4. Characteristics of enzymes as biological catalysts. Structure, names and classification of enzymes. Mechanisms of enzyme catalysis. Enzyme-substrate complex. Active site. Specificity of the enzyme action.

Define biological catalysts and explain why enzymes are classified as such.

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Explain how enzymes contribute to the homeostasis of living organisms.

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Discuss the importance of enzyme evaluation and pharmacological regulation in diagnosis and therapy.

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List the different locations of enzymes in the body and provide specific examples of enzymes and their functions in each location.

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Explain in detail how enzymes affect reaction rates without altering chemical equilibrium.

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Discuss the energy distribution of substrate molecules and the concept of activation energy.

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Explain how catalysts, including enzymes, increase reaction rates by lowering activation energy.

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Describe the concept of reaction intermediates and their role in enzyme catalysis.

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Define the rate-limiting step in an enzymatic reaction and its importance.

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Compare and examine different levels of catalytic efficiency between enzymes and non-biological catalysts.

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Explain why enzymes are considered highly efficient catalysts.

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Emphasize the significance of enzymes remaining unchanged during the reactions they catalyze.

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Describe the two naming systems for enzymes: recommended names and systematic names

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Explain how systematic enzyme names reflect the chemical reaction they catalyze.

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Provide examples of common enzyme names and discuss their limitations in conveying enzymatic reaction details.

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Analyze potential confusions in enzyme nomenclature, highlighting examples like synthetase vs. synthase, phosphatase vs. phosphorylase, and dehydrogenase vs. oxidase vs. oxygenase.

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List the six major classes of enzymes, describe the types of reactions they catalyze, and provide a specific example for each class

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Differentiate the two classes of enzymes based on their chemical composition: simple enzymes and complex enzymes.

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Define apoenzymes, cofactors, prosthetic groups, and holoenzymes, explaining their roles in enzymatic function.

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Distinguish between cofactors and prosthetic groups in terms of their binding to the apoenzyme.

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Provide a complete table of cofactor examples, specifying the involved metal ions and the corresponding enzymes they assist.

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List examples of coenzymes derived from water-soluble vitamins, indicating the precursor vitamin and the specific reactions catalyzed by each coenzyme.

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Provide examples of nucleotide derivatives and thiol compounds functioning as cofactors and describe their enzymatic roles.

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Explain the concept of the active site and its importance in enzyme catalysis.

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Describe the structural characteristics of the active site, including its shape and how it forms within the enzyme structure.

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List and define the four types of amino acid residues in active sites, explaining their specific roles in catalysis and substrate binding.

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Illustrate how substrate binding to the active site contributes to enzymatic catalysis, including the types of bonds involved.

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Discuss the induced fit model and how it explains the conformational change of the enzyme upon substrate binding.

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Describe the two main approaches used to understand enzymatic action mechanisms: energy changes and active site chemistry.

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Explain the concept of activation energy (Ea) and its role in determining reaction rates.

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Graphically illustrate how enzymes lower activation energy to accelerate chemical reactions.

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Define the transition state (T) and explain how its stabilization by enzymes contributes to catalytic efficiency.

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Detail the catalytic mechanisms employed by enzymes, including: Transition state stabilization, General acid-base catalysis, Covalent catalysis

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Provide a specific example, such as chymotrypsin, to illustrate how enzymes utilize multiple catalytic mechanisms to facilitate substrate-to-product conversion.

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Use an appropriate analogy, like a sweater and a child, to explain the transition state concept and the enzyme's role in facilitating its formation.

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Explain how the formation of the enzyme-substrate (ES) complex affects the energy profile of the reaction.

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Define enzyme specificity and discuss its importance in the context of cellular metabolism.

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2. List and describe the different types of substrate specificity exhibited by enzymes, supporting each type with specific examples:

   • Substrate string specificity

   • Group specificity

   • Bond specificity

   • Stereoisomer specificity

   • Geometric specificity

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Explain how the unique structure of an enzyme's active site, including shape, charge, and chemical properties of amino acid residues, determines its specificity for a particular substrate.

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Describe how substrate concentration affects the rate of an enzymatic reaction.

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Explain the concept of maximum velocity (Vmax) and its significance in relation to enzyme saturation.

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Graphically illustrate the effect of substrate concentration on reaction rate and discuss the curve's shape.

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Differentiate Michaelis-Menten kinetics from allosteric kinetics, highlighting their distinct curve shapes.

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Analyze how temperature affects enzymatic activity, including the increase in reaction rate at higher temperatures and enzyme denaturation at excessive temperatures.

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Explain the concept of optimal temperature for enzymes and provide examples of how it varies among different organisms.

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Discuss the effect of pH on enzymatic reaction rates, emphasizing the roles of active site ionization and enzyme denaturation.

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Explain why different enzymes have distinct optimal pH values, relating this concept to their location and function in the body.

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Graphically illustrate the effect of pH on reaction rates for various enzymes, such as pepsin and enzymes functioning at neutral pH.

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