Well defined reading frames are critical in protein synthesis. That’s common knowledge so why are they important? In order to build proteins, the genetic code and DNA needs to be deciphered.
This is all done by RNA. RNA is single stranded and each one of the 4 bases has a nucleic acid attached to it, hence RNA stands for ribonucleic acid. It’s able to duplicate itself because it has a 3D shape that acts as a template. A well-defined reading frame is vital because it would be like reading something out of context or skipping part of the story.
Reading frames
Proteins are made up of chains of amino acids, which are the building blocks of proteins. Each protein has a unique sequence of amino acid residues that is defined by the sequence of the coding DNA. In order to make a protein, the cell first copies the coding DNA into messenger RNA (mRNA) in a process called transcription.
The mRNA is then translated into an amino acid chain in a process called translation, in which each set of three bases (a codon) on the mRNA specifies one amino acid.
The three-base codon system means that there are 64 possible combinations that can be used as codons and hence specify 20 different amino acids and 3 stop signals.
However, since only 4 different bases occur in DNA, there may be more than one possible DNA sequence that encodes any given protein. Therefore, it is important for this information to be encoded unambiguously so that there is no doubt about the protein that is being synthesized from the mRNA transcript.
The genetic code is degenerate; this means that more than one DNA sequence may code for a single amino acid when read as codons in linear triplets. For example, serine can be coded for by 6 different DNA sequences – TCG, AGT, AGC.
Initiation of translation
Initiation of translation is the process by which translation of a messenger RNA (mRNA) molecule into a polypeptide begins. In eukaryotes, it begins at the cap structure, while in prokaryotes it begins with the recognition of the Shine-Dalgarno sequence near the 5′ end. The initiation step is followed by elongation and termination steps.
The process of translation in eukaryotes is similar to that in prokaryotes, however there are some unique steps involved in eukaryotic translation initiation. Eukaryotic mRNAs are polyadenylated at their 3′ ends and also contain a 7-methylguanosine cap at their 5′ ends.
Both of these modifications help in ribosome binding during translation initiation. The 5′ cap binds to a complex called eukaryotic initiation factor 4F (elF4F). This complex consists of three subunits: elF4E, elF4A and elF4G. The bound mRNA is then recruited to a large ribonucleoprotein particle called pre-initiation complex (PIC). It consists of small ribosomal subunits, initiation factors and other proteins involved in mRNA recruitment and scanning for initiating.
The ribosome and genetic code
The genetic code is the set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. Specifically, the code defines a mapping between tri-nucleotide sequences called codons and amino acids.
For example, the sequence GGG specifies the amino acid glycine and the sequence GAU specifies the amino acid aspartic acid. Because the genetic code contains multiple codons that specify the same amino acid, there are several synonymous codons that code for only 20 amino acids.
The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries. The code defines how sequences of nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. While the “genetic code” determines a protein’s amino acid sequence, other genomic regions determine when and where these
A well-defined reading frame is critical in protein synthesis because the way the left and right hand side of the frame to frame like a mirror image
A well-defined reading frame is critical in protein synthesis because the way the left and right hand side of the frame to frame like a mirror image. This means that there is no overlap between the first and last nucleotide of a triplet codon.
The start codon is a special case, in which it has two possible reading frames. Since this codon has only one possible reading frame, it is the only start codon used for gene transcription.
The stop codons have three possible reading frames, and each of them is used for gene transcription. This means that there are four different possible ways that a gene can be transcribed from DNA to mRNA, and four different ways that an amino acid sequence can be read from mRNA to form a protein.
Conclusion
Overall, well-defined reading frames are critical for the production of proteins made up of amino acid sequences. In the absence of such a frame, the protein translation system will not be able to accurately translate your DNA sequences and you will therefore get off-target proteins instead. Don’t let this happen to your research or lab!