Supercharge your learning!

Use adaptive quiz-based learning to study this topic faster and more effectively.

Protein structure

Amino acids are the basic units of proteins. They are important organic molecules that consist of:

  • An amino group, $$\ce{-NH2}$$
  • A carboxyl group, $$\ce{-COOH}$$
  • An R-group (a side chain).

These groups are linked via a central carbon, known as the $$\alpha$$-carbon.

The R-group varies across amino acids.

In glycine, the R group is simply a hydrogen.
In glycine, the R group is simply a hydrogen.

The R-group influences the way an amino acid can interact through intermolecular (between molecules) or intramolecular (within the molecule itself) bonding.

Amino acids can be classified as non-polar, polar, acidic or basic based on the R-group. Glycine is a special case where the R-group is a single hydrogen atom.

There are 22 amino acids found in proteins. Humans use 20 of them.

There are nine amino acids that the human body cannot produce. These must be obtained from the diet, and are called essential amino acids.

Proteins are large polymers composed of long chains of amino acids.

Amino acids are the building blocks of proteins. There are 20 different amino acids commonly found in proteins. These can be arranged in any order to create lots of different proteins.

The sequence of amino acids in a protein determines the protein's shape and function.

Most amino acids can be synthesised by the body. However, some essential amino acids need to be taken from food.

Meat and nuts are rich in essential amino acids.

Proteins are necessary for almost all biological processes, including:

  • Controlling the speed of chemical reactions as enzymes
  • Providing structural support for the cell
  • Transporting molecules around the cell
  • Protecting the body from disease as antibodies
  • Used as an energy source during starvation.

The primary structure of a protein is the sequence of amino acids in the protein. The amino acid sequence is encoded by genes in the DNA.

The only bonds relevant for the primary structure of a protein are the peptide bonds between individual amino acids.

The sequence of amino acids dictates the overall structure of the protein, because their R-groups influence the folding and bonding at every level of the protein structure.

Small changes in the primary structure can result in an alteration of the protein's function.

Sickle cell anaemia is a genetic disease that arises from the change in one amino acid in the primary structure of a protein.

The secondary structure of proteins describes the folding or coiling of the polypeptide chain to form local substructures. The structures are sustained by hydrogen bonds.

There are two main types of secondary structure:

$$\alpha$$-helix $$\beta$$-pleated sheet
  • Spiral shaped
  • The most common secondary structure
  • Zigzag shaped
  • Exists as parallel or antiparallel sheets

A protein may consist of more than one secondary structure. For instance, a short section may form an $${\alpha}$$ helix, whilst another may form a $${\beta}$$ sheet.

Overall, proteins formed from a combination of secondary structures.
Overall, proteins formed from a combination of secondary structures.

The tertiary structure is the overall 3D structure of one polypeptide chain. It describes the overall folding of the protein and the forces that influence this folding.

The tertiary structure of artemin, a protein found in the human body.
The tertiary structure of artemin, a protein found in the human body.

There is a subtle difference between secondary and tertiary structure.

The secondary structure only describes local folding of the protein, while the tertiary structure describes the overall structure of the protein.

The tertiary structure is influenced by the nature of interactions between amino acids brought together when the protein folds against itself. These amino acids may have many others in the chain between them, but be close in the folded 3D structure.

The following bonds are heavily involved in the tertiary structure:

  • Ionic bond
  • Hydrogen bond
  • Disulphide bridge, a type of covalent bond that is unique to cysteine.
  • Hydrophobic (or van der Waals) interactions

The quaternary structure is formed by interactions between multiple polypeptide chains. This includes non-protein groups (known as cofactors) that may associate with the protein.

The molecular interactions involved (same as interactions at tertiary structures) are as follows:

  • Hydrogen bond
  • Disulphide bond
  • Ionic bond
  • Hydrophobic interaction
Haemoglobin (left) and collagen (right).
Haemoglobin (left) and collagen (right).

Fibrous proteins and globular proteins are the two main classes of protein within the quaternary structure.

Fibrous proteins are long and thin and tend to take on structural roles.

Collagen, the main component in connective tissue, is a fibrous protein. It is formed of three strands coiled into a triple helix.

Globular proteins are roughly spherical and usually water-soluble. Globular proteins tend to participate in metabolic reactions.

Haemoglobin (the oxygen carrier in red blood cells) is an example of a globular protein. It is made up of four polypeptide chains.

Haemoglobin is a globular protein formed of four polypeptide chains. The chains are held together by hydrogen bonds, ionic bonds and hydrophobic interactions.

Haemoglobin is the oxygen transport protein present in red blood cells.

The blue and red ribbons represent folded polypeptide chains in haemoglobin (left), each associated with a haem group (magnified on the right).
The blue and red ribbons represent folded polypeptide chains in haemoglobin (left), each associated with a haem group (magnified on the right).

Each of the polypeptide chains is tightly associated with a haem group which is a non-protein molecule. Haem is a hydrocarbon ring with an iron ion in the centre.

Haemoglobin contains four haem groups, and each of these groups can carry one oxygen molecule. Overall, haemoglobin can carry up to four oxygen molecules.

Haem binds to oxygen at high concentrations of the gas, such as in the blood vessels of the lungs, and then releases it elsewhere in the body.

Haemoglobin is water-soluble. The solubility is achieved through the arrangement of the amino acids in the tertiary structure. Amino acids with hydrophilic R-groups are arranged around the outside of the protein.

The three polypeptide chains of collagen are indicated in different colours.
The three polypeptide chains of collagen are indicated in different colours.

Collagen is a fibrous protein with a structural role. It is a major component in mammalian connective tissue, providing elasticity to skin, muscles, tendons and bone.

Collagen is long protein and due to its length, it is insoluble in water.

Collagen consists of three polypeptides. The polypeptides are wound together in a triple helix (like a plait).

Every third amino acid in collagen is glycine, the smallest amino acid. This allows for tight packing of the polypeptide chains.

Tight packing makes collagen compact. Compactness increases the tensile strength of the protein, allowing it to stretch.

Collagen also contains a significant amount of lysine . Lysine R-groups on neighbouring collagen proteins form covalent bonds between the strands.

This formation of covalent bonds allows individual collagen proteins to associate and form fibres.

A sample can be tested for proteins using the Biuret test.

The Biuret test actually tests for the links between amino acids in a protein, called peptide bonds.

  • Grind up the sample and dissolve in distilled water in a test tube.
  • Add Biuret reagent (blue coloured) to the solution.
  • Biuret reagent contains two solutions: potassium hydroxide and copper sulphate.

If the resulting solution changes colour from blue to purple , the sample contains protein. If there is no colour change (i.e. stays blue), no protein is present!

Biuret reagent is normally premixed for you to use.
Biuret reagent is normally premixed for you to use.

For each chemical test, it is important to know when to you it, how to do it and what it tells you! Below is a summary table:

Biological molecule Chemical test Positive result
Simple sugars Benedict's test Brick red colour
Starch Iodine test Dark blue colour
Lipids Ethanol emulsion test Cloudy white solution
Protein Biuret test Purple colour