The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a single-stranded chain of nucleotides. Each nucleotide is composed of the five-carbon sugar ribose. The carbon molecules of ribose are numbered one through five. Carbon number five carries a phosphate group and carbon number one carries a nitrogenous base.
There are four nitrogenous bases in RNA—adenine (A), guanine (G), cytosine (C), and uracil (U). Uracil is the only base in RNA that is not present in DNA, which uses thymine (T) instead. During transcription, RNA is synthesized from a DNA template by complementary binding of the new RNA bases to the DNA bases; A binds to T, G binds to C, C binds to G, and U binds to A.
Like DNA, adjacent nucleotides in RNA are linked together through phosphodiester bonds. These bonds form between the phosphate group of one nucleotide and a hydroxyl (–OH) group on the ribose of the adjacent nucleotide.
This structure lends RNA its directionality—that is, the two ends of the chain of nucleotides are different. Carbon number five of ribose carries an unbound phosphate group which gives rise to the name 5’ end. The last ribose at the other end of the nucleotide chain has a free hydroxyl (–OH) group at carbon number 3; hence, this end of the RNA molecule is called the 3’ end. As nucleotides are added to the chain during transcription, the 5’ phosphate group of the new nucleotide reacts with the 3’ hydroxyl group of the growing chain. Therefore, RNA is always assembled in the 5’ to 3’ direction.
Secondary structures are formed by complementary base pairing between distant nucleotides on the same single-stranded RNA. While hairpin loops are formed by pairing of bases within 5-10 nucleotides of each other, stem-loops are formed by pairing of bases that are separated by 50 to hundreds of nucleotides. In prokaryotes, these secondary structures function as transcriptional regulators. For instance, a hairpin loop can serve as a termination signal such that when transcription enzymes encounter this structure, they detach from the mRNA, and transcription stops. Stem-loops or hairpin loops at the 3’ or 5’ ends also regulate mRNA stability in eukaryotes by preventing the binding of ribonucleases—enzymes that degrade RNA.
Secondary structures can form more complicated tertiary structures called pseudoknots. Pseudoknots are formed when bases in the loop regions of secondary structures interact with complementary bases outside the loop. These tertiary structures play essential roles in RNA structure and function.
tRNAs serve as adaptor molecules during the translation of mRNA into proteins. The three-dimensional structure of tRNA is L-shaped, with the amino acid binding site at one end and an anticodon at the other end. Anticodons are sequences of three nucleotides complementary to the mRNA codon—a sequence of three nucleotides that encode a specific amino acid. This peculiar shape of the tRNA enables it to bind to ribosomes, where protein synthesis occurs. tRNA molecules are usually 70-80 nucleotides long and fold into a stem-loop structure that resembles a cloverleaf. Three of the four stems have loops containing 7-8 bases. The fourth stem is unlooped and includes the free 5’ and 3’ ends of the RNA strand. The 3’ end acts as the amino acid acceptor site.
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