Proteins are ordered molecular polymers of 50-1000 amino acids, of 20 different types. Each of the approximately 500-10,000 protein types in a typical cell consists of a unique sequence of the 20 amino acids. Moreover, each protein chain folds into a characteristic three-dimensional structure, which is necessary for its activity.
Many proteins, called enzymes, act as exquisitely selective catalysts for specific chemical reactions, allowing these reactions to take place dramatically faster than they would under normal circumstances. The presence or absence of an enzyme effectively switches reactions on and off within a cell.
The amino acid sequence (and thus the properties) of a particular protein is controlled by the sequence of DNA codons in the associated gene. Triplets of the four DNA nucleotides, A, T, G, and C specify one of 64 code words. These 64 code words specify a start code, three stop codes, and a redundant specification of which of the 20 amino acids should be inserted next into a partially constructed protein molecule.
The information in the DNA is not directly used to manufacture protein. Instead, the primary DNA sequence for a gene is first copied, in a process called transcription, into an intermediate form of RNA, called messenger RNA (mRNA). This copying process is under the control of an enzyme complex called RNA polymerase. The copying process is not automatic, and control is carefully exercised over which portions of the DNA are copied into mRNA. We will use these control mechanisms as the basis for our logic gates.
The mRNA transcript is then (often in a pipelined manner) used by an enzyme/RNA complex called the ribosome to manufacture proteins. This process of manufacturing proteins from mRNA transcripts is called translation. The protein manufacturing process is sometimes used as a control mechanism, but is far less widely used than control of mRNA synthesis. mRNA is degraded quite rapidly by the cell, and requires continual replenishment by the creation of new mRNA copies by RNA polymerase from the primary DNA gene.
Proteins are also gradually degraded within the cell, at a sequence dependent rate. The continuing presence of a particular protein thus depends upon its creation by the translation of mRNA transcripts.
