Transcription of DNA

For the hereditary information in DNA to be useful, it must be “expressed,” that is, used to direct the growth and functioning of an organism. The first step in the processes that constitute DNA expression is the synthesis of RNA, by a template mechanism that is in many ways analogous to DNA replication. Because the RNA that is synthesized is a complementary copy of information contained in DNA, RNA synthesis is referred to as transcription.

There are three key differences between replication and transcription: (1) RNA molecules are much shorter than DNA molecules; only a portion of one DNA strand is copied or transcribed to make an RNA molecule. (2) RNA is built from ribonucleotides rather than deoxyribonucleotides. (3) The newly synthesized RNA strand does not remain associated with the DNA sequence it was transcribed from.

The DNA sequence that is transcribed to make RNA is called the template strand, while the complementary sequence on the other DNA strand is called the coding or informational strand. To initiate RNA synthesis, the two DNA strands unwind at specific sites along the DNA molecule. Ribonucleotides are attracted to the uncoiling region of the DNA molecule, beginning at the 3′ end of the template strand, according to the rules of base pairing. Thymine in DNA calls for adenine in RNA, cytosine specifies guanine, guanine calls for cytosine, and adenine requires uracil. RNA polymerase—an enzyme—binds the complementary ribonucleotide and catalyzes the formation of the ester linkage between ribonucleotides, a reaction very similar to that catalyzed by DNA polymerase (Figure 1.1). Synthesis of the RNA strand takes place in the 5′ to 3′ direction, antiparallel to the template strand. Only a short segment of the RNA molecule is hydrogen-bonded to the template strand at any time during transcription. When transcription is completed, the RNA is released, and the DNA helix reforms. The nucleotide sequence of the RNA strand formed during transcription is identical to that of the corresponding coding strand of the DNA, except that U replaces T.

Figure 1.1 A Schematic Diagram of RNA Transcription from a DNA Template. The representation of RNA polymerase is proportionately much smaller than the actual molecule, which encompasses about 50 nucleotides at a time.

Three types of RNA are formed during transcription: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). These three types of RNA differ in function, size, and percentage of the total cell RNA (Table 1.1). mRNA makes up only a small percent of the total amount of RNA within the cell, primarily because each molecule of mRNA exists for a relatively short time; it is continuously being degraded and resynthesized. The molecular dimensions of the mRNA molecule vary according to the amount of genetic information a given molecule contains. After transcription, which takes place in the nucleus, the mRNA passes into the cytoplasm, carrying the genetic message from DNA to the ribosomes, the sites of protein synthesis. Elsewhere, we shall see how mRNA directly determines the sequence of amino acids during protein synthesis.

Ribosomes are cellular substructures where proteins are synthesized. They contain about 65% rRNA and 35% protein, held together by numerous noncovalent interactions, such as hydrogen bonding, in an overall structure consisting of two globular particles of unequal size.

Molecules of tRNA, which bring amino acids (one at a time) to the ribosomes for the construction of proteins, differ from one another in the kinds of amino acid each is specifically designed to carry. A set of three nucleotides, known as a codon, on the mRNA determines which kind of tRNA will add its amino acid to the growing chain. Each of the 20 amino acids found in proteins has at least one corresponding kind of tRNA, and most amino acids have more than one.

The two-dimensional structure of a tRNA molecule has three distinctive loops, reminiscent of a cloverleaf (Figure 1.2). On one loop is a sequence of three nucleotides that varies for each kind of tRNA. This triplet, called the anticodon, is complementary to and pairs with the codon on the mRNA. At the opposite end of the molecule is the acceptor stem, where the amino acid is attached.