Читать книгу Algorithms in Bioinformatics - Paul A. Gagniuc - Страница 15

Life on Earth was classified by us into three major domains, namely Bacteria, Archaea, and Eukarya (Figure 1.1) [29]. Bacteria (Greek – bakterion, “small stick”) and Archaea (Greek – Arkhē, “origin”) are prokaryotes (Greek – pro, “before”; karyon, “kernel” or “core”). Prokaryotes are single-cell organisms (unicellular) without a “core,” namely without a nucleus, and are considered similar or close in sophistication to the first living organisms on Earth. Eukarya (Greek – eu, “well” or “true”) includes all unicellular and multicellular organisms with cells that contain nuclei, and it refers to animals (including us), plants, fungi, and single-celled protists.

Figure 1.1 The tree of life – basic diagram. The prebiotic period shown on the bottom-left represents the formation of primordial chemical molecules necessary for the ignition of life. Next, the diagram indicates the appearance of LUCA (last universal common ancestor), the first “rudimentary” form of life. The first prokaryotes appear later based on the evolution of LUCA, namely bacteria and archaea. Eukaryotes appear next in the evolutionary chain. Eukaryotes divide the tree of life into four other main subdivisions (eukaryotic kingdoms), namely: protists, fungi, animals, and plants. Note that the approximate number of known species is presented for each subdivision.

Source: Refs. [29, 74, 252, 253].

All contemporary forms of life store information in DNA molecules. DNA molecules are polymers consisting of four types of organic molecules linked together by phosphate groups, namely: adenine (A), thymine (T), cytosine (C), and guanine (G). Indirectly, all cellular processes are orchestrated by the information contained in the DNA molecule. Cellular processes store and use energy in the form of discrete packets (adenosine triphosphate molecules or ATP). In prokaryotes, DNA shows a double-stranded circular (usually) form and it is located in the internal environment of the cell (cytoplasm). Cells of eukaryotic organisms contain a double-stranded linear (usually) DNA folded inside a membrane-bound organelle, named the nucleus (from Latin – nucleus, “kernel” or “seed”; pl. nuclei). The nuclear membrane is a controlled barrier that separates the DNA molecules from the cytoplasm (Figure 1.2). Naturally, images based on electron microscopy can best show the classic structure and the inner “frozen” dynamics of eukaryotic cells (Figure 1.2). In double-stranded DNA, a cytosine molecule from one strand and a guanine molecule from the other strand, form three hydrogen bonds while adenine and thymine form two hydrogen bonds. The successive alternation of these simple hydrogen bonds along the double-stranded DNA molecule dictates the energy required to separate the two strands and establishes the local stability of the duplex. In both eukaryotes and prokaryotes, the order of the four types of nucleotides defines the information structure throughout a DNA molecule. These structures include the well-known “genes” (Greek – geneá, “generation”). Genes are regions of different lengths, found along the DNA molecule. Broadly, gene regions are in turn accompanied by regulatory structures, such as gene promoters and enhancers. Genes are involved in transcription, namely in the synthesis of RNA transcripts. Note that RNA molecules are also polymers consisting of four types of organic molecules, namely: adenine (A), uracil (U), cytosine (C), guanine (G). The RNA transcript is a single-stranded nucleotide sequence that is complementary to the DNA strand harboring the gene. In turn, the information on the RNA transcript dictates whether the transcript becomes a functional molecule within the cell or whether it becomes a template for protein synthesis.