RNAs, Structure and Function

RNA structure
Ribonucleic acid or RNA is a biopolymer macromolecule along with DNA. It consists if small subunits called nucleotides which are composed by: The nucleobase is attached on the D-ribose by an N-glycosidic bond, the ribose is bonded on the phospate group through ester bonds, and the backbone bonding between phosphate group and an adjacent ribose sugar through phosphodiester bonds.A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. RNA is relatively unstable in comparison with the DNA molecule as it contains a 2'-OH hydroxyl group that acts as a nucleophil enhancing the cleavage of the phosphodiester bond between adjacent nucleotides.
 * Purine(adenine, guanine) or pyrimidine (cytosine,uracil) nucleobase
 * D-ribose pentose sugar
 * Phosphate group

RNA / DNA differences
RNA and DNA are very similar in structure but they differ in 4 major points:
 * 1) DNA nucleotides include adenine, guanine, thymine or cytosine whereas RNA nucleotides instead of thymine they involve uracil.
 * 2) DNA is always in a double helix structure with 2 strands always running in antiparallel orientation whereas RNA usually exists as a single strand but it has the ability to form a double strand structure too.
 * 3) DNA has a 2'-deoxy-D-ribose pentose sugar whereas RNA has a D-ribose.
 * 4) DNA has equal portions of adenine-thymine and guanine-cytosine nucleobases as it exists as a double stranded molecule where as RNA does not as it usually exists in a single stranded form

Types of RNA
RNA in contrast to DNA is not self replicated in order to proliferate but it is encoded by DNA genes. The different types of RNA are synthesized so that translation of the DNA into products is achieved. In other words with no RNA no product synthesis can occur, so DNA is useless without its RNA genes. RNA genes of DNA encode for 3 major types of RNA:
 * ribosomal RNA,
 * messenger RNA and
 * transfer RNA

Ribosomal RNA - rRNA
Ribosomes are the non membranous organelles that participate in the translation of th mRNA into a protein product. The ribosome structure is composed of 2 subunits. A small and a large subunit each of which consists primarily of rRNA of various size and a small quantity of proteins which constitute the 80% of the whole RNA. The large subunit consists of rRNA of 5S, 5.8S and 28S sizes whereas the small subunit consists of rRNA of 18S size. (where the S is the unit for rRNA size). These rRNAs are synthesized by transcription of the rRNA genes. However, the rRNA genes encode for all rRNAs apart from the 5S rRNA which is tfromed by the tRNA genes along with all tRNAs. RNA polymerase type I is responsible for the transcription of rRNA genes by binding on the core element-CE, which overlaps the Transcription Start Site-TSS, along with the Transcription Factors inducing the so called Transcription Initiation Complex designated as TIC. The rate of the transcription is controlled by an Upstream Control Sequence-UCS found 100 base pairs upstream to the TSS. The transcription begins and the genes are transcribed into pre-rRNA in the following order: 18S - 5.8S - 28S. The transcription ends when the Transcription Complex reaches an area rich in adenines found at about 600 base pairs after the gene, indicating the end of the gene. The pre-rRNA formed includes all rRNAs on a single strand so that cleavage has to be performed so that different size rRNAs are separated. This task is untertaken by RNases that cleave the rRNA giving rise to the differential size rRNAs.

Messenger RNA - mRNA
mRNA genes are the genes that encode only for proteins but this encoding has an RNA intermediate. The DNA is firstly transcribed into mRNA and subsequently this mRNA is translated into a protein product. So the mRNA genes are the genes that encode for mRNA in order to synthesize proteins. mRNA constitutes only the 5% of the total RNA. RNA polymerase II is the enzyme responsible for the transcription of the corresponding genes into mRNA. The polymerase binds on the TATA box which acts more or less as a promoter, located about 25 base pairs upstream the Transcription Start Site - TSS, along with the transcription factors giving rise to the Transcription Initiation Complex - TIC. In order for this complex to be functional a proper sequence of events of binding the TF and the polymerase on the promoter must occur as: TFII-D, TFII-A, TFII-B, RNA pol II, TFII-F, TFII-H TFII-E TFII-J. As soon as the TIC is formed then transcription begins giving rise to pre-mRNA which include both exons and introns. Transcription ends without recognition of an adenine rich area but rather by automatic disassembling οf the Transcription Complex. The pre-mRNA is then submitted to processing that involves splicing - removal of introns and merging of the adjacent exons- and capping - addition of 7-methylguanosine on the 5' end of the mRNA so that mRNA cannot be cleaved by exonucleases and also serves as a recognition site of the mRNA prior to translation.

Transfer RNA - tRNA
Transfer RNA is encoded by genes that also encode for the 5S size rRNA. RNA polymerase III is responsible for the transcription of these genes by binding on the promoter, situated about 100 base pairs downstream the Transcription Start Site -TSS, along with the Transcription Factors giving rise to the Transcription Initiation Complex. As soon as this complex is formed transcription process can begin and when the Transcription Complex faces an adenine rich region transcription comes to an end as this area is an indication for the gene end. tRNA constitutes 15% of the total RNA and is directly involved in the translation of the mRNA. More specificaly tRNA binds onto a specific amino acid and brings it along the translation site so that it is bound on the newly synthesized peptide.
 * tRNA binds to its specific amino acid recognized by its side R chain in presence of the aminoacyl tRNA synthetase enzyme. The synthetase binds the 5'-CCA-OH-3' acceptor arm with the -COOH group of the amino acid.
 * When the small ribosomal subunit faces an AUG codon on the mRNA it indicates the commencing of the peptide formation. As soon as the AUG codon is recognized then the first tRNA binds on the small ribosomal subunit and on the mRNA through its anticodon arm, giving rise to the Translation Initiation Complex designated as tRNAimet. Eventually the large ribosomal subunit binds on the complex indicating the initiation of the translation process. Translation always begins with the methionine amino acid on the newly synthesized peptide.
 * After translocation of the Translation complex the tRNAimet enter the Peptidyl site of the complex leaving the Aminoacyl site vacant for the next tRNA to enter, bringing together the two adjacent amino acids so that a peptide bond can be formed in presence of the peptidyl transferase enzyme. As soon as the peptide bond is formed, the tRNA is released from its amino acid in presence of the tRNA deacylase.