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User:Benjah-bmm27/degree/2/DNW

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Proteins, DNW

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"Amino Acids, Peptides and Proteins: Chemistry, Structure and Function"

Polyamides

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nH2N-(CH2)6-NH2 + nClOC-(CH2)4-COCl(-HN-(CH2)6-NH-CO-(CH2)4-CO-)n (nylon 6,6 with amide bond in bold) + 2nHCl

Amino acids

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  • Amino acids
  • All naturally-occurring amino acids have the (S) configuration, except cysteine which is (R):
    (because of its C-S side chain, which unlike all other side chains, has a higher priority than the CO2H group)

Proteins

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Protein structure

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Amino acids by polarity and structure

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It's a secondary amino acid (AKA imino acids, although this nomenclature is disputed)
It's conformationally locked (backbone dihedral angle φ fixed to about −75°) → very rigid, loses less conformational entropy upon folding, found in turns

More protein structure

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Primary structure

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Secondary structure

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Tertiary structure

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Quaternary structure

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  • Quaternary structure: arrangement of multiple folded protein molecules in a multi-subunit complex - XRD again

Ramachandran plots

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  • UV-Vis spectroscopy can be used to determine protein concentration - aromatic amino acid side chains (K, Y, W, H) absorb UV

Supersecondary structure

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  • Supersecondary structure
    • EF hand - chiral, right-handed enantiomer only (with one exception). Aspartic acid residues bind Ca2+ (important in calcium signaling) in loop between two alpha helices.
    • Beta hairpin - major structural unit, two beta strands antiparallel
    • βαβ motif - two beta strands parallel, chiral (alpha helix either above or below plane of beta strands), only right-handed enantiomer found in nature
    • Coiled coil - left-handed(!) - HPPHPPP repeat gives 3.5 not 3.6 residues per turn, so hydrophobic seam slowly curves - myosin, keratin
    • Polyproline helix?
    • Collagen helix?
  • Plastocyanins - Cu redox centre converts between Cu(I) and Cu(II), coordination geometry of Cu is not optimal for either oxidation state, making neither favoured and thus interconversion facile. Structures: PDB 3BQV, PDB 1PNC.

Reactions

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