# 3-notes - 580.221 BME Molecules and Cells L04 Protein...

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L04 Protein Structure p 1 Lecture Three – Protein Structure (1) Outline: Structure determines Function. Peptide Bond Importance of weak bonds Amino acid side chains Levels of protein structure Review : Henderson – Hasselbach Equation Henderson-Hasselbach is useful for determining pH, fractional charge, etc. Note: Typical Buffer concentrations are 10-100 mM. Typical Protein concentrations in the nM range. This means that there are plenty of protons available from the buffer. pH = pKa + log([A-]/[HA]) Some examples using Henderson-Hasselbach: pH=pKa so [A-]/[HA] = 1 and [A-] = [HA] at equilibrium pH=pKa + 1 so [A-]/[HA] = 10 and [A-] = 10*[HA] at equilibrium pH=pKa - 1 so [A-]/[HA] = 0.1 and 10*[A-] = [HA] at equilibrium Note: The Henderson-Hasselbach equation is important because it shows that most amino acids exist as zwitterions (see below). Peptide Bonds Proteins, aka polypeptides, are made up of amino acids. When amino acids link together, via peptide bonds, a protein is formed (condensation reaction – lecture 2). Peptide bonds, between N and C, are polar and planar (see large figure above). The planar character is due to resonance of the C=O double bond and the C–N bond. Because of this planar group, rotation is strictly limited to rotation of the entire group (the peptide unit) about the α -Carbons. The angles of rotation (

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## This note was uploaded on 04/15/2008 for the course BME 580.221 taught by Professor Dr.vidal during the Fall '08 term at Johns Hopkins.

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3-notes - 580.221 BME Molecules and Cells L04 Protein...

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