ORGANIC COMPOUNDS
Chapter 3
Organic compounds are so name because they were thought to be produced only by
living organisms.


Compounds containing a backbone of covalently bonded carbon atoms.
Many organic compounds are synthetic, e.g. plastics.
There are simple carbon compounds that are considered inorganic especially if they do
not contain hydrogen, e.g. CO, CO2.
Carbon atoms form an enormous variety of structures.






Four valence electrons.
Each bond can link to another carbon or another element.
Bonds are not easily broken.
Produce a variety of three-dimensional molecules.
Single bonds allow rotation; double and triple bonds do not allow rotation.
Carbon backbones have a zigzag shape.
ISOMERS
Isomers have the same molecular formula and different structural formula. Cells can
distinguish between these molecules. Normally one is biologically active and the other
not.
1. Structural isomers differ in the arrangement of their atoms.
2. Geometric isomers differ in the spatial arrangements of their atoms.
3. Enantiomers are mirror images of each other.
FUNCTIONAL GROUPS
These are groups of atoms that give distinctive chemical properties to the molecule they
become attached.

LEARN THE NAME AND STRUCTURE OF THE SEVEN FUNCTIONAL GROUPS
GIVEN ON PAGES 27 AND 28.
BIOLOGICAL MOLECULES
The major groups of biologically important molecules are carbohydrates, lipids, proteins
and nucleic acids.
Usually they are very large containing thousands of atoms: macromolecules.
Most macromolecules are polymers. These are long chains formed by linking small
organic molecules called monomers.
1. Condensation is the chemical process by which monomers are linked together.

A molecule of water is removed (dehydration synthesis).
2. Hydrolysis is the chemical process by which polymers can be degraded into
monomers.

A molecule of water is broken into H and OH and added to the broken bonds.
CARBOHYDRATES
Carbohydrates contain carbon hydrogen and oxygen in a ratio of 1:2:1.
Monosaccharides are simple sugars.




Normally containing 3 to 7 carbon atoms.
A hydroxyl group is bonded to each carbon except one.
That carbon is double bonded to an oxygen atom forming a carbonyl group:
aldhyde or ketone.
Glucose, fructose.
Dissaccharides are made of two monosaccharide units.



Two monosaccharide rings joined by a glycosidic linkage.
They can be split by the addition of water, hydrolyzed.
Maltose, sucrose.
Polysaccharides.





Repeating chains usually of glucose.
Single long chain or branched chain.
Starch is the main storage carbohydrate of plants:  1-4 linkages.
Glycogen is the main storage carbohydrate of animals:  1-4 linkages
Cellulose is a structural carbohydrate:  1-4 linkages.
Some modified and complex carbohydrates have special roles:

Galactosamine is a structural carbohydrate present in cartilage, and
glucosamine is found in chitin, in which OH groups are replaced by NH2 groups.

Glycoproteins and glycolipids are commonly found on the outer surface of
cells.
LIPIDS
Lipids are diverse group of compounds made mostly of carbon and hydrogen, with a
few oxygen atoms found mainly in functional groups.




Hydrophobic molecules.
Soluble in nonpolar solvents.
For energy storage, hormones, structure of cell membrane.
Neutral fats, carotenoids, phospholipids, waxes, steroids.
1. Neutral fats are made of glycerol and three fatty acids.






Glycerol is a 3-carbon alcohol.
Fatty acids are long unbranched hydrocarbon chain with a carboxyl group
(COOH) at one end.
Triglyceride (triacylglycerol) is a synonym for fat.
Saturated fats have a maximum number of hydrogen atoms in the chain, and are
usually are solid at room temperature.
Unsaturated fats have double bonds between some of the carbon atoms and
have less than the maximum number of hydrogen atoms.
Unsaturated fats have bends in the chains that prevent the aligning with the
adjacent chain and prevent the van der Waals forces from acting.
When a fatty acid combines with a glycerol molecule a molecule of water is removed
and an ester linkage is formed.
2. Phospholipids are similar to fats but contain a phosphate group at one end and only
two fatty acids.





The phosphate group is bonded to an organic molecule that varies, e.g. choline,
lecithin.
The fatty acid chains are hydrophobic.
The phosphate-organic molecule head is hydrophilic.
Amphipathic molecule.
Important in cell membrane structure.
3. Carotenoids are isomers of isoprene molecules.


Plant pigments involved in photosynthesis.
Insoluble in water.
4. Steroids have their carbon skeleton bent into four fused rings with a carbon chain
attached to one of the rings.



They are made from isoprene units.
Three rings have six carbon atoms and one has five carbons.
The length and structure of the chain distinguishes one steroid from another.
5. Waxes are lipids made of a fatty acid linked to an alcohol.


Hydrophobic
Coating of fruits, leaves, some insects.
PROTEINS
Proteins are large complex molecules, polymers of amino acids, joined by peptide
bonds.







20 amino acids involved.
Carbon, hydrogen, oxygen, nitrogen and usually sulfur.
Two AA combine to form a dipeptide; three form a tripeptide; many form a
polypeptide.
AA contain an amino group, NH2, and a carboxyl group, COOH.
AA have a variable side chain (R group) that determines the specific properties of
that AA.
Bacteria and plants can synthesize all AA. There are a few exceptions.
Animals synthesize some but not all AA. Essential AA must be obtained from
the diet.
Polypeptide chain may contain thousands of AA.
Proteins consist of one or more polypeptide chains twisted into a unique shape.
Proteins have four levels of organization.




Primary organization: the sequence of AA.
Secondary organization results from hydrogen bonds between certain atoms of
the chain resulting in coiling (helix) or folding (pleated sheet).
Tertiary structure is the overall shape of the polypeptide due to the interaction
among the side chains, R groups.
Quaternary structure is the relationship among several polypeptide chains of a
protein.
Proteins become denatured when they loose their specific shape.
The shape of the proteins determines its function.
NUCLEIC ACIDS
Two classes: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).


Transmit hereditary information.
Determine what the cells manufacture.
Nucleic acids are polymers that serve blueprints of proteins.
Nucleic acids are polymers of nucleotides.
Nucleotides are made of...



One five-carbon sugar: deoxyribose or ribose.
One or more phosphate groups, which make the molecule acidic.
One nitrogenous base: a double-ringed purine or a single-ringed pyrimidine.
The linear chain of nucleotides is linked together by phosphodiester linkages.

A phosphate group attached to sugars of adjacent nucleotides.
DNA consists of double helix held together by hydrogen bonds between opposite
nucleotides.

It contains the bases adenine, cytosine, guanine and thymine.
RNA is mad of a single chain of nucleotides.

It contains the bases adenine, cytosine, guanine and uracil.
ATP, adenosine triphosphate, and NAD+ , nicotinamide adenine dinucleotide, are
nucleotides important in energy metabolism.