The backbone of RNA is composed of ribose rather than 2ˈ-deoxyribose. That is, it has a hydroxyl group at its 2ˈ position. RNA has uracil in place of thymine. Uracil lacks the 5ˈ methyl group which is present in thymine. RNA is a single polynucleotide chain. RNA functions as an intermediate (the mRNA) between the gene and the protein synthesizing machinery. It also functions as an adaptor (the tRNA) between the codons in the mRNA and the amino acids. RNA as a regulatory molecule binds to and interferes with translation process of certain mRNAs. Some of the RNAs act as essential enzymes to catalyze reactions inside a cell. RNA chains frequently fold back on themselves to from base paired segments between short stretches of complementary sequences. It adopts stem loop structure in case of closely placed complementary sequences. Special properties exhibited by the loop such as tertraloop sequence UUCG provides stability to the complete loop. Pseudoknots appear in their structure when base pairing occurs between sequences that are not contiguous. A non-Watson-Crick base pair adds to the tendency of RNA to form double helical structures. This is the G:U base pair, which has the hydrogen bonds between N3 of Uracil and the carbonyl on C6 of Guanine and between the carbonyl on C2 of Uracil and N1 of Guanine. RNAs possess an enhanced capacity for self-complementarity. RNA fails to adopt a B-form helix due to the presence of 2ˈhydroxyl in its backbone. The minor groove in double helical RNA is wide and shallow and hence accessible, but it holds little sequence specific information. Whereas, the major groove is narrow and deep that is not very accessible to amino acid side chains from interacting proteins. Proteins can assist the formation of tertiary structure of large RNA molecules. Proteins shield the negative charges of backbone phosphates, which otherwise would be destabilized by the electrostatic repulsions. RNAs that adopt complex tertiary structure and act as biological catalysts are called ribozymes. They exhibit active site, a binding site for a substrate and a binding site for a cofactor, such as a metal ion.
Different types of RNA
Messenger RNA (mRNA): The DNA is firstly transcribed into mRNA and subsequently translated into a protein product. mRNA constitutes only 5% of the total RNA. RNA polymerase II is the enzyme responsible for the transcription of corresponding genes into mRNA.
• mRNA carry copies of genetic instructions that are used to assemble amino acids into proteins/polypeptide chains.
• Transcribes code from DNA strand.
• mRNA genes are the genes that encode only for proteins in order to synthesize protiens but this encoding has an RNA intermediate.
Ribosomal RNA (rRNA): Ribosomal RNA (rRNA), along with ribosomal protein subunits, makes up the ribosome, the site of protein assembly. A functional ribosome consists of two subunits, a large subunit and a small subunit, each of which consists of one or more pieces of RNA and a number of proteins.rRNA are combined with proteins to form ribosomes. It is a component of the ribosome.
- Ribosome is the site of protein synthesis.
- Ribosome holds the mRNA and tRNA close together.
- It positions each new amino acid for addition to polypeptide.
- It combines each new amino acid together.
- Regulatory elements for the expression of rRNA genes resides in the non-transcribe spacer genes.
Following are the three active sites
i. Aminoacyl tRNA site (A-site) Site where binding of new incoming tRNA takes place.
ii. Peptidyl tRNA site (P-site) Site where tRNA adds its amino acid to the growing polypeptide chain. Site of the tRNA holding the growing chain.
iii. Exit site (E-site) For the tRNA to release and exit ribosome.
S-Svedberg 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 synthesized by the tRNA genes along with all nuclear tRNAs. RNA polymerase type I is responsible for the transcription of rRNA genes by binding on the core element, which overlaps the TSS, along with the Transcription Factors inducing the TIC. The rate of the transcription is controlled by an Upstream Control Sequence (UCS) located 100 base pairs upstream to the TSS. The transcription ends when the Transcription Complex reaches an area rich in Adenines found at about 600 base pairs downstream of the gene, indicating its end. This task is undertaken by RNAses that cleave the rRNA giving rise to the differential size rRNAs.
• Small interfering RNA (siRNA) Known as short interfering RNA, a class of double stranded RNA molecules involved in the RNA interference (RNAi) pathway. It interferes with the expression of specific genes controlling the stability of the mRNA. The mRNA disintegrates (when required), avoiding its overexpression with a consequent overproduction of proteins. siRNA has 21-25 nucleotide sequence with 2 nucleotide overhang at 3‘ end. It is generally induced by viruses.
• Small nuclear ribonucleic acid (snRNA) They are RNA molecules transcribed by either RNA polymerase II along with mRNA or by RNA polymerase III along with all nuclear tRNAs and the 5S rRNA. They are primarily involved in mRNA processing such as splicing by removal of introns. They are always associated with proteins giving rise to complexes called small nuclear ribonucleoproteins (snRNP) that are directly associated with the splicing process.
• Heterogeneous nuclear ribonucleic acid (hnRNA) hnRNA is an immature single strand of mRNA. The hnRNA and pre-mRNA are almost identical
Transfer RNA (tRNA): Transfer RNA is about 76-90 nucleotide in length. tRNA serve as temporary carrier of amino acids. It helps decode a messenger RNA sequence into a protein.
tRNA brings the appropriate amino acids to the ribosome based on the messenger RNA (mRNA) nucleotide sequence
i. tRNA transfers each amino acid to the ribosome.
ii. tRNA acts as the interpreter of the mRNA code.