BIOC 2580 Lecture Notes - Lecture 6: Crystallography, Physical Chemistry, Bond Order
9 Jan 2017
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Secondary structure: regular repetitive patterns such as helix, in short sections of the polypeptide chain. The polypeptide chains forms a backbone which appears to be linked by c-c and c-n singular bonds. Single bonded structures are flexible due to bond rotation. Groups connected by single bonds can rotate about bond axis. Chain flexibility arises from bond rotation, not bond bending. Normal 109 degree tetrahedral or 120 degree trigonal planor bond angles are present. Bond rotation allows the peptide chain to adopt a variety of shapes. Conformations represent states of a molecule that can be interconverted by bond rotations, without breaking covalent bonds. Configurations can only be interchanged by breaking covalent bonds, not by bond rotation. Cis and trans forms of molecules with a -c=c- double bond. Two chiral forms of amino acids (d- and l-) For macromolecules such as proteins, we are usually concerned with conformations. X-ray diffraction measures regular repeating patterns on the molecular scale.
