Eukaryotic cells, by definition, keep their DNA in a separate membrane-bound organelle, the nucleus; they also typically contain 3-30 times as many genes in prokaryotes and in many cases contain thousands more non-coding DNA. The large amount of non-coding DNA is responsible for the complex regulation of gene expression.
It was thought that a gene contained all the information needed to construct a complete protein, such as an enzyme. However, it has now been proven that many proteins contain more than one polypeptide chain, so these molecules are coded for by more than one gene. The location of a gene on a chromosome is referred to as its locus, which remains in that fixed position (Boyle and Senior, 2008). It is customary to divide organisms in two groups, prokaryotes whose DNA directly interacts with cytoplasm and eukaryotes whose DNA is separated from the cytoplasm by a nuclear membrane (Bendich and Drlica, 2000). It is estimated that the human genome encodes approximately 25,000 genes which is nearly twice as many compared to that of the common fruit fly; the 25,000 genes that are encoded account for around 1.5% of the genome. The rest of the genome is considered to contain the extensive instructions that direct gene transcription, indicating the complexity of eukaryotes (Phillips, 2008).
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In all species, transcription begins with the binding of the RNA polymerase complex to a certain DNA sequence at the beginning of a gene which can be defined as the promoter. The activation of the RNA polymerase complex initiates the transcription process; this is then followed by the elongation of the transcript. This process leads to the clearing of the promoter which allows the transcription process to begin yet again; it can be controlled in two different ways, cis (Promoter) and polymerase (Trans) levels (Clancy, 2008)
While there are basic similarities involved with gene transcription between prokaryotes and eukaryotes; which include the fact that RNA polymerase binds upstream of the gene on the promoter which then initiates transcription. Multicellular eukaryotes control cell differentiation through more precise, complex and spatial regulation of gene expression (Phillips, 2008). Specifically, in eukaryotes, transcription is undertaken by three different types of RNA polymerase, each differ in the number and type of subunits as well as the class of RNAâ€™s in which they transcribe. For example, RNA pol I transcribes rRNA (ribosomal RNA) whereas RNA pol II transcribes mRNA (messenger RNA) (Clancy, 2008). Transcription and translation occur simultaneously; therefore, changes that affect one process automatically affect the other. This relationship provides a gene regulatory mechanism which is unique to prokaryotes (Ralston, 2008).
In prokaryotes all transcription is performed by a single type of RNA polymerase, it contains four catalytic subunits and a single regulatory subunits referred to as sigma (Clancy, 2008). Prokaryotic RNA polymerases recognise promoters by specific sequences directly upstream from the initiation site; transcription is initiated more efficiently on purified DNA templates (Struhl, 1999).
The final level of protein in the cell depends on the efficiency of each step and the rate in which the RNA and protein molecules are degraded. In the eukaryotic cell the RNA molecule resulting from transcription contains both exon (coding) and intron (non-coding) sequences. Before it can go through the process of translation, the two ends of the RNA molecule are modified, the introns are removed by an enzyme catalysed RNA splicing reaction, which results in an mRNA molecule. This molecule can now be transported through the nuclear pore, as it is single stranded, into the cytoplasm. However, in prokaryotes the production of mRNA is much less complex, the five prime end of the RNA molecule is produced by the imitation of transcription and the three prime end when the transcription process is terminated. As prokaryotes lack the presence of a nucleus, both transcription and translation occur in a common compartment (Alberts, 2008).
The sequencing of various genomes has produced a significant amount of information on the genome architecture and the different features such as intron-exon organisation, regulatory regions and non-coding RNAâ€™s. The information acquired by the sequencing of genomes has challenged our understanding and the underlying principles that are involved in genome evolution (Chavali et al., 2011).
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Genomic architecture of eukaryotic cells is considerably different compared to that of prokaryotic cells; this is due to the presence of spliceosomal introns, which can be defined as pre-mRNA introns characterised by specific intron sequence located on the boundaries between introns and exons. These spliceosomal introns have been conserved over a long evolutionary period; they are responsible for interrupting protein-coding genes (Koonin, 2009). However, the density and content of these introns can differ dramatically from 1-2 introns per genome in various unicellular eukaryotes, for example, diplomonands, to approximately 5-8 introns per gene in vertebrates. Majority of eukaryotes have relatively small introns with a size of around 20-200 nucleotides; however in some plants they possess a fraction of longer introns whereas in mammals the average intron size is roughly 2kb. The wide variance of size and density of introns could indicate they are, on average, well conserved elements of the eukaryotic genome architecture (Koonin, 2009).
Eukaryotic chromosomes possess more than one origin of replication and with the accumulation of repetitive elements this accounts for the 80,000-fold genome size variation in this domain. In many cases, increases in the genome size are not related to selection, some eukaryotic genomes are only limited by replication (MooreSchools, 2007).
Prokaryote genomes only contain a single bidirectional replication site per chromosome, which indicates it can occur in both directions using a switch point between the leading and lagging strand (Koonin and Wolf 2008); consequently, the genome size limits the rate in which the chromosomes replicate. A number of prokaryote genomes are spread across a number of chromosomes which are not the copies of one another; this allows the genome to have a larger size but does not slow down the process of replication (Poole et al., 2004). Circular chromosomes are only found in prokaryotes, it has been suggested that prokaryotes linages occurred through the adaptation to high temperatures, this theory arose from the fact that circular DNA is more thermostable than linear DNA (Forterre, 1995).
Linear chromosomes can however occur in some prokaryotes such as bacteria; species which consist of linear chromosomes include Borrelia Burgdorferi and Streptomyces species. As well as having linear chromosomes these bacterial chromosomes resemble those of eukaryotic chromosomal telomeres, designed to solve the â€˜ends problemâ€™ of linear DNA replication. Chromosomes in eukaryotic cells are thought to be linear, however, circular forms of these chromosomes can be maintained under certain conditions (Bendich and Drlica, 2000).
Prokaryotes and eukaryotes have evolved the best mechanism to suite their individual particular needs; while prokaryotes take advantage of pairing transcription and translation by it allowing an increase in the rate of the process, eukaryotes have developed a more complex system with different mechanisms of gene regulation. This complex system involved in eukaryotes makes it less susceptible to DNA degrading and mutations as it is protected inside a membrane bound organelle such as a nucleus (Ralston, 2008). Key aspects of eukaryotic genome architecture appear to be conserved from a very early period in evolution, pre-dating the last common ancestor. Compared to that of prokaryote genome architecture that is the result from one or more periods of reductive evolution (Poole et al., 2004). As stated above not all bacteria have circular chromosomes, since there have been so few species that have been analysed adequately it is unclear whether circle is the most common structure for chromosomes amongst prokaryotes. The evidence that supports the idea of circular chromosomes is purely based on mapping data, which alone cannot distinguish between linear and circular chromosomal form (Bendich and Drlica, 2000).