8.1: Specifying a polypeptide’s sequence

You may be asking yourself, if there are so many different possible polypeptides and no inherent bias favoring the addition of one amino acid over another, what determines the sequence of amino acids within a polypeptide - presumably it is not random. Here we connect the specification of polypeptide sequence to the information stored in DNA. We begin with a description of the process in bacteria and then extend it to archaea and eukaryotes. We introduce them in this order because, while basically similar (homologous), the system is somewhat simpler in bacteria, although you might find it complex enough for your liking. We will leave most of the complexities for subsequent courses. We will consider the network dynamics of these systems and ask you to make plausible predictions about their behavior in response to various perturbations, mutations and such. A point to keep in mind is that the system is continuous. The machinery required for protein synthesis is inherited by the cell; new copies of it are synthesized as the cell grows. Each new polypeptide is synthesized in an environment full of pre-existing proteins and ongoing metabolic processes.

A bacterial cell synthesizes thousands of different polypeptides. The sequence of these polypeptides, the exact amino acids from the N-terminal start to the C-terminal end, is encoded within the organism’s DNA. The bacterial genome is a double-stranded circular DNA molecule that is (typically) millions of base pairs in length. Each polypeptide is encoded by a specific region of this DNA molecule. So, how are specific DNA regions recognized? transcribed into RNA and how is the information in DNA translated into a polypeptide?

To address the first question think back to the structure of DNA. Perhaps the one-dimensional sequence of a polypeptide could be encoded in the one-dimensional sequence of a polynucleotide chain.^[322] The question was how to translate the language of nucleic acids, sequences of four different nucleotides, into the language of polypeptides, sequences of the 22 different amino acids. As pointed out by the physicist George Gamow (1904-1968)^[323] the minimum set of nucleotides needed to encode all 20-22 amino acids is three; a sequence of one nucleotide (4¹) could encode at most four different amino acids, a two nucleotide sequence could encode (4²) or 16 different amino acids (not enough), while a three nucleotide sequence (4³) could encode 64 different amino acids (more than enough).^[324]Although the actual coding scheme that Gamow proposed was wrong, his thinking about the coding capacity of DNA influenced those who set out to experimentally determine the actual rules of the “genetic code”.

The genetic code is not the information itself, but the algorithm by which nucleotide sequences are “decoded” to determine polypeptide sequences. A polypeptide is encoded by the sequence of nucleotides. This nucleotide sequence is read in groups of three nucleotides, known as a codon. Each codons is read in a non-overlapping manner, with no spaces (that is, non-coding nucleotides) between them. Since there are 64 possible codons but only 22 different amino acids used in organisms, the code is redundant, that is, certain amino acids are encoded for by more than one codon. In addition there are three codons, UAA, UAG, and UGA, that (in most organisms) do not encode any amino acid but are used to mark the end of a polypeptide, they encode “stops” or periods (→). The amino acids selenocysteine and pyrrolysine are encoded for by stop codons that occur in a specific "context" of surrounding nucleotides.^[325]

The region of the nucleic acid that encodes a polypeptide begins with what is known as a “start” codon and continues with a number of In-frame codons until one or more of the three stop codons is reached.^[326] This "coding" sequence is known as an open reading frame, an ORF. While the information encoding a polypeptide is present in the DNA, this information is not used directly to specify the sequence of a polypeptide. The process involves an intermediate. The information in the DNA is first copied (transcribed) into an mRNA molecule. The mRNA moleculedirects polypeptide synthesis. As noted, the process of copying information from a DNA into an RNA molecule is known as transcription because DNA and RNA use the same nucleotide sequence language. In English, as opposed to molecular biology, transcription is the process of making a written copy of what someone says - the language of both is the same. In contrast polypeptides are written in a different language, amino acid sequences. The process of RNA-directed polypeptide synthesis is known as translation; it involves changing between languages, from nucleic acid-ese to polypeptide-ese.

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