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10_02_10_Notes - Asn and Gln – both polar hydrogen-bond...

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1.1 Natural proteins have precise length and exact sequences of amino acids - Capable of three-dimensional folded conformation Proline – imino acid All amino acids (naturally occurring) are L amino acids (except for glycine, which does not have a stereocenter) Linkage through peptide bonds to form a polypeptide chain - Including side chain, unit of polypeptide backbone is an amino acid residue 1.2 3.80 A is the MAXIMUM length between adjacent residues 3.63 A is the length in a fully extended chain Peptide bond has partial double bond character! Length of peptide bond = 1.33 A Length of C-N single bond – 1.45 A Length of C=N double bond – 1.25 A Thus, coplanar (atoms bonded to double bond) Trans conformation is much more stable than cis, unless the following residue is Pro, which will make stability of cis comparable to that of trans 1.3 Peptide bond before pro residue is more likely to adopt a cis conformation
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Unformatted text preview: Asn and Gln – both polar, hydrogen-bond donors and acceptors Extreme pHs and high temperature Asp and Glu Asn more likely than Gln Amino groups (such as that of Lysine) can be detected by 2-4-6-trinitrobenzene sulfonate (TNBS) which absorbs at 367 nm Histidine – imadazole ring In the non ionized form, nitrogen with hydrogen atom is an electrophile and donor for hydrogen bonding, and the other hydrogen atom is a nucleophile and acceptor for hydrogen bonding Aromatic side chains – Phe, Tyr Trp Responsible for most of the UV absorbance and fluorescence properties of proteins Phe – non polar, chemically unreactive Tyr – because of OH group, electrophilic substitutions -hydroxyl group can participate in OH bonding-electrophilic attack occurs at ortho position BULKINESS increases hydrophobicity 4.1.1 – impenetrable volume of atoms are defined by van der Waals radius...
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