Action Zones 

Exploring Psalm 119 from a scientist’s perspective: introduction part 3 

Peter Gray-Read BSc MSc

Molecular biology - analogy

My journey of discovery in science started with being amazed at the sight of protozoa (‘pond-life’) swimming around in a drop of water under a microscope.  I asked the question ‘What gives them life?  What chemistry is driving them?  It led to studying biochemistry and molecular biology to Master’s Degree level.  So I am inclined to see parallels in this area.  I found this very compelling

When I was at first at university in the 70s we had to learn the structure of 20 amino acids making up the primary sequence of a protein chain.  These are the basic building blocks of many structures in animal and plant cells.  Today they recognise 22 amino acids – 2 more recently found to have an important role in a few specialist enzymes

I need to outline the ‘central dogma’ of the cell to help you appreciate this second analogy which I believe has real significance.  The information needed to make every enzyme and protein structure in the cell is coded in the long thread-like DNA by a sequence of four special molecules called ‘bases’ designated by the letters A, T, C, and G.  A triplet of these is called a CODON and each of the 22 amino acids has at least one specific codon which signifies its position in the protein chain.  It is like translating from one language into another – the nucleic acid code to an amino acid / protein code

However there is one more level between the DNA and protein.  The DNA is the master blue-print.  It does not go to the protein ‘building site’ itself which is in the cytoplasm, but stays protected in the nucleus inside the nuclear membrane.  The cell produces a working copy of the particular sequence of its code that is needed by the builders.  This copy is a 1-dimensional molecule similar to DNA, called RNA – in this case messenger or mRNA.  But it is only as long as the information needed to make one protein molecule.  The single stranded mRNA is exported through the nuclear membrane and reaches a sort of submersible platform called endoplasmic reticulum where the machinery to make the protein can be assembled

To enable the amino acids to be incorporated into the growing protein chain they are identified by being attached to a specific RNA ‘adapter molecule’ called transfer or tRNA.  Again there are 22 varieties, distinguished by a specific sequence of bases called an anti-CODON triplet (see Fig.3) which can ‘recognise’ its matching CODON sequence on the mRNA molecule.  This matching is achieved by the very specific ‘base pairing’ that takes place between the three bases in the mRNA codon being transcribed and the anti-codon on the tRNA.  It was a ‘ureka moment’ when Watson and Crick in 1953 found that a jig-saw like fit could be achieved between the DNA strands if the following pairing was adhered to:  A = T and C≡G.  So the sequence information is maintained and reproduced in either strand of DNA, or mRNA and determines the amino acid sequence in proteins via complimentary base pairing by the tRNA. The only difference being that in RNA a based designated by U replaces the T – but the ‘fit’ is the same. The new amino acid is attached to the growing chain by a special type of ester link called a ‘peptide’ bond

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