This horrifies me... This is why I'm not a biologist.
3 DNA base pairs abstract to an amino acid which has chemical properties. It's just theres some redundancy which 3 base pairs get converted to an amino acid. And if there's a single mistake somewhere with just one amino acid, the structure of the thousand amino acid long protein probably has some fault tolerance there.
Those amino acids are arranged in a way in the DNA code to make bigger motifs, alpha helices, beta sheets, active sites, coordinating complexes with inorganic ions.
It's all in the DNA code, though I suspect this train of thoughts is influenced by epigenetics. Parts of the DNA code also responsible for the regulation of how much the protein itself is expressed. That can still abstract to conditional and loop structures.
Yes some of the base pairs strongly bind together in the double helice which can influence stability of the DNA strand. The GC pairing has 3 hydrogen bonds, where AT has 2, but I think this influences the distribution of junk DNA, as you still need codons to make proteins which is the central dogma of biology.
The first level of problems is that what you're describing applies to only a tiny percentage of the DNA in a cell, and even for that DNA, it may overlap/exist in parallel with completely different "codings" that are more to do with structure, packing and replication machinery than protein coding.
I don't mean to distress you, but you are a biological computer.
Just rejoice that you needn't read the release notes.
“Thanks for being human. This update changes your DNA and may contain bug fixes and performance improvements. Keep on humaning!”