6.1 An Introduction to Enzymes in Chapter 6 Enzymes

6.1 An Introduction to Enzymes

Much of the history of biochemistry is the history of enzyme research. Biological catalysis was first recognized and described in the late 1700s, in studies on the digestion of meat by secretions of the stomach. The science of biochemistry can be traced to an experiment by Eduard Buchner in 1897, which demonstrated that cell-free yeast extracts could ferment sugar to alcohol. Buchner thus proved that fermentation was promoted by molecules that continued to function when removed from cells. This work marked the end of vitalistic notions advanced by Louis Pasteur that biological catalysis was a process inseparable from living systems. Frederick W. Kühne later gave the name enzymes (from the Greek enzymos, “leavened”) to the molecules detected by Buchner.

A photo of Eduard Buchner, 1860-1917, a German chemist and zymologist. — Eduard Buchner, 1860–1917

Not until the late 1920s did it become clear that enzymes were proteins. In 1926, James Sumner provided the first breakthrough, isolating and crystallizing the enzyme urease. Further work by Northrop, Kunitz, and others led to general acceptance of the enzyme-protein association by the early 1930s. Since the latter part of the twentieth century, thousands of enzymes have been purified, their structures elucidated, and their mechanisms explained.

The power of enzyme catalysts is often astonishing. The enzyme orotidine phosphate decarboxylase, an enzyme involved in the biosynthesis of pyrimidine nucleotides, provides a special example, with a rate enhancement of $mathml alt text5$ $10 Superscript 17$ . The uncatalyzed reaction has a half-life of 78 million years. On the enzyme, the reaction occurs on a time scale of milliseconds.

Most Enzymes Are Proteins

With the exception of a few classes of catalytic RNA molecules (Chapter 26), enzymes are proteins. Their catalytic activity depends on the integrity of their native protein conformation. If an enzyme is denatured or dissociated into its subunits, catalytic activity is usually lost. The catalytic activity of each enzyme is intimately linked to its primary, secondary, tertiary, and quaternary protein structure.

Enzymes, like other proteins, have molecular weights ranging from about 12,000 to more than 1 million. Some enzymes require no chemical groups for activity other than their amino acid residues. Others require an additional chemical component called a cofactor — either one or more inorganic ions, such as $mathml alt text6$ $Fe Superscript 2 plus$ , $mathml alt text7$ $Mg Superscript 2 plus$ , $mathml alt text8$ $Mn Superscript 2 plus$ , or $mathml alt text9$ $Zn Superscript 2 plus$ (Table 6-1), or a complex organic or metalloorganic molecule called a coenzyme. Coenzymes act as transient carriers of specific functional groups (Table 6-2). Most are derived from vitamins, organic nutrients required in small amounts in the diet. We consider coenzymes in more detail as we encounter them in the metabolic pathways discussed in Part II. Some enzymes require both a coenzyme and one or more metal ions for activity. A coenzyme or metal ion that is very tightly or even covalently bound to the enzyme protein is called a prosthetic group. A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions is called a holoenzyme. The protein part of such an enzyme is called the apoenzyme or apoprotein. Finally, some enzyme proteins are modified covalently by phosphorylation, glycosylation, and other processes. Many of these alterations are involved in the regulation of enzyme activity.

TABLE 6-1 Some Inorganic Ions That Serve as Cofactors for Enzymes
Ions	Enzymes
$mathml alt text10$ $Cu Superscript 2 plus$	Cytochrome oxidase
$mathml alt text11$ $Fe Superscript 2 plus$ or $mathml alt text12$ $Fe Superscript 3 plus$	Cytochrome oxidase, catalase, peroxidase
$mathml alt text13$ $upper K Superscript plus$	Pyruvate kinase
$mathml alt text14$ $Mg Superscript 2 plus$	Hexokinase, glucose 6-phosphatase, pyruvate kinase
$mathml alt text15$ $Mn Superscript 2 plus$	Arginase, ribonucleotide reductase
Mo	Dinitrogenase
$mathml alt text16$ $Ni Superscript 2 plus$	Urease
$mathml alt text17$ $Zn Superscript 2 plus$	Carbonic anhydrase, alcohol dehydrogenase, carboxypeptidases A and B

TABLE 6-2 Some Coenzymes That Serve as Transient Carriers of Specific Atoms or Functional Groups
Coenzyme	Examples of chemical groups transferred	Dietary precursor in mammals
Biocytin	$mathml alt text18$ $CO Subscript 2$	Biotin (vitamin $mathml alt text19$ $upper B Subscript 7$ )
Coenzyme A	Acyl groups	Pantothenic acid (vitamin $mathml alt text20$ $upper B Subscript 5$ ) and other compounds
$mathml alt text21$ $5 prime$ -Deoxyadenosylcobalamin (coenzyme $mathml alt text22$ $upper B Subscript 12$ )	H atoms and alkyl groups	Vitamin $mathml alt text23$ $upper B Subscript 12$
Flavin adenine dinucleotide	Electrons	Riboflavin (vitamin $mathml alt text24$ $upper B Subscript 2$ )
Lipoate	Electrons and acyl groups	Not required in diet
Nicotinamide adenine dinucleotide	Hydride ion $mathml alt text25$ $left-parenthesis bold colon upper H Superscript minus Baseline right-parenthesis$	Nicotinic acid (niacin, vitamin $mathml alt text26$ $upper B Subscript 3$ )
Pyridoxal phosphate	Amino groups	Pyridoxine (vitamin $mathml alt text27$ $upper B Subscript 6$ )
Tetrahydrofolate	One-carbon groups	Folate (vitamin $mathml alt text28$ $upper B Subscript 9$ )
Thiamine pyrophosphate	Aldehydes	Thiamine (vitamin $mathml alt text29$ $upper B Subscript 1$ )
Note: The structures and modes of action of these coenzymes are described in Part II.

Enzymes Are Classified by the Reactions They Catalyze

Many enzymes have been named by adding the suffix “-ase” to the name of their substrate or to a word or phrase describing their activity. Thus, urease catalyzes hydrolysis of urea, and DNA polymerase catalyzes the polymerization of nucleotides to form DNA. Other enzymes were named by their discoverers for a broad function, before the specific reaction catalyzed was known. For example, an enzyme known to act in the digestion of foods was named pepsin, from the Greek pepsis, “digestion,” and lysozyme was named for its ability to lyse (break down) bacterial cell walls. Still others were named for their source: trypsin, named in part from the Greek tryein, “to wear down,” was obtained by rubbing pancreatic tissue with glycerin. Sometimes the same enzyme has two or more names, or two different enzymes have the same name. To limit ambiguity, biochemists worldwide have adopted a system for naming and classifying enzymes. This system divides enzymes into seven classes, each with subclasses, based on the type of reaction catalyzed (Table 6-3). Each enzyme is assigned a four-part classification number and a systematic name, which identifies the reaction it catalyzes. As an example, the formal systematic name of the enzyme catalyzing the reaction

ATP + D -glucose \to ADP + D -glucose 6 -phosphate

$ATP plus upper D hyphen glucose right-arrow ADP plus upper D hyphen glucose 6 hyphen phosphate$

is ATP:d-hexose 6-phosphotransferase, which indicates that it catalyzes the transfer of a phosphoryl group from ATP to glucose. Its Enzyme Commission number (E.C. number) is 2.7.1.1. The first number (2) denotes the class name (transferase); the second number (7), the subclass (phosphotransferase); the third number (1), a phosphotransferase with a hydroxyl group as acceptor; and the fourth number (1), d-glucose as the phosphoryl group acceptor. For many enzymes, a trivial name is more frequently used — in this case, hexokinase. A complete list and description of the thousands of known enzymes is maintained by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (www.qmul.ac.uk/sbcs/iubmb).

TABLE 6-3 International Classification of Enzymes
Class number	Class name	Type of reaction catalyzed
1	Oxidoreductases	Transfer of electrons (hydride ions or H atoms)
2	Transferases	Group transfer
3	Hydrolases	Hydrolysis (transfer of functional groups to water)
4	Lyases	Cleavage of $mathml alt text31$ $upper C em-dash upper C$ , $mathml alt text32$ $upper C em-dash upper O$ , $mathml alt text33$ $upper C em-dash upper N$ , or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds
5	Isomerases	Transfer of groups within molecules to yield isomeric forms
6	Ligases	Formation of $mathml alt text34$ $upper C em-dash upper C$ , $mathml alt text35$ $upper C em-dash upper S$ , $mathml alt text36$ $upper C em-dash upper O$ , and $mathml alt text37$ $upper C em-dash upper N$ bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
7	Translocases	Movement of molecules or ions across membranes or their separation within membranes

SUMMARY 6.1 An Introduction to Enzymes

Life depends on powerful and specific catalysts: enzymes. Almost every biochemical reaction is catalyzed by an enzyme.
With the exception of a few catalytic RNAs, all known enzymes are proteins. Many require nonprotein coenzymes or cofactors for their catalytic function.
Enzymes are classified according to the type of reaction they catalyze. All enzymes have formal E.C. numbers and names, and most have trivial names.