RNA: Structure, Function, and Types in Protein Synthesis
Ribonucleic Acid (RNA)
Ribonucleic acid (RNA) is a nucleic acid comprising a chain of ribonucleotides. It is present both in prokaryotes and eukaryotes and is the only genetic material of certain viruses (virus RNA). The cellular RNA is linear and single-stranded, but in the genome of some viruses, it is double-stranded.
Cellular organisms use RNA in different roles. The molecule directs the intermediate stages of protein synthesis. DNA cannot act alone, and RNA is used to transfer this vital information during protein synthesis (production of proteins needed by the cell for its activities and development). Several types of RNA regulate gene expression, while others have catalytic activity. RNA is, therefore, much more versatile than DNA.
RNA differs from DNA in that the constituent nucleotides’ pentose is ribose instead of deoxyribose and that instead of the four bases A, G, C, and T, it is A, G, C, and U (i.e., uracil instead of thymine). RNA chains are shorter than DNA, although this feature is due to biological considerations, as there is no chemical limitation to forming RNA chains as long as DNA. The phosphodiester bond is chemically identical. RNA is formed mostly by a single string (that is single-stranded), although in certain situations, such as tRNAs and rRNAs, it can form complex folded structures.
While DNA contains the information, RNA expresses that information from a linear sequence of nucleotides in a linear sequence of amino acids in a protein.
Chemical Structure
As with DNA, RNA consists of a repetitive chain of monomers called nucleotides. The nucleotides are joined one after another by negatively charged phosphodiester bonds.
Each nucleotide consists of one molecule of a five-carbon monosaccharide (pentose) called ribose (deoxyribose in DNA), a phosphate group, and one of four possible nitrogen compounds called bases: adenine, guanine, uracil (thymine in DNA), and cytosine.
Ribose carbons are numbered from 1′ to 5′ clockwise. The nitrogenous base is attached to carbon 1′; the phosphate group binds to the carbon 5′ and 3′ carbon of the ribose of the next nucleotide. The phosphate has a negative charge at physiological pH, which gives the RNA its polyanionic character. Purine bases (adenine and guanine) can form hydrogen bonds with the pyrimidine (uracil and cytosine) under the schedule C=G and A=U. In addition, other interactions are possible, such as base stacking or pairing tetrabucles with G=A.
Many RNAs also contain modified nucleotides, which originate by transformation of the typical nucleotides; they are characteristic of transfer RNA (tRNA) and ribosomal RNA (rRNA). Methylated nucleotides are also present in eukaryotic messenger RNA.
Secondary Structure
Unlike DNA, RNA molecules are single-stranded and do not often form extensive double helices. However, they fold as a result of the presence of short regions with intramolecular base pairing, i.e., base pairs formed by complementary sequences within the same strand. tRNA possesses around 60% of base-paired arms with a four double-helix structure.
A major structural feature that distinguishes RNA from DNA is the presence of a hydroxyl group in position 2′ of ribose, which causes the RNA double helices to adopt a conformation instead of the conformation that is most common in DNA.
A second consequence of the presence of the hydroxyl is that of RNA phosphodiester bonds in regions where no double helix forms are more susceptible to chemical hydrolysis than DNA. RNA phosphodiester bonds are hydrolyzed rapidly in an alkaline solution, while DNA links are stable. The half-life of RNA molecules is much shorter than that of DNA, a few minutes in some bacterial RNA or a few days in human tRNAs.
Tertiary Structure
The tertiary structure of RNA is the result of base stacking and hydrogen bonds between different parts of the molecule. tRNAs are a good example; in solution, they are folded to form an “L” compact stabilized by Watson-Crick pairing conventional (A=U, C=G) and base interactions between two or more nucleotides, including triplets. Foundations can donate hydrogen atoms to join the phosphodiester backbone; the OH of carbon 2′ of ribose is also a major donor and acceptor of hydrogen.
Types of RNA
Messenger RNA (mRNA) is the type of RNA that carries information from DNA to ribosomes, where protein synthesis occurs. The nucleotide sequence of mRNA determines the amino acid sequence of the protein. Therefore, the mRNA is called RNA-coding.
However, many RNAs are non-protein-coding and are called non-coding RNA, originating from their own genes (RNA genes or introns are rejected during the process of splicing). Non-coding RNAs include transfer RNA (tRNA) and ribosomal RNA (rRNA), which are key elements in the translation process, and various types of RNA regulators. Some non-coding RNAs, called ribozymes, are able to catalyze chemical reactions such as cutting and joining other RNA molecules or peptide links between amino acids in the ribosome during protein synthesis.
RNA Involved in Protein Synthesis
- Messenger RNA: Messenger RNA (mRNA) carries information on the amino acid sequence of the protein from the DNA, where it is registered, to the ribosome, where proteins are synthesized from the cell. It is, therefore, an intermediary molecule between DNA and protein, and the nickname of “messenger” is totally descriptive. In eukaryotes, mRNA is synthesized in the nucleoplasm of the cell nucleus and enters the cytosol, where there are ribosomes, through the pores of the nuclear envelope.
- Transfer RNA: Transfer RNA (tRNA) are short polymers of about 80 nucleotides that transfer a specific amino acid to the growing polypeptide chain. They bind to specific sites on the ribosome during translation. They have a specific site for the fixation of amino acid (3′) and an anticodon consisting of a triplet of nucleotides that binds to the mRNA codon through complementary hydrogen bonding.
- Ribosomal RNA: Ribosomal RNA (rRNA) combines with proteins to form ribosomes, which represent about 2/3 of them. In prokaryotes, the large ribosomal subunit contains two molecules, and the small subunit contains one rRNA molecule. In eukaryotes, the large subunit contains three rRNA molecules and the small one. In both cases, the frame consists of the rRNA associated with specific proteins. rRNA is abundant and represents 80% of the RNA found in the cytoplasm of eukaryotic cells. Ribosomal RNA is the catalytic component of ribosomes; it is responsible for creating the peptide bonds between amino acids, forming the polypeptide during protein synthesis, acting therefore as ribozymes.