Organic Chemistry

1. Empirical formula is the simplest formula that shows the ratio of each kind of atom in a
molecule. e.g. C2H5 is the empirical formula for C4H10

2. Molecular formula shows the actual number of each kind of atoms in a molecule. e.g. C4H10

3. Structural formula shows how the atoms are connected to each other in a molecule. e.g.
CH3CH2CH2CH3

4. Displayed/full formula shows all the bonds and relative placing of all the atoms in a
H H H H

H C C C C H

molecule. e.g. H H H H

5. Homologous series are compounds have the same general formula and functional group
and each homologue differs from its neighbor by a fixed group of atoms (e.g.CH2). As we go
down a homologous series, the chemical properties remain unchanged but there is a gradual
change in physical properties. Examples of homologous series are alkanes, alkenes,
alcohols..

6. Structural isomerism refers to compounds with the same molecular formula but different
structural formula. E.g. CH3COOCH3 and C2H5COOH

7. Stereoisomerism refers to compounds that have the same molecular formula but with
different spatial arrangements. [STPM 2007 SB Q9]

Geometric isomers have same carbon skeleton with double bonds restricting free
rotation. For geometric isomerism to exist, there must be two different groups of
atoms bonded to each side of the C=C bond.

Optical isomers are non-superimposable mirror images of each other (enantiomers).

Isomers have at least one chiral C atom, i.e. there are four different groups attached
and have no plane of symmetry. An equal proportion of enantiomers forms a racemic
mixture which is optically inactive.

8.* Alkane are unsaturated aliphatic hydrocarbons with one or more double bonds;

STPM Chemistry Definitions [Organic Chemistry - Term 3] 1

9. The primary structure of a protein shows the exact order (or unique sequence) of the -
amino acids held by peptide/amide linkages along the polypeptide chain. The primary
structure determines what the protein is, how it folds and its function.

10. The secondary structure refers to the detailed configurations of the polypeptide chain. In a
protein molecule, the long chain of amino acid units may be coiled into an -helix or folded
into a -pleated sheet. Both structures are stabilized by hydrogen bonds between the N-H
group of one amino acid residue and the C=O group of another along the main chain.

11. The tertiary structure of the protein refers to the overall 3-dimensional shape of the entire
protein involving folding or coiling of the chains. It shows how protein molecules are
arranged in relation to each other.

There are four types of R group interactions which hold the tertiary structure in its shape.
van der Waals forces (induced dipole-induced dipole bonding) exist when non-polar
R groups (e.g. alkyl or aryl groups) come close together. They are usually found on
the inside of globular proteins where, because they are hydrophobic, they do not
interfere with solubility.
hydrogen bonding between polar groups (e.g.. CH2OH, -COOH and NH2 groups).
ionic bonding eg. COO-, -NH3+, and >NH2+.
disulfide linkages eg. SH or CH2-S-S-CH2- groups.

12. Quaternary structure of proteins refers to the spatial arrangement of its protein subunits. It
shows how the individually folded protein subunits are packed together to yield large
structures. This only applies to proteins that contain two or more polypeptide chains. The
individual polypeptide chains are called the subunits. E.g. haemoglobin contains 4 subunits,
each containing a haem group.

It is stabilized by the same R-group interactions that stabilise the tertiary structure.

13. Denaturation is the loss of biological activity of a native protein. When proteins are
denatured, the secondary and tertiary structures are disrupted i.e. the R group interactions
are broken or destroyed. Note that the primary structure remains unaffected.
Factors that can lead to denaturation include extremes in pH, temperature, ionic salts, heavy
metal compounds, presence of organic solvents etc.

14. Denaturation is the loss of biological activity of a native protein. When proteins are denatured, the
secondary and tertiary structures are disrupted i.e. the R group interactions are broken or destroyed.
Note that the primary structure remains unaffected.
Factors that can lead to denaturation include extremes in pH, temperature, ionic salts, heavy metal
compounds, presence of organic solvents etc.

15. Zwitterion is a neutral molecule with both positive and negative electrical charges

16. Double Helix is two interlinked spirals/chains/strands woven round each other

17. Transcription is the process where DNA/RNA/nucleic acid unravels, strands is used as a template,
mRNA reads the sequence on this strand and produces a complementary strand.
18. Translation is the process where mRNA binds to ribosome , tRNA translate the codon from mRNA,
tRNA carries amino acids to ribosome and adds amino acid to chian.

STPM Chemistry Definitions [Organic Chemistry - Term 3] 2

18

19 In tertiary structure:

20 Polypeptide are natural polymers whose monomers are bonded to each other
via the amide link, -CONH-, and whose monomers are amino acids. [STPM 2008 P2 SA Q4]

21 Electrophile is a species that can act as an acceptor of a pair of electrons in an organic

mechanism. [STPM 2009 P2 SB Q9]
22 Nucleophile is species that can act as a donor of a pair of electrons.

23 Propagation Step a step in a free-radical mechanism in which the radicals formed can then attack
reactant molecules generating more free-radicals, and so on.
24 Nucleophilic Addition the mechanism of the reaction in which a nucleophile attacks the carbon atom
in a carbonyl group and adds across the C=O bond,
e.g. aldehydes or ketones reacting with hydrogen cyanide.
25 FriedelCrafts reaction is the electrophilic substitution of an alkyl or acyl group into a benzene
ring.

STPM Chemistry Definitions [Organic Chemistry - Term 3] 3

Polymerisation

1 Condensation Polymerisation is a process where the (many) monomers are added together
to form a polymer and small molecule (such as H2O, HCl)
2 Additional Polymerisation is a process where the (many) monomers are joined together
to form a polymer without lost of small molecule (such as H2O, HCl)
3

4* Monomer is a small, reactive molecule that reacts to make long-chain molecules called polymers.
5* Polymer is a long-chain molecule made up of many repeating units.
6* Repeating Units is a part of a polymer whose repetition would produce the complete polymer chain
(except for the end-groups) by linking the repeat units together successively along the chain.
7* Homopolymers is a polymer derived from one species of monomer.
8* Copolymers is a polymer derived from more than one species of monomer

STPM Chemistry Definitions [Organic Chemistry - Term 3] 4