Protein Synthesis – Machinery & Mechanism of Protein Synthesis

Protein Synthesis: Proteins are essential for the maintenance of structural attributes and the functioning of all living cells and viruses. Protein comprises approximately 50% of cellular dry weight. A protein is a high molecular weight organic compound and is a biopolymer of amino acids that are joined together by peptide bonds.
Even though proteins are made up of 20 different amino acids, each protein is different in structure and function due to the sequence in which these amino acids are arranged. Does a question now arise that how the sequence of amino acids is decided during the synthesis of a specific protein? To understand the entire process of protein synthesis, let’s read the article till the end.

What is Protein Synthesis?

Protein synthesis, also called translation, is the stepwise process of the production of specific and different types of proteins. This process involves DNA, RNA, and various enzymes. The process initiates with transcription (formation of RNA over DNA template), and actual synthesis of proteins takes place on ribosomes which is called translation, and is terminated with post-translational events such as protein folding, modification, and proteolysis.

Learn About Genetic Code Here

Fig: A Overview of Protein Synthesis

Machinery for Protein Synthesis

The machinery of protein synthesis involves the following components:
1. Amino acids as Raw materials: Amino acids are the raw material for the synthesis of different types of proteins in the biological system. There are about 20 types of amino acids that are available in the cytoplasmic matrix as an amino acid pool.
2. DNA for Specificity Control: The DNA provides instructions for the synthesis of exactly alike protein by following the same sequence of amino acids in a polypeptide chain, therefore serves as a specificity control. DNA exercises specificity control through mRNA. Sequences of three consecutive nucleotides (triplet) in RNA from the genetic code. Each genetic code carries the information for a specific amino acid.
3. tRNA the Carrier of amino acids: tRNA is also known as soluble RNA. The Clover-leaf model of tRNA consists of an acceptor arm that contains a sequence CCA at the 3’ end. It is not base-paired and is the point of attachment of amino acids. The anticodon loop recognises the genetic codon sequence on mRNA and therefore determines the specificity of a sequence of amino acids in the protein chain.
4. Ribosomes: The site of protein synthesis: Ribosomes are the sites of protein synthesis that consist of a smaller and larger unit. Both the units join only at the time of protein synthesis. Prokaryotes have 70S types of ribosomes, and eukaryotes contain 80S types of ribosomes. Each ribosome has three binding sites, E-site (Exit site), A-site (aminoacyl site), and P-site (peptidyl site).

Mechanism of Protein Synthesis: Translation

The process of translation occurs in the cytoplasm in eukaryotes and prokaryotes. Protein synthesis is an elaborated process that involves the following steps:
1. Activation of amino acids: Twenty naturally occurring amino acids participate in protein synthesis. Activation of amino acids is brought about under the direction of an enzyme, aminoacyl tRNA synthetase, in the presence of Mg⁺² which is highly specific for a specific amino acid.

The amino acid reacts with ATP in the presence of a specific aminoacyl tRNA synthetase to produce the activated form called aminoacyladenylic acid (Amino acid-AMP-enzyme complex). The complex formed is called an activated amino acid.

2. Charging of tRNA: The AA-AMP-E complex further reacts with a particular tRNA. The -COOH group of the complex binds to the -OH group at the terminal base triplet CCA at 3’ end. This results in the formation of tRNA-AA-Complex (aminoacyl tRNA). This complex is called charged tRNA. The aminoacyl tRNA synthetase enzyme catalyses the reaction.
The sum-up of this process is the transfer of amino acid to tRNA in the presence of the same enzyme.

Fig: Activation of Amino Acid and tRNA Charging

3. Polypeptide Chain formation: A polypeptide chain is formed by the assembly of several amino acids. The formation of a polypeptide chain involves the following three steps:
I. Initiation of polypeptide chain: The translation of mRNA begins with the formation of the initiation complex.
i. In this stage, the smaller subunit of the ribosome, an mRNA, a tRNA bearing the first amino acid of the polypeptide chain, GTP, Mg⁺², and proteinaceous initiation factors are assembled. GTP supplies the energy for the formation of the pre-initiation complex.
ii. These initiation factors are designed as IFs. In prokaryotes, IF₁, IF₂, and IF₃ are the initiation factors, whereas eukaryotes have nine initiation factors.
iii. The initiation factors bind to the smaller subunit of the ribosome. The complex then attaches to the mRNA and a specifically charged initiator tRNA.
iv. The ribosome subunit binds to the leader segment at the 5’ end of mRNA, preceding the initiator AUG codon, which signals the start of translation.
v. The initiator tRNA joins the initiation codon (AUG) by its anticodon loop through hydrogen bonds. It carries the amino acid formylmethionine (formyl-met) in prokaryotes and methionine in eukaryotes.
vi. Binding of charged formyl-met tRNA (fMet-tRNA) to all the components assembled at 30S subunit form initiation complex.
vii. Later, when the large 50S subunit joins the initiation complex, the initiation factors are released, and a complete 80S ribosome is formed. It is called the activation of ribosomes. The mRNA is thread through the groove between the larger and the smaller subunit of the ribosome. The initiating formyl methionine tRNA can bind only with the P-site, whereas all other aminoacyl tRNA bind to the A-site.
viii. The ribosome has two binding sites. The initiator tRNA (fMet-tRNA) lies at the P-site at this stage, leaving the triplet (three bases of mRNA or codon) at the A-site to remain unoccupied to allow the entry of another charged tRNA.

Fig: Initiation of the Polypeptide Chain

II. Elongation of polypeptide chain: The elongation of the polypeptide chain involves the addition of amino acids one by one to the first amino acid (formylmethionine or methionine).

The addition of amino acids requires certain proteins called elongation factors. In prokaryotes, the elongation factors are termed EF-Tu, EF-Ts, and EF-G. There is a more complex set of elongation factors in eukaryotes.

The process of elongation of the polypeptide chain occurs in a three-step cycle:
a. Codon recognition: A charged tRNA molecule, along with its amino acid, enters the ribosome at the A-site. Its anticodon reads and binds to the complementary codon of the mRNA chain by hydrogen bonds. Hydrolysis of GTP provides energy in this step.
b. Peptide bond formation: The amino acid on the tRNA at P-site and the newly attached tRNA at A-site join by a peptide bond. The reaction is catalysed by the peptidyl transferase enzyme.

In the peptide bond formation, the linkage between the first amino acid and its tRNA is broken, and the -COOH group now forms a peptide bond with the -NH₂ group of the second amino acid. Therefore, the second tRNA carries a dipeptide, formylmethionine/methionine-proline, and the first tRNA is without amino acid. The tRNA in P-site, without its amino acid, is called deacylated. The whole assembly is called dipeptidyl tRNA.

Translocation: The tRNA at A site, carrying a dipeptide, moves to the P-site. This process is termed translocation. The codon that was waiting in the wings to the right moves into A-site, ready to interact with aminoacyl tRNA. Translocation requires an elongation factor called EF-G and energy from GTP.
The process then repeats itself to add another amino acid:
i. EF-Tu, in conjugation with GTP, brings the appropriate aminoacyl-tRNA to match the new codon in the A-site.
ii. EF-Tu, in conjugation with GTP, brings the appropriate aminoacyl-tRNA to match the new codon in the A-site.
iii. EF-G, using energy from GTP, translocates the tripeptidyl-tRNA, together with its mRNA codon, to the P site.
This process continues over and over until the ribosome reaches the last codon in the message. The protein is now complete, and further goes for termination.

Fig: Elongation of the Polypeptide Chain

III. Termination and release of polypeptide chain: The synthesis of a polypeptide chain is concluded when a signal in the form of a termination codon is reached. There are three termination codons (UAG, UGA, and UAA) that do not code for amino acids, and therefore the translation stops. These three codons are frequently referred to as nonsense codons because they do not code for any amino acid.
A release factor (RF₁, RF₂, and RF₃) joins to the stop codon in the A-site, which cleaves the polypeptide from the terminal tRNA. RF₁ leads to a mismatched pairing between the P-site codon and the anticodon of the peptidyl-tRNA. RF₁ /RF₂ and RF_{3 lead} to premature termination of protein synthesis.
The polypeptide is now from the ribosome. The ribosome jumps off the mRNA chain at the stop codon and dissociates into its two subunits.

Fig: Termination of the Polypeptide Chain

4. Polysome Formation

When the ribosome reaches the 3’ end of the mRNA, another ribosome is attached to the initiator codon at the 5’ end, synthesising the exact copy of the previous polypeptide chain. The continuation of the process leads to the attachment of a number of ribosomes in a linear fashion over the mRNA strand, forming the polysome or polyribosome.

Fig: Polysome formation

5. Modification of released polypeptide: The released polypeptide chain can be modified in different ways.
i. The first amino acid of the polypeptide chain in prokaryotes is formyl methionine. An enzyme deformylase removes the formyl group of methionine.
ii. Besides, the exopeptidase enzyme may remove some amino acids from the N-terminal and the C-terminal end of the polypeptide chain.
iii. Besides, the exopeptidase enzyme may remove some amino acids from the N-terminal and the C-terminal end of the polypeptide chain.
iv. Two or more tertiary structures may unite into a functional quaternary structure.

Summary

Proteins are body-building organic biomolecules that support body growth. These are the polymers of amino acids. Twenty amino acids are arranged in a different sequential manner, form different types of proteins. Protein synthesis is a complex and elaborate process that involves the translation of genetic messages carried by mRNA into a polypeptide chain.
Ribosomes serve as the site of protein synthesis that attaches to the mRNA at its 5’end and causes the initiation of the polypeptide chain with the help of initiation factors. The translation begins with the initiator codon AUG. The tRNA recognises and joins the initiation codon carrying the specific amino acid. The elongation of the polypeptide chain is further carried by elongation factors. At the terminal, the presence of nonsense codons indicates the termination and release of the polypeptide chain.

Frequently Asked Questions (FAQs) on Protein Synthesis

Q.1. What is required for protein synthesis?
Ans: Ribosomes, mRNA, tRNA, and amino acids are required for protein synthesis.

Q.2. What is the initiation codon of protein synthesis in protein synthesis?
Ans: AUG is the initiation codon in protein synthesis.

Q.3. What are the termination codons in protein synthesis?
Ans: UAG, UAA, and UGA are the termination codons in protein synthesis.

Q.4. Where does protein synthesis occur?
Ans: Ribosomes are the site for protein synthesis.

Q.5. What is another word for protein synthesis?
Ans: Translation is another word used for the biosynthesis of proteins.

Learn About The DNA Model Here

We hope this article on Protein Synthesis helps you in your preparation. Do drop in your queries in the comments section if you get stuck and we will get back to you at the earliest.