Carbon
Organic chemistry is the branch of chemistry that specializes in the study of carbon
compounds.
Organic molecules are molecules that contain carbon.
The carbon atom
Has an atomic number of 6; therefore has 4 valence electrons.
4 valence electrons means that carbon completes its outer energy shell by
forming 4 covalent bonds.
The tetravalent electron configuration makes large, complex molecules possible,
with the carbon atom at a central point from which the molecule branches off in 4
directions.
This electron configuration also gives carbon covalent compatibility with many
different elements.
The 4 major atomic components of organic molecules are:
Hydrogen
Valence of 1
Oxygen
Valence of 2
Nitrogen
Valence of 3
Carbon
Valence of 4
Fig 4.3
The electron configuration of carbon determines the molecule’s three-dimensional
shape. Three-dimensional shapes are important to function.
Fig 4.2
Variations in carbon skeletons contribute to the diversity of organic molecules.
Covalent bonds link carbon atoms together in long chains that form the skeletal
framework for organic molecules. These vary in:
Length
Shape (straight chain, branched, rings)
Number and location of double bonds
Other elements covalently bonded to available sites
Fig 4.4
Hydrocarbons = molecules containing only carbon and hydrogen
Fossil fuels
Diverse in lengths and shapes
Hydrocarbons are hydrophobic because of nonpolar bonds, C-C and C-H
Fig 4.5
Isomers are compounds with the same molecular formula but with different structures
and hence different properties.
There are 3 types of isomers:
1
Structural isomers = isomers that differ in the covalent arrangement of
their atoms. Number of possible isomers increases as the carbon skeleton size
increases.
Geometric isomers = isomers which share the same covalent
partnerships but differ in their spatial arrangements. This is due to the fact that double
bonds will not allow the atoms they join to rotate about the axis of the bonds.
Enantiomers = isomers that are mirror images of each other. Can occur
when four different atoms or groups of atoms are bonded to the same carbon
(asymmetric carbon). There are 2 different spatial arrangements. Often one form is
biologically active and the other is not.
Fig 4.6
Fig 4.7
Functional groups
Functional groups also contribute to the molecular diversity of life.
Small characteristic groups of atoms (functional groups) are frequently bonded to
the carbon skeleton of organic molecules. These functional groups:
Have specific chemical and physical properties
Are the regions of organic molecules that are chemically reactive.
Behave consistently from one organic molecule to another.
Determine the unique chemical properties of organic molecules in which
they occur.
These molecules can be viewed as hydrocarbon derivatives with functional groups in
place of H, bonded to carbon at various sites along the molecule.
Hydroxyl group = a functional group that consists of a hydrogen atom bonded to an
oxygen atom, which in turn is bonded to carbon (-OH).
It is a polar group, the bond between the oxygen and hydrogen is a polar
covalent bond.
Polarity makes the molecule to which it is attached water soluble.
Organic compounds with hydroxyl groups are called alcohols.
Carbonyl group = functional group that consists of a carbon atom double-bonded to
oxygen (-CO)
It is a polar group, water soluble
Is a functional group found in sugars
If the carbonyl is at the end of the carbon skeleton, the compound is an
aldehyde--if in another region of the skeleton it is a ketone.
Carboxyl group = functional group that consists of a carbon atom which is both doublebonded to an oxygen and single-bonded to the oxygen of a hydroxyl group (-COOH)
Polar and water soluble. The covalent bond between oxygen and hydrogen is so
polar that the hydrogen reversibly dissociates as H+. The polarity results from the
combined effect of the 2 electronegative oxygen atoms bonded to the same carbon.
2
Since it can donate protons (H+ ions), this group is acidic, and these compounds
are called carboxylic acids.
Amino group = functional group that consists of a nitrogen atom bonded to two
hydrogens and to the carbon skeleton (-NH2)
Polar and water soluble
Acts as a weak base because the nitrogen can accept a proton (H+).
These compounds are called amines
Sulfhydryl group = functional group that consists of an atom of sulfur bonded to an
atom of hydrogen (-SH).
Helps stabilize the structure of proteins (disulfide bridges)
These compounds are called thiols.
Phosphate group = functional group which is the dissociated form of phosphoric acid
(H3PO4)
Loss of 2 protons (H+) by dissociation leaves the phosphate group with a
negative charge.
Has acid properties since it donates protons
Polar and water soluble
Organic phosphates are important in cellular energy storage and transfer (e.g.
ATP).
Methy group = functional group that consists of a carbon bonded to 3 hydrogen atoms.
Nonpolar and not water soluble
3