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
1. Messenger RNA (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.
First, the DNA is transcribed into mRNA which is then translated into protein. The enzyme RNA Pol II is the enzyme that catalyze transcription of corresponding genes into mRNA. mRNA is approximately 2-5% of the total RNA.
2. 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.
Ribosomes holds the mRNA and tRNA close together.
It combines each new amino acid together.
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. The synthesis of these rRNA is done 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 is completed when the Transcription Complex reaches around 600bp downstream of the gene which is an area rich in Adenines. This task is undertaken by RNAses that cleave the rRNA giving rise to the differential size rRNAs.
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. rRNA are responsible for mRNA processing and splicing.
Heterogeneous nuclear ribonucleic acid (hnRNA:) hnRNA is an immature single strand of mRNA. The hnRNA and pre-mRNA are almost identical
3. Transfer RNA (tRNA)
tRNA helps in decoding mRNA sequence into a protein. It is also responsible for the insertion codon specific amino acids in a synthesising protein chain in ribosome during the process called translation.
i. tRNA transfers each amino acid to the ribosome.
ii. tRNA acts as the interpreter of the mRNA code.
Genes that also encode for the 5S rRNA encode transfer RNA. RNA polymerase III is responsible for the transcription of these genes by binding on the promoter. Situated about 100 base pairs downstream the TSS, along with the transcription factors they form the Transcription Initiation Complex. tRNA constitutes 15% of the total RNA and is directly involved in the translation of the mRNA. More specifically 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 specificity of the tRNA recognition by a aminoacyl tRNA synthetase that is intrinsic to the tRNA molecule lies on the acceptor stem and anticodon loop. The synthetase binds the 5ˈ-CCA-OH-3ˈ acceptor arm with the —COOH group of the amino acid.