Biomolecules

Biomolecules - All the carbon compounds that we get from living tissues can be called ‘biomolecules’.

a small amount of a living tissue (say a leaf or liver and this is called wet weight) and dry it. All the water, evaporates. The remaining material gives dry weight

if the tissue is fully burnt, all the carbon compounds are oxidised to gaseousare removed the remaining is called ‘ash’. This ash contains inorganic elements (like calcium, magnesium etc).

Amino acids are organic compounds containing an amino group and an acidic group as substituents on the same carbon i.e., the α-carbon. Hence, they are called α-amino acids.

They are substituted methanes.
There are four substituent groups occupying the four valency positions. These are hydrogen, carboxyl group, amino group and a variable group designated as R group.
Based on the nature of R group there are many amino acids.
in proteins are only of twenty types.
The R group in these proteinaceous amino acids could be a hydrogen (the amino acid is called glycine), a methyl group (alanine), hydroxy methyl (serine), etc.
ased on number of amino and carboxyl groups, there are acidic

(e.g., glutamic acid), basic (lysine) and neutral (valine) amino acids. Similarly

there are aromatic amino acids (tyrosine, phenylalanine, tryptophan). A particular property of amino acids is the ionizable nature of –NH2 and –COOH groups. Hence in solutions of different pH, the structure of amino acids changes.
Lipids are generally water insoluble and are not polymer.(NEET 2017)
A fatty acid has a carboxyl group attached to an R group.

The R group could be a methyl (–CH3), or ethyl (– C2H5) or higher number of –CH2 groups (1 carbon to 19 carbons).

For example, palmitic acid has 16 carbons including carboxyl carbon.

Arachidonic acid has 20 carbon atoms including the carboxyl carbon.
Fatty acids could be saturated (without double bond) or unsaturated (with one or more C=C double bonds).
Another simple lipid is glycerol which is trihydroxy propane
Many lipids have both glycerol and fatty acids.
Fatty acids are found esterified with glycerol and can be monoglycerides, diglycerides and triglycerides also called fats and oils based on melting point.
Oils have lower melting point (e.g., gingelly oil) and hence remain as oil in winters.
Some lipids have phosphorous and a phosphorylated organic compound in them. These are phospholipids found in cell membrane. Lecithin is one example. (NEET 2016)
Some tissues especially the neural tissues have lipids with more complex structures.
Some of these are nitrogen bases – adenine, guanine, cytosine, uracil, and thymine.
When found attached to a sugar, they are called nucleosides.
Adenosine, guanosine, thymidine, uridine and cytidine are nucleosides.
If a phosphate group is also found esterified to the sugar they are called nucleotides.
Adenylic acid, thymidylic acid, guanylic acid, uridylic acid and cytidylic acid are nucleotides.

• Nucleic acids like DNA and RNA consist of nucleotides only. DNA and RNA function as genetic material.

PRIMARY AND SECONDARY METABOLITES

Metabolites: The essential organic compounds present in living tissue.

Primary Metabolites: Biochemicals formed as product of vital metabolic pathways of organism example sugars, Amino Acids.

Secondary Metabolites: Specialised products formed by alteration of normal metabolic pathway example alkaloides, rubbers. scents gums, spices, pigments, drugs, etc..

Biomacromolecules

Biomacromolecules: Biomolecules with mass more than 800 Daltons. These are polymers example proteins, polysaccharides, Nucleic acids.

living tissue (a vegetable or a piece of liver, etc.) and grind it in trichloroacetic acid (Cl3CCOOH) using a mortar and a pestle. We obtain a thick slurry. If we were to strain this through a cheesecloth or cotton we would obtain two fractions.
One is called the filtrate or more technically, the acid-soluble pool,
and the second, the retentate or the acid-insoluble fraction.
The acid soluble pool represents roughly the cytoplasmic composition. The macromolecules from cytoplasm and organelles become the acid insoluble fraction.

PROTEINS

Proteins are polypeptides. They are linear chains of amino acids linked by peptide bonds.
As there are 20 types of amino acids (e.g., alanine, cysteine, proline, tryptophan, lysine, etc.),
a protein is a heteropolymer and not a homopolymer.
A homopolymer has only one type of monomer repeating ‘n’ number of times.
amino acids can be essential or non-essential.

• Collagen is the most abundant protein in animal world and Ribulose bisphosphate Carboxylase- Oxygenase (RuBisCO) is the most abundant protein in the whole of the biosphere. (NEET 2012)

POLYSACCHARIDES

Polysaccharides are long chains of sugars.
Carbonyl and Hydroxyl two functional groups are Characteristic of sugar. (NEET 2018)
monosaccharides as building blocks. For example, cellulose is a polymeric polysaccharide consisting of only one type of monosaccharide i.e., glucose. Cellulose is a homopolymer.
Starch is a variant of this but present as a store house of energy in plant tissues. Animals have another variant called glycogen. Inulin is a polymer of fructose.
In polysaccharide chain (say glycogen), the right end is called the reducing end and the left end is called the non-reducing end.
Starch forms helical secondary structures.
They have as building blocks, amino-sugars and chemically modified sugars (e.g., glucosamine, N-acetyl galactosamine, etc.). Exoskeletons of arthropods, for example, have a complex polysaccharide called chitin. (NEET 2013,2015)

Nucleic Acid

Together with polysaccharides and polypeptides these comprise the true macromolecular fraction of any living tissue or cell.
A nucleotide has three chemically distinct components. One is a heterocyclic compound, the second is a monosaccharide and the third a phosphoric acid or phosphate.
The sugar found in polynucleotides is either ribose (a monosaccharide pentose) or 2’ deoxyribose.
A nucleic acid containing deoxyribose is called deoxyribonucleic acid (DNA)
while that which contains ribose is called ribonucleic acid (RNA).

Structure of Protein

Nature of Bond linking monomers in a Polymer

In a polypeptide or a protein, amino acids are linked by a peptide bond which is formed when the carboxyl (-COOH) group of one amino acid reacts with the amino (-NH2) group of the next amino acid with the elimination of a water moiety (the process is called dehydration)
In a polysaccharide the individual monosaccharides are linked by a glycosidic bond. This bond is also formed by dehydration. This bond is formed between two carbon atoms of two adjacent monosaccharides.
The bond between the phosphate and hydroxyl group of sugar is an ester bond. As there is one such ester bond on either side, it is called phosphodiester bond .
For Detail Molecular Basis of Inheritance Ch. 6 Class 12 Biology

DYNAMIC STATE OF BODY CONSTITUENTS – CONCEPT OF METABOLISM

One of the greatest discoveries ever made was the observation that all these biomolecules have a turn over.
Turn over means that they are constantly being changed into some other biomolecules and also made from some other biomolecules and this breaking and making is through chemical reactions constantly occuring in living organisms. Together all these chemical reactions are called metabolism.
Metabolic reactions is that every chemical reaction is a catalysed reaction.

There is no uncatalysed metabolic conversion in living systems. Even carbon dioxide dissolving in water, a physical process, is a catalysed reaction in living systems.
The catalysts which hasten the rate of a given metabolic conversation are also proteins and proteins with catalytic power are named enzymes.

METABOLIC BASIS FOR LIVING

Metabolic pathways can lead to a more complex structure from a simpler structure are called biosynthetic pathways or anabolic pathways. (Consume energy)

example, acetic acid becomes cholesterol

Metabolic pathways lead to a simpler structure from a complex structure are called catabolic pathways (release energy)

example, glucose becomes lactic acid in our skeletal muscle.

important form of energy currency in living systems is the bond energy in a chemical called adenosine triphosphate (ATP).

THE LIVING STATE

the blood concentration of glucose in a normal healthy individual is 4.2 mmol/L–6.1 mmol/L, while that of hormones would be nanograms/mL.
the living state is a non-equilibrium steadystate to be able to perform work; living process is a constant effort to prevent falling into equilibrium. This is achieved by energy input.
Without metabolism there cannot be a living state.

Enzymes

Almost all enzymes are proteins. There are some nucleic acids that behave like enzymes.

These are called ribozymes. (NEET 2016)

An enzyme like any protein has the secondary and the tertiary structure. When you look at a tertiary structure you will notice that the backbone of the protein chain folds upon itself, the chain criss-crosses itself and hence, many crevices or pockets are made.
One such pocket is the ‘active site’. An active site of an enzyme is a crevice or pocket into which the substrate fits. Thus enzymes, through their active site, catalyse reactions at a high rate.
Enzymes get damaged at high temperatures (say above 40°C).
enzymes isolated from organisms who normally live under extremely high temperatures (e.g., hot vents and sulphur springs), are stable and retain their catalytic power even at high temperatures (upto 80°-90°C).
Thermal stability is thus an important quality of such enzymes isolated from thermophilic organisms.

Chemical Reactions

when bonds are broken and new bonds are formed during transformation, this will be called a chemical reaction.
hydrolysis of starch into glucose is an organic chemical reaction.
Rate of a physical or chemical process refers to the amount of product formed per unit time can also be called velocity if the direction is specified.
A general rule of thumb is that rate doubles or decreases by half for every 10°C change in either direction.
The enzyme has accelerated the reaction rate by about 10 million times.
There are thousands of types of enzymes each catalysing a unique chemical or metabolic reaction.

How do Enzymes bring about such High Rates of Chemical Conversions ?

The chemical which is converted into a product is called a ‘substrate’. Hence enzymes, i.e. proteins with three dimensional structures including an ‘active site’, convert a substrate (S) into a product (P).
obligatory formation of an ‘ES’ complex. E stands for enzyme. This complex formation is a transient phenomenon a new structure of the substrate called transition state structure is formed. intermediate structural states are unstable.

The energy level difference between S and P. If ‘P’ is at a lower level than ‘S’, the reaction is an exothermic reaction. One need not supply energy (by heating) in order to form the product.

The chemical which is converted into a product is called a ‘substrate’. Hence enzymes, i.e. proteins with three dimensional structures including an ‘active site’, convert a substrate (S) into a product (P).
obligatory formation of an ‘ES’ complex. E stands for enzyme. This complex formation is a transient phenomenon a new structure of the substrate called transition state structure is formed. intermediate structural states are unstable.
The energy level difference between S and P. If ‘P’ is at a lower level than ‘S’, the reaction is an exothermic reaction. One need not supply energy (by heating) in order to form the product.

Nature of Enzyme Action

The catalytic cycle of an enzyme action can be described in the following steps:

First, the substrate binds to the active site of the enzyme, fitting into the active site.

The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.
The active site of the enzyme, now in close proximity of the substrate breaks the chemical bonds of the substrate and the new enzyme- product complex is formed.
The enzyme releases the products 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.

Factors affecting Enzyme Activity

The activity of an enzyme can be affected by temperature, pH, change in substrate concentration or binding of specific chemicals that regulate its activity.

Temperature and pH

Each enzyme shows its highest activity at a particular temperature and pH called the optimum temperature and optimum pH.
Activity declines both below and above the optimum value.
Low temperature preserves the enzyme in a temporarily inactive state whereas high temperature destroys enzymatic activity because proteins are denatured by heat.

Concentration of substrate

With the increase in substrate concentration, the velocity of the enzymatic reaction rises at first. The reaction ultimately reaches a maximum velocity (Vmax) which is not exceeded by any further rise in concentration of the substrate.
This is because the enzyme molecules are fewer than the substrate molecules and after saturation of these molecules, there are no free enzyme molecules to bind with the additional substrate molecules.
The activity of an enzyme is also sensitive to the presence of specific chemicals that bind to the enzyme. When the binding of the chemical shuts off enzyme activity, the process is called inhibition and the chemical is called an inhibitor.
When the inhibitor closely resembles the substrate in its molecular structure and inhibits the activity of the enzyme, it is known as competitive inhibitor. (NEET 2015)

Example - inhibition of succinic dehydrogenase by malonate which closely resembles the substrate succinate in 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.

• Oxidoreductases/dehydrogenases: Enzymes which catalyse oxidoreduction between two substrates S and S’

e.g., S reduced + S’ oxidised →S oxidised + S’ reduced.

• Transferases: Enzymes catalysing a transfer of a group, G (other than hydrogen) between a pair of substrate S and S’

e.g., 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, geometric or positional isomers.
Ligases: Enzymes catalysing the linking together of 2 compounds, e.g., enzymes which catalyse joining of C-O, C-S, C-N, P-O etc. bonds.