286

18

Transcriptomics and Proteomics

designer of digital electronic circuits, ²³ in which an output is made available to

multiple devices. If the response to the external stimulus triggering the cascade

requires the activation of multiple enzymes, for which the genes encoding them

might be located on different chromosomes, the cascade is a way of achieving rapid

diffusion of the signal in a relatively unstructured milieu. Furthermore, as a protein,

each element of the cascade is only able to interact with a relatively small number

of other molecules bearing information. ²⁴ There may be more potentially blocking

molecules than sites on a single member of the cascade; the blocking effect can

nevertheless be achieved by interacting with any member, since the entire cascade

essentially constitutes a single linear channel for information flow.

The fact that information is conveyed by material objects, whose supply is vari-

able and limited and which occupy an appreciable proportion of the volume of the

cell, creates a situation that is significantly different from that of regulatory net-

works based on fixed (e.g., electrical or optical) connexions. As was already stressed

in the discussion of the kinase-based signalling pathways, the information-bearing

“quanta” have to be regenerated by phosphatases. There is, moreover, an ultimate

constraint in the form of the finiteness of the attributes of a cell; conceivably, it could

happen that all of the kinases were converted to the active form and no resources

were available for regenerating them, and hence no resources for communicating the

need for regeneration.

Problem. Elaborate some examples of signalling cascades (e.g., blood clotting,

glycogenolysis).

Problem. Using the formalism of Figs. 7.1 and 3.1, analyse one of the cascades

described in the previous problem, or the MAPK signalling system, from an

information-theoretic viewpoint.

References

Bell AW et al (2009) A HUPO test sample study reveals common problems in mass spectrometry-

based proteomics. Nat Methods 6:423–430

Chumakov S et al (2005) The theoretical basis of universal identification systems for bacteria and

viruses. J Biol Phys Chem 5:121–128

Dyson HJ (2011) Expanding the proteome: disordered and alternatively folded proteins. Q Rev

Biophys 44:467–518

Fearn S (2015) Characterisation of biological material with ToF-SIMS: a review. Mater Sci Technol

31:148–161

Fodor SPA et al (1991) Light-directed, spatially addressable parallel chemical synthesis. Science

251:767–773

23 And, indeed, to the neurologist.

24 This limitation is imposed physicochemically; for example, there is only room for a small number

of other proteins to cluster round and interact with a central one and, of course, the entire surface

of the central protein is unlikely to be sensitive to the presence of other proteins; the possibilities

for interaction are typically limited to a small number of specific binding sites.