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Introduction

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High-Yield Terms

  • Fibrous protein: any protein that is generally insoluble in water and exists in an elongated and rigid conformation; most structural proteins are fibrous

  • Globular protein: any protein that is generally soluble in water and exists in more compact spherical conformation; most functional proteins are globular

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Primary Structure in Proteins

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The primary structure of peptides and proteins refers to the linear number and order of the amino acids present. The convention for the designation of the order of amino acids is that the N-terminal end (ie, the end bearing the residue with the free α-amino group) is to the left (and the number 1 amino acid) and the C-terminal end (ie, the end with the residue containing a free α-carboxyl group) is to the right.

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Murray RK, Bender DA, Botham KM, Kennelly PJ, Rodwell VW, Weil PA. Harper's Illustrated Biochemistry, 29th ed. New York, NY: McGraw-Hill; 2012.

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Secondary Structure in Proteins

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The ordered array of amino acids in a protein confers regular conformational forms upon that protein. These conformations constitute the secondary structures of a protein. In general, proteins fold into 2 broad classes of structure termed globular proteins or fibrous proteins. Globular proteins are compactly folded and coiled, whereas, fibrous proteins are more filamentous or elongated. It is the partial double-bond character of the peptide bond that defines the conformations a polypeptide chain may assume. Within a single protein, different regions of the polypeptide chain may assume different conformations determined by the primary sequence of the amino acids.

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The α-Helix

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The α-helix is a common secondary structure encountered in proteins of the globular class. The formation of the α-helix is spontaneous and is stabilized by H-bonding between amide nitrogens and carbonyl carbons of peptide bonds spaced 4 residues apart. This orientation of H-bonding produces a helical coiling of the peptide backbone such that the R-groups lie on the exterior of the helix and perpendicular to its axis (Figure 5-1).

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FIGURE 5-1:

Orientation of the main chain atoms of a peptide about the axis of an α helix. Murray RK, Bender DA, Botham KM, Kennelly PJ, Rodwell VW, Weil PA. Harper's Illustrated Biochemistry, 29th ed. New York, NY: McGraw-Hill; 2012.

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Not all amino acids favor the formation of the α-helix due to steric constraints of the R-groups. Amino acids, such as A, D, E, I, L, and M, favor the formation of α-helices, whereas, G and P favor disruption of the helix. This is particularly true for P since it is a pyrrolidine-based imino acid (HN=) whose structure significantly restricts movement about the peptide bond in which it is present, thereby, interfering ...

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