Three major types of RNA have been recognized: mRNA, tRNA, and rRNA

RNA SUMMARY

Three major types of RNA have been recognized: mRNA, tRNA, and rRNA. There are three key differences between the chemistry of RNA and that of DNA: RNA has the sugar ribose instead of deoxyribose; RNA has the base uracil instead of the base thymine; and except in certain viruses, RNA is not double stranded. RNA acts at two levels, genetic and functional. At the genetic level, RNA can carry the genetic information from DNA. At the functional level, RNA acts as a macromolecule in its own right, serving a structural role in ribosomes or an amino acid transfer role in protein synthesis. Some

RNA even has catalytic activity.

The transcription of the genetic information from DNA to RNA is carried out through the action of enzyme RNA polymerase, which catalyzes the formation of the phosphodiester bonds between ribonucleotides. RNA polymerase requires the presence of DNA, which acts as a template. The precursors of RNA are ATP, GTP, UTP, and CTP. The chemistry of RNA synthesis is very similar to DNA synthesis. RNA polymerase, unlike DNA polymerase, can start chains (the initial nucleotide in an RNA chain then retains all three phosphates). The first base in the RNA is almost always a purine, either adenine or guanine.

All RNA polymerases studied from bacteria are complex enzymes with closely related subunit structures. The enzyme from E.coli has four different types of protein subunits designated beta, beta prime, alpha, and sigma, with alpha appearing in two copies. The subunits interact to form the active enzyme, but sigma factor is not as tightly bound as the others, and easily dissociated, leading to formation of what is called the core enzyme. The core enzyme alone can catalyze the formation of RNA, and the role of sigma is in the recognition of the appropriate site on the DNA for the initiation of RNA synthesis.

The binding of RNA polymerase to the DNA occurs at particular sites called promoters. RNA polymerase travel away from the promoter region, synthesizing RNA as it moves.

Once the RNA polymerase has bound the process of transcription can proceed.

Termination of RNA synthesis occurs at specific base sequences on the DNA. A common termination sequence on the DNA is one containing an inverted repeat with a central nonrepeating segment. When such a DNA sequence is transcribed, the RNA can form a stem-loop structure by intrastrand base pairing. When such stem-loop structures in the RNA are followed by runs of uridines, they are effective transcription terminators. Other termination sites are regions where a GC rich region is followed by an AT rich sequence. Such kinds of structures lead to termination without addition of any extra factors. Another type of transcription terminator has been recognized which involves a distinct protein called rho. Rho does not bind to RNA polymerase or to DNA, but binds tightly to RNA and moves down the chain toward the RNA polymerase-DNA complex. Once RNA polymerase has paused at a termination site, rho can then cause the RNA and polymerase to leave the DNA, thus terminating transcription. Whether rho-dependent or rho-independent, transcription termination is ultimately determined by specific nucleotide sequences on the DNA.

A single organism can have several different sigma factors and these can recognize different promoter sequences. For E.coli, two sequences within the promoter region are highly conserved between promoters, and it is these that are recognized by sigma. Both sequences are upstream of the start of transcription. One is a region 10 bases before the start of transcription, the –10 region (Pribnow box). This has a consensus sequence of TATAAT. The second region of conserved sequence is about 35 bases from the start of transcription. The consensus sequence in the –35 region is TTGACA.

The RNA carrying the information that is translated into a protein is called mRNA. Most mRNA is unstable and is degraded by cellular nucleases. This is in contrast to rRNA and tRNA, which are sometimes referred to as stable RNA. In prokaryotes, a single mRNA molecule often codes for more than one protein. In prokaryotic genetic elements, genes coding for related enzymes are often clustered together. In these situations the RNA polymerase proceeds down the chain and transcribes the whole series of genes into a single long mRNA molecule. An mRNA coding for such a group of genes is called polygenic mRNA or a polycistronic mRNA. Subsequently, when this polycistronic mRNA participates in protein synthesis several polypeptides coded by a single mRNA can be synthesized at one time.

AN operon is a complete unit of gene expression, generally involving genes coding for several polypeptides on a polycistronic mRNA or genes coding for rRNA. In some cases, the transcription of the mRNA for an operon is under the control of a specific region of the DNA, the operator, which is adjacent to the coding region of the first gene in the operon. The operator is nearby and may overlap with the promoter. Within the cell are specific proteins, known as repressor proteins, which are able to bind to specific operators. If the repressor protein is attached to the operator, then transcription of that operon cannot occur.

In prokaryotes, a transcript of a protein-encoding gene is used directly to make protein, but transcripts of many other genes generally need to be trimmed before being used. The conversion of a precursor RNA into a mature RNA is called RNA processing. For instance, in prokaryotes, tRNA and rRNA are made initially as long precursor molecules, which are then cut at several places to make the final mature RNAs.

Catalytic RNAs, referred to as ribozymes, are involved in a number of important cellular reactions. RNA enzymes work like protein enzymes in that an active site exists that binds the substrate and catalyzes formation of a product. Most ribozymes are self-splicing introns. They are RNA-splicing enzymes that remove themselves from an RNA molecule while joining adjacent exons together. The intron ribozyme acts as a sequence-specific endoribonuclease, and once removed from the precursor RNA, circularizes with the further removal of a short oligonucleotide fragment. Most self-splicing introns can only act once.

The translation of the RNA message into the amino acid sequence of protein is brought about through the action of tRNA. Transfer RNA is an adaptor molecule having two specificities, one for a codon on mRNA, the other for an amino acid. The transfer RNA and its specific aa are brought together by means of specific enzymes that ensure that a particular tRNA receives its correct aa. The enzymes, called amino acid activating enzymes or animoacyl-tRNA synthetases, have the important function or recognizing both the aa and the specific tRNA for that aa. TRNA molecules contain some purine and pyrimidine bases differing slightly form the normal bases found in RNA in that they are chemically modified, often methylated. These modifications are added to the bases after transcription. The structure of tRNA is generally drawn in cloverleaf fashion. One of the variable parts of the tRNA molecule contains the anti-codon, the site recognizing the codon of mRNA. The anti-codon is found in the anti-codon loop and there are three nucleotides that are involved in the recognition process and with base pair with the codon. Other portions of the tRNA interact with the ribosome, other proteins, and with the activating enzyme.

REFERENCE:

Biology of Microorganisms. 7^th edition. Brock, Madigan, Martinko, and Parker. 1994.