Chapter 3 : Organic molecules

Organic molecules - contain Carbon atoms. They are found in all living things.
Hydrocarbons - consist of only carbon and hydrogen.
	Prefix		       Suffix

Meth -     1 carbon atom     - ane    No double bonds
Eth -      2 carbon atoms									    
Prop -     3 carbon atoms    - ene    At least 1 double bond
But -      4 carbon atoms
Pent -     5 carbon atoms      ( Fig 3-1 )
Hex -      6 carbon atoms
Isomers
Isomers are compounds with the same molecular formula, but different structural formulas.
a) Structural isomers - vary in the arrangement of their atoms
b) Geometric isomers - differ around the atoms in a double bond
c) Enantiomers - are molecules that are mirror-images of each other

Different isomers have different effects on the body eg Ibuprofen, Prozac, Thalidomide Nobel Prize.

Functional groups ( Table 3-1 )
Chemical properties of molecules depend on their functional groups ( atoms on the outside of the molecule ). 
Functional   Structure	  Example      Comments
  group  

Hydroxyl     - OH           Sugars       Dissolve in water
Carboxyl     - COOH         Fatty acids  Are acid
Amino        - NH2          Proteins     Are basic ( alkali)
Phosphate    - PO4          DNA          Dissolve  & are acid
Macromolecules : very large molecules, made of hundreds, or thousands, of atoms. Most are polymers : large molecules made of similar, small monomers joined together

Hydrolysis : a chemical reaction that breaks polymers into monomers eg digestion
Condensation synthesis : a chemical reaction that joins monomers together by removing water.

There are 4 types of macromolecule in living things : carbohydrates, lipids, proteins and nucleic acids.

1). Carbohydrates
Carbohydrates contain only C , H and O. They are made of simple sugars called monosaccharides (Fig 3-6) such as glucose (C6H12O6) and glyceraldehyde (C3H6O3). Monosaccharides dissolve in water.

Disaccharides consist of 2 monosaccharides joined by condensation synthesis such as maltose or brewing sugar (2 glucose) and sucrose or table sugar (glucose + fructose . Monosaccharides and some disaccharides react with Benedicts reagent.

Polysaccharides are made of many monosaccharides, such as :
2). Lipids
Lipids contain C , H , and O. They do not dissolve in water. Lipids can be fats, phospholipids , waxes or steroids.

A) Fats ( triglycerides ) Fig 3-12.
They are made of glycerol and 3 fatty acids. Fats are used for energy storage and insulation.

Saturated fats : no double bonds (only single bonds); straight molecules; solids; found in animals; eg butter.
Eating a lot of saturated fat increases your risk of heart attack.

Unsaturated fats : have 1 or more double bonds; bent molecules; liquids; in plants; eg corn oil.
Unsaturated fats are more healthy for you than saturated.

Some foods, like margarine, cookies and snack foods are hydrogenated (have hydrogen added to them) to make them more solid. This produces trans fat which is as bad for you as saturated fat. Since January 2006, food labels have been required to list any trans fat in the food.

B) Phospholipids Fig 3-13
Phospholipids are made of glycerol, 2 fatty acids and phosphate. Part of the molecule is hydrophobic, part is hydrophilic.
Phospholipids make up most of the cell membrane.

C) Waxes
Waxes consist of a fatty acid joined to an alcohol.They are used for waterproofing in plants (and some animals).

D) Steroids Fig 3-15
Steroids are made of 4 rings of carbon. They form sex hormones eg estrogen, testosterone. Animals often need small amounts in their diet eg cholesterol. Drugs in world athletics. High levels of steroids can damage the brain.

3). Proteins
Proteins contain C , H , O and N. They are made of amino acids joined together with a peptide bond. There are 20 different amino acids (Fig 3-16 do not learn the names). The order of amino acids in a protein is important (see sickle cell anemia below).
Primary structure : the order of amino acids (Fig 3-19)
Secondary structure : the protein folds, and is held by hydrogen bonds (Fig 3-20)
Tertiary structure : covalent or ionic bonds between different side chains of the protein.
Sickle cell anemia : an often fatal genetic disease caused by one amino acid in the wrong place in the protein hemoglobin.

Proteins are unusual because their shape is mainly affected by hydrogen bonds which are weak. This means that if a protein is heated it denatures : the shape changes. For example if you boil an egg (which contains lots of protein) it changes from a raw egg to a cooked egg because the proteins are denatured. This denaturing will usually kill a cell. Proteins are found in cell membranes, blood, hair, enzymes and muscles.

4). Nucleic acids
Nucleic acids contain C , H , O , N and P. They are made of nucleotides, ( phosphate, sugar and base ) Fig 3-24

DNA ( Deoxyribonucleic acid ) DNA has deoxyribose as the sugar. It has 4 bases : 

	Adenine		Thymine	
	Guanine		Cytosine
DNA bases pair up and join with hydrogen bonds to form a double helix. The code on DNA carries information the cell needs to make proteins ( the primary structure).

DNA can be used in vaccines. DNA vaccine Closely related animals have similar DNA. Humans and primates. A new study will trace human migrations by looking at DNA. DNA study

RNA ( ribonucleic acid )
RNA has ribose as the sugar. It also has 4 bases : with Uracil instead of Thymine.

RNA is a single strand. RNA moves from the nucleus of the cell to the cytoplasm to allow the cell to make proteins ( mRNA : messenger RNA ). New RNA drugs could be very useful, for example to prevent blood clots, or treat cancer.RNA drugs

 Last edited August 2009, by David Byres, dbyres@fccj.edu