Chapter 18

Transcriptomics and Proteomics

DNA is transcribed into RNA—the ensemble of the proteome is the ensemble of

expressed proteins in a cell (cf. Fig. 14.1), and proteomics is the study of that ensemble

(i.e., the identification and determination of the amounts, locations, and interactions

of all the proteins). It could also include disordered and alternatively folded proteins. ¹

The tasks of proteomics are summarized in Fig. 18.1.

We have seen in Chap. 14 how the gene is first transcribed into messenger RNA

(mRNA), and a given gene, especially in a eukaryotic cell in which the gene resembles

a mosaic of introns (upper II) and exons (upper EE), can be assembled to form different mRNAs

(e.g., if the gene is upper E 1 upper I upper E 2 upper I upper E 3 upper I upper E 4 upper I upper E 5E1I E2I E3I E4I E5, one could form mRNAs upper E 1 upper E 2 upper E 3 upper E 4 upper E 5E1E2E3E4E5,

upper E 1 upper E 3 upper E 4 upper E 5E1E3E4E5, and upper E 1 upper E 3 upper E 5E1E3E5). The ensemble of these transcripts is called the transcrip-

tome, and its study is called transcriptomics (Sect. 18.1). Due to the variety of assem-

bly possibilities, the transcriptome is considerably larger (i.e., contains more types

of objects) than the genome.

After the mRNA is translated into a protein, the polypeptide may be modified by

the following:

1. Cutting off a block of amino acids from either end;

2. Covalently adding a large chemical group to an amino acid (e.g., a fatty acid or

an oligosaccharide);

3. Covalently modifying an amino acid (e.g., by serine or threonine phosphorylation,

or acetylation);

4. Oxidizing or reducing an amino acid (e.g., arginine deimination or glutamine

deamidation).

Modifications 2 and 3 may well be reversible; that is, there may be a pool of both mod-

ified and unmodified forms in the cell at any instant. More than 200 post-translational

modifications (PTM) have been identified. They can significantly change the confor-

mation, which in turn implies (for example) that the catalytic activity of an enzyme

may change. Conformation is also a determinant of intermolecular specificity, which

1 Dyson (2011).

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https://doi.org/10.1007/978-3-030-45607-8_18

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