course brief notes on protein synthesis

Sophia Kossida (
Wed, 10 Jan 1996 18:13:45 +0000

Dear Dr. John Walshaw,

below I wrote few notes for the 1st term lesson of
protein synthesis. Obviously enough the below notes are not suppoed to
cover the subject in any detail at all. They are mostly addressed to
students that are not familar with biology, giving the most important
facts, trying to avoid details.
If wanted, I could translate the below text into HTML. Comments and
suggestions are always welcome.

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 lighter (one-fifth of the mass) 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