![]() Hydrogen bonds can be formed between different parts of a single chain that is doubled back on itself (intrachain bonds) or between different chains (interchain bonds). If the peptide chains run in the same direction (i.e., if they are all aligned in terms of their N-terminal and C-terminal ends), a parallel pleated sheet is formed.\)) in the side chain of hydroxyproline allows more hydrogen bonding in the collagen peptide, which makes connective tissues stronger. Chemistry Polymers Protein Definition Alpha Helix and Beta Sheet Alpha-Helix and Beta-Sheet Alpha-Helix and Beta-Pleated sheets are types of the secondary structure of the protein. The peptide backbone in the β-sheet is almost completely extended. The arrangement of atoms in the β-pleated sheet conformation differs markedly from that in the α-helix. How is the B -sheet different from the A -helix? The α -carbon is just outside the helix, and crowding can occur if it is bonded to two atoms other than hydrogen, as is the case with valine, isoleucine, and threonine. In the α-helical conformation, all the side chains lie outside the helix there is not enough room for them in the interior. This means that it results from the folding of a single amino acid chain. Another possibility is crowding (steric repulsion) caused by the proximity of several bulky side chains. The alpha helix is a secondary structure in proteins. Other localized factors involving the side chains include strong electrostatic repulsion owing to the proximity of several charged groups of the same sign, such as groups of positively charged lysine and arginine residues or groups of negatively charged glutamate and aspartate residues. Now, because of its secondary alpha amino group, proline introduces kinks into this alpha helix. And an alpha helix is just a coiled up polypeptide chain that kind of looks like this. It cannot fit into the α-helix because (1) rotation around the bond between the nitrogen and the α-carbon is severely restricted, and (2) proline’s α-amino group cannot participate in intrachain hydrogen bonding. Well, they both play a role in disrupting a particular pattern found in secondary protein structure called the alpha helix. The amino acid proline creates a bend in the backbone because of its cyclic structure. Proteins have varying amounts of α-helical structures, varying from a few percent to nearly 100%. Figure 4.3 shows the structures of two proteins with a high degree of α-helical content. The sidechains comprise the R groups, and dangle from the backbone like charms from a bracelet. ![]() In SI units, the pitch of the α-helix is 0.54 nm or 540 pm. The backbone comprises the amide nitrogen, the alpha carbon and the carbonyl carbon that are contributed by each amino acid unit. Analysis of -helical conformations acquired from the Protein Data Bank (PDB) demonstrates that a conformational energy function of the -helix backbone can be harmonically approximated on. Nanometers (1 nm 5 10 –9 m) and picometers (1 pm 5 10 –12 m) are the SI units used for interatomic distances. ![]() The angstrom unit, 1 Å 5 10 –8 cm 5 10 –10 m, is convenient for inter-atomic distances in molecules, but it is not a Système International (SI) unit. There are 3.6 residues for each turn of the helix, and the pitch of the helix (the linear distance between corresponding points on successive turns) is 5.4 Å (Figure 4.2). The helical conformation allows a linear arrangement of the atoms involved in the hydrogen bonds, which gives the bonds maximum strength and thus makes the helical conformation very stable. The two most common folding patterns are the alpha helix. Counting from the N-terminal end, the C-O group of each amino acid residue is hydroge n bonded to the N-H group of the amino acid four residues away from it in the covalently bonded sequence. Protein secondary structure refers to regular, repeated patterns of folding of the protein backbone. ![]() The α-helix is stabilized by hydrogen bonds parallel to the helix axis within the backbone of a single polypeptide chain. The β -pleated sheet structure can give a two-dimensional array and can involve one or more polypeptide chains. The α -helix is rodlike and involves only one polypeptide chain. The α -helix and β -pleated sheet are periodic structures their features repeat at regular intervals. ![]()
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