This chapter inventories classes of DNA sequences in the genomes of organisms, mitochondria, chloroplasts, and viruses.
Part of an organism's genome consists of functional sequences – genes, regulatory sequences, telomeres, centromeres, and origins of replication. However, genomes also include DNA sequences that either are clearly nonfunctional or appear to be nonfunctional. The genomes of bacteria and archaea are mostly free of nonfunctional sequences, but, in many eukaryal genomes, the junkyard is larger than the portion that encodes RNA.
Some genes are present in multiple, identical copies. There are also sets of functionally related, homologous genes, called gene families. Nonfunctional DNA sequences may also be present in multiple copies. Repeated DNA sequences are often arranged in tandem.
What Is a Gene?
Dear reader, I have bad news for you: geneticists cannot agree on what a gene is, even though we do agree that genes are fundamental biological objects. Worse still, gene can change its meaning with context. Though this situation wants a strong remedy, none is available. The best I can offer you is a simple, natural concept of gene, contrasted with widely used, alternative concepts.
Consistently in this book, a gene is defined as a chromosomal segment of nucleic acid that encodes an RNA transcript (a freshly synthesized piece of RNA), along with nearby regulatory sequences needed to initiate RNA synthesis. This applies even when the transcript codes for several peptides or polypeptides.