Chapter06

Chapter06 - BCH 4053 Summer 2001 Chapter 6 Lecture Notes...

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Chapter 6, page 1 BCH 4053 Summer 2001 Chapter 6 Lecture Notes Slide 1 CHAPTER 6 Proteins: Secondary, Tertiary, and Quaternary Structure Slide 2 Levels of Protein Structure • Primary (sequence) • Secondary (ordered structure along peptide bond) • Tertiary (3-dimensional overall) • Quaternary (subunit relationships) Slide 3 Forces Contributing to Overall Structure • Strong (peptide bond, disulfide bond) • Weak • Hydrophobic (40 kJ/mol) • Ionic bonds (~20 kJ/mol) • Figure 6.1 • Hydrogen bonds (~12-30 kJ/mol) • Dispersion (van der Waals) (0.4-4 kJ/mol)
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Chapter 6, page 2 Slide 4 Effect of Sequence on Structure • Sufficient information for folding into correct 3-dimensional structure is in the sequence (primary structure) of the protein • Experiments of Anfinsen and White on Ribonuclease • However—the “folding problem” is one of the major unsolved problems of biochemistry and structural biology Slide 5 Secondary Structure • Folding probably begins with nucleation sites along the peptide chain assuming certain stable secondary structures. • Planarity of the peptide bond restricts the number of conformations of the peptide chain. Rotation is only possible about the • C(alpha)-N bond (the Φ (phi) angle) • C(alpha)-C bond (the Ψ (psi) angle) • See Figure 6.2 Slide 6 Steric Constraints on Φ and Ψ Angles • Examine the effects of rotation about the Φ and Ψ angles using Kinemage • Download Kinemage • Download Peptide file • Note that some angles are precluded by orbital overlap: • Figure 6.3
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Chapter 6, page 3 Slide 7 Ramachandran Map • Plot of Φ versus Ψ angle for a peptide bond is called a Ramachandran Map • Ordered secondary structures have repeats of the Φ and Ψ angles along the chain. • See Figure 6.4
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This note was uploaded on 05/22/2011 for the course BCH 4053 taught by Professor Logan during the Fall '06 term at FSU.

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Chapter06 - BCH 4053 Summer 2001 Chapter 6 Lecture Notes...

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