4 2.1 Prokaryotic and eukaryotic cells differ in structure. (Left to right: T.J. Beveridge/Visuals Unlimited; W. Baumeister/Science Photo/Library/Photo Researchers; Biophoto Associates/Photo Researchers; G. Murti/Phototake.)

Research indicates that dividing life into two major groups, the prokaryotes and eukaryotes, is incorrect. Although similar in cell structure, prokaryotes include at least two fundamentally distinct types of bacteria. These distantly related groups are termed eubacteria (the true bacteria) and archaea (ancient bacteria). An examination of equivalent DNA sequences reveals that eubacteria and archaea are as distantly related to one another as they are to the eukaryotes. Although eubacteria and archaea are similar in cell structure, some genetic processes in archaea (such as transcription) are more similar to those in eukaryotes, and the archaea may actually be evolutionarily closer to eukary-otes than to eubacteria. Thus, from an evolutionary perspective, there are three major groups of organisms: eubacteria, archaea, and eukaryotes. In this book, the prokaryotic-eukaryotic distinction will be used frequently, but important eubacterial - archaeal differences also will be noted.

From the perspective of genetics, a major difference between prokaryotic and eukaryotic cells is that a eukaryote has a nuclear envelope, which surrounds the genetic material to form a nucleus and separates the DNA from the other cellular contents. In prokaryotic cells, the genetic material is in close contact with other components of the cell — a property that has important consequences for the way in which genes are controlled.

Another fundamental difference between prokaryotes and eukaryotes lies in the packaging of their DNA. In eukary-otes, DNA is closely associated with a special class of proteins, the histones, to form tightly packed chromosomes. This complex of DNA and histone proteins is termed chromatin, which is the stuff of eukaryotic chromosomes ( FIGURE 2.2). Histone proteins limit the accessibility of enzymes and other proteins that copy and read the DNA but they enable the DNA to fit into the nucleus. Eukaryotic DNA must separate from the histones before the genetic information in the DNA can be accessed. Archaea also have some histone proteins that complex with DNA, but the structure of their chromatin is different from that found in eukaryotes. However, eubacteria do not possess histones, so their DNA does not exist in the highly ordered, tightly packed arrangement found in eukary-otic cells ( FIGURE 2.3). The copying and reading of DNA are therefore simpler processes in eubacteria.

Genes of prokaryotic cells are generally on a single, circular molecule of DNA, the chromosome of the prokaryotic cell. In eukaryotic cells, genes are located on multiple, usually linear DNA molecules (multiple chromosomes). Eukaryotic cells therefore require mechanisms that ensure that a copy of each chromosome is faithfully transmitted to each new cell. This generalization — a single, circular chromosome in prokaryotes and multiple, linear chromosomes in eukaryotes—is not always true. A few bacteria have more than one chromosome, and important bacterial genes are frequently found on other DNA molecules called plasmids. Furthermore, in some eukaryotes, a few genes are located on circular DNA molecules found outside the nucleus (see Chapter 20).

Histone proteins

Histone proteins

I 2.2 In eukaryotic cells, DNA is complexed to histone proteins to form chromatin.

I 2.3 Prokaryotic DNA (a) is not surrounded by a nuclear membrane nor is the DNA complexed with histone proteins; eukaryotic DNA (b) is complexed to histone proteins to form chromosomes that are located in the nucleus. (Part a, Dr. G. Murti/Science Photo Library/Photo Researchers; Part b, Biophoto Associates/Photo Researchers.)

I 2.4 A virus consists of DNA or RNA surrounded by a protein coat. (Hans Gelderblam/Visuals Unlimited.)

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