Proteins

The structure of proteins

The basic unit in the protein structure is an amino acid. Amino acids join together by covalent peptide bonds to form polymers called polypeptides. Polypeptides are then combined to form proteins. Therefore, you can conclude that proteins are polymers composed of monomers that are amino acids.

Amino acids

Amino acids are organic compounds composed of five parts:

• the central carbon atom, or the α-carbon (alpha-carbon)
• amino group -NH2
• carboxyl group -COOH
• hydrogen atom -H
• R side group, which is unique to each amino acid.

There are 20 amino acids naturally found in proteins, and each one has a different R group. Figure 1. shows the general structure of amino acids, and in figure 2. you can see how the R group differs from one amino acid to another. All 20 amino acids are shown here for you to be familiar with their names and structures. It is not necessary to memorize them at this level!

Fig. 1 - The structure of an amino acid

Fig. 2 - The side chain of an amino acid (R group) determines the characteristics of that amino acid

The formation of proteins

Proteins form in a condensation reaction of amino acids. Amino acids join together by covalent bonds called peptide bonds.

A peptide bond forms, with the carboxylic group of one amino acid reacting with the amino group of another amino acid. Let's call these two amino acids 1 and 2. The carboxylic group of amino acid 1 loses a hydroxyl -OH, and the amino group of amino acid 2 loses a hydrogen atom -H, creating water that is released. The peptide bond always forms between the carbon atom in the carboxyl group of amino acid 1 and the hydrogen atom in the amino group of amino acid 2. Observe the reaction in figure 3.

Fig. 3 - The condensation reaction of formation of a peptide bond

When amino acids join together with peptide bonds, we refer to them as peptides. Two amino acids joined together by peptide bonds are called dipeptides, three are called tripeptides, etc. Proteins contain more than 50 amino acids in a chain, and are called polypeptides (poly- means 'many').

Proteins can have one very long chain or multiple polypeptide chains combined.

Four types of protein structure

Based on the sequence of amino acids and the complexity of the structures, we can differentiate four structures of proteins: primary, secondary, tertiary and quaternary.

The primary structure is the sequence of amino acids in a polypeptide chain. The secondary structure refers to the polypeptide chain from the primary structure folding in a certain way. When the secondary structure of proteins starts to fold further to create more complex structures, the tertiary structure is formed. The quaternary structure is the most complex of them all. It forms when multiple polypeptide chains, folded in their specific way, are bonded with the same chemical bonds.

You can read more about these structures in the article Protein structure.

The function of proteins

Proteins have a vast array of functions in living organisms. According to their general purposes, we can group them into three groups: fibrous, globular, and membrane proteins.

1. Fibrous proteins

Fibrous proteins are structural proteins that are, as the name suggests, responsible for the firm structures of various parts of cells, tissues and organs. They do not participate in chemical reactions but strictly operate as structural and connective units.

Structurally, these proteins are long polypeptide chains that run parallel and are tightly wound to one another. This structure is stable due to cross-bridges that link them together. It makes them elongated, fiberlike. These proteins are insoluble in water, and that, along with their stability and strength, makes them excellent structural components.

• Collagen and elastin are building blocks of skin, bones, and connective tissue. They support the structure of muscles, organs, and arteries as well.

• Keratin is found in the outer layer of human skin, hair and nails, and feathers, beaks, claws, and hooves in animals.

2. Globular proteins

Globular proteins are functional proteins. They perform a much wider range of roles than fibrous proteins. They act as enzymes, carriers, hormones, receptors, and much more. You can say that globular proteins carry out metabolic functions.

Structurally, these proteins are spherical or globe-like, with polypeptide chains that fold to form the shape.

• Haemoglobin transfers oxygen from the lungs to cells, giving the blood its red colour.

• Insulin is a hormone that helps to regulate blood glucose levels.

• Actin is essential in muscle contraction, cell motility, cell division and cell signalling.

• Amylase is an enzyme that hydrolyses (breaks down) starch into glucose.

Amylase belongs to one of the most significant types of proteins: enzymes. Mostly globular, enzymes are specialized proteins found in all living organisms where they catalyze (accelerate) biochemical reactions. You can find out more about these impressive compounds in our article on enzymes.

3. Membrane proteins

Membrane proteins are found in plasma membranes. These membranes are cell surface membranes, meaning they separate the intracellular space with everything extracellular or outside the surface membrane. They are composed of a phospholipid bilayer. You can learn more about this in our article on the cell membrane structure.

Membrane proteins serve as enzymes, facilitate cell recognition, and transport the molecules during active and passive transport.

Integral membrane proteins

Integral membrane proteins are permanent parts of the plasma membrane; they are embedded within it. Integral proteins that span across the entire membrane are called transmembrane proteins. They serve as transport proteins, allowing ions, water and glucose to pass through the membrane. There are two types of transmembrane proteins: channel and carrier proteins. They are essential for the transport across cell membranes, including active transport, diffusion and osmosis.

Peripheral membrane proteins

Peripheral membrane proteins are not permanently attached to the membrane. They can attach and detach either to the integral proteins or either side of the plasma membrane. Their roles include cell signalling, the preservation of the structure and the shape of the cell membrane, protein-protein recognition, and enzymatic activity.

Fig. 4 - Structure of the cell plasma membrane which involve various types of proteins

It is important to remember that membrane proteins differ according to their position in the phospholipid bilayer. This is especially important when discussing channel and carrier proteins in transports across cell membranes such as diffusion. You might be required to draw the fluid-mosaic model of the phospholipid bilayer, indicating its relevant components, including membrane proteins. To learn more about this model, check out the article on cell membrane structure.

Biuret test for proteins

Proteins are tested using a biuret reagent, a solution that determines the presence of peptide bonds in a sample. That is why the test is called the Biuret test.

To perform the test, you would need:

• A clean and dry test tube.

• A liquid test sample.

• Biuret reagent.

The test is performed as follows:

1. Pour 1-2 ml of the liquid sample into the test tube.

2. Add the same amount of Biuret reagent to the tube. It is blue.

3. Shake well and allow to stand for 5 minutes.

4. Observe and record the change. A positive result is the colour change from blue to deep purple. The purple colour indicates the presence of peptide bonds.

If you are not using Biuret reagent, you can use sodium hydroxide (NaOH) and dilute (hydrated) copper (II) sulfate. Both solutions are components of the biuret reagent. Add an equal amount of sodium hydroxide to the sample, followed by a few drops of dilute copper (II) sulfate. The rest is the same: shake well, allow to stand and observe the colour change.

Fig. 5 - Purple colour indicates a positive result of the Biuret test: proteins are present