Chapter 4: Life is based on molecules with carbon (organic molecules).


I.         Much of the chemistry of life is based on organic compounds

A.      organic compounds have at least one carbon atom covalently bound to another carbon atom or to hydrogen; the chemistry of organic molecules is organized around the carbon atom

B.       carbon atoms have six electrons - 2 in level 1, and 4 in their valence (outer) shell (level 2)

1.        Carbon is not a strongly electron seeking element, and it does not readily give up its electrons.  Thus carbon does not readily from ionic bonds.  It almost always shares electrons, forming covalent bonds.

2.        carbon can form up to 4 covalent bonds (and typically does form all four)

C.       wide diversity in organic compounds

1.        over 5 million identified

2.        variety partially because carbon tends to bond to carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus

·         hydrocarbons – contain only hydrogen and carbon

·         single carbon-carbon bonds allow rotation around them and lend flexibility to molecules

3.        building of organic macromolecules also leads to diversity

·         carbon works well as a molecular “backbone” for forming long chain molecules due to the number and strength of its bonds, particularly carbon-carbon bonds

·         stronger carbon-carbon bonds can be made with double and triple covalent bonds

·         carbon chains can branch

D.      the shape of a molecule is important in determining its chemical and biological properties

1.        the 4 bonds formed by carbon are formed at 109.5 degree angles from each other and form a pyramid with a triangular base called a tetrahedron

2.        when double bonds are formed the bonds are formed at angles 120 degrees apart, and they all lie in the same plane

3.        These bond angles for carbon play a critical role in determining the shape of molecules.

4.        generally there is freedom to rotate around carbon to carbon single bonds, but rotation around double bonds is not permitted

II.       Isomers are molecules that have the same molecular formula but different structures; there are two kinds of isomers

A.      structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms; example: ethanol and dimethyl ether (C2H6O)

B.       stereoisomers - substances with the same arrangement of covalent bonds, but the order in which the atoms are arranged in space is different; two important types for our use

1.       cis-trans isomers

·         associated with compounds that have carbon-carbon double bonds

·         since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in relationship to each other

·         larger items together = cis; larger items opposite = trans

·         examples: trans-2-butene and cis-2-butene

2.        enantiomers – substances that are mirror images of each other and that cannot be superimposed on each other

·         sometimes called optical isomers

·         typically, only one form of an enatiomer pair is found in and/or used by organisms

·         the enantiomers are given designations such as [(+)- vs. (−)-] or  [D- vs. L-] or  [(R)- vs. (S)-]

·         biologically important enantiomers include

§         amino acids (found in proteins) – most are L-amino acids (e.g. L-leucine, L-alanine, etc)

§         sugars – most are D-sugars (e.g. D-glucose, D-fructose, etc.)

III.     Functional groups determine most of the reactive properties (functions) of organic molecules

A.      functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond

B.       the properties of the major classes of organic compounds (carbohydrates, lipids, proteins, and nucleic acids) are determined mostly by their functional groups

C.       learn these seven functional groups (note: X here stands for the “rest” of the molecule)

1.        hydroxyl group (X-OH): polar; found in alcohols

2.        carbonyl group (X-C=O): polar; found in aldehydes and ketones

3.        carboxyl group (X-COOH): weakly acidic; found in organic acids (such as amino acids)

4.        amino group (X-NH2): weakly basic; found in such things as amino acids

5.        sulfhydryl group (X-SH): essentially nonpolar; found in some amino acids

6.        phosphate group (X-PO4H2): weakly acidic; found in such things as phospholipids and nucleic acids

7.        methyl group (X-CH3): nonpolar (thus hydrophobic); found in such things as lipids, other membrane components