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Classes of Biomolecules

Classes of Biomolecules. Proteins (amino acids) Nucleic Acids – DNA & RNA (nucleotides) Carbohydrates (monosaccharides) Lipids (fatty acids) Vitamins and Cofactors Metabolites. Classes of Biomolecules. Proteins (amino acids) Nucleic Acids – DNA & RNA (nucleotides)

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Classes of Biomolecules

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  1. Classes of Biomolecules • Proteins (amino acids) • Nucleic Acids – DNA & RNA (nucleotides) • Carbohydrates (monosaccharides) • Lipids (fatty acids) • Vitamins and Cofactors • Metabolites

  2. Classes of Biomolecules • Proteins (amino acids) • Nucleic Acids – DNA & RNA (nucleotides) • Carbohydrates (monosaccharides) • Lipids (fatty acids) • Vitamins and Cofactors • Metabolites • Proteins (amino acids) • Nucleic Acids – DNA & RNA (nucleotides)

  3. Structures of the Amino Acids

  4. pK values of Amino Acids Each of these function groups contain potential donor atoms for metal ion coordination

  5. Likely Metal Ion Binding Sites Which groups are involved depends on the type of metal and on the conditions

  6. Primary Structure of Proteins • Metal ions can coordinate to: • side chain functional groups • backbone functional groups • N- and C-terminal functional groups A combination of donor atom types and geometric orientation that best matches the metal ion preferences will dictate where and how a particular metal ion binds

  7. Secondary Structure of Proteins Dashed lines indicate hydrogen bonds These bonding interactions will compete with metal ion binding

  8. Tertiary Structure of Proteins Additional side chain and backbone interactions contribute to protein folding and stability These interactions further limit the opportunities for metal ion binding

  9. Structure of a Ferredoxin The two regions of the polypeptide chain are linked together by Fe-S clusters

  10. Backbone Structure of DNA and RNA

  11. Nucleoside bases in DNA and RNA

  12. Likely Metal Ion Binding Sites N1 (in pyrimidines) and N9 (in purines) are not available for metal ion binding since these are the points of attachment to the ribose backbone in DNA and RNA Backbone phosphate groups provide a rich environment for metal ion binding

  13. Base pairing in Nucleic Acids Base pairing in DNA (and duplex sections of RNA) will prevent metal ion binding at these sites

  14. DNA Structures

  15. Transfer-RNA Structure The secondary structures of DNA and tRNA provide multiple opportunities for metal ion binding

  16. Other Biomoleculesvitamins and cofactors

  17. Other Biomoleculescofactors

  18. Summary • Proteins, nucleic acids, carbohydrates and lipids are the major groups of biomolecules • Metal ions can potentially interact with a wide range of functional groups in protein and nucleic acid structures • A optimal combination of donor atoms and coordination geometries will produce metal ion binding sites with high affinity and high selectivity • Many other biomolecules (vitamins, cofactors, metabolites) exist primarily as metal complexes

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