Biomolecules

Introduction

• There is a wide diversity in living organisms in our biosphere.
• If we perform such an analysis on a plant tissue, animal tissue or a microbial paste, we obtain a list of elements like carbon, hydrogen, oxygen and several others and their respective content per unit mass of a living tissue.
• If the same analysis is performed on a piece of earth’s crust as an example of non-living matter.
• All the elements present in a sample of earth’s crust are also present in a sample of living tissue.

How to Analyse Chemical Composition

• Analytical techniques, when applied to the compound give us an idea of the molecular formula and the probable structure of the compound.
• All the carbon compounds that we get from living tissues can be called ‘biomolecules’.
• Living organisms have also got inorganic elements and compounds in them. Inorganic compounds like sulphate, phosphate, etc., are also seen in the acid-soluble fraction.

• Therefore elemental analysis gives elemental composition of living tissues in the form of hydrogen, oxygen, chlorine, carbon etc. while analysis for compounds gives an idea of the kind of organic and inorganic constituents present in living tissues.

• From a chemistry point of view, one can identify functional groups like aldehydes, ketones, aromatic compounds, etc. But from a biological point of view, we shall classify them into amino acids, nucleotide bases, fatty acids etc.
• Amino acids are organic compounds containing an amino group and an acidic group as substituents on the same carbon i.e., the a-carbon. Hence, they are called a-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.
• Those which occur 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.

• Based on number of amino and carboxyl groups, there are acidic (e.g., glutamic acid), basic (lysine) and neutral (valine) amino acids.
• 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.
• 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), 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).
• Simple lipid is glycerol which is trihydroxy propane.
• Many lipids have both glycerol and fatty acids.
• They can be then monoglycerides, diglycerides and triglycerides.
• These are 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.
• They are found in cell membrane.
• Lecithin is one example.
• Some tissues especially the neural tissues have lipids with more complex structures.

Primary and Secondary Metabolites

• Thousands of organic compounds including amino acids, sugars, etc.
• In animal tissues, the presence of all such categories of compounds are called primary metabolites.
• When one analyses plant, fungal and microbial cells, one would see thousands of compounds other than these called primary metabolites, e.g. alkaloids, flavonoids, rubber, essential oils, antibiotics, coloured pigments, scents, gums, spices are called secondary metabolites primary metabolites play roles in normal physiologial processes, ‘secondary metabolites’ are useful to ‘human welfare’ (e.g., rubber, drugs, spices, scents and pigments).
• Some secondary metabolites have ecological importance.

Biomacromolecules

• All those compounds found in the acid soluble pool have molecular weights ranging from 18 to around 800 daltons (Da) approximately.
• The acid insoluble fraction, has only four types of organic compounds i.e., proteins, nucleic acids, polysaccharides and lipids.
• These classes of compounds with the exception of lipids, have molecular weights in the range of ten thousand daltons and above.
• Biomolecules, found in living organisms are of two types One, those which have molecular weights less than one thousand dalton and are usually referred to as micromolecules or simply biomolecules while those which are found in the acid insoluble fraction are called macromolecules or biomacromolecules.
• The molecules in the insoluble fraction with the exception of lipids are polymeric substances.
• Lipids, molecular weights do not exceed 800 Da.
• Lipids are indeed small molecular weight compounds and are present not only as such but also arranged into structures like cell membrane and other membranes.
• Lipids are not strictly macromolecules.
• Water is the most abundant chemical in living organisms.

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.
• Certain amino acids are essential for our health and they have to be supplied through our diet. Hence, dietary proteins are the source of essential amino acids.
• Therefore, amino acids can be essential or non-essential. The latter are those which our body can make, while we get essential amino acids through our diet/food.
• Proteins carry out many functions in living organisms, some transport nutrients across cell membrane, some fight infectious organisms, some are hormones, some are enzymes, etc.
• 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.

Polysaccharides

• Polysaccharides are long chains of sugars.
• They are threads (literally a cotton thread) containing different 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.
• Insulin 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.
• It has branches as shown in Figure 9.2.

• Starch forms helical secondary structures.
• In fact, starch can hold I₂ molecules in the helical portion.
• The starch-I2 is blue in colour.
• Cellulose does not contain complex helices and hence cannot hold I2.
• Plant cell walls are made of cellulose.
• Paper made from plant pulp and cotton fibre is cellulosic.
• There are more complex polysaccharides in nature.
• 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. These complex polysaccharides are mostly homopolymers.

Nucleic Acids

• Nucleic acid are polynucleotides.
• For nucleic acids, the building block is a nucleotide.
• 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 the rest are substituted pyrimidines.
• The skeletal heterocyclic ring is called as purine and pyrimidine respectively.
• 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 Proteins

• Proteins, are heteropolymers containing strings of amino acids.
• Biologists describe the protein structure at four levels.
• The sequence of amino acids i.e., the positional information in a protein - which is the first amino acid, which is second, and so on - is called the primary structure.
• A protein is imagined as a line, the left end represented by the first amino acid and the right end represented by the last amino acid.
• The first amino acid is also called as N-terminal amino acid.
• The last amino acid is called the C-terminal amino acid.
• A protein thread does not exist throughout as an extended rigid rod. The thread is folded in the form of a helix (similar to a revolving staircase).
• Only some portions of the protein thread are arranged in the form of a helix.
• In proteins, only right handed helices are observed. Other regions of the protein thread are folded into other forms in what is called the secondary structure.
• The long protein chain is also folded upon itself like a hollow woolen ball, giving rise to the tertiary structure.
• Tertiary structure is absolutely necessary for the many biological activities of proteins.
• Some proteins are an assembly of more than one polypeptide or subunits.
• The manner in which these individual folded polypeptides or subunits are arranged with respect to each other (e.g. linear string of spheres, spheres arranged one upon each other in the form of a cube or plate etc.) is the architecture of a protein otherwise called the quaternary structure of a protein.
• Adult human haemoglobin consists of 4 subunits
• Two of these are identical to each other. Hence, two subunits of a type and two subunits of b type together constitute the human haemoglobin (Hb)·

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.
• 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.
• 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
• Nucleic acids exhibit a wide variety of secondary structures.
• One of the secondary structures exhibited by DNA is the famous Watson-Crick model.
• This model says that DNA exists as a double helix.
• The two strands of polynucleotides are antiparallel i.e., run in the opposite direction.
• The backbone is formed by the sugarphosphate- sugar chain.
• The nitrogen bases are projected more or less perpendicular to this backbone but face inside.
• A and G of one strand compulsorily base pairs with T and C, respectively, on the other strand.

• There are two hydrogen bonds between A and T and three hydrogen bonds between G and C.
• At each step of ascent, the strand turns 36°. One full turn of the helical strand would involve ten steps or ten base pairs.
• The pitch would be 34Å. The rise per base pair would be 3.4Å. This form of DNA called BDN-A.

Dynamic State of Body Constituents-Concept of Metabolism

• Living organisms, be it a simple bacterial cell, a protozoan, a plant or an animal, contain thousands of organic compounds. These compounds or biomolecules are present in certain concentrations (expressed as mols/cell or mols/litre etc.).
• All these biomolecules have a turn over. This means that they are constantly being changed into some other biomolecules and also made from some other biomolecules.
• This breaking and making is through chemical reactions constantly occurring in living organisms.
• Together all these chemical reactions are called metabolism.
• Each of the metabolic reactions results in the transformation of biomolecules.
• A few examples for such metabolic transformations are: removal of CO2 from amino acids making an amino acid into an amine, removal of amino group in a nucleotide base; hydrolysis of a glycosidic bond in a disaccharide, etc.
• Metabolites are converted into each other in a series of linked reactions called metabolic pathways.
• These pathways are either linear or circular.
• These pathways crisscross each other, i.e., there are traffic junctions. Flow of metabolites through metabolic pathway has a definite rate and direction like automobile traffic.
• This metabolite flow is called the dynamic state of body constituents.
• Another feature of these metabolic reactions is that every chemical reaction is a catalysed reaction.
• There is no uncatalysed metabolic conversion in living systems.
• Even CO2 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.
• These proteins with catalytic power are named enzymes.

Metabolic Basis for Living

• Metabolic pathways can lead to a more complex structure from a simpler structure (for example, acetic acid becomes cholesterol) or lead to a simpler structure from a complex structure (for example, glucose becomes lactic acid in our skeletal muscle).
• The former cases are called biosynthetic pathways or anabolic pathways.
• The latter constitute degradation and hence are called catabolic pathways.
• Anabolic pathways, consume energy.
• Catabolic pathways lead to the release of energy.
• When glucose is degraded to lactic acid in our skeletal muscle, energy is liberated.
• This metabolic pathway from glucose to lactic acid which occurs in 10 metabolic steps is called glycolysis.
• The most 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 mmoI/L-6.1 mmol/L. while that of hormones would be nano grams/mL.
• The most important fact of biological systems is that all living organisms exist in a steady-state characterised by concentrations of each of these biomolecules.
• These biomolecules are in a metabolic flux.
• Living organisms work continuously, they cannot afford to reach equilibrium.
• Hence the living state is a non-equilibrium steadystate to be able to perform work.
• Metabolism provides a mechanism for the production of energy. Hence the living state and metabolism are synonymous.
• 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.
• 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. Enzyme catalysts differ from inorganic catalysts in many ways, but one major difference needs mention.
• Inorganic catalysts work efficiently at high temperatures and high pressures, while enzymes get damaged at high temperatures (say above 40°C).
• However, 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

• Chemical compounds undergo two types of changes. A physical change simply refers to a change in shape without breaking of bonds.
• Another physical process is a change in state of matter: when ice melts into water, or when water becomes a vapour. These are also physical processes.
• 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 is an inorganic 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. It can be expressed as:

Rate=δP/δT

• Rate can also be called velocity if the direction is specified.
• 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.
• Catalysed reactions proceed at rates vastly higher than that of uncatalysed ones.
• When enzyme catalysed reactions are observed, the rate would be vastly higher than the same but uncatalysed reaction. For example:

• 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.
• The power of enzymes is incredible indeed.
• A multistep chemical reaction, when each of the steps is catalysed by the same enzyme complex or different enzymes, is called a metabolic pathway. For example,

Glucose → 2 Pyruvic acid

C6H12O6 + O₂ → 2C3H4 O₃ + 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).

How do Enzymes bring about such

High Rates of Chemical Conversions?

• The chemical or metabolic conversion refers to a reaction.
• 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). Symbolically, this can be depicted as:

S→ P

the substrate ’S’ has to bind the enzyme at its ‘active site’ within a given cleft or pocket.

• The substrate has to diffuse towards the ‘active site’.
• There is thus, an obligatory formation of an ‘ES’ complex. E stands for enzyme.
• This complex formation is a transient phenomenon.
• During the state where substrate is bound to the enzyme active site, a new structure of the substrate called transition state structure is formed.
• The structure of substrate gets transformed into the structure of product(s).
• All other intermediate structural states are unstable.
• Stability is something related to energy status of the molecule or the structure.
• The y-axis represents the potential energy content. The x-axis represents the progression of the structural transformation or states through the ‘transition state’.
• The energy level difference between Sand P. If ‘P’ is at a lower level than ’S’, the reaction is an exothermic reaction.
• The difference in average energy content of ’S’ from that of this transition state is called ‘activation energy’.

• Enzymes eventually bring down this energy barrier making the transition of ’S’ to ‘P’ more easy.

Nature of Enzyme Action

• Each enzyme (E) has a substrate (S) binding site in its molecule so that a highly reactive enzyme-substrate 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.

• 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

• 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.

• 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 substrate binding 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

• Thousands of enzymes have been discovered, isolated and studied.
• 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 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.

Co-factors

• Enzymes are composed of one or several polypeptide chains.
• There are a number of cases in which non-protein constituents called cofactors are bound to the enzyme to make the enzyme catalytically active. In these instances.
• The protein portion of the enzymes is called the apoenzyme.
• Three kinds of cofactors may be identified: prosthetic groups, co-enzymes and metal ions.
• 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, haem is the prosthetic group and it is a part of the active site of the enzyme.
• Co-enzymes are also organic compounds but their association with the apoenzyme is only transient, usually occurring during the course of catalysis.
• Co-enzymes serve as co-factors in a number of different enzyme catalyzed reactions.
• The essential chemical components of many coenzymes are vitamins, e.g., coenzyme nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin.
• A number of 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.
• Catalytic activity is lost when the co-factor is removed from the enzyme which testifies that they play a crucial role in the catalytic activity of the enzyme.

NEET Special

NEET Special

• Rama chandran was an Indian physicist who proposes a triple helical model for the structure of collagen protein.
• The amino acids that are involved in protein synthesis are known as protein amino acids such as alanine, valine etc. and those amino acids which are not involved in protein synthesis are called as non-protein amino acids such as citrulline ornithine etc.
• Keratin is a type of fibrous protein and it is hard due to the presence of high amount of cysteine amino acid in its structure
• The concentration of glucose in the blood of a normal healthy individual is 4.2 mmol/L - 6.1 mmol/L.
• In isomaltose the linkage is a-1,6-glycosidic linkage.
• Zymogen is an inactive precursor of a proteolytic enzyme