The DNA molecule that stores the genetic information in the nucleus is a long, double-stranded, helical structure. DNA is composed of nucleotides, which consist of phosphoric acid, a five-carbon sugar called deoxyribose, and one of four nitrogenous bases (Fig. 6.1). These nitrogenous bases carry the genetic information and are divided into two groups: the pyrimidine bases, thymine (T) and cytosine (C), which have one nitrogen ring, and the purine bases, adenine (A) and guanine (G), which have two. The backbone of DNA consists of alternating groups of sugar and phosphoric acid, with the paired bases projecting inward from the sides of the sugar molecule.
Double Helix and Base Pairing
The native structure of DNA, as elucidated by James Watson and Frances Crick in 1953, is that of a spiral staircase, with the paired bases representing the steps (see Fig. 6.1). A precise complementary pairing of purine and pyrimidine bases occurs in the double-stranded DNA molecule in which A is paired with T and G is paired with C. Each nucleotide in a pair is on one strand of the DNA molecule, with the bases on opposite DNA strands bound together by hydrogen bonds that are extremely stable under normal conditions. The double- stranded structure of DNA molecules allows them to replicate precisely by separation of the two strands, followed by synthesis of two new complementary strands. Similarly, the base complementary pairing allows for efficient and correct repair of damaged DNA molecules.
Several hundred to almost 1 million base pairs can represent a gene, the size being proportional to the protein product it encodes. Of the two DNA strands, only one is used in transcribing the information for the cell’s protein-building machinery. The genetic information of one strand is meaningful and is used as a template for transcription; the complementary code of the other strand does not make sense and is ignored. Both strands, however, are involved in DNA duplication. Before cell division, the two strands of the helix separate and a complementary molecule is duplicated next to each original strand. Two strands become four strands. During cell division, the newly duplicated double-stranded molecules are separated and placed in each daughter cell by the mechanics of mitosis. As a result, each of the daughter cells again contains the meaningful strand and the complementary strand joined together as a double helix. In 1958, Meselson and Stahl characterized this replication of DNA as semiconservative, as opposed to conservative replication in which the parental strands reassociate when the two strands are brought together (Fig. 6.2).
Packaging of DNA
The genome or total genetic content is distributed in chromosomes. Each human somatic cell (cells other than the gametes [sperm and ovum]) has 23 pairs of different chromosomes, one pair derived from the individual’s mother and the other from the father. One of the chromosome pairs consists of the sex chromosomes. Genes are arranged linearly along each chromosome. Each chromosome contains one continuous, linear DNA helix. The DNA in the longest chromosome is more than 7 cm in length. If the DNA of all 46 chromosomes were placed end to end, the total DNA would span a distance of about 2 m (>6 feet).
Because of their large size, DNA molecules are combined with several types of protein and small amounts of RNA into a coiled structure known as chromatin. The organization of DNA into chromatin is essential for controlling transcription and for packaging the molecule. Some DNA-associated proteins form binding sites for repressor molecules and hormones that regulate genetic transcription; others may block genetic transcription by preventing access of nucleotides to the surface of the DNA molecule. A specific group of proteins called histones is thought to control the folding of the DNA strands. Each double-stranded DNA molecule periodically coils around histones, which keeps the DNA organized.3 With cells that do not divide the DNA strands are in a less compact form called chromatin. Figure 6.3 illustrates how both the chromosomes and chromatin, which consist of chromosomal DNA, are coiled around histones.
Although solving the structural problem of how to fit a huge amount of DNA into the nucleus, the chromatin fiber, when complexed with histones and folded into various levels of compaction, makes the DNA inaccessible during the processes of replication and gene expression. To accommodate these processes, chromatin must be induced to change its structure, a process called chromatin remodeling. Several chemical interactions are now known to affect this process. One of these involves the acetylation of a histone amino acids group that is linked to the opening of the chromatin fiber and gene activation. Another important chemical modification involves the methylation of histone amino acids, which is correlated with gene inactivation.
Four bases—guanine, adenine, cytosine, and thymine (uracil is substituted for thymine in RNA)—make up the alphabet of the genetic code. A sequence of three of these bases forms the fundamental triplet code used in transmitting the genetic information needed for protein synthesis. This triplet code is called a codon (Table 6.1). An example is the nucleotide sequence UGG (uracil, guanine, guanine), which is the triplet RNA code for the amino acid tryptophan. The genetic code is a universal language used by most living cells (i.e., the code for the amino acid tryptophan is the same in a bacterium, a plant, and a human being). Stop codons, which signal the end of a protein molecule, are also present. Mathematically, the four bases can be arranged in 64 different combinations. Sixty-one of the triplets correspond to particular amino acids, and three are stop signals. Only 20 amino acids are used in protein synthesis in humans. Several triplets code for the same amino acid; there- fore, the genetic code is said to be redundant or degenerate. For example, AUG is a part of the initiation or start signal as well as the codon for the amino acid methionine. Codons that specify the same amino acid are called synonyms. Synonyms usually have the same first two bases but differ in the third base.
Rarely, accidental errors in duplication of DNA occur. These errors are called mutations. Mutations result from the substitution of one base pair for another, the loss or addition of one or more base pairs, or rearrangements of base pairs. Many of these mutations occur spontaneously, whereas others occur because of environmental agents, chemicals, and radiation. Mutations may arise in somatic cells or in germ cells. Only those DNA changes that occur in germ cells can be inherited.
Considering the millions of base pairs that must be duplicated in each cell division, it is not surprising that random changes in replication occur. Most of these defects are corrected by DNA repair mechanisms. Several repair mechanisms exist, and each depends on specific enzymes called endonucleases that recognize local distortions of the DNA helix, cleave the abnormal chain, and remove the distorted region. The gap is then filled when the correct deoxyribonucleotides, created by a DNA polymerase using the intact complementary strand as a template, are added to the cleaved DNA. The newly synthesized end of the segment is then joined to the remainder of the DNA strand by a DNA ligase. The normal regulation of these gene repair mechanisms is under the control of DNA repair genes. Loss of these gene functions renders the DNA susceptible to accumulation of mutations. When these affect protooncogenes or tumor suppressor genes, cancer may result.
As the Human Genome Project was progressing, it became evident that the human genome sequence is almost exactly (99.9%) the same in all people. It is the small variation (0.01%) in gene sequence (termed a haplotype) that is thought to account for the individual differences in physical traits, behaviors, and disease susceptibility. These variations are sometimes referred to as polymorphisms (from the existence of more than one morphologic or body form in a population). An international effort has been organized to develop a map (HapMap) of these variations with the intent of providing a link between genetic variations and common complex diseases such as cancer, heart disease, diabetes, and some forms of mental disease.
In addition to nuclear DNA, part of the DNA of a cell resides in the mitochondria. Mitochondrial DNA is inherited from the mother by her offspring (i.e., matrilineal inheritance). It is a double-stranded closed circle, containing 37 genes, 24 of which are needed for mitochondrial DNA translation and 13 of which encode enzymes needed for oxidative metabolism. Replication of mitochondrial DNA depends on enzymes encoded by nuclear DNA. Thus, the protein-synthesizing apparatus and molecular components for oxidative metabolism are jointly derived from nuclear and mitochondrial genes. Genetic disorders of mitochondrial DNA, although rare, commonly affect tissues such as those of the neuromuscular system that have a high requirement for oxidative metabolism.