Basic concepts of molecular evolution

Abstract

The phenotype of living organisms is always a result of the genetic information that they carry and pass on to the next generation and of the interaction with the environment. The genome, carrier of this genetic information, is in most organisms deoxyribonucleic acid (DNA), whereas some viruses have a ribonucleic acid (RNA) genome. Part of the genetic information in DNA is transcribed into RNA, either mRNA, which acts as a template for protein synthesis; rRNA, which together with ribosomal proteins constitutes the protein translation machinery; or tRNA, which offers the encoded amino acid. The genomic DNA also contains elements, such as promotors and enhancers, that orchestrate the proper transcription into RNA. A large part of the genomic DNA of eukaryotes consists of genetic elements, such as introns, alu-repeats, the function of which is still not entirely clear. Proteins, RNA, and to some extent DNA, through their interaction with the environment, constitute the phenotype of an organism. DNA is a double helix in which the two polynucleotide strands are antiparallelly oriented, whereas RNA is a single-stranded polynucleotide. The backbone in each DNA strand consists of deoxyriboses with a phosphodiester linking each 5′ carbon with the 3′ carbon of the next sugar. In RNA, the sugar moiety is ribose. On each sugar, one of the following four bases is linked to the 1′ carbon in DNA: the purines, adenine (A) or guanine (G ); or the pyrimidines, thymine (T ), or cytosine (C ); in RNA, thymine is replaced by uracil (U ). Hydrogen bonds and base stacking result in binding of the two DNA strands, with strong (triple) bonds between G and C, and weak (double) bonds between T/U and A (Figure 1.1). These hydrogen-bonded pairs are called complementary. During DNA duplication or RNA transcription, DNA or RNA polymerase synthesizes a complementary 5′–3′ strand starting with the lower 3′–5′ DNA strand as template, such that the genetic information is preserved. This genetic information is represented by a oneletter code, indicating the 5′–3′ sequential order of the bases in the DNA or RNA