Molecular Biotechnology: Principles and Applications - Glick, B., & Pasternak, J. 2002

Fundamentals of Molecular Biotechnology
DNA, RNA, and Protein Synthesis
DNA Structure

All information regarding the Structure and functioning of any living Organism is encoded within its genetic material, which is primarily composed of deoxyribonucleic acid (DNA). In most organisms, DNA exists as a long double-stranded polymer. The sequence of monomeric units (deoxyribonucleotides) in one strand corresponds to—and is complementary to—the sequence of deoxyribonucleotides in the other strand. This principle of complementarity ensures that newly synthesized DNA molecules, formed during duplication (Replication), are identical to the parent molecules. Genes are individual genetic elements with strictly specific nucleotide sequences that encode particular products; some encode Proteins, while others encode RNA molecules exclusively. The information contained in protein-encoding genes (structural genes) is decoded through two consecutive processes: RNA Synthesis (METABOLISM/31.html">Transcription) and Protein Synthesis (Translation). First, Messenger RNA (mRNA) is synthesized using a specific region of DNA AS A template. Subsequently, through the coordinated action of a multi-component system involving Transfer RNA (tRNA), mRNA, Enzymes, and various protein factors, the protein molecule is assembled. Together, these processes ensure the accurate translation of Genetic information—encrypted in DNA in the language of NUCLEOTIDES—into the language of Amino Acids. The Amino Acid Sequence of a protein molecule uniquely dictates its three-dimensional structure and biological Functions.

To obtain valuable biotechnological products, scientists utilize genes from A wide variety of organisms. To better understand how biotechnological systems function, let us examine The structure of the DNA molecule along with the processes of replication, transcription, and translation.

The first insights into The chemical properties of DNA emerged in 1868. By the early 1940s, it was established that the DNA molecule is a linear polymer. Its monomeric units are nucleotides, which consist of a nitrogenous base, a five-carbon sugar (pentose), and a phosphate group (Fig. 3.1, A). The phosphate group is attached to the 5' carbon of the sugar residue, while the organic base is attached to the 1' carbon. There are two types of bases in DNA: Purines [adenine (A) and guanine (G)] and Pyrimidines [cytosine (C) and thymine (T)] (Fig. 3.1, B). In DNA, the monosaccharide is 2'-deoxyribose, which contains a single hydroxyl group (OH), whereas in RNA, it is ribose, which has two hydroxyl groups. Nucleotides are linked together by phosphodiester bonds, where the phosphate group at the 5' carbon of one nucleotide is joined to the 3'-OH group of the deoxyribose in the adjacent nucleotide (Fig. 3.2). One end of the polynucleotide chain features a free 3'-OH group (the 3' end), while the opposite end features a 5'-phosphate group (the 5' end).

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Fig. 3.1. Structural formulas of DNA components. A. Nucleotide. The base may be adenine, guanine, cytosine, or thymine. The colored dashed line outlines the sugar residue (deoxyribose), with carbon atoms indicated by numbers. B. Bases. The colored dashed line outlines the nitrogen atom through which deoxyribose attaches to the base.

Fig. 3.2. A single strand of a DNA molecule.

Fig. 3.3. Model of the DNA double helix. The rungs represent complementary Base Pairs, and the side rails represent the sugar-phosphate backbone.

In 1953, James Watson and Francis Crick, building upon X-Ray Diffraction data from DNA crystals, concluded that native DNA consists of two polymer chains forming a double helix (Fig. 3.3). The intertwined polynucleotide chains are held together by Hydrogen Bonds formed between complementary bases on opposite chains (Fig. 3.4). Specifically, adenine pairs exclusively with thymine, and guanine pairs with cytosine. The A—T base pair is stabilized by two hydrogen bonds, whereas the G—C pair is stabilized by three. The length of double-stranded DNA is typically measured in base pairs (bp). For DNA molecules comprising thousands or millions of base pairs, the units kilobase pairs (kbp) and megabase pairs (Mbp) are used, respectively. For example, the DNA of human chromosome 1 is a single double helix measuring 263 Mbp in length.

Fig. 3.4. A fragment of double-stranded DNA.

The sugar-phosphate backbone of the molecule—consisting of phosphate groups and deoxyribose residues linked by 5'—3' phosphodiester bonds—forms the side rails of the spiral staircase, while the A—T and G—C base pairs form its rungs (Fig. 3.4). The strands of the DNA molecule are antiparallel: one runs in the 3'→5' direction, while the other runs 5'→3'. In accordance with THE PRINCIPLE OF complementarity, if one strand has The nucleotide sequence 5'-TAGGCAT-3', the complementary strand must feature the sequence 3'-ATCCGTA-5' at that Location. Consequently, the double-stranded form appears as follows:

By convention, the 5' end of the top strand is always positioned on the left, and the 3' end on the right.

The carrier of genetic information must satisfy two primary requirements: it must replicate with high fidelity, and it must dictate (code for) the synthesis of protein molecules. The Watson-Crick DNA model fully satisfies both criteria. First, According to the principle of complementarity, each DNA strand can serve as a template for the synthesis of a new complementary strand. Consequently, following a single round of replication, two daughter molecules are produced, each possessing the exact same nucleotide sequence as the parent DNA molecule. Second, the nucleotide sequence of a structural Gene uniquely defines The amino acid sequence of the protein it encodes.