Untitled Quiz

Biochemistry Overview

• Biochemistry studies the chemical basis of life, focusing on the structures and reactions within living cells.
• Encompasses cell biology, molecular biology, and molecular genetics.
• Explores life forms from simple viruses to complex humans.

Metabolism

• Metabolic pathways consist of enzymatic reactions producing specific products called metabolites.
• Catabolism (degradation) breaks down nutrients to generate energy.
• Anabolism (biosynthesis) synthesizes biomolecules from simpler precursors, using ATP and NADPH for energy.
• Central oxidative pathways convert diverse substances into common intermediates, especially acetyl-CoA.

Enzymes

• Enzymes are biocatalysts that increase reaction rates without changing themselves.
• Most enzymes are proteins; some are nucleic acids (ribozymes).
• Enzymes are typically denoted with names ending in “-ase” (e.g., amylase).
• The International Union of Biochemistry classifies enzymes according to the type of reaction catalyzed.

Enzyme Classification

• Enzyme Commission (EC) classification contains four numbers indicating the main class, subclass, sub-subclass, and serial number.
• Enzymes are categorized into six classes, including oxidoreductases, transferases, and hydrolases.

Cofactors and Coenzymes

• Cofactors are vital for enzyme function; they include inorganic ions (e.g., Fe²⁺, Mg²⁺) and organic molecules (coenzymes).
• Many vitamins serve as coenzyme precursors.
• Examples include Biotin (Vitamin B7) for carboxylation and Coenzyme A derived from Pantothenic acid (Vitamin B5).

Active Site and Specificity

• The active site is crucial for substrate binding and catalysis, often featuring hydrophilic and hydrophobic environments.
• Enzyme specificity can include group specificity (multiple substrates) and absolute specificity (one substrate).
• Stereochemical specificity refers to the action on specific isomers (e.g., L-amino acids).

Enzyme Structure

• Monomeric enzymes consist of a single polypeptide chain, usually 100-300 amino acids long.
• Oligomeric enzymes consist of multiple polypeptide chains, typically more than 35 kDa, and are more common.

Free Energy and Reaction Spontaneity

• Free energy indicates the energy available for work in a system; reactions tend to occur spontaneously when ΔG is negative.
• Gibbs free energy change (ΔG) is influenced by reactant and product concentrations and temperature.

Enzyme Kinetics

• Chemical reactions depend on molecular collisions; reaction rates increase with higher concentrations or temperature.
• Activation energy must be overcome for reactions to occur; catalysts lower this energy without affecting the overall energetics.
• The law of mass action relates the rate of reaction to the concentration of reactants.

Kinetics of Enzyme-Catalyzed Reactions

• Enzyme-catalyzed reactions can exhibit first-order, second-order, or zero-order kinetics depending on substrate concentration relative to enzyme concentration.
• The initial velocity (v0) is determined at time zero and correlates with reactant concentration.
• The Michaelis-Menten equation describes the relationship between substrate concentration and reaction velocity.

Catalysis and Reaction Progress

• Enzymes form enzyme-substrate (ES) complexes leading to transition states that yield products.
• The Henri and Michaelis-Menten equations use kinetic constants to relate enzyme activity and substrate concentration, resulting in the Michaelis constant (Km), which provides insight into enzymatic function.### Enzyme Kinetics and the Michaelis-Menten Equation
• Maximal Velocity (Vmax): Achieved at high substrate concentrations, indicating enzyme saturation in the ES form.
• Michaelis Constant (Km): Represents substrate concentration at which reaction velocity is half of Vmax. A low Km reflects high enzyme-substrate affinity.
• Turnover Number (kcat): Defined as the maximum number of substrate molecules converted to product per enzyme active site per unit time. kcat can vary based on enzyme mechanism complexity.
• Catalytic Efficiency: Calculated as kcat/Km; a measure of how efficiently an enzyme converts a substrate into product.
• Lineweaver-Burk Plot: Inverted form of the Michaelis-Menten equation, allowing linear representation to facilitate determination of Vmax and Km.

Enzyme Units and Specific Activity

• Enzyme Unit (U): The amount of enzyme that catalyzes a specific amount of substrate (e.g., 1 nmol) per minute under standard conditions.
• SI Unit - Katal (kat): Defined as the amount of enzyme catalyzing the transformation of one mole of substance per second.
• Specific Activity: Measured in units/mg, it reflects the activity of an enzyme per milligram of total protein.

Factors Affecting Enzyme Activity

• pH Sensitivity: Each enzyme has an optimum pH for maximal activity; deviations can reduce activity.
• Ionic Strength: Influences binding of charged substrates and internal active site dynamics.
• Temperature Impact: High temperatures can denature enzymes while moderate increases generally accelerate catalytic rates.

Cooperativity and Allosteric Regulation

• Cooperativity: Interaction between multiple ligand-binding sites affects binding affinities, distinguishing between cooperative and non-cooperative behavior.
• Allosteric Enzymes: Feature regulatory sites for modulators; activators enhance substrate binding, while inhibitors reduce it, affecting the enzyme's activity.

Metabolic Pathway Characteristics

• Irreversibility: Highly exergonic reactions dictate pathway directionality.
• Differing Pathways: Catabolic and anabolic pathways diverge, allowing independent regulation.
• First Committed Steps: Each pathway has an initial irreversible reaction, ensuring commitment to the path.
• Regulation: Metabolic pathways are regulated based on enzyme controlling first committed steps to avoid unnecessary metabolite synthesis.

ATP and Energy Transfer

• ATP Functionality: ATP serves as the primary energy currency in cells, facilitating endergonic processes via hydrolysis.
• Phosphate Hydrolysis: Negative ΔG of ATP hydrolysis signifies the tendency to release energy; actual free energy is influenced by cellular concentration and conditions.
• Formation Methods: ATP is generated through substrate-level phosphorylation and oxidative/photophosphorylation.

Biological Oxidation-Reduction Reactions

• Electron Transfer: Redox reactions involve electron transfer, essential for cellular energy generation.
• Photosynthesis vs. Aerobic Metabolism: CO2 reduction and water oxidation in photosynthesis is reversed in cellular respiration to harness energy.
• Standard Reduction Potential (Eo): Indicates the electron affinity of redox pairs, aiding in the understanding of electron transfer efficiency; calculated via the Nernst equation.

Practical Applications

• Enzyme Kinetics Studies: Understanding enzyme behavior under varying conditions aids in research and application in biotechnology, medicine, and industry.### Standard Reduction Potentials and Free Energy Change
• ΔEo calculated: Difference in standard reduction potentials between electron acceptor and donor.
• Reaction: Acetaldehyde + NADH → Ethanol + NAD+ results in ΔEo of 0.123 V.
• Relevant half-reactions:
  • Acetaldehyde reduction: Acetaldehyde + 2H+ + 2e– → Ethanol, Eo = –0.197 V.
  • NAD+ reduction: NAD+ + 2H+ + 2e– → NADH + H+, Eo = –0.320 V.
• ΔGo calculation: ΔGo = –n ℱ ΔEo, where n = 2, ℱ = 96,500 J/V·mol, yields ΔGo = –23,700 J/mol = –23.7 kJ/mol.

Actual Free Energy Change Calculation

• Actual free energy change ΔG is influenced by concentrations of reactants/products.
• Formula: ΔG = ΔGo + RT ln([ethanol][NAD+]/[acetaldehyde][NADH]).
• Given concentrations: [acetaldehyde] = 1.00 M, [NADH] = 1.00 M, [ethanol] = 0.100 M, [NAD+] = 0.100 M.
• Resulting ΔG calculation gives ΔG = –35,100 J/mol = –35.1 kJ/mol.

Importance of Metabolic Regulation

• Metabolic flow control ensures product availability matches demand.
• Maintains stable concentrations of intermediates for homeostasis.
• Homeostasis is essential for maximum thermodynamic efficiency in metabolism.
• Intermediates often involved in multiple pathways, requiring delicate balance control.
• Large fluctuations in intermediate concentrations can disrupt cellular osmotic properties and slower response to control signals.

Mechanisms of Metabolic Control

• Each pathway has a rate-limiting step, often controlled by pivotal regulatory enzymes.
• Regulatory enzymes are typically allosteric and may be influenced by feedback inhibition or covalent modification.

Mechanisms of Regulatory Enzymes Control

• Allosteric Control: Enzymes regulated by substrates, products, or coenzymes as effectors, enhancing control sensitivity.
• Covalent Modification: Enzymes can be phosphorylated or modified on specific residues, altering activity substantially.
• Substrate Cycles: Opposing reactions increase the sensitivity of control relative to a single reaction in equilibrium.
• Genetic Control: Long-term mechanism where enzyme concentrations adjust based on metabolic requirements via protein synthesis.

Time Scale of Control Mechanisms

• Short-term control (seconds to minutes): Mechanisms 1-3 (allosteric, covalent modification, substrate cycles).
• Long-term control (hours to days): Mechanism 4 (genetic control).