Biomolecules

Key concepts

All the elements present in a sample of earth’s crust are also present in a sample of living tissues.
* However, carbon and hydrogen are relatively abundant in living tissues.
* Living tissues are composed of inorganic elements and Biomolecules.
* All the carbon compounds produced by living tissues are called Biomolecules.
* We can analyze the chemical composition of a tissue by two methods.
        * Chemical analysis 
        * Elemental analysis
 

Chemical analysis:
* For chemical analysis a known weight of living tissue is grinded with trichloroacetic acid and filtered.
* The filtrate is called acid soluble fraction which contains organic compounds with low molecular weights or micro molecules. (Between 18 to 800 Daltons).
* Inorganic sulphates and phosphates are also present in acid soluble fraction.
* The acid soluble pool represents cytoplasmic composition.
* The retentate is called acid insoluble fraction and contains organic compounds with high molecular weights or bio macro molecules. (10,000 Daltons and more).
e.g.: Proteins, nucleic acids, polysaccharides and lipids.
* The acid insoluble fraction represents macromolecules from cytoplasm and organelles.

Elemental analysis:
* For elemental analysis we will find out the fresh weight of the tissue (leaf, liver etc.)
* The tissue is dried and its dry weight is estimated.
* Later the tissue is burnt to oxidize organic compounds in the form of CO₂ and H₂O and get ash.
* The ash contains inorganic elements like Calcium, magnesium etc.

Primary and secondary metabolites:
* The molecules formed and used in metabolic reactions are called metabolites.
* Primary metabolites are those Biomolecules which have known functions in the metabolism of a living organism. e.g.: aminoacids, sugars etc.
* Secondary metabolites are those metabolites which do not have known functions or whose functions are not known to us.
e.g.: alkaloids, essential oils etc.
* However secondary metabolites are of great use to human welfare as rubber, drugs, spices, scents, antibiotics, pigments etc.
 

Amino acids and Proteins
Amino acids:
* Amino acids are organic compounds which contain an amino group (NH₂) and acidic group (COOH) on the same carbon (α- carbon).
* Amino acids are substituted methanes.
* The four substituent groups on carbon are :
            * Hydrogen 
            * Carboxyl group
            * Amino group 
            * Variable group called R group

* The R group determines the nature of amino acid. 
            * If the R group is hydrogen it is Glycine.
            * If the R group is methyl group it is Alanine.
            * If the R group is hydroxymethyl group it is Serine.
* 21 types of amino acids make up the structures of proteins.
* The amino acids may be acidic (glutamic acid), basic (lysine), neutral (Valine) or aromatic
    (tyrosine, phenylalanine, and tryptophan).
* As both –NH₂ and –COOH groups are ionizable amino acids form zwitter ions.
* Amino acids play a main role in human diet.
* The aminoacids which our body can make are called non-essential aminoacids. These aminoacids are not required in our protein diet.
* The aminoacids which our body cannot make are called essential aminoacids. These aminoacids are supplied by our protein diet.
Proteins:
* Proteins are polymers of amino acids linked by peptide bonds.
* All proteins are heteropolymers, i.e. they are made up of 21 different types of amino acids. 
A peptide bond is formed when the carboxyl group (COOH) of one amino acid reacts with the amine group (NH₂) of next amino acid by eliminating a water molecule.
* The structure of proteins is determined by the number and sequence of aminoacids. Proteins show four levels of structures:
   * Primary structure: A thread like linear chain of aminoacids.
   * Secondary structure: The threads folded into other forms.
   * Tertiary structure: Long protein chains folded into hollow woolen ball like structure.
   * Quaternary structure: More than one polypeptide chains folded into spheres, cubes  or plates.
 Proteins have different functions in our body:
     * Transport nutrients across cell membranes.
     * Fight infectious agents (antibodies)
     * Hormones (insulin)
     * Enzymes (trypsin)
* Collagen is the most abundant protein in animal world. Rubisco is the most abundant protein in the whole biosphere.

Nitrogen bases and Nucleic acids:
* Nitrogen bases are a type of heterocyclic ring compounds present in nucleic acids of living organisms.
 They are of two types: 
       * Purines: Adenine and Guanine
       * Pyrimidines: Thymine, Cytosine and Uracil.
* The nitrogen bases along with sugars form nucleosides.
          For example Adenine + sugar = Adenosine
          Guanine + sugar = Guanosine
          Thymine + sugar = Thymidine
          Uracil + sugar = Uridine 
          Cytosine + sugar = Cytidine 
* When nucleosides combine with phosphate group nucleotides are formed.
Example: Adenosine  + Phosphate = Adenylic acid
                 Guanosine + Phosphate = Guanylic acid
                 Thymidine + Phosphate = Thymidylic acid
                Uridine + Phosphate = Uridylic acid
                Cytidine + Phosphate = Cytidilic acid
 

Nucleic acids
* Nucleic acids like DNA and RNA contain nucleotides.
* Nucleic acids are found in acid insoluble fraction because they are macromolecules called poly nucleotides.
* Each nucleotide in the nucleic acid contains 3 parts:
   Heterocyclic compound – nitrogen base
   Mono saccharide - ribose or deoxyribose sugar
   Phosphoric acid or phosphate
* A nucleic acid with deoxyribose sugar is called DNA or Deoxyribonucleic acid.
* A nucleic acid with ribose sugar is called RNA or Ribonucleic acid.
In a nucleic acid a phosphate moiety links the 3’ carbon of one sugar to the 5’ carbon of next sugar by phosphor diester bonds.
 

Structure of DNA:
* According to Watson and Crick model of DNA, the B-DNA exists as a double helix.  
* Two polynucleotide strands run anti parallel to each other in opposite direction.
* Sugar-phosphate-sugar forms the backbone.
* Nitrogen bases are present perpendicular to the backbone.
* Adenine pairs with Thymine by two hydrogen bonds.
* Guanine pairs with cytosine by three hydrogen bonds.
* Thus the DNA molecule appears like a helical stair case.
* At each step of ascent the strand turns 360^o .
* One full turn of helical strand involves ten base pairs.
* The pitch is 34 A0 and rise per base pair is 3.4 A⁰.
 

Lipids:
* Lipids are organic molecules with molecular weight less than 800 Daltons.
*  They may be present freely or arranged in structures like cell membranes.
*  As they are a part of cell membrane they are not water soluble and obtained as vesicles in acid insoluble portion.
*  Based on the complexity of structure lipids may be of the following types:
         * Simple fatty acids
         * Glycerol 
         * Fatty acids esterified with glycerol (Fats and Oils)
         * Phospholipids 
         * More complex lipids found in neural tissues.
*  A simple fatty acid has a carboxyl group attached to an R group (methyl, ethyl etc)
e.g.: Palmitic acid (16 carbons)
Arachidonic acid (20 carbons)

* Fatty acids may be saturated (without double bonds) or unsaturated (with one or more double bonds).
* Glycerol is another simple lipid which is chemically trihydroxy propane.
* Monoglycerides, diglycerides and triglycerides are fatty acids esterified with glycerol. These are also called fats or oils based on melting point.
* Oils have low melting points and hence remain as liquids even in winter.
e.g.: Gingelly oil.
* Lipids having phosphorous and a phosphorylated organic compound in them are called phospholipids. They are found in cell membranes.
e.g.: Lecithin.
* Neural tissues show lipids with more complex structure.
 

Polysaccharides:
* Polysaccharides are long chains of sugars which are polymers of monosaccharides.
* The individual monosaccharides are linked by glycosidic bonds between two carbon atoms formed by dehydration.
* In a polysaccharide chain the right end is called reducing end and left end is called non-reducing end.
* Polysaccharides may be homopolymers or heteropolymers.
* Homopolymers are composed of only one type of monosaccharide.
e.g.: Cellulose (made up of glucose units)
           Starch
           Insulin (made up of fructose)
* Starch forms helical secondary structures and can hold I2 (Iodine) molecules. Hence starch gives blue colour with Iodine.
* Cellulose does not have helical structures hence cannot hold Iodine molecules. Hence it does not give blue colour with Iodine.
* Heteropolymers are complex polysaccharides with monosaccharides and other molecules like amino groups.
e.g.: Amino sugars like glucosamine and N-acetyl galactosamine.
       Chitin (present in skeletons of arthropods and cell wall of fungi)
Note: Polysaccharides, nucleic acids and proteins are considered as bio macro molecules.
 

Concept of metabolism:
* Biomolecules are constantly changed into some other Biomolecules and also made from some other Biomolecules which is known as turn over.
* This breaking and making is through chemical reactions constantly occurring in living organisms called metabolism.
* All metabolic reactions are catalyzed by enzymes.

Metabolic basis for living:
* Anabolic pathways and catabolic pathway constitute metabolism.
* During anabolic pathways complex structures are synthesized. (Synthesis of glucose during photosynthesis). Anabolism consumes energy.
* During catabolic pathways complex structures are broken to form simple ones. (Breakdown of glucose into lactic acid in skeletal muscles). Catabolism liberates energy.
* ATP (Adenosine Tri Phosphate) is the energy currency of the cell.
 

The living state:
* All living organisms exist in a steady-state with determined concentrations of Biomolecules.
* Systems at equilibrium cannot perform work.
* Living organisms work continuously and cannot reach equilibrium.
* Hence the living state is a non-equilibrium steady state to be able to perform work.
* Living state and metabolism are synonymous.
* Without metabolism there cannot be a living state.