Protein Structure

A living system develops, maintains, and reproduces itself. The most amazing feature of the living system is that it is made up of many non-living substances which are existent in their cells in a very complex but highly organized form. These are called biomolecules. hereby, biomolecules are the sophisticated Inanimate organic substances that make up living organisms and are essential for their growth and maintenance. They form the basis of life. Several generic paradigms are enzymes, nucleic acids, lipids, carbohydrates, proteins, amino acids, fats, etc. These biomolecules socialize with each other and form the molecular logic of life processes.

The branch of science that deals with the study of biomolecules and their role in the living system are called biochemistry.

These biomolecules conspicuously interact with each other to produce life. Many of these biomolecules are polymers. For example, starch, protein, nucleic acid are condensation polymers of simple sugars, amino acids, and nucleotides respectively. In addition, the umpteenth clear molecules such as vitamins and mineral salts also play a grand role in the functions of organisms.

What are Proteins?

Proteins are advanced molecular mass labyrinthine biomolecules of amino acids present in all living cells. The primary sources of protein are milk, rice, pulses, groundnut, fish, meat, etc. They occur in every portion of the body and form the foundation of the structure and functions of life. 

The name protein is derived from the Greek word protein which means primary or prime significance. They are so named because proteins are important chemical substances compulsory for the growth and upkeep of life. They are operating in almost all living cells of plants and animals. The protoplasm of plants or animals consists of 10-20% protein. 

Some important proteins required by our body are-

• Enzymes: As biocatalysts to catalyze biochemical reactions, hormones: to regulate various body functions,
• Antibodies: To protect the body from toxins and infections,
• Transport proteins: To carry different substances in the blood to different tissues of the body,
• Structural proteins: Structural elements of the cells and tissues,
• Contractile proteins: To help in the contraction of muscles and other cells etc. All proteins restrain the elements carbon, hydrogen, oxygen, nitrogen, and sulphur. Few of these may also contain phosphorus, iodine, and traces of metals such as iron, copper, zinc, manganese, etc.

All proteins on partial hydrolysis give peptides of varying molecular masses which on integrated hydrolysis give a-amino acids.

Proteins  ⇢  Peptides  ⇢  ∝ – Amino acids

Structure of Proteins

Proteins are biopolymers consisting of a large number of amino acids linked together through peptide bonds having three-dimensional (3D) structures. The structure of proteins is very complex. Protein structure and shape can generally be studied at four different levels, namely primary, secondary, tertiary, and quaternary structures. Their discussion is as follows:

Primary Structure

Proteins can contain one or more polypeptide chains. Each polypeptide is a protein consisting of amino acids linked to each other in a specific order. This sequence of amino acids is called the primary structure of that protein. Thus, the sequence in which amino acids are linked in one or more polypeptide chains of a protein is called the primary structure of the protein.

The primary structure is usually determined by its gradual hydrolysis with enzymes or mineral acids. The amino acid sequence of a protein determines its function and is important for its biological activity. Frederick Sanger determined the primary structure of a protein (insulin) for the first time in 1953. The importance of the primary structure of a protein lies in the fact that even a change of one amino acid can substantially alter the properties of the whole protein. It also makes a different protein. For example, normal haemoglobin has 574 amino acid units and changing only one amino acid in the sequence results in defective haemoglobin in patients with sickle cell anaemia.

Primary Structure of Protein

Secondary Structure

The secondary structure describes how the polypeptide chains are folded or arranged. Hence, it gives the shape or structure of the protein molecule. This arises from the plane geometry of the peptide bond and hydrogen bond between the >C= 0 and N-H groups of different peptide bonds.

Pauling and Corey investigated the structures of many proteins with the help of X-ray patterns. It is observed that there are two general types of structures.

Secondary Structure of Protein

• α – Helix structure: The ∝-helix model was proposed by Linus Pauling in 1951 based on theoretical considerations. However, was later verified experimentally. It is the majority generic form in which a polypeptide chain forms all possible types of hydrogen bonds by twisting into a right-handed screw helix) with the -NH group of each amino acid residue hydrogen-bonded to the C=0 group of an imminent turn of the helix. This is called ∝-helix. This structure can be conjectured as if one can coil a polypeptide chain next to an invisible cylinder. 
• β-pleated sheet structure: In this structure, all polypeptide chains are stretched out to almost supreme extension and then lay down side by side in a zig-zag manner to form a flat sheet. Each sheet is held to bonds. These sheets are stacked in one structure called β-pleated sheet structure. The structure resembles the pleated stratum of the drapery and, as closely as possible, is referred to as a β-pleated sheet.

Tertiary Structure

The tertiary structure originates due to the folding, coiling, and bending of polypeptide chains manufacturing three-dimensional structures. This structure gives the overall shape of the protein. 

In other words, the tertiary structure of a protein is the overall folding of the polypeptide chains i.e. further folding of the secondary structure. The two major molecular shapes are found to be fibrous and globular.  Fibrous proteins such as silk collagen and C-keratin have large helical material and a rigid rod-like shape and are insoluble in water. 

On the other hand, in globular proteins such as haemoglobin, polypeptide chains consist of partially helical segments that are bent about at random cuts to remain in a globular shape. Perutz and Kendrew determined the tertiary structure of haemoglobin and myoglobin through X-ray determination. The main forces that stabilize the secondary and tertiary structures of Steins are hydrogen bonds, disulfide linkages, van der Waals and electrostatic attraction forces.

Tertiary Structure of Protein

Quaternary Structure

Many proteins exist as a single polypeptide chain but some proteins exist as a combination of two or more polypeptide chains called subunits or protomers. These sub-units may be similar or different. These are held together by non-covalent forces such as hydrogen bonds, electrostatic interactions, and van der Waal’s interactions. 

Quaternary structure refers to the determination of the number of subunits and their arrangement in an overall protein molecule. The best-known example of a protein with a quaternary structure is haemoglobin that carries oxygen from the lungs to the cells and carbon dioxide from the cells to the lungs through the bloodstream. 

It is an aggregate of four polypeptide chains or sub-units, two identical alpha chains (each containing 141 amino acid residues) and two identical beta chains (each containing 146 amino acid residues). These four sub-units lie more or less at the vertices of a regular tetrahedron. At the end of each polypeptide chain is a heme follicle (iron-protoporphyrin complex).

There are four types of protein structures in this structure, each ball representing an amino acid.

Quaternary Structure of Protein

Sample Questions

Question 1: Differentiate between the primary and secondary structure of proteins. 

Answer:

The primary structure is the order in which amino acids join one or more polypeptide chains of a protein. This serves its function and is important for its biological activity.

The secondary structure determines how the protein chain is folded. This results from the geometry of peptide bonds and hydrogen bonds from one region of the backbone to another.

Question 2: Which α-amino acid link can cross peptide chains?

Answer:

Cysteine can cross-link peptide chains via disulfide bonds.

Question 3: Describe the use of interferon and insulin in medicines.

Answer:

Interferon is an antiviral agent. Insulin is used in the treatment of diabetes.

Question 4: What type of linkages hold the α-Helix structure of proteins?

Answer:

Hydrogen bonding between -NH and >C=O groups of peptide bond immobilize the α-Helix structure.

Question 5: Where does the water present in the egg go after boiling the egg?

Answer:

When an egg is boiled in water, the water present in the egg is used in the denaturation of the protein, possibly through H-bonding. In this process, the globular protein in e turns into a rubber-like insoluble mass.

Question 6: What is the effect of denaturation on the structure of proteins?

Answer:

During denaturation, the protein molecule uncoils from an ordered and specific structure to a more random conformation. Denaturation does not change the primary structure of the protein but results from the rearrangement of secondary and tertiary structures.