Structure of Proteins

Introduction

All proteins comprise long chains of ⍺-amino acids (alpha-amino acids). Amino acids are organic compounds and form the building components for the living system necessary for the growth and development of human beings. About 300 amino acids occur in nature. The key elements of amino acids consist of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N); also, sulfur (S) is present in the side chains of cysteine and methionine. The major functional groups present in the amino groups include amine (-NH₂), carboxyl (-COOH) and side chain (R group). A chain of amino acids forms a protein. In other words, proteins are polymers of amino acids. Chains of amino acids are together through peptide bonds.

Altogether, there are a total of 20 amino acids that combine to form proteins of different structures and functions. Based on the position of the amino group concerning carboxyl group, amino acids are classified as α, β, ץ, δ and so on. On hydrolysis of proteins, α-amino acids are obtained. The α-amino acids may have other functional groups. The ⍺-amino acids are called so because they carry an amino group (-NH₂) and a carboxyl group (-COOH) at the α-carbon atom.

In acidic solution, pH = less than 4, -COO combines with H+ ions and converts into the -COOH i.e., uncharged form whereas in alkaline solution, pH above 9, ammonium ion (-NH₃⁺) loses a H⁺ ion and converts into amino groups (-NH₂). pH ranging between 4-8, amino acids carry both positive and negative charges and do not create electrical fields in the chemical solution. These structures are called zwitterions.

Structure of Amino Acids:

All 20 naturally occurring amino acids have common structural features – an amino group (-NH3+), carboxylate (-COO-) group and a hydrogen-bonded to the same carbon atom. The difference lies in the side-chain called the R group. 4 different groups are attached to α-carbon.

These 4 groups are:

• Amino group(-NH₂)
• -COOH
• Hydrogen atom
• Side-chain (R)

Amino acids are linked together via peptide bonds or peptide linkage. Peptide bonds are formed between -COOH and -NH₂ groups.

When two same or different amino acids combine, this results in the elimination of a water molecule and hence the formation of peptide bonds occurs. The end product obtained is called dipeptide as it is made up of two amino acids. Similarly, when third amino acids combine to dipeptide then the product obtained is called tripeptide. In the same way, tetrapeptide, pentapeptide, or hexapeptide products can be obtained. More than ten amino acids combine to form a product called a polypeptide.

Based on structure, proteins can be classified into the following types:

Fibrous proteins: In this structure of a protein, the polypeptide chain runs parallel and held together with the help of hydrogen and disulphide bonds and thus forming a fiber-like structure called fibrous proteins. These are insoluble in water.

E.g.- keratin (present in hair, silk) and myosin (muscle protein) etc.

Globular proteins: When polypeptide coils result in the spherical shape. These are soluble in water.

E.g.- Insulin and albumin.

Characteristics of peptide bonds are as follows:

1. Peptide bonds have partial double bond character.
2. Peptide bonds cannot be broken by the high salt concentration or by heat.
3. Peptide bonds are rigid and hence provide a definite shape to the protein structure.
4. They contain partial positive charge and negative charge groups.

Different types of peptide bonds

• Dipeptides have 2 amino acid units
• Tripeptides have 3 amino acid units
• Tetrapeptides have 4 amino acid units
• Oligopeptide contains 2 to 20 amino acid units
• Micropeptides have more than 100 amino acids

Level of Structural organization in proteins

The primary , secondary, tertiary, and quaternary structure applies to the configuration of protein. The nomenclature is provided by the committee of the International Union Biochemistry.(IUB)

Primary Structure of Protein

Analytical procedures revealed that the primary structure of the protein is the sequence of the peptide bonds. Concerning the arrangement of amino acids in the primary structure of a protein, amino acids are present in a sequence of long chains like a long thread or are irregularly coiled. Any change in the sequence of the linear arrangement of amino acids results in the formation of different proteins. Mutual attraction and repulsion between polar and nonpolar groups i.e. The R-group in side chains of amino acids determines the configuration of protein. .

Secondary Structure of Protein

All amino acids except glycine have asymmetric L-amino acids. The peptide bond in this structure of protein assumes helical shape asymmetrically. Such structural features are the secondary structure of a protein. Also, this structure is characterized by the presence of alpha-helix and beta-pleated sheets. Chains of amino acids are linked together via peptide as well as hydrogen bonds

The Tertiary Structure of Protein

The tertiary structure of a protein is formed as a result of interaction side chains (R-group) of amino acids. Some of them have positively or negatively charged groups or some are polar and non-polar. Several carbon atoms range from 2 in glycine to 11 in tryptophan. Positive and negative charges in the structure of protein attract each other whereas if the same charges are present then they tend to repel each other. Negatively charged amino acids include aspartic or glutamic acid while positively charged amino acids include lysine or arginine. Amino acids are linked via peptide and hydrogen bonds. Hydrogen bonds are formed between the nitrogen bonded hydrogen atom i.e., the imide hydrogen and the oxygen atom in the carbonyl group. The hydrogen bond is much weaker than the covalent bond. In the side chains of amino acids like valine, leucine, isoleucine and phenylalanine, the nature of the interaction is hydrophobic interaction. In cysteine, the configuration is determined by the disulfide bonds present.

Tertiary structure is formed by further folding of the secondary structure of a protein. This structure is characterized by hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces of attraction.

Quaternary Structure of Protein

An example of this structure of a protein is hemoglobin (Hb). Each Hb molecule has 4 peptide chains, 2 α-chains and 2 β-chains forming a tetramer. All 4 subunits are linked together via hydrogen bonds and hydrophobic interactions and no covalent bonds occur between the sub-units. Covalent bonds are present in other proteins as disulfide bridges.

Conclusion

Proteins are polymers of amino acids linked together by peptide bonds. Proteins are the building blocks for the human organ system. Condensation of amino acids results in the formation of 4 levels of protein, these are primary, secondary, tertiary, and quaternary respectively. All these levels of protein differ in structure as well as in chemical composition. Although bonds present in them are peptide bonds and hydrogen bonds. Some amino acids are also linked by disulfide bonds. With respect to stability of all 4 levels of protein, the stability chart is as follows- quaternary>tertiary>secondary>primary respectively. The Hb molecule shows quaternary structure of protein. Proteins or amino acids assume themselves either in linear structure or fibrous or fold themselves into globular shape. Keratin is an example of fibrous protein whereas insulin is an example of globular protein.