secondary_structure

secondary_structure - Biochemistry 462a Proteins: Secondary...

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1 Biochemistry 462a – Proteins: Secondary Structure and Fibrous Proteins Reading - Chapter 6, pp. 159-175 Practice problems - Chapter 6 - #1,4 (sec. struct.), #2,3 (fibrous prots); Proteins extra problems Levels 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 o Primary Structure is the amino acid sequence of its polypeptide chain(s). Every protein has a unique amino acid sequence. o Secondary Structure is the spatial arrangement of the polypeptide backbone, ignoring the conformation of the sidechains. o Tertiary Structure is the three dimensional structure of the entire polypeptide. o Quaternary Structure refers 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 OCNH atoms 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 C α carbon - phi ( φ) φ) or psi (ψ). (ψ). However, there are significant limitations as to which angles of φ and ψ can be used due to steric clashes between atoms. A Ramachandran Plot shows those regions of φ and ψ where there are no steric conflicts.
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2 For proteins, there are two major regions. In one the polypeptide chain adopts a
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secondary_structure - Biochemistry 462a Proteins: Secondary...

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