Bright Mind Academy Kamra

Chap:03 Enzymes
 Metabolism: Sum of all chemical reactions in a cell; essential for quick product utilization in life
activities.
 Enzymes: Biological catalysts that speed up biochemical reactions without being consumed.
 Historical Note: Early 19th-century French chemists Payen and Persoz discovered that a crude mixture
from barley seeds could digest starch; they named this substance "diastase."
 Definition: Enzymes are biological polymers that catalyze biochemical reactions.
 Enzyme Structure:
 Enzymes are globular proteins made up of one or more polypeptide chains.
 Ribozymes, which are RNA-based enzymes found in ribosomes, include peptidyl transferase
involved in protein synthesis.
 Active Site:
 Definition: Specific, charge-bearing, three-dimensional cavity on an enzyme where the substrate
binds.
 Components:
o Binding Site: Region where substrate attaches via non-covalent interactions (e.g., hydrogen
bonding, hydrophobic interactions).
o Catalytic Site: Region responsible for converting the substrate into the product.
 Structure: Made up of 3-12 amino acids that are spread out in the enzyme but come together when
the enzyme folds.
 Example: Active site for aldolase includes glycine, histidine, and alanine.
 Specificity: The shape of the active site is made to fit a specific substrate, but sometimes it can also
fit similar substrates
 Cofactors:
 Definition: Non-protein components required by some enzymes.
 Functions: helps in substrate attachment to the active site and participate in the catalytic process.
 Active Site Formation: The final shape of the active site is established after the cofactor attaches.
 Holoenzyme:
 The enzyme becomes active only when the cofactor is combined with it.
 Apoenzyme:
Apoenzyme or apoprotein is an enzymatically inactive protein part of an enzyme, which requires a cofactor
for its activity.
apoenzyme is the enzyme's catalytically inactive protein component, whereas holoenzyme is the enzyme's
catalytically active form, consisting of the apoenzyme and the cofactor.

 Pepsin Example:
 Inactive Form: Pepsinogen, secreted by the gastric gland, has an additional polypeptide fragment
that blocks substrate binding.
 Activation: Exposure to HCl in the stomach removes the additional fragment, converting
pepsinogen (apoenzyme) into active pepsin (holoenzyme).

 Enzyme Formation:
 Enzymes are proteins formed according to the genetic message encoded in DNA.
  Enzymes can retain their catalytic action even when extracted from cells and can act in vitro.
 Modern enzymes are also produced using recombinant DNA technology.
 Types of Cofactors:
1. Inorganic Ions:
o Examples: Fe²⁺, Mg²⁺, Cu²⁺, Zn²⁺.
o Function: Detachable cofactors that act as activators(Enzyme activators are molecules that
bind to enzymes and increase their activity); they attach to enzymes when the substrate binds.

2. Organic Molecules:
o Coenzymes:
 Definition: Organic cofactors derived from vitamins.
 Examples: ATP, NAD⁺, FAD.
 Function: Detachable cofactors that attach to enzymes when the substrate binds.
o Prosthetic Groups:
 Definition: Organic molecules covalently bonded to enzymes.
 Function: Permanently attached and do not detach after the reaction.
 Example: An iron-containing porphyrin ring in cytochromes.

 Mechanism of Enzyme Action:

 Formation of ES Complex: The substrate binds to the enzyme's active site to form an enzyme-
substrate (ES) complex.
 Conversion to EP Complex: The substrate is converted into the product while still attached to the
enzyme, forming an enzyme-product (EP) complex.
 Release of Product: The product is released from the enzyme, allowing the enzyme to repeat the
process.

 Models of Enzyme Action:

1. Lock and Key Model (Proposed by Emil Fischer in 1894):
o Concept: The enzyme is like a lock, and the substrate is like a key.
o Mechanism: The substrate has a shape that fits precisely into the enzyme's active site,
similar to how a key fits into a lock.
o Binding: The enzyme-substrate binding is specific; if the substrate does not match the shape
of the active site, binding will not occur.
o Enzyme Rigidity: The enzyme's active site does not change shape during the binding
process.
o Alternate Representation: Sometimes, the model is depicted with the key as the enzyme
and the lock as the substrate.

Specificity of Enzymes:
 Notched Key Analogy: The notched portion of the key represents the active site of the enzyme,
illustrating the high specificity of enzymes.
  Non-Regulatory Enzymes: Enzymes that follow the Lock and Key model and perform only one
specific reaction. Examples include sucrase and maltase.
 Absolute Specificity: Enzymes that catalyze only one specific substrate, such as urease which
catalyzes the hydrolysis of urea to ammonia and carbon dioxide.

2. Induced Fit Model (Proposed by Daniel Koshland in 1959):

 Concept: The active site of the enzyme is flexible and changes shape as the substrate interacts with
it.
 Mechanism: The amino acids in the active site mold into a precise shape to better facilitate the
catalytic process. The active site adjusts to accommodate the substrate, enhancing the enzyme's
effectiveness.
 Post-Reaction: After the reaction, the active site returns to its original shape.
 Versatility: The flexibility allows the enzyme to bind with a range of related substrates and perform
multiple related reactions.
 Example: Carbonic anhydrase, which can add O₂ to hemoglobin and also manage the formation of
carbonic acid and bicarbonates in the blood.

 Regulatory or Allosteric Enzymes:

 Definition: Enzymes that follow the Induced Fit model and can catalyze multiple related reactions.
 Example: Hexokinase, which demonstrates flexibility in its substrate interactions.

 Energy of Activation:
 This is the energy needed to start a chemical reaction.
 In non-living systems, we often use heat to provide this energy. Heat makes molecules move faster and
collide more, which helps start the reaction.
 In living things, using heat isn’t practical because cells can’t handle high temperatures. Instead, enzymes
help by lowering the amount of energy needed to start the reaction.
 Enzymes work by binding to the reactants and forming a temporary complex. This makes it easier for the
reaction to occur.
 Enzymes reduce the energy barrier, so less energy is needed to start the reaction.
 Enzymes make chemical reactions happen faster by making it easier for molecules to react without
needing extra heat

 Effect of Enzymes:
 Lower Activation Energy: Enzymes lower the energy of activation required for reactions, making it
easier for reactants to be converted into products.
 Energy Efficiency: Enzymes convert energy-dependent processes into energy-independent
processes, facilitating biochemical reactions under mild conditions.
 Energy Diagram: Enzymes decrease the activation energy required to start a reaction,
Factors affecting rate of enzymatic reaction
 Rate Measurement:
 Definition: The rate of enzymatic reaction is assessed by measuring the amount of substrate
converted or the amount of product formed over time.
 Factors Affecting Enzymatic Action:
1. Temperature
2. pH
3. Concentration of Enzyme
4. Substrate Concentration

Temperature
 Increasing Temperature:
o Raises the rate of reaction by increasing molecular motion.
o A 10°C increase can double the reaction rate, up to a point.
 Optimal Temperature:
o Maximum enzyme activity is at the optimum temperature.
o Human enzymes: ~37-38°C.
o Thermophilic bacteria: ~70°C or higher.
 Denaturation:
o Occurs above the optimum temperature.
o Enzyme structure is disrupted, losing activity.
o Temperature causing denaturation is the maximum temperature.
 Low Temperatures:
o Near freezing: Enzymes become inactive but not denatured.
o Activity resumes when temperature returns to optimal levels.
o Temperature where enzyme becomes active again is the minimum temperature.
 Optimum pH:
 Definition: The narrow pH range where an enzyme functions most effectively.
 Effect of pH on Enzyme:
o Optimal pH: Maximum rate of reaction is achieved.
o Slight pH Changes: Cause temporary inactivation due to ionization of amino acids.
o Extreme pH Changes: Disrupt ionic bonding and enzyme structure, leading to denaturation.
 Enzyme Examples:
 Pepsin: Active in acidic conditions (pH 2).
 Trypsin: Active in alkaline conditions (pH 8).
 Papain: Functions in both acidic and alkaline conditions (pH 5-8).
 Industrial Pollution Impact:
 Effect on Aquatic Plants: Changes in water pH can disrupt the enzyme activity and metabolic
pathways of plants, affecting their growth and health.

 Enzyme Concentration:
 Effect on Reaction Rate:
o Proportional Relationship: As enzyme concentration increases (with constant substrate
concentration, pH, and temperature), the reaction rate increases proportionally.
o Active Sites: More enzymes provide more active sites, speeding up substrate conversion.
o Equilibrium State: Reaction rate increases until enzyme and substrate concentrations reach
equilibrium. Beyond this point, adding more enzymes does not further increase the reaction
rate.

 Enzyme Inhibition:
 Definition: When an enzyme fails to catalyze a reaction due to interference by inhibitor molecules.
 Inhibitors: Include poisons, cyanides, antibodies, anti-metabolites, penicillin, and sulfa drugs.
  Poisons: Toxins
  Cyanides: Toxins
  Antibodies: Proteins
  Anti-metabolites: Drugs
  Penicillin: Antibiotic
  Sulfa drugs: Antibiotics

 Types of Inhibition:
o Competitive Inhibition: Inhibitor competes with the substrate for the active site.
o Non-competitive Inhibition: Inhibitor binds to a different site on the enzyme, altering its
function.
 Definition:
 Competitive Inhibition: Occurs when an inhibitor competes with the substrate for the active site of
an enzyme.
 Mechanism:
 Inhibitor Characteristics: Typically structurally similar to the substrate but cannot fully participate
in the reaction.
 Effect: Blocks substrate binding and prevents enzyme activity.
 Reversibility:

 Temporary: Inhibition can be reversed, depending on the amounts of substrate and inhibitor.
 Increased Substrate: More substrate can outcompete(perform better) the inhibitor and stop the
inhibition.

 Example:
 Malonate: A competitive inhibitor of succinate dehydrogenase, blocking the conversion of succinate
to fumarate.
 Critical Thinking:
 Substrate Concentration in Non-Competitive Inhibition: Substrate concentration does not affect
non-competitive inhibition because the inhibitor binds to a different site on the enzyme, not the
active site.

 Definition:
 Non-Competitive Inhibition: The inhibitor binds to a site other than the enzyme's active site,
known as the allosteric site.
 Types of Non-Competitive Inhibition:
 Reversible Non-Competitive Inhibition:
o Mechanism: Inhibitor binds to the allosteric site, preventing enzyme-substrate complex from
converting to enzyme-product complex.
o Effect: Temporary inactivation; substrate binding is unaffected, but product formation is
inhibited.
o Example: Feedback inhibition is an examle of this, (It means that the final product of a process
can stop an enzyme that helps make it. This prevents the process from making too much of the
product.)
 Irreversible Non-Competitive Inhibition:
o Mechanism: Inhibitor binds permanently, altering the enzyme’s shape and rendering the
active site unusable.
o Examples:
 Cyanides: Bind to iron in cytochrome oxidase, blocking cellular respiration.
 Heavy Metal Salts: Bind to thiol groups, breaking disulfide bridges and denaturing
the enzyme.
 Significance:
 Reversible Inhibition: Can be overcome by increasing substrate concentration.
 Irreversible Inhibition: Permanent and often toxic; requires enzyme replacement or regeneration.

Feedback Inhibition:
 A regulatory mechanism where the end product of a metabolic pathway inhibits an enzyme involved
in the pathway.
 Type:
 Reversible Non-Competitive Inhibition: The inhibition is reversible, and the enzyme can return to
its active state once the end product is removed.
 Mechanism:
 Product Binding: The end product binds to an allosteric site on an enzyme, altering its shape and
inhibiting its activity.
  Pathway Regulation: When the end product concentration is high, it reduces the enzyme’s activity
to prevent overproduction. When the end product is used up, inhibition is removed, and the pathway
resumes.
 Example:
 Aspartate to Threonine: Threonine, the end product of the pathway, binds to an allosteric site on
enzyme 1, inhibiting its activity. This prevents excess production of threonine. When threonine
levels decrease, the enzyme becomes active again.
 Significance:
 Regulation: Ensures balance in metabolic pathways and prevents the overproduction of substances.

Classification of enzymes Based on Reaction Type

1. Oxidoreductases
 Function: Catalyze oxidation/reduction reactions by adding or removing electrons or H+ ions.
 Example: Cytochrome oxidase (oxidizes cytochrome).
2. Transferases
 Function: Transfer specific functional groups (other than hydrogen) from one substrate to another.
 Example: Hexokinase (transfers a phosphate group from ATP).
3. Hydrolases
 Function: Break down large organic molecules into smaller ones by adding water (hydrolysis) and
breaking specific covalent bonds.
 Example: Pepsin, trypsin (break down proteins into peptides).
4. Lyases
 Function: Break down specific covalent bonds and remove groups without hydrolysis.
 Example: Histidine decarboxylase (removes carbon dioxide from histidine).
Isomerases
 Function: Facilitate intra-molecular rearrangement of atoms to form isomers.
 Example:
o Phosphohexose Isomerase: Converts glucose 6-phosphate to fructose 6-phosphate.
6. Ligases (Synthetases)
 Function: Join two molecules together, utilizing energy from ATP hydrolysis.
 Example:
o Polymerases: Link monomers into polymers, such as DNA or RNA.

Classification of Enzymes Based on Substrate

1. Proteases
 Function: Act upon proteins, breaking them down into smaller peptides or amino acids.
 Examples:
o Pepsin: Digests proteins into polypeptides and peptones(partially digested proteins)
o Trypsin: Digests polypeptides into smaller peptides.
o Carboxypeptidases: Digests peptones into dipeptides and amino acids.
2. Lipases
 Function: Hydrolyze lipids into fatty acids and glycerol.
 Examples:
o Pancreatic Lipase: Breaks down triglycerides into fatty acids and glycerol.
3. Carbohydrases
 Function: Break down carbohydrates into simpler sugars.
  Examples:
o Amylase: Digests starch or glycogen into maltose.
o Cellulase: Digests cellulose into cellobiose(diassacharide sugar).
o Maltase: Digests maltose into glucose.
o Sucrase: Digests sucrose into glucose and fructose.
o Lactase: Digests lactose into glucose and galactose.
4. Nucleases
 Function: Break down nucleic acids (DNA and RNA) into nucleotides.
 Examples:
o RNAases: convert RNA into ribonucleotides.
o DNAases: convert DNA into deoxyribonucleotides.
o ATPases: Hydrolyzes ATP into ADP and inorganic phosphate.