Human Biochemistry, Volume 2 - Murray R. 1993

Structure, Function, and Replication of Information Macromolecules
Recombinant DNA Technology
Basic Properties of DNA

Introduction/20.html">DNA Structure

DNA is a complex biopolymer organized into a double helix. Its fundamental building blocks are purine (adenine and guanine) and pyrimidine (thymine and cytosine) bases. These bases are attached to the C-1' carbon of the sugar moiety (deoxyribose). The sugar residues are linked together via 3'- and 5'-phosphodiester bonds (Fig. 37.1). The alternating deoxyribose residues and phosphate groups form the backbone of The Double Helix (Fig. 37.2). The direction of the 3'→5' bonds determines the orientation of a given strand, and since the orientations of the two complementary strands are opposite, they are referred to as antiparallel.

THE PRINCIPLE OF complementary base pairing (the base-pairing rule) underlies the Structure and function of DNA molecules. Adenine always pairs with thymine, and guanine with cytosine. These Base Pairs are termed complementary. The content of guanine residues in any DNA fragment always exactly matches the content of cytosine. Similarly, the amounts of adenine and thymine are equal. The two strands of DNA are held together by complementary base-pairing interactions and hydrophobic stacking interactions. These interactions can be disrupted by heating, leading to DNA Denaturation (melting). The rules of base pairing dictate that upon renaturation, the two complementary strands of DNA should re-associate to form the original structure. This is indeed what happens when a thermally denatured DNA solution is slowly cooled (annealed).

The denaturation-renaturation Temperature profile allows for an estimation of the degree of complementarity between nucleotide bases in DNA strands. Denaturing DNA segments characterized by a high degree of complementarity requires a correspondingly greater input of energy. Consequently, the Separation of such DNA fragments occurs at higher temperatures. This physical phenomenon is used in practice to determine the degree of affinity (Homology) between various Nucleic Acids and forms The basis of Hybridization—one of the core techniques in Genetic Engineering.

The human haploid genome consists of approximately 3·10⁹ base pairs (bp). Assuming an average Gene size of 3,000 bp, and given that genes do not overlap and METABOLISM/31.html">Transcription proceeds in only one direction, one might calculate that The Human Genome contains up to 10⁶ different genes. However, it is estimated that there are no more than 10⁵ genes in the human genome, and only 10% of genomic DNA directly encodes Proteins. The Functional Significance of the remaining 90% remains largely unknown.

The double helix is packaged into a compact structure formed through interactions with a group of predominantly basic proteins known as Histones. This compaction can exert regulatory Functions and also serves a clear practical purpose: if fully unraveled, the DNA in a single Cell Nucleus would reach a length of 1 meter. Chromosomal proteins package this gigantic molecule into a nucleus with a volume of just a few cubic microns.

Gene Organization

As a rule, prokaryotic genes consist of a small regulatory region (100–500 bp) and a large protein-coding segment (500–10,000 bp). Often, multiple genes are controlled by the same regulatory element. Most mammalian genes have a more complex architecture. The coding regions of eukaryotic genes are interrupted and interspersed with non-coding sequences. Once transcribed, these sequences are removed during the Processing of the primary transcript. The coding regions (which remain in the mature mRNA) are designated as exons. The DNA nucleotide sequences located between exons are called introns (Fig. 36.1). Introns are excised from the primary transcript prior to the export of the RNA into the Cytoplasm. The process of intron removal and the subsequent joining (ligation) of the coding segments is known as RNA splicing. Aberrant splicing can lead to human disease (see below), highlighting the critical importance of this post-transcriptional stage. The regulatory regions of eukaryotic genes are typically located 5' to the Transcription initiation site (the 5'-flanking DNA sequence). Occasionally, regulatory sequences reside within the gene itself or even in the 3'-flanking region. In mammalian Cells, each gene possesses its own regulatory element. Many eukaryotic genes (as well as those of certain Viruses replicating in mammalian cells) contain specialized DNA regions called enhancers, which enhance The rate of transcription. Some genes also contain silencers—regions that downregulate transcription. Mammalian genes are complex, multicomponent structures.

Gene Transcription

The Central dogma of molecular biology outlines the flow of Genetic information along the pathway DNA → mRNA → protein (Fig. 36.1, see also Ch. 41). This process is tightly controlled and comprises a series of intricate steps, each regulated by one or more Enzymes or factors. An error at any stage can result in pathology.