This would make the peptide bond rigid and unable to rotate freely, and it can only form distinct cis and trans geometric isomers. Figure 6.5 The resonance structure of the peptide bond gives it double-bond characteristics.įrom bond length measurements, Pauling first worked out that the peptide bond actually behaves more like a double bond, due to the contribution of the second resonance form of the amide (Figure 6.5). Pauling understood the importance of knowing precise atomic radii, bond lengths, angles and used these to create exact scale models of possible structures. The structural basis of these repeated distances were worked out by Linus Pauling. For example, the hydrogen atom and the C-H bond are both about 1 Å in size. The angstrom unit (Å), 1 x 10 -10 meter, is a measure of distance commonly used for atomic structures. X-ray diffraction gave the following measurements for repeating patterns: Since different wavelengths are deflected at different angles, white light breaks up into a spectrum. The music is recorded on the CD as a pattern of closely spaced dots, and the dots are spaced at a similar distance to light wavelengths. Visible light can also be diffracted, for example, a spectrum of colours can be seen reflected from the back of a compact disk. However, detailed theory of X-ray diffraction is beyond the scope of this book. X-ray diffraction is discussed in Stryer Section 27.1.1. Figure 6.4 X-ray diffraction is used to determine the atomic structure of molecules. If the X-ray wavelength is known, the size of the repeating pattern in the protein can be calculated. Since X-rays have the same dimensions as atoms and bonds, repetitive features in molecular structure can be detected. The reflected X-rays form a characteristic pattern if the repetitive spacing in the sample is comparable to X-ray wavelengths (Figure 6.4). The keratins were studied by X-ray diffraction, a technique in which X-rays are reflected off a regular repetitive structure such as a crystal or fibre of protein. Β-keratin or fibroin – spider and silkmoth silk. Α-keratin – protein of hair, skin and wool Orderly arrangements of the polypeptide backbone were first studied by examining fibrous proteins called keratins: The organization of the native state places amino acids in 3-dimensional space in the arrangement required for proper function, and this poses the question of why any special patterns should exist at all. Most proteins also have an ordered arrangement called the native state. Because there is no orderly arrangement, denatured protein is non-functional. Proteins become denatured at elevated temperature or in the presence of disruptive solvents. This is called the denatured state of the protein. All polypeptides can adopt a form which is flexible, but it is random and disordered in bond orientation. Figure 6.3 A chain made up of only single bonds is highly flexible.Ī chain made only of single bonds is highly flexible (Figure 6.3). Instead, different shapes are obtained by rotation about the axis of single bonds (Figure 6.2). Figure 6.2 Different shapes in chain structures occur by rotation about the axis of single bonds.įlexing in a covalent chain structure does not occur by bending bonds, or can be achieved while the normal tetrahedral or trigonal planar bond angles are maintained. Therefore, it should be as flexible as a simple hydrocarbon chain. On first inspection, this structure appears to be connected entirely by single C-C or C-N bonds (Figure 6.1). The polypeptide chain forms a backbone structure in proteins. Why is there a pattern? Figure 6.1 The backbone of polypeptides appears to be connected by single bonds. Secondary structure is the occurrence of regular repetitive patterns, such as α-helix, over short sections of the polypeptide chain. Amino acid can be grouped in three classes: amino acids with bulky side chains prefer to form β-sheet, a second group of amino acids have side chains that disrupt secondary structure and the remaining amino acids tend to form α-helix. The particular secondary structure is dependent on the local amino acid sequence. Two arrangements result in regular repetitive structure, α-helix and β-sheet. Synopsis: The polypeptide backbone flexes by rotation about its single bonds.
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