Unit I: Biochemistry (CH. 4)
I. Hydrocarbons

A. Carbon is the basic element of organic compounds.

-Carbon has 4 valence electrons and likes to share electrons with other atoms (including itself) to make four stable covalent bonds.

-Most common partners are hydrogen, oxygen, and nitrogen.

-Hydrocarbons are a group which have only carbon and hydrogen. These are what we use as fuel because of the huge amount of energy stored in these bonds. Living organisms can not use pure hydrocarbons but many biological compounds, especially fatty acids, have long carbon-hydrogen chains with other groups attached.

-Hydrocarbons are non-polar and are not water soluble (called hydrophobic).

B. Aliphatic Compounds (chain type or non-aromatic rings)

1. Alkanes

-Hydrocarbons in which the carbons are joined by a single non-polar covalent bond.

-Structural formula uses single lines to indicate bonds between the carbons (also hydrogens).
Ex.



-Alkanes allow for the rotation of bonded atoms around the singly bonded carbons without causing isomers. Alkanes can also make structural isomers (vary in covalent arrangement) and enantiomers (vary in spatial arrangement). See below.

-To name these compounds use the prefixes
(for the number of carbons) below and add -ane to the end of the name:

Meth- 1
Eth- 2
Prop- 3
But- 4
Pent- 5
Hex- 6
Hept- 7
Oct- 8
Non- 9
Dec- 10

2. Alkene and Alkynes-

- Alkenes have double covalent bonds between the carbons and bonds between carbons in structural formula is annotated by a double line.

- Alkynes have triple covalent bonds between the carbons. Three lines are used to indicate the triple bond in the structural formula.

- To name these compounds use the correct prefix and add -ene for an alkene and –yne for an alkyne and you must give the number carbon that the double bond/triple bond is attached to. If there are more than one double/triple bond you must add a number prefix such as di, tri, etc. to the ending and you must give the lowest numbers to those carbons with the double bonds.

- Ex.

- Considered to be unsaturated and are not able to rotate like an alkane. Allows for geometric isomers (vary in arrangement around double bonds).

C. Branched Chains and Substitute Groups

1. Alkyls -
-Branched alkanes with substitute hydrocarbon groups. Can be one to several carbons long but is always one hydrogen less than usual alkane. It is named by dropping the –ane with –yl.

Ex. C2H6 (ethane)---- C2H5 (ethyl)

-To name the whole chain you must:
a. Find the longest continuous chain of carbons for parent name.
b. Number the carbons in the chain (must number the carbons so the substitute group is the lowest number possible).
c. Identify the substituents on the chain.
d. Use the appropriate prefixes if there are more than one of a particular substituent.
e. Write down the number carbon and the type of substitute group on that carbon (follow same rules as above but add –yl at the end) in alphabetical order if more than one.
f. Write down name of carbon chain using above rules (-ane if single bond, etc.).
Ex.

• Same for alkenes and alkynes but you must number the double or triple bond so that it has the lowest number possible and place that number before alkene/alkyne name at the end.

Ex.

2. Other Substituted Compounds

-Naming of these compounds vary but usually follow rules that involve using the prefix for the number of carbons and adding the ending that pertains to the substituted groups.

-Addition of these functional groups increase the solubility of the molecules and make them more hydrophilic (more hydrogen bonding). These functional groups will give them unique properties to biological compounds.

a. Hydroxyl-
-OH added
-called alcohols when added to a carbon chain
-ending changes to –ol
Ex.

b. Carbonyl-
-have a double bonded oxygen added.
-if oxygen is at the number one of molecule it is called an aldehyde (ending with –al) if it is in the middle of the carbon chain it is called a ketone (ending with -one).
Ex.

c. Carboxyl-
-have a double bonded oxygen and a hydroxyl group (-COOH) at endo of molecule on number one carbon.
-called carboxylic acids
-ending is –oic or -ic acid.

Ex.

d. Amino Group-
-have a –NH2 group attached
-called amines
-forms amino acids (proteins)
Ex.

e. Sulfhydryl Group-
-have a –SH group attached
-called thiols
-help stabilize proteins
Ex.

f. Phosphate Group-
-have a –PO4 group attached
-essential for energy molecules and DNA
-doesn’t follow any naming pattern
Ex.

D. Cyclic Hydrocarbons and Aromatic Compounds

1. Cyclic Hydrocarbons
-When two ends of carbon chain are attached to form a ring.
-use prefix –cyclo before name of compound
-only number substitute groups if there are more than one and then by the lowest number going clockwise or counter clockwise.
-complex naming system
Ex.

2. Aromatic Compounds or Arenes-
-benzene compounds that are six carbon rings with resonating double bonds with varying substituents.
-very stable