In the regulation of molecular switches, protein kinases and guanine nucleotide exchange

All second messengers are water-soluble and diffuse freely through the cytosol.

In the regulation of molecular switches, protein kinases and guanine nucleotide exchange factors (GEFs) always turn proteins on, whereas protein phosphatases and GTPase-activating proteins (GAPs) always turn proteins off.

Most intracellular signaling pathways provide numerous opportunities for amplifying the responses to extracellular signals.

Binding of extracellular ligands to receptor tyrosine kinases (RTKs) activates the intracellular catalytic domain by propagating a conformational change across the lipid bilayer through a single transmembrane helix.

Protein tyrosine phosphatases display exquisite specificity for their substrates, unlike most serine/threonine protein phosphatases, which have rather broad specificity

Even though plants and animals independently evolved multicellularity, they use virtually all the same signaling proteins and second messengers for cellcell communication.

Suppose that the circulating concentration of hormone is 1010 M and the Kd for binding to its receptor is 108 M. What fraction of the receptors will have hormone bound? If a meaningful physiological response occurs when 50% of the receptors have bound a hormone molecule, how much will the concentration of hormone have to rise to elicit a response? The fraction of receptors (R) bound to hormone (H) to form a receptorhormone complex (RH) is [RH]/ ([R] + [RH]) = [RH]/[R]TOT = [H]/([H] + Kd).

Cells communicate in ways that resemble human communication. Decide which of the following forms of human communication are analogous to autocrine, paracrine, endocrine, and synaptic signaling by cells. A. A telephone conversation B. Talking to people at a cocktail party C. A radio announcement D. Talking to yourself

Why do signaling responses that involve changes in proteins already present in the cell occur in milliseconds to seconds, whereas responses that require changes in gene expression require minutes to hours?

How is it that different cells can respond in different ways to exactly the same signaling molecule even when they have identical receptors?

Why do you suppose that phosphorylation/ dephosphorylation, as opposed to allosteric binding of small molecules, for example, has evolved to play such a prominent role in switching proteins on and off in signaling pathways?

Consider a signaling pathway that proceeds through three protein kinases that are sequentially activated by phosphorylation. In one case, the kinases are held in a signaling complex by a scaffolding protein; in the other, the kinases are freely diffusible (Figure Q151). Discuss the properties of these two types of organization in terms of signal amplification, speed, and potential for cross-talk between signaling pathways.

Describe three ways in which a gradual increase in an extracellular signal can be sharpened by the target cell to produce an abrupt or nearly all-or-none response.

Activation (maturation) of frog oocytes is signaled through a MAP kinase signaling module. An increase in the hormone progesterone triggers the module by stimulating the translation of Mos mRNA, which is the frogs MAP kinase kinase kinase (Figure Q152). Maturation is easy to score visually by the presence of a white spot in the middle of the brown surface of the oocyte (see Figure Q152). To determine the doseresponse curve for progesterone-induced activation of MAP kinase, you place 16 oocytes in each of six plastic dishes and add various concentrations of progesterone. After an overnight incubation, you crush the oocytes, prepare an extract, and determine the state of MAP kinase phosphorylation (hence, activation) by SDS polyacrylamide-gel electrophoresis (Figure Q153A). This analysis shows a graded response of MAP kinase to increasing concentrations of progesterone.

Propose specific types of mutations in the gene for the regulatory subunit of cyclic-AMP-dependent protein kinase (PKA) that could lead to either a permanently active PKA or a permanently inactive PKA.

Phosphorylase kinase integrates signals from the cyclic-AMP-dependent and Ca2+-dependent signaling pathways that control glycogen breakdown in liver and muscle cells (Figure Q154). Phosphorylase kinase is composed of four subunits. One is the protein kinase that catalyzes the addition of phosphate to glycogen phosphorylase to activate it for glycogen breakdown. The other three subunits are regulatory proteins that control the activity of the catalytic subunit. Two contain sites for phosphorylation by PKA, which is activated by cyclic AMP. The remaining subunit is calmodulin, which binds Ca2+ when the cytosolic Ca2+ concentration rises. The regulatory subunits control the equilibrium between the active and inactive conformations of the catalytic subunit, with each phosphate and Ca2+ nudging the equilibrium toward the active conformation. How does this arrangement allow phosphorylase kinase to serve its role as an integrator protein for the multiple pathways that stimulate glycogen breakdown?

The Wnt planar polarity signaling pathway normally ensures that each wing cell in Drosophila has a single hair. Overexpression of the Frizzled gene from a heatshock promoter (hs-Fz) causes multiple hairs to grow from many cells (Figure Q155A). This phenotype is suppressed if hs-Fz is combined with a heterozygous deletion (Dsh) of the Dishevelled gene (Figure Q155B). Do these results allow you to order the action of Frizzled and Dishevelled in the signaling pathway? If so, what is the order? Explain your reasoning.