This is a thread-like structure consisting of a single molecule of DNA, but in the case of archaea and eukaryotes, it also includes histone proteins. The DNA carries the genetic information of the cell. In the bacteria and archaea, the chromosome lies free in the cytoplasm of the cell and consists of a single circle of DNA. In the case of eukaryotes the DNA consists of several separate strands of DNA, each chromosome of which carries different information and all of which are enclosed together in a membrane-bound nucleus inside the cell. The totality of the genetic information in a cell is referred to as the genome.
Comparisons of genomes between various organisms reveal some interesting differences. Humans have 23 pairs of different chromosomes which include more than 3 billion nucleotides (with about 20,000 genes) while the fruit fly has 4 pairs of chromosomes with 175 million nucleotides (about 16,000 genes). By comparison, the bacterium E. coli exhibits about 4.6 million nucleotides all located on single chromosome, Arabidopsis (a type of radish plant) has 5 pairs of chromosomes and 135 million nucleotides, and ferns have 720 or more chromosome pairs with total number of nucleotides as high as 148 billion. There does not seem to be any particular reason for any of these numbers!
The main point of interest however is what happens to the chromosomes in the different kinds of cell. A brief examination of this will reveal a major gulf between the cells with an organized nucleus (eukaryotes) and those which lack such a feature (bacteria and archaea).
The process of cell division (binary fission) is rapid and quite uncomplicated in bacteria and archaea. In bacteria there is one point of replication where the duplication of DNA begins. This point of origin copies itself as the duplication of DNA moves in opposite directions. Once the copying is completed, the duplicated points of origin move apart, each one carrying a circular chromosome with it. In the archaea, the process is similar except that there are a number of points on the chromosome where the duplicating process begins.
For the eukaryotes, the process (mitosis) is much more complicated and much slower. As there are a number of linear chromosomes in the nucleus, care must be taken to make sure all the right chromosomes get into the new identical daughter cells. This multi-step process proceeds as follows:
There are many special innovations in this process, including: the centromere which is a region of condensed DNA forming the ‘waist-line’ in the chromosome; the kinetochore, a histone-type of protein body; the appearance of spindle microtubules; the attachment of kinetochore to microtubule; the disappearance and later reforming of the complicated nuclear envelope (which is also unique to eukaryotes); the coordinated pulling of the chromosomes by the spindle fibres; and the subsequent process of cell division.
But those are not all the innovations in the eukaryotic cell!
Some single celled eukaryotes exhibit only mitotic cell division (and asexual reproduction) but most multicellular eukaryotes exhibit meiosis as well (and sexual reproduction). Meiosis is necessary for sexual reproduction. Sexual reproduction occurs in an individual whose cells are diploid. A diploid cell has 2 complete sets of chromosomes. One set comes from the mother and the other set comes from the father. However, to keep the number of chromosomes from escalating in every following generation, there must be a process to reduce the number of chromosomes in the sex cells (eggs and sperm) down to one set again (haploid) before a new fertilization event. This process of going down to one set of chromosomes is called meiosis. It is much more complicated than mitosis!
There are four novel steps in meiosis which are not present in mitosis:
There is a great deal of information required to coordinate this activity and bring about meiosis! This all has to be programmed into the DNA.
Scientists really have no plausible ideas for how meiosis could have developed through evolutionary processes. However, meiosis is only one problem with the origin of the eukaryotic cell. Mitosis is also a huge problem. There are several competing theories as to how all these features of the eukaryotic cell could have appeared through spontaneous unguided processes. It goes without saying that many scientists believe that the common ancestor of all eukaryotes arose from some kind of cell without a nucleus, but whether it was bacterial or archaeal is much debated, and exactly how this might happen remains unknown.
The special capabilities of the eukaryotic cell actually cry out that they were designed. The complexity and finesse of these features simply could not develop from the unpromising material of bacteria and archaea.