Ribosome

Ribosomes are roughly-spherical bodies that are contained
within the cell.  They are very small and can be seen only under
the electron microscope.  They are formed from two subunits, one
being larger than the other.

Ribosomes are the factory where a given protein is
manufactured.  Put in a simple way:  the mRNA brings the
instructions needed to synthesize the protein; the Amino Acids
(AA) required for the protein are carried to the site by the
tRNA; finally, as already mentioned, rRNA is part of the
machinery (and part of the ribosome itself) that manufacture the
protein.

Protein Synthesis

Physically you are made out of countless proteins.  Your
tissues, your bones, your blood, your organs, your enzymes, your
hormones, even your thoughts and memories are presumably
proteins.  The majority of proteins (within the same gender) are
similar.  Some proteins, however, are peculiar to a given
individual; indeed no two individuals have the exact same
proteins, not even identical twins!  (Because of the impact of
the environment, and its effect on the epigenetic code, identical
twins are not 100% identical.  This will be discussed in the
section on identical twins).

As discussed, proteins are synthesized in the ribosome of
the cell.  The assembly, following the blueprint provided by the
DNA and transported to the ribosome by the mRNA involves:

1) Controlled formation of a peptide bond between two AA.
This operation is repeated many times as each AA in turn is added
to the polypeptide chain.

Remember that at the end of the section on RNA I mentioned
that the DNA instructions include promoters and terminators
sequences.  These sequences in effect indicate to the ribosome
where to start and at what point to stop.  At the end of the
process, the manufactured protein is released to be used by the
body.  This operation is repeated million of times with a balance
maintained throughout the whole organism!  One question remains,
however.  How does the cell codes for the various AA?

2) The code

A great deal of work was carried out to crack the code.
Ultimately, the research was done in test tubes!  When many
biologists expressed doubt as to whether such a system really
operated in living organisms, more work was done on viruses with
a single strand of RNA.  To make a long story short, the validity
of the code was eventually verified.  If interested, you can
research and read further the fascinating story behind one of the
most extraordinary achievements of the 20th century!

So what is the code?

Remember that the four bases for RNA are: A,C,G,U.  Also
keep in mind that there are 20 AA and that we need different
codes for each one.

One base is insufficient to code a single AA.  Pairs of
bases could be arranged in 16 different ways (AA, UU, UA, etc.).
But we are still short since we have 20 AA.  Triplets of bases,
on the other hand, can be arranged in 64 different ways, more
than enough to code for 20 AA.  Because of this coding
relationship, a triplet of bases is called a codon.  To add to
the complexity, each AA is coded by one or more (up to six)
codons.

Three of the 64 possible codons (UAA, UAG & UGA) have not
been found to code for any AA.  They act as chain terminators.
When the ribosome reaches them, the polypeptide chain is
completed and is released to carry out its function in the cell.

Some examples of the code together with the corresponding
AA:

AUG for Methionine; UCG for Tryptophan; UUU & UUC for
phenylalanine; UUA & UUG for Leucine; CUU, CUC, CUA & CUG for
Leucine; GGU, GGC, GGA & GGG for Glycine.

Note the following:

1 to 4 codons codes for the above AA.

Leucine is coded by 2 or 4 codons (in most cases, several
codons code for a single AA, and one codon may be “preferred” by
one organism, another by a different organism).

I said that three codons (UAA, UAG & UGA) act as chain
terminators; what indicates the starting point?  AUG is used for
that purpose when it is at the beginning; when it is within the
message being decoded it is used (as shown above) to code for
Methionine.

Most of the codons have been assigned as a result of studies
with E.Coli; there is evidence that the code is the same for all
organisms.

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