1. Functional Groups

3. aldehyde
Definition: an organic compound containing a Carbonyl group ( C=O ).
The aldehyde group is generaly written -CHO
the name Aldehyde comes from Alcohol-dehydrogenated meaning the loss of hydrogen:
                                                                        
Benzaldehyde: aroma in cherries, almonds, perfumes

4. The Carboxyl group is generally written -COOH
Definition: a Carboxyl group ( -COOH), double bonded to an oxygen and single-bonded to the oxygen of the hydroxyl group
Polar, water-soluble
The H+ dissociates and thus has acidic properties. Compounds with this functional group are called carboxylic acids
The Carboxyl group is generally written -COOH
Carboxylic acids are the most important acids of organic chemistry. They are present or in derived form in many natural substances:
Amino acids (building blocks of proteins). Note that the amino acids also contain an amine group. Below is given the structure of alanine
Fatty acids (building blocks of lipids) are long aliphatic chains terminated by the carboxyl group. The structure of stearine is given below.
Fatty acid
Glutamic acid

5. Carbonyl Group
Definition: functional group consisting of a carbon atom double-bonded to oxygen
(-CO)
Polar, involved in H-bonding and molecules with this functional group are water-soluble
Found in sugars
If the carbonyl is at the end off the carbon skeleton-the compound is an aldehyde
If the carbonyl is at the end of the carbon skeleton, the compound is a ketone

6. Alcohol
Definition: an alcohol is an organic compound containing a hydroxyl group ( O-H ). The molecule on the left (methanol) shows the alcohol functional group
OH-CH2-CH2-OH ethylene glycol (antifreeze)

7. Amine
Definition: an Amine is a derivative of ammonia ( NH3 ) in which hydrogen atoms are replaced by R group
caffeine
Alanine & cysteine

8. Phosphate group
Definition: functional group which is the dissociated form of phosphoric acid
Has acid properties since it loses H+ (protons)
Polar and soluble in water
Important in cellular energy storage and transfer (ATP)

9. Sulfhydryl group
Definition: functional group consisting of an atom of sulfur bonded to an atom of hydrogen
Help stabilize structure of proteins-disulfide bridges in the tertiary structure of proteins
Called thiols when found in organic compounds

10. Carbon atoms and molecules of carbon
hexane
Methane & ethane
Branching-isohexane
Ring-cyclohexane
Single, double, triple bonds

11. Isomers have the same molecular formula but different structures and different properties
STRUCTURAL
BOTH HAVE THE SAME MOLECULAR FORMULA C6H14
BUT DIFFERENT STRUCTURAL FORMULAS

12. Structural isomers

13. GEOMETRIC
These two chlorine atoms are locked on opposite sides of the double bond. This is known as the trans isomer the two chlorine atoms are locked on the same side of the double bond. This is know as the cis isomer. (Hint: if you build models and have to take it apart-geometric isomer)
free rotation about single bonds; these two structures represent the same molecule (Hint: if you build model-you just have to rotate c-c bond- not an isomer)

14. Cis/trans geometric isomers
In triglycerides fatty acids may contain double bonds, which can be in either the cis or trans configuration .
Fats with at least one double bond between carbon atoms are unsaturated fats. When some of these bonds are in the cis configuration, the molecules cannot pack tightly, so they remain liquid (oil) at room temperature.
triglycerides with trans double bonds (called trans fats), have are linear fatty acids that are able to pack tightly together at room temperature and form solid fats.

15. ENANTIOMERS
Whenever a carbon atom has four different structures bonded to it, two different molecules can be formed. (chiral means the central C is bonded to 4 different groups or atoms)
EXAMPLE: the amino acid alanine. Bonded to its alpha carbon atom are:
a carboxyl group (COO−)
an amino group (NH3+)
a methyl group (CH3)(its R group)
a hydrogen atom
If you orient the molecule so that you look along it from the COO− group to the NH3+ group, the methyl (R) group can extend out
to the left, forming L-alanine (shown below on the left) or
to the right, forming D-alanine (on the right).

16. Although they share the same chemical formula, they are not interchangeable any more than a left-hand glove is interchangeable with right-hand glove.
19 of the 20 amino acids used to synthesize proteins can exist as L- or D- enantiomorphs. The exception is glycine, which has two (indistinguishable) hydrogen atoms attached to its alpha carbon.
L amino acids are used exclusively for protein synthesis by all life on our planet. (Some D amino acids are used for other purposes.)

17. The function of a protein is determined by its shape.
A protein with a D amino acid instead of L will have its R group sticking out in the wrong direction.
Many other kinds of organic molecules exist as enantiomers. Usually only one form is active in biological systems. For example, if one form binds to a receptor protein on the surface of a cell, the other probably cannot.
Cells usually synthesize only one form. However, chemical synthesis in the laboratory or pharmaceutical factory usually produces equal amounts of the two enantiomers — called a racemic mixture.
Example: The drug albuterol (e.g., Proventil®) contains equal amounts of two enantiomers. Only one of them is effective, and the other may be responsible for the occasional unpleasant side-effects associated with the drug (which is used to dilate the bronchi, e.g, during an attack of asthma).

18. Chiral compounds
Some chemical compounds have optical activity in the sense that these compounds have the ability to rotate the plane of polarized light. Polarized light has light waves all traveling parallel to each other. Ordinary light has light waves traveling in all directions. When polarized light is passed through a solution of an optically active compound, the plane of polarization is rotated to the right or the left. The angle of rotation can be measured in a polarimeter.
An optically active organic compound can be identified by finding a chiral carbon. A chiral carbon is one that has four different "groups" attached to it. The groups can be anything from a single H to functional groups to one or more other carbons. See bromochloroiodomethane on the left - it has 3 halogens and one hydrogen.
In relatively complicated compounds, each carbon must be examined carefully to determine whether it is chiral. Some compounds may have two or more chiral carbon centers such as in carbohydrates.
See glyceraldehyde : Carbon # 1 has only three groups attached. Carbon # 3 has two hydrogens which count as 2 of the same groups. Finally, carbon # 2 has four different groups attached.