The structure and function of proteins

In a nutshell

Proteins are important biological molecules made up of amino acid monomers that form polypeptide chains. The sequence of amino acids allows proteins to have primary, secondary, tertiary and quaternary structures. These structures allow proteins to carry out their specific function in organisms. It is possible to detect the presence of protein in a sample by performing the biuret test.

Proteins

Definition

Proteins are polymers made up of monomers known as amino acids. Two amino acids bond together to form a dipeptide. A chain of two or more amino acids is known as a polypeptide. Proteins are then made up of one or more polypeptide(s).

Amino acid structure

All amino acids have the same general structure. They each have a carboxyl group (- $COOH$ ), an amino group (- $NH_2$ ) and a variable side group known as the R group.

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — 1. Amino group, 2. R group, 3. Carboxyl group

There are $20$ amino acids, each with a different side chain.

Examples

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — **The amino acid alanine.**

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — **The amino acid lysine.**

The different bases will code for different amino acids. These can be seen below.

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins

Condensation reactions

Polypeptides are formed when amino acids join together via a peptide bond. This releases a molecule of water. The reverse is known as hydrolysis, which happens when a polypeptide is broken down and requires a molecule of water.

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins

1 and 2.	Amino acids
3.	Dipeptide
4.	Forward condensation reaction
5.	Backwards hydrolysis reaction
6.	Release of a water molecule
7.	Peptide bond

Protein structure

Proteins are large molecules and their structures can be divided into four levels. These levels are known as primary, secondary, tertiary and quaternary structures.

Primary structure

This is the sequence of amino acids in the polypeptide chain. It is specific for each protein.

Secondary structure

Hydrogen bonds form between carboxyl and amino groups in nearby amino acid monomers. This makes the protein coil into a secondary structure known as an $\alpha$ -helix or fold into a $\beta$ -pleated sheet.

An $\alpha$ -helix happens when hydrogen bonds form between every fourth peptide bond and a $\beta$ -pleated sheet occurs when proteins fold in a way that causes two parts of the polypeptide to be parallel to each other. This allows the parallel amino acids to form hydrogen bonds.

Note: Fibrous proteins such as collagen and keratin have secondary structures.

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — 1. Alpha helix, 2. Beta-pleated sheet

Tertiary structure

This describes the three-dimensional structure of the protein. The coiled chain of amino acids is coiled and/or folded further. This allows more bonds to form between different amino acids.

Bond	Description
Hydrogen	These occur between R groups.
Ionic	These occur between charged (negative or positive) R groups.
Disulfide bridges	These only occur between two cysteine molecules. Cysteine is an amino acid that has a sulfur atom.
Weak hydrophobic interactions	These occur between non-polar R groups.

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — 1.Primary structure, 2. Secondary structure, 3. Tertiary structure, 4. Hydrogen bonds, 5. Disulfide bridge, 6. Weak hydrophobic interactions, 7. Ionic bond

Quaternary structure

Proteins made up of several different polypeptide chains have a quaternary structure. Each chain in the quaternary structure makes up one subunit of the protein.

Example

Haemoglobin

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — The quaternary structure of haemoglobin. 1. Alpha-globin subunit, 2. Beta-globin subunit, 3. Haem group, 4. Oxygen molecule

Overall protein structure

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — The four levels of protein structure: 1. Amino acid, 2 and 3. Polypeptide chains

Types of proteins

There are two main types of protein shape you need to know about.

Type	Description	Example
Fibrous	Fibrous proteins are made up of long and coiled polypeptide chains.	Collagen is formed of three polypeptide chains held together through covalent and hydrogen bonds.
Globular	Globular proteins are more spherical in shape as they fold so that their hydrophilic amino acids are at their surface whereas their hydrophobic amino acids are in the centre.	Haemoglobin.

Function of proteins

There are many different proteins found in living organisms, each with different structures and shapes that are suited to their function.

Examples

Protein	Function
*Enzymes*	Enzymes are roughly spherical as there is tight folding of the polypeptide chains. They're soluble, often involved in metabolism and can help make large molecules.
*Antibodies*	Antibodies form part of the acquired immune response. They are made up of two light polypeptide chains and two heavy polypeptide chains. They also have variable regions which are regions where the amino acid sequence varies greatly.
*Transport proteins*	These include channel proteins which are present in cell membranes. They contain hydrophobic and hydrophilic regions which mean the protein folds up and forms a channel that can transport molecules and ions across the membrane.
*Structural proteins*	These are long polypeptide chains that lie parallel to each other which cross-links. They are often very strong. Examples include keratin, which is found in hair and nails, and collagen which is found in connective tissue.

Biuret test

The biuret test can be used to detect protein in a sample.

Procedure

1.	To make the test solution alkaline, add a few drops of sodium hydroxide solution to the sample.
2.	Next, add copper(II) sulfate solution to the sample.
3.	If protein is present, the solution will turn purple. If there is no protein, the solution will remain blue. *Note:* The colour change is subtle so you must look carefully.

Biology; Biological molecules; KS5 Year 12; The structure and function of proteins — 1. Negative result, 2. Positive result