Biomolecules

Analysis Of Chemical Composition

To do this one extracts the compounds, then subjects the extract to various separation techniques till one has separated a compound from all other compounds. In other words, one isolates and purifies a compound. 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’.

Analysis of Inorganic Compounds

A slightly different but destructive experiment has to be done. One weighs 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. Now if the tissue is fully burnt, all the carbon compounds are oxidised to gaseous form (CO2, water vapour) and are removed. What is remaining is called ‘ash’. This ash contains inorganic elements (like calcium, magnesium etc). 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:

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. However, those which occur in proteins are only of twenty one types. The R group in these proteinaceous amino acids could be a hydrogen (the amino acid is called glycine), a methyl group (alanine), hydroxyl methyl (serine), etc. The chemical and physical properties of amino acids are essentially of the amino, carboxyl and the R functional groups. Based 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 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), 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. 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 point (e.g., gingely 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.

Living organisms have a number of carbon compounds in which heterocyclic rings can be found. Some of these are nitrogen bases – adenine, guanine, cytosine, uracil, and thymine. When found attached to a sugar, they are called nucleosides. If a phosphate group is also found esterified to the sugar they are called nucleotides. Adenosine, guanosine, thymidine, uridine and cytidine are nucleosides. 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

Primary metabolites have identifiable functions and play known roles in normal physiologial processes, we do not at the moment, understand the role or functions of all the ‘secondary metabolites’ in host organisms. However, many of them 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 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.

Average Composition of Cells

The acid soluble pool represents roughly the cytoplasmic composition. The macromolecules from cytoplasm and organelles become the acid insoluble fraction. Together they represent the entire chemical composition of living tissues or organisms.

Proteins

Each protein is a polymer of amino acids. As there are 21 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, 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.

Some Proteins And Their Functions

POLYSACCHARIDES

Polysaccharides are long chains of sugars. They are threads 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. Inulin is a polymer of fructose.

Three-D Structure of Cellulose

In a 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. In fact, starch can hold I2 molecules in the helical portion.

Cellulose does not contain complex helices and hence cannot hold I2. Plant cell walls are made of cellulose. Paper made from plant pulp is cellulose. Cotton fibre is cellulose.

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 heteropolymers.

NUCLEIC ACIDS

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

Primary Structure: 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 of a protein. 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 aminoacid 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.

Secondary Structure: Regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the alpha helix, beta sheet and turns. Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule.

Tertiary structure: The overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even post-translational modifications. The term "tertiary structure" is often used as synonymous with the term fold. The Tertiary structure is what controls the basic function of the protein.

Quaternary Structure: 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.

NATURE OF BOND LINKING MONOMERS IN A POLYMER

Glycosidic Bond: A glycosidic bond is a certain type of functional group that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.

Peptide Bond: A peptide bond (amide bond) is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting CO-NH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called an amide group or (in the context of proteins) a peptide group. Polypeptides and proteins are chains of amino acids held together by peptide bonds, as is the backbone of PNA. Polyamides, such as nylons and aramids, are synthetic molecules (polymers) that possess peptide bonds.

Phospho-diester Bond: A phospho-diester bond is a group of strong covalent bonds between a phosphate group and two other molecules over two ester bonds. Phosphodiester bonds are central to all life on Earth, as they make up the backbone of the strands of DNA. In DNA and RNA, the phosphodiester bond is the linkage between the 3' carbon atom of one sugar molecule and the 5' carbon of another, deoxyribose in DNA and ribose in RNA.

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. 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.

Majority of these metabolic reactions do not occur in isolation but are always linked to some other reactions. In other words, 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. What is most important is that this interlinked metabolic traffic is very smooth and without a single reported mishap for healthy conditions. Another feature of these metabolic reactions is that every chemical reaction is a catalysed reaction. There is no uncatalysed metabolic conversion 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

Anabolic Pathways: Anabolic pathways convert simpler structure molecules to complex molecules. Anabolic pathways consume energy to synthesize something.

Catabolic Pathways: Catabolic pathways convert complex molecules into simple molecules. Catabolic pathways release energy while breaking down molecules. Living organisms have learnt to trap this energy liberated during degradation and store it in the form of chemical bonds. As and when needed, this bond energy is utilized for biosynthetic, osmotic and mechanical work that we perform. 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 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. Any chemical or physical process moves spontaneously to equilibrium. The steady state is a non-equilibirium state.

As living organisms work continuously, they cannot afford to reach equilibrium. Hence the living state is a non-equilibrium steady-state to be able to perform work; living process is a constant effort to prevent falling into equilibrium. This is achieved by energy input. 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. An enzyme like any protein has a primary structure, i.e., amino acid sequence of the protein. An enzyme like any protein has the secondary and the tertiary structure.

"Lock and Key" Model:

Enzymes are very specific, and it was suggested by Emil Fischer in 1894 that this was because both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This is often referred to as "the lock and key" model. However, while this model explains enzyme specificity, it fails to explain the stabilization of the transition state that enzymes achieve. The "lock and key" model has proven inaccurate, and the induced fit model is the most currently accepted enzyme-substrate-coenzyme figure.

(ref: http://en.wikipedia.org/wiki/File:Induced_fit_diagram.svg accessed on 9th Oct 2009)

Induced Fit Model

Diagrams to show the induced fit hypothesis of enzyme action.In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continually reshaped by interactions with the substrate as the substrate interacts with the enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side chains which make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases, the substrate molecule also changes shape slightly as it enters the active site. The active site continues to change until the substrate is completely bound, at which point the final shape and charge is determined.

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.

Mechanisms of Enzymatic Actions

• Lowering the activation energy by creating an environment in which the transition state is stabilized (e.g. straining the shape of a substrate—by binding the transition-state conformation of the substrate/product molecules, the enzyme distorts the bound substrate(s) into their transition state form, thereby reducing the amount of energy required to complete the transition).

• Lowering the energy of the transition state, but without distorting the substrate, by creating an environment with the opposite charge distribution to that of the transition state.

• Providing an alternative pathway: For example, temporarily reacting with the substrate to form an intermediate ES complex, which would be impossible in the absence of the enzyme.

• Reducing the reaction entropy change by bringing substrates together in the correct orientation to react. Considering ΔH‡ alone overlooks this effect.

• Increases in temperatures speed up reactions. Thus, temperature increases help the enzyme function and develop the end product even faster. However, if heated too much, the enzyme’s shape deteriorates and only when the temperature comes back to normal does the enzyme regain its shape. Some enzymes like thermolabile enzymes work best at low temperatures.

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

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 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.

Effect of Inhibitor: 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

Thousands of enzymes have been discovered, isolated and studied. Most of these enzymes have been classified into different groups based on the type of reactions they catalyse. 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’.

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

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. However, there are a number of cases in which non-protein constituents called cofactors are bound to the 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: 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: Co-enzymes are also organic compounds but their association with the apoenzyme is only transient, usually occurring during the course of catalysis. Furthermore, 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.

Metal Ions: 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 cordination 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.