Enzymes in Biochemistry

Enzyme Structure, Classification, and Mechanism of Action

• Enzymes play roles in metabolism, diagnosis, and therapeutics
• All biochemical reactions are enzyme-catalyzed in living organisms
• Enzyme levels in blood are of diagnostic importance and can indicate myocardial infarction
• Enzymes can be used therapeutically, such as digestive enzymes

Definition of Enzymes and Related Terms

• Enzymes are proteins that accelerate reaction rates by lowering activation energy
• Enzymes catalyze almost all chemical reactions in the body's cells
• Enzymes are not altered or consumed during the reaction and are reusable

Active Sites

• Enzyme molecules contain special pockets or clefts called active sites

Lock-and-Key Model of Enzyme Action

• The active site has a rigid shape
• Only substrates with a matching shapes can fit
• The substrate acts as the key, and the active site acts as the lock

Apoenzyme and Holoenzyme

• An enzyme without its non-protein moiety is called an apoenzyme and is inactive
• A holoenzyme is an active enzyme with its non-protein component

Cofactors

• A cofactor is a non-protein chemical compound bound to an enzyme, either tightly or loosely, and is required for catalysis
• Coenzymes and prosthetic groups are types of cofactors

Coenzyme

• The non-protein component of an enzyme is loosely bound to the apoenzyme by a non-covalent bond
• Vitamins or compounds derived from vitamins are examples of coenzymes

Prosthetic Group

• A prosthetic group is the non-protein component of an enzyme that is tightly bound to the apoenzyme by covalent bonds

Enzyme Specificity

• Enzymes have degrees of specificity for substrates and may catalyze a single substrate (absolute specificity), a group of similar substrates (group specificity), or a particular type of bond (bond specificity)

Types of Enzyme Specificity

• Absolute specificity: Urease catalyzes only the hydrolysis of urea.
• Group specificity: Hexokinase adds a phosphate group to hexoses.
• Linkage specificity: Chymotrypsin catalyzes the hydrolysis of peptide bonds.

Activation Energy

• Activation energy is the amount of energy required to start a chemical reaction

Mechanism of Action of Enzymes

• Enzymes increase reaction rates by decreasing activation energy

• Enzyme-substrate interactions involves the formation of an enzyme-substrate complex via the lock-and-key model or the induced fit model

• Step 1: Enzyme and substrate combine to form a complex

• Step 2: An enzyme-product complex is formed

• Step 3: Enzyme and product separate

Lock-and-Key Model

• The active site has a rigid shape
• Only substrates fits into active site
• An older model that does not work for all enzymes

Induced-Fit Model

• Active site is flexible
• Shapes of the enzyme, active site, and substrate adjust to improve catalysis, allowing a greater range of substrate specificity
• A more consistent model with a wider range of enzymes

Factors affecting enzyme activity

• Environmental conditions
• Cofactors and coenzymes
• Enzyme inhibitors

Environmental Conditions

• Extreme temperatures are the most dangerous, high temperatures may denature the enzyme
• Optimal pH is typically near neutral (pH 6 - 8)
• Substrate concentration also plays a key role

Cofactors and Coenzymes

• Proper enzymatic activity requires some inorganic substances (zinc, iron) and vitamins
• For example, the quaternary structure of hemoglobin needs iron to pick up oxygen

Environmental Factors

• Optimum temperature is the temperature at which enzymatic reactions occur fastest
• Enzymes prefer a pH of around 7, but some prefer acidic or basic conditions based on the enzyme type.
• The rate of reaction increases as substrate concentration increases
• Maximum activity occurs when the enzyme is saturated

Reversible Competitive Inhibition

• A competitive inhibitor that Has a similar struture to the substrate
• It competes with the substrate for the active site
• The effect is reversed by increasing substrate concentration

Noncompetitive Inhibition

• Inhibitor has a structure different than substrate
• It distorts the shape of the enzyme, which alters the shape of the active site
• It prevents the binding of the substrate, and can not be reversed by adding more substrate.

Naming Enzymes

• Many enzyme names end in -ase
• For example, sucrase catalyzes the hydrolysis of sucrose
• Enzyme names describe their function
• For example, oxidases catalyze oxidation reactions
• Some names are common, typically for digestion enzymes such as pepsin and trypsin
• Some names describe both substrate and function, with enzymes such as alcohol dehydrogenase oxidizing ethanol

Enzyme Classification

• Enzymes are grouped by the International Union of Biochemists (I.U.B.) into 6 functional classes based on the types of reaction they catalyze:
  • Oxidoreductases (EC 1)
  • Transferases (EC 2)
  • Hydrolases (EC 3)
  • Lyases (EC 4)
  • Isomerases (EC 5)
  • Ligases (EC 6)
• Each enzyme has a classification number including four digits
• For example, EC: (2.7.1.1) HEXOKINASE

Enzyme classifications

• EC: (2.7.1.1) indicates groups of enzymes:
  • 2. Class (Transferase)
  • 7. Subclass (Transfer of Phosphate)
  • 1. Sub-sub class (Alcohol is phosphate acceptor)
  • 1. Specific name (ATP,D-HEXOSE-6-PHOSPHOTRANSFERASE (Hexokinase))
• Hexokinase catalyzes: Glucose + ATP → glucose-6-P + ADP

Oxidoreductases, Transferases, and Hydrolases

• Oxidoreductases catalyze oxidation-reduction reactions,
• Transferases catalyze the transfer of functional groups
• Hydrolases catalyze hydrolysis reactions

Lyases, Isomerases, and Ligases

• Lyases catalyze the addition of a group to a double bond or removal of a group from a double bond without hydrolysis or oxidation

Kinetic properties of enzymes

• Leonor Michaelis and Maud Menten were the first researchers who explained the shape of the rate curve (1913)
• Rate constant indicate the speed or efficiency of a reaction
• [S] is small but is nearly independent of [S] when [S] is large
• Rate rises linearly as [S] increases and then levels off at high [S] (saturated)

Michaelis-Menten Equation

• Basic equation derived by Michaelis and Menten to explain enzyme-catalyzed reactions as V。= Vmax[S] / Km + [S]
  • Km - Michaelis constant
  • Vo - initial velocity caused by substrate concentration, [S]
  • Vmax - maximum velocity
• The higher the enzyme concentration [E], the greater the initial reaction rate

Enzyme inhibition

• Different chemical agents can inhibit enzyme activity
• Such agents can be metabolites, substrate analogs, toxins, drugs, metal complexes etc
• Inhibitor (I) binds to an enzyme, preventing ES complex formation or breakdown to E + P

Reversible and Irreversible inhibitors

• Reversible inhibitors combine with an enzyme can rapidly dissociate
• Enzyme is inactive only when bound to inhibitors through a weak, noncovalent interaction
• The basic types of reversible inhibition can be competitive, uncompetitive or noncompetitive.

Reversible inhibition

• Competitive inhibition can bind to the same active site

Competitive inhibition

• Has a structure similar to the substrate,
• Substrate competes, and enzyme cannot differentiate between the two compounds
• When inhibitor binds, the substrate is prevented
• Released by increased concentration

Noncompetitive inhibition

• binds to an enzyme site different from the active site
• Inhibitor and substrate can bind enzyme at the same time
• Cannot be overcome by increasing the substrate concentration
• Inhibitors only bind to ES not a free enzyme
• This type of inhibition only occurs in multisubstrate reactions

Irreversible Enzyme Inhibition

• EI complex has very dissociation
• Tightly bound through interactions
• group-specific reagents
• substrate analogs
• suicide inhibitors
• Group-specific reagents react with specific R groups of amino acids
• Substrate analogs are structurally similar to substrate
• Covalently modify active site residues
• Suicide inhibitors bind as a substrate, initial processed by the catalytic process
• generates a chemically reactive intermediate to inactivate enzyme
• through covalent modification
• Enzyme participates in own inhibition

Explore the role of enzymes in biochemical reactions, differentiating between holoenzymes and apoenzymes. Understand enzyme specificity, active sites, and models like 'lock-and-key' and 'induced-fit'. Discover the role of coenzymes and prosthetic groups, and the diagnostic importance of serum enzyme levels.