Some intracellular signaling molecules are small chemicals, which are often called second messengers (the “first messengers” being the extracellular signals). They are generated in large amounts in response to receptor activation and diffuse away from their source, spreading the signal to other parts of the cell. Some, such as cyclic AMP and Ca2+, are water-soluble and diffuse in the cytosol, while others, such as diacylglycerol, are lipid-soluble and diffuse in the plane of the plasma membrane. In either case, they pass the signal on by binding to and altering the behavior of selected signaling or effector proteins.
Most intracellular signaling molecules are proteins, which help relay the signal into the cell by either generating second messengers or activating the next signaling or effector protein in the pathway. Many of these proteins behave like molecular switches. When they receive a signal, they switch from an inactive to an active state, until another process switches them off, returning them to their inactive state. The switching off is just as important as the switching on. If a signaling pathway is to recover after transmitting a signal so that it can be ready to transmit another, every activated molecule in the pathway must return to its original, unactivated state.
The largest class of molecular switches consists of proteins that are activated or inactivated by phosphorylation (discussed in Chapter 3). For these proteins, the switch is thrown in one direction by a protein kinase, which covalently adds one or more phosphate groups to specific amino acids on the signaling protein, and in the other direction by a protein phosphatase, which removes the phosphate groups (Figure 15–7A). The activity of any protein regulated by phosphorylation depends on the balance between the activities of the kinases that phosphorylate it and of the phosphatases that dephosphorylate it. About 30–50% of human proteins contain covalently attached phosphate, and the human genome encodes about 520 protein kinases and about 150 protein phosphatases. A typical mammalian cell makes use of hundreds of distinct types of protein kinases at any moment.
Protein kinases attach phosphate to the hydroxyl group of specific amino acids on the target protein. There are two main types of protein kinase. The great majority are serine/threonine kinases, which phosphorylate the hydroxyl groups of serines and threonines in their targets. Others are tyrosine kinases, which phosphorylate proteins on tyrosines. The two types of protein kinase are closely related members of a large family, differing primarily in the structure of their protein substrate binding sites.
Many intracellular signaling proteins controlled by phosphorylation are themselves protein kinases, and these are often organized into kinase cascades. In such a cascade, one protein kinase, activated by phosphorylation, phosphorylates the next protein kinase in the sequence, and so on, relaying the signal onward and, in some cases, amplifying it or spreading it to other signaling pathways.
The other important class of molecular switches consists of GTP-binding proteins (discussed in Chapter 3). These proteins switch between an “on” (actively signaling) state when GTP is bound and an “off” state when GDP is bound. In the “on” state, they usually have intrinsic GTPase activity and shut themselves off by hydrolyzing their bound GTP to GDP (Figure 15–7B). There are two major types of GTP-binding proteins. Large, trimeric GTP-binding proteins (also called G proteins) help relay signals from G-protein-coupled receptors that activate them (see Figure 15–6B). Small monomeric GTPases (also called monomeric GTP-binding proteins) help relay signals from many classes of cell-surface receptors.