4 - Kuo, 580.221 14 Sept 2004 Concepts/Vocabulary Molecules...

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Kuo, 580.221 14 Sept 2004 1 BME 580.221 Protein Structure Lecture #04, 14 Sep 2004 Scot C. Kuo 14 Sept 2004 Kuo, 580.221 Concepts/Vocabulary • Evolution: local, rather than global, optimization – “trapped” in structural motifs • Secondary: alpha helix (H-bonds local), beta sheet; geometry & periodicity (for structural predictions) • Amino acids: zwitterion; sidechain chemistries and weak forces 14 Sept 2004 Kuo, 580.221 Specificity of An Antibody Cartoon #2 How to decipher the structure of a protein (e.g. antibody molecule)? Chemistry – What’s the connectivity of covalent bonds? 14 Sept 2004 Kuo, 580.221 Formation of peptides condensation of amino acids 14 Sept 2004 Kuo, 580.221 Notes for 2005 • In 2004, students did not have Orgo yet. • Should use molecular model kit to demonstrate: – Chirality (e.g. left-hand vs. right-hand) • Definition : Without breaking bonds, no way to reorient molecules of different chirality to super-impose identically with each other. • Only certain atoms are chiral (i.e. ‘chiral centers’). – Must be 4 bond directions (tetrahedral), or more (metal bonds) – Different things in at least 4 directions. • Example: L- vs. D- amino acids – Freedom of single-bond to rotate
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Kuo, 580.221 14 Sept 2004 2 14 Sept 2004 Kuo, 580.221 Handedness of amino acids CO-R-N , Clockwise with H visible towards you 14 Sept 2004 Kuo, 580.221 What are amino acids? Role of ‘side chain’ in the assembled peptide. Zwitterion - stable positive & negative charges at neutral pH. pK
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4 - Kuo, 580.221 14 Sept 2004 Concepts/Vocabulary Molecules...

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