Biology Chapter on Enzymes and Reactions

Enzymes

• Enzymes are biological catalysts, proteins that speed up chemical reactions in living organisms.
• They are crucial for metabolic processes and other essential chemical reactions within cells.
• They accelerate reactions without being consumed in the process.

Types of Chemical Reactions

• Endergonic Reactions: Require energy input.
  • These reactions are non-spontaneous.
  • Energy is absorbed.
  • ∆G > 0 (Gibbs Free Energy is greater than 0)
  • Product Energy > Substrate Energy
• Exergonic Reactions: Release energy during the reaction.
  • These reactions are spontaneous.
  • Energy is released.
  • ∆G < 0 (Gibbs Free Energy is less than 0).
  • Product Energy < Substrate Energy

Enzyme Action

• Catalyst: A substance that increases the rate of a chemical reaction without being a reactant.
• Function: Enzymes increase the rate of chemical reactions but do not affect the equilibrium of the reaction.
• Activation Energy (Ea): The minimum energy required for reactants to undergo a chemical reaction. Enzymes lower the activation energy needed for reactions to occur. The lower the activation energy, the faster the reaction rate.
• Enzyme-Substrate Complex: The temporary complex formed when an enzyme binds to its substrate. This binding often creates a specific shape to aid in reaction progression.
• Active Site: The region of an enzyme where the substrate binds. The shape of the active site is crucial for determining the specificity of the enzyme. This involves modifications at the active site for matching the substrate.
• Transition State: The high-energy, unstable state that reactants must reach before converting to products. Enzymes stabilize this transition state to aid in reaction progression.

Enzyme Structure

• Protein Catalysts: Enzymes are primarily composed of proteins.
• Structure: Enzymes have four levels of structure (primary, secondary, tertiary, and quaternary). These structures are essential for enzyme function and specificity.
• Primary Structure: A sequence of amino acids.
• Secondary Structure: Repeated folding of the protein chain.
• Tertiary Structure: 3D structure of the protein.
• Quaternary Structure: The structure of multiple polypeptide chains that interact to form a complete enzyme.
• Active Site: A specific region of the enzyme where the substrate binds.
• Apoenzyme: The protein component of an enzyme
• Cofactors/Coenzymes: The non-protein components necessary for enzyme activity.
  • Cofactors: Inorganic ions (e.g. iron, zinc).
  • Coenzymes: Organic molecules (e.g. vitamins, NAD+, FAD).
  • The binding of a cofactor or coenzyme to an apoenzyme creates an active enzyme called a holoenzyme.
• Prosthetic Groups: Non-protein molecules tightly bound to the enzyme and essential for its catalytic function. Often permanently attached.
• Allosteric Sites: A specific region distinct from the active site, where regulatory molecules (allosteric effectors) bind. This binding often changes the enzyme shape, affecting its activity at the active site.
• Allosteric Modulation: Regulation of enzyme activity through allosteric sites. Allosteric effectors bind and induce conformational changes. This binding is crucial for enzyme regulation in metabolic pathways.

Enzyme Specificity

• 1-Optical (Stereo) Specificity: Enzymes catalyze the conversion of an optically active isomer of a substrate, and do not catalyze the conversion of its mirror image. Enzymes act on one of two possible isomers. (Example: L-lactate dehydrogenase acts only on L-lactic acid, not D-lactic acid).
• 2-Group Specificity: Enzymes require a particular functional group, such as phosphate, amino, or methyl, for their function. They often target particular functional groups on a substrate (e.g., hexokinase catalyzes the phosphorylation of hexose sugars)
• 3-Absolute Substrate Specificity: Enzymes act only on one particular substrate. (e.g. Urase enzyme acts only on Urea).
• 4-Linkage Specificity: Enzymes act on a particular chemical bond within a substrate, regardless of the rest of the molecule's structure. (e.g. lipase enzymes act on the ester bond of different triglycerides).
• **5-Reaction Specificity: ** Enzymes are specific to a particular reaction, not a specific substrate.
• 6-Dual Specificity: Some enzymes act on two different substrates. (e.g., isocitrate dehydrogenase acts on isocitrate and oxaloacetate).

Enzyme Nomenclature

• Trivial Names: Common names (e.g. hexokinase).
• Systematic/Descriptive Names: Follows standardized structural guidelines using the substrate and reaction type. (e.g. ATP: D-hexose-6-phosphotransferase).

Enzyme Classification

• EC (Enzyme Commission) Number: A unique numerical identifier assigned for each enzyme, based on the reaction it catalyzes. This system helps classify enzymes' function and activity into categories and subclasses.

Enzyme Mechanism of Action

• Lock-and-Key Model: A rigid enzyme with an inflexible active site fits a specific substrate.
• Induced-Fit Model: A flexible enzyme changes shape to adapt to its substrate to stabilize the transition state. This is a more complete representation of enzyme function, accounting for the flexibility of enzymes

Enzyme Site

• Intracellular Enzymes: Located inside cells, function within specific organelles.
• Extracellular Enzymes: Synthesized inside cells but secreted outside to perform functions outside the cell.
• Transmembrane Enzymes: Integrated into cell membranes, with active sites exposed on both the internal and external membrane surfaces.

Enzyme Functions

• Cell Maintenance: Envision supporting fundamental cellular processes.
• Growth: Facilitate processes that drive cell division.
• Metabolism/Energy Production: Catalyze metabolic processes required to generate energy. These involve the use of energy and creation of energy from chemical processes.
• Digestion: Enzymes aid in breaking down food for nutrient absorption.
• Nutrient Breakdown: Support metabolic reactions for nutrient absorption and utilization.
• Microbial Pathogenesis: Enzymes involved in microbial processes.
• Signal Transduction: Enzymes are essential in how cells respond to their environment.
• Metabolic Pathways: Enzymes are catalysts throughout all metabolic pathways.

Enzyme Characters

• Nature: Most enzymes are proteins, some are RNA (Ribozymes).
• Size: Enzymes are typically larger than their substrates.
• Enzyme-Substrate Complex: The interaction between enzyme and substrate is vital for catalysis.
• Catalytic Power: Enzymes significantly enhance reaction speed, and lower activation energy.
• Efficiency: Enzymes require minimal amounts to catalyze many reaction cycles. They maintain their structure and function to catalyze reactions multiple times.
• Specificity: Enzymes act on a specific substrate, and specific reaction type.
• Reusability: Enzymes are not consumed by reactions and maintain their structure to be reusable.
• Site: The locations of enzymes, and how they affect the enzyme reaction process.
• Sensitivity: Enzymes are affected by environmental conditions like temperature and pH.
• Active Sites: Regions on the enzyme where the substrate binds to carry out catalysis.
• Cofactors and Coenzymes: Necessary components of enzymes (inorganic and organic).
• Ability to produce Products: Enzymes are critical for the formation of products via catalysis.

Test your understanding of enzymes and biochemical reactions with this quiz. Examine the role of enzymes, the nature of endergonic and exergonic reactions, and energy changes involved in these processes. Perfect for students studying biological chemistry!