28), between ligands and hormone receptors, and between enzymes and their substrates are particularly intimate and selective. The topic of protein–protein interactions is discussed further in Chapter 23.
Most of the cellular building blocks are inert molecules that are not prone to react chemically. Significant activation energy has to be overcome in order to start an energy‐consuming chemical reaction. In the laboratory, this can be achieved by heating and adding acids or bases. In biological systems, evolution has developed enzymes as biological catalysts that are able to catalyze all necessary reactions without higher temperatures being necessary. Enzymes do not change the reaction equilibrium, but usually alter the reaction rate. Enzymes contain an active center in which a substrate is bound. After the enzyme has catalyzed a reaction, the product is released, but the enzyme remains unchanged and is ready for a new reaction. Noncovalent interactions (hydrogen bonds, ionic bonds) and transient covalent bonds between protein and substrate play a key role during the binding and catalysis. Detailed elucidation of such interactions at the atomic scale is the task of biophysics and biochemistry. This research is also important for biotechnology in relation to the synthesis of new enzyme inhibitors or enzyme modulators.
Enzymes show high substrate specificity. It is believed that for almost every biosynthetic step that happens in the cell, a specific enzyme is also present. This does not rule out that enzymes that catalyze chemically similar reactions can be derived from a common original enzyme. Such enzymes belong to a common protein family. Most enzymes have particular pH and temperature optima. Enzymes are divided into different classes according to the processes catalyzed (Table 2.5). Coenzymes or inorganic ions often take part in the catalysis itself. Many coenzymes must be ingested in the forms of vitamins (Table 2.6) because the human body cannot synthesize them themselves. Biochemists and biotechnologists are interested in the elucidation of the enzymatic reaction mechanisms because hints for new catalysts for organic synthesis can be obtained. Apart from this, scientists are attempting to create new biological catalysts through the production of artificial enzymes through genetic engineering of existing enzymes.
Table 2.5 Important classes of enzymes.
| Enzyme | Reaction catalyzed |
|---|---|
| Hydrolases | Catalyze hydrolytic cleavage (amylase, lipase, glucosidase, esterase) |
| Nucleases | Hydrolyze nucleic acids (DNase, RNase) |
| Proteases | Cleave peptides (pepsin, trypsin, chymotrypsin) |
| Isomerases | Catalyze the rearrangement of bonds within a molecule |
| Synthases | General name for an enzyme that catalyzes condensation reactions in anabolic processes |
| Polymerases | Catalyze the formation of RNA and DNA |
| Kinases | Transfer phosphate residues; the protein kinases (PKA, PKC) are particularly important |
| Phosphatases | Remove phosphate residues from a molecule |
| ATPases | Hydrolyze ATP (e.g. H+‐ATPase, Na+, K+‐ATPase, Ca2+‐ATPase); motor proteins, such as myosin |
| GTPases | Hydrolyze GTP; many GTP‐binding proteins work as GTPases |
| Oxidoreductases | Enzymes that catalyze redox reactions, in which one molecule is reduced and another is oxidized; they are grouped into oxidases, reductases, and dehydrogenases |
Table 2.6 Many vitamins serve as essential coenzymes for enzyme reactions.
| Vitamin | Coenzyme | Enzyme reactions that require the coenzyme |
|---|---|---|
| Thiamine (vitamin B1) | Thiamine pyrophosphate | Activation and transfer of aldehydes |
| Pyridoxine (vitamin B6) | Pyridoxal phosphate | Transaminases and decarboxylases |
| Biotin (vitamin B7) | Biotin | Activation and transfer of CO2 |
| Riboflavin (vitamin B2) | FADH | Oxidations–reductions |
| Niacin (vitamin B3) | NADH, NADPH | Oxidations–reductions |
| Pantothenic acid (vitamin B5) | Coenzyme A | Activation and transfer of acyl groups |
| Lipoic acid | Lipoamide | Activation of acyl groups; oxidation–reductions |
| Folic acid (vitamin B9) | Tetrahydrofolate | Activation and transfer of single‐carbon groups |
| Vitamin B12 | Cobalamin | Isomerization and methyl group transfer |
In addition to a catalytic center, many enzymes (especially those composed of several subunits) also have a regulatory center where allosteric ligands bind. For example, the second messenger cAMP binds to the tetrameric protein kinase A complex; after binding both regulatory protein subunits dissociate from both catalytic subunits, which results in their activation (Figure 3.9). Enzymes can be inhibited by inhibitors. We distinguish between reversible, irreversible, competitive, and noncompetitive inhibitors.
A further important way to regulate the activity of enzymes or regulatory proteins is that of reversible conformational change. This is achieved by phosphorylation/dephosphorylation with the help of protein kinases or phosphatases, respectively. Most of the protein kinases utilize adenosine triphosphate (ATP); other molecular switches work through the binding of guanosine triphosphate (GTP) and guanosine diphosphate (GDP) (Figure 2.16, Table 2.7). A reversible reduction of disulfide bridges (e.g. through thioredoxin) plays an important role during the regulation of light‐dependent chloroplast enzymes. Biochemists
