Proteins

Proteins are the most abundant biomolecules of the living system. Chief sources of proteins are milk, cheese, pulses, peanuts, fish, meat, etc. They occur in every part of the body and form the fundamental basis of structure and functions of life. They are also required for growth and maintenance of body. The word protein is derived from Greek word, “proteios” which means primary or of prime importance. All proteins are polymers of α-amino acids.

Amino Acids

There are some 20 amino acids in the proteins that we consume. These amino acids bond together to form a larger protein molecule. Amino acid being organic compound molecules can form various different links with each other due to the versatile nature of carbon. This enables the great diversity of proteins that can be found in nature. These are an essential nutrient in our diet because of the functions they perform.

Structure of Amino Acids

There are actually thousands of amino acids occurring in nature. But only about 20 amino acids form a part of the proteins in the human body. These twenty acids will be our focus here. Although all these have varied structures, the basic structure of amino acid remains uniform.

Ø All amino acids contain a carbon atom in the middle of the molecule, the alpha-carbon

Ø This atom is surrounded by three chemical groups.

Ø One is an amine group -NH₂

Ø The second one is a carboxyl group -OOOH

Ø The third group is denoted by R. This is the variable radical group and is different for every amino acid. This R group makes the amino acid unique.

Classification of Amino Acids

Amino Acid can be classified based on their structure and the structure of their side chains i.e. the R chains. Now two basic subcategories are

1. Non-Polar Amino Acids

These are also known as Hydrophobic. The R group can be either of Alkyl groups (with an alkyl chain) or Aromatic groups. The acids falling in this group are stated below. Numbers one to seven are Alkyl and the last two are aromatic

i. Glycine (H)

ii. Alanine (CH₃)

iii. Valine  (CH(CH₃)₂)

iv. Methionine (CH₂CH₂SCH₃)

v. Leucine (CH₂CH(CH₃)₂)

vi. Isoleucine (-CH(CH₃)CH₂CH₃)

vii. Proline (special structure)

viii. Phenylalanine

ix. Tryptophan

2. Polar Amino Acids

If the side chains of amino acid contain different polar groups like amines, alcohols or acids they are polar in nature. These are also known as Hydrophilic Acids. These are further divided into three further categories.

a) Acidic:

If the side chain contains an extra element of carboxylic acid component these are acid-polar amino acids. They tend to donate their hydrogen atom. These are:

i. Aspartic Acid (CH₂COOH)

ii. Glutamic Acid (CH₂CH₂COOH)

b) Basic:

These have an extra nitrogen group that tend to attract a hydrogen atom. The three basic polar amino acids are

i. Histidine

ii. Lysine (CH₂(CH₂)2NH₂)

iii. Arginine

c) Neutral:

These are neither acidic nor basic. They have an equal number of amino and carboxyl groups. Also, they have at least one hydrogen component connected to electronegative atoms. Some of these neutral acids are

i. Serine (CH₂OH )

ii. Threonine (CH(OH)CH₃)

iii. Asparagine (CH₂OHNH₂)

iv. Glutamine (CH₂CH₂CONH₂)

v. Cysteine (CH₂SH)

vi. Tyrosine

Amino acid can also be classified on the basis of their need to the human body and their availability in the human body

1. Essential Amino Acids

These are the acids that cannot be synthesized in our bodies. We must rely on food sources to obtain these amino acids. They are

Ø Leucine

Ø Isoleucine

Ø Lysine

Ø Theorine

Ø Methionine

Ø Phenylalanine

Ø Valine

Ø Tryptophan

Ø Histidine (conditionally essential)

2. Non-Essential

These acids are synthesized in our bodies itself and we need not rely on outside sources for them. They are either produced in our bodies or obtained from protein breakdowns.

Properties of Amino Acids

Ø Each amino acid has both an acidic and basic group as you can see from its structure. This is the reason they behave like salts.

Ø Any amino acid in the dry state is in crystalline form. They exist as a dipolar ion. The COOH group exists as an anion. And the NH₂ group exists as a cation. This dipolar ion has a special name “Zwitter ions’. 

Ø In aqueous solution, alpha amino acids exist in equilibrium between a cationic form, an anionic form and dipolar ion.

Ø The Isoelectric point is the pH point at which the concentration of zwitter ions is the highest ad the concentration of cationic and anionic form is equal. This point is definite for every α-amino acid.

Ø They are generally water soluble and also have high melting points.

Structure of Proteins

Proteins are what we call biological polymers (i.e. they occur naturally in nature). Now we previously learnt that amino acids are the building blocks of proteins. What this actually entails is that proteins are long chain-like structure, with amino acids being the main ingredient.  These amino acids are connected together with peptide bonds, and a few such bonds linking together form a polypeptide chain. Now one or more of these polypeptide chains twist or fold spontaneously and a protein is formed.

The size of the proteins varies greatly. It actually depends on the number of polypeptide molecules it contains. One of the smallest protein molecules is insulin, and the largest being Titin which consist of 34,350 amino acids.  The four types of protein structure that make up a protein molecule are:

1. Primary Protein Structure

The primary structure is the unique formation and order in which the amino acids (the building blocks) combine and link to give us a protein molecule. Protein gets all its properties from its primary structure.

There are in all twenty amino acids in the human body. All of these have a carboxyl group and an amino group. But each has a different variable group known as the “R” group. It is this R group that lends a particular protein its unique structure.

Every protein is determined by the sequencing of the amino acids. The formation and ordering of these amino acids in proteins are extremely specific. If we alter even one amino acid in the chain it results in a non-functioning protein or what we call a gene mutation.

2. Secondary Protein Structure

After the sequencing of amino acids, we now move on to the secondary structure. This is when the peptide backbone of the protein structure will fold onto itself, to give proteins their unique shape. This folding of the polypeptide chains happens due to the interaction between the carboxyl groups along with the amine groups of the peptide chains.

There are two kinds of shapes formed in the secondary structure. These are

· α-helix: The backbone follows a helical structure. The hydrogen bonds with the oxygen between the different layers of the helix, giving it this helical structure.

· β-pleated sheet: here the polypeptide chains are stacked next to each other and their outer hydrogen molecules form intramolecular bonds to give it this sheet-like structure

3. Tertiary Structures

This is the structure that gives protein the 3-D shape and formation. After the amino acids form bonds (secondary structure) and shapes like helices and sheets, the structure can coil or fold at random. This is what we call the tertiary structure of proteins. If this structure is disrupted or disturbed a protein is said to be denatured which means it is chemically affected and its structure is distorted.

4. Quaternary Structure

Finally, we come to the fourth structure. The spatial arrangement of two or more peptide chains leads to this structure. It is important to note it is not necessary for proteins to have quaternary structures. Primary, secondary and tertiary structures are present in all natural proteins, but the same is not true for quaternary structure. Hence if a protein has only the first three structures it is considered to be a protein.

Denaturation of Proteins

Ø Protein found in a biological system with a unique three-dimensional structure and biological activity is called a native protein.

Ø When a protein in its native form, is subjected to physical change like change in temperature or chemical change like change in pH, the hydrogen bonds are disturbed.

Ø Due to this, globules unfold and helix get uncoiled and protein loses its biological activity. This is called denaturation of protein.

Ø During denaturation 2° and 3° structures are destroyed but 1° structure remains intact.

Ø The coagulation of egg white on boiling is a common example of denaturation.