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