Protein Synthesis – Definition and Step-by-Step Mechanism

Protein synthesis is the process by which a cell makes protein. : <-Definition

In this article we would be knowing about how synthesize of protein take place in animal cell. Also, I would be guiding you through the process or mechanism of protein synthesis, role of protein, the relation of DNA for the synthesis and much more.

Let us now dive into the this interesting topic.

Introduction to Protein Synthesis

Before knowing about knowing about protein synthesis, let us first know what is protein?

Proteins are complex organic compounds forming the main building materials of the cell.

Some of the proteins are enzymes which act as biocatalysts and control the essential chemical processes carried on in the living system.

Proteins are the most important group of chemical compounds. Through protein inherited characters are expressed.

Many hormones are composed of different kinds of proteins also. The individuality of the organism is known by the proteins it possesses.

Proteins are giant molecules (macromolecules) and are made up of hundred to several hundred building blocks of aminoacid molecules.

Amino acids are so called because they have an amino group (-NH2) and carboxyl group (-COOH). These amino acids are held together by covalent peptide bond (-CO-NH-).

Living cells build more living substances from these amino acids. There are only 20 kinds of amino acids commonly met with, through which a number of proteins can be formed.

In each kind of protein, the amino acids are arranged in particular sequence, thus forming single peptide chain called monomere or may be polypeptide chain called as polymers.

The mechanism by which the characteristic proteins of the organism can be synthesized is present in the cells.

The general structure of an amino acid is represented by the formula have been given below:

amino acid structure
Amino Acid structure

where -NH2, is an amino group, -COOH, carboxylic group and -R, an organic group which varies in structure from one amino acid to the other.

For example, the simplest amino acid is glycine, where R = H. If R = CH3, the amino acid is alanine and if R=CH2OH, the acid is called serine.

The twenty essential amino acids are namely:

  1. Alanine
  2. arginine
  3. asparagine
  4. aspartic acid
  5. cysteine
  6. glutamic acid
  7. glutamine
  8. glycine
  9. histidine
  10. isoleucine
  11. leucine
  12. lysine
  13. methionine
  14. phenylalanine
  15. proline
  16. serine
  17. threonine
  18. tryptophan
  19. tyrosine
  20. valine.

All these amino acids need not be present in a particular protein.

Role of Nucleic Acid in Protein Synthesis

Nucleic Acid plays the main role in transmitting the required genetic information for protein synthesis.

The proteins are synthesized under the control of genetic instructor DNA but actual synthesis occurs in the cytoplasm in association with the ribosomes.

Because the information regarding protein synthesis is contained in the nuclear DNA which has a particular base composition from its one end to the other.

All the hereditary characters or information depend on the sequence of nitrogenous bases in the molecules of DNA. The three kinds of RNA, namely m-RNA, t-RNA and r-RNA are directly related with the protein synthesis.

The m-RNA molecule serves to carry the message of the genetic code (described earlier) from nuclear DNA to the cytoplasm. The m-RNA is formed from DNA template during replication and the base components in m-RNA are complementary to those of DNA.

The length of m-RNA molecule depends upon the length of the polypeptide chain for which it is coded.

The role of t-RNA is to bring the proper amino acid molecules from other location of the cell to m-RNA already placed on the surface of the ribosomes, where protein synthesis occurs.

It thus acts as intermediate or adaptor molecule between the amino acid and m-RNA. One kind of t-RNA serves only for one specific amino acid. So there are at-least 20 different t-RNA molecules; one for each amino acid.

The ribosomes are composed of ribosomal RNA and protein. The exact function of r-RNA in protein synthesis is not yet known.

But it may be possible that the unpaired bases in the molecule of r-RNA may serve to bind m-RNA and t-RNA to ribosomes or t-RNA may serve as a template for the synthesis of ribosomal proteins.

Relation Between DNA and Protein Synthesis

As the DNA remains locked up so to say in the nucleus, it directs protein synthesis through RNA. Now three questions arise in this connection:

  1. In what language is the genetic information written in DNA?
  2. How is this information carried from DNA to the cytoplasm?
  3. In what form is the information expressed?

The information for the structure of a polypeptide is stored in a polynucleotide chain. The sequence of four bases (A, T, C, G) in a particular segment of DNA (polynucleotide chain) will determine the sequence of amino acids in a particular polypeptide.

The relationship between these two sequence is popularly known as ‘central dogma‘. Central dogma explains how synthesis of protein is controlled by DNA while undergoing self-replication. It also controls the synthesis of all kinds of RNA.

These RNA then control the synthesis of specific proteins. The flow of information is one way i.e., from DNA, the information is transferred to RNA (m-RNA) and from RNA to protein.

Mechanism/Process of Protein Synthesis

You know that a particular unit of DNA acts as a template and provides genetic information through m-RNA for coding of amino acids during protein synthesis.

The entire mechanism of the synthesis of protein is as follows:

Entire mechanism of protein synthesis
Entire Mechanism of Protein Synthesis

Above diagram is showing entire mechanism of Protein synthesis. DNA acts as a template for the synthesis of mRNA (transcription), activation of amino acids, tRNA amino acids complexes, translation and growth of peptide chain on the ribosomes and its release.

Step I: Synthesis of m-RNA and Its Association with Ribosomes

The m-RNA is synthesized on DNA template. The process of copying of the message from DNA on m-RNA is known as transcription.

The synthesis takes place through the enzymatic action of DNA, directed by RNA polymerase. By this process, the single strand of DNA resembles the m-RNA.

For example, if thymine is present in DNA strand, then adenine would remain in m-RNA.

Similarly, if adenine is present in DNA strand, corresponding base uracil would remain in m-RNA.

Because adenine alone is linked with thymine or vice versa in DNA helix but in m-RNA adenine is linked with uracil (in place of thymine). So similar case happens with cytosine and guanine.

Diagram showing entire mechanism of protein synthesis. DNA acts as a template for the synthesis of m-RNA (transcription), activation of amino acids, t-RNA amino acid complexes, translation and growth of peptide chain on the ribosomes and its release.

After the formation of m-RNA chain, m-RNA comes out of the nucleus into cytoplasm where it becomes associated with ribosomes.

The protein synthesis in fact takes place on a group of ribosomes, called polyribosomes. This increases the efficiency of the process.

The m-RNA molecule becomes attached to a group of 3 to 10 ribosomes; on all of which synthesis of protein takes place simultaneously.

Step II: Activation of Amino Acids

The required amino acids which were obtained from the protein food, are present in the cytoplasm. Most of the amino acids which form the raw materials for protein synthesis, remain in inactive state in the cytoplasm.

Now the different amino acids must be brought into high energy state. The energy for the reaction of activation comes from ATP (Adenosine triphosphate).

The ATP is the chief high energy exergonic reactant in the cell. There are also specific enzymes catalyzing the reaction for each individual amino acid.

The process of amino acid activation is as follows:

amino acid activation
Amino Acid activation | Activated amino acid or aminoacyl adenylate

(activated amino acid or aminoacyl adenylate) where PP and AMP denote pyrophosphate and adenosine monophosphate respectively.

Step III: Attachment of Activated Amino Acid with t-RNA

Now in the cytoplasm, we have the proper site (ribosomes), the instruction (m-RNA) and activated amino acids.

What more is needed, is a machinery to pick up the required amino acids and to place them according to the coded instructions.

The t-RNA molecules exist as free floaters in the cytoplasm and act as biochemical middlemen to pick up amino acids from the intracellular amino acid pool in the cytoplasm i.e., outside the ribosomes and to bring them to the ribosomal surface.

Here the role of t-RNA is like that of a railway engine, which picks up bogies or wagons from various places in the yard to assemble the train.

There is at-least one t-RNA molecule for each kind of amino acid and each amino acid has its own activating enzyme.

Each t-RNA takes up specific amino acid because it has the triplet CCA at one end and the amino acid becomes bound to adenine.

In the presence of activating enzyme called aminoacyl transfer RNA synthetase, the activated amino acid or aminoacyl adenylate (of Step II) gets attached with t-RNA forming transfer RNA-amino acid complex.

The reaction is as follows:

AA tRNA complex
AA tRNA complex

This t-RNA-amino acid complex is moved to the site of protein synthesis (Ribosomal surface) empowered by ATP.

Step IV: Release of Amino Acids from t-RNA on the Ribosomes

The proper amino acid is released from the transfer RNA by guanosine triphosphate (GTP) in the presence of specific ribosomal enzyme and is collected on the ribosome and incorporated into a polypeptide chain to form a protein.

The liberated t-RNA again takes up another specific amino acid and thus cycle is repeated. The reaction is as follows:

release of amino acid
Release of amino acid

where GDP denotes guanosine diphosphate.

Step V: Translation and Coding of Amino Acids

Now the coded message in the form of bases of m-RNA after transcription, is translated to the specific amino acid sequence of protein molecules with the help of ribosomes. This process is known as translation.

So the amino acids become joined in a particular sequence determined by the m-RNA (bringing the specific message for the codon of amino acids) associated with the ribosomes.

A triplet code of m-RNA is recognized by a particular t-RNA. Each t-RNA molecule has two recognition sites.

One of them recognizes the correct amino acid and other recognizes the m-RNA codon due to a triplet of bases called anticodon which is complementary of the m-RNA codon for the amino acid carried by it.

Under the direction of m-RNA, amino acid molecules brought by t-RNA are joined in proper order to form a particular polypeptide chain.

Step VI: Growth of Polypeptide Chain

The synthesis of protein chain begins at the amino end of the polypeptide and progresses to the carboxyl end. In this process of formation of polypeptide chain the m-RNA moves along the groove of the ribosomes, so as to expose the next triplet.

Another t-RNA molecule with its amino acid becomes attached to exposed triplet and a new amino acid is added to the chain by the repetition of the process.

The amino acids are linked together by the formation of peptide bonds which later take place in the presence of an enzyme called peptide synthetase and ATP.

After the complete formation, the protein chain is released from the surface of ribosomes and moves into the cytoplasm. But what happens to m-RNA is not clearly known.

Hence the central dogma of the process can be indicated as:

growth of polypeptide chain
Growth of Polypeptide Chain

In this process, there must be a signal to start and another to stop the synthesis. The codon AUG (codes for methionine) signals for the start of synthesis. Similarly the codon UAA, UAG and UGA serve as the chain terminating codons.

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