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 Figure 4 Hydrogen bonding between two peptide links. |
3.2 Secondary structure Secondary structure is the term protein chemists give to the arrangement of the peptide backbone in space (conformation). The backbone can form regular, repeating structures held together by the attractions between peptide links along it. Structural proteins (e.g. skin, hair and nails) have their polypeptide chains twisted regularly and arranged in bundles or sheets. Protein chemists call them fibrous proteins. Other, more water soluble proteins such as enzymes have their polypeptide chains twisted and folded with less regularity to form molecular `blobs’. Protein chemists call these globular proteins. The fibrous proteins have extensive regions of regular secondary structure. In general globular proteins have many small regions of regular secondary structure. |
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 Figure 5 The geometry of a peptide link. Ca refers to the a carbon atom: the one to which both COOH and NH2 are joined |
Hydrogen bonding is one of the main sources of attraction between the backbone peptide links.
For the hydrogen bond to have its maximum strength (approximately 25 kJ mol-1) the C=O and N-H groups must be arranged in space so that the O, H and N atoms lie along a straight bline (Figure 4). Bonds along the peptide backbone rotate so this can happen. There are some limits, though, on how the backbone bonds can rotate. There are three types of bond: Ca-CO, CO-N,N-Ca (see Figure 5). It is usual to draw out the peptide link showing the carbonyl group with a C=O double bond and a single CO-N bond. This is not entirely accurate since the lone pair of electrons on the N atom and the pair of p electrons from the C=O bond are, smeared out (delocalised) across all three atoms - the C, O and N. This gives the CO-N bond some double bond character and some characteristics of the C=C bond in alkenes. Delocalisation makes the bond shorter than you would expect for a single bond but, more importantly, it makes it difficult to rotate and it forces the six atoms involved in the peptide link into a single plane (figures 5 and 6). |
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 Figure 6 Delocalisation of electrons in the peptide link. |
The freedom of the Ca - CO and N - Ca bonds to rotate is not restricted in this way, but rotation may be limited by steric factors. This is where particular rotations would cause atoms to collide with each other. In general large side chain groups restrict bond rotation more than small groups. Rotations that bring together the oxygens or hydrogens from adjacent peptide links are unlikely to occur.
Proline and hydroxyproline are unusual as their peptide N atom is also part of the side chain, severely limiting rotation about the N _ Ca bond. You can picture, then, a polypeptide molecule as a chain made from flat rectangular plates (the peptide links) joined by the Ca atoms. The plates have some freedom to twist (Figure 7). |
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 Figure 7 A chain of peptide plates joined by Ca atoms. |
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Unilever Education Advanced Series: Proteins | ||||||||||
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