Proteins

PROTEINS

Introduction

Proteins are the most abundant organic compounds to be found in cells and comprise over 50% of their total dry weight. They are present in all types of cells and in all parts of the cell.

Function

Proteins perform many functions. Some of their important functions are;

1. They build many structures of the cell.
2. All enzymes are proteins and in this way they control the whole metabolism of the cell.
3. Somehormones are also proteins and regulate metabolic processes.
4. Some proteins (e.g. haemoglobin) work as carriers and transport specific substances such as oxygen, lipid, metal ions etc.
5. Some proteins called antibodies, defend the body against pathogens.
6. Blood clotting proteins prevent the loss of blood from the body after an injury.
7. Movement of organs and organisms and movement of chromosomes during anaphase of cell division, are caused by proteins.

Amino acids as units of protein

1. Proteins are polymers of amino acids, the compounds containing carbon, nitrogen, oxygen and hydrogen.
2. The number of amino acids varies from a few to 3000 or even more in different proteins.

• About 170 types of amino acids have been found to occur in cells and tissues.
• Out of these about 25 are constituents of proteins.
• Most of the proteins are however made of 20 types of amino acids.

Chemical composition of amino acids

All the amino acids have an amino group (-NH2) and carboxyl group (-COOH) attached to the same carbon atom, also known as alpha carbon. They have the general formula as:

R may be Hydrogen atom as in glycine and CH3 group as in alanine. So amino acids mainly differ due to the type or nature of R group.

Linkage between amino acids

• Amino acids are linked together to form polypeptide proteins. The amino group of one amino acid may react with the carboxyl group of another, releasing a molecule of water. For example, glycine and alanine may combine and form a dipeptide.
• The linkage between the hydroxyl group of carboxyl group of one amino acid and the hydrogen of amino group of another amino acid release H2O and C-N link to form a bond called peptide bond.
• The resultant compound glycylalanine, has two amino acid subunit and is dipeptide.

• A dipeptide has an amino group at one end and a carboxyl group at the other end of the molecule. So both reactive parts are again available for further peptide bonds to produce tripeptides, tetrapeptides and pentapeptide etc, leading to polypeptide chains.

Peptide linkage-formation of peptide bond

Arrangement of amino acids in proteins

• There are over 10,000 proteins in the human body, which are composed of unique and specific arrangement of 20 types of amino acids.
• The sequence of amino acid in protein is determined by the order of nucleotides in the DNA.
• The arrangement of amino acids in a protein molecule is highly specific for its proper functioning.
• If any amino acid is not at its normal place, the protein fails to carry on its normal function.

Example

The best example is the sickle cell haemoglobin. In this case only one amino acid in each beta chain out of the 574 amino acids do not occupy the normal place in the proteins and the heamoglobin fails to carry any or sufficient oxygen, hence leading to death of the patient.

Size of proteins

The size of protein molecules is determined by the type of amino acids and the number of amino acids comprising the particular protein molecule.

Structure of Proteins

Each protein has specific properties, which are determined by the number and the specific sequence of amino acids in a molecule and upon the shape, which the molecule assumes as the chain folds into its final, compact form.

There are four levels of organization, which are described below.

(i) Primary structure

Primary structure comprises the number and sequence of amino acids in a protein molecule.

F. Sanger was the first scientist who determined the sequence of amino acids in a protein molecule.

Example

• F. Sanger concluded that insulin is composed of 51amino acids in two chains. One of the chains has 21amino acids and the other has 30 amino acids and they are held together by disulphide bridges.
• Haemoglobin is composed of four chains, two alpha and two beta chains. Each alpha chain contains 141amino acids, while each beta chain contains 146amino acids.

(ii) Secondary structure

Secondary structure tells us about the helix structure or other regular configuration of polypeptide chains.

Polypeptide chains do not lie flat. They usually coil in a helix or into some other regular configuration.

Example

• One of the common secondary structure is the α -helix. It involves a spiral formation of the basic polypeptide chain. The α-helix is a very uniform geometric structure with 3.6 amino acids in each turn of the helix.
• The helical structure is kept by the formation of hydrogen bonds among amino acid molecules in successive turns of the spiral
• -pleated sheet is formed by fold backs of the polypeptide.

(iii) Tertiary structure

Usually a polypeptide chain bends and folds upon itself forming a globular shape. Tertiary structure tells us about shape of protein after bending and folding.

Tertiary structure is maintained by three types of bonds, namely ionic, hydrogen and disulphide (-S-S-).

Example

In aqueous environment, the most stable tertiary structure (conformation) is that in which hydrophobic amino acids are buried inside while hydrophilic amino acids are on the surface of the molecule.

Polypeptide chains in keratin (fibrous protein) and in hemoglobin

(globular protein) are held together to form respective functional proteins.

(iv) Quaternary structure

In many highly complex proteins, polypeptide tertiary chains are aggregated and held together by hydrophobic interactions, hydrogen and ionic bonds. This specific arrangement is the quaternary structure.

Example

Hemoglobin, the oxygen carrying protein of red blood cells, which exhibits such a structure.

Classification of proteins

Because of complexity of structure and diversity in their function, it is very difficult to classify proteins in a single well defined fashion. However, according to their structure, proteins are classified as follows:

(i) Fibrous proteins

• They consist of molecules having one or more polypeptide chains in the form of fibrils.
• Secondary structure is most important in them.
• They are insoluble in aqueous media.
• They are non-crystalline and elastic in nature.
• They perform structural role in cells and organisms.

Examples

Examples are silk fiber (from silk worm and spiders’ web), myosin (in muscle cells), fibrin (of blood clot) and keratin (of nails and hair).

(ii) Globular proteins

• They are spherical or ellipsoidal due to multiple folding of polypeptide chains.
• Tertiary structure is most important in them.
• They are soluble in aqueous media such as salt solution, solution of acids and bases or aqueous alcohol.
• They can be crystallized.
• They disorganize with changes in the physical and physiological environment.

• Example

  Examples are enzymes, antibodies, hormones and hemoglobin.
  
  Three levels of protein structures compared with a telephone wire.