Biology: Biomolecules

: Bio-Molecules

Living cells are composed of both organic and inorganic components.

How to analyse chemical composition:

For organic compounds:

·         Living tissue + trichloro acetic acid and grind it to form slurry.

·         Filter the slurry to obtain 2 fractions like  Filtrate/ acid soluble and Retentate/ acid insoluble

For inorganic compounds:

Sample of tissue should be burnt to obtain ash and different kinds of inorganic compounds were identified.

Types of biomolecules  - Micro molecules and Macro molecules

·         Micro molecules are known as monomers

·         Macromolecules are known as polymers

Primary and Secondary metabolites: These are biomolecules in living cells metabolites.

Primary metabolites are those which have identifiable functions and play specific roles in normal physiological processes. Eg. Amino acids, nitrogenous bases, proteins and nucleic acid.

Secondary metabolites are product of certain metabolic pathways from primary metabolites.

·         Pigments – anthocyanin, carotenoids

·         Drugs – vinblastin, curcumin

·         Alkaloids - morphine, codeine

·         Essential oils – lemon grass oil

·         Polymeric compounds - rubber gum, cellulose, resins

Biomacromolecules



It is molecules with weight greater than 1000 dalton found in acid insoluble fraction.

Eg- polysaccharides, nucleic acid, proteins and lipids.

Polysaccharides :

·         Long chain of polymers of monosaccharides – 2 types of Mono-polysaccharides (cellulose, starch – made of only Glucose monomers).

·         Heteropolymer – chitin

·         Inulin  -is a polymer of fructose

·         Glycogen – polymer of glucose in animal tissues

·         Monosaccharides are joined by Glycosidic acid bond, right end is reducing and left end is non reducing.

·         Starch forms helical secondary structures. Starch can hold Iodine molecules in helical portion and form blue colour. But Cellulose does not contain complex helices and cannot hold iodine.

·         Complex polysaccharide: .Plant cell wall (cellulose ), Paper (plant pulp ), Cotton, Fibre (cellulose) Exoskeleton of animals, building blocks, amino-sugars and chemically modified Sugars like, Eg. – Giucosamine (N – acetyl galactosamine).

Nucleic acids: 



·         DNA – Polynucleotide chain, double stranded (deoxy ribose sugar) – nitrogenous bases are A, G, C and T

·         RNA – single stranded Polymer of ribo-nucleotides (ribose sugar) – A, G, C and U

·         Nucleotides – nitrogenous base + pentose sugar + phosphate group

·         Nucleoside – nitrogenous base + pentose sugar

·         Nitrogenous  bases

1.       Adenine (A)

2.       Guanine(G)

3.       Cytosine( C )

4.       Thymine (T)



Phospho-diester bonds – covalent bond formed between nucleotides.

Proteins: 



·         Polymer of amino acids (peptide bonds)

1.       Primary structure – linear chain of aminoacids linked by peptide bonds – non functional.

2.       Secondary structure – alpha-helix or beta-pleated structure with peptide and hydrogen bonds.

3.       Tertiary structure – long chain of coiled structure with peptide, hydrogen, disulphide and ionic bonds – functional structurte of protein.

4.       Quaternary structure – group of more than two tertiary structured proteins (eg- haemoglobin – made of two alpha and two beta chains).

Nature of bonds linking monomers in a polymer:



1.       Amino acids are linked by Peptide bonds

2.       Monosaccharides are linked by Glycosidic bond

3.       Nucleotides are linked by  Phosphodiester bond between 3-C of one nucleotide with

5-C of another - Each helix of DNA contains 10 base pairs with the length of 3.4 nm (34 Ao).

Concept of Metabolism:  



·         Biomolecules have turn over (because constantly changing from one form to another)

·         Chemical reactions are called metabolism.

Examples:

·         Amino acids can be formed by the removal of amino group in a nucleotide base.

·         Hydrolysis of disaccharides – 2  monosacharides

·         Linked chemical reactions are called Metabolic pathways, it is a catalysed reaction by enzymes.

Metabolic pathways in living system:

·         Anabolic pathways - making / constructing big molecules from micromolecules (eg – photosynthesis)

·         Catabolic pathways – breaking down of big molecules in to smaller ones  (eg – respiration)

·         For both ATP is required (energy currency)

The living state

·         Blood glucose – should be 4.5 -5.0mM

·         Hormones – in nanograms/mL

·         System at equilibrium cannot perform work

·         As living organisms work constantly, it is non equilibrium.

·         Hence the living state is non equilibrium steady state to be able to perform work.

Enzymes Vs Catalysts:



·         Enzyme –  helps in chemical reactions

·         Inorganic reaction :- Ba(OH)2 + H2SO4 --> BaSO4 + 2 H2O – No enzyme used.

·         Organic reaction  - Enzyme used

·         Carbonic anhydrase – fastest enzyme - without enzyme 200 molecules / hr - with enzyme 600,000 molecules / sec.

·         Activation energy  is the energy needed to do work.

Nature of enzyme action:

Enzyme + Substrate --> ES complex --> Enzyme + Product

ENZYME

CATALYST

1.

It is produced by living cells and made of protein.

It is chemical substances and help in chemical reactions.

2.

It can work well at optimum temperature of 40o C.

It can work even at 80 – 90o C.

3.

It reduces the activation energy.

It requires different level of energy.

Properties of Enzymes:

1.       All enzymes are proteins, but all proteins are not enzymes.

2.       Enzymes are specific with their substrates as their active sites are different for different substrates.

3.       Enzymes are of 2 types 1. Builders. 2. Breakers

4.       Enzyme does not get used up during the reaction, as it does not change its shape – hence less enzymes are required.

Denaturation: 

The enzyme changes its shape and the substrate cannot bind with the enzyme - affect tertiary structure of the protein.



Factors affecting enzyme activity:

·         Effect of temperature: temperature at which the enzyme gives its maximum rate of reaction is known as optimum temperature (40o C).

·         Effect of pH  - different enzymes work at different pH, for example, enzyme pepsin works at pH 2, and enzyme amylase at pH 7, it is called optimum pH.

·         Substrate concentration -

Enzyme inhibition – enzyme action can be inhibited by other chemical molecules called inhibitors.

Competitive inhibition: Inhibitor chemical molecule resembles the structure of substrate and bind with

                                          the active site of enzyme instead of substrate, hence there is no production of

                                          products.

Eg. Inhibition of Succinic dehydrogenase by Malonate (inhibitor), which resembles the

       substrate Succinate  in structure.

·         All enzymes are proteins but all proteins are not enzymes. Eg. Heamoglobin is a protein but not an enzyme.

·         Enzymes at low temperature become inactive, enzymes at high temperature denatures.

Classification and nomenclature of enzymes: Based on type of reaction they classified into 6 classes.

1.       Dehydrogenases/ oxidoreductases -

S reduced + S’ oxidized  ------ S oxidized + S’ reduced

2.       Transferases -

S-G + S’------- S+S’-G

3.       Hydrolases -

Hydrolysis of ester ether, peptide and glycoside

C –C , C- halides , P-N bonds

4.       Lyases -

Removal of group from substrates other than hydrolysis ( from double bond )

X Y

l   l

C  C  ------ X-Y+C =C

5.       Isomerases  - Inter-conversion of optical geometrical or positional isomers.

6.       Ligases – linking two compounds. C-O, C-S, C-N, P-O

Co-factors:

·         It is a non – protein part, makes enzyme more active – protein part is called Apoenzyme.

·         There are 3 kinds of factors:

1.       Prosthetic group - tightly bound with apoenzyme. Eg. Peroxidase, Catalases.

2.       Co-enzyme – bound transient form. Eg. NAD, NADP (Nicotinamide Adenine Dinucleotide Phosphate)

3.       Metal ions -  Form coordination bonds. Eg. Fe, Zn.