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 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 unequal electronegativities

NaCl is an ionic compound Figure 2.13

H 2 is a covalent compound Figure 2.8

Bonding capacities Table 2.2

Electronegativities Table 2.3

H 2 O is a polar covalent compound Figure 2.11

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

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

interactions of nonpolar molecules Table 2.1

Many Biological Molecules are Polar Figure 2.12

bond energies of biologically important molecular interactions Table 2.1

Ionic Compounds Dissociate in an Aqueous (Polar) Solvent Figure 2.14

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

biological molecules come in different sizes Figure 2.9

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]

Molarity : how much stuff is in the water? standard prefixes modify molar concentrations prefix M milli mM = 0.1 M micro µM = 0.1 mM nano nM = 0.1 µM pico pM = 0.1 nM fempto fM = 0.1 pM

Acids/Bases and the pH Scale Figure 2.18 pH=-log 10 [H + ] H + donors H + acceptors

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

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

common functional groups Figure 2.20

isomers of organic molecules C 2 H 6 O H 3 C-CH 2 -OH H H Ethyl alcohol H-C-C-H H OH H 3 C-O-CH 3 HH H-C-O-C-H Diethyl ether HH

optical isomers Figure

amino acids are optically active H H 3 N + -C-COO - R