The process of mapping from DNA sequence to folded protein in eucaryotes involves many steps (see Figure 3). The first step is the transcription of a portion of DNA into an RNA molecule, called a messenger RNA (mRNA). This process begins with the binding of a molecule called RNA polymerase 26 ARTIFICIAL INTELLIGENCE & MOLECULAR BIOLOGY to a location on the DNA molecule.
Exactly where that polymerase binds determines which strand of the DNA will be read and in which direction. Parts of the DNA near the beginning of a protein coding region contain signals which can be recognized by the polymerase; these regions are called promoters. (Promoters and other control signals are discussed further below.) The polymerase catalyzes a reaction which causes the DNA to be used as a template to create a complementary strand of RNA, called the primary transcript.
This transcript contains introns as well as exons. At the end of the transcript, 250 or more extra adenosines, called a poly-A tail, are often added to the RNA. The role of these nucleotides is not known, but the distinctive signature is sometimes used to detect the presence of mRNAs. The next step is the splicing the exons together. This operation takes takes place in a ribosome-like assembly called a spliceosome. The RNA remaining after the introns have been spliced out is called a mature mRNA.
It is then transported out of the nucleus to the cytoplasm, where it then binds to a ribosome. A ribosome is a very complex combination of RNA and protein, and its operation has yet to be completely understood. It is at the ribosome that the mRNA is used as a blueprint for the production of a protein; this process is called translation.
The reading frame that the translation will use is determined by the ribosome. The translation process depends on the presence of molecules which make the mapping from codons in the mRNA to amino acids; these molecules are called transfer-RNA or tRNAs. tRNAs have an anti-codon (that binds to its corresponding codon) near one end and the corresponding amino acid on the other end.
The anti-codon end of the tRNAs bind to the mRNA, bringing the amino acids corresponding the mRNA sequence into physical proximity, where they form peptide bonds with each other. How the tRNAs find only the correct amino acid was a mystery until quite recently.
This process depends on the three dimensional structure of the RNA molecule, which is discussed in Steeg’s chapter of this volume. As the protein comes off the ribosome, it folds up into its native conformation. This process may involve help from the ribosome itself or from chaperone molecules, as was described above.