Organic Chemistry

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

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

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

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

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

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.

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

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

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

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

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

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