BIOC12H3 Study Guide - Midterm Guide: Pyranose, Glycocalyx, Collagen
1 Dec 2016
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Document Summary
Modelling 3-d structures: space-filling: to show surface ligand binding, ball-and-stick: to show bonding arrangement, backbone: to show general course of polypeptide chain, cartoon ribbon: shows folding (no side chains) Amide bond is shorter than normal c-n bond and rotation around bond is restricted due to resonance with carbonyl. N has partial + and c has partial . Peptide group = carbonyl + amide (with h) + adjacent alpha carbons. Can rotate around alpha carbon pivot; 0 deg means protein is in cis conformation. 108 deg when protein is fully extended (trans) Capping of n-h and c-o groups for hydrogen bonds providing a pitch distance of 5. 4 . Alpha helix has a net dipole in the c n direction. Helix may have hydrophilic amino acids on one face and hydrophobic on the opposite face (amphipathic) Proline disrupts right hand helix, glycine/serine destabilizes due to unconstrained rotation, and bulky side chains such as asparagine and tyrosine are less common in alpha helix.
