Compared with bacteria, most eukaryotic cells are enormous. Bacteria are rarely larger than a few thousandths of a millimetre (a few microns) or so in length. In contrast, although some eukaryotes, known as the pico-eukaryotes, are of bacterial size, the majority are ten to a hundred times those dimensions, giving them a cell volume about 10 000 to 100 000 times that of bacteria.
Size is not the only thing that matters. The cardinal feature of eukaryotes, from which their Greek name derives, is the possession of a 'true' nucleus. This nucleus is typically a spherical, dense mass of DNA (the genetic matter) wrapped up in proteins and enveloped in a double membrane. Here, already, are three big differences with bacteria. First, the bacteria lack a nucleus at all, or else have a primitive version that is not enclosed by a membrane. For this reason bacteria are also termed 'prokaryotes', from the Greek 'before the nucleus'. While this is potentially a prejudgement—some researchers argue that cells with a nucleus are just as ancient as those without—most specialists agree that prokaryotes are well named: they really did evolve before cells with a nucleus (the eukaryotes).
The second big difference between bacteria and eukaryotes is the size of their genomes as a whole—the total number of genes. Bacteria generally have far less DNA than even simple single-celled eukaryotes such as yeast. This difference can be measured either in terms of the total number of genes—usually adding up to hundreds or thousands—or the total DNA content. This latter value is known as the C-value, and is measured in 'letters' of DNA. It includes not only the genes, but also the stretches of so-called non-coding DNA—DNA that does not code for proteins, and so can't really be called 'genes'. The differences in both the number of genes and the C-value are revealing. Single-celled eukary-otes like yeasts have several times as many genes as most bacteria, whereas humans have perhaps twenty times as many. The difference in the C-value, or total DNA content, is even more striking, as eukaryotes contain far more non-coding DNA than bacteria. The total DNA content of eukaryotes spans an extraordinary five orders of magnitude. The genome of a large amoeba, Amoeba dubia, is more than 200 000 times larger than that of the tiny eukaryotic cell, Encephalitozoon cuniculi. This enormous range is unrelated to complexity, or the total number of genes. Amoebae dubia actually has 200 times more DNA than do humans, even though it has far fewer genes and is obviously less complex. This odd discrepancy is known as the C-value paradox. Whether all this non-coding DNA has any evolutionary purpose is debated. Some of it certainly does, but a large part remains puzzling, and it is hard to see why an amoeba should need so much (we will return to this in Part 4). Nonetheless, it is a fact, requiring an explanation, that eukaryotes generally have orders of magnitude more DNA than prokaryotes. This is not without a cost. The energy required to copy all this extra DNA, and to ensure it is copied faithfully, affects the rate and circumstances of cell division, with implications that we will explore later.
The third big difference lies in the packing and organization of DNA. As we noted in the Introduction, most bacteria possess a single circular chromosome. This is anchored to the cell wall, but otherwise floats freely around the cell, ready for quick replication. Bacteria also carry genetic 'loose change' in the form of tiny rings of DNA called plasmids, which replicate independently and can be passed from one bacterium to another. The daily exchange of loose plasmids in this way is equivalent to shopping with loose change, and explains how the genes for drug resistance spread so quickly in a population of bacteria— just as a coin may find itself in twenty different pockets in a day. Returning to their main gene bank, few bacteria wrap their main chromosome in proteins—
rather, their genes are 'naked', making them easily accessible—a current account rather than a savings account. Bacterial genes tend to be ordered in groups that serve a similar purpose, and act as a functional unit, which are known as operons. In contrast, eukaryotic genes give no semblance of order. Eukaryotic cells possess quite a number of disparate, straight chromosomes, which are usually doubled up to give pairs of equivalent chromosomes, such as the 23 pairs of chromosomes found in humans. In eukaryotes, the genes are strung along these chromosomes in virtually a random order, and to make matters worse they are often fragmented into short sections with long stretches of non-coding DNA breaking up the flow. To build a protein, a great tract of DNA often needs to be read off, before it is spliced up and melded together to form a coherent transcript that codes for the protein.
Eukaryotic genes are not just randomized and fragmented, they are also tricky to get at. The chromosomes are tightly wrapped in proteins called his-tones, which block access to the genes. When the genes are being replicated during cell division, or copied to make transcripts for building proteins, the configuration of the histones must be altered to allow access to the DNA itself. This in turn has to be controlled by proteins called transcription factors.
Altogether, the organization of the eukaryotic genome is a complicated business that fills library after library with footnotes. We'll come to another aspect of this complicated set-up in Part 5 (sex, which is not found in bacteria). For now, though, the most important take-home point is that there is an energetic cost to all of this complexity. Where bacteria are almost always ruthlessly streamlined and efficient, most eukaryotes are lumbering and labyrinthine.
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