Small Molecules in Biology
Remember General Chemistry
• Atomic structure
• Names and relationships of elements
• Interactions among atoms
Biology Occurs in the First Few RowsFigure 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
compoundFigure 2.13
H2
is a covalent
compoundFigure 2.8
Bonding capacitiesTable 2.2
ElectronegativitiesTable 2.3
H2O is a polar covalent compoundFigure 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 moleculesTable 2.1
Many Biological Molecules are PolarFigure 2.12
bond energies
of biologically important molecular
interactionsTable 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 sizesFigure 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 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
Acids/Bases and the
pH ScaleFigure 2.18
pH=-log10[H+]
H+ donors
H+ acceptors
Acids/Bases and BuffersFigure 2.19 Buffers
minimizethe 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
groupsFigure 2.20
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
optical isomersFigure 2.21
1
2
3
4
amino acids
are optically
active
HH3N+-C-COO-
R
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