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Questions and Answers
What is the term for the change in free energy of a reaction?
What is the term for the change in free energy of a reaction?
- T∆Srxn
- ∆Grxn (correct)
- ∆Hrxn
- Ea
Catalysts change the overall free energy change, ∆G, of a reaction.
Catalysts change the overall free energy change, ∆G, of a reaction.
False (B)
What is the effect of enzymes on the activation energy of a reaction?
What is the effect of enzymes on the activation energy of a reaction?
Enzymes lower the activation energy.
The systematic name for an enzyme typically begins with _____ and ends with -ase.
The systematic name for an enzyme typically begins with _____ and ends with -ase.
Match the following enzymes with their requirements:
Match the following enzymes with their requirements:
What is the rate law for the reaction A + 2B → C if it is governed by a single elementary step?
What is the rate law for the reaction A + 2B → C if it is governed by a single elementary step?
Enzymes can enhance reaction rates by factors ranging from 10^6 to 10^14.
Enzymes can enhance reaction rates by factors ranging from 10^6 to 10^14.
Define thermodynamically unstable in the context of ATP.
Define thermodynamically unstable in the context of ATP.
What is one role of metal ions in enzymatic catalysis?
What is one role of metal ions in enzymatic catalysis?
Acid-base catalysis involves the transfer of H+ ions.
Acid-base catalysis involves the transfer of H+ ions.
Name the amino acids that are part of the catalytic triad in serine proteases.
Name the amino acids that are part of the catalytic triad in serine proteases.
In acid-base catalysis using RNase, His 12 acts as a ______ and His 119 acts as a ______.
In acid-base catalysis using RNase, His 12 acts as a ______ and His 119 acts as a ______.
Match the following enzymes with their specific action:
Match the following enzymes with their specific action:
What does the Michaelis-Menten equation primarily describe?
What does the Michaelis-Menten equation primarily describe?
Which of the following is not a mechanism of catalysis mentioned?
Which of the following is not a mechanism of catalysis mentioned?
The Michaelis constant (KM) is independent of the binding affinity of the enzyme for its substrate.
The Michaelis constant (KM) is independent of the binding affinity of the enzyme for its substrate.
The act of transiently forming a covalent bond during a reaction is called ______ catalysis.
The act of transiently forming a covalent bond during a reaction is called ______ catalysis.
The preferential stabilization of the transition state is a characteristic of electrostatic catalysis.
The preferential stabilization of the transition state is a characteristic of electrostatic catalysis.
What is the significance of kcat in enzyme kinetics?
What is the significance of kcat in enzyme kinetics?
At steady state, the rate of formation of ES is equal to the rate of __________.
At steady state, the rate of formation of ES is equal to the rate of __________.
Match the following terms with their definitions:
Match the following terms with their definitions:
What represents the efficiency of an enzyme?
What represents the efficiency of an enzyme?
In the Michaelis-Menten model, the ES complex is assumed to be in a steady state.
In the Michaelis-Menten model, the ES complex is assumed to be in a steady state.
What does the rate equation v0 = Vmax[S]/(KM + [S]) indicate about substrate concentration?
What does the rate equation v0 = Vmax[S]/(KM + [S]) indicate about substrate concentration?
Flashcards
Change in Free Energy (ΔG)
Change in Free Energy (ΔG)
The change in free energy during a reaction, indicating whether it's spontaneous or not. Negative delta G indicates a spontaneous reaction.
Free Energy
Free Energy
Energy available to do work as a reaction reaches equilibrium.
Thermodynamically Unstable
Thermodynamically Unstable
A molecule like ATP that is thermodynamically unstable but kinetically stable, meaning it has a high potential energy for release but doesn't readily break down.
Activation Energy (Ea or ΔG++)
Activation Energy (Ea or ΔG++)
The activation energy needed for a reaction to occur, measured as the free energy difference between the reactants and the transition state.
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Catalyst
Catalyst
A substance that speeds up a reaction without being consumed in the process, by lowering the activation energy.
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Enzymes
Enzymes
Biological catalysts made of proteins (or RNA), specifically designed to speed up biochemical reactions in living organisms.
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Reaction Rate
Reaction Rate
A measure of how fast a reaction proceeds, determined by factors like concentration and temperature.
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Rate Law
Rate Law
The rate of a reaction is proportional to the concentration of reactants, raised to a specific power reflecting their involvement in the reaction's mechanism.
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Enzyme Catalysis
Enzyme Catalysis
Enzymes speed up reactions by providing an alternative pathway with a lower activation energy (ΔG‡). They do this by binding and orienting substrates, favoring the formation of the transition state, and participating in chemical reactions.
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Acid-Base Catalysis
Acid-Base Catalysis
Enzymes can use acid-base catalysis, where amino acid residues donate or accept protons, to facilitate reactions.
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Covalent Catalysis
Covalent Catalysis
A type of catalysis where a transient covalent bond forms between the enzyme and the substrate.
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Metal Ion Catalysis
Metal Ion Catalysis
Metal ions, often found in active sites of enzymes, can contribute to enzyme catalysis by stabilizing charges, orienting substrates, and participating in redox reactions.
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Electrostatic Catalysis
Electrostatic Catalysis
The preferential stabilization of a transition state by an enzyme, often through hydrogen bonding or ionic interactions.
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Schiff Base Formation
Schiff Base Formation
A special type of covalent catalysis where a Schiff base is formed between an enzyme and its substrate.
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Serine Proteases
Serine Proteases
A family of proteolytic enzymes responsible for breaking peptide bonds in proteins.
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Transition State Analog
Transition State Analog
A stable molecule that mimics the transition state of a reaction, designed to inhibit enzyme activity.
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Why Study Enzyme Kinetics?
Why Study Enzyme Kinetics?
The study of enzyme kinetics involves analyzing the rates of enzymatic reactions to understand how enzymes function, their reaction mechanisms, and their interactions with substrates and inhibitors. It's a fundamental aspect of biochemistry and is essential for drug development and understanding how enzymes contribute to metabolic pathways.
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Michaelis-Menten Equation
Michaelis-Menten Equation
The Michaelis-Menten equation describes the rate of an enzymatic reaction as a function of substrate concentration. It helps us understand how the rate changes with varying substrate amounts and provides key parameters like KM and Vmax.
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What is KM?
What is KM?
KM is the Michaelis constant, representing the substrate concentration at which the enzyme operates at half its maximum velocity (Vmax). It's a measure of how tightly the enzyme binds to the substrate and influences the efficiency of the reaction.
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What is Kcat?
What is Kcat?
Kcat (also known as turnover number) is a measure of the maximum number of substrate molecules an enzyme can convert into product per unit time, when fully saturated with substrate. It's essentially the enzyme's catalytic efficiency.
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What is the specificity constant?
What is the specificity constant?
The specificity constant, kcat/KM, reflects the overall efficiency of an enzyme at low substrate concentrations, indicating how good an enzyme is at choosing its correct substrate.
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Enzymes
- Enzymes are proteins that catalyze biochemical reactions.
- Enzymes lower the activation energy for both forward and reverse reactions.
- Enzymes do not change the overall free energy (ΔG) change of a reaction.
Rate vs Direction of Biochemical Reactions
- Free energy is the energy available to do work as a reaction approaches equilibrium.
- ΔGrxn = ΔΗrxn - TAS
- ΔGrxn < 0 for spontaneous reactions.
- ATP is thermodynamically unstable but kinetically stable. This is shown in a free energy diagram for ATP hydrolysis. ΔG° = -30.5 kJ/mol.
Biochemical Kinetics
- Rate = k [A][B]2, where k is the rate constant.
- Rate constant, k, is defined by the Arrhenius equation and includes the temperature and activation energy (Ea = ΔG++).
- Ea = Ae-Ea/RT, where A is the frequency factor, R is the gas constant, and T is the Kelvin temperature.
Catalysts
- Catalysts increase the rate of reactions toward equilibrium by lowering ΔG++.
- Enzymes can provide enhancements of 106 to 1014 in reaction rates.
Enzyme Classification
- Oxidoreductases: catalyze oxidation-reduction reactions.
- Transferases: transfer functional groups.
- Hydrolases: catalyze hydrolysis reactions.
- Lyases: catalyze group elimination to form double bonds.
- Isomerases: catalyze isomerization reactions.
- Ligases: catalyze bond formation coupled with ATP hydrolysis.
Enzyme Nomenclature
- Enzymes usually end in "-ase."
- Common names are often ambiguous; systematic names are established by the enzyme commission of IUBMB (e.g., carboxypeptidase A, systematic name: peptidyl-L-amino acid hydrolase EC.3.4.17.1).
How do enzymes lower ΔG‡?
- Binding and orientation of substrate(s) to increase reactivity and proximity of chemical groups.
- Preferential binding of X+.
- Provide an alternative pathway with a lower ΔG‡.
Chemical Bases for Enzymatic Catalysis
- Acid-base catalysis (H+ transfer)
- Covalent catalysis (transient covalent bond)
- Metal ion catalysis
- Transition metal ions in active site play a role in catalysis (Fe, Cu, Zn, Mn, Co).
- Contributions to electrostatic catalysis.
- Increase reactivity of H2O by polarization.
- Redox reactions.
- Electrostatic effects (stabilization of X+, binding, and orientation of substrate S)
- Electron transfer (redox)
- Polarization of H2O (e.g., carbonic anhydrase)
- Charge-shielding on substrate (e.g., Mg-ATP).
Specific Example: RNase
- Two key histidine residues in the active site: His 12 (base) and His 119 (acid).
- An example of a hydrolysis reaction.
Enzyme Kinetics
- Michaelis-Menten Equation describes the reaction rate of non-allosteric enzymes
- Rate equation: v = Vmax[S]/ (KM + [S])
- Vmax = maximum velocity
- KM= (k-1 + k2)/ k1 or rate of dissociation of ES
Significance of KM
- KM is the substrate concentration at which the reaction rate is half-maximal (Vmax/2)
- related to the equilibrium binding affinity of E for S
Catalytic Constant, kcat
- kcat is a first-order rate constant that represents the maximum rate of a substrate turnover in an enzyme catalyzed reaction.
- kcat = Vmax/ET , (where ET is the total enzyme concentration)
Specificity Constant, kcat/KM
- A measure of catalytic efficiency. A higher rate generally means better efficiency
Two-Substrate Reactions
- Sequential mechanism
- Both substrates bind to the enzyme, producing a ternary complex, before any product is formed.
- Ping-pong mechanism
- One substrate binds, then the first product is released before the second substrate binds.
Allosteric Enzymes
- Multi-subunit proteins (multiple catalytic and regulatory subunits).
- Subunit interactions stabilize low-affinity (T) state.
- Allosteric effectors (modulators) can be positive or negative.
- Substrate binding can show positive cooperativity.
Example: Aspartate Transcarbamoylase
- First step in pyrimidine biosynthesis.
- Complex of six catalytic and six regulatory subunits (C6R6).
- Allosteric effectors: substrates (+), CTP (-), ATP (+).
Covalent Modifications
- Phosphorylation, adenylation, acetylation, myristoylation are common covalent modifications that produce allosteric-like changes.
Regulation of Enzyme Activities
- Rapid: noncovalent modification (competitive inhibition, substrate/effector binding).
- Slower: covalent modifications (phosphorylation), degradation and synthesis of mRNA/polypeptides.
Enzyme Inhibition
- Irreversible inhibitors: inactivators (typically very reactive electrophiles)
- Reversible inhibitors: bind noncovalently and reversibly.
Different types of Enzyme Inhibition
- Competitive Inhibition
- Uncompetitive Inhibition
- Mixed Inhibition
- Noncompetitive Inhibition
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