Protein (Bio Molecules)

PROTEIN

Proteins are biomolecules that are essential for the survival of the living organismsAmino acids are the building blocks of the proteins. There are 22 naturally occurring amino acids. Amino acid is composed of amino group, carboxyl group, hydrogen atom and R group (alkyl group). The R group is variable, that is, varies with different amino acids. These 4 groups are attached to single carbon atom known as Alpha-Carbon

Structure of Amino Acid

 

The simplest amino acid is glycine. In glycine, the R group is replaced by hydrogen atom. The bond between the two amino acid is peptide bond.

Fig.. Amino Acid Sequence-Protein

 

Amino acids

  • Amino acids are organic compounds made from an amine group and a carboxylic acid group.

 

  • It is the smallest unit of proteins.
  • Twenty types of amino acids are incorporated into proteins inside the human body. 

Classification of Amino Acids

·         Depending upon the relative position of amino group with respect to carboxyl group, the amino acids can be classified as α, β, γ, δ and so on.

·         For example:

·        

 

·         All naturally occuring amino acids are laevo-rotatory (except glycine).

•   Depending upon the relative number of amino and carboxyl groups in their molecule, Amino acid may be categorized as:

     o   Neutral: These are the amino acids containing equal number of NH2 and COOH groups.

     o   Acidic: These are the amino acids containing more COOH groups than NH2  groups

     o   Basic: These are the amino acids containing more NH2 groups than COOH groups

Peptides

·         Peptides are condensation products of two or more amino acids.

Peptide Linkage

·         Peptide linkage is an amide linkage formed by condensation of two amino acids involving −NH2  group of one amino acid and the −COOH group of the other amino acid with the loss of water.

For example:

·        

Classification of Peptides:

•   On the basis of number of amino acids undergoing the condensation, the peptides can be classified as:

     o    Dipeptide: It is a peptide composed of two amino-acid residues.

     o    Tripeptide: It is a peptide composed of three amino-acid residues.

     o    Polypeptide: It is a peptide composed of more than ten amino-acid residues.

 

Zwitterion form of amino acids:

·        In aqueous solution, the carboxyl group can lose a proton and amino group can accept a proton, giving rise to a dipolar ion known as zwitter ion. This is neutral but contains both positive and negative charges.

·        In zwitterionic form, amino acids show amphoteric behaviour as they react both with acids and bases.

 

Isoelectronic point: 

The pH at which the dipolar ion exists as neutral ion and does not migrate to either electrode cathode or anode is called isoelectronic point.

 

Essential and non essential amino acids

  • These are divided into essential amino acids, which cannot be synthesized inside the body, and non-essential amino acids. 

Essential amino acids :

  • Nine of the twenty amino acids are categorized as essential, which include leucine, isoleucine, valine, lysine, methionine, phenylalanine, threonine, histidine and tryptophan.
  • Tryptophan is used to make niacin, melatonin, and serotonin, which promote healthy sleep and a positive mood state.
  • leucine helps stimulate muscle protein synthesis.

Non-Essential amino acids :

  • Nonessential amino acids are those that your body naturally produces and therefore not essential to acquire through dietary sources.
  • Alanine, asparagine, aspartic acid, glutamic acid, arginine, cysteine, glutamine, glycine, proline, serine, tyrosine are all considered nonessential amino acids.

 

Structure of protein

Primary Protein Structure -Each polypeptide in a protein has amino acids linked with each other in a specific sequence and it is this sequence of amino acids that is said to be the primary structure of that protein. Any change in this primary structure i.e., the sequence of amino acids creates a different protein

 

Secondary protein structure

Two basic forms: alpha-helices and beta-sheets

·        Hydrogen bond interactions within the alpha-helix and beta-sheet provide the stability of the secondary structure of proteins.

Alpha-helices

·        An α-helix can be either right- or left-handed.

·        The α-helices found in proteins are almost always right-handed.

 

Beta-pleated sheets

·        When two adjacent β-strands line up they can from bridges of hydrogen bonds. This creates a very stable structure known as a β-sheet.

·        There are two ways the β-strands can position themselves to form a β-sheet.

·        They can be in either parallel or anti-parallel orientation.

 

·        Parallel — the peptide chain advances in a single direction.

·        Anti-parallel — the peptide chain advances in two opposite directions.

Tertiary protein structure

·        The tertiary structure of proteins represents overall folding of the polypeptide chains i.e., further folding of the secondary structure. It gives rise to two major molecular shapes viz. fibrous and globular.

·        The main forces which stabilise the 2° and 3° structures of proteins are hydrogen bonds, disulphide linkages, van der Waals and electrostatic forces of attraction.

 

Quaternary protein structure

 

·        Some of the proteins are composed of two or more polypeptide chains referred to as sub-units.

·        The spatial arrangement of these subunits with respect to each other is known as quaternary structure.

 

 

Fibrous and Globular protein

Fibrous proteins

·        When the polypeptide chains run parallel and are held together by hydrogen and disulphide bonds, then fibre– like structure is formed.

·        These proteins are generally insoluble in water

·        Examples: keratin (present in hair, wool, silk) and myosin (present in muscles), etc

Globular proteins

·        This structure results when the chains of polypeptides coil around to give a spherical shape.

·        These are usually soluble in water.

·        Examples: Insulin and albumins

 

Denaturation of proteins

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

·        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.

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

·        During denaturation secondary and tertiary structures are destroyed but primary structure remains intact. The coagulation of egg white on boiling is a common example of denaturation.

·        Another example is curdling of milk which is caused due to the formation of lactic acid by the bacteria present in milk.

 

Enzyme

•     Enzymes are proteinaceous substances which are used as biological catalysts.

•     Almost all the enzymes are globular proteins.

•     Being proteins, they have colloidal nature and get inactivated during reactions and have to be constantly replaced by synthesis in the body.

•     Enzymes are needed only in small quantities for the progress of a reaction.

•     Enzymes are very selective and specific for a particular reaction.

•     Enzymes lower the energy barrier that reactants must pass over to form the products.

•      An enzyme molecule may contain a nonprotein part which is known as prosthetic group.

It is of two types:

      o     Cofactor: The prosthetic group which is covalently attached with the enzyme molecule is known as cofactor.

      o     Coenzyme: The prosthetic group which get attached to the enzyme at the time of a reaction is known as coenzyme.

Nomenclature of Enzymes

Enzymes are usually named by adding the suffix ‘ase’ to the root name of the substrate, e.g., urease, maltase, invertase, etc.

Mechanism of Enzyme Action

•   There is a lock and key arrangement between the an enzyme and a substrate.

•   Substrates bind at active site, temporarily forming an enzyme-substrate (E-S) complex.

•   The E-S complex undergoes internal rearrangements that form the product.

•   The enzyme gets regenerated for the next molecule of the substrate.