Protein Synthesis Process: Step By Step

In simple terms, protein synthesis means to produce the production of protein molecules either from scratch or by breaking or converting other biomolecules.

Protein synthesis entails many smaller steps including- synthesis of amino acids, transcription of mRNA, translation of the mRNA to protein and post-transcriptional processing of that protein.  Proteins are nothing but long chains of amino acids joined together in an orderly fashion.

The process of making new proteins is known as protein synthesis. In biological systems, it occurs within the cell. Prokaryotes have it in their cytoplasm. It starts in the nucleus with the production of a transcript (mRNA) of the DNA’s coding sequence in eukaryotes. This mRNA transcript then leaves the cell nucleus. It makes its way to the ribosomes attached to the Golgi bodies in the cytoplasm, where it is translated into a protein molecule with a codon-specific amino acid sequence.

Steps of protein synthesis process:

There are 5 major steps of the protein synthesis process are:

  1. Activation of amino acids
  2. Transfer of amino acids to tRNA
  3. Initiation of the polypeptide chain
  4. Chain termination and
  5. Translocation of the protein molecule

This is the basic thumb rule for prokaryotes, while eukaryotes have some extra steps due to their cell complexity. Hereafter we will discuss the above-mentioned steps in detail.

1024px Summary of the protein biosynthesis process
Comprehensive protein synthesis process
Image: Wikipedia

Activation of amino acids:

Thereaction is brought about when amino acids come to interact with ATP molecules catalyzed by aminoacyl RNA synthetase. The aminoacyl – AMP – enzyme complex is generated as a result of the reaction between amino acid (AA) and adenosine triphosphate (ATP), which is mediated by the aforementioned enzyme. The complex is as follows:

AA + ATP Enzyme -AA – AMP – enzyme complex + PP

Process of DNA transcription
Image showing DNA transcription to mRNA
Image: Wikipedia

 It’s worth noting that different amino acids require different aminoacyl RNA synthetases.

Transfer of the amino acid to tRNA:

The generated AA–AMP–enzyme complex responds with a particular tRNA. As a result, amino acids are transported to tRNA. As a result, the enzyme, as well as the AMP, are released.

So the complex becomes:

AA – AMP – enzyme Complex + tRNA- AA – tRNA + AMP enzyme

Initiation of a polypeptide chain:

The ribosome accepts charged tRNA. In all organisms, protein synthesis occurs in the ribosome that is normally attached to the Golgi bodies in the cytoplasm. The SOS subunit of the 70S type ribosome interacts with the mRNA. Ribosomes are small complex molecules, responsible for protein synthesis and made up of 2 components- rRNA (ribosomal RNA) and proteins. Ribosomes also catalyze the creation of peptide bonds (the enzyme—ribozyme—in bacteria). Ribosomes are classified into two types: large and tiny.

Scientists represent each amino acid by three nucleic acid sequences known as codons. Based on the arrangement of the nitrogenous bases, this information is present in the mRNA. The amino acid methionine is transcribed as an initiating codon by the codon AUG but rarely by GUG (for valine), which is always responsible for starting polypeptide chains in prokaryotes. In prokaryotes, the formation of the starting amino acid methionine is a must.

Translation cycle
Illustration showing translation process with the cycle of tRNA codon-anti-codon pairing and amino acid incorporation into the growing polypeptide chain by the ribosome
Image: Wikipedia

Ribosomes have two binding sites for amino-acyl-tRNA.

  1. A site or amino-acyl (acceptor site).
  2. The peptidyl site, often known as the “P” site, is a kind of peptide (donor site). Each site is made up of different parts of the SOS and 30S subunits. Only the P site may attach to the starting formyl methionine tRNA (AA, f Met tRNA).

In the first stage, the amino-acyl-tRNA complex is bound to an elongation factor called the “ Tu complex”. This complex contains a molecule of bound GTP. Thereafter the amino-acyl-tRNA-Tu-GTP complex is tied to the 70S initiation complex. The Tu-GDP complex is released from the 70S ribosome when the GTP molecule hydrolyzes. The new aminoacyl tRNA now comes and connects itself to the aminoacyl or A site of the ribosome.

The tRNAs on the A site and P sites of the ribosomes are connected using peptide bonds. We consider this as the initiation of the second step of elongation. In the next phase, the formyl methionine acyl group that was initially formed is transferred from the tRNA it was attached to to the amino group of the new amino acid that arrived at the A site. Peptide synthesis is catalysed by peptidyl transferase, a ribosomal enzyme found in the 50 S subunit. A dipeptidyl-tRNA molecule is generated at the A site, all the while with an empty tRNA remaining attached to the P site of the mRNA.  

The ribosome travels down the codons along the mRNA towards its 3′ terminal in the third phase of elongation (i.e., 1st to 2nd codon and then from 2nd to 3rd on the mRNA). Because the dipeptidyl tRNA is still connected to the second codon, ribosome movement causes the dipeptidyl tRNA to shift from the A site to the P-site. The empty tRNA is released as a result of this translocation.

The third mRNA codon is now on the A-site, while the second codon is on the P-site. The translocation step is the movement of ribosomes along mRNA. Elongation factor G is required for this step (also called translocase). In addition, another molecule of GTP is hydrolyzed at the same time. The translocation requires energy, which is provided by the hydrolysis of GTP.

The actions of three termination or releasing factors known as R1, R, and S are also required for termination. The translocation requires energy, which is provided by the hydrolysis of GTP. The polypeptide chain lengthens as a result of this recurrent process for chain elongation. As the ribosome moves down every codon towards the 3’ end of the mRNA, it is at this time that the polypeptide chain with the final amino acid comes to attach to it.

Chain termination:

One of the 3 terminal codons of mRNA marks the end of the polypeptide.  UAG (amber), UAA (ocher) and UGA (opal) are called stop codons. They can also be considered as stop signals.

The terminal codon follows immediately after the last and last amino acid codon. The polypeptide chain, tRNA, and mRNA are then released. Ribosome subunits become detached. The actions of three termination or releasing factors known as R1, R, and S are also required for termination.

Translocation of the protein molecule:

Two types of polyribosome shave been discovered that are involved in this process:

  • Free polyribosomes
  • Membrane-bound polyribosomes.

Upon termination of protein synthesis in the free ribosome, the prepared ribosome releases the protein into the cytoplasm. Special types of processes are used to transport some of these specialised proteins to the mitochondria and nucleus.

In membrane-bound polyribosomes, on the other hand, a polypeptide chain that develops on mRNA is introduced into the ER membrane’s lumen. Some of the proteins also compose parts of the membrane structure.

Even yet, only a few proteins are released into the lumen and integrated into Golgi body vesicles. They can also change the protein through glycosylation, which is the addition of sugar residues. As a result, the vesicles shape a bond with the plasma

membrane and the proteins are sooner or later released.

Protein synthesis process in prokaryotes:

Prokaryotes are simple creatures and have only these 5 steps involved in protein synthesis.

  • Activation of amino acids
  • Transfer of amino acid to tRNA
  • Initiation of the polypeptide chain
  • Chain Termination and
  • Translocation of the protein molecule

Prokaryotes have a single DNA molecule that is used for protein synthesis by transcription and translation. The DNA molecule is so simple that it doesn’t even require post-transcriptional and post-translational modifications for its protein synthesis process.

Process of protein synthesis in eukaryotes:

Protein synthesis in eukaryotes is a bit more complicated due to the presence of introns in the RNA that is transcribed. Hence the introns must be removed by the transcriptional process of splicing to ligate only the exons and produce mRNA which can be translated into protein.

Biochemistry of RNA splicing
Image: Wikipedia

Post-transcriptional processing consists of a total of 4 steps in eukaryotic hnRNA:

  1. Introns are removed from mRNA during splicing. Introns are areas of the genome that don’t code for a protein. The remaining portion of the mRNA is made up entirely of protein-coding parts called exons. In the diagram, ribonucleoproteins are tiny nucleoproteins that contain RNA and are required for the splicing process.
  2. Some of the nucleotides in mRNA are changed during editing. Because of editing, a human protein called APOB, which aids in the transport of lipids in the blood, has two distinct versions. Because editing inserts an earlier stop signal in mRNA, one version is smaller than the other.
  3. The “head” of the mRNA is given a methylation cap via 5’- capping. This cap helps the ribosomes identify where to bind to the mRNA and prevents it from breaking down.
  4. Polyadenylation gives mRNA a “tail.” A series of As makes up the tail (adenine bases). It means that the mRNA has now exhausted its functional requirement and is no longer of any use and can be discarded. It also aids in the export of mRNA from the nucleus and shields mRNA from enzymes that could degrade it.

Protein synthesis example:

A type of protein synthesis that occurs in neurons is called de novo protein synthesis.

In neurons, “de novo protein synthesis” refers to protein synthesis that occurs outside of the soma or cell body’s limits. Both compartments of neurons i.e. dendritic compartment(the longer cavity) and the axonal compartment(the star or spider-shaped cavity) can produce such “extrasomal” proteins.

This means that the protein is synthesized without any prior knowledge of its codon composition, so the protein produced is also the origin and a puzzle for scientists as to regarding their function

Also Read: