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)