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4 Biosynthesis and Function of Macromolecules (DNA, RNA, and Proteins)

       Michael Wink

       Heidelberg University, Institute of Pharmacy and Molecular Biotechnology (IPMB), Im Neuenheimer Feld 329, 69120, Heidelberg, Germany

4.1 Genomes, Chromosomes, and Replication

In the past few decades, genomics has developed into a new specialized area of genetics and biotechnology. The aim is the complete molecular and functional characterization of genomes of all important organisms. It is divided into structural and functional genomics (see Chapter 21). When the human genome project HUGO (Human Genome Organization) determined the nucleotide sequence of a human haploid chromosome in 2001, this was a real breakthrough. Since then, sequencing technologies have changed. Instead of cloning and sequencing individual genes, today complete genomes are determined by massive parallel sequencing using next generation sequencing (NGS) (see Chapters 14 and 21). More than 1150 other genomes are already completely sequenced (as of 2010), including 100 genomes of Eukarya, 970 of Bacteria, and 70 of Archaea (Table 4.1). In 2020, the number of species with sequenced genomes is higher than 10000 (see https://en.wikipedia.org/wiki/List_of_sequenced_bacterial_genomes, https://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes for an update) and new sequenced are published every eeek. By comparing nucleotide sequences and derived amino acid sequences obtained from various organ‐ and tissue‐specific cDNA and expressed sequence tag(EST) banks, or through the construction of knockout RNAi, or antisense mutants, assigning the genomic sequences to functional units or genes is being attempted. Finally, functional genomics (see Chapters 21 and 22) will supply an exact answer to the question of which regions of the genome have a function (today it is estimated that the information necessary for survival constitutes 85–95% of bacteria and only 10% of the whole DNA for vertebrates) and which parts can be regarded as apparently functionless evolutionary remnants. However, parts of the genome, which were considered functionless a few years ago, do have functions.

Table 4.1 Overview of a few of the genomes that are already sequenced and published.

      Mb, one million bases.

      4.1.1 Genome Size

The total DNA of a cell is referred to as a genome. Genome sizes of major organismal groups are shown schematically in Figure 4.1. When the minimal genome size of organisms is examined (i.e. only the left side of the bar), an increase in size can be seen that mainly runs parallel to the organizational level. Bacteria and fungi with simple structures have smaller genomes than structurally complicated multicellular organisms. It is presumed that the genome was enlarged particularly through genome duplications. Protostomia and the Deuterostomia ancestors of the vertebrates (see Chapter 6) contain generally only one copy of a gene, while several copies of a gene are often found in the genomes of chordates. As a result, it is supposed that the chordate genomes have doubled at least two or three times (1‐2‐4 rule). The first genome duplication during the evolution of chordates has already taken place before the Cambrian explosion, whereas the second and next doubling occurred in the early Devonian period. In the evolution of fish, a further doubling of the genome occurred with up to eight copies of the original Deuterostomia (1‐2‐4‐8 hypothesis) in the late Devonian period. This took place after the Actinopterygii and Sarcopterygii had already divided. Among the Sarcopterygii are the famous Coelacanthus and lungfishes. All land vertebrates (amphibians, reptiles, birds, and mammals) have apparently descended from them. Within the eukaryotes, the maximum genome size has only a small relationship

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