1. Organic Chemistry

2. Chemistry Basics All elements can react to form chemical bonds.
There are three classifications for true chemical bonds
Covalent: Share electrons equally, between two atoms of the same type. Ex: O2
Polar Covalent : Share electrons (almost) equally, between non-metals Ex: CO
Ionic: Electrons are transferred from one element to another, between metals and non-metals; uncommon in biology and organic chemistry

3. Intermolecular Forces
These are interactions between molecules that allow attractions like cohesion and adhesion
Hydrogen Bonding: Not a true chemical bond but is when hydrogen is attracted to Nitrogen, Oxygen or Fluorine (and sometimes Sulfur)
Dipole-Dipole: attractions caused by polar bonds and ionic bonds
London Dispersion: weak attractions between covalent molecules

4. Chemistry Basics
All elements will create chemical bonds until their orbitals are full (8 total electrons) giving them noble gas configurations
Elements can only make bonds to fill empty orbital spaces
So…Oxygen can make 2 bonds, Nitrogen can make 3 bonds, Carbon can make 4 bonds

5. Organic Molecules
Organic molecules are named using the longest carbon chain – which is not always in a strait line
Prefixes are used to identify how many carbons are in the chain
Meth, Eth, Prop, But, Pent, Hex, Hept, Oct, Non, Deca

6. Alkanes, Alkenes and Alkynes
Alkanes are hydro-carbons that are saturated, meaning they have only single bonds.
Alkenes contain one or more double bonds that are identified by the carbon number they start on
Alkynes contain one or more triple bonds identified by the carbon they start on

7. Functional Groups
Most organic molecules contain at least one functional group. These are groupings of elements that change the properties of the organic molecule.
Functional groups will allow hydrogen bonding, di-sulfide bridges and polar interactions.

8. Functional Groups Hydroxyl Group Carbonyl Group
H bonded to O; alcohols;
soluble in water because they are polar
Carbonyl Group
C double bond to O;
some polarity
At end of chain:
aldehyde
Otherwise:
ketone

9. Functional Groups, II Carboxyl Group Amino Group
O double bonded to C to hydroxyl; carboxylic acids; bond between O and H; polar;
likely to dissociate an H ion creating an acidic environment and the ability to easily bond with a positively charged functional group
Amino Group
N to 2 H atoms; called amines;
the name amino acids is derived from this functional group
acts as a base (+1) and will attract the carboxyilic acid

10. Functional Groups Sulfhydral Group sulfur bonded to H;
called thiols; used in proteins to create di-sulfide bridges in 3-D structure
Phosphate Group phosphate ion; covalently attached by 1 of its O to the C skeleton; is used in ATP to store energy within this bond or release energy by breaking it

11. Cyclic Molecules Sometimes organic molecules can form ring structures.
These ring structures are not as reactive as linear molecules but can still be involved in chemical reactions.
The most common ring structure in Biology is a benzene ring containing 6 Carbons, 6 Hydrogens and 3 double bonds

12. Bonding in Molecules
Bonds are created in organic molecules using functional groups.
These bonds most often produce water when formed in a condensation reaction
The most common involve amino groups and carboxylic acids or carbonyl groups and carboxylic acids

13. Isomers
Isomers are molecules that contain the same number of each element but have those elements arranged in a differently.
Structural Isomer: Differ in arrangement
Butane v. Isobutane
Geometric Isomers: Differ in spacial arrangement
Cis and Trans arrangements
Enatiomers: mirror images
Right v. Left Hand