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.


  1. 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

    =


  2. How many carbons are connected together in sequence:

    1. methane
    2. ethane  
    3. propane
    4. butane  
    1. pentane
    2. hexane
    3. heptane
    4. octane
    1. nonane
    2. decane
    3. undecane
    4. dodecane, etc


  1. 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


  2. Alternate - approved IUPAC names - based on the longest straight chain of carbons:

    n-butanebutane
    iso-butane2-methyl-propane
    n-pentanepentane
    iso-pentane2-methyl-butane
    neo-pentane2,2-dimethyl-propane
    "octane" as in gasoline2,2,4-trimethyl-pentane


  3. 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
    propane1-propanol
    n-propyl alcohol
    propanal propionic acid
     2-propanol
    isopropyl alcohol
    propanone
    acetone
    general form
    the alcohol
    the aldehyde

    the ketone
    the carboxylic acid
     


  4. Other oxidation states (not involving oxygen but rather caused by multiple bonds):
    Single bondsDouble bondsTriple bonds
    ethane
    ethylene
    acetylene or ethyne
    propane
    propylene
    propyne


  5. CYCLIC MOLECULES

    turn n-hexane into cyclo-hexane:
    benzene (the basis of "aromatic" organic chemistry):
    positions on ring relative to a given side group:
    orthonext, either side
    metatwo carbons away, either side
    paraopposite side of ring
    remember pun: orthodox, paradox, and meta-what?


  6. SIDE GROUPS:
    -OHalcohol
    =Oketone
    -CHOaldehyde
    -COOHcarboxyl


  7. When two "respectible" organic molecules are linked together:
    ClassCompositionRelevance
    esteralcohol-acidcommon in biochemistry
    etheralcohol-alcoholwaxes
    anhydrideacid-acidbiochemical energy reactions (e.g.: ATP)
    hemi-acetalalcohol-aldehydesimple sugars
    acetalalcohol-aldehyde-alcoholpolysaccharides


  8. 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")


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