14.9 Ontogeny (Development)

207

membrane of the cell. The overall process comprises initiation (at the start codon),

elongation, and termination (when the stop codon is reached). Elongation has two

phases: In the first (decoding) phase, a codon of the mRNA is matched with its

cognate tRNA carrying the corresponding amino acid, which is then added to the

growing polypeptide; in the second phase, the mRNA and the tRNA are translocated

one codon to make room for the next tRNA. As established by Crick et al. (1961),

the mRNA is decoded sequentially in nonoverlapping groups of three nucleotides. ⁵⁸

A messenger RNA may be used several times before it is degraded.

Some of the synthesized proteins are used internally by the cell; for example, as

enzymes to metabolize food and degrade toxins and to build up structural components

within the cell, such as lipid membranes and cytoskeletal filaments, and organelles

such as the chloroplast. Other proteins are secreted to fulfil extracellular functions

such as matrix building (for supporting tissue; or for biofilm) and other special-

ized functions, which become more and more complicated as the organism becomes

more and more sophisticated. Another group of proteins modulate transcriptional,

translational, and enzymatic activities. Many proteins have a dual function as a regu-

lator and as something else—for example, an enzyme may also be able to modulate

transcription, either of its own RNA or that of another protein.

It is estimated that about a third of newly synthesized proteins are immediately

degraded by proteasomes, because they have recognizable folding errors.

14.9

Ontogeny (Development)

A multicellular organism begins life as a zygote, which is the diploid result of the

union of two (haploid) gametes, male and female. The zygote then undergoes a series

of divisions, the number of cells doubling each time; when 16 cells are present,

the zygote has developed into a morula. Its cells then compactify to form a two-

dimensional shell (the blastoderm) enclosing a cavity (the blastocoele) filled with

fluid, the overall object being called a blastocyst or blastula. The presence of maternal

transcription factors regulates the initial pattern of gene activation. Rich possibili-

ties ensue once several cells are formed, for they can emit and receive substances

that activate or inhibit internal processes (including the ability to emit and receive

these substances). At this stage, the developing embryo can be modelled as a two-

dimensional cellular automaton. The blastula then invaginates into two or three layers

of cells, the ectoderm on the outside and the endoderm on the inside, with possibly a

mesoderm between them (see also footnote a to Table 14.7). This object is called the

gastrula, which may be modelled as a three-dimensional cellular automaton. The

ectoderm forms the epidermis and the nervous system; the mesoderm forms bone,

cartilage, muscle, blood, etc.; and the endoderm forms the epithelium of the digestive

and respiratory systems and their organs such as the liver.

58 See Table 7.1 for the nucleic acid to amino acid transformation.