RNA and Types

Most proteins are enzymes that catalyze the myriad of chemical reactions in cells that are necessary for life; other proteins form structural functions as in bone and muscle. The information for making proteins resides in the sequence of bases in DNA in chromosomes and in organelles such as mitochondria. Converting the information contained in genes into proteins involves two complex processes. Transcription is the first step in which the sequence of bases in a gene is converted into a complementary sequence of bases in a molecule of RNA. Three chemically identical but functionally quite different molecules of RNA are transcribed from DNA: messenger RNA (mRNA) carries the genetic information contained in a gene; transfer RNA (tRNA) and ribosomal RNA (rRNA) are also transcribed from genes but are used to convert the information in the sequence of bases in mRNA into the corresponding sequence of amino acids in a protein.

Structure of RNA:

RNA is a single-stranded polynucleotide containing the nucleosides adenosine, guanosine, cytosine, and uridine. Roughly one-third to one-half of the nucleotides are engaged in intrastrand hydrogen bonds, with single-stranded segments interspersed between double-stranded regions that may contain up to about 30 base pairs. The base pairing produces conformations that are important to the function of the particular RNA molecules.

Ribosomal RNA (rRNA):

Ribosomes contain many different RNA molecules, three in prokaryotic ribosomes and four in eukaryotic ribosomes. Each class is characterized by its sedimentation coefficient, which represents a typical size. For prokaryotes, the three Escherichia coli rRNA molecules are used as size standards; they have sedimentation coefficients of 5S, 16S, and 23S. The E. coli rRNA molecules have been sequenced and contain 120, 1541, and 2904 nucleotides, respectively. The sizes of the prokaryotic rRNA molecules vary very little from one species of bacterium to another. Eukaryotic rRNA molecules are generally larger and there are four eukaryotic rRNA molecules. Rat liver rRNA molecules are taken as standards; the S values and the average number of nucleotides are 5S (120), 5.8S (150), 18S (2100), and 28S (5050), respectively. The eukaryotic 5.8S species corresponds functionally to the prokaryotic 5S species; no prokaryotic rRNA molecule corresponds to the eukaryotic 5S rRNA.

Transfer RNA (tRNA):

Transfer RNA molecules range in size from 73 to 93 nucleotides. All tRNA molecules studied contain extensive double stranded regions and form a clover leaf structure in which open loops are connected by double-stranded stems. By careful comparison of the sequences of more than 200 different tRNA molecules, common features have been found and a "consensus" tRNA molecule consisting of 76 nucleotides arranged in a cloverleaf form has been defined. By convention, the nucleotides are numbered 1 through 76 starting from the 5'-P terminus. The standard tRNA molecule has the following features:
1. The 5'-P terminus always is base-paired, which probably contributes to the stability of tRNA.
2. The 3'-OH terminus always is a four-base single-stranded region containing the base sequence
XCCA-3'-OH, in which X can be any base. This is called the CCA or acceptor stem. The adenine in the CCA sequence is the amino acid attachment site catalyzed by the cognate synthetase.
3. tRNA has many "modified" bases. A few of these, dihydrouridine (DHU), ribosylthymine (rT),
pseudouridine (Ψ), and inosine (I), occur in specific regions.
4. tRNA has three large single-stranded loops. The anticodon loop contains seven bases. The loop
with bases 14-21 is called the DHU loop; it is not constant in size in various tRNA molecules. The loop containing bases 54-60 almost always possesses the sequence TΨC and is called the TΨC loop.
5. Four double-stranded regions called stems (or arms) often possess GU base pairs. The names of the stems match the respective loop.
6. Another loop with bases 44-48, is also present. In the smallest tRNAs it contains four bases, whereas in the largest tRNA molecule it contains 21 bases. This highly variable loop is known as the extra arm.

tRNA

Messenger RNA:

Messenger RNA molecules in prokaryotic and eukaryotic cells are similar in some structural aspects but also differ significantly. All messenger RNAs contain the same four nucleotides, A, C, G, and U, and utilize the codon AUG to initiate translation of a polypeptide and the codons UAG, UGG, and UAA to terminate translation. Prokaryotic mRNAs are polycistronic (polygenic) and usually carry information for the synthesis of several polypeptides from a single mRNA. The triplet codons in prokaryotic mRNA are transcribed from the sense strand of DNA and subsequently are translated continuously from the 5’-PO4 end of the mRNA to the 3'-OH end. Since prokaryotic DNA is not isolated from the cytoplasm by a nuclear membrane, translation starts on mRNA molecules before transcription is completed. Thus, transcription and translation are coupled in prokaryotes. Synthesis of each polypeptide chain in a polycistronic mRNA is decided by an AUG initiation codon and one or more nonsense codons that release the finished polypeptide from the ribosome. Eukaryotic mRNAs differ from prokaryotic mRNAs in several respects. Eukaryotic genes invariably possess information for only a single polypeptide but each gene may consist of millions of nucleotides because eukaryotic genes contain introns and exons. The mRNA that is transcribed (primary transcript) is processed in several ways:

1. The introns (intervening sequences) are spliced out of the primary transcript and the exons (expressed sequences) are joined together. The splicing reactions and removal of introns from the primary transcript are done by small nuclear ribonucleoproteins (snRNPs).
2. While transcription is in process, the 5' end of the mRNA is capped with a methyl guanine nucleotide ( m7Gppp ) .
3. After the primary transcript is complete, a polyA tail (-AAAn AoH) is added to the 3' terminus.

mRNA

4. Other changes of the primary transcript are possible such as alternative splicing which gives
mRNAs with different sets of exons and RNA editing in which bases are modified or changed in the original transcript.
5. The functional mRNA is transported to the cytoplasm where translation occurs on ribosomes bound to the endoplasmic reticulum of the cell.