Biomolecules

Acid-soluble pool: Scientists have found thousands of organic compounds in the acid-soluble pool. The compounds of the acid-soluble pool have molecular weights ranging from 18 to around 800 Daltons (Da) approximately.

Acid insoluble pool: The acid insoluble fraction, has only four types of organic compounds i.e., proteins, nucleic acids, polysaccharides, and lipids. These classes of compounds apart from lipids, have molecular weights in the range of ten thousand Daltons and above.

AMINO ACIDS:

• 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 the R group there are many amino acids.

• However, those which occur in proteins are only of twenty types. The R group in these proteinaceous amino acids could be hydrogen (the amino acid is called glycine), a methyl group (alanine), hydroxy methyl (serine), etc.

• Based on the number of amino and carboxyl groups, there are acidic (e.g., glutamic acid), basic

• A particular property of amino acids is the ionizable nature of –NH2 and –COOH groups.

• Hence in solutions of different pHs, the structure of amino acids changes.

LIPIDS:

• Lipids are generally water-insoluble. They could be simple fatty acids.

• A fatty acid has a carboxyl group attached to an R group. The R group could be a methyl (– CH3), ethyl (–C2H5), or a higher number of –CH2 groups (1 carbon to 19 carbons). For example, palmitic acid (16 carbons) and arachidonic acid (20 carbon atoms) including the carboxyl carbon.

• Fatty acids could be saturated (without double bonds) or unsaturated (with one or more C=C double bonds).

• Glycerol is a simple lipid which is trihydroxy propane.

• Many lipids have both glycerol and fatty acids. Here the fatty acids are found esterified with glycerol. They can be then monoglycerides, diglycerides and triglycerides. These are also called fats and oils based on melting point.

• Oils have lower melting points (e.g., gingerly oil) and hence remain as oil in winter.

• Phospholipids are found in cell membranes. Lecithin is one example.

NITROGENOUS BASES:

• Nitrogenous bases are heterocyclic rings having a number of carbon compounds.

• Nitrogen bases are – adenine, guanine, cytosine, uracil, and thymine.

• Nucleosides - Nitrogenous base + sugar. Ex: Adenosine, guanosine, thymidine, uridine, and cytidine.

• Nucleotides - Nitrogenous base + sugar + Phosphate group. Ex: Adenylic acid, thymidylic acid, guanylic acid, uridylic acid, and cytidylic acid are nucleotides.

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

PRIMARY AND SECONDARY METABOLITES

A primary metabolite is a kind of metabolite that is directly involved in normal growth, development, and reproduction. Primary metabolites have identifiable functions and play known roles in normal physiological processes.

The analyses of plant, fungal, and microbial cells, contain thousands of compounds other than primary metabolites, e.g. alkaloids, flavonoids, rubber, essential oils, antibiotics, colored pigments, scents, gums, and spices. These are called secondary metabolites.

Many secondary metabolites are useful to ‘human welfare’ (e.g., rubber, drugs, spices, scents, and pigments). Some secondary metabolites have ecological importance.

BIOMACROMOLECULES:

Chemical compounds found in living organisms are of two types.

One, those which have molecular weights less than one thousand Dalton (18-800 Dalton) and are usually referred to as micromolecules or simply biomolecules.

The acid insoluble fraction has only four types of organic compounds i.e., proteins, nucleic acids, polysaccharides and lipids. These classes of compounds apart from lipids, have molecular weights in the range of ten thousand Daltons and above are usually referred to as biomacromolecules.

PROTEINS

• Proteins are polypeptides.

• They are linear chains of amino acids linked by peptide bonds.

• Each protein is a polymer of amino acids. 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 (does not make up in our body, we get through our diet/food) or non-essential (are those which our body can make).

• 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.

Functions of proteins:

• Some proteins transport nutrients across cell membrane.

• Some fight infectious organisms (Antibodies).

• Some are hormones like insulin - helps in regulating blood sugar level.

• Some are enzymes like trypsin – helps in digestion

• Collagen is a protein acts as intercellular ground substance, binds other tissues.

• GLUT-4 enables glucose transport into cells.

STRUCTURE OF PROTEINS

Proteins are heteropolymers containing strings of amino acids.

Primary structure: Found in the form of linear sequence of amino acids. The first amino acid is also called as N-terminal amino acid. The last amino acid is called the C-terminal amino acid.

Secondary structure: A protein thread does not exist throughout as an extended rigid rod. The thread is folded in the form of a helix (like a revolving staircase). Other regions of the protein thread are folded into other forms in what is called the secondary structure.

Tertiary structure: the long protein chain is also folded upon itself like a hollow woolen ball, giving rise to the tertiary structure. This gives us a 3-dimensional view of a protein.

Quaternary structure: Composed of more than one polypeptide or subunits. Linear string of spheres, spheres arranged one upon each other in the form of a cube or plate is the architecture of a protein otherwise called the quaternary structure of a protein. EX: Adult human haemoglobin consists of 4 subunits. Two of these are identical to each other. Hence, two subunits of α type and two subunits of β type together constitute the human haemoglobin (Hb).

POLYSACCHARIDES

• Polysaccharides are long chains of sugars.

• They are threads (literally a cotton thread) containing different monosaccharides as building blocks.

• 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 a polysaccharide chain (say glycogen), the right end is called the reducing end and the left

  end is called the non-reducing end.

Significance of Polysaccharides:

• Plant cell walls are made of cellulose.

• Glycogen found as storage polysaccharide in animals. • Paper made from plant pulp and cotton fibre is cellulosic.

• There are more complex polysaccharides in nature. They have as building blocks, aminosugars and chemically modified sugars (e.g., glucosamine, N-acetyl galactosamine, etc.).

• Exoskeletons of arthropods, for example, have a complex polysaccharide called chitin. These complex polysaccharides are mostly homopolymers.

NUCLEIC ACIDS

• These are polynucleotides.

• Together with polysaccharides and polypeptides these comprise the true macromolecular fraction of any living tissue or cell.

• Nucleotide is a building block of nucleic acids.

• 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 heterocyclic compounds in nucleic acids are the nitrogenous bases named adenine, guanine, uracil, cytosine, and thymine.

• Adenine and Guanine are substituted purines while uracil, cytosine, and thymine are substituted pyrimidines.

• 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).

NATURE OF BOND LINKING MONOMERS IN A POLYMER

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). [Peptide bond formed between two amino acids of protein].

A glycosidic bond: 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.

Ester bond: The bond between the phosphate and hydroxyl group of sugar is an ester bond. In a nucleic acid a phosphate moiety links the 3’-carbon of one sugar of one nucleotide to the 5’-carbon of the sugar of the succeeding nucleotide.

Phosphodiester bond: As there is one such ester bond on either side, it is called phosphodiester bond.

ENZYMES

• Almost all enzymes are proteins.

• There are some nucleic acids that behave like enzymes. These are called ribozymes.

• An enzyme like any protein has a primary structure, the secondary and the tertiary structure.

• In tertiary structure of an enzyme we can 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. • Inorganic catalysts work efficiently at high temperatures and high pressures, while 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.

For example:

Ba(OH)2 + H2SO4 → BaSO4 + 2H2O

Rate of a physical or chemical process refers to the amount of product formed per unit time. It can

be expressed as:

Rate = δP/δt

Rates of physical and chemical processes are influenced by temperature among other factors. A

general rule of thumb is that rate doubles or decreases by half for every 10°C change in either

direction.

Catalyzed reactions proceed at rates vastly higher than that of uncatalyzed ones. When enzyme

catalyzed reactions are observed, the rate would be vastly higher than the same but uncatalyzed

reaction.

For example

CO2 + H2O Carbonic anhydrase H2CO3 (Carbonic acid)

In the absence of any enzyme this reaction is very slow, with about 200 molecules of H2CO3 being formed in an hour. However, by using the enzyme present within the cytoplasm called carbonic anhydrase, the reaction speeds dramatically with about 600,000 molecules being formed every second. The enzyme has accelerated the reaction rate by about 10 million times.

C6H12O6 + O2 → 2C3H4O3 + 2H2O

is actually a metabolic pathway in which glucose becomes pyruvic acid through ten different

enzyme catalysed metabolic reactions.

In our skeletal muscle, under anaerobic conditions, lactic acid is formed.

Under normal aerobic conditions, pyruvic acid is formed.

In yeast, during fermentation, the same pathway leads to the production of ethanol (alcohol).

Hence, in different conditions different products are possible.

Nature of Enzyme Action

Each enzyme (E) has a substrate (S) binding site in its molecule so that a highly reactive enzymesubstrate complex (ES) is produced. This complex is short-lived and dissociates into its product(s) P and the unchanged enzyme with an intermediate formation of the enzyme-product complex (EP).

The formation of the ES complex is essential for catalysis.

E + S → ES → EP → E + P

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

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

2. The binding of the substrate induces the enzyme to alter its shape, fitting more tightly around the substrate.

3. 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.

4. 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 a change in the conditions which can alter the tertiary structure of the protein. These include temperature, pH, change in substrate concentration or binding of specific chemicals 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 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 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. Due to its close structural similarity with the substrate, the inhibitor competes with the substrate for the substratebinding site of the enzyme. Consequently, the substrate cannot bind and as a result, the enzyme action declines, e.g., inhibition of succinic dehydrogenase by malonate which closely resembles the substrate succinate in structure. Such competitive inhibitors are often used in the control of bacterial pathogens.

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’ oxidized → S oxidized + S’ reduced.

Transferases: Enzymes catalyzing 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 catalyzing hydrolysis of ester, ether, peptide, glycosidic, C-C, C-halide or PN bonds.

Lyases: Enzymes that catalyze removal of groups from substrates by mechanisms other than hydrolysis leaving double bonds.

Isomerases: Includes all enzymes catalyzing inter-conversion of optical, geometric or positional

isomers.

Ligases: Enzymes catalyzing the linking together of 2 compounds, e.g., enzymes which catalyze joining of C-O, C-S, C-N, P-O etc. bonds.

Co-factors

Enzymes are composed of one or several polypeptide chains. However, there are a number of cases in which non-protein constituents called cofactors are bound to the enzyme to make the enzyme catalytically active.

The protein portion of the enzymes is called the apoenzyme.

Three kinds of cofactors may be identified prosthetic groups, co-enzymes and metal ions.

a. Prosthetic groups: are organic compounds and are distinguished from other cofactors in that they are tightly bound to the apoenzyme.

For example, in peroxidase and catalase, which catalyze the breakdown of hydrogen peroxide to water and oxygen.

b. Co-enzymes: are also organic compounds but their association with the apoenzyme is only transient, usually occurring during catalysis. The essential chemical components of many coenzymes are vitamins, e.g., co-enzyme nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin.

c. Metal ions: A few enzymes require metal ions for their activity which form coordination bonds with side chains at the active site and at the same time form one or more coordination bonds with the substrate.

e.g., zinc is a cofactor for the proteolytic enzyme carboxypeptidase.