Download - Biochemistry
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