Beginning Organic Chemistry for Biology Students
There is a horrendous deficiency in high school chemistry (including A.P. Chemistry): carbon compounds are ignored. Thus the burden of teaching organic- and biochemistry falls on the shoulders of biology teachers. At the end of the summer of 1993, three high school teachers of A.P.Biology sat down with the instructor of Biology 80 at UC San Diego to go over what components of organic chemistry ought to be taught to AP Biology students at the beginning of that course. A number of students in the class also contributed their insights into this process. It is also recommended that not all the following be given at once, but rather given as needed so as to not overwhelm the students.
ORGANIC CHEMISTRY
(The following assumes a chalk-talk for further explanation.)
This type of chemistry covers most compounds that contain the element carbon. (Occasionally however, even the single-carbon compounds are not considered in inorganic chemistry.)
Most high schoolers and college students have trouble with organic chemistry because suddenly they encounter molecules that are much larger than they have seen before. Despite sizes that can be overwhelming, most follow are rather simple set of rules. It is as if in earlier courses the students learned about bricks and pieces of wood. Now they are looking at whole buildings made of bricks and pieces of wood. Thus big molecules such as DNA can be understood chemically if taken in piece-meal bits. What follows are a few elementary rules dealing with (1) how to name the bits, (2) the many oxidation states of carbon, and (3) a new concept of various 3-D states.
- The concept of writing in a sort of short-hand must be mentioned. Here the method is to link together dots, which indicate carbon atoms. Since carbons usually have four bonds, any unwritten ones below are filled with H-atoms. For example: CO2 is
and | = |  |
- How many carbons are connected together in sequence:
- methane
 - ethane
 - propane
 - butane

| - pentane
- hexane
- heptane
- octane
| - nonane
- decane
- undecane
- dodecane, etc
|
- Naming the bits when carbon is in its most reduced (least oxidized state). Learn what an isomer is:
methane
 | ethane
 | propane
 | n-butane
 iso-butane  | n-pentane
 iso-pentane
 neo-pentane
|
- Alternate - approved IUPAC names - based on the longest straight chain of carbons:
| n-butane | butane |
|
| iso-butane | 2-methyl-propane |
|
| n-pentane | pentane |
|
| iso-pentane | 2-methyl-butane |
|
| neo-pentane | 2,2-dimethyl-propane |
|
| "octane" as in gasoline | 2,2,4-trimethyl-pentane |
|
- Now let's look at some oxidation states in methane, ethane, and propane and find out what "oxidized" and "reduced" means:
| Reduced and Oxidized Carbon Compounds
|
|---|
| Reduced | | ↔ | | Oxidized
|
|---|
methane cooking gas | methanol wood alcohol | methanal formaldehyde | methanoic acid formic acid | CO2
|
|
|
ethane | ethanol  grain alcohol | ethanal acetaldehyde | ethanoic acid acetic acid |
|
|
|
| propane | 1-propanol  n-propyl alcohol | propanal  | propionic acid
 |
|
| | 2-propanol isopropyl alcohol
 | propanone acetone
 | |
|
general form
 | the alcohol
 | the aldehyde
 the ketone
 | the carboxylic acid
 |
|
- Other oxidation states (not involving oxygen but rather caused by multiple bonds):
| Single bonds | Double bonds | Triple bonds
|
|---|
ethane
 | ethylene
 | acetylene or ethyne
|
propane
 | propylene
 | propyne
|
- CYCLIC MOLECULES
turn n-hexane into cyclo-hexane:
|
benzene (the basis of "aromatic" organic chemistry):
|
| | positions on ring relative to a given side group:
|
| | ortho |  | next, either side
|
| | meta |  | two carbons away, either side
|
| | para |  | opposite side of ring
|
| | remember pun: orthodox, paradox, and meta-what?
|
-
| SIDE GROUPS:
|
|---|
| -OH | alcohol |
|
| =O | ketone |
|
| -CHO | aldehyde |
|
| -COOH | carboxyl |
|
- When two "respectible" organic molecules are linked together:
| Class | Composition | Relevance
|
|---|
| ester | alcohol-acid | common in biochemistry
|
| ether | alcohol-alcohol | waxes
|
| anhydride | acid-acid | biochemical energy reactions (e.g.: ATP)
|
| hemi-acetal | alcohol-aldehyde | simple sugars
|
| acetal | alcohol-aldehyde-alcohol | polysaccharides
|
- Miscellaneous OTHER SIDE GROUPS frequently encountered in biochemistry:
| -amine | -NH2
|
| mercapto- (sulfidryl) | -SH
|
| -phosphate (phospho-) | -OPO3H2 (usually as a "phospho-ester")
|
| -sulfate (sulfo-) | -OSO3H (usually as a "sulfo-ester")
|
| HOME PAGE | TEACHERS' PAGE |