Organic chemistry - study of carbon-containing compounds
Hydrocarbons - compounds made of only carbon and hydrogen
Biochemistry - organic chemistry involved in life processes


(1) Single bond


Each - represents 2 electrons

(2) Double Bond                 H-C=C-H
                                                H H

Double and triple bonds are referred to as "unsaturated"
Unsaturated fatty acids have double bonds. Polyunsaturated means several double bonds. Saturated fatty acids have no double bonds - saturated with hydrogens

(3) Triple Bond             H-C/ C-H


(1) Molecular formula-number and kinds of atoms, but no idea what it looks like C4H10

(2) Structural formula - order of attachment of atoms in a molecule.

     H H H H
H-C-C-C-C-H                             CH3CH2CH2CH3
H H H H                                  Condensed structural formula
expanded structural formula

(3) Dimensional formula - geometry stressed. Important biochemically to fit in the active sites of enzymes.


Types of reactions

1. Isomerization Isomers have the same molecular formula but the atoms are arranged differently. Both glucose & fructose have the same formula C6H12O6 but they are different sugars.

2. Hydrogenation Adding hydrogen atoms to the compound. Plant oils have a lot of unsaturated fatty acids and they are liquid. To make solid shortening (solid Crisco), or solid margarine, hydrogen atoms are added across the unsaturated bonds of the plant oils. When this is done, some of the new fatty acids have a different configuration in space and are called >trans= fatty acids. These are bad for health


3. Dehydrogenation Taking away hydrogens to make a double bond or to give the hydrogens to another compound.

Hydrogenation/dehydrogenation reactions are very important in biochemistry. We make energy called ATP by these transfers.

4. Hydration Adding a water molecule


5. Dehydration Taking a water molecule out


6. Halogenation Adding chlorine, fluorine, bromine, or iodine to a compound.


7. Deamination Amines have Nitrogen. Ammonia is NH3. To deaminate a compound means to take the N containing group off. Amino acids have NH2 groups.

8. Oxygenation To add oxygen






gain of oxygen

 loss of oxygen

loss of hydrogen

 gain of hydrogen

loss of electrons

 gain of electrons

Ca ---> Ca++

Organic compounds have endings that tell what type of compound they are. Alkanes end in Aane@

so pentane is a 5 carbon alkane. Alcohols end in Aol@ so pentanol is 5 carbon alcohol.


Number of carbons:    meth = 1      eth = 2      prop = 3    but = 4      pent = 5     hex = 6    hept = 7
                                  oct = 8         non = 9     dec = 10

Classes of compounds:

alkanes end in >ane=


 octane is an 8 carbon alkane

alkenes end in >ene=

 pentene is a 5 carbon alkene

alkynes end in >yne=  

butyne is a 4 carbon alkyne

alcohols end in >ol=

 ethanol is a 2 carbon alcohol

acids end in >oic acid=

 pentoic acid is a 5 carbon acid

aldehydes end in >al=

 methanal is a 1 carbon aldehyde

ketones end in >one=

 butanone is a 4 carbon ketone

amines just say amine

 methyl amine

ethers just say ether

 methyl ethyl ether

esters end in >oate=

 pentyl ethanoate


Alkanes are hydrocarbons having hydrogen and carbon and have the formula CnH2n+2

pentane             C5H12                  H   H   H   H     H
                                            H C - C - C - C - C H
                                                H   H   H   H    H

CH4 is methane take away 1 hydrogen -CH3 is called methyl
C2H6 is ethane take away 1 hydrogen - C2H5 is called ethyl
C3H8 is propane take away 1 hydrogen - C3H7 is called propyl

What would be butyl?

What would be pentyl?

    H    H   H   H    H
H C - C - C - C - C H
    H    H    |    H    H

short hand representation

C - C - C - C - C

            These two formulas are called 3-methyl pentane. Why?


Just like alkanes but with one or more double bonds.

C - C - C - C- C = C - C             2- heptene             The 2 tells where the double bond is. Count from
                                                     the lowest number 5- heptene and 2- heptene are the same.

C - C = C - C = C - C - C           2,4-heptadiene diene = 2 double bonds triene = 3 double bonds


Just like alkanes but with a triple bond. We don=t see them in biochemistry



Have OH groups. Very important in biochemistry.

C - C- OH ethanol

C - C - C-OH propanol

C- OH methanol (fill in the extra bonds with H=s)

OH groups hold water loosely. Glycerol is used to retain moisture. Hydrogen bonding with H2O

C - OH
C - OH <----- This is glycerol. It is the backbone for triglycerides
C - OH            C - O - fatty acid
                                    C - O - fatty acid           This is a triglyceride. If the bottom fatty acid
                                     |                                    is replaced with a phosphate group PO4 , it
                                    C - O - fatty acid           becomes a phospholipid. If choline is attached
                                                                          to the phospho group, it becomes phosphatidyl
                                                                          choline or LECITHIN


The sugars have many alcohol (OH) groups

C =O

































ribose found in RNA

deoxyribose found in DNA


Reactions of alcohols

1) Take out a water - dehydrase get a double bond

2) Add a water across a double bond to get an alcohol


3) Oxidize to an aldehyde                     H
                                                        HCOH             HC=O
                                                        HCOH             HCOH
                                                        HCOH             HCOH
                                                            H                      H
                                                        glycerol         glyceraldehyde

4) Oxidize to an acid                             H
                                                        HCOH             HOC=O
                                                        HCOH             HCOH
                                                        HCOH             HCOH
                                                            H                     H
                                                        glycerol             glyceric acid

5) Oxidize to a ketone                         H                      H
                                                        HCOH             HCOH
                                                        HCOH             HC=O
                                                        HCOH             HCOH
                                                            H                      H
                                                        glycerol             acetone

We see these types of reactions when glucose gets oxidized to carbon dioxide and water.

Every time a compound gets oxidized, another compound gets reduced.

In the oxidation of sugars the compounds that get reduced are NAD and FAD, which go to NADH and FADH. This is tied to phosphorylation - adding a phoshpate group.



Oxidative phosphorylation

The sugars get oxidized. NAD and FAD get reduced to NADH & FADH which are in the mitochondria (the energy producing part of the cell).

ADP (adenosine diphosphate) goes to ATP (adenosine triphosphate) ATP is the energy of the cell

C6H12O6 + 6 O2 ---------> 6 CO2 + 6 H2O + 30 ATP


- C=O The carbon has a double bond with oxygen and also a single bond with a hydrogen atom
Simpliest is methanal HC=O also known as formaldehyde. One teaspoon of formaldehyde can cause blindness. In the old days of stills, people actually became 'blind drunk'. Instead of having only ethanol (2C) some methanol was formed (1C). The methanol got oxidized to formaldehyde. Draw the structures of methanol and methanal. Was the oxidation reaction due to a gain of oxygen or a loss of hydrogen?

                                                                    H                         C=O
                                                                    C=O                   HCOH
                                                                    HCOH                HOCH
                                                                    HCOH                HCOH
                                                                       H                     HCOH
                                                                   glyceraldehyde         glucose

Aldehydes get oxidized to acids.

   H  H                                                       H OH
H C-C=O     +     O2     ----------->     HC-C=O             CH3 CHO -----> CH3COOH
   H                                                          H
ethanal                                                 acetic acid
                                                           ethanoic acid

Another name for acetic acid is vinegar. Fermentation process - sugar --> ethanol

Oxidation continues ethanol ---> ethanal ---> vinegar



C                   The carbon that has the double bond with oxygen also has to have 2 other carbons
|                     attached to it. The simpliest ketone has 3 carbons propanone (a.k.a. acetone
C=O             & dimethyl ketone)
|                                         Fructose has a ketone group.
C                                                         COH
acetone                                                C=O

Biochemically we see ketones

1) as ketone sugar - fructose
2) intermediate in glycolysis - dihydroxyacetone phosphate & pyruvate (pyruvic acid)
3) intermediate in citric acid cycle - a ketoglutarate & oxaloacetic acid
4) amino acids going to a keto acids
5) ketone bodies in blood



                                                  OH                                                                    O-
|                                                                        |
The acid group is -COOH         -C=O         Only the H from the OH comes off. -C=O

HCOOH     methanoic acid     aka formic acid     If the H comes off it is called formate

H3CCOOH     ethanoic acid     aka acetic acid     If the H comes off it is called acetate.


Acetate is the precursor for

1. the Krebs Cycle aka Tricarboxylic Acid or Citric Acid Cycle Acetate comes into this pathway and 2 carbon dioxides come off every time the cycle turns and 10 ATP=s are formed. See sheet

2. synthesis of fatty acids

3. synthesis of sterols - cholesterol, bile acids, hormones

4. the formation of glycine, an amino acid.



R - C

Palmitic 16:0
Stearic 18:0
Oleic 18:1

Where is the double bond?
If you count from carboxyl group is at carbon 9 it is delta Δ9
If you count from the methyl group is also at 9 omega ω 9

Δ 9 organic chemistry
ω 9 biochemistry

Polyunsaturated Fatty Acids

linoleic 18:2 ω6,9
linolenic 18:3 ω3,6,9
Arachidonic 20:4 ω6,9,12,15

All three used to be called essential fatty acids. Now 18:2 and 18:3. Needed for growth.

Linoleic -----> arachidonic

Draw 18:2 ω6,9

Omega 3 Fatty Acids

Monkeys fed high cholesterol diets developed atherosclerosis giving rise to a correlation between high fat diets and heart disease. Eskimo diets were very high in fat, yet they had a low incidence heart attacks. Eskimo diets had a five fold excess of omega 3 fatty acids compared to the diets of the Danes. This prompted research into the omega 3 fatty acids.

SFA                                         fully Saturated Fatty Acids
MUFA                                     MonoUnsaturated Fatty Acids
PUFA                                      PolyUnsaturated Fatty Acids
EPA                                         EicosaPentanoic Acid 20:5 Very high concentrations in fish: anchovies,
DHA                                        DocosaHexanoic Acid 22:6 herring, sardines, fresh tuna, whitefish.

Diets high in omega 3 fatty acids :

Normalized blood pressure
Reduced triglycerides
Slower progression of atherosclerosis
Enhanced defenses against cancer

Diets too high in omega 3 fatty acids:

Increased susceptibility to strokes to the same extent it reduces heart attacks
Can precipitate vitamin E deficiency

Trans Fatty Acids

Trans refers to the spacial arrangement of the carbon atoms. A trans configuration gives a 'kink' in the molecule. The trans formation is found in ruminant fat, made by microorganisms in thr rumen. The major source is due to an artifact in the hydrogenation of unsaturated fatty acids.

Trans fatty acids are metabolized like the saturated fatty acids. It is though that the trans may antagonize the metabolism of the essential fattya cids and make the deficiency worse.

Trans raises the LDL cholesterol levels and lowers the HDL cholesterol levels, has an increase in cancer. On autopsy 15% of the fatty acids were found to be trans.


C20 comes from arachidonic acid Put in where the double bonds would be if the prostaglandins come from arachidonic acid.

Prostanoic Acid

Function as hormones: raising or lowering blood pressure, constricting or dilating vessels, or muscle contraction.


Amines generally have an unpleasant odor.

Amines have NH2 groups. Amines are basic in nature. Amino acids have an acid group and an amine group. These are polar groups, so amino acids are soluable in polar solvents, ie blood.

H - C - N-H is methyl amine CH3NH2
H    N

H - C - C = O is glycine, the simpliest amino acid. Circle the amine and acid groups.
       |      |
   H N OH

H2N-C-NH2 is urea, a breakdown product of amino acids and proteins.

BUN - blood urea nitrogen

Positive nitrogen balance means more proteins are being made rather than being destroyed.

Negative nitrogen balance means more proteins are being destroyed than being made. Anorexia and cancer give negative nitrogen balance.


Esters generally have a pleasant odor.

acid + alcohol -------> ester + water

               O                                                            O
             2                                                           2
-C - C -OH      +      HO-CH3 -------> -C - C- O - CH3 + HOH
         acetic acid           methanol               methyl ethanoate
                                                                   methyl acetate (acetic acid is the common name)

Fatty acids + glycerol -------> triglyceride (what kind of structure do you think a TG is?)

Strawberry = ethyl butyrate

Apple = methyl butyrate

Rum = methyl formate (formic acid = methanoic acid)

Aspirin is an ester

Biochemically we see esters

1) triglycerides - glycerol + fatty acid
2) esterified cholesterol cholesterol + fatty acid


    C- O - C         dimethyl ether             C-C-O-C             is ethyl methyl ether

The old anesthetic is diethyl ether. What does it look like?

Bunny - O - Bunny Ether Bunny

Wednesday, March 21, 2007 01:28:02 PM