1Biochemistry 462a – Proteins: Secondary Structureand Fibrous ProteinsReading - Chapter 6, pp. 159-175Practice problems - Chapter 6 - #1,4 (sec. struct.), #2,3 (fibrous prots); Proteins extra problemsLevels of Protein Organization• The function of a protein can only be understood in terms of its structure. The three dimensional structures of many proteins have been determined and from these structures a few general principles can be derived. Protein structure is discussed in terms of oPrimary Structureis the amino acid sequence of its polypeptide chain(s). Every protein has a unique amino acid sequence. oSecondary Structure is the spatial arrangement of the polypeptide backbone, ignoring the conformation of the sidechains. oTertiary Structureis the three dimensional structure of the entire polypeptide. oQuaternary Structurerefers to the three dimensional structure of proteins that are composed of two or more polypeptide chains, called subunits. Secondary Structure• Recall that peptide bond has partial double bond character that forces the OCNHatoms of the polypeptide backbone to be planar. • Thus, the only degrees of freedom for rotation in the polypeptide backbone are around the bonds to the Cαcarbon - phi (φ) or psi(ψ).• However, there are significant limitationsas to which angles of φandψ can be used due to steric clashes between atoms. A Ramachandran Plotshows those regions of φ andψ where there are no steric conflicts.
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