The RNA Translation
The process of translation or protein synthesis is one of a cell’s most energy-consuming metabolic processes. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform a wide variety of the functions of a cell. The process of translation involves decoding an mRNA message into a polypeptide product. Amino acids are covalently strung together in lengths ranging from approximately 50 amino acids to more than 1,000.
The protein synthesis machinery
In addition to the mRNA template, many other molecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of ribosomal RNAs (rRNA) and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors (Figure 7.6).
Figure 7.6: The protein synthesis machinery includes the large and small subunits of a ribosome, mRNA, and tRNA.
The genetic code
The information needed for protein synthesis is stored in DNA macromolecules, whose language is encoded using 4 symbols (A, T, C and G) corresponding to the 4 nitrogenous bases (adenine, thymine, cytosine, guanine). The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of four symbols: A (adenine), U (uracil), C (cytosine), and G (guanine). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Nature’s protein sequences consist of 20 commonly occurring amino acids, ordered and arranged in countless ways (Figure 7.7). The remarkable variety of the structure and functions of proteins in an organism is a consequence of the variety of configurations of the 20 amino acids within the polypeptide chains.
Figure 7.7: The structures of the 20 amino acids found in proteins. Each amino acid is composed of an amino group (NH3+), a carboxyl group (COO–), and a side chain (blue). The side chain may be nonpolar, polar, or charged, as well as large or small. It is the variety of amino acid side chains that gives rise to the incredible variation of protein structure and function.
Since DNA is made up of 4 types of nucleotides and proteins are made up of 20 types of amino acids, it is not possible to make a one-to-one correspondence between a nucleotide and an amino acid. The mathematician George Gamow showed that for the coding of the 20 types of amino acids 3 nucleotides would be needed. His reasoning is expressed by the following formula:
16 = 42 < 20 <= 64 = 43
Thus, each amino acid is defined by a three nucleotide sequence called triplet codon or simply codon. The genetic code is the biochemical system that establishes the correspondence between nucleic acids and proteins, or equivalently, between triplet codons and amino acids. Since there are 64 (4 × 4 × 4) codons and only 20 amino acids, a given amino acid may be encoded by more than one codon (Figure 7.8), which makes the genetic code degenerate. Such codons are called synonymous codons and they differ only in their third nucleotide. With the exception of tryptophan and methionine, each amino acid is encoded by at least 3 synonymous codons. There also are three amino acids – arginine, leucine, and serine – that are encoded by 6 synonymous codons.
Of the 64 codons of the genetic code, 61 codons encode amino acids and are called sense codons. Among them, there are two sense codons, denoted AUG and GUG, which require a special mention. These codons, which encode methionine and valine, have also the role of starting the translation phase of the protein synthesis process, which is why they are called START or BEGIN codons.
The 3 codons that are not involved in the coding of amino acids are called nonsense codons. They are important for reading the genetic message carried by mRNA. The nonsense codons are denoted UAA, UGA and UAG and they mark the place where the decoding of genetic information stops, which is why they are called STOP or END codons. These 3 codons practically release the polypeptide from the translation machinery, otherwise they end the protein synthesis process. The START and STOP codons are sometimes called the punctuation marks of the genetic code.
The reading frame for translation is set by a START codon near the 5′ end of the mRNA “recipe” and moves toward the 3′ end, similarly to replication and transcription.
The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis, which is a powerful evidence that all life on Earth shares a common origin.
Figure 7.8: The genetic code for translating each nucleotide triplet, or codon, in mRNA into an amino acid or a termination signal in a nascent protein (credit: modification of work by NIH).
The mechanism of protein synthesis
Just as with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we will explore how translation occurs in Escherichia coli, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.
Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small ribosome subunit, the mRNA template, three initiation factors, and a special initiator tRNA. The initiator tRNA interacts with the AUG start codon, and links to a special form of the amino acid methionine that is typically removed from the polypeptide after translation is complete.
In prokaryotes and eukaryotes, the basics of polypeptide elongation are the same, so we will review elongation from the perspective of E. coli. The large ribosomal subunit of E. coli consists of three compartments. The A site binds incoming charged tRNAs (tRNAs with their attached specific amino acids). The P site binds charged tRNAs carrying amino acids that have formed bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E site releases dissociated tRNAs so they can be recharged with free amino acids. The ribosome shifts one codon at a time, catalyzing each process that occurs in the three sites. With each step, a charged tRNA enters the complex, the polypeptide becomes one amino acid longer, and an uncharged tRNA departs. The energy for each bond between amino acids is derived from guanosine triphosphate (GTP), a molecule similar to adenosine triphosphate (ATP) (Figure 7.9). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid polypeptide could be translated in just 10 seconds.
Termination of translation occurs when a stop codon (UAA, UAG, or UGA) is encountered. When the ribosome encounters the stop codon, the growing polypeptide is released and the ribosome subunits dissociate and leave the mRNA. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.
Figure 7.9: Translation begins when a tRNA anticodon recognizes a codon on the mRNA. The large ribosomal subunit joins the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed. Entry of a release factor into the A site terminates translation and the components dissociate.
References:
- Fowler, Samantha, et al. Concepts of Biology. OpenStax College, Rice University, 2013. Download for free at: https://openstax.org/details/books/concepts-biology.
- Clark, Mary, Jung Choi, and Matthew Douglas. Biology 2E. 2018. Access for free at https://openstax.org/details/books/biology-2e.