Biochemical Engineering Fundamentals, Part 1 - Bailey J., Ollis D. 1989

Chemical Foundations of Life
Amino Acids and Proteins
Primary Structure

The Introduction/19.html">Primary Structure of a protein refers to its characteristic sequence of amino acid residues. Insulin was the first protein for which the complete primary structure was determined (Sanger et al., 1955). It is now well established that any given protein is characterized not only by a specific Amino Acid Composition, but also by a unique Amino Acid Sequence. As we will see below (Section 6.1), this sequence is determined by The nucleotide sequence of DNA.

A detailed Study of the Methods used to determine Amino acid sequences is beyond The Scope of this book, so we will limit ourselves to only the most General Overview. There are many methods for cleaving a protein into various polypeptide fragments. For example, Enzymes are known that can cleave bonds between specific amino acid residues. The amino acid sequence of the resulting relatively short polypeptide chains can then be determined using methods developed by Sanger and other researchers. The known, partially overlapping sequences of these protein fragments are then aligned and combined to ultimately reconstruct the complete amino acid sequence of the entire protein. Automated protein sequenators utilizing a spinning cup reaction vessel can sequentially determine up to 100 amino acid residues in a chain, requiring about 2 hours to identify a single residue. The recently introduced gas-phase method has significantly reduced The amount of protein required for sequencing. For example, determining the complete primary structure of a 50-residue polypeptide requires 50—100 picomoles of material on a gas-phase sequenator, compared to 1—5 nanomoles on a spinning-cup analyzer. As we will see later in Chapter 6, the amino acid sequence of a protein can also be deduced indirectly from the experimentally determined nucleotide sequence of its corresponding Gene.

At present, the amino acid sequences of many Polypeptides and Proteins are known. So far, no repeating regions with identical sequences have been found in proteins, although some data suggest that such a pattern may occur in certain Fibrous proteins. As an example, Fig. 2.17 shows the amino acid sequence of hen egg-white Lysozyme. As we have repeatedly noted, the numbering of amino acid residues begins at the N-terminus (Lysine, in this case) and ends at the C-terminal residue, which in this enzyme is leucine.

The side chains of amino acid residues interact with one another and with the protein's immediate environment, thereby determining the geometric configuration of the protein molecule. The folding of the polypeptide chain into a highly specific three-dimensional structure results in a protein molecule of complex, intricate shape, such as that shown in Fig. 2.17,b for lysozyme. This complex spatial arrangement of the protein is determined primarily by its primary structure.

The Significance of the Primary Structure of Proteins becomes especially clear when we consider that it is, in turn, determined by The Cell's coding system (Section 6.1). Thus, the amino acid sequence of proteins serves as the link connecting the cell's master control center, DNA, with the complex, highly specific protein molecules that carry out and regulate the diverse biochemical processes essential for cell growth and survival.

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FIG. 2.17. a — amino acid sequence or primary STRUCTURE OF THE hen egg-white lysozyme enzyme; b — three-dimensional (tertiary) structure of the crystalline lysozyme molecule. [Reproduced with permission of the author and publisher from: Blake, C. C. F., Structure of Hen Egg-White Lysozyme; Nature, 206, 757 (1965).]