mRNA Bases

Exploring the Function of mRNA Bases in Gene Expression

The central dogma of molecular biology explains that DNA codes for RNA, which codes for proteins. Proteins do everything from helping plants grow to protecting the body.

mRNA carries genetic code from the nucleus to ribosomes in the cytoplasm, where it is translated into amino acids for protein synthesis. Chemical modifications of mRNA have profound consequences for gene expression regulation.


The first step in protein synthesis involves coupling amino acids to tRNA molecules. Because the genetic code is redundant, several codons can specify the same amino acid. To avoid miscoding, tRNAs are designed to base-pair with a specific codon accurately. They must match perfectly at the first two positions of a codon and can tolerate a mismatch, or wobble, in the third position.

tRNAs are trimmed and spliced to remove non-coding sequences before they can be used for protein synthesis. This processing is a quality-control measure that helps ensure that the tRNAs are correctly folded and located on the ribosome.

Once a tRNA has been correctly processed, it is covalently attached to an amino acid by the action of a peptidyl transferase enzyme. The peptidyl transferase reaction is catalyzed by the same enzyme that makes tRNAs, and it is one of many cellular reactions coupled to the energy-releasing hydrolysis of ATP.

In bacteria, the ribosome moves along the three mRNA bases simultaneously, from the 5′ end to the 3′ end. New tRNAs whose anticodons complement the mRNA codons arrive with their corresponding amino acids. The tRNA-amino acid complex is then joined to the carboxyl end of the growing polypeptide chain by a peptide bond, and the resulting peptide is folded into a functionally distinct protein.

mRNA Codons

In the next step of gene expression, translation, the nucleotide sequence in an mRNA molecule is decoded to specify an amino acid sequence that will ultimately form a protein. This process occurs inside a ribosome and requires adapter molecules called tRNAs. The tRNAs have three nucleotides sticking out of one end that can match (base-pair) with a specific codon in the mRNA sequence and an amino acid attached to the other end. Each tRNA binds temporarily to the codon, then releases its amino acid into the ribosome, replaced with another amino acid, and so on until a protein is formed.

Because there are only 20 different amino acids and 64 possible combinations of codons, many codons code for more than one amino acid. This is called redundancy and is made possible by a phenomenon known as wobble base-pairing.

The ribosome is a large structure composed of two subunits, the small and large ribosomal subunits. The small ribosomal subunit scans the mRNA sequence to identify a start codon. Once a start codon is recognized, a particular protein called an initiation factor, dissociates from the small ribosomal subunit to allow the tRNA to bind to the mRNA and begin a new round of translation.

mRNA Anticodons

By recognizing and pairing with their complementary codons, tRNA molecules bring the appropriate amino acids to the correct sites on the ribosome. These interactions, known as wobble base-pairing, explain why it is possible to fit 20 different amino acids into 61 different codons: each codon can be represented by several sequences that differ only in the third nucleotide.

When a tRNA binds to a particular codon in the ribosome’s P site, its three-nucleotide anticodon loop recognizes the corresponding amino acid residue. The loop forms a complex L-shaped structure, and its ends make specific Watson-Crick base pairs with the first two nucleotides of the mRNA codon. This way, the tRNA helps the ribosome correctly read the mRNA’s genetic instructions to build protein chains.

The specific shape of tRNAs helps them orient themselves on the ribosome to bind their codon partners and then move towards the E site once the codon-anticodon interaction is complete.


UTRs can contain sequences that influence mRNA stability, splicing, or translation. They also often have structural characteristics that can affect subcellular localization. For example, genes that bind to protein complexes in the cytoplasm tend to have shorter 5′ and 3′ UTRs than genes that need to attach to the mitochondrion.

UTR cis-elements can also affect protein function by influencing the abundance or activity of RBPs that bind them. This is the case with AU-rich elements, initially thought to repress translation but later found to increase protein production after lipopolysaccharide stimulation of T cells.

Some cis-elements in UTRs have been shown to regulate the stability of specific mRNAs by binding to the RISC complex or other RNA-binding proteins.

Another type of cis-element that influences translation is the zipper code. These sequences interact with a specific zip-code binding protein to control mRNA localization in the cytoplasm and nucleus. Several examples of zipper codes exist in the mRNAs of various cancers, including some whose mutations can lead to uncontrolled cell growth and tumorigenesis.

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