Types of Enzymes and Their Roles
Type of Reaction Catalyzed
Hydrolase Splits substrate by hydrolysis. Includes many sub-categories, including nucleases, proteases, glycosidases and phosphatases.
Nuclease Cleaves nucleic acids by hydrolyzing phosphodiester bonds between nucleotides. Includes restriction enzymes that cut DNA at specific sequences.
Protease Cleaves polypeptide chains by hydrolyzing peptide bonds between amino acids.
Glycosidase Cleaves polysaccharides by hydrolyzing glycoside bonds between sugars.
Includes p-galactosidase, lysozyme and cellulase.
Phosphatase Removes phosphate groups by hydrolysis.
p-Lactamase Hydrolase that inactivates antibiotics of the p-lactam group (penicillins and cephalosporins) by opening the lactam ring.
ATPase General name for enzymes that hydrolyse ATP so releasing energy that is used to drive a reaction
Synthase General name for a biosynthetic enzyme. Includes ligases, polymerases, transferases and other classes.
Ligase Forms new bonds by joining fragments together. The term "ligase" alone is usually understood to refer to DNA ligase.
Polymerase Type of ligase that synthesizes polymers by linking the subunits. Includes
DNA polymerase and RNA polymerase.
Transferase Transfers chemical groups from one molecule to another. Includes methylases, acetylases, kinases and others.
Methyl ase Transferase that adds m ethyl groups to a molecule. Includes modification enzymes that m ethylate DNA.
Acetylase Transferase that adds acetyl groups to a molecule. Includes histone acetyl transferase (HAT), which acetylates histones.
Kinase Transferase that adds phosphate groups to a molecule. Includes protein kinases, which attach phosphate groups to proteins.
Isomerase Interconverts the isomers of a molecule.
Racemase Specialized isomerase that interconverts the D- and L- isomers of an optically active molecule such as an amino acid.
Oxidoreductase Catalyzes oxidation and reduction reactions. Includes dehydrogenases, which remove hydrogen atoms from molecules.
Enzymes provide alternative reaction routes of lower energy for organic reactions.
In any chemical reaction, the reactants are converted to the products via the reaction intermediate or transition state. In an enzyme catalyzed reaction, the substrate(s) is bound by the enzyme and the reaction occurs within the active site. In either case, energy may be needed to prime the reaction. This transition state energy, AG*, is the difference in free energy between the starting materials and the transition state (Fig. 7.33). When AG* is positive, as shown, energy must be supplied to reach the transition state. Even if this energy is released once the overall reaction is over, the higher the transition state energy, the slower the reaction. Enzymes cannot change the overall free energy of a reaction, i.e., the energy difference between reactants and products. The role of an enzyme is to lower the transition state energy, either by stabilizing the transition state Another term for the activated intermediate in a chemical reaction transition state energy Energy difference between the reactants and the activated reaction intermediate or transition state
Enzymes Act by Lowering the Energy of Activation 183
FIGURE 7.33 Energy is Required to Reach the Transition State
Initiation of a chemical reaction requires an input of energy to reach the transition state. The required energy is called the energy of activation, or transition state energy, AG+, and is needed even if the reaction is exothermic (as shown) and will eventually release more energy overall than originally put in. The net energy released is AG.
intermediates in the active site, or by providing an alternative reaction mechanism that proceeds by a pathway of lower energy.
The rate of a reaction may be slow without an enzyme. Rate increases by enzymes range from 108 to 1020 relative to the uncatalyzed, spontaneous reaction (e.g., 109 for alcohol dehydrogenase; 1016 for alkaline phosphatase). A high enzymatic rate occurs when enzymes can position the substrate correctly relative to the catalytic groups in the active site. Several factors are involved in enzyme rate increases:
1. Proximity—(up to 106 fold increase). The enzyme binds the substrate so that the susceptible bond is very close to the catalytic group in the active site. The local concentration of substrate in the active site may be as much as 50 Molar whereas its concentration in the cytoplasm may be less than 1 mM. Chemical reaction rates are proportional to the concentrations of the reactants.
2. Orientation—(up to 102 fold). When the substrate is bound, the reacting groups must be properly oriented. The orbital steering hypothesis suggests that the binding of the substrate(s) to the enzyme aligns the reactive groups so that the relevant molecular orbitals involved in bond formation overlap. This increases the probability of forming the transition state.
3. Covalent intermediates—(around 1010 fold). The strategy is to lower the transition state energy "hump" by taking an alternative reaction pathway. Consider the transfer of a chemical group "X" from molecule A to molecule B. Here "X" is a molecular fragment such as a phosphate group, acyl group or glycosyl group.
The enzyme may react in two steps, picking up group "X" from molecule A and then transferring it to molecule B in a second reaction:
4. Acid-base catalysis—(around 1010 fold). Acid-base catalysis is due to proton donors (acids) or proton acceptors (bases), that donate protons to or remove protons from the reaction intermediate. Enzymes use the side chains of acidic or basic amino acids to attack the substrate. An acidic group in one part of the active site may donate a proton and a basic group in another part of the active site may remove another proton from the reaction intermediate. This referred to as concerted acid-base catalysis. Most hydrolytic enzymes use acid/base catalysis.
5. Metal ion catalysis—(around 1010 fold). Many enzymes have metal ions at the active site. Sometimes these are used as redox centers, as in cytochromes. Often, o o w Z w w w
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