Organic Chemistry
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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
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The simplest organic molecules are made of
chains or rings of only carbon and hydrogen
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methane, CH4
ethane, C2H6
propane, C3H8
butane, C4H10
pentane, C5H12
hexane, C6H14
heptane, C7H16
octane, C8H18
nonane, C9H20
decane, C10H22
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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.
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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
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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.
Hydroxyl
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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
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Suffix for alcohols is –ol.
Examples:
◦ Methanol
◦ Ethanol
◦ Propanol
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Location of hydroxyl group on longer chains
is indicated in the name
Examples:
◦ 2-propanol (isopropanol)
◦ 1-propanol
Carbonyl
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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 - Aldehydes
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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 – Ketones
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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)
Carboxyl
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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:
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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
Amines
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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
Methylamine
Putrescine
Amides
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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
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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
Sulfhydryl
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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
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Ethanethiol is added to natural gas to make it
immediately noticeable in case of a leak
Sulfhydryl
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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 threedimensional 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
Phosphate
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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)