on DNA. They may also be divided into exonuclease and endonuclease. The exonuclease progressively splits off single nucleotides from one end of DNA or RNA. The endonuclease splits DNA or RNA at internal sites.

Phosphatase catalyzes dephosphorylation (removal of phosphate groups). Example: calcineurin. The immunosuppressive drugs FK506 and Cyclosporin A are the inhibitors of calcineurin.

4. Lyases catalyze the cleavage of C-C, C-O, C-S and C-N bonds by means other than hydrolysis or oxidation. Common names include decarboxylase and aldolase.

5. Isomerases catalyze atomic rearrangements within a molecule. Examples include rotamase, protein disulfide isomerase (PDI), epimerase and racemase.

6. Ligases catalyze the reaction which joins two molecules. Examples include peptide synthase, aminoacyl-tRNA synthetase, DNA ligase and RNA ligase.

The IUBMB committee also defines subclasses and sub-subclasses. Each enzyme is assigned an EC (Enzyme Commission) number. For example, the EC number of catalase is EC1.11.1.6. The first digit indicates that the enzyme belongs to oxidoreductase (class 1). Subsequent digits represent subclasses and sub-subclasses.

4.General principles

Because of their close interdependence, it is convenient to deal with the classification and nomenclature together.

The first general principle of these 'Recommendations' is that names purporting to be names of enzymes, especially those ending in -ase, should be used only for single enzymes, i.e. single catalytic entities. They should not be applied to systems containing more than one enzyme. When it is desired to name such a system on the basis of the overall reaction catalysed by it, the word system should be included in the name. For example, the system catalysing the oxidation of succinate by molecular oxygen, consisting of succinate dehydrogenase, cytochrome oxidase, and several intermediate carriers, should not be named succinate oxidase, but it may be called the succinate oxidase system. Other examples of systems consisting of several structurally and functionally linked enzymes (and cofactors) are the pyruvate dehydrogenase system, the similar 2-oxoglutarate dehydrogenase system, and the fatty acid synthase system.

In this context it is appropriate to express disapproval of a loose and misleading practice that is found in the biological literature. It consists in designation of a natural substance (or even of an hypothetical active principle), responsible for a physiological or biophysical phenomenon that cannot be described in terms of a definite chemical reaction, by the name of the phenomenon in conjugation with the suffix ase, which implies an individual enzyme. Some examples of such phenomenase nomenclature, which should be discouraged even if there are reasons to suppose that the particular agent may have enzymic properties, are: permease, translocase, reparase, joinase, replicase, codase, etc..

The second general principle is that enzymes are principally classified and named according to the reaction they catalyse. The chemical reaction catalysed is the specific property that distinguishes one enzyme from another, and it is logical to use it as the basis for the classification and naming of enzymes.

Several alternative bases for classification and naming had been considered, e.g. chemical nature of the enzymes (whether it is a flavoprotein, a hemoprotein, a pyridoxal-phosphate protein, a copper protein, and so on), or chemical nature of the substrate (nucleotides, carbohydrates, proteins, etc.). The first cannot serve as a general basis, for only a minority of enzymes have such identifiable prosthetic groups. The chemical nature of the enzyme has, however, been used exceptionally in certain cases where classification based on specificity is difficult, for example, with the peptidases (subclass EC 3.4). The second basis for classification is hardly practicable, owing to the great variety of substances acted upon and because it is not sufficiently informative unless the type of reaction is also given. It is the overall reaction, as expressed by the formal equation, that should be taken as the basis. Thus, the intimate mechanism of the reaction, and the formation of intermediate complexes of the reactants with the enzyme is not taken into account, but only the observed chemical change produced by the complete enzyme reaction. For example, in those cases in which the enzyme contains a prosthetic group that serves to catalyse transfer from a donor to an acceptor (e.g. flavin, biotin, or pyridoxal-phosphate enzymes) the name of the prosthetic group is not normally included in the name of the enzyme.

Nevertheless, where alternative names are possible, the mechanism may be taken into account in choosing between them.

A consequence of the adoption of the chemical reaction as the basis for naming enzymes is that a systematic name cannot be given to an enzyme until it is known what chemical reaction it catalyses. This applies, for example, to a few enzymes that have so far not been shown to catalyse any chemical reaction, but only isotopic exchanges; the isotopic exchange gives some idea of one step in the overall chemical reaction, but the reaction as a whole remains unknown.

A second consequence of this concept is that a certain name designates not a single enzyme protein but a group of proteins with the same catalytic property. Enzymes from different sources (various bacterial, plant or animal species) are classified as one entry. The same applies to isoenzymes (see below). However, there are exceptions to this general rule. Some are justified because the mechanism of the reaction or the substrate specificity is so different as to warrant different entries in the enzyme list. This applies, for example, to the two cholinesterases, EC 3.1.1.7 and 3.1.1.8, the two citrate hydro-lyases, EC 4.2.1.3 and 4.2.1.4, and the two amine oxidases, EC 1.4.3.4 and 1.4.3.6. Others are mainly historical, e.g. acid and alkaline phosphatases (EC 3.1.3.1 and EC 3.1.3.2).

A third general principle adopted is that the enzymes are divided into groups on the basis of the type of reaction catalysed, and this, together with the name(s) of the substrate(s) provides a basis for naming individual enzymes. It is also the basis for classification and code numbers.

Special problems attend the classification and naming of enzymes catalysing complicated transformations that can be resolved into several sequential or coupled intermediary reactions of different types, all catalysed by a single enzyme (not an enzyme system). Some of the steps may be spontaneous non-catalytic reactions, while one or more intermediate steps depend on catalysis by the enzyme. Wherever the nature and sequence of intermediary reactions is known or can be presumed with confidence, classification and naming of the enzyme should be based on the first enzyme-catalysed step that is essential to the subsequent transformations, which can be indicated by a supplementary term in parentheses, e.g. acetyl-CoA:glyoxylate C-acetyltransferase (thioester-hydrolysing, carboxymethyl-forming) (EC 2.3.3.9, cf. section 3).

To classify an enzyme according to the type of reaction catalysed, it is occasionally necessary to choose between alternative ways of regarding a given reaction. Some considerations of this type are outlined in

section 3 of this chapter. In general, that alternative should be selected which fits in best with the general system of classification and reduces the number of exceptions.

One important extension of this principle is the question of the direction in which the reaction is written for the purposes of classification. To simplify the classification, the direction chosen should be the same for all enzymes in a given class, even if this direction has not been demonstrated for all. Thus the systematic names, on which the classification and code numbers are based, may be derived from a written reaction, even though only the reverse of this has been actually demonstrated experimentally. In the list in this volume, the reaction is written to illustrate the classification, i.e. in the direction described by the systematic name. However, the common name may be based on either direction of reaction, and is often based on the presumed physiological direction.

Many examples of this usage are found in section 1 of the list. The reaction for EC 1.1.1.9 is written as an oxidation of xylitol by NAD+, in parallel with all other oxidoreductases in subgroup EC 1.1.1, and the systematic name is accordingly, xylitol:NAD+ 2-oxidoreductase (D-xylulose-forming). However, the common name, based on the reverse direction of reaction, is D-xylulose reductase.

2. Common and Systematic Names

The first Enzyme Commission gave much thought to the question of a systematic and logical nomenclature for enzymes, and finally recommended that there should be two nomenclatures for enzymes, one systematic, and one working or trivial. The systematic name of an enzyme, formed in accordance with definite rules, showed the action of an enzyme as exactly as possible, thus identifying the enzyme precisely. The trivial name was sufficiently short for general use, but not necessarily very systematic; in a great many cases it was a name already in current use. The introduction of (often cumbersome) systematic names was strongly criticised. In many cases the reaction catalysed is not much longer than the systematic name and can serve just as well for identification, especially in conjunction with the code number.

The Commission for Revision of Enzyme Nomenclature discussed this problem at length, and a change in emphasis was made. It was decided to give the trivial names more prominence in the Enzyme List; they now follow immediately after the code number, and are described as Common Name. Also, in the index the common names are indicated by an asterisk. Nevertheless, it was decided to retain the systematic names as the basis for classification for the following reasons:

(i) the code number alone is only useful for identification of an enzyme when a copy of the Enzyme List is at hand, whereas the systematic name is self-explanatory;

(ii) the systematic name stresses the type of reaction, the reaction equation does not;

(iii) systematic names can be formed for new enzymes by the discoverer, by application of the rules, but code numbers should not be assigned by individuals;

(iv) common names for new enzymes are frequently formed as a condensed version of the systematic name; therefore, the systematic names are helpful in finding common names that are in accordance with the general pattern.

It is recommended that for enzymes that are not the main subject of a paper or abstract, the common names should be used, but they should be identified at their first mention by their code numbers and source. Where an enzyme is the main subject of a paper or abstract, its code number, systematic name, or, alternatively, the reaction equation and source should be given at its first mention; thereafter the common name should be used. In the light of the fact that enzyme names and code numbers refer to reactions catalysed rather than to discrete proteins, it is of special importance to give also the source of the enzyme for full identification; in cases where multiple forms are known to exist, knowledge of this should be included where available.

When a paper deals with an enzyme that is not yet in the Enzyme List, the author may introduce a new name and, if desired, a new systematic name, both formed according to the recommended rules. A number should be assigned only by the Nomenclature Committee of IUBMB.

The Enzyme List contains one or more references for each enzyme. It should be stressed that no attempt has been made to provide a complete bibliography, or to refer to the first description of an enzyme. The references are intended to provide sufficient evidence for the existence of an enzyme catalysing the reaction as set out. Where there is a major paper describing the purification and specificity of an enzyme, or a major review article, this has been quoted to the exclusion of earlier and later papers. In some cases separate references are given for animal, plant and bacterial enzymes.

3. Scheme for the classification of enzymes and the generation of EC numbers

The first Enzyme Commission, in its report in 1961, devised a system for classification of enzymes that also serves as a basis for assigning code numbers to them. These code numbers, prefixed by EC, which are now widely in use, contain four elements separated by points, with the following meaning:

(i) the first number shows to which of the six main divisions (classes) the enzyme belongs,

(ii) the second figure indicates the subclass,

(iii) the third figure gives the sub-subclass,

(iv) the fourth figure is the serial number of the enzyme in its sub-subclass.

The subclasses and sub-subclasses are formed according to principles indicated below.

The main divisions and subclasses are:

Class 1. Oxidoreductases.

To this class belong all enzymes catalysing oxidoreduction reactions. The substrate that is oxidized is regarded as hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The common name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor.

The second figure in the code number of the oxidoreductases, unless it is 11, 13, 14 or 15, indicates the group in the hydrogen (or electron) donor that undergoes oxidation: 1 denotes a -CHOH- group, 2 a CHO or -CO-COOH group or carbon monoxide, and so on, as listed in the key.

The third figure, except in subclasses EC 1.11, EC 1.13, EC 1.14 and EC 1.15, indicates the type of acceptor involved: 1 denotes NAD(P)+, 2 a cytochrome, 3 molecular oxygen, 4 a disulfide, 5 a quinone or similar compound, 6 a nitrogenous group, 7 an iron-sulfur protein and 8 a flavin. In subclasses EC 1.13 and EC 1.14 a different classification scheme is used and sub-subclasses are numbered from 11 onwards.

It should be noted that in reactions with a nicotinamide coenzyme this is always regarded as acceptor, even if this direction of the reaction is not readily demonstrated. The only exception is the subclass EC 1.6, in which NAD(P)H is the donor; some other redox catalyst is the acceptor.

Although not used as a criterion for classification, the two hydrogen atoms at carbon-4 of the dihydropyridine ring of nicotinamide nucleotides are not equivalent in that the hydrogen is transferred stereospecifically.

Class 2. Transferases.

Transferases are enzymes transferring a group, e.g. a methyl group or a glycosyl group, from one compound (generally regarded as donor) to another compound (generally regarded as acceptor). The systematic names are formed according to the scheme donor:acceptor grouptransferase. The common names are normally formed according to acceptor grouptransferase or donor grouptransferase. In many cases, the donor is a cofactor (coenzyme) charged with the group to be transferred. A special case is that of the transaminases (see below).

Some transferase reactions can be viewed in different ways. For example, the enzyme-catalysed reaction

X-Y + Z = X + Z-Y may be regarded either as a transfer of the group Y from X to Z, or as a breaking of the X-Y bond by the introduction of Z. Where Z represents phosphate or arsenate, the process is often spoken of as 'phosphorolysis' or 'arsenolysis', respectively, and a number of enzyme names based on the pattern of phosphorylase have come into use. These names are not suitable for a systematic nomenclature,

because there is no reason to single out these particular enzymes from the other transferases, and it is better to regard them simply as Y-transferases.

In the above reaction, the group transferred is usually exchanged, at least formally, for hydrogen, so that the equation could more strictly be written as:

X-Y + Z-H = X-H + Z-Y. Another problem is posed in enzyme-catalysed transaminations, where the -NH2 group and -H are transferred to a compound containing a carbonyl group in exchange for the =O of that group, according to the general equation:

R1-CH(-NH2)-R2 + R3-CO-R4 R1-CO-R2 + R3-CH(-NH2)-R4. The reaction can be considered formally as oxidative deamination of the donor (e.g. amino acid) linked with reductive amination of the acceptor (e.g. oxo acid), and the transaminating enzymes (pyridoxalphosphate proteins) might be classified as oxidoreductases. However, the unique distinctive feature of the reaction is the transfer of the amino group (by a well-established mechanism involving covalent substrate-coenzyme intermediates), which justified allocation of these enzymes among the transferases as a special subclass (EC 2.6.1, transaminases).

The second figure in the code number of transferases indicates the group transferred; a one-carbon group in EC 2.1, an aldehydic or ketonic group in EC 2.2, an acyl group in EC 2.3 and so on.

The third figure gives further information on the group transferred; e.g. subclass EC 2.1 is subdivided into methyltransferases (EC 2.1.1), hydroxymethyl- and formyltransferases (EC 2.1.2) and so on; only in subclass EC 2.7, does the third figure indicate the nature of the acceptor group.

Class 3. Hydrolases.

These enzymes catalyse the hydrolytic cleavage of C-O, C-N, C-C and some other bonds, including phosphoric anhydride bonds. Although the systematic name always includes hydrolase, the common name is, in many cases, formed by the name of the substrate with the suffix -ase. It is understood that the name of the substrate with this suffix means a hydrolytic enzyme.

A number of hydrolases acting on ester, glycosyl, peptide, amide or other bonds are known to catalyse not only hydrolytic removal of a particular group from their substrates, but likewise the transfer of this group to suitable acceptor molecules. In principle, all hydrolytic enzymes might be classified as transferases, since hydrolysis itself can be regarded as transfer of a specific group to water as the acceptor. Yet, in most cases, the reaction with water as the acceptor was discovered earlier and is considered as the main physiological function of the enzyme. This is why such enzymes are classified as hydrolases rather than as transferases.

Some hydrolases (especially some of the esterases and glycosidases) pose problems because they have a very wide specificity and it is not easy to decide if two preparations described by different authors (perhaps from different sources) have the same catalytic properties, or if they should be listed under separate entries. An example is vitamin A esterase (formerly EC 3.1.1.12, now believed to be identical with EC 3.1.1.1). To some extent the choice must be arbitrary; however, separate entries should be given only when the specificities are sufficiently different.

Another problem is that proteinases have 'esterolytic' action; they usually hydrolyse ester bonds in appropriate substrates even more rapidly than natural peptide bonds. In this case, classification among the peptide hydrolases is based on historical priority and presumed physiological function.

The second figure in the code number of the hydrolases indicates the nature of the bond hydrolysed; EC 3.1 are the esterases; EC 3.2 the glycosylases, and so on.

The third figure normally specifies the nature of the substrate, e.g. in the esterases the carboxylic ester hydrolases (EC 3.1.1), thiolester hydrolases (EC 3.1.2), phosphoric monoester hydrolases (EC 3.1.3); in the glycosylases the O-glycosidases (EC 3.2.1), N-glycosylases (EC 3.2.2), etc. Exceptionally, in the case of the peptidyl-peptide hydrolases the third figure is based on the catalytic mechanism as shown by active centre studies or the effect of pH.

Class 4. Lyases.

Lyases are enzymes cleaving C-C, C-O, C-N, and other bonds by elimination, leaving double bonds or rings, or conversely adding groups to double bonds. The systematic name is formed according to the pattern substrate group-lyase. The hyphen is an important part of the name, and to avoid confusion should not be omitted, e.g. hydro-lyase not 'hydrolyase'. In the common names, expressions like decarboxylase, aldolase, dehydratase (in case of elimination of CO2, aldehyde, or water) are used. In cases where the reverse reaction is much more important, or the only one demonstrated, synthase (not synthetase) may be used in the name. Various subclasses of the lyases include pyridoxal-phosphate enzymes that catalyse the elimination of a - or -substituent from an -amino acid followed by a replacement of this substituent by some other group. In the overall replacement reaction, no unsaturated end-product is formed; therefore, these enzymes might formally be classified as alkyltransferases (EC 2.5.1...). However, there is ample evidence that the replacement is a two-step reaction involving the transient formation of enzyme-bound ,(or ,)-unsaturated amino acids. According to the rule that the first reaction is indicative for classification, these enzymes are correctly classified as lyases. Examples are tryptophan synthase (EC 4.2.1.20) and cystathionine -synthase (EC 4.2.1.22).

The second figure in the code number indicates the bond broken: EC 4.1 are carbon-carbon lyases, EC 4.2 carbon-oxygen lyases and so on.

The third figure gives further information on the group eliminated (e.g. CO2 in EC 4.1.1, H2O in EC 4.2.1).

Class 5. Isomerases.

These enzymes catalyse geometric or structural changes within one molecule. According to the type of isomerism, they may be called racemases, epimerases, cis-trans-isomerases, isomerases, tautomerases, mutases or cycloisomerases.

In some cases, the interconversion in the substrate is brought about by an intramolecular oxidoreduction (EC 5.3); since hydrogen donor and acceptor are the same molecule, and no oxidized product appears, they are not classified as oxidoreductases, even though they may contain firmly bound NAD(P)+.

The subclasses are formed according to the type of isomerism, the sub-subclasses to the type of substrates.

Class 6. Ligases.

Ligases are enzymes catalysing the joining together of two molecules coupled with the hydrolysis of a diphosphate bond in ATP or a similar triphosphate. The systematic names are formed on the system X:Y ligase (ADP-forming). In earlier editions of the list the term synthetase has been used for the common names. Many authors have been confused by the use of the terms synthetase (used only for Group 6) and synthase (used throughout the list when it is desired to emphasis the synthetic nature of the reaction). Consequently NC-IUB decided in 1983 to abandon the use of synthetase for common names, and to replace them with names of the type X-Y ligase. In a few cases in Group 6, where the reaction is more complex or there is a common name for the product, a synthase name is used (e.g. EC 6.3.2.11 and EC 6.3.5.1).

It is recommended that if the term synthetase is used by authors, it should continue to be restricted to the ligase group.

The second figure in the code number indicates the bond formed: EC 6.1 for C-O bonds (enzymes acylating tRNA), EC 6.2 for C-S bonds (acyl-CoA derivatives), etc. Sub-subclasses are only in use in the CN ligases.

In a few cases it is necessary to use the word other in the description of subclasses and sub-subclasses. They have been provisionally given the figure 99, in order to leave space for new subdivisions.

From time to time, some enzymes have been deleted from the List, while some others have been renumbered. However, the old numbers have not been allotted to new enzymes; rather the place has been left vacant and cross-reference is made according to the following scheme: