Basic Structure / Components of Proteins

Amino Acids:
- They are the monomers (basic units) from which proteins are constructed.
- Each amino acid consists of a carbon atom bonded to a -COOH (carboxyl group), an -NH2
(amine group), a hydrogen atom, and an R group.
The R group is a group of atoms bonded to the central atom, which dictate whether amino
acids differ from each other. There are 20 amino acids which occur in living organisms (the
only difference between them is the R groups).
- Amino acids are joined together by condensation reactions, in which peptide bonds form
between the amino acids.
As a result of these reactions dipeptides (molecules made up of 2 joined amino acids) and
polypeptides (macromolecules / polymers made of many amino acids joined together) are
formed.
A complete protein molecule may contain one, two, or more polypeptide chains interacting
with each other!
- In living cells, ribosomes are the site where amino acids are joined together. This process is
controlled by enzymes.
- Proteins can be broken down again to amino acids by hydrolysis. This occurs naturally in the
stomach and small intestine during digestion before the amino acids are absorbed into the the
blood.

The Structure of Proteins:

- Primary Structure: It is the sequence of amino acids within a polypeptide chain.
There are many possible primary structures (a change in one amino acid= different protein).

- Secondary Structure: It is the structure of a polypeptide chain resulting from the coiling or

folding of a sequence of amino acids.

-helix: It is a corkscrew shape which a polypeptide chain gains because of (intramolecular)
hydrogen bonds between the oxygen atom of the -CO- group and the hydrogen atom of the
-NH- group four amino acids ahead.
-pleated sheet: It is the looser, straighter, pleated shape which are created by similar
bonds to the -helix.
Some proteins or part of proteins have no regular arrangement. It depends in the R groups
of the amino acids and what attractions are possible.
The bonds (H bonds) which hold together the secondary structure can be broken by
changes in temperature and pH.
- Tertiary Structure: It is the compact structure of a polypeptide chain resulting from the 3D
coiling of already-folded chain of amino acids.

 The 3D shape of these molecules is very precise and are held together by bonds between
amino acids
1. Hydrogen Bonds: Form between highly polar groups (e.g.. -NH-, -CO-, -OH-)
2. Disulfide Bonds: Form between cysteine molecules and can be broken by reducing
agents (add H+ ions).
3. Ionic Bonds: Form between amino acids that have ionised amine (-NH3-) and
carboxyl (-COO-) groups and can be broken by changes in pH.
4. Hydrophobic Interactions: The weak bonds occur between non-polar R groups.
They stay together because they are repelled by their watery surroundings (the
enemy -the non-polar R group- of my enemy -the water molecules- is my friend).

- Quaternary Structure:It is the 3D arrangement of two or more polypeptide chains or a

polypeptide chain and a non-protein component such as a haem group.
The different polypeptide chains are held together by the same bonds as the tertiary
structure.