Secondary Structure and Amino Acids

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Secondary structure & amino acids Proteins are large macromolecules which are made up of a long chain of amino acids. The naturally occurring amino acids have a common structure. Amino acids, as the name implies, have two functional groups, an amino group (–NH2) and a carboxyl group (–COOH). These groups are joined to a single (aliphatic) carbon. In organic chemistry, the carbon directly attached to a carboxyl group is the alpha (α) position, so the amino acids in proteins are all alpha-amino acids. The side chains that distinguish one amino acid from another are attached to the alpha carbon, so the structures are often written as shown in Figure 1 , where R stands for one of the 20 side chains The side chains of amino acids give them their different chemical properties and allow proteins to have so many different structures. Each α-amino acid consists of a backbone part that is present in all the amino acid types, and a side chain that is unique to each type of residue. An exception from this rule is proline. Because the carbon atom is bound to four different groups it is chiral, however only one of the isomers occurs in biological proteins. Glycine however, is not chiral since its side chain is a hydrogen atom. In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure. In 1951 Linus Pauling and Robert Cory predicted the secondary structure. Secondary structure can be formally defined by the hydrogen bonds of the biopolymer, as observed in an atomic-resolution structure. In proteins, the secondary structure is defined by the patterns of hydrogen bonds between backbone amino and carboxyl groups. .. Both the
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