Organic Chemistry

 Molecule made of carbon and hydrogen in a chain or a ring is considered organic  This includes carbohydrates, lipids, proteins, nucleic acids, as well as a multitude of other synthetic molecules (such as plastics)  Carbon is at the center of such a wide variety of molecules because it can form four stable covalent bonds – this allows for an infinite number of possible configurations

 The simplest organic molecules are made of chains or rings of only carbon and hydrogen ◦ methane, CH 4 ◦ ethane, C 2 H 6 ◦ propane, C 3 H 8 ◦ butane, C 4 H 10 ◦ pentane, C 5 H 12 ◦ hexane, C 6 H 14 ◦ heptane, C 7 H 16 ◦ octane, C 8 H 18 ◦ nonane, C 9 H 20 ◦ decane, C 10 H 22

 Hydrocarbons with only single C-C bonds are alkanes (-ane ending)  Hydrocarbons with at least one double C=C bond are alkenes (-ene ending)  Hydrocarbons with at least one triple C≡C bond are alkynes (-yne ending)  All are nonpolar, hydrophobic molecules.

 Other elements are often found attached to hydrocarbons  These reactive clusters of atoms are called functional groups  They will affect the amount of intermolecular forces and thus other factors such as solubility and melting/boiling points.

Halides  Organic hydrocarbons with at least one halogen atom attached in place of a hydrogen  Not frequently found in living organisms  More often used in industry; as refrigerants, in production of PVC and DDT, and several pharmaceuticals such as ciproflaxin are organic halides.

 characteristic of alcohols  electronegative oxygen atom increases the intermolecular forces  alcohols are polar molecules  more hydroxyl groups increases the melting/boiling points  compare the melting points of propanol (−126.5 °C) and glycerol (18 °C) Hydroxyl

 Suffix for alcohols is –ol.  Examples: ◦ Methanol ◦ Ethanol ◦ Propanol  Location of hydroxyl group on longer chains is indicated in the name  Examples: ◦ 2-propanol (isopropanol) ◦ 1-propanol Hydroxyl

 Carbon atom double bonded to an oxygen  Two types: aldehyde and ketone  Both are polar, and have increased boiling points and solubility compared to similar sized alkanes or alkenes ◦ Aldehydes – carbonyl group occurs at one of the terminal carbon - names end with –al  methanal, ethanal ◦ Ketones – carbonyl group occurs at one of the internal carbons - names end with –one  propanone, butanone Carbonyl

 Commonly occur as natural or artificial fragrances, such as in essential oils like cinammaldehyde or vanillin  Other common examples include methanal (formaldehyde) and ethanal (acetaldehyde) Carbonyl - Aldehydes

 Used frequently as solvents in industrial processes, or in some pharmaceutical drugs, but are found in nature as animal pheromones  Examples: ◦ acetone (propanone) ◦ Muscone (animal scent - musk) Carbonyl – Ketones

 A combination of hydroxyl and carbonyl groups attached to the same carbon atom  Highly polar functional groups – tend to have higher melting/boiling points than similar sized alkanes  Examples: ◦ ethanoic acid (acetic acid or vinegar) ◦ butanoic acid – found in rancid butter ◦ citric acid (a tricarboxylic acid) – in citrus fruit ◦ fatty acids – such as stearic acid or oleic acid ◦ the acid end of all amino acids Carboxyl

Carboxyl

 Includes nitrogen atom attached to a carbon chain or ring  Similar to an ammonia molecule, but with a carbon chain replacing one or more hydrogens.  Found in all amino acids, urea, nitrogenous bases, some insect pheromones  Methylamine – strong odour of fish  Putrescine and cadaverine – responsible for the odour of putrefying flesh (during the breakdown of amino acids) Amines

Amines Methylamine Putrescine

 Similar to amines, but with a carbonyl group attached to one of the carbon chains  Or thought of another way, they can be derived from a carboxyl group, where the – OH part of the -COOH is replaced by an – NH 2  Examples: ◦ methanamide: HCONH 2 ◦ ethanamide: CH 3 CONH 2 ◦ propanamide: CH 3 CH 2 CONH 2 Amides

 Amides are weak bases and are generally less soluble than similar-sized amines  They are extremely common in nature as structural materials – in particular as proteins  Amino acids are bonded together with peptide bonds, which are essentially amide linkages Amides

 Have a similar structure to hydroxyls – the oxygen is replaced with a sulfur atom  Are also referred to as thiols, they have very strong pungent odours, similar to garlic.  Skunk odour is composed of several different thiol compounds  examples: ◦ Methanethiol ◦ Ethanethiol  Ethanethiol is added to natural gas to make it immediately noticeable in case of a leak Sulfhydryl

 Thiols are important in proteins – especially ones that contain the amino acid cysteine  Two cysteines can form a covalent bond called a disulfide bond (-S-S-) in a protein  Disulfide bonds contribute to the three- dimensional structure of proteins  Coenzyme A is an important thiol used in the synthesis of fatty acids and also a critical step in the Kreb’s cycle of cellular respiration Sulfhydryl

 An inorganic salt related to phosphoric acid  When attached to hydrocarbon(s), they are called organophosphates  In biological systems, phosphates are part of molecules such as phospholipids (in the plasma membrane), nucleic acids (DNA, ATP)  When phosphates are unattached to a compound (such as during the ATP-ADP cycle) they are referred to as inorganic phosphate (P i ) Phosphate