Gene Organisation: Prokaryotes verus Eukaryotes

Prokaryotes
In bacteria, the genes that encode proteins that serve a particular function together are found in a contiguous (sharing a common border) array in the DNA. These arrangements are called operons. The operons form a single unit and will share a promoter, and when transcribed, will produce a single strand of mRNA. From there, the various proteins will be translated, and thus, results in the coordinate expression of all of the genes in the operon. This means that all of the genes in the operon are transcribed and translated. Note that in prokaryotes, very few gaps of noncoding DNA are found, and so mRNA is transcribed directly from the get-go. Also, as DNA is not sequestered in a nucleus, as prokaryotes do not have organelles, translation starts by ribosomes at the 3' end of the nascent mRNA while the polymerase is still attached and carrying out transcription. Such processes are known as dynamic.

Eukaryotes
As eukaryotes are more complex, genes are not organized into operons that code for proteins that serve a particular function. In fact, the genes are physically separated in the DNA, and are located on different chromosomes for instance. Co-regulation in eukaryotes is not achieved simply by physical linkage like in prokaryotes. Instead, each gene is transcribed from its own promoter, which is translated to form a single polypeptide. This contrasts with prokaryotes which from various polypeptides from the same operon. Also the protein-coding sequence of mRNA is discontinuous with the template DNA strand. How is this possible? After all, the mRNA was transcribed directly from this strand, so they should contain identical information. Not so. The eukaryotic gene contains pieces of coding sequence called exons, separated by pieces of noncoding sequence called introns. During mRNA processing, the introns are removed from the initial primary transcript (the RNA copy of the entire DNA sequence).

Eukaryotic mRNA Processing

Since transcription occurs in the nucleus, for eukaryotes, no translation can occur until the mRNA is processed. First, the DNA is transcribed to form a pre-cursor mRNA, also known as the primary transcript. This long sequence contains all of the information of the original DNA strand.

As soon as the 5' end of the RNA emerges from the polymerase, it is given a 5' cap, a 7-methylguanylate which identifies it as an mRNA so it will eventually be exported to the cytoplasm and stabilizes the structure from being degraded by other enzymes. The capping is done by enzymes and it is connected by 5' 5' triphosphate linkage.

Then, the primary transcript is cleaved at a 3' end site to yield a free 3' hydroxyl group to which adelylinic acid residues (100-250) are added to form a poly(A) tail. This is done by poly(A) polymerase.

Finally, RNA splicing occurs, where the transcript is cleaved and the introns are removed (intron excision), and the exons are connected together again (exon ligation).

Eukatryotic mRNAs contain untranslated regions or (UTRs) at both ends, with the 5' UTR having around 100 nucleotides and the 3' UTR having around several kilobases. Bacteria also have UTRs, but they are smaller, around 10 nucleotides only.

Alternative RNA Splicing

Alternative RNA splicing leads to greater diversity in the types of proteins encoded by the genomes of higher organisms. How this works is a single gene can have exons spliced out of its sequence giving rise to different forms of a protein called isoforms that are encoded by the same gene.

For example, fibronectin, a multidomain protein found in mammals, is processed by alternative splicing. In fibroblasts, the fibronectin mRNAs contain exons EIIIA and EIIIB, which then encode amino acid sequences that bind tightly to proteins in the fibroblast plasma membrane. In heptatocytes (liver cells), mRNAs do not contain exons EIIIA and EIIIB, as they have been excised from the mRNA sequence. Thus, fibronectin produced by the liver, does not adhere to proteins. More than 20 different kinds of fibronectin exist; all produced by alternative splicing.