Fundamentals of Molecular Biology. Part 2: Molecular Genetic Mechanisms - A. N. Ogurtsov 2011

DNA Transcription
Ribonucleotide Polymerization

A Gene is a segment of DNA that contains the information determining the synthesis of a single polypeptide chain or functional RNA (such as tRNA, for example).

The vast majority of genes carry information about The Structure of protein molecules, and RNA copies of such protein-coding genes are represented by Messenger RNA (mRNA). Viral DNA molecules contain only a few genes, whereas the DNA molecule of A eukaryotic chromosome can contain several thousand genes.

During RNA Synthesis, the four-letter (A, C, G, T) "language" of DNA is simply copied, or transcribed (METABOLISM/31.html">Transcription - rewriting), into the four-letter (A, G, C, U) "language" of RNA, in which thymine is replaced by uracil (Figure 8).

Unlike transcription, during Protein Biosynthesis (Translation), the four-letter "language" of DNA and RNA is translated into the 20-symbol amino acid language of Proteins.

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Figure 8 - Polymerization of ribonucleotides by RNA polymerase during transcription. N.B. - nitrogenous bases; rNTP - ribonucleoside triphosphate

During transcription, one of the DNA strands acts as a template that determines the order in which rNTP monomers, or ribonucleoside triphosphates, polymerize to form an RNA strand complementary to the DNA template.

The bases of the DNA template pair with complementary rNTPs, which are then added to the growing polynucleotide RNA chain via a polymerization reaction catalyzed by the enzyme RNA polymerase.

Polymerization involves the nucleophilic attack of the 3'-oxygen of the hydroxyl group at the end of the growing RNA chain on the α-phosphate of the next nucleotide to be added to the chain, which is already paired with the next Base of the DNA template (Figure 8).

As a result, a phosphodiester bond is formed and pyrophosphate (PP_i) is released. A consequence of this reaction is that the RNA molecule is always synthesized in the 5'→3' direction.

The addition of each successive ribonucleotide to the growing RNA molecule is energetically favorable because the high-energy bond between the α and β phosphates of the rNTP monomer is replaced by a low-energy phosphodiester bond between the ribonucleotides.

The chemical equilibrium of the polymerization reaction is driven toward further chain elongation by the presence within The Cell of pyrophosphatase, an enzyme that catalyzes the Cleavage of pyrophosphate into two molecules of inorganic phosphate.

Much like the DNA double helix, the template DNA strand and the complementary growing RNA strand have opposite 5'→3' orientations.

It is standard convention to number the positions of the nitrogenous bases on the DNA template strand along which the RNA molecule is synthesized in the following manner. The nitrogenous base where RNA polymerization begins (the transcription start site) is designated as (+1).

The direction in which the RNA chain elongates is considered positive, while the reverse direction is considered negative. Accordingly, the numbering of NUCLEOTIDES starting from the (+1) position in the positive direction (often referred to as "downstream") carries a plus (+) sign, and in the opposite direction ("upstream"), a minus (-) sign.