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Biomolecules




BIOMOLECULES

Biomolecules are the organic substances that play a major role in the structure and function of the living organism.
 

Primary and Secondary Metabolites:

A large number of organic biomolecules are present  in the cells which are used in various metabolic reactions of cells. Hence, these compounds are called metabolites.
 
Primary metabolites: These are metabolites which are found in animal tissues. They play specific roles in the normal physiological processes.
For example: Amino acids, carbohydrates, nitrogenous bases, proteins, nucleic acids etc.
 
Secondary metabolites: These are metabolites which are generally found in plants, fungal and microbial cells. These are the products of certain metabolic pathways.
For example: Alkaloids, coloured pigments, Essential oils etc.
Both primary and secondary metabolites serves the following functions-
  • Many of them are useful in human welfare, for example: Rubber, drugs, spices, pigments, scents.
  • Some have ecological importance.

 

Proteins:

  • These are the most important and abundant intracellular organic biomolecule.
  • They are polypeptide having chain of amino acids, arranged linearly that are linked by peptide bonds.
  • Proteins are considered as heteropolymer.
 
Structure Of Protein:
 
Primary structure:
  • This includes the number and sequence of amino acids in each polypeptide.
  • The left end of the protein is represented by first amino acid also called as the N-terminal amino acid and the right end is represented by C-terminal amino acid.
For example: Insulin, Ribonuclease
 
Secondary Structure:
  • The thread of the primary protein is folded in the form of Alpha helix.
For example- keratin
  • In beta -pleated secondary structure two or more polypeptide chains get interconnected by hydrogen bonds.
For example: Silk fibre
 
Tertiary structure:
  • There is bending and folding of various types to form a hollow woolen ball like sphere, rods or fibres.
  • It is established by several types of bonds that are ionic bonds, Vander waals interactions, covalent bonds and hydrophobic bonds.
  • It gives information about a three-dimensional conformation of the protein.
For example: Myoglobin
 
Quaternary structure: 
Certain proteins consist of an assembly of more than one polypeptide or subunit.
For example: Hemoglobin.

 
Function of Proteins:
  • Help in transportation of nutrients across the cell membrane by acting as protein transporter.
  • These are helpful in Movement of muscles. For example: myosin and actin.
  • Help in maintenance of ph and regulation of volume of body fluid.
  • Help in fighting with infectious organisms.
  • Help in growth and repair of body tissues.
  • Some proteins function as hormones and some as enzyme and catalyse the reactions.
 

Amino Acid:

  • Amino acids are organic compounds containing an amino group, an acidic group as substituents on the same carbon i. e., the alpha-carbon.
  • Alpha-carbon also bear a hydrogen and a variable group designated as R group. Thus, there are 4 substituent group present on alpha carbon i.e., hydrogen, carboxyl, amino and R-group.
  • Based on the nature of amino, carboxyl and R-functional group, the chemical and physical properties of amino acids are decided.

 
Based on the number of amino and carboxyl group present, amino acids are categorised into following types:
 
Acidic amino acid: These contain 1 amino group and 2 carboxyl groups per molecule.
For example: Glutamic acid, Aspartic acid
 
Basic amino acid: These contain 2 amino group and 1 carboxyl group per molecule.
For example: Arginine, Lysine and Histidine.
 
Neutral amino acid: These contain 1 amino group and 1 carboxyl group per molecule.
For example: Methionine, Serine, glycine and alanine etc.
 
Aromatic amino group: These contain aromatic ring in their side chain.
For example: Phenylalanine, Tyrosine, Tryptophan.
 
 
Zwitter ion:
It is a neutral molecule (with positive and negative charge) having the ionizable nature of amino (-NH2) and carboxyl (-COOH) groups.
Hence in solution of different pH the structure of amino acid changes variably.

 
Note
  • The amino group accepts a Proton whereas the carboxyl group donates a Proton so an amino acid can act as both acid and base. So it is amphoteric in nature.
  • The amino acids in proteins are joined by peptide bond.
 

Carbohydrates:

  • These are the organic compounds mainly made up of carbon, hydrogen and oxygen.
  • They are defined as polyhydroxy aldehyde and ketones.
  • Carbohydrates are also known as saccharides because their major constituents are sugar.
  • They are produced directly by plants during photosynthesis. 
These are divided into following types:
Monosaccharides:
  • These are the simplest carbohydrates which can't be hydrolysed further into smaller carbon compounds.
  • These are generally composed of three to seven carbon atoms per molecule.
  • Monosaccharides are also known as reducing Sugars because they have a free aldehyde and Ketone group and can also reduced cupric ion Cu2+ of Benedict's or Fehling's solution to Cuprous Cu+.
  • For example: Ribose, glucose etc.

 
Oligosaccharides:
  • These are formed by condensation of 2 to 6 monosaccharide molecules.
  • The bond between two monosaccharide units is called Glycosidic Bond.
They are classified according to number of monosaccharide units-
Disaccharides: Sugar containing two monomeric units and can be further hydrolysed into smaller components.
These are known as non -reducing sugar because free aldehyde and Ketone group is absent.
For example: Sucrose, maltose, lactose etc.
Trisaccharides: It contains three monomer units. For example: raffinose.
Tetrasaccharides: It contains four monomeric units. For example: stachyose
 
Polysaccharides (Acid insoluble fraction):
Polysaccharides are long chains of Sugars. These are made up of two ends, the right end is called reducing end, and the other left end is called non-reducing end.
They are the thread containing different monosaccharides as building blocks.
Types of polysaccharides:
Homopolysaccharides: These are those Complex carbohydrates which are formed by polymerization of only one type of monosaccharide monomers.
For example: Starch (glucose monomer), cellulose (glucose monomer),glycogen (glucose monomer), Inulin (Fructose monomer).
Heteropolysaccharides: These are complex carbohydrates formed by the polymerization of two or more than two types of monosaccharide monomers.
For example: Chitin (N- acetylglucosamine), pectin, peptidoglycans (Murein), hyaluronic acid.
 
Functions of polysaccharides:
  • Act as a structural compound in the cell wall of plants, certain fungi and protists.
For example: Cellulose, Chitin.
  • Help in anticoagulation and prevents blood clotting inside the vessels.
For example: Heparin
  • Help in lubrication of joints between bones.
For example: hyaluronic acid
  • Also used in tissue culture.
For example: Agar
  • Act as reserve food.
For example: Starch

Nucleic Acids (Acid Insoluble Fraction):

These are polymeric compounds of nucleotides i. e.,polynucleotides.
A nucleotide is composed of three chemically distinct components-
  1. Heterocyclic compound: Nitrogenous base.

It is of two types

Purine (Dicyclic)- Adenine (A) and Guanine (G).

Pyrimidine (Monocyclic)- Cytosine  (C), Thymine (T) and Uracil (U).

  1. Monosaccharide sugar: Ribose and deoxyribose sugar.
  2. Phosphoric acid or phosphate.
A nucleic acid which contains deoxyribose sugar is called DNA that is deoxyribonucleic acid.
While which contain ribose sugar is called RNA that is ribonucleic acid.
When sugar is attached to base, then it forms nucleoside and when phosphate group is attached to it, then it is called nucleotide.
The two nucleotides of nucleic acids are joined by phosphodiester bond.

 
Structure of DNA:
  • The structure of DNA was elucidated by Watson and Crick based on X-Ray diffraction method.
  • DNA exists as a double helix and consists of two strands of polynucleotides that are antiparallel to each other that is one in 5' to  3' direction and other is 3' to 5' direction.
  • The backbone of DNA is formed by the sugar-phosphate-sugar chain.
  • A always paired with T with two hydrogen bonds and G always paired prepared with C with three hydrogen bonds.
  • One turn of DNA measures 3.4nm and consists of 10 nucleotides. This form of DNA is called B- DNA.

Functions of Nucleic Acid:
  • It enables cell to grow,  maintain and divide by directing the synthesis of structural proteins.
  • Act as genetic material i.e, transfer hereditary characters from one generation to the next.

Lipids:

  • Lipids are the esters of fatty acid and alcohol and insoluble in water.
  • Fatty acids are organic acids having hydrocarbon chains (R- group) that end in a Carboxyl Group (-COOH).
  • For example- Palmitic acid has 16 carbon including carboxyl carbon.
Arachidonic acid has 20 carbon including Carboxyl carbon.
 
Fatty acids are following two types:
Saturated fatty acids:
Fatty acids which do not have double bond (C-C) and are generally solid at room temperature.
CH3-(CH2)14-COOH        Palmitic acid
They have relatively higher melting points and are present in most animal fat.
 
Unsaturated fatty acid:
Fatty acids which contain one or more than one double bonds (C=C) and are generally liquid at room temperature.
CH3-(CH2)7-CH=CH(CH2)7COOH
They have relatively lower melting points and are present in most plant fat.
 
Lipids are classified into following subgroups-
Simple Lipids:
These are esters of fatty acids and various alcohol.
  1. Natural or True fats: These are esters of fatty acid with glycerol (glycerides).
  2. Waxes: These are esters of fatty acids with alcohol other than glycerol.
 
Compound or Conjugated Lipids:
These are esters of fatty acids and alcohol but contain other substances also.
For example- Phospholipids (lipids having Phosphorus and phosphorylated organic compounds) for example: Lecithin
Glycolipids: Suberin, cutin etc.
 
Derived Lipids:
These are lipids like substances such as sterol  or derivatives of lipids. For example- Steroids.
 
Fats are also differentiated on the basis of their melting point at room temperature-
  • Hard fats are solid at room temperature and contain a long chain of fatty acids. For example- Animal fat.
  • Oils are usually liquid at room temperature because they have low melting point. For example- groundnut oil, cottonseed oil, mustard oil etc.

Although lipids have their molecular weight not exceeding above 800Da but still it comes under an acid insoluble fraction that is biomacromolecule. Because these are small molecular weight compounds and are present not only as such but also arranged into structures like cell membrane and other membrane.
 
When we grind the tissue which disrupts the cell structure, cell membrane and other membranes are broken down into pieces and form vesicles that are not water soluble. So these are separated along with acid insoluble pool and are placed in macromolecules.
 

Concept of Metabolism (Dynamic state of body constituents):

  • Turn over of biomolecule is the phenomenon in which biomolecule change constantly into some other biomolecules or made from some other biomolecules.
  • All these, transfer of one molecule into other occur due to chemical reaction which continuously takes place in an organism. The chemical reactions together are called Metabolism, which do not occur in isolation but they takes place in a series of linked reactions known as metabolic pathways.
  • Flow of metabolites through metabolic pathways has a definite rate and direction and are always catalyzed reactions. The catalyst which hasten the rate of a given metabolic conversion are also proteins. These proteins with catalytic power are called enzymes.
 
 
Anabolic Pathways
Catabolic Pathways
These include formation of complex structures from simple ones.
These include the formation of simple structure i.e., the breakage of complex structure into simpler ones.
Example- Formation of cholesterol from acetic acid, protein synthesis etc.
Example- Conversion of glucose into lactic acid in skeletal muscles
These are energy consuming pathways.
These are energy releasing pathways.
 

Enzymes-

The term enzymes was coined by Kohne  enzymes are colloidal organic macromolecules, which are mostly proteinaceous in nature.
These are essential for normal metabolism in the cells.
Enzymes are water soluble in nature.
These are useful for catalyzing biochemical reactions in living cells so also called Biocatalyst.
 
Properties of Enzymes:
  1. They enhance the rate of chemical reaction without themselves being changed or used.
  2. Enzymes are efficient in very small amounts.
  3. Enzymes are highly specific, as each of them catalyzes only a specific reaction.
  4. For example- Maltase acts only on maltose. Enzymes can be denatured by heat (thermolabile or heat sensitive).
  5. Human enzymes are active at 35° to 40° Celsius and denatured at 50° to 55°Celsius.
 
Active site:
It is a crevice or pocket of an enzyme into which a particular substrate fix. Thus, enzymes catalyse reaction at a higher rate through their active sites. Each enzyme functions at a specific pH and temperature.
 
Functioning of enzymes:
For a chemical reaction to proceed the substrate (S) must bind to enzyme at the active site within a cleft or pocket.
During conversion of substrate into product formation of an enzyme-substrate complex takes place.
This complex formation is a transient phenomenon.
The active site of enzyme, now enclosed proximity of the substrate, breaks the chemical bonds of the substrate and a new enzyme-product complex is formed.
The enzyme releases the product of the reaction and the free enzyme is ready to bind to another molecule of the substrate and run through the catalytic cycle once again.
The formation of the ES complex is essential for catalysis.

 
Concept of Activation Energy:

Enzymes catalyzes the transition of substrate (S) to product (P) by lowering the activation energy.
 
Factors Affecting Enzyme Activity:
Factors include temperature, pH, change in substrate concentration or binding of specific chemical that regulate its activity.
 
Temperature and pH:
Enzymes generally function in a narrow range of temperature and pH.
Each enzyme shows its highest activity at a specific temperature and pH known as optimum temperature and optimum pH.
For example- Amylase function at 37°Celsius.
 

Concentration of Substrate:
With the increase in concentration of substrate, the velocity of the enzymatic reaction rises at first. The reaction finally reaches the maximum velocity that is Vmax.
Vmax is the maximum velocity which does not exceed even by any further rise in concentration of the substrate. This is because at this stage the enzyme molecule becomes fully saturated and no active site is left free to bind to additional substrate molecules.
 
Enzyme inhibition:
The enzyme activity is also sensitive to the presence of specific chemicals that shut off the enzyme, the moment they bind to the enzyme.
This process is known as inhibition and the chemical responsible is known as inhibitor.
 
Competitive inhibition:
When the inhibitor closely resembles the substrate in its molecular structure and inhibits the activity of the enzyme, it is known as competitive inhibitor. Due to its close structural similarity with the substrate, the inhibitor completes with the substrate for the substrate binding site of the enzyme. So the substrate cannot bind and as a result, the enzyme action declines.
For example- inhibition of succinic dehydrogenase by malonate which closely resembles the substrate succinate and structure.
 
Classification and Nomenclature of Enzymes:
Enzymes are divided into 6 classes each with 4-13 subclasses and named accordingly by a four-digit number.
 
 
Enzyme
Function
Oxidoreductases/dehydrogenases
Enzymes which catalyse oxidoreduction between two substrates S and S'.
For example:
S reduced + S' oxidised ----- S oxidised + S' reduced.
Transferases
Enzyme catalysing a transfer of a group, G (other than hydrogen) between a pair of substrate S and S'.
For example:
S-G + S' ------- S + S'-G
Hydrolases
Enzymes catalysing hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide Or P-N bonds.
Lyases
Enzymes that catalyse removal of groups from substrates by mechanisms other than hydrolysis leaving double bonds.
Isomerases
Includes all enzymes catalysing inter-conversion of optical, geometrical for positional isomers
Ligases
Enzyme catalyzing the linking together of 2 compounds, for example, enzymes which catalyse joining of C-O, C-S, C-N, P-O etc. bonds.
 
Co-factor:
Enzyme is known as Holoenzyme. The protein portion of the enzyme is known as apoenzyme. There are a number of cases in which non-protein constituents called Co- factor are bound to the enzyme to make the enzyme catalytically active.
Three kinds of Co-factors may be identified
Prosthetic group
Co-enzyme
Metal ion
 
Prosthetic Group:
They are organic compounds which are tightly bound to the apo-enzyme.
For example- in peroxidase and catalase, which catalyze the breakdown of H2O2 to water and oxygen, haem is the prosthetic group and it is a part of the active site of enzyme.
 
Co -enzyme:
Coenzymes are organic compounds which usually occur during the course of catalysis and they serve as co-factor in a number of different enzyme catalyzed reactions.
The essential chemical components of many coenzymes are vitamins, for example, coenzyme nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin.
 
Metal Ion:
They form coordination bonds with the side chain at the active site and at the same time form one or more coordination bonds with the substrate.
For example- Zinc is a cofactor for proteolytic enzyme carboxypeptidase.
 
Catalytic activity is lost when the Co-factor is removed from the enzyme.
 


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