Chapter-9: Biomolecules

Chapter 9

Biomolecules

The biosphere has a vast variety of living species. Carbon, hydrogen, oxygen, and numerous other elements, as well as their respective contents, are acquired per unit mass of living tissue when an elemental analysis is done on plant tissue, animal tissue, or microbial paste. A similar list of elements will be obtained if the same analysis is performed on a piece of the earth's crust as an example of non-living stuff. A sample of live tissue contains all of the elements found in a sample of the earth's crust. However, a closer look reveals that any living organism has a higher relative quantity of carbon and hydrogen in relation to other elements than the earth's crust.

How to Analyse Chemical Composition?

A natural substance's elemental analysis reveals that it is made up of several elements such as carbon, hydrogen, oxygen, chlorine, and so on. Analytical procedures provide information on various organic and inorganic compounds, as well as their molecular formulas and structures. They also aid in the separation and purification of one component from another. Simple experiments can be used to determine the chemical composition of biomolecules. Crush and combine a piece of living tissue with an acid. We get two pieces after filtering it. The acid-soluble fraction of the filtrate is retained on the filter membrane, while the acid-insoluble fraction is retained on the filter membrane. This indicates that there are two or more substances with distinct characteristics within the tissues.Thousands of organic molecules have been discovered in the acid-soluble pool by scientists.

Constituents of Living Tissues

Take another piece and burn it till all the moisture in it is evaporated. When carbon compounds are burned, they are all oxidized. Inorganic substances such as calcium, magnesium, sulfate, phosphate, and others are formed in the tissue by the ash that has been left out.

Analytical techniques, when applied to a chemical, provide us with an estimate of its molecular formula and likely structure. 'Biomolecules' refers to all carbon compounds obtained from living tissues. All carbon-containing chemicals (organic compounds) found in living organisms are classified as biomolecules. They are organic substances found in living cells that have a role in the organism's maintenance and metabolic activities. Inorganic elements and compounds, on the other hand, are found in living beings. As a result, elemental analysis provides information on the composition of live tissues in terms of hydrogen, oxygen, chlorine, carbon, and other elements, whereas compound analysis provides information on the types of organic and inorganic constituents found in living tissues.

Functional groups such as aldehydes, ketones, aromatic molecules, and others can be detected in living tissues from a chemical standpoint. However, amino acids, nucleotide bases, fatty acids, and carbohydrates make up living tissues from a biological standpoint.

Amino acids are chemical molecules that have both an amino and an acidic group as substituents on the same carbon, the -carbon. As a result, they are known as -amino acids. They're methanes that have been replaced. The four valency locations are occupied by four substituent groups. Hydrogen, carboxyl group, amino group, and a variable group known as R group are the four groups. There are numerous amino acids in the R group due to its nature. However, there are only twenty varieties of those found in proteins. The R group in these proteinaceous amino acids could be a hydrogen (glycine), a methyl group (alanine), hydroxy methyl (serine), or something else entirely. The amino, carboxyl, and R functional groups make up the chemical and physical properties of amino acids.Acidic (e.g., glutamic acid), basic (lysine), and neutral (valine) amino acids are classified by the number of amino and carboxyl groups they contain.

Similarly, aromatic amino acids exist (tyrosine, phenylalanine, tryptophan). The ionizability of the –NH2 and –COOH groups of amino acids is a unique feature. As a result, the structure of amino acids alters in different pH solutions.

Figure 2 (a): Diagrammatic representation of small molecular weight organic compounds in living tissues

Figure 2(b): Diagrammatic representation of small molecular weight organic compounds in living tissues

Heterocyclic rings can be found in a variety of carbon compounds found in living beings. Adenine, guanine, cytosine, uracil, and thymine are examples of nitrogen bases. They're called nucleosides when they're found linked to sugar. Nucleotides are formed when a phosphate group is additionally esterified to the sugar. Nucleosides include adenosine, guanosine, thymidine, uridine, and cytidine. Nucleotides include adenylic acid, thymidylic acid, guanylic acid, uridylic acid, and cytidylic acid. Only nucleotides make up nucleic acids like DNA and RNA. DNA and RNA are two types of genetic material.

Primary and Secondary Metabolites

The most interesting component of chemistry is extracting thousands of small and large chemicals from live creatures, establishing their structure, and, if possible, synthesizing them. A list of biomolecules might contain thousands of organic chemicals, such as amino acids, carbohydrates, and other substances. These biomolecules can be referred to as metabolites. All of these kinds of chemicals can be found in animal tissues. Primary metabolites are what these are called. Thousands of additional substances termed secondary metabolites can be found in the plant, fungal, and microbial cells, such as alkaloids, flavonoids, rubber, essential oils, antibiotics, colored pigments, fragrances, gums, and spices. Secondary metabolites are what these are called.While primary metabolites have well-defined functions and roles in normal physiological processes, the role and functions of all secondary metabolites' in host organisms are currently unknown. Many of them, however, are beneficial to 'human welfare (e.g., rubber, drugs, spices, scents and pigments). Secondary metabolites play an important role in ecology.

Biomacromolecules

Proteins, nucleic acids, polysaccharides, and lipids are the only organic molecules found in the acid-insoluble fraction. With the exception of lipids, these substances have molecular weights in the tens of thousands of Daltons or higher. Biomolecules, or chemical substances found in living beings, are divided into two categories for this reason. One, those which have molecular weights less than one thousand daltons and are commonly referred to as micromolecules or simply biomolecules whereas those which are discovered in the acid-insoluble fraction are dubbed macromolecules or biomacromolecules. All of the chemicals in the acid-soluble pool have one thing in common. They have molecular weights that range from 18 to 800 daltons (Da).

With the exception of lipids, the molecules in the insoluble fraction are polymeric. Lipids are small molecular weight substances that can be found in a variety of forms, including cell membranes and other membranes. When the cell structure is disturbed and the tissue ispulverized, the breakdown of cell membranes and other membranes results in the formation of vesicles that are not water-soluble. As a result, membrane fragments in the form of vesicles separate from the acid-insoluble pool, resulting in the macromolecular fraction. The cytoplasmic composition is generally represented by the acid-soluble pool. The acid-insoluble fraction contains macromolecules from the cytoplasm and organelles. They represent the total chemical composition of biological tissues when put together.In summation, it is observed that water is the most abundant component in living organisms upon characterizing the chemical makeup of living tissue from the standpoint of abundance and classifying them accordingly.

Carbohydrates

Carbohydrate is a group of organic compounds occurring in living tissues and foods in the form of starch, cellulose, and sugars. It is one of the three micronutrients via which a human body obtains energy. The properties of carbohydrate biology include carbon, hydrogen, and oxygen atoms at their chemical level. Cn(H₂O)n is the generic formula for all carbohydrates. This formula is only valid for simple sugars, which are made up of the same amount of carbon and water.

There are two types of carbohydrates, simple and complex. This division is primarily based on their chemical structure along with their degree of polymerization. 

Simple Carbohydrates: Simple carbohydrates carry one or two molecules of sugar. Such examples of carbohydrates are found abundantly in dairy products, refined sugar, etc. Since these carbohydrates do not comprise any fiber, vitamin, or mineral, they are regarded as empty calories. Simple carbohydrates can be further divided into three categories. These are as follows:

Monosaccharides: Carbohydrates consisting of one sugar molecule are called monosaccharides. Monosaccharides can be further classified based on the number of carbon atoms. These are trioses, tetroses, pentoses, hexoses, and heptoses. One of the most significant monosaccharides is glucose. The following are the two most frequent methods for preparing glucose. Sucrose is converted to glucose and fructose when it is cooked with dilute acid in an alcohol solution. From Starch, Glucose can also be made by hydrolyzing starch and boiling it with weak sulphuric acid at 393 degrees Fahrenheit under high pressure. Glucose, commonly known as dextrose and aldohexose, is abundant on the planet.

Disaccharides: Two monosaccharides combine to form a disaccharide. Sucrose, Lactose, and Maltose are some of the prime examples of this carbohydrate.

Oligosaccharides: Carbohydrates consisting of 2-9 monomers are classified as oligosaccharides.

The term “monosaccharide” refers to a carbohydrate derivative possessing a single carbon chain; “disaccharide” and “trisaccharide” refer to molecules containing two or three such monosaccharide units joined together by acetal or ketal linkages. “Oligosaccharide” and “polysaccharide” refer to larger such aggregates, with “a few” and many monosaccharide units, respectively. Current usage seems to draw the distinction between “few” and many at around 10 units.

Complex Carbohydrate: Complex carbohydrates are made up of two or more molecules of sugar. Such carbohydrates are found abundantly in food items like corn, lentils, peanuts, beans, etc. Complex carbohydrates are also known as polysaccharides as they are formed due to polymerization.

Polysaccharides are another macromolecule family found in the acid-insoluble pellet. Polysaccharides are lengthy sugar chains. They're threads (literally, cotton threads) made up of various monosaccharides as building blocks. cellulose, for example, is a polymeric polysaccharide made up of only one type of monosaccharide, glucose. Cellulose is a homopolymer, which means it is made up of only one type of molecule. Starch is a type of this that is found in plant tissues as a source of energy. Glycogen is a different type of carbohydrate found in animals. Inulin is a fructose polymer. The right end of a polysaccharide chain (such as glycogen) is known as the reducing end, while the left end is known as the non-reducing end. It has branches. Secondary helical structures are formed by starch.In fact, the helical part of starch can retain I2 molecules. The colour of starch-I2 is blue. Because cellulose lacks complex helices, it is unable to retain I2.

Cellulose is the main component of plant cell walls. Cellulosic paper is created from plant pulp and cotton fibre. In nature, there exist more complicated polysaccharides. Amino-sugars and chemically modified sugars are used as building blocks (e.g., glucosamine, N-acetyl galactosamine, etc.). Arthropod exoskeletons, for example, contain a complex polymer called chitin. The majority of these complex polysaccharides are homopolymers.

Amino Acids

Amino acids are chemical molecules with amino and carboxylate functional groups as well as a side chain that is unique to each amino acid. Amino Acids are chemical substances that combine to produce proteins, which is why they are known as the building blocks of proteins. These biomolecules have a role in a variety of biological and chemical functions in the human body and are essential for human growth and development. There are around 300 amino acids found in nature. Amino acids' general features include:

1. A high melting and boiling point.

2. Amino acids are crystalline solids that are white in color.

3. Few amino acids have a pleasant, tasteless, or bitter flavour.

4. The majority of amino acids are water-soluble and insoluble in organic solvents.

There are 20 amino acids found in nature, all of which have the same structural features: an amino group (-NH3+), a carboxylate group (-COO-), and a hydrogen-bonded to the same carbon atom. Their side-chain, known as the R group, distinguishes them from one another. The - carbon of each amino acid is connected to four distinct groups namely: Amino group, COOH, Hydrogen atom, and Sidechain.

Amino acids have a general structure which can be represented as:

 

Our bodies can easily produce a few non-essential amino acids out of a total of 20 amino acids. Alanine, asparagine, arginine, aspartic acid, glutamic acid, cysteine, glutamine, proline, glycine, serine, and tyrosine are examples of these amino acids.

Besides these, there are nine other amino acids that are extremely important because our bodies cannot make them. Isoleucine, histidine, lysine, leucine, phenylalanine, tryptophan, methionine, threonine, and valine are examples of important amino acids.

Amino acids are essential for a variety of biological and chemical tasks in our bodies, including tissue construction and repair, enzyme production and activity, food digestion, molecule transportation, and so on. Only a few amino acids can be synthesized by our bodies, thus the rest, known as essential amino acids, must be obtained from protein-rich foods in our daily diet. Plant-based foods with high levels of amino acids include broccoli, beans, beets, pumpkin, cabbage, almonds, dry fruits, chia seeds, oats, peas, carrots, cucumber, green leafy vegetables, onions, soybeans, whole grain, peanuts, legumes, lentils, and so on. Apples, bananas, berries, figs, grapes, melons, oranges, papaya, pineapple, and pomegranates are high in amino acids.Dairy products, eggs, seafood, poultry, beef, pork, and other animal products are examples of other animal goods.

Functions of Essential Amino acids

1. Phenylalanine helps in maintaining a healthy nervous system and in boosting memory power.

2. Valine acts as an important component in promoting muscle growth.

3. Threonine helps in promoting the functions of the immune system.

4. Tryptophan is involved in the production of vitamin B3 and serotonin hormones. This serotonin hormone plays a vital role in maintaining our appetite, regulating sleep and boosting our moods.

5. Isoleucine plays a vital role in the formation of hemoglobin, stimulating the pancreas to synthesize insulin, and transporting oxygen from the lungs to the various parts.

6. Methionine is used in the treatment of kidney stones, maintaining healthy skin and also used in controlling invade of pathogenic bacteria.

7. Leucine is involved in promoting protein synthesis and growth hormones.

8. Lysine is necessary for promoting the formation of antibodies, hormones, and enzymes and in the development and fixation of calcium in bones.

9. Histidine is involved in many enzymatic processes and in the synthesizing of both red blood cells (erythrocytes) and white blood cells (leukocytes).

Functions of Non-Essential Amino acids

1. Alanine functions by removing toxins from our body and in the production of glucose and other amino acids.

2. Cysteine acts as an antioxidant and provides resistance to our body; it is important for making collagen. It affects the texture and elasticity of the skin

3. Glutamine promotes a healthy brain function and is necessary for the synthesis of nucleic acids – DNA and RNA.

4. Glycine is helpful in maintaining the proper cell growth, and its function, and it also plays a vital role in healing wounds. It acts as a neurotransmitter.

5. Glutamic acid acts as a neurotransmitter and is mainly involved in the development and functioning of the human brain.

6. Arginine helps in promoting the synthesis of proteins and hormones, detoxification in the kidneys, healing wounds, and maintaining a healthy immune system.

7. Tyrosine plays a vital role in the production of the thyroid hormones -T3 and T4, in synthesizing a class of neurotransmitters and melanin, which are natural pigments found in our eyes, hair, and skin.

8. Serine helps in promoting muscle growth and in the synthesis of immune system proteins.

9. Asparagine is mainly involved in the transportation of nitrogen into our body cells, formations of purines and pyrimidine for the synthesis of DNA, the development of the nervous system and improving our body stamina.

10. Aspartic acid plays a major role in metabolism and in promoting the synthesis of other amino acids.

11. Proline is mainly involved in the repairing of the tissues and the formation of collagen, preventing the thickening and hardening of the walls of the arteries (arteriosclerosis) and in the regeneration of new skin.

Proteins

Polypeptides are the building blocks of proteins. They are peptide bonds that connect linear chains of amino acids. A polymer of amino acids makes up each protein. A protein is a heteropolymer, not a homopolymer because there are 20 different types of amino acids. A homopolymer is made up of only one type of monomer that repeats 'n' times. Specific amino acids are necessary for human health and must be obtained through our food. As a result, necessary amino acids are obtained from food proteins. As a result, amino acids can be classified as either essential or non-essential. The latter are those that our bodies can produce, whereas essential amino acids must be obtained through our diet.Proteins have a variety of activities in living creatures, including transporting nutrients across cell membranes, fighting pathogenic organisms, acting as hormones, and enzymatic reactions. The most abundant protein in the animal kingdom is collagen, and the most abundant protein in the biosphere is Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO).

Structure of Proteins:

Proteins are heteropolymers made up of strings of amino acids, as previously stated. In different situations, the structure of molecules means different things. Physicists visualize molecular structures in three dimensions, while biologists explain protein structure on four levels. The primary structure of a protein is the sequence of amino acids, or the positional information in a protein — which amino acid is the first, which is the second, and so on.A protein can be visualized as a line, with the initial amino acid on the left end and the last amino acid on the right.

N-terminal amino acid is another name for the first amino acid. The C-terminal amino acid is the last one in the chain. As an extended stiff rod, a protein thread does not exist throughout. The thread is folded into a helix shape (similar to a revolving staircase). Naturally, only a piece of the protein thread is organized in a helix shape. Only right-handed helices are found in proteins. In what is known as the secondary structure, various portions of the protein thread are folded into other configurations.

Furthermore, the lengthy protein chain folds in on itself like a hollow woollen ball, forming the tertiary structure. This allows us to see a protein in three dimensions. Proteins' tertiary structure is required for many of their biological functions. Some proteins are made up of several polypeptides and subunits. The architecture of a protein, also known as the quaternary structure of a protein, is the way these individual folded polypeptides or subunits are arranged with regard to one other (e.g., a linear string of spheres, spheres placed one upon another in the form of a cube or plate, etc.).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).

Nature of bond linking monomers in a polymer

A peptide bond is produced when the carboxyl (-COOH) group of one amino acid combines with the amino (-NH2) group of the next amino acid with the elimination of a water molecule in a polypeptide or protein (the process is called dehydration). Individual monosaccharides in a polysaccharide are joined by a glycosidic bond. Dehydration also contributes to the formation of this link. Two carbon atoms from two neighboring monosaccharides make a peptide bond. A phosphate moiety of a nucleic acid connects the 3'-carbon of one sugar of one nucleotide to the 5'-carbon of the sugar of the next nucleotide. An ester link exists between the phosphate and the sugar's hydroxyl group.The phosphodiester bond is named after the fact that there is one such ester bond on each side.

Lipids

Lipids are organic molecules containing hydrogen, carbon, and oxygen atoms that provide the structural and functional foundation for living cells. Because water is a polar molecule, these organic compounds are nonpolar molecules that are only soluble in nonpolar solvents and insoluble in water. These molecules are produced in the human liver and can be found in the oil, butter, whole milk, cheese, fried foods, and some red meats.

Structure of Lipids

Lipids are fatty acid polymers with a long, non-polar hydrocarbon chain and a short polar area that contains oxygen.Lipids are often insoluble in water. It's possible that they're just simple fatty acids. A carboxyl group is connected to the R group in a fatty acid. The R group could be methyl (–CH3), ethyl (–C2H5), or a combination of the two (1 carbon to 19 carbons). Palmitic acid, for example, comprises 16 carbons, including the carboxyl carbon. Arachidonic acid, including carboxyl carbon, has 20 carbon atoms.Saturated fatty acids have no double bonds, while unsaturated fatty acids have one or more C=C double bonds. Glycerol, which is trihydroxy propane, is another simple lipid. Glycerol and fatty acids are found in many lipids. The fatty acids are esterified with glycerol. Monoglycerides, diglycerides, and triglycerides are the three types of lipids. Based on their melting point, these are also known as fats and oils. Oils (e.g., gingely oil) have a lower melting point and hence remain as oil in the winter. Phosphorus and a phosphorylated organic molecule are found in some lipids. Phospholipids are what they're called. They're located in the membranes of cells. One example is lecithin. Lipids with more complicated structures are found in some tissues, particularly brain tissues.

Listed below are some important characteristics of Lipids.

1. Lipids are oily or greasy nonpolar molecules, stored in the adipose tissue of the body.

2. Lipids are a heterogeneous group of compounds, mainly composed of hydrocarbon chains.

3. Lipids are energy-rich organic molecules, which provide energy for different life processes.

4. Lipids are a class of compounds characterized by their solubility in nonpolar solvents and insolubility in water.

5. Lipids are significant in biological systems as they form a mechanical barrier dividing a cell from the external environment known as the cell membrane.

Classification of Lipids:

Lipids serve a critical role in our bodies. They are a component of the cell membrane's structure. They aid in the production of hormones and provide energy to our bodies. They aid in appropriate meal digestion and absorption. If we eat them in the right amounts, they constitute a nutritious element of our diet. They play a vital function in signaling as well.

Nucleic Acids

The nucleic acid is another form of macromolecule found in the acid-insoluble portion of any living tissue. Polynucleotides are a type of nucleotide. They make up the real macromolecular fraction of any living tissue or cell, together with polysaccharides and polypeptides. A nucleotide is the building block of nucleic acids. A nucleotide is made up of three chemically different parts. A heterocyclic molecule is one, a monosaccharide is another, and phosphoric acid or phosphate is the third. The nitrogenous bases adenine, guanine, uracil, cytosine, and thymine are heterocyclic molecules in nucleic acids. The purines Adenine and Guanine are substituted, with the pyrimidines Thymine and Cytosine. Purine and pyrimidine are the components for the skeletal heterocyclic ring.Polynucleotides include either ribose (a monosaccharide pentose) or 2' deoxyribose as a sugar. Deoxyribonucleic acid (DNA) is a nucleic acid that contains deoxyribose, whereas ribonucleic acid (RNA) contains ribose sugar.

Secondary structures in nucleic acids come in a range of shapes and sizes. The famous Watson - Crick Model, for example, is one of DNA's secondary structures. According to this idea, DNA is a double helix. Polynucleotide strands are antiparallel, meaning they run in opposite directions. The sugar-phosphate-sugar chain makes up the backbone. The nitrogen bases are positioned perpendicular to the backbone but on the inside. One strand's A and G must base pair with the other strand's T and C, respectively. Between A and T, there are two hydrogen bonds, while between G and C, there are three hydrogen bonds.

Each thread resembles a spiral staircase. A pair of bases represent each stage of the ascent. The strand rotates 36 degrees with each climbing step. Ten steps or ten base pairs would be required to complete a full turn of the helical strand. It would be a 34 pitch. The increase would be 3.4 per base pair. B-DNA is a type of DNA that has the characteristics listed above. More than a dozen kinds of DNA named after English alphabets with unique structural properties are known to exist.

Concept of metabolism and living state

Thousands of organic chemicals can be found in living species, whether they be bacteria, protozoa, plants, or animals. These substances or biomolecules exist at specific concentrations (mols/cell, mols/litre, and so on). The discovery that all biomolecules have a turnover was one of the most significant discoveries ever made. This means they're continually changing into and out of different biomolecules. Chemical reactions occur frequently in living organisms, breaking and making this possible. Metabolism refers to the sum of all these chemical events. The change of biomolecules occurs in each of the metabolic processes.

Removal of carbon di oxide from amino acids, resulting in an amine, removal of amino group in a nucleotide base, hydrolysis of a glycosidic bond in a disaccharide, and so on are some examples of metabolic transformations. There are tens of thousands of examples like this. The majority of these metabolic events are always related to other reactions and do not occur in isolation. In other words, metabolites are changed into one another through metabolic pathways, which are a set of related reactions. These metabolic pathways are comparable to city traffic in terms of complexity. There are two types of pathways: linear and circular. There are traffic crossroads where these paths cross one other.Like car traffic, the flow of metabolites through the metabolic pathway has a set rate and direction. The dynamic state of bodily constituents refers to this metabolite flux. What matters most is that this interconnected metabolic traffic runs smoothly and without a single reported hiccup under normal circumstances. Every chemical reaction in these metabolic pathways is a catalysed reaction, which is another distinguishing trait. In biological systems, there is no metabolic conversion that is not catalysed. Even the physical process of CO₂ dissolving in water is a catalysed reaction in biological systems. Proteins are also catalysts that speed up the tempo of a metabolic conversation. Enzymes are the name given to these catalytic proteins.

Metabolic basis for living

Metabolic pathways can either lead to a more complex structure from a simpler structure (e.g., acetic acid becomes cholesterol) or a simpler structure from a complex structure (e.g., acetic acid becomes cholesterol) (for example, glucose becomes lactic acid in our skeletal muscle). The former are referred to as biosynthetic or anabolic pathways. The latter are referred to as catabolic pathways since they involve degradation. Anabolic pathways, use a lot of energy. Energy is required to assemble a protein from amino acids. Catabolic pathways, on the other hand, result in the release of energy. When glucose is metabolized to lactic acid in skeletal muscles, for example, energy is released. Glycolysis is a metabolic mechanism that takes glucose and converts it to lactic acid in ten stages.

Living organisms have figured out how to capture the energy released during breakdown and store it as chemical bonds. This bond energy is used as needed for biosynthetic, osmotic, and mechanical tasks that we do. The bond energy in a molecule called adenosine triphosphate is the most essential kind of energy currency in living systems (ATP).

The living state

Tens and thousands of chemical compounds in a living organism, otherwise called metabolites, or biomolecules, are present at concentrations characteristic of each of them. For example, the blood concentration of glucose in a normal healthy individual is 4.5-5.0 mM. The most important fact of biological systems is that all living organisms exist in a steady-state characterized by concentrations of each of these biomolecules. These biomolecules are in metabolic flux. Any chemical or physical process moves spontaneously to equilibrium. The steady state is a non-equilibrium state. One should remember from physics that systems at equilibrium cannot perform work. As living organisms work continuously, they cannot afford to reach equilibrium.

Thus, to be able to conduct work, the living state is a non-equilibrium steady-state; the living process is a constant endeavour to avoid slipping into equilibrium. This is accomplished by the use of energy. Metabolism is the process by which energy is produced. As a result, the terms "living state" and "metabolism" are interchangeable. There can be no living condition without metabolism.

Enzymes

Proteins make up almost all enzymes. Some nucleic acids have enzyme-like properties. Ribozymes are the name for these proteins. A line diagram can be used to represent an enzyme. An enzyme, like any other protein, has a primary structure, which is the amino acid sequence. Secondary and tertiary structures are present in enzymes, as they are in other proteins. When you look at a tertiary structure, you'll observe that the protein chain's backbone folds in on itself, the chain crisscrosses itself, and many crevices or pockets form. The 'active site' is one such pocket. An enzyme's active site is a crevice or pocket that the substrate fits into. As a result, enzymes catalyze processes at a rapid pace through their active site.

In many aspects, enzyme catalysts differ from inorganic catalysts, but one key distinction stands out. At high temperatures and pressures, inorganic catalysts perform efficiently, but enzymes are destroyed at high temperatures (say, above 40°C). Enzymes extracted from organisms that dwell in severe heat (e.g., hot vents and sulphur springs) are stable and keep their catalytic power even at extreme temperatures (up to 80°-90°C). The capacity of such enzymes extracted from thermophilic organisms to maintain their thermal stability is thus critical.

Chemical reactions

Chemical compounds go through two sorts of transformations. A physical change is merely a change in shape that does not involve the breaking of connections.This is a bodily function. A change in state of matter is another physical process, such as when ice melts into water or when water becomes vapour. These are physical processes as well. A chemical reaction, on the other hand, occurs when bonds are broken and new bonds are generated during transformation. For example

Ba (OH)2+ H2SO4 ® BaSO4 + 2H2O

is a chemical process that takes place in an inorganic state. The conversion of starch to glucose is also an organic chemical reaction. The amount of product created per unit time is referred to as the rate of a physical or chemical process. It can be written as:

rate=dP/ dT

If the direction is indicated, rate is also known as velocity. Temperature, among other things, affects the rates of physical and chemical processes. For every 10°C change in either direction, the rate doubles or declines by half, according to a common rule of thumb. Catalyzed reactions proceed at a much faster rate than uncatalyzed reactions. For every 10°C change in either direction, the rate of enzyme catalysed reactions would be substantially larger than the same but uncatalyzed reaction. Catalyzed reactions proceed at a much faster rate than uncatalyzed reactions. When enzyme-catalyzed reactions are detected, the rate is much higher than when the identical process is not catalysed. As an example,

In the absence of any enzyme, this reaction is extremely sluggish, producing just around 200 molecules of H₂CO₃ per hour. The reaction speeds up substantially when carbonic anhydrase, an enzyme found in the cytoplasm, is used, with roughly 600,000 molecules generated every second. The enzyme has sped up the reaction rate by a factor of ten million. The power of enzymes is very amazing! Thousands of different enzymes exist, each catalysing a different chemical or metabolic reaction. A metabolic route is a multistep chemical reaction in which each step is catalysed by the same enzyme complex or separate enzymes. As an example,

is a metabolic pathway in which glucose is converted to pyruvic acid via 10 enzyme-catalyzed chemical events. At this point, you should be aware that this metabolic pathway, when supplemented with one or two additional processes, produces a wide range of metabolic end products. Lactic acid is produced in skeletal muscle under anaerobic circumstances. Pyruvic acid is generated under typical aerobic circumstances. The similar route leads to the generation of ethanol in yeast during fermentation (alcohol). As a result, different products are possible depending on the circumstances.

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

The concept of an active site is already known. A reaction is referred to as a chemical or metabolic change. A'substrate' is the chemical that is transformed into a product. As a result, enzymes, which are three-dimensional proteins with a 'active site,' convert a substrate (S) into a product (P). This can be represented symbolically as

Within a specific cleft or pocket, the substrate 'S' must bind the enzyme at its'active site.' The substrate must diffuse into the 'active site.' As a result, the creation of a 'ES' complex is required. The letter E stands for enzyme. This intricate structure is a one-time occurrence. A new structure of the substrate called the transition state structure is created when the substrate is attached to the enzyme active site. The product is quickly removed from the active site after the intended bond breaking/making is completed. In other words, the substrate's structure is changed into the product's structure (s). This transformation must pass via a structure known as a transition state structure.Between the stable substrate and the result, there could be many additional 'altered structural states.' The notion that all other intermediate structural states are unstable is implicit in this assertion. Stability has to do with the molecule's or structure's energy status.

The potential energy content is shown by the y-axis. The x-axis depicts the structural transformation or states as they proceed through the 'transition stage.' There would be two things that you would notice. The difference in energy levels between S and P. When 'P' is less than 'S,' the reaction is exothermic. It is not necessary to provide energy (through heating) in order to manufacture the product. Regardless of whether the reaction is exothermic or spontaneous or endothermic or energy-demanding, the 'S' must pass through a significantly higher energy level or transition state. 'Activation energy' is the difference between the average energy content of 'S' and that of this transition state. Enzymes gradually break down this energy barrier, allowing the 'S' to become 'P' more easily.

Nature of Enzyme Action

In order to create a highly reactive enzyme-substrate complex (ES), each enzyme (E) has a substrate (S) binding site in its molecule. This complex has a brief half-life and dissociates into its product(s) P and the unmodified enzyme, with the enzyme-product complex forming in the middle (EP). Catalysis requires the creation of the ES complex.

E+S → ES → EP → E+P

An enzyme's catalytic cycle can be broken down into the following steps:

1. The substrate first binds to the enzyme's active site, fitting into the active site.

2. The enzyme's shape changes as a result of the substrate's binding, causing it to fit more tightly around the substrate.

3. The enzyme's active site, which is now in close proximity to the substrate, breaks the substrate's chemical bonds, forming a new enzyme-product complex.

4. The reaction products are released by the enzyme, and the free enzyme is ready to bind to another molecule of the substrate and repeat the catalytic cycle.

Factors Affecting Enzyme Activity

A change in the circumstances can impact the activity of an enzyme by altering the protein's tertiary structure. Temperature, pH, changes in substrate concentration, and the binding of certain molecules that affect its activity are examples of these.

Temperature and pH: Enzymes typically operate within a narrow temperature and pH range. The optimum temperature and pH for each enzyme are defined as the temperature and pH at which the enzyme is most active. Both below and above the ideal value, activity decreases. Because proteins are denatured by heat, low temperatures maintain the enzyme in a temporarily inactive state, but high temperatures eliminate enzymatic function.

Substrate Concentration: At first, the enzymatic reaction's velocity increases as the substrate concentration rises. The reaction eventually achieves a maximum velocity (Vmax) that isn't exceeded by any further increase in substrate concentration. This is because there are fewer enzyme molecules than substrate molecules, and there are no free enzyme molecules to interact with the additional substrate molecules after these molecules have been saturated. An enzyme's activity is also affected by the presence of certain molecules that bind to it. The process of inhibition occurs when a chemical binds to an enzyme, and the chemical is referred to as an inhibitor.Competitive inhibitors are those that have a chemical structure that closely mimics that of the substrate and inhibits the enzyme's activity. Because of its structural similarity to the substrate, the inhibitor competes with it for the enzyme's substrate binding site. As a result, the substrate is unable to attach, and the enzyme's activity is reduced, as seen in the inhibition of succinic dehydrogenase by malonate, which is structurally similar to the substrate succinate. Competitive inhibitors like these are frequently employed to combat bacterial infections.

Classification and Nomenclature of Enzymes

There have been thousands of enzymes identified, isolated, and analyzed. The majority of these enzymes have been divided into groups depending on the kind of reactions that they catalyze. Enzymes are classified into six classes, each having four to thirteen subclasses, and given a four-digit number.

Co-factors

Enzymes are polypeptide chains made up of one or more polypeptide chains. However, in other situations, non-protein elements known as cofactors are coupled to the enzyme in order for it to be catalytically active. The apoenzyme refers to the protein part of the enzyme in these cases. Prosthetic groups, co-enzymes, and metal ions are all examples of cofactors. Prosthetic groups are chemical molecules that are strongly attached to the apoenzyme, distinguishing them from other cofactors. The prosthetic group haem is a component of the active site of enzymes like peroxidase and catalase, which catalyze the breakdown of hydrogen peroxide to water and oxygen.Co-enzymes are organic substances as well, although their relationship with the apoenzyme is very temporary, occurring most often during catalysis. Co-enzymes are also used as co-factors in a variety of enzyme-catalyzed processes. Many coenzymes contain vitamins as important chemical components; for example, the coenzymes nicotinamide adenine dinucleotide (NAD) and NADP contain the vitamin niacin. Metal ions that create coordination bonds with side chains in the active site while also forming one or more coordination bonds with the substrate are required for the activity of a number of enzymes, for example, zinc is a cofactor for the proteolytic enzyme carboxypeptidase. When a co-factor is removed from an enzyme, its catalytic activity is lost, indicating that they play an important part in the enzyme's catalytic activity.