Questions and Answers
What is biochemistry concerned with?
The chemical basis of life and the chemical constituents of living cells.
Which of the following categories divide metabolic pathways?
What are metabolites?
The reactants, intermediates, and products in metabolic pathways.
Enzymes are typically proteins.
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What does the International Union of Biochemistry's classification system assign to enzymes?
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The energy of activation is also known as the __________ barrier.
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What is the role of cofactors in enzymatic reactions?
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What is the primary source of free energy in anabolic pathways?
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What does the term 'isoenzyme' refer to?
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What is the definition of free energy in the context of chemical reactions?
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The rate of a reaction is proportional to the active mass of reactants.
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What type of reaction is indicated by a pseudo-first-order reaction?
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What is the enzyme-product complex?
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What does the Michaelis constant (Km) represent?
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What is turnover number (kcat)?
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What is the formula to calculate catalytic efficiency?
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What is the effect of pH on enzyme activity?
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What is the significance of the Lineweaver-Burk plot?
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The unit of enzyme activity, defined as the amount of enzyme that catalyzes the reaction of a specific amount of substrate per minute, is called _____.
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What does ATP stand for?
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An enzyme's activity generally decreases at higher pH levels.
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What is the primary role of kinases in cells?
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What is the standard Gibbs free energy change (ΔG'0) of ATP hydrolysis?
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What does the term 'allosteric regulation' refer to?
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What are the typical intracellular concentrations of ATP and ADP?
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What happens to the equilibrium of ATP synthesis during high metabolic activity?
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How long can a resting vertebrate skeletal muscle rely on phosphocreatine for free energy?
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What is the primary role of oxidation-reduction reactions in living organisms?
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In photosynthesis, which compound is reduced?
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Match the following components with their roles in redox reactions:
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What is the Nernst equation used for in the context of redox reactions?
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What is the standard reduction potential, Eo?
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How do you calculate the standard free-energy change, ΔGo?
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Why must metabolic flow be controlled?
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What type of enzymes are usually involved in the rate-limiting steps of metabolic pathways?
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Most enzymes involved in regulatory processes are ___ enzymes.
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What is an example of a short-term control mechanism in metabolic flux?
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Study Notes
Biochemistry Overview
- Biochemistry is the science of the chemical basis of life, focusing on the constituents and processes of living cells.
- It integrates concepts from cell biology, molecular biology, and molecular genetics, essential for understanding all biological sciences.
Metabolism
- Metabolic pathways consist of sequential enzymatic reactions, converting substrates into products known as metabolites.
- Two types of metabolic pathways:
- Catabolism: Breakdown of molecules to generate energy and salvage components.
- Anabolism: Synthesis of complex molecules from simpler precursor molecules, utilizing energy-rich compounds like ATP and NADPH.
Enzymes
- Biocatalysts that accelerate chemical reactions without being consumed in the process; most are proteins, some are ribozymes (nucleic acids).
- Enzymes typically end with "-ase"; exceptions include proteolytic enzymes (e.g., trypsin).
Enzyme Classification
- Enzymes classified by the International Union of Biochemistry fall into six main classes based on reaction types:
- Oxidoreductases: Transfer of electrons.
- Transferases: Transfer of functional groups.
- Hydrolases: Hydrolysis reactions.
- Lyases: Group removal, not through hydrolysis.
- Isomerases: Isomerization processes.
- Ligases: Join two molecules with ATP breakdown.
- Each enzyme receives a four-digit code for classification and an associated systematic name.
Isoenzymes
- Isoenzymes are different enzymes catalyzing the same reaction, sharing identical four-number EC codes.
Enzyme Structure and Synthesis
- Enzymes are synthesized from amino acids, undergo transcription and translation, and may have post-translational modifications.
Cofactors
- Cofactors assist in enzyme activity and include inorganic metal ions (e.g., Fe²⁺, Mg²⁺) and organic molecules (coenzymes).
- Key coenzymes and their functions:
- Biotin: Carboxylation (from Vitamin B7).
- Coenzyme A: Acyl transfer (from Pantothenic acid/Vitamin B5).
- Flavin coenzymes: Oxidation-reduction (from Riboflavin/Vitamin B2).
Active Site
- The active site comprises the binding and catalytic sites of an enzyme, allowing substrate interaction and reaction catalysis.
- Specificity in enzyme action includes:
- Group specificity: Acts on similar substrates.
- Absolute specificity: Only one substrate is accepted.
- Stereochemical specificity: Specific for one isomer of a compound.
Enzyme Types
- Monomeric enzymes consist of a single polypeptide chain, usually hydrolyze substrates, and lack cofactors.
- Oligomeric enzymes consist of multiple polypeptide chains, often interacting non-covalently, and represent the majority of enzymes (e.g., glycolytic enzymes).
Free Energy and Reaction Spontaneity
- Free energy (G) indicates potential work in a system; expressed as G = H - TS (enthalpy, entropy, temperature).
- Reactions occur spontaneously when ΔG is negative; ATP hydrolysis under physiological conditions releases energy.
Enzyme Kinetics
- Reaction rates can be increased by higher concentrations of reactants or temperature.
- Activation energy is the minimum energy to trigger a reaction; catalysis lowers this energy barrier.
- The law of mass action states the rate is proportional to reactant concentrations.
Kinetics of Enzyme-Catalyzed Reactions
- Initial velocity (v0) reflects the reaction rate at time zero and depends on reactant concentration.
- The Michaelis-Menten equation describes enzyme kinetics, relating substrate concentration to reaction rate and accounting for enzyme saturation.
This structured overview creates a clear understanding of the fundamental concepts in biochemistry, particularly related to metabolism, enzyme function, and kinetics.### Michaelis-Menten Kinetics
- Vmax represents the maximal velocity of an enzymatic reaction at saturation when all enzymes are in the ES (enzyme-substrate) complex.
- At high substrate concentrations, [S0] is significantly greater than [E0], allowing [S] to be approximated as [S0].
- Km is the Michaelis constant, the substrate concentration where V0 equals ½ Vmax.
- A smaller Km indicates higher enzyme affinity for its substrate.
- kcat, also known as turnover number, is the rate at which an enzyme converts a substrate into a product, depicting the maximum number of substrates converted per active site per time unit.
Catalytic Efficiency
- Catalytic efficiency is measured as the ratio kcat/Km, highlighting how efficient an enzyme is at converting substrates under physiological conditions.
Lineweaver-Burk Plot
- A linear transformation of the Michaelis-Menten equation helps derive Vmax and Km more accurately.
- This plot, derived from reciprocal values of [S] and V0, presents a clearer method for measuring enzyme kinetics.
Enzyme Units and Specific Activity
- 1 unit (U) of enzyme activity is defined as the amount that catalyzes 1 nmol of substrate per minute under standard conditions.
- SI unit for enzyme activity is katal (kat), indicating the transformation of one mole per second.
- Specific activity reflects an enzyme's activity per milligram of protein, expressed in units/mg.
Environmental Effects on Enzyme Activity
- pH: Each enzyme has an optimal pH reflecting its native environment, with activity declining outside this range.
- Ionic Strength: Influences the binding of substrates and the movement of charged groups, affecting enzyme catalysis and structure.
- Temperature: High temperatures can denature enzymes while moderate increases usually enhance catalytic rates.
Enzyme Cooperativity and Allosteric Regulation
- Cooperativity occurs when ligand binding to one site affects the binding at another, enhancing or inhibiting activity.
- Allosteric enzymes have sites for modulators, which can either enhance (activators) or inhibit (inhibitors) substrate binding, influencing enzyme activity through structural changes.
Metabolic Pathway Characteristics
- Irreversibility: Pathways often contain exergonic reactions making them directional.
- Distinct Catabolic and Anabolic Pathways: Each pathway requires unique steps for interconversion of metabolites, allowing independent regulation.
- First Committed Step: Metabolic pathways have an initial irreversible step that commits intermediate products down the pathway.
- Regulation is primarily controlled at the enzyme level, ensuring supply aligns with metabolic demand.
ATP and Energy Transfer
- ATP serves as the primary energy currency in cells, facilitating energy transfer during biochemical reactions.
- The ΔG of ATP hydrolysis is significant, influencing the thermodynamics of phosphorylation reactions in cellular processes.
Formation and Consumption of ATP
- Substrate-level Phosphorylation: Direct transfer of a phosphate group from a molecule to ADP.
- Oxidative and Photophosphorylation: Both utilize proton gradients for ATP synthesis during cellular respiration and photosynthesis.
- ATP consumption rates vary with cellular activity; ATP turnover is rapid, indicating its role as a transient energy carrier rather than a long-term reservoir.
Biological Oxidation-Reduction Reactions
- Redox reactions are fundamental for energy extraction from nutrients, involving electron transfer.
- Standard reduction potential (Eo) indicates the affinity of substances for electrons, influencing the direction of electron flow in metabolism.
- Nernst equation relates the actual reduction potential to standard potentials, crucial for understanding cellular redox processes.
Summary
- Understanding enzyme kinetics, regulatory mechanisms, and energy transfer through ATP is vital for comprehending metabolic processes and maintaining cellular functions.### Standard Free Energy Change in Redox Reactions
- Standard free-energy change (ΔGo) is calculated using the equation: ΔEo = Eo of electron acceptor - Eo of electron donor.
- For the reaction of acetaldehyde and NADH yielding ethanol and NAD+:
- ΔEo = –0.197 - (–0.320) = 0.123 V.
- The relevant half-reactions:
- (1) Acetaldehyde + 2H+ + 2e– → ethanol; Eo = –0.197 V.
- (2) NAD+ + 2H+ + 2e– → NADH + H+; Eo = –0.320 V.
- The equation for ΔGo is: ΔGo = –nℱΔEo, where n = 2 and ℱ = 96,500 J/V.mol.
- Calculation of ΔGo yields: ΔGo = –2 x 96500 J/V.mol x 0.123 V = –23,700 J/mol = –23.7 kJ/mol.
Actual Free Energy Change Calculation
- Given concentrations: [acetaldehyde] and [NADH] = 1.00 M; [ethanol] and [NAD+] = 0.100 M.
- Actual free-energy change (ΔG) formula: ΔG = ΔGo + RT ln([products]/[reactants]).
- Substituting in values: ΔG = –23,700 J/mol + (8.315 J/mol.K x 298 K x ln(0.1 x 0.1/1 x 1)).
- Calculation results in ΔG = –35,100 J/mol = –35.1 kJ/mol.
Importance of Metabolic Regulation
- Metabolic flow must be controlled to align product supply with demand.
- Maintaining steady-state concentrations of intermediates promotes homeostasis.
- Homeostasis in metabolism ensures thermodynamic efficiency in open systems.
- Concentration changes can disrupt balance in shared intermediates across pathways.
- Regulatory control prevents large fluctuations in intermediates that could affect osmotic balance.
Metabolic Control Mechanisms
- Each metabolic pathway contains a rate-limiting step primarily regulated by specific enzymes.
- Regulatory enzymes are typically allosteric and can be affected by feedback inhibition and covalent modification.
- Questions arise regarding whether a single step is truly rate-limiting or if multiple enzymes contribute to regulation.
Mechanisms of Metabolic Flux Control
- Flux through rate-determining steps can be adjusted by several mechanisms:
- Allosteric Control: Enzymes may be regulated by effectors that are substrates, products, or coenzymes.
- Covalent Modification: Enzymes can be phosphorylated or modified at specific residues, altering activity.
- Substrate Cycles: Opposing reactions catalyzed by different enzymes increase sensitivity to control.
- Genetic Control: Enzyme concentrations can change over time (hours to days) via protein synthesis based on metabolic needs.
- Short-term mechanisms (1 to 3) operate rapidly, whereas long-term control (4) is slower responding to conditions.
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