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Ch. 3 Notes: Organic Chemistry
Aside from water, most biologically important molecules are carbon-based (organic).
Organic Chemistry = study of C (and H) compounds.
THE CARBON ATOM
Valence Electrons: 4
Lewis Dot Structure:
.
∙C∙
∙
It makes large, complex molecules possible, due to its:
 Small size
 Ability to form up to 4 covalent bonds (single, double, or triple)
o In organic compounds, usually bonded to members of CHNOPS
 Ability to be arranged in long carbon chains = carbon skeleton
o C-C bonds are very stable
o These are the framework for organic molecules
o These determine the organic molecule’s 3-D shape, which affects its function!
Hydrocarbons = molecules made of only C’s and H’s
 Major components of fossil fuels
 Are hydrophobic because the C-C and C-H bonds are nonpolar
FUNCTIONAL GROUP = a specific combination of bonded atoms that always reacts in the
same way, regardless of the C-skeleton it is bonded to
 Are often the chemically reactive part of the molecule
 Determine the unique chemical properties of the organic molecules in which they occur
Please note that chemists use the letter R to represent the C-skeleton these groups are attached
to, which is considered the “remainder” of the molecule.
1. Hydroxyl Group = R-OH
 Polar  this makes the molecule water soluble!
 Called alcohols
2. Carbonyl Group = R-C=O
 Polar and water soluble
 Found in sugars
 If on the end of the carbon skeleton = aldehyde
 If in the middle of the C-skeleton = ketone
O
║
May also see as: R-C=O
3. Carboxyl Group = R-COOH or
 Polar and water soluble
 Can donate the last H as H+ (a proton), so it has acidic properties
 Things with these attached are often called carboxylic acids
4. Amino Group = R-NH2
May also see as: R-NH3+
 Polar and water soluble
 Acts as a weak base by accepting a proton (H+)
 Called amines
5. Sulfhydryl Group = R-SH
 Nonpolar group
 Helps stabilize structure of proteins
 Called thiols
6. Phosphate Group
 Actually the dissociated form of phosphoric acid
 Looks like:
O│
O - P – O║
O



Has acid properties
Polar and water soluble
Important for energy storage
7. Methyl Group = -CH3
 Nonpolar
 Useful in making nonpolar amino acids and in controlling genes
ISOMERS = organic molecules with the same molecular formula but with different
arrangements of atoms
 Will also have different properties
BIOMOLECULES
Polymer = (poly = many; mer = part); large molecules made of many identical or similar
subunits connected together
Monomer = a single subunit of a polymer
Macromolecule = large organic polymer
Put together by DEHYDRATION (a.k.a. CONDENSATION) reactions = reaction that link two
or more small monomers to form larger polymer by the net removal of a water molecule

An –OH is removed from one molecule and a –H is removed from the other  H2O

Each leave behind an unpaired electron on their monomer which can then be used to
create a new covalent bond between them

A Dehydration Reaction looks like:

Requires energy

Requires biological catalysts or enzymes

Hydrolysis (hydro- = water; lysis = to split); a reaction that breaks covalent bonds
between monomers by the addition of a water molecule (-OH and –H)

Ex. Digestive enzymes work this way