Chapter 20: Enzymes and Vitamins – Structure, Function, and Regulation

Enzymes: Biological Catalysts

Definition and Importance

• Enzymes are proteins that act as biological catalysts, increasing the rate of chemical reactions without being consumed in the process.

• They are essential for life, facilitating processes such as digestion, metabolism, DNA replication, and repair.

• Most biochemical reactions in living organisms are catalyzed by protein enzymes, though some RNA molecules (ribozymes) also have catalytic activity.

• Enzymes are highly specific, each recognizing particular substrates and catalyzing specific reactions.

• Enzyme-catalyzed reactions are highly regulated to meet the needs of the cell or organism.

Comparison to Chemical Catalysts

• Like chemical catalysts, enzymes speed up reactions by lowering the activation energy.

• Unlike most chemical catalysts, enzymes are highly specific for their substrates and operate under mild biological conditions (temperature, pH).

How Enzymes Work

Mechanism of Action

• Enzymes increase reaction rates by lowering the activation energy required for the reaction, often by stabilizing the transition state.

• They do not change the standard free energy ($\Delta G$) of the reaction.

Example: The enzyme carbonic anhydrase catalyzes the reaction:

$\mathrm{CO_2 + H_2O \xrightleftharpoons[\text{carbonic anhydrase}]{} HCO_3^- + H^+}$

Active Site and Substrate Binding

• The active site is the region of the enzyme where the substrate binds and the reaction occurs.

• Binding is highly specific, involving interactions similar to those responsible for the tertiary structure of proteins (hydrogen bonds, ionic interactions, hydrophobic effects).

Steps of an Enzyme-Catalyzed Reaction

1. The enzyme binds its substrate in the active site, forming an enzyme-substrate complex (ES).

2. The enzyme catalyzes the reaction, converting the substrate to product within the active site (forming an enzyme-product complex (EP)).

3. The product is released, and the enzyme is free to catalyze another reaction.

Models of Enzyme Action

• Lock and Key Model: The active site is rigid and only substrates with the correct shape can bind.

• Induced Fit Model: The enzyme and substrate can change shape to achieve a better fit, lowering the activation energy further.

Enzyme Nomenclature and Classification

Naming Enzymes

• Enzyme names are often derived from their substrate or the type of reaction they catalyze, usually ending in "-ase" (e.g., lactase hydrolyzes lactose).

• Some exceptions exist (e.g., pepsin, trypsin).

• Example: Pyruvate decarboxylase catalyzes:

$\mathrm{CH_3COCOO^- + H^+ \xrightarrow{pyruvate\ decarboxylase} CH_3CHO + CO_2}$

Enzyme Classification

Enzymes are classified into six major categories based on the type of reaction they catalyze:

Type of Reaction	Class of Enzyme
Oxidation-reduction reactions	Oxidoreductases
Group transfer reactions	Transferases
Hydrolysis reactions	Hydrolases
Hydration and dehydration reactions	Lyases
Isomerization reactions	Isomerases
Condensation reactions and ATP/ADP hydrolysis	Ligases

1. Oxidoreductases

• Catalyze oxidation-reduction reactions.

• Oxidases oxidize substrates; dehydrogenases add or remove two H atoms (require coenzymes such as NAD+).

• Example: Alcohol dehydrogenase:

$\mathrm{CH_3CH_2OH + NAD^+ \rightarrow CH_3CHO + NADH + H^+}$

2. Transferases

• Catalyze the transfer of functional groups between molecules.

• Transaminases transfer amino groups; kinases transfer phosphate groups.

3. Hydrolases

• Catalyze hydrolysis reactions (breaking bonds with water).

• Proteases hydrolyze peptide bonds; lipases hydrolyze ester bonds in lipids; amylase hydrolyzes glycosidic bonds in starch.

4. Lyases

• Catalyze addition or removal of groups to form double bonds.

• Decarboxylases remove CO2; deaminases remove NH3; dehydratases remove H2O; hydratases add H2O.

5. Isomerases

• Catalyze isomerization (rearrangement) of atoms within a molecule.

6. Ligases

• Catalyze the joining of two molecules, often using ATP.

• Synthetases form new bonds; carboxylases add CO2 to substrates.

Factors Affecting Enzyme Activity

Key Factors

• Temperature: Enzymes have an optimum temperature (usually ~37°C in humans). High temperatures can denature enzymes.

• pH: Each enzyme has an optimum pH, often around 7.4, but this varies by location and function. Extreme pH can denature enzymes.

• Enzyme Concentration: Increasing enzyme concentration increases reaction rate (if substrate is not limiting).

• Substrate Concentration: Increasing substrate increases rate until all enzyme active sites are saturated.

• Presence of Inhibitors: Inhibitors can decrease enzyme activity.

Table: Optimum pH for Selected Enzymes

Enzyme	Location	Substrate	Optimum pH
Pepsin	Stomach	Peptide bonds	1.5–2.0
Sucrase	Small intestine	Sucrose	6.2
Amylase	Pancreas	Amylose	6.7–7.0
Urease	Liver	Urea	7.0
Trypsin	Small intestine	Peptide bonds	7.7–8.0
Lipase	Pancreas	Lipid (ester bonds)	8.0
Arginase	Liver	Arginine	9.7

Enzyme Regulation

Types of Regulation

• Allosteric Enzymes: Regulated by molecules binding at sites other than the active site (allosteric sites), causing conformational changes that affect activity. Can be positive (activators) or negative (inhibitors).

• Feedback Control: The end product of a metabolic pathway inhibits an enzyme earlier in the pathway, preventing overproduction.

• Covalent Modifications: Enzyme activity is regulated by covalent addition or removal of groups (e.g., phosphorylation, activation of zymogens).

Zymogens (Proenzymes)

• Inactive enzyme precursors activated by cleavage when needed (e.g., digestive enzymes, blood clotting factors).

Zymogen (Inactive Enzyme)	Produced in	Activated in	Enzyme (Active)
Chymotrypsinogen	Pancreas	Small intestine	Chymotrypsin
Pepsinogen	Gastric chief cells	Stomach	Pepsin
Trypsinogen	Pancreas	Small intestine	Trypsin
Fibrinogen	Liver	Damaged tissues	Fibrin
Prothrombin	Liver	Damaged tissues	Thrombin
Proinsulin	Pancreas	Pancreas	Insulin

Phosphorylation

• Kinases add phosphate groups to enzymes, often activating them.

• Phosphatases remove phosphate groups, often deactivating enzymes.

Enzyme Inhibitors

Types of Inhibition

• Irreversible Inhibitors: Bind covalently to the enzyme, permanently inactivating it (e.g., penicillin, nerve gases).

• Competitive Inhibitors: Resemble the substrate and compete for binding at the active site. Inhibition can be overcome by increasing substrate concentration.

• Noncompetitive Inhibitors: Bind to a site other than the active site, causing conformational changes that reduce activity. Cannot be overcome by increasing substrate concentration.

Example: Penicillin irreversibly inhibits transpeptidase, an enzyme involved in bacterial cell wall synthesis.

Cofactors and Coenzymes

Role in Enzyme Function

• Cofactors are non-protein molecules (often metal ions or small organic molecules) required for enzyme activity.

• Coenzymes are organic cofactors, often derived from vitamins.

• Example: Carboxypeptidase requires a zinc ion as a cofactor.

Vitamins: Essential Micronutrients

Definition and Classification

• Vitamins are organic molecules required in small amounts for normal health and growth, often functioning as coenzymes or precursors to coenzymes.

• They are classified as water-soluble or fat-soluble:

Water-Soluble Vitamins	Fat-Soluble Vitamins
Polar, soluble in water Excess excreted in urine Most are coenzymes Sensitive to heat, UV, oxygen Examples: B vitamins, vitamin C	Nonpolar, soluble in fat Excess accumulates in tissues Diverse functions (vision, bone, antioxidants, blood clotting) Examples: Vitamins A, D, E, K

Biological Roles of Water-Soluble Vitamins

• Many act as coenzymes in metabolic reactions.

• NAD+ (from niacin), FAD (from riboflavin), and Coenzyme A (from pantothenic acid) are key metabolic cofactors.

Example: NAD+ is reduced to NADH in oxidation reactions, carrying electrons to the electron transport chain.

$\mathrm{NAD^+ + 2e^- + 2H^+ \rightarrow NADH + H^+}$

FAD is reduced to FADH2 in reactions forming C=C bonds:

$\mathrm{FAD + 2e^- + 2H^+ \rightarrow FADH_2}$

Coenzyme A forms high-energy thioesters with acetyl groups:

$\mathrm{Acetyl~group + CoA \rightarrow Acetyl{-}CoA}$

Biological Roles of Fat-Soluble Vitamins

• Vitamin A (Retinol): Vision, RNA synthesis, antioxidant.

• Vitamin D (Cholecalciferol): Regulates calcium and phosphorus absorption for bone growth.

• Vitamin E (Tocopherol): Antioxidant.

• Vitamin K (Menaquinone): Synthesis of blood clotting factors.

Summary Table: Fat-Soluble Vitamins

Vitamin	Main Function	Deficiency Symptoms
Vitamin A	Vision, antioxidant	Night blindness, immune suppression
Vitamin D	Calcium/phosphorus absorption, bone health	Rickets, bone weakness
Vitamin E	Antioxidant	Neurological issues (rare)
Vitamin K	Blood clotting	Prolonged bleeding, bruising

Practice and Application

• Enzyme classification and inhibition are common exam topics. Practice matching enzyme types to reactions and identifying types of inhibition (competitive, noncompetitive, irreversible).

• Understand the role of cofactors and vitamins in enzyme function and metabolism.

Additional info: This chapter integrates concepts from biochemistry and organic chemistry, focusing on the structure, function, and regulation of enzymes, as well as the chemical and biological roles of vitamins as enzyme cofactors.