Protein Synthesis

Protein synthesis, a one-dimensional procedure - the information in a linear sequence of nucleotides is used to specify a linear chain of amino acids - depends on the collaboration of several classes of RNA molecules and requires a series of preparatory steps:

A messenger RNA (mRNA) which encodes the protein to be synthesised is generated by the DNA in nucleus in a process called DNA transcription. Transcription generates not only the mRNAs that carry the information for protein synthesis but transfer, ribosomal and other RNA molecules that have structural and catalytic functions. All these RNA molecules are synthesised by RNA polymerase enzymes which bind very tightly when they collide with a specific DNA sequence: the promoter. The promoter sequence is the one which defines which DNA strand is to be transcribed by defining the direction of RNA polymerase movement. All the above is based upon the fact that the DNA strand serving as template must be traversed from its 3' end to its 5' end.
Discussion question: Plausible explanations for the complicated molecules of both bacterial and eucaryotic RNA polymerases in contrast with the single-chain and with one fifth of the mass of the later; RNA polymerases of some bacterial viruses depicting the same efficiency though.
Each of the 20 amino acids from which the protein is to be built must be attached to its specific transfer RNA (tRNA) molecule. Actually, only the tRNA molecule, and not its attached amino acid, determines where the amino acid is added during protein synthesis. Specific enzymes called aminoacyl-tRNA synthetases couple each amino acid to its appropriate tRNA molecule. Then the tRNA molecule binds to the appropriate nucleotide sequence on the mRNA. Amino acids are added to the carboxyl-terminal end of a growing polypeptide chain. Most of the amino acids are represented by more than one codon and the genetic code is said to be degenerate.
Discussion question: Existence of tRNAs. Is it necessary? In which sense? Could the tRNAs be replaced by other mechanisms?
The events in protein synthesis are catalysed on the ribosomes which are large complexes of RNA and protein molecules. The ribosome moves stepwise along the mRNA chain. The elongation phase of protein synthesis on a ribosome requires a three-step cycle which is repeated over and over during the synthesis of a protein chain. An aminoacyl-tRNA molecule binds to the A-site on the ribosome in step 1; a new peptide bond is formed in step 2; and the ribosome moves a distance of three nucleotides along the mRNA chain in step 3, ejecting an old tRNA molecule and "resetting" the ribosome so that the next aminoacyl-tRNA molecule can bind. A protein chain is released from the ribosome when one of three of different stop codons is reached. In eucaryotes only one species of polypeptide chain is usually synthesised from each mRNA molecules. The binding of many ribosomes to an individual mRNA molecule generates polyribosomes. The overall rate of protein synthesis in eucaryotes is controlled by initiation factors.
Discussion question: Why should rRNA molecules exist at all, and how did they come to play an important role in the structure and function of the ribosome?