Proteins
Quick Notes
- Proteins are polymers of α-amino acids.
- Amino acids contain both –NH2 (basic) and –COOH (acidic) groups.
- Protein structure is modelled as primary, secondary, tertiary, quaternary.
- Two types of protein: fibrous (structural) and globular (functional).
- Denaturation alters protein structure but not primary sequence.
Full Notes
Proteins are large biomolecules made up of amino acids, joined by peptide bonds. They perform a wide range of structural and functional roles in living organisms and are fundamental to life processes.
Amino Acids
Amino acids are organic compounds containing an amino (–NH2) group and a carboxyl (–COOH) group attached to the same carbon (α-carbon).

where R = side chain
The amine (-NH₂) group acts as a base (accepts a H+ ion) and the carboxylic acid (-COOH) group acts as an acid (donates a H+ ion).

Zwitterions: Isoelectric Point
At a specific pH (isoelectric point), amino acids exist as zwitterions.

The zwitterion contains both a positive (–NH3+) and a negative (–COO−) charge but is overall neutral.
They form at a specific pH when the amine (NH2) group accepts a H+ ion and the carboxylic acid (COOH) group loses a H+ ion.
Classification of Amino Acids
Amino acids can be classified based on the number of amino and carboxyl groups:
- Acidic amino acids: have an extra –COOH group.
- Basic amino acids: have an extra –NH2 group.
- Neutral amino acids: have an equal number of –NH2 and –COOH groups.
Also classified based on origin:
- Essential amino acids – Must be obtained through diet.
- Non-essential amino acids – Synthesised in the body.
There are 20 standard amino acids commonly found in proteins.
Structure of Proteins
Proteins are naturally occurring polymers of amino acids linked by peptide bonds (–CONH–).

Peptide bonds form by condensation reactions between amino acids, releasing water:

The process can keep happening between more amino acids, forming a polypeptide chain (polymer).

Peptide bonds can be broken apart in hydrolysis reactions. The hydrolysis of proteins (with acid or alkali) releases the amino acids that made up the protein.


The conditions used for hydrolysis determine the form of the amino acids released. If acidic conditions are used, then the amino acids may exist as positively charged ions with the NH2 group accepting a H+ ion to form NH3+. Equally, if alkaline conditions are used, then the carboxylic acid groups may be forced to lose H+ ions and exist as carboxylate ions (COO−).
Types of Protein
Proteins can be fibrous or globular.
Fibrous Proteins
- Linear and thread-like.
- Insoluble in water.
- Provide structural support (e.g., keratin, collagen).
Globular Proteins
- Folded and spherical.
- Soluble in water.
- Functional proteins (e.g., enzymes, hormones, antibodies).
Levels of Protein Structure
Proteins can have very complicated shapes that are difficult to analyse.
To help, we describe the structure of proteins in terms of a Primary, Secondary and Tertiary structure. (Proteins made up of more than one polymer chain also have a quaternary structure).
Primary Structure

- The sequence of amino acids in a polypeptide chain
- Determines the overall structure and function of the protein
Secondary Structure
Folding of the polypeptide due to hydrogen bonding between C=O and N–H bonds from different amino acids in the polymer chain.

The hydrogen bonding can form two shapes or patterns in the protein:

- α-helix – a right handed coil (spiral) structure stabilised by hydrogen bonds.
- β-pleated sheet – strands linked side by side with hydrogen bonds.
Tertiary Structure
3D folding of the protein due to interactions between R groups.

The interactions between different R groups causes the protein to ‘fold’ into complicated shapes, with the final shape between determined by the locations (and type) of amino acids in the chain.

- Hydrogen bonding (between polar groups that can form Hydrogen bonds).
- Disulfide (S–S) bonds (between cysteine residues that contain sulfur (S)).
- Ionic bonds (between charged R groups).
- Hydrophobic interactions (between non-polar R groups).
Quaternary Structure
Association of two or more polypeptide chains.
Example: Haemoglobin (4 subunits)

Denaturation of Proteins
Denaturation is the loss of the biological activity of a protein due to disruption of its conformation and shape.
- Caused by physical or chemical agents (e.g., heat, acids, alcohol, heavy metals).
- Affects secondary, tertiary, and quaternary structures.
- Primary structure remains intact.
Summary
- Proteins are polymers of α-amino acids linked by peptide bonds.
- Amino acids exist as zwitterions at the isoelectric point.
- Protein structures include primary, secondary, tertiary and quaternary levels.
- Fibrous proteins are structural and insoluble while globular proteins are functional and soluble.
- Denaturation changes structure beyond the primary sequence.