BiochemistryOrganic 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

Organic molecules

The simplest organic molecules are made of chains or rings of only carbon and hydrogen◦ methane, CH4

◦ ethane, C2H6

◦ propane, C3H8

◦ butane, C4H10

◦ pentane, C5H12

◦ hexane, C6H14

◦ heptane, C7H16

◦ octane, C8H18

◦ nonane, C9H20

◦ decane, C10H22

Hydrocarbons

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.

Alkanes, alkenes, and alkynes

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.

Functional groups

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 –NH2

Examples:◦ methanamide: HCONH2

◦ ethanamide: CH3CONH2

◦ propanamide: CH3CH2CONH2

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 (Pi)

Phosphate