Friday, June 8, 2012

Biomolecules

Biomolecules are chemical compounds found in living organisms. They include organic and inorganic compounds.

BIOMICROMOLECULES

Include amino acids, sugars, nitrogen bases, lipids etc.

1. Amino acids

A typical amino acid is formed of an amino group (-NH2), an acid group (-COOH), H & a variable group (R). –NH2 and  –COOH are attached to the same carbon atom (α-carbon).
20 amino acids are used for protein synthesis. They include
·   Acidic amino acids (e.g. glutamic acid)
·   Basic amino acids (e.g. Lysine)
·   Neutral amino acids (e.g. Valine)
Some amino acids are aromatic (e.g. tyrosine, phenyl alanine, and tryptophan).
Amino acids have ionizable nature of –NH2 & –COOH groups.

2. Lipids
-    Water insoluble. Contains fatty acids and glycerol.
-    A fatty acid has –COOH group attached to an R- group.
-    Palmitic acid has 16 carbons (CH3-(CH2)14-COOH) and Arachidonic acid has 20 Carbons.
-    Fatty acids are 2 types:
o Saturated fatty acids: No double or triple bonds between 2 carbon atoms.
o Unsaturated Fatty acids: One or more C=C bonds.
-    Structure of glycerol (trihydroxy propane):
CH2-OH
|
CH-OH
|
CH2-OH
-    Many lipids have both glycerol and fatty acids to form fats. (Fatty acids are esterified with glycerol).
-    It includes monoglycerides, diglycerides & triglycerides.
-    Based on melting point lipids are 2 types: fats and oils.

3. Sugars (Carbohydrates)

Sugars are sweet and water soluble carbohydrates. They are formed of C, H and O in the ratio of 1:2:1.

4. Nitrogen Bases

Includes Purines (Adenine & Guanine) and Pyrimidines (Cytosine, Thymine & Uracil) 

   Nucleoside: Nitrogen base + Sugar.
Adenine + sugar           =         Adenosine
Guanine + sugar           =         Guanosine
Cytosine + sugar         =         Cytidine
Thymine + sugar         =         Thymidine
Uracil + sugar             =         Uridine 


   Nucleotide: Nitrogen base + Sugar + phosphate.
Adenine + sugar + phosphate    =     Adenylic acid
Guanine + sugar + phosphate    =     Guanylic acid
Cytosine + sugar + phosphate   =     Cytidylic acid
Thymine + sugar + phosphate    =     Thymidylic acid
   Uracil + sugar + phosphate        =      Uridylic acid 


Nucleotides are heterocyclic compounds.
Nucleic acids (DNA & RNA) are made up of nucleotides.

BIOMACROMOLECULES

-    Molecules having molecular weight greater than 1000 Dalton (Da) is called biomacromolecules.
-    Molecules having molecular weight less than 1000 Da are called micromolecules.
-    Molecular weight of compounds found in the acid soluble pool ranges from 18 to 800 Da. The acid soluble pool represents the cytoplasmic composition.
-    Biomacromolecules are found in acid insoluble fraction.
-   

Molecular weight is 10,000 Da and above except lipids.
Acid insoluble fraction includes
o Proteins
o Nucleic acids            
o Polysaccharides
o Lipids
-    Molecular weight of lipids does not exceed 800 Da. But it comes under acid insoluble fraction because lipids are arranged into structures like cell membranes. When a tissue is grinded, these membranes are broken and form vesicles which are water insoluble, i.e. lipids are not strictly macromolecules.
-    Acid insoluble fraction: Includes macromolecules from cytoplasm and organelles.

Average composition of cells
Water                : 70-90 %
Protein              : 10-15%
Carbohydrates    : 3%
Lipids               : 2%
Nucleic acids     : 5-7%
                        Ions                  : 1%


2. Polysaccharides

These are polymers of sugars (monosaccharides). E.g.
§ Starch (polymer of glucose)
§ Cellulose (polymer of glucose)
§ Inulin (polymer of fructose)
§ Glycogen
§ Glucosamine
§ N-acetyl galactosamine
  § Chitin (Exoskeleton of arthropods) 
§ Glycosidic bond in polysaccharides: It is the bond formed when individual monosaccharides are linked between 2 carbon atoms by dehydration.
§ Starch forms helical secondary structure. Starch holds I2 molecules in the helical portion giving blue colour.
§ Cellulose has no complex helices and so cannot hold I2.
§ Diagrammatic representation of a portion of glycogen is given below:









3. Nucleic acids (DNA and RNA)

Secondary structure of DNA (Watson - Crick Model)

-    DNA exists as a double helix. The 2 polynucleotide strands are arranged antiparallely.
-    One full turn of helical strand have 10 steps (10 base pairs).
-    Length of one full turn = 34 Å (i.e. 3.4 Å for each step).
-    At each step the strand turns 360 (3600 for a full turn).
-    A polynucleotide chain is heteropolymer of nucleotides.
-    A nucleotide consists of nitrogen bases, deoxyribose sugar and phosphate group
-    The backbone of DNA is formed by the sugar-phosphate-sugar chain. Nitrogen base pairs form the steps of DNA.
-    Nitrogen bases include Adenine (A), Guanine (G), Thymine (T) and Cytosine (C).
-    A pairs with T (A=T) by 2 hydrogen bonds.
-    G pairs with C (G≡C) by 3 hydrogen bonds.
-    A phosphate molecule links the 3’-carbon atom of one sugar of one nucleotide to the 5’-carbon of the sugar of the succeeding nucleotide.
-    There is an ester bond between PO43- and –OH group of sugar. As there is one such ester bond on either side, it is called phosphodiester bond.



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