In this article we will discuss about:- 1. Structure of Protein 2. The Role of Nucleic Acids in Protein Synthesis 3. The General Scheme and the Mechanism of Protein Synthesis.
Structure of Protein:
Proteins are giant molecules, formed of long chains of about hundred to several hundred amino acid molecules arranged in a variety of sequences.
Although, amino acid molecules in a protein are counted up to several hundreds, they number only twenty two in variety. Each amino acid has a asymmetric carbon, which is joined by covalent bonds to 4 different groups-a carboxyl, an amino, hydrogen and R groups. The R groups are different in different amino acids.
Since the carboxyl and amino groups are present, amino acids may act as either an acid or a base. The amino acid molecules are attached together by establishing peptide bond between them and the chain thus formed is known as polypeptide chain. A peptide bond connects amino groups of one amino acid and the carboxyl group of another.
The various types of proteins are formed by only different arrangements of these amino acids. The sequence of amino acid in a protein molecule is determined by the sequence of bases in DNA. The amino acid sequence is referred to as the Primary Protein Structure.
The configuration of the polypeptide backbone refers to the Secondary Structure of protein. Almost all proteins exist in a helical configuration called as α-helix. Tertiary structure of protein refers to the topological pattern of the folded chain.
The Role of Nucleic Acids in Protein Synthesis:
Nucleic acid play the chief role in the synthesis of protein. The synthesis is governed by the genetic information contained in the DNA molecules which determine the amino acid sequence of proteins. Ribonucleic acids play a key role in transmitting the genetic information for protein synthesis.
There are mainly three kinds of RNAs, concerned with protein synthesis. Recent studies have shown the mRNA and tRNA play the main role in coding the sequence of amino acids whereas rRNA remains inactive inside the ribosome.
The General Scheme and the Mechanism of Protein Synthesis:
We can distinguish three important processes in the scheme of protein synthesis.
1. Exact replication of DNA by an enzyme DNA polymerase. This replication ensures that all the cells in a multicellular organism will have the same genetic information and will have the same ability to synthesise specific protein molecule.
2. Transcription process:
We know that the genetic information for linking of amino acids in a definite sequence to form particular protein is coded in DNA molecules. These information’s are transmitted to mRNA molecules, which are copied from one of the strands of their respective DNA molecules. This process is governed by the enzyme RNA polymerase.
The mRNA thus synthesised by DNA diffuses into the cytoplasm. Several ribosomes become attached to one molecule of mRNA, thereby, forming a sort of cluster or grouping. This grouping of ribosomes on mRNA molecule is known as Polyribosome or Polysome.
3. The Translation process that takes place when the information in mRNA is translated in to the amino acid sequence of the newly synthesised peptide chain. This takes place in the active ribosomes.
It involves the arrival of amino acids in the form of activated aminoacyl- tRNA molecules, their assembly in sequence on the mRNA template in the ribosome and the combination of amino acid to form peptide bonds. This is followed by the release of tRNA. The finished polypeptide chain is released from the polysome. A specific enzyme is supposed to involve in this process.
Mechanism of Protein Synthesis:
Protein synthesis involves two steps:
1. The activation and charging reaction.
2. The transfer reaction.
1. The activation and charging reaction:
Amino acids in the cytoplasm occur in an inactive stage and they cannot take part in protein synthesis. Hence, these are activated by giving them energy. The activation is facilitated through ATP. In this reaction the carboxyl group of the amino acids react with ATP forming aminoacyl adenylate and releasing pyrophosphate.
This reaction is catalysed by a large number of enzymes, but each is specific for a particular amino acid. This means at least twenty two enzymes must function at this stage. These enzymes are generally known as amino acid activating enzyme. Magnesium ion (as well as ATP) is involved in this reaction.
Then each enzyme bound aminoacyl adenylate reacts immediately with tRNA and form aminoacyl-tRNA product. The same enzyme that is involved in activation also functions to transfer the amino acid to tRNA. These enzymes are then called aminoacyl-tRNA synthetase. They are unique catalysts, as they not only activate the amino acid but are also capable of recognizing a particular tRNA molecule.
During the formation of aminoacyl-tRNA product, the amino acid is transferred to the adenine that is present at one end of the tRNA molecules. When aminoacyl-tRNA product is formed, adenosine monophosphate and the aminoacyl synthetase are released. The tRNA functions as an adapter accepting amino acid and there is a group of three bases called anticodon. The anticodon is complementary with a triplet codon present in mRNA.
2. Transfer reaction:
Perhaps the most important step in protein synthesis is the transfer reaction. It involves aminoacyl-tRNA, ribosomes, and mRNA resulting in peptide-bond formation. For this reaction two enzymes are required as well as guanosine triphosphate (GTP) and several inorganic ions.
The ribosomes are not active until they are first combined with mRNA. A small ribosomal subunit become attached to the mRNA near initiation codon (AUG). The first step in transfer reaction is the binding reaction which occurs between aminoacyl- tRNA and the mRNA ribosome complex. It appears to be non enzymatic process, however, the binding is very specific.
That is an aminoacyl-tRNA carrying a specific anticodon fits in a proper position of the mRNA containing the corresponding codon. Initiator tRNA (with format) pairs with this codon and then a large ribosomal subunit joins to the small sub unit to initiate translation.
Magnesium ions are required for the stable bonding of mRNA to tRNA and also for the stability of the ribosomes. Each ribosome contains two sites, the P (for polypeptide) site and the A (for amino acid) site. A t-RNA with attached polypeptide is at the P-site and a t-RNA amino acid complex just arrives at the A- site. Further the attachment of the ribosome to the messenger is also quite specific and always occurs in a single site on the 5′- hydroxyl end of the mRNA.
The mRNA in a linear form passes through or over the ribosome. At the ribosome surface the complementary tRNAs with amino acids line up along the mRNA. The amino acid of each tRNA molecule interacts with the preceding amino acid forming a peptide link and releasing the preceding tRNA molecule. The enzyme peptidyl transferase and the energy rich molecule GTP are involved in the process.
As the mRNA moves through the ribosome from a site to the empty -P site and becomes free, again another ribosome may attach itself to the beginning of the molecule. Since the ribosome has moved forward three nucleotides, there is a new codon now located at the empty A-site.
Electron microscopic picture show many ribosomes attached at intervals along the length of a mRNA molecule. This complex is known as Polysome. When a peptide chain is completed, it is released and becomes a protein molecule. All the released tRNA molecules are once again charged with amino acids and the transfer reaction is repeated again and again.
The synthesis of protein chain begins at the amino end of polypeptide chain and progresses to the carboxyl end at the rate of two amino acids per second. Termination of polypeptide synthesis occurs at a stop codon i.e., UAA, UGA and UAG which does not code for any amino acid.
The arrival of stop codon in A- site results in the completion of protein synthesis and enzymatic cleavage of last tRNA from polypeptide. Although we know so much about protein synthesis, we still need to know which of the two strands of DNA, double helix acts as a template to form mRNA.