Biosynthesis: What is it? Genetic Code, Mechanism of Protein Synthesis and Genetic Translation

The term is sometimes used to refer to a multi-step process, which begins with synthesizing amino acids and is then used for genetic translation.

It is the formation of biomolecules using anabolism, a process responsible for synthesizing or constructing more complex organic molecules (biomolecules) from more simple ones or nutrients, with energy requirement (endergonic reactions), unlike catabolism.

Protein biosynthesis, although very similar, differs between prokaryotes and eukaryotes.

The synthesis of proteins consumes more of a cell’s energy than any other metabolic process.

In turn, proteins represent more mass than any other macromolecule of living organisms.

They perform all the functions of a cell virtually, serving as functional (e.g., Enzymes) and structural elements.

The translation process, or protein synthesis, the second part of gene expression, involves the decoding by a ribosome of an mRNA message in a polypeptide product.


The genetic code

The translation of the mRNA template converts genetic information based on nucleotides into the “language” of amino acids to create a protein product.

A protein sequence consists of 20 standard amino acids.

Each amino acid is defined within the mRNA by a triplet of nucleotides called a codon. The relationship between a codon of mRNA and its corresponding amino acid is called a genetic code.

The three-nucleotide code means 64 possible combinations (43, with four different possible nucleotides in each of the three different positions within the codon).

This number is greater than the number of amino acids, and a given amino acid is encoded by more than one codon.

This redundancy in the genetic code is called degeneration.

Typically, while the first two positions in a codon are essential in determining which amino acid will be incorporated into a growing polypeptide, the third position, called the oscillation position, is less critical.

In some cases, if the nucleotide in the third position is changed, the same amino acid is still incorporated.

While 61 of the 64 possible triplets encode amino acids, three of the 64 codons do not code for an amino acid; they finish the synthesis of proteins, releasing the polypeptide from the translation machinery.

These are called stop codons or nonsense codons. Another codon, AUG, also has a particular function.

In addition to specifying the amino acid methionine, it also typically serves as the start codon to initiate translation.

The reading frame, how the nucleotides in the mRNA are grouped into codons, for translation is established by the AUG start codon near the 5 ‘end of the mRNA.

After this start codon, each set of three nucleotides is a codon in the mRNA message.

The genetic code is almost universal.

With some exceptions, virtually all species use the same genetic code for protein synthesis, robust evidence that all life on earth shares a common origin.

However, unusual amino acids such as selenocysteine ​​and pyrrolysine have been observed in archaea and bacteria.

In the case of selenocysteine, the codon used is UGA (usually a stop codon).

However, UGA can encode selenocysteine ​​using a stem-loop structure (known as the selenocysteine ​​insert sequence, or SECIS element), which is found in the three untranslated regions of the mRNA.

Pyrolysis uses a different stop codon, UAG. Incorporating pyrrolysine requires the pylS gene and a single transfer RNA (tRNA) with a CUA anticodon.

The protein synthesis machinery

In addition to the mRNA template, many molecules and macromolecules contribute to the translation process.

The composition of each component varies according to the taxa; for example, ribosomes may consist of different numbers of ribosomal RNA (rRNA) and polypeptides depending on the organism.

However, the structures and general functions of the protein synthesis machinery are comparable from bacteria to human cells.

The translation requires the entry of a template of mRNA, ribosomes, tRNA, and various enzymatic factors.


A ribosome is a complex macromolecule composed of catalytic rRNA (called ribozymes), structural rRNA, and polypeptides.

Mature rRNA constitutes approximately 50% of each ribosome.

Prokaryotes have 70S ribosomes, while eukaryotes have 80S ribosomes in the cytoplasm and rough endoplasmic reticulum and 70S ribosomes in mitochondria and chloroplasts.

Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during translation initiation.

In E. coli, the small subunit is described as the 30S (containing the 16S rRNA subunit), and the large subunit is 50S (containing the 5S and 23S rRNA subunits), for a total of 70S (the Svedberg units do not they are additive).

The eukaryotic ribosomes have a small 40S subunit (containing the 18S rRNA subunit) and a large 60S subunit (5S, 5.8S, and 28S rRNA subunits), for a total of 80S.

The small subunit is responsible for binding the mRNA template, while the large subunit binds to the tRNAs (discussed in the following subsection).

Each mRNA molecule is translated simultaneously by many ribosomes, all synthesizing protein in the same direction: by reading the mRNA from 5 ‘to 3’ and synthesizing the polypeptide from the N-terminus to the C-terminus.

The complete structure that contains an mRNA with multiple associated ribosomes is called polyribosome (or polysome).

In both bacteria and archaea, before the transcriptional termination occurs, each transcript encoding a protein is already used to begin the synthesis of numerous copies of the encoded polypeptides because transcription and translation processes can occur concurrently, forming polyribosomes.

Transcription and translation can co-occur because both processes occur in the same direction from 5 ‘to 3’.

Both occur in the cell’s cytoplasm because the RNA transcript is not processed once transcribed.

This allows a prokaryotic cell to quickly respond to an environmental signal that requires new proteins.

On the contrary, simultaneous transcription and translation are impossible in eukaryotic cells.

Although polyribosomes are also formed in eukaryotes, they can not do so until RNA synthesis is complete and the RNA molecule has been modified and transported out of the nucleus.

RNA transfer:

Transfer RNAs (tRNAs) are structural molecules of RNA and, depending on the species, there are many different types of tRNA in the cytoplasm.

Bacterial species usually have between 60 and 90 types.

Serving as adapters, each type of tRNA binds to a specific codon in the mRNA template and adds the corresponding amino acid to the polypeptide chain.

Therefore, tRNAs are the molecules that actually “translate” the language of RNA into the language of proteins.

Surprisingly, tRNAs can adapt to such specificity in a small package like translation adapter molecules.

The tRNA molecule interacts with three factors: aminoacyl tRNA synthetases, ribosomes, and mRNA.

Mature tRNAs acquire a three-dimensional structure when the complementary bases are exposed in the hydrogen bond of the single-stranded RNA molecule to each other.

This form positions the amino acid binding site called the amino acid sharp end CCA, a cytosine-cytosine-adenine sequence at the 3 ‘end of the tRNA, and the anticodon at the other end.

The anticodon is a sequence of three nucleotides that binds to a codon of mRNA through the pairing of complementary bases.

An amino acid is added to the end of a tRNA molecule through tRNA’s “loading” process. Each tRNA molecule binds to its correct amino acid or affinity for a group of enzymes called aminoacyl tRNA synthetases.

There is at least one type of aminoacyl tRNA synthetase for each of the 20 amino acids.

The amino acid is activated for the first time by adding adenosine monophosphate (AMP) and then transferred to the tRNA, which converts it into a charged tRNA and releases AMP.

The mechanism of protein synthesis

The translation is similar in prokaryotes and eukaryotes. Here we will explore how translation occurs in E. coli, a representative prokaryote, and specify any difference between bacterial and eukaryotic translation.


The initiation of protein synthesis begins with the formation of an initiation complex.

In E. coli, this complex involves the small 30S ribosome, the mRNA template, three initiation factors that help the ribosome assemble correctly, and guanosine triphosphate (GTP) acts as an energy source a special initiator tRNA that carries N -formyl-methionine (fMet-tRNA met).

The initiator tRNA interacts with the AUG start codon of the mRNA and carries a formylated methionine (fMet).

Due to its participation in initiation, feet are inserted at the beginning (N-terminus) of each polypeptide chain synthesized by E. coli. In E. coli mRNA, a leader sequence upstream of the first AUG codon is called the Shine-Dalgarno sequence.

It is also known as the ribosomal binding site AGG AGG); it interacts by pairing complementary bases with the rRNA molecules that make up the ribosome.

This interaction anchors the 30S ribosomal subunit in the correct location in the mRNA template.

At this point, the 50S ribosomal subunit binds to the initiation complex, forming an intact ribosome.

In eukaryotes, the formation of the initiation complex is similar, with the following differences:

The initiator tRNA is a specialized tRNA that transports methionine, called Met-RNAi.

Instead of binding to the mRNA in the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 5 ‘cap of the eukaryotic mRNA, then traces along the mRNA in the 5’ to 3 ‘direction until the codon is recognized. Start AUG.

At this point, the 60S subunit binds to the Met-tRNA complex, mRNA, and the 40S subunit.

Elongation or elongation:

The basic concepts of translation elongation in prokaryotes and eukaryotes are the same.

In E. coli, the binding of the 50S ribosomal subunit to produce the intact ribosome forms three functionally important ribosomal sites: site A (aminoacyl) binds to incoming loaded aminoacyl tRNAs.

The P (peptidyl) site binds to charged tRNAs that carry amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA.

The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids.

There is one notable exception to this tRNA assembly line. During the initiation complex formation, bacterial fMet-tRNA met, or eukaryotic Met-RNAi, enters the P site directly without first entering site A, providing a free A place to accept the tRNA corresponding to the first codon after the AUG.

Elongation continues with movements of a single codon of the ribosome; each is called a translocation event.

During each translocation event, charged tRNAs enter site A, then switch to site P and finally site E for their removal.

The ribosomal movements, or steps, are induced by conformational changes that advance the ribosome in three bases in the 3 ‘direction.

Peptide bonds are formed between the amino group of the amino acid attached to the tRNA of the A site and the carboxyl group of the amino acid linked to the tRNA of the P site.

The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based ribozyme that is integrated into the 50S ribosomal subunit.

The amino acid linked to the tRNA of the P site is also attached to the growing polypeptide chain.

As the ribosome traverses the mRNA, the anterior tRNA of site P enters site E, separates from the amino acid, and is expelled.

Several of the steps during elongation, which include the binding of an aminoacyl rebate loaded to site A and translocation, require energy derived from the hydrolysis of GTP, which is catalyzed by specific elongation factors.

Surprisingly, the translation apparatus of E. coli takes only 0.05 seconds to add each amino acid, which means that a protein of 200 amino acids can be translated in only 10 seconds.


Translation termination occurs when a nonsense codon (UAA, UAG, or UGA) is found for which there is no complementary tRNA.

By aligning with site A, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that result in the amino acid in the P site being released from its tRNA, releasing the newly created polypeptide.

The small and large ribosomal subunits dissociate from the mRNA and each other; they are recruited almost immediately in another translation initiation complex.