A simplified model of protein assembly

Nucleotide: elementary DNA unit
DNA: linear set of nucleotides (universal)
Codon: a nucleotide triplet
RNA: mapping of a codon to an  amino acid (universal)
Start-codon Stop-codon define the domain of RNA mapping. They are also  the initial conditions of RNA mapping
Gene A linear set of codons
Protein: A linear set of amino acids.
Protein conformation: Mapping of the linear protein into a coil. Given a sequence of amino acids, each coil is a different protein

Alternative splicing: A shift of the start and stop-codons (new domain) so that the gene sequence is mapped into different amino acids. 
Mutation: A change of a codon which is then mapped into a different amino acid.
microRNA: Modifies RNA mapping (by silencing genes)  so that the same gene (domain)  may be translated into a different set of amino acids.

Each gene is a source (initial condition) of a protein assembly process. Amino acids that are formed from  a gene stream away and grow into chains which incorporate other molecules. Later on they coil (become different protein)  and finally die (are broken into molecules) . In the healthy organism, for each dead protein a new one is born  which is known as steady state condition. 

v. streaming proteins

A simple illustration with cellular automata (CA)

The gene  is a CA string which serves as an initial state for future iterations.  The CA is born when the initial state has been specified.
CA rule is the RNA
CA structure is the protein
Alternative splicing: Applying the same rule to different initial states (domains)
A gene set generates different CA (proteins) which interact as they go.
The life of a CA is finite. For each dying CA a new one is born (steady state conditions)


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