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Small Molecules in Biology

Small Molecules in Biology. Remember General Chemistry. Atomic structure Names and relationships of elements Interactions among atoms. Biology Occurs in the First Few Rows Figure 2.3. Chemistry is the Rearrangement of Valence Electrons Figure 2.7. Rearrangement of Valence Electrons.

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Small Molecules in Biology

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  1. Small Molecules in Biology

  2. Remember General Chemistry • Atomic structure • Names and relationships of elements • Interactions among atoms

  3. Biology Occurs in the First Few RowsFigure 2.3

  4. Chemistry is the Rearrangement of Valence ElectronsFigure 2.7

  5. Rearrangement of Valence Electrons • Outer Shells are Filled by Ionic Bonds or Covalent Bonds • ionic bonds involve exchanged electrons • covalent bonds involve shared electrons • Remember the number of bonds formed by H, O, S, N, C, P • polar covalent bonds join atoms of unequalelectronegativities

  6. NaCl is an ionic compoundFigure 2.13

  7. H2is a covalent compoundFigure 2.8

  8. Bonding capacitiesTable 2.2

  9. ElectronegativitiesTable 2.3

  10. H2O is a polar covalent compoundFigure 2.11

  11. Polar and Non-polar Covalent Compounds Do Not Interact • Non-polar covalent compounds • Polar covalent compounds • hydrogen bonds • ionic bonds • hydrophilic bonds

  12. Oil (non-polar)and Water (polar)Do Not Mix

  13. interactions of nonpolar moleculesTable 2.1

  14. Many Biological Molecules are PolarFigure 2.12

  15. bond energies of biologically important molecular interactionsTable 2.1

  16. Ionic Compounds Dissociate in an Aqueous (Polar) SolventFigure 2.14

  17. some properties of water • water (mw = 18) • is a liquid at RT • has high heat capacity • has a high heat of vaporization • dissolves polar and ionic compounds • is cohesive/adhesive to polar materials • because it is polar

  18. biological molecules come in different sizesFigure 2.9

  19. Molarity: how much stuff is in the water? • biological reactions occur in solution • molar solutions are directly comparable • 0.2 M solution of glucose • 0.1 M solution of sucrose • biological solutions • millimolar (mM) [10-3 M] • micromolar (µM) [10-6 M]

  20. Molarity: how much stuff is in the water? • standard prefixes modify molar concentrations prefixM milli 10-3 100 mM = 0.1 M micro 10-6 100 µM = 0.1 mM nano 10-9 100 nM = 0.1 µM pico 10-12 100 pM = 0.1 nM fempto 10-15 100 fM = 0.1 pM

  21. Acids/Bases and thepH ScaleFigure 2.18 pH=-log10[H+] H+ donors H+ acceptors

  22. Acids/Bases and BuffersFigure 2.19 Buffers minimize the pH change when acid or base is added

  23. Functional Groups of organic compounds • properties of molecules depend on • polarity • 3-dimensional shape • reactivity • solubility • functional groups with particular properties confer those properties on whichever molecules they are attached

  24. common functional groupsFigure 2.20

  25. isomers of organic molecules C2H6O H3C-CH2-OH H H Ethyl alcohol H-C-C-H H OH H3C-O-CH3 H H H-C-O-C-H Diethyl ether H H

  26. optical isomersFigure 2.21 1 2 4 3

  27. amino acids are optically activeHH3N+-C-COO-R

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