Chapter  9:  Molecular Structure of Genes and Chromosomes

Male human chromosomes visualized by the method of chromosome “painting.” Metaphase chromosomes were hybridized to multiple DNA probes specific for sequences along the length of each chromosome. A different combination of fluorochromes that fluoresce with different spectra was used to label the probes for each chromosome. Following hybridization, digital images of the fluorescently labeled chromosomes were collected using a charge-coupled device (CCD) camera and multiple exposures with separate optical filters specific for each of the fluorochromes. The images were then analyzed by computer and a composite image was generated in which each chromosome can be clearly distinguished from chromosomes of a similar size by a pseudocolor assigned on the basis of its fluorochrome composition. Note that there are two homologs of each chromosome. This same method can be used to recognize abnormal chromosomal translocations with great sensitivity (see Figure 9 -38b). [See P. Lichter, 1997, Trends Genet. 13:475 – 479; photograph courtesy of M. Speicher and D. C. Ward.]

Sequencing and other molecular analyses have revealed that a very large fraction of all vertebrate genomes, perhaps well over 90 percent, does not encode precursors to mRNAs or any other RNAs. In multicellular organisms, this noncoding DNA contains many regions that are similar but not identical. Variations within some stretches of this repetitious DNA are so great that each single person can be distinguished by a DNA “fingerprint” based on these sequence variations. Moreover, some repetitious DNA sequences are not found in constant positions in the DNA of individuals of the same species. Such “mobile” DNA segments, which are present in both prokaryotic and eukaryotic organisms, can cause mutations when they move to new sites in the genome. These mobile segments probably have played an important role in evolution, even though they generally have no function in the life cycle of an individual organism.

In higher eukaryotes, DNA regions encoding proteins — that is, genes — lie amidst this expanse of nonfunctional DNA. In addition to the apparently nonfunctional DNA between genes, noncoding introns are common within genes of multicellular plants and animals. Introns are less common, but sometimes present, in single-celled eukaryotes and very rare in bacteria. Sequencing of the same protein-coding gene in a variety of eukaryotic species has shown that evolutionary pressure selects for maintenance of relatively similar sequences in the coding regions, or exons. In contrast, wide sequence variation, even including total loss, occurs among introns, suggesting that most of the sequence of introns is nonfunctional. Cloning and sequencing have also confirmed the widespread existence of “families” of similar genes encoding proteins with related, but distinct, specialized functions.

The sheer length of cellular DNA is a significant problem with which cells must contend. The DNA in a typical bacterial cell, which is about 10³ times longer than the length of the cell, is folded and organized to fit within the cell. The total length of the DNA in eukaryotic cells is even longer compared with the cell diameter. Specialized eukaryotic proteins associated with nuclear DNA organize it into the structures of DNA and protein visualized as individual chromosomes during mitosis. Mitochondria and chloroplasts also contain DNA, probably evolutionary remnants of their origins, that encodes essential components of these vital organelles.

In this chapter we first present a molecular definition of genes and then discuss the main classes of eukaryotic DNA and the special properties of mobile DNA. Next we describe several examples of functional rearrangements of chromosomal DNA, including the process for generating functional antibody genes. We also consider the packaging of DNA and proteins into compact complexes, the large-scale structure of chromosomes, and the functional elements required for chromosome duplication and segregation. In the final section, we discuss organelle DNA.