The living world exhibits immense diversity. A fundamental question is whether living organisms are composed of the same basic chemical elements and compounds as non-living matter.

Performing an elemental analysis on living tissue (like a plant, animal tissue, or microbial paste) and comparing it to a sample of non-living matter (like the Earth's crust) reveals that all elements found in the Earth's crust are also present in living tissues.

However, a key difference lies in the relative abundance of certain elements. Carbon and hydrogen, in particular, are significantly more abundant in living organisms compared to the Earth's crust (Table 9.1).

Element	% Weight of Earth’s crust	% Weight of Human body
Hydrogen (H)	0.14	0.5
Carbon (C)	0.03	18.5
Oxygen (O)	46.6	65.0
Nitrogen (N)	very little	3.3
Sulphur (S)	0.03	0.3
Sodium (Na)	2.8	0.2
Calcium (Ca)	3.6	1.5
Magnesium (Mg)	2.1	0.1
Silicon (Si)	27.7	negligible

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How To Analyse Chemical Composition?

To understand the types of organic compounds present in living organisms, a chemical analysis is performed.

Method for analysing organic compounds:

1. Take a sample of living tissue (e.g., vegetable, liver).
2. Grind it in trichloroacetic acid (Cl$_3$CCOOH) using a mortar and pestle to create a thick slurry.
3. Strain the slurry through cheesecloth or cotton.
4. This process yields two fractions:
   • Filtrate (Acid-soluble pool): Contains thousands of organic compounds with smaller molecular weights.
   • Retentate (Acid-insoluble fraction): Contains organic compounds with larger molecular weights (macromolecules), and lipids.

Scientists use various separation techniques to isolate and purify individual compounds from these fractions. Analytical techniques then help determine the molecular formula and structure of these compounds.

All the carbon compounds obtained from living tissues are collectively called biomolecules.

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Method for analysing inorganic constituents:

A different method is used to identify inorganic elements and compounds:

1. Weigh a small amount of living tissue (wet weight).
2. Dry the tissue completely to evaporate all water. The remaining material is the dry weight.
3. Burn the dry tissue completely. All carbon compounds are oxidized into gaseous forms (CO$_2$, water vapour) and removed.
4. The remaining residue is called ash.
5. The ash contains inorganic elements (e.g., calcium, magnesium).

Inorganic compounds (e.g., sulphate, phosphate) are also found in the acid-soluble fraction.

Thus, elemental analysis identifies the composition of living tissues in terms of elements (H, O, Cl, C, etc.), while analysis for compounds identifies the types of organic (Figure 9.1 provides examples of small organic molecules) and inorganic constituents (Table 9.2 lists examples of inorganic ions and compounds) present.

Component	Formula
Sodium ion	Na$^+$
Potassium ion	K$^+$
Calcium ion	Ca$^{++}$
Magnesium ion	Mg$^{++}$
Water	H$_2$O
Compounds (e.g., salts, carbonates)	NaCl, CaCO$_3$, PO$_4^{3-}$, SO$_4^{2-}$

From a chemistry perspective, compounds can be grouped by functional groups (aldehydes, ketones, etc.). Biologically, they are often classified into categories like amino acids, nucleotide bases, fatty acids, etc.

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Examples of small molecular weight organic compounds (Figure 9.1):

• Amino acids: Organic compounds with both an amino group ($-\textsf{NH}_2$) and an acidic carboxyl group ($-\textsf{COOH}$) attached to the same carbon atom (the $\alpha$-carbon). They are substituted methanes, with the other two valencies occupied by hydrogen and a variable 'R' group. About 20 types of amino acids are commonly found in proteins, differing based on their R group (e.g., Glycine has H, Alanine has $-\textsf{CH}_3$, Serine has $-\textsf{CH}_2\textsf{OH}$).

Properties of amino acids vary based on the R group and the number of amino and carboxyl groups. They can be acidic (e.g., glutamic acid), basic (e.g., lysine), or neutral (e.g., valine). Some are aromatic (e.g., tyrosine, phenylalanine, tryptophan). The amino and carboxyl groups are ionizable, leading to changes in structure (e.g., zwitterionic form) at different pH levels.

• Lipids: Generally insoluble in water. Can be simple fatty acids, or compounds involving glycerol and fatty acids.
  • Fatty acids: Have a carboxyl group attached to an R group (hydrocarbon chain, 1-19 carbons). Can be saturated (no C=C double bonds, e.g., palmitic acid - 16 carbons) or unsaturated (one or more C=C double bonds, e.g., arachidonic acid - 20 carbons).
  • Glycerol: Trihydroxy propane.
  • Glycerides: Fatty acids esterified with glycerol. Can be monoglycerides, diglycerides, or triglycerides (fats and oils). Oils have lower melting points than fats.
  • Phospholipids: Lipids containing phosphorous and a phosphorylated organic compound (e.g., lecithin). Important components of cell membranes.
• Nitrogen bases: Heterocyclic compounds containing nitrogen (e.g., adenine, guanine, cytosine, uracil, thymine). Adenine and Guanine are purines (double-ring structure), while Cytosine, Uracil (in RNA), and Thymine (in DNA) are pyrimidines (single-ring structure).
• Nucleosides: Formed when a nitrogen base is attached to a sugar (ribose or deoxyribose). Examples: Adenosine (Adenine + Ribose), Guanosine, Cytidine, Uridine (Uracil + Ribose), Thymidine (Thymine + Deoxyribose).
• Nucleotides: Formed when a phosphate group is esterified to the sugar in a nucleoside. Examples: Adenylic acid (Adenosine + Phosphate), Guanylic acid, Cytidylic acid, Uridylic acid, Thymidylic acid.

Nucleic acids (DNA and RNA) are polymers made up solely of nucleotides and serve as genetic material.

Primary And Secondary Metabolites

The thousands of small and large compounds isolated from living organisms are called metabolites.

• Primary metabolites: Compounds that have identifiable functions and play known, essential roles in the normal physiological processes of an organism (e.g., amino acids, sugars, fatty acids, nitrogen bases, etc. found in Figure 9.1). These are found in all animal tissues.
• Secondary metabolites: Thousands of other compounds found primarily in plant, fungal, and microbial cells (not typically found in animal tissues). These do not have obvious, known roles in the host organism's normal physiology (at least currently).

Examples of Secondary Metabolites (Table 9.3):

Category	Examples
Pigments	Carotenoids, Anthocyanins, etc.
Alkaloids	Morphine, Codeine, etc.
Terpenoides	Monoterpenes, Diterpenes etc.
Essential oils	Lemon grass oil, etc.
Toxins	Abrin, Ricin
Lectins	Concanavalin A
Drugs	Vinblastin, curcumin, etc.
Polymeric substances	Rubber, gums, cellulose

Although the specific role of many secondary metabolites in the producing organism is not fully understood, many are highly valuable to human welfare (e.g., rubber, drugs, spices, scents, pigments). Some also have ecological importance (e.g., defense against herbivores or microbes).

Biomacromolecules

Biomolecules can be broadly classified based on their molecular weight and presence in the acid-soluble or acid-insoluble fraction after chemical analysis:

• Micromolecules: Organic compounds found in the acid-soluble pool. They typically have molecular weights ranging from approximately 18 to 800 Daltons (Da). These are often referred to as simple biomolecules.
• Macromolecules (Biomacromolecules): Organic compounds found in the acid-insoluble fraction. With the exception of lipids, these compounds have molecular weights of ten thousand Daltons (10,000 Da) and above. They are typically polymeric substances.

The macromolecules in the acid-insoluble fraction consist of four main types:

• Proteins
• Nucleic acids
• Polysaccharides
• Lipids (exception)

Lipids are an exception to the molecular weight definition of macromolecules. Their molecular weights are typically below 800 Da. However, they are found in the acid-insoluble fraction because they are organized into structures like cell membranes and other cellular membranes. When tissues are ground, these membranes break into small vesicles. These vesicles are not water-soluble and therefore get separated into the acid-insoluble pellet along with the macromolecules. Thus, lipids are technically micromolecules but are included in the macromolecular fraction due to their structural association in cells.

The acid-soluble pool roughly represents the cytoplasmic composition, containing monomers and smaller molecules. The acid-insoluble fraction primarily represents the macromolecules from the cytoplasm and organelles. Together, these fractions reflect the entire chemical composition of a living tissue.

When considering the abundance of different chemical components in a cell, water is the most abundant (Table 9.4).

Component	% of the total cellular mass
Water	70-90
Proteins	10-15
Carbohydrates	3
Lipids	2
Nucleic acids	5-7
Ions	1

Proteins

Proteins are polypeptides. They are linear polymers formed by joining amino acids together.

The bond linking amino acids in a protein is a peptide bond.

Amino acids are the monomers of proteins. There are 20 different types of amino acids found in proteins (e.g., alanine, cysteine, proline, tryptophan, lysine). Because a protein chain is typically composed of multiple different types of amino acids, proteins are considered heteropolymers (polymers made of different types of monomers), not homopolymers (polymers made of only one type of repeating monomer).

Amino acids needed by our body can be classified as:

• Essential amino acids: Cannot be synthesized by the body and must be obtained from the diet. Dietary proteins are a crucial source of essential amino acids.
• Non-essential amino acids: Can be synthesized by the body.

Proteins perform a vast array of functions in living organisms (Table 9.5):

Protein	Functions
Collagen	Provides structural support, forms intercellular ground substance.
Trypsin	Enzyme (involved in protein digestion).
Insulin	Hormone (regulates blood glucose levels).
Antibody	Part of the immune system, fights infectious agents.
Receptor	Receives signals (sensory reception like smell, taste, or hormone binding).
GLUT-4	Transport protein, facilitates glucose transport into cells.

Collagen is the most abundant protein in the animal kingdom. Ribulose bisphosphate Carboxylase-Oxygenase (RuBisCO) is the most abundant protein in the entire biosphere (including plants, which make up a huge biomass).

Polysaccharides

Polysaccharides are another class of macromolecules found in the acid-insoluble pellet. They are long chains (polymers) of sugars (monosaccharides).

Monosaccharides are the building blocks (monomers) of polysaccharides. These monomers are linked together by glycosidic bonds.

Polysaccharides can be homopolymers (made of one type of monosaccharide) or heteropolymers (made of different types).

Examples of Polysaccharides:

• Cellulose: A homopolymer made up solely of glucose units. Forms the major structural component of plant cell walls. Paper and cotton fiber are examples of cellulosic material. Cellulose does not form complex helical structures.
• Starch: A homopolymer of glucose, serving as the primary energy storage carbohydrate in plants. Starch molecules form helical secondary structures, which can bind iodine (I$_2$) molecules, resulting in a characteristic blue colour.
• Glycogen: A branched homopolymer of glucose, serving as the energy storage carbohydrate in animals and fungi. It is highly branched (Figure 9.2). The ends of a polysaccharide chain are referred to as the reducing end (typically the right end in diagrams) and the non-reducing end (the left end in diagrams).
• Inulin: A polymer of fructose.
• Chitin: A complex polysaccharide that is a homopolymer of a modified sugar called N-acetyl glucosamine (an amino-sugar). It forms the exoskeleton of arthropods (insects, crustaceans) and the cell walls of fungi.

More complex polysaccharides can have amino-sugars and other chemically modified sugars as building blocks (e.g., glucosamine, N-acetyl galactosamine).

Nucleic Acids

Nucleic acids are macromolecules found in the acid-insoluble fraction, along with proteins and polysaccharides. They are polymers called polynucleotides.

The building block (monomer) of a nucleic acid is a nucleotide.

Each nucleotide has three chemically distinct components:

1. A heterocyclic compound (nitrogenous base).
2. A monosaccharide (pentose sugar - 5 carbons).
3. A phosphoric acid or phosphate group.

Nitrogenous Bases (Heterocyclic compounds): Adenine (A), Guanine (G), Cytosine (C), Uracil (U), and Thymine (T). They are derived from two parent structures:

• Purines: Adenine (A) and Guanine (G) are substituted purines (double-ring structure).
• Pyrimidines: Cytosine (C), Uracil (U), and Thymine (T) are substituted pyrimidines (single-ring structure).

Pentose Sugar: The sugar is either:

• Ribose: A five-carbon sugar (found in RNA).
• 2’-deoxyribose: A ribose sugar with a hydroxyl group removed from the 2' carbon (found in DNA).

Phosphoric acid ($H_3PO_4$): The phosphate group.

Combining the components:

• Nucleoside: A nitrogen base attached to a sugar. Examples: Adenosine (Adenine + Ribose), Guanosine, Cytidine, Uridine, Thymidine.
• Nucleotide: A nucleoside with a phosphate group esterified to the sugar. Examples: Adenylic acid, Guanylic acid, Cytidylic acid, Uridylic acid, Thymidylic acid. Nucleotides are also called nucleoside phosphates.

Types of Nucleic Acids:

• Deoxyribonucleic acid (DNA): A nucleic acid containing 2'-deoxyribose sugar.
• Ribonucleic acid (RNA): A nucleic acid containing ribose sugar.

DNA and RNA function as the genetic material in most organisms.

Structure Of Proteins

Proteins are complex macromolecules with structures described at four levels (Figure 9.3).

1. Primary Structure: This is the linear sequence of amino acids in a polypeptide chain. It specifies which amino acid is first, second, third, and so on, from the N-terminal end (amino group end) to the C-terminal end (carboxyl group end). The N-terminal amino acid is the first in the sequence, and the C-terminal is the last. This linear sequence is determined by the genetic code.
2. Secondary Structure: The polypeptide chain does not exist as a straight rod. It folds or coils into specific repeating patterns. Common secondary structures are:
   • $\alpha$-helix: The polypeptide chain coils into a right-handed spiral shape, stabilized by hydrogen bonds between amino acids in different turns of the helix.
   • $\beta$-pleated sheet: Portions of the polypeptide chain lie parallel or anti-parallel to each other and are connected by hydrogen bonds, forming a pleated, sheet-like structure.
3. Tertiary Structure: The overall three-dimensional folding of the entire polypeptide chain. This involves further bending and folding of the secondary structures into a compact, globular, or fibrous shape, resembling a hollow woolen ball. The tertiary structure is stabilized by various types of bonds and interactions (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bonds between cysteine residues). This 3D conformation is absolutely essential for the biological activity of most proteins.
4. Quaternary Structure: This level of organization occurs in proteins that are composed of more than one polypeptide chain (subunit). The quaternary structure describes the specific arrangement of these individual polypeptide subunits relative to each other in the complete protein complex. For example, adult human haemoglobin (Hb) is a tetramer (has 4 subunits): two identical $\alpha$ subunits and two identical $\beta$ subunits are arranged together to form the functional protein.

Nature Of Bond Linking Monomers In A Polymer

Polymers in living organisms are formed by linking monomers through specific chemical bonds, typically involving the removal of a water molecule (dehydration or condensation reaction).

• Peptide Bond: Links amino acids in a polypeptide (protein). Formed between the carboxyl group ($-\textsf{COOH}$) of one amino acid and the amino group ($-\textsf{NH}_2$) of the next amino acid, with the elimination of water.
• Glycosidic Bond: Links monosaccharides in a polysaccharide. Formed between two carbon atoms of adjacent monosaccharides, also by the elimination of water.
• Phosphodiester Bond: Links nucleotides in a nucleic acid (DNA or RNA). Formed between the phosphate group of one nucleotide and the sugar of the next nucleotide. Specifically, the phosphate moiety is esterified to the 3'-carbon of the sugar of one nucleotide and also to the 5'-carbon of the sugar of the succeeding nucleotide via ester bonds. Since there are two ester bonds involving the phosphate group, it is called a phosphodiester bond (Figure 9.5). This bond forms the backbone of the nucleic acid chain (sugar-phosphate-sugar).

Nucleic acids can form various secondary structures. The most well-known is the DNA double helix, famously described by Watson and Crick:

• DNA exists as two polynucleotide strands coiled around each other to form a double helix.
• The two strands are antiparallel, meaning they run in opposite directions (one from 5' to 3', the other from 3' to 5').
• The sugar-phosphate chain forms the backbone of the helix, located on the outside.
• The nitrogen bases project inwards, more or less perpendicular to the backbone.
• Base Pairing: Specific bases on one strand pair with specific bases on the other strand via hydrogen bonds:
  • Adenine (A) always pairs with Thymine (T) by two hydrogen bonds.
  • Guanine (G) always pairs with Cytosine (C) by three hydrogen bonds.
• The specific base pairing (A with T, G with C) means the two strands are complementary.
• The double helix resembles a helical staircase, with each step represented by a base pair.
• Each base pair turn is $36^{\circ}$.
• One full turn of the helix involves ten base pairs.
• The pitch (length of one full turn) of the helix is approximately $34 \textsf{ Å}$ ($3.4 \textsf{ nm}$).
• The rise per base pair (distance between adjacent base pairs) is approximately $3.4 \textsf{ Å}$ ($0.34 \textsf{ nm}$).

This specific form of DNA described is called B-DNA, which is the most common form under physiological conditions. Other forms of DNA exist with different structural features.

Dynamic State Of Body Constituents - Concept Of Metabolism

Living organisms contain thousands of organic compounds (biomolecules or metabolites) present at specific concentrations (e.g., glucose concentration in blood is $4.2 \textsf{ mmol/L} - 6.1 \textsf{ mmol/L}$).

A fundamental characteristic of living organisms is the constant turnover of these biomolecules. They are continuously being broken down and synthesized from other biomolecules through a series of interconnected chemical reactions.

The sum total of all chemical reactions occurring in a living organism is called metabolism.

Metabolic reactions result in the transformation of biomolecules (e.g., converting an amino acid to an amine by removing CO$_2$, hydrolyzing a disaccharide).

Metabolic reactions rarely occur in isolation; they are typically linked to other reactions, forming structured sequences called metabolic pathways. These pathways can be linear or circular and often intersect at 'traffic junctions', allowing for complex interactions and regulation.

The flow of metabolites through these pathways occurs at a definite rate and direction, representing the dynamic state of body constituents.

A crucial feature of metabolic reactions in living systems is that almost every reaction is a catalysed reaction. Even simple processes like CO$_2$ dissolving in water are catalysed in living systems.

The catalysts that speed up metabolic conversions are primarily proteins called enzymes (some nucleic acids, called ribozymes, also have catalytic activity).

Metabolic Basis For Living

Metabolic pathways can be categorized based on their overall outcome and energy requirements:

• Anabolic pathways (Biosynthetic pathways): Build more complex structures from simpler ones (e.g., synthesis of cholesterol from acetic acid, assembly of proteins from amino acids). These pathways consume energy.
• Catabolic pathways (Degradation pathways): Break down complex structures into simpler ones (e.g., breakdown of glucose to lactic acid). These pathways release energy.

Living organisms are able to capture the energy released during catabolic reactions and store it in the chemical bonds of specific molecules. The most important energy currency in living systems is adenosine triphosphate (ATP). The bond energy in ATP can then be used to power various cellular processes, including biosynthetic reactions (anabolism), transport (osmotic work), and movement (mechanical work).

Understanding how organisms obtain, store, and utilize energy is the domain of Bioenergetics.

The Living State

In a living organism, metabolites and biomolecules are present at specific, characteristic concentrations, but they are constantly being interconverted through metabolic reactions. This continuous turnover means the system is in a state of metabolic flux.

Physically or chemically, spontaneous processes tend towards equilibrium. However, living organisms are in a steady-state, which is a non-equilibrium state.

Organisms continuously perform work (biosynthesis, transport, movement). Systems at equilibrium cannot perform work.

The living state is fundamentally a non-equilibrium steady state maintained by a constant input of energy derived from metabolism. This energy is used to prevent the system from reaching equilibrium.

Therefore, the living state and metabolism are intrinsically linked and can be considered synonymous; metabolism is necessary to provide the energy required to maintain the non-equilibrium steady state characteristic of life.

Enzymes

Most enzymes are proteins. Some nucleic acids, called ribozymes, also exhibit catalytic activity.

Structure: Proteinaceous enzymes have primary, secondary, and tertiary structures. The specific folding of the polypeptide chain in the tertiary structure creates three-dimensional pockets or crevices. One such pocket is the active site.

Active site: A crevice or pocket on the enzyme surface where the substrate molecule binds and the catalytic reaction takes place.

Enzyme catalysts differ from inorganic catalysts in several ways. A key difference is their sensitivity to temperature:

• Inorganic catalysts are often efficient at high temperatures and pressures.
• Most enzymes are sensitive to heat and can be damaged or lose activity (denatured) at temperatures above $\sim 40^\circ\textsf{C}$. However, enzymes from thermophilic organisms (living in extreme heat) can remain stable and active at much higher temperatures ($\sim 80^\circ\textsf{-}90^\circ\textsf{C}$).

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Chemical Reactions

Chemical compounds undergo physical changes (change in shape or state, no bond breaking) or chemical reactions (bonds are broken and formed, leading to transformation).

Example chemical reactions:

• Inorganic: $\textsf{Ba(OH)}_2 + \textsf{H}_2\textsf{SO}_4 \rightarrow \textsf{BaSO}_4 + 2\textsf{H}_2\textsf{O}$
• Organic: Hydrolysis of starch into glucose.

The rate of a physical or chemical process is the amount of product formed per unit time. It can be expressed as rate $= \frac{\textsf{dP}}{\textsf{dt}}$. Rate can also be called velocity if direction is specified.

Rates are influenced by factors like temperature. Generally, the rate doubles or halves for every $10^\circ\textsf{C}$ change.

Catalysed reactions occur at rates significantly higher than uncatalysed ones. Enzymes are highly efficient biological catalysts.

Example: The reaction of carbon dioxide with water to form carbonic acid:

$\textsf{CO}_2 + \textsf{H}_2\textsf{O} \xrightarrow{\textsf{Carbonic anhydrase}} \textsf{H}_2\textsf{CO}_3$

• Without enzyme: $\sim 200$ molecules formed per hour.
• With enzyme (carbonic anhydrase): $\sim 600,000$ molecules formed per second.

The enzyme increases the reaction rate by about 10 million times, demonstrating incredible catalytic power.

Metabolic pathways involve a series of enzyme-catalysed reactions. For instance, the breakdown of glucose to pyruvic acid (glycolysis) is a 10-step metabolic pathway, with each step catalyzed by a specific enzyme or enzyme complex.

Metabolic pathways can lead to different end products depending on conditions (e.g., glucose to lactic acid in skeletal muscle under anaerobic conditions, or ethanol in yeast during fermentation).

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How Do Enzymes Bring About Such High Rates Of Chemical Conversions?

Enzymes accelerate reactions by lowering the activation energy. The molecule converted into a product is called the substrate (S).

The mechanism involves the following steps:

1. The substrate (S) binds to the enzyme's active site, forming an enzyme-substrate (ES) complex. This binding is often highly specific.
2. The binding induces a change in the enzyme's shape, causing it to fit more tightly around the substrate (induced fit).
3. Within the active site, the enzyme facilitates the breaking and formation of chemical bonds in the substrate, transforming it into the product(s). This intermediate state is called the enzyme-product (EP) complex. The substrate passes through a high-energy state called the transition state during this transformation.
4. The enzyme releases the product(s) (P) from the active site.
5. The free enzyme is then available to bind another substrate molecule and repeat the catalytic cycle.

The overall reaction pathway is: E + S $\rightleftharpoons$ ES $\rightarrow$ EP $\rightarrow$ E + P

Activation Energy: For any chemical reaction to occur, the substrate must reach a higher energy state, the transition state, before being converted to product. The difference in energy between the stable substrate molecule and the transition state is called the activation energy (Figure 9.6).

Enzymes function by lowering the activation energy barrier required for the reaction to proceed, thereby significantly increasing the reaction rate.

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Nature Of Enzyme Action

The catalytic cycle describes the sequence of events during enzyme action:

1. The substrate (S) attaches to the enzyme's active site, creating the enzyme-substrate complex (ES). The active site's shape precisely fits the substrate.
2. Binding of the substrate slightly alters the enzyme's shape for a tighter fit (induced fit).
3. Within the active site, positioned optimally, the enzyme promotes bond breaking/making in the substrate, converting it to product(s). An intermediate enzyme-product complex (EP) is formed.
4. The product(s) (P) are released from the active site.
5. The enzyme is regenerated in its original form, ready for a new substrate molecule.

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Factors Affecting Enzyme Activity

Enzyme activity can be influenced by changes in conditions that affect the enzyme's tertiary structure or the substrate-enzyme interaction (Figure 9.7).

• Temperature: Each enzyme has an optimum temperature at which its activity is highest. Activity decreases both below and above this optimum. Low temperature preserves the enzyme in an inactive state. High temperature above the optimum leads to denaturation of the protein structure, irreversibly destroying enzyme activity.
• pH: Similar to temperature, each enzyme has an optimum pH for maximal activity. Deviations from this optimum pH can reduce or abolish enzyme activity by altering the ionization state of amino acid residues in the active site.
• Concentration of Substrate ([S]): As substrate concentration increases, the reaction velocity (enzyme activity) initially increases. However, the rate eventually plateaus and reaches a maximum velocity (Vmax). This occurs because the number of enzyme molecules is limited. At high substrate concentrations, all enzyme active sites become saturated with substrate molecules, and the rate is limited by how fast the enzyme can process the substrate.

Enzyme Inhibitors: Specific chemicals can bind to an enzyme and reduce or stop its activity. These are called inhibitors, and the process is inhibition.

Competitive Inhibitor: An inhibitor that closely resembles the substrate in molecular structure. It competes with the substrate for binding to the enzyme's active site. This reduces the chances of the substrate binding, thus lowering enzyme activity. Increasing substrate concentration can often overcome competitive inhibition. Example: Malonate inhibits succinic dehydrogenase because it is structurally similar to the enzyme's substrate, succinate. Competitive inhibitors are sometimes used as drugs to target bacterial enzymes.

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Classification And Nomenclature Of Enzymes

Enzymes are systematically classified into 6 major classes based on the type of chemical reaction they catalyze. Each class has subclasses, and individual enzymes are assigned a unique four-digit number.

1. Oxidoreductases/Dehydrogenases: Catalyze oxidation and reduction reactions, transferring hydrogen or electrons between two substrates. $\textsf{S}_{\text{reduced}} + \textsf{S'}_{\text{oxidised}} \rightarrow \textsf{S}_{\text{oxidised}} + \textsf{S'}_{\text{reduced}}$
2. Transferases: Catalyze the transfer of a specific functional group (other than hydrogen) from one substrate to another. $\textsf{S}-\textsf{G} + \textsf{S'} \rightarrow \textsf{S} + \textsf{S'}-\textsf{G}$
3. Hydrolases: Catalyze the hydrolysis (breakdown using water) of various bonds, including ester, ether, peptide, glycosidic, C-C, C-halide, or P-N bonds. (e.g., digestive enzymes like amylase, protease).
4. Lyases: Catalyze the removal of groups from substrates by mechanisms other than hydrolysis, often resulting in the formation of double bonds. (e.g., Fumarase removes water from malate to form fumarate).
5. Isomerases: Catalyze the inter-conversion of different isomeric forms (optical, geometric, or positional isomers) of a molecule. (e.g., Phosphohexose isomerase converts glucose-6-phosphate to fructose-6-phosphate).
6. Ligases: Catalyze the joining together of two molecules, forming bonds such as C-O, C-S, C-N, or P-O bonds. This process typically requires energy input (e.g., DNA ligase joins DNA fragments).

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Co-Factors

Some enzymes consist solely of one or more polypeptide chains. However, many enzymes require non-protein components called co-factors to be catalytically active.

Holoenzyme: The catalytically active enzyme, consisting of the protein portion (apoenzyme) bound to its co-factor.

Co-factors can be of three types:

1. Prosthetic groups: Organic compounds that are tightly and firmly bound to the apoenzyme. Often a part of the enzyme's active site. Example: Haem is the prosthetic group in enzymes like peroxidase and catalase, which break down hydrogen peroxide.
2. Co-enzymes: Organic compounds whose association with the apoenzyme is transient or temporary, typically occurring only during the catalytic reaction. Co-enzymes can function as co-factors for several different enzymes. Many co-enzymes are derived from vitamins (e.g., NAD and NADP contain the vitamin niacin).
3. Metal ions: Inorganic ions required by some enzymes for activity. They form coordination bonds with side chains of amino acids at the active site and also with the substrate. Example: Zinc (Zn$^{2+}$) is a metal ion cofactor for the proteolytic enzyme carboxypeptidase.

The removal of the co-factor typically results in the loss of the enzyme's catalytic activity, demonstrating their crucial role.

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