Translation: Protein synthesis from RNA
Specific directions for synthesis of protein are transcribed from sense DNA template in mRNA. Each molecule of mRNA has information essential to assemble specific sequence of amino acids into complete polypeptide chain; this chain may be either complete protein molecule or polypeptide submit the protein molecule. Information transformed to, and contained on mRNA are in form of three linear nucleotides forming the codeword or codon. Using four bases in all different 3-base combinations, 64 different codewords can be formed. This is more than enough for 20 known amino acids that make up protein molecules. Therefore we can have more than one codon coding for every amino acid, but no one codon can code for more than one. The ribosomes, of course are RNA particles coupled with proteins. Surrounding ribosomes is a pool of different tRNA's with joined amino acids. Each tRNA has a recognition site (known as an anti-codon) for code designating these amino acids in mRNA. For instance tRNA carrier of threonine would have anti-codon UGG (or UGA, UGU or UGC).
When right anti-codon on tRNA finds right codon on mRNA temporary bonding will be created. Then next t-RNA comes around and binds to next set of codons. Two amino acids are now united in the chain and first t-RNA dissociates from its codon to search for another amino acid to hook up with. Ribosome move along m-RNA and subsequent codons dictate amino acid to be joined to growing chain. The set of triplets on mRNA dictate end for that specific protein synthesis; to this triplet set, known as terminator, no t-RNA binds. At the sight of terminator protein synthesis ends, and polypeptide chain detaches; it can on its own fold up in its tertiary structure to create protein, or join up with other polypeptide chains to create protein.
Initiation of Protein Synthesis:
First step in initiation of protein synthesis is binding of mRNA to ribosome. mRNA combines with smaller 30s unit of ribosome. First amino acid to be laid down in synthesis of any bacterial protein is N-formyl-L-methionine.
Initiation of protein synthesis depends on interactions between mRNA, fmet - tRNA, initiation codon AUG and 30s ribosomal subunit to create initiation complex, this procedure needs GTP and mg2+. Once formed whole complex then combines with 50s subunit to make up during formation of initiation complex, it is hydrolyzed when two subunits (30s - 50s) unite. These ribosomal proteins just called F3 or initiation factors have been shown to be needed for process of chain initiation. Two of these appear to be necessary for binding of fmet - tRNA and normal mRNA to 30s subunit; third protein is concerned with linking two ribosomal subunits. Therefore it appears that bacterial ribosomes are disassociate until 30s subunits form initiation complex.
GUG triplet that usually codes for valine, can also code for fmet - tRNA and therefore, services as initiation codon. Investigations have shown that region between chain termination of one protein and initiation codon of another one is not translated.
Once initiation complex has combined with 50s subunit of ribosome actual polypeptide synthesis then starts. Next codon is then employed by second amino acyl - tRNA complex bering suitable anticodon; this happens at A site GTP, mg2+ and two elongation factors EFTU and EFTs, are involved. Peptide bond is then created between fmet's carbonyl group and amino group of newly-attached amino-acyl tRNA. Reaction is catalyzed by the enzyme known as peptidyl transferase, that is constituent of 50s ribosomal subunit; as a result of transfer, +-RNA that was initially attached to f-met is freed, and dipeptide is left attached to second tRNA. Next codon on mRNA is filled, in similar manner by acyt-tRNA with correct anticodon; peptide bond will be formed with preceding amino acid with subsequent hydrolisis and release of its tRNA. The sequence carries on until end of chain is reached.
Peptide chain continues to grow until set of triplets on mRNA dictates end of that particular protein synthesis. This triplet is known as termination codon or terminator and doesn't bind any tRNA. Three of such terminators exist - UAA, UAG and UGA. Upon reaching termination codon, protein synthesis stops and polypeptide chain detaches. Release of ribosomal proteins releasing factors, R1 and R2.
The Peptide Bond:
In the protein or polypeptide amino acid are joined together by carboxyl and amino groups by amide linkage. This linkage is called as peptide bond. For alanine and glycine, this provides alanylglycine which is dipeptide.
Peptide bond itself is -CO-NH- link, and it can be split by hydrolysis in acid solution or in presence of appropriate enzyme. If third amino acid is attached to alanylglycine dipeptide, it will become tripeptide. A peptide chain having three or more amino acids is called as polypeptide. If third amino acid is leucine, we get alanylglycylleucine.
Protein Structure and Conformation:
i) Primary Structure:
Sequential arrangement of amino acids as synthesized from mRNA on polysomes is called as primary structure of protein. Released polypeptide chain can suffer structural modifications; these alterations will result in polypeptide assuming secondary, tertiary and quaternary structures.
ii) Secondary Structure:
Secondary structure of protein engages formation of hydrogen - bond interactions between amino acid residues fairly close to one another in primary structure.
iii) Tertiary Structure:
This engages extensive coiling or folding to generate complex, fairly rigid structures. This folding usually takes place from interactions between amino acid residues relatively far apart in sequence.
iv) Quaternary Structure:
This results from interaction between separate polypeptide units of protein having more than one subunit. Where subunits are same protein has homogeneous quartenary structure (or promoter); where different the protein has heterogenous quartenary structure (=oligomeric protein like haemoglobin).
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