Lecture 3 - Lecture 3 Chapter 4 3-D structure of a protein...

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Lecture 3 Chapter 4 - 3-D structure of a protein is determined by its amino acid sequence – the function of a protein depends on its structure – an isolated protein usually exists in one or a small number of stable structural forms – the most important forces stabilizing the specific structures maintain by a given protein are noncovalent interactions - Conformation – spatial arrangement of atoms in a protein – possible conformations of a protein include an structural state it can achieve w/o breaking covalent bonds - Secondary structure – refers to any chosen segment of a polypeptide chain & describes the local spatial arrangement of its main-chain atoms, without regard to the conformation of its side chains or its relationship to other segments - Tertiary structure – overall 3-D arrangement of all atoms in a protein amino acids that are far apart in the polypeptide sequence and are in different types of secondary structure may interact within the completely folded structure of a protein interacting segments of polypeptide chains are held in their characteristic tertiary positions by several kinds of weak interactions between the segments - Quaternary structure – arrangement of protein subunits in 3-D complexes o Collagen – coiled coil, but one w distinct tertiary and quaternary structures: 3 separate polypeptides, called α chains, are supertwisted about each other - C α – C – N - C α peptide C-N bond is somewhat shorter than the C-N bond in a simple amine & that the atoms associated w the peptide bond are coplanar – indicated a resonance or partial sharing of 2 pairs of electrons between the carboxyl oxygen and the amide nitrogen – the oxygen has a partial negative charge & the nitrogen a partial positive charge, setting up a small electric dipole – the 6 atoms of the peptide group lie in a single plane, w the oxygen atom of the carbonyl group trans to the hydrogen atom of the amide nitrogen bc of their partial double-bond character, peptide C-N bonds cannot rotate freely – rotation is permitted around the N - C α and the C α – C bonds backbone of a polypeptide chain can thus be pictured as a series of rigid planes, w consecutive planes sharing a common point of rotation at C α – the
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