Biochemistry (MC 101) 1st Semester

1. Introduction to Organic Compounds.

Organic Compounds
Organic Compounds are substances that came from an organism. It always contains C (carbon)
and H (hydrogen), sometimes nonmetal such as O (oxygen), S (sulfur), N (Nitrogen), P (Phosphorus), or a
X (Halogens).
Halogen elements: Early scientists believe the existence of “vital force” in organisms which
 fluorine (F) is said to be required in order for it to synthesize. However, in 1828,
 chlorine (Cl)
 bromine (Br)
Friedrich Wöhler, a German scientist, disprove this theory by synthesizing
 iodine (I) organic compound from an inorganic compound.
 astatine (At)
 tennessine (Ts).

Friedrich Wöhler (31 July 1800 – 23 September 1882)

 Was a German chemist

 known for his work in inorganic chemistry, being the
first to isolate the chemical elements beryllium and
yttrium in pure metallic form.
 known for seminal contributions in organic
chemistry, in particular the Wöhler synthesis of urea.
 contradicted the belief that organic compounds could
only be produced by living organisms due to a "vital
force"

Wohler’s Synthesis:
Organic: CH3-CH2-CH3 (Propane)
Inorganic: Na+ and Cl- (Sodium chloride)

2. Classes of Organic Compounds

Hydrocarbons
 It is any of a class of organic chemicals made up of only the elements carbon (C) and
hydrogen (H).
 Hydrocarbons are examples of group 14 hydrides.

Carbon can be bond 4 times

Types of Hydrocarbons:

 Alkanes – are a series of compounds that contain

carbon and hydrogen atoms with SINGLE
COVALENT BONDS.
Methane, propane, ethane, and butane are four alkanes.

o Cycloalkanes – are alkanes with carbon atoms attached in the form of a closed ring.
 Examples: cyclopentane, Cyclobutene, cyclohexane, and cycloheptane, cyclooctane,
etc.

o Alkanes with Substituents – when an alkane has four or more carbon atoms, the atoms
can be arranged so that a side group called a branch or substituent is attached to a carbon
chain.

Alkyl group

Parent chain

Physical Properties of Alkanes:

 Methane (1 carbon), ethane (2 carbons), propane (3 carbons), and butane (4
carbons) are gasses at room temperature  widely used as heating fuels.
 Alkanes with 5-8 carbons are liquids at room temperature  highly volatile
(easily evaporated at normal temperatures.)
 9-17 carbons: higher boiling points.
  Nonpolar  insoluble in water (polar)

 Alkenes – is a hydrocarbon containing a carbon–carbon DOUBLE BOND. It forms when

adjacent carbon atoms share two pairs of valence electrons.

o Cycloalkenes or cycloolefin – is a type of alkene hydrocarbon which contains a closed

ring of carbon atoms and either one or more double bonds, but has no aromatic character
Examples: Cyclopropene, Cyclobutene, Cyclopentene, Cyclohexene,
Cycloheptene, etc.

o Cis-
trans isomers – exhibit a type of stereoisomerism where the atoms have different spatial
arrangements in three-dimensional space.
CIS – the same side
Trans – opposite side
 Physical Properties of Alkenes:
 Ethene, Propene, and Butene: colorless gases.
 5 or more carbons: liquid
 15 carbons or more: solids
 Alkenes are insoluble in water.
 BP (boiling point): similar to alkanes of the same # of C, ↑MM (Molar
Mass) =↑BP (boiling point)
 MP (Melting point): similar to alkanes, depends on the packaging of the
molecules
 In cis-substituted alkenes there is a net dipole, therefore contributing to
higher boiling in cis-isomers than trans-isomers.
 Alkynes – are hydrocarbons which contain carbon-carbon TRIPLE BONDS. A triple bond
forms when two carbon atoms share three pairs of valences.

 Terminal Alkyne – an alkyne in whose

molecule there is at least one hydrogen atom

bonded to a triply bonded carbon atom.
 Internal Alkyne – is an alkyne in whose molecule there are no hydrogen atoms
bonded to triply bonded carbon atoms.
Physical properties of Alkynes:

Organic solvents  Triple bond contributes to the nonpolar bonding strength, linearity, and
the acidity of alkynes.
– carbon-based substances
capable of dissolving or
 Dissolves in organic solvents.
dispersing one or more  Slight solubility in polar solvents.
other substances.  Insoluble in water.
Polar solvent  BP: slightly higher boiling points than alkanes and alkenes.
- is a type of solvent that
has large partial charges or
dipole moments.
Aromatic
 one that has special stability and properties due to a closed loop of electrons.
 consists of a ring of six carbon atoms with one hydrogen atom attached to each carbon.
 had fragrant odors, the family of benzene compounds →aromatic compound.

Physical properties of Aromatic Compounds:

  Generally nonpolar.
 Stable  aromaticity
 Insoluble in water
 Unreactive
 Useful solvents for nonpolar compounds.
 MP: higher than non-planar hydrocarbons with similar MM

 Hydrogenation is a chemical reaction between molecular hydrogen (H2) and another

compound or element, usually in the presence of a catalyst such as nickel, palladium or
platinum. The process is commonly employed to reduce or saturate organic compounds.

ALCOHOLS, THIOLS, ETHERS, ALDEHYDES, AND KETONES

Alcohols
 Contain the hydroxyl group (-OH) that replaces H atom in a hydrocarbon. Functional group on an
aliphatic carbon atom.
 Primary (1˚)
 Secondary (2˚)
 Tertiary (3˚)

Physical properties of Alcohols:

 Colorless, acidic
 Flammable
 Generally liquid at room temperature
 1-3 carbon atoms: miscible water
 4 C’s: Slightly soluble in water
 5 or more C’s: insoluble in water
 BP: higher than haloalkanes
 MP: higher than alkanes

Phenol
 molecular formula: C6H5OH
  -OH, group replaces a H atom attached to a benzene ring

Physical properties of Phenol:

 Slightly soluble in water

 Weak acid
 Pure phenol is a white crystalline solid, smelling of disinfectant
 MP and BP: higher

THIOL
 contains a sulfur atom
 Similar to an alcohol except -OH is replaced by -SH group

Physical properties of Thiol:

 Has a strong, sometimes disagreeable, odor

 Lower BPs and Less soluble in water and other polar solvents compared to
alcohols

ETHER
 Functional group consists of an O atom, attached to 2 C atoms (—O—)
 Physical properties of
Ether:

 Very volatile
 Highly flammable
 At room temperature: pleasant-smelling colorless liquids
 Relative to alcohols: less dense
 BP: comparable to alkanes but much lower than alcohols
 Miscible in water

ALDEHYDES AND KETONES

Contain a carbonyl group that consist of a carbon-oxygen double bond with 2 groups of atoms
attached to the carbon at angles of 120˚.
The polarity of the carbonyl group strongly influences the physical and chemical properties of
aldehydes and ketones.

Aldehyde
 Carbonyl group is bonded to at least 1 H atom
 C may also be bonded to another H atom, C of alkyl group, or aromatic ring.
 —CHO
Ketone
 carbonyl group is bonded to 2 alkyl groups or aromatic rings
 Keto group (C=O) can be written as CO

Physical Properties of Aldehydes and Ketones:

 Up to 11 C’s: colorless liquids

 Higher → solids
 Lower aldehydes have unpleasant odors
 ↑size = less pungent, more fragrant
 Up to 4Cs: miscible in water
 ↑length of alkyl chain = ↓solubility
 Fairly soluble in organic solvents
 BP: lower than alcohols or carboxylic acids
CARBOXYLIC ACIDS, ESTERS, AMINES, AND AMIDES