Enzymes - Detailed Study Notes
Enzymes - Chapter 6
Objectives
- Describe the shared characteristics of enzymes and how they differ from chemical catalysts.
- Investigate the relationship between free energy and reaction properties, including the influence of enzymes on these parameters.
- Discriminate binding and chemical effects on enzyme catalysis.
- Apply the plots and equations used to quantify enzyme kinetics.
- Explain the catalytic mechanism of serine protease.
- Elucidate the molecular basis of the different classes of reversible enzyme inhibition.
- Examine the mechanisms and logic of biological regulation of enzymes.
- Text Readings: Stryer 2nd or 3rd Edition All of Chapters 6, 7 and 8
Enzymes - Introduction
- Life depends on the ability to efficiently and selectively catalyze chemical reactions.
- Most biomolecules are very stable with rates of uncatalyzed transformations that are too slow to permit life.
- Enzymes provide a mechanism for acceleration, regulation, and coordination of these reactions.
- The most striking feature about enzymes is their catalytic power and specificity.
- Side reactions leading to useless or dangerous molecules must be avoided.
- Some enzymes are information sensors as well as catalysts.
Enzymes - Vitalism
- Eduard Buchner demonstrated that dead yeast still convert sugars into alcohol, indicating the reactions of life were separate from life.
- There was a factor in yeast catalyzing the reaction; the term "enzyme" is from the Greek "in yeast".
- This work won Eduard Buchner the Nobel Prize, ten years before he was killed in WWI.
- Originally biochemical reactions were believed to be inseparable from life.
- Vitalism is the belief that living things are fundamentally different from non-living things; that they contain some non-physical element and are governed by different principles that inanimate objects.
- Vitalism had some famous supporters, including Louis Pasteur.
Enzymes - Co-Enzymes and Co-Factors
- Proteins are well suited to form a variety of complex three-dimensional structures that enable binding of a variety of substrates.
- For some enzymes, the protein component alone is fully active.
- Other enzymes require co-factors (inorganic ions (, , etc.)) or co-enzymes (complex organic molecules (vitamins)) for activity.
- A co-enzyme or co-factor that is tightly associated with the enzyme is called a prosthetic group (the difference is the degree of association).
- Different enzymes that use the same coenzyme usually perform similar types of reactions.
Catalysts - General
Catalysts:
- lower the amount of energy required for a reaction to proceed.
- sped up attainment of equilibrium but do not change equilibrium.
- are unchanged by the reaction; recycled to participate in another reaction.
- Enzymes offer incredible catalytic power in the rate enhancements they provide.
Catalysts - Enzymes vs Chemical Catalysts
- Speed: Enzymes are often much faster than chemical catalysts, some approaching catalytic perfection.
- Conditions: Many chemical catalysts that require extremes of temperature, pressure and pH while enzymes function under physiological conditions.
- Specificity: Enzymes have a higher degree of specificity (including stereospecificity) than most chemical catalysts. This includes specificity for what they act upon and what they produce.
- Regulation: Unlike chemical catalysts, many enzymes are responsiveness to the dynamic needs of the cell and organism.
Enzymes - Circe Effect
- Enzyme rates of catalysis can approach the physical limit of rates of diffusion of molecules in solution.
- Some enzymes have rate-determining steps that are roughly as fast as the binding of substrates to the enzymes.
- Some enzymes are able to catalyze reaction faster than predicted by diffusion-control limits.
- This is called the Circe effect, named after a figure in Greek mythology who was renowned for her ability to draw her enemies to her, then transform them into animals.
Enzymes - Equilibrium and ES Complex
- Enzymes catalyze the interconversion of substrate and product.
- Substrate (S): the molecule acted upon by the enzyme.
- Product (P): the molecule produced by the enzyme.
- Active Site: the portion of enzyme (E) responsible for binding the substrate to formation of an enzyme-substrate (ES) complex.
Enzymes - The Active Site
- The active site is a 3D cleft formed from different parts of the polypeptide chain.
- The active site represents just a small part of the enzyme.
- Active sites are unique microenvironments.
- Substrates are bound to enzymes by multiple weak interactions.
- The specificity of substrate binding depends on the precisely defined arrangement of atoms in the active site.
- Enzymes and their active sites can be quite flexible.
- Substrate binding can caused “induced fit” or “conformation selection”.
Enzyme Specificity - Lock-and-key vs Hand-in-Glove
- Lock and Key model: The substrate fits perfectly into the active site of the enzyme, like a key in a lock.
- Hand in Glove (Induced Fit) model: The enzyme's active site changes shape slightly to accommodate the substrate.
Enzymes - Free Energy (Rates and Equilibrium)
- A reaction is spontaneous only if is negative. Spontaneous means the reaction will proceed without the input of energy and the reaction releases energy (exergonic).
- A reaction cannot take place spontaneously if is positive. An input of free energy is required to drive such reactions (endergonic).
- In a system at equilibrium, there is no net change in the concentrations of the products and reactants, and the is zero.
- The of a reaction depends only on the free energy of the product minus the free energy of the reactants. The of a reaction is independent of the steps of the transformation.
- The provides no information about the rate of a reaction. A negative indicates that a reaction can take place spontaneously but does not signify whether it will proceed at a perceptible rate.
Enzymes - Free Energy (Rates and Equilibrium)
- Activation energy, , between S and P determines the rate at which equilibrium is reached.
- Enzymes provide an alternate, lower-energy pathway between the substrate and product, lowering .
- The relationship between the rate of a reaction and the activation energy is inverse and exponential.
- Difference in free energy between S and P determines the equilibrium of the reaction.
- Enzymes do not influence the difference in free energy between S and P and therefore do not influence the equilibrium.
Enzymes - Rate Enhancements and Equilibrium
- Enzymes provide a lower-energy pathway between the substrate and product, decreasing the activation energy of the transition state and increasing the rate of reaction.
- Enzymes do not affect the difference in free energy between the substrate and product and therefore do not influence the equilibrium of a reaction.
Enzymes - Modes of Enzyme Catalysis
- What are the forces that lower the activation energy?
- Catalytic capabilities of enzymes result from both chemical and binding effects.
Binding Effects
- Substrate Binding
- Transition-state Stabilization
Chemical Effects
- Acid/base catalysis
- Covalent catalysis
Binding Effects - Reaction Specificity and Catalysis
- Binding of substrate in the active site provides specificity and catalytic power.
- Catalytic mechanisms limited to binding properties can still increase reaction rates by over 10,000-fold.
Binding Effects
- Substrate Binding
- Transition-state Stabilization
- There is conceptual overlap between substrate binding and transition state stabilization.
Binding Effects - Substrate Binding
Substrate binding promotes reactions by:
- Reducing entropy (decreased freedom of motion of two molecules in solution).
- Alignment of reactive functional groups of the enzyme with the substrate.
- Desolvation of the substrate (removal of water molecules) to expose reactive groups.
- Distortion of substrates.
- Induced fit of the enzyme in response to substrate binding.
Binding Effects - Transition-State (TS) Stabilization
- An increased interaction of the enzyme and substrate occurs in the transition-state.
- The essence of catalysis is stabilization of the transition state.
- The enzyme distorts the substrate, forcing it toward the transition state.
- The active site is complementary to the transition-state in shape and chemical character.
- Enzymes may bind their transition states to times more tightly than their substrates.
- Active site must be similar enough to substrate to ensure specificity, different enough to promote change.
Transition-State Analogs - Competitive Inhibitors
- Transition-state analogs (TSAs) are stable compounds that resemble unstable transition states.
- They have potential therapeutic applications as competitive inhibitors.
- Competitive Inhibitors are molecules that bind to the active site of an enzyme, they tend to resemble the substrate molecule.
- TSAs can bind the active site of a target enzyme active site with high affinity, preventing substrate binding.
Enzymatic Catalysis - Chemical Effects
- After substrate binding, the enzyme can act upon the substrate to promote formation of the product.
- The active site often contains chemically reactive side chains.
- This includes polar, ionizable side chains (triprotics) such as Asp, Glu, His, Cys, Tyr, Lys, Arg, and Ser.
- Two commonly observed mechanisms of chemical catalysis are:
- Acid/base Catalysis
- Covalent Catalysis
Chemical Modes of Enzymatic Catalysis - Acid-Base Catalysis
- Reaction acceleration is achieved by catalytic transfer of a proton.
- The side chains of some amino acids can acts as either bases (proton acceptors) or acids (proton donors).
- Histidine, with a pKa near physiological pH, is often involved in acid/base catalysis.
- The pKa of a functional group is influenced by the chemical microenvironment.
- Functional groups of amino acids can have different pKas within the active site which make them more suitable for acid/base catalysis.
Chemical Modes of Enzymatic Catalysis - Covalent Catalysis
As a part of the reaction mechanism the substrate is covalently bound to the enzyme to form a reactive intermediate.
In this example, group is transferred from A-X to B in two steps via the covalent complex of X-Enz.
Covalent catalysis often involves two steps, the first which forms a covalent linkage to the enzyme, the second to regenerate the free enzyme.
Covalent Catalysis - Sucrose Phosphorylase
- Sucrose* + Pi → Fructose + Glucose-1-P (*Sucrose is a disaccharide of glucose and fructose)
- Step one: Glucosyl residue is transferred to enzyme
- Step two: Glucose is transferred to phosphate
Enzyme Kinetics - General
- Kinetics is the study of the velocity of reactions.
- The velocity of a reaction is quantified as the change in concentration of product over time.
- Enzyme kinetics measured in sunits of concentration over time, for example mmoles/sec or moles/min.
Enzymes Kinetics - Variables that Enzyme Velocity
- As enzymes are proteins, any variable that influences protein structure may influence enzyme activity.
- The activity of enzymes is temperature and pH sensitive.
- Enzymes can have different optimum temperatures and pHs.
Enzymes Kinetics - Variables that Enzyme Velocity
- Enzyme velocities are also influenced by enzyme and substrate concentration.
- For kinetics, we are most interested in the relationship between velocity and substrate concentration.
Kinetics - Initial Velocity (Vo)
- As velocity is defined as the change in product concentration over time, it is necessary to measure product formation before equilibrium is reached.
- Initial velocity () is the velocity at the beginning of an enzyme catalyzed reaction, prior to product accumulation.
- and represent rapid, non-covalent interactions between enzyme and substrate.
- is rate constant of formation of product from ES.
Michaelis-Menton Kinetics - Steady State Assumption
- In deriving the Michaelis and Menton equation they worked from the assumption that the rate of formation of the ES complex was equal to the rate of its breakdown.
- This is known as the steady-state assumption.
- Mathematically the steady state assumption states that:
- Rate of formation of the ES complex is
- Rate of breakdown of the ES complex is
Michaelis-Menten - Equation and Plot
- The Michaelis-Menten equation and plot describe the relationship between substrate concentration and initial velocity.
- is the concentration of substrate required to reach 1/2 .
- is the maximum velocity of the enzyme.
Michaelis-Menten - Km
- is the concentration of substrate required for the enzyme to function at half maximal velocity.
- For many enzymes, provides an accurate approximation of the in vivo substrate concentration.
- This means that most enzymes are usually functioning at about half their maximum velocity.
Michaelis-Menten - Km
- When [S] < K_m, enzymes are highly sensitive to changes in substrate concentration but have very little activity.
- When [S] > K_m, enzymes have high activity but are insensitive to changes in substrate concentration.
- When , enzyme has significant activity and is responsive to changes in substrate concentration.
Michaelis-Menten - Sample Question #1
- What is the velocity of a reaction when substrate concentration is equal to ?
- Step 1: Pick values of and that are consistent with the question. Here we can say that and are both equal to 2 mM.
- Step 2: Substitute these values into the equation.
- Step 3: Express the velocity as a fraction of .
Michaelis-Menten - Sample Question #2
- What is reaction velocity when substrate concentration is double ?
- Step 1: Pick values of and that are consistent with the question. Here we can say that is equal to 2 mM and is equal to 4 mM.
- Step 2: Substitute these values into the equation.
- Step 3: Express the velocity as a fraction of .
Michaelis-Menten - Sample Question #3
- What is the reaction velocity when substrate concentration is a third of ?
- Step 1: Pick values of and that are consistent with the question. Here we can say that is equal to 3 mM and is equal to 1 mM.
- Step 2: Substitute these values into the equation.
- Step 3: Express the velocity as a fraction of .
Kinetics - Lineweaver-Burk Plots
Lineweaver-Burke plots:
- also describe the relationship between and .
- are a double-reciprocal plot of vs .
- are a more precise method of analysis of kinetic data.
- are used to determine and .
Kinetics - Enzyme Turnover Number
Enzyme Turnover Number:
- also called
- equals the number of molecules of substrate converted to product per unit time under saturating conditions.
- is calculated by .
Reversible Enzyme Inhibition - General
- An inhibitor is a compound that binds to an enzyme to interfere with its activity.
- Inhibitors can prevent formation of ES or the breakdown to E and P.
- Reversible inhibitors bind to the enzyme by non-covalent interactions.
- We will consider two classes of reversible enzyme inhibitors with different mechanisms and kinetic consequences.
- Competitive
- Uncompetitive
- Noncompetitive
Reversible Enzyme Inhibition - Competitive
- Competitive inhibitors resemble the substrate and compete with the substrate for binding the active site.
- The antibiotic sulfanilamide is a competitive inhibitor of a bacterial enzyme that has PABA as a substrate.
- Competitive inhibitors bind only the free enzyme.
- The effect of competitive inhibitors can be overcome with an excess of substrate (washing out).
- is the same but apparent is increased.
Reversible Enzyme Inhibition - Uncompetitive
- Uncompetitive inhibitors bind only to the ES complex.
- is decreased by conversion of ES to ESI which cannot form product.
- Uncompetitive inhibitors reduce [ES].
- As E binds S to replenish ES this apparent increase in affinity of the E for S causes a decrease in .
- The Herbicide “Round-Up” is an uncompetitive inhibitor of a plant enzyme involved in amino acid metabolisms.
Reversible Enzyme Inhibition - Non-competitive
- Non-competitive inhibitors bind to E and ES.
- is decreased with no change in .
- Non-competitive inhibitors don’t influence S binding, therefor there is no change in .
- Essentially reduces the number of active enzyme molecules.
- The antibiotic doxycycline is a non-competitive inhibitor of a bacterial enzyme (collagenase).
Serine Proteases - General Properties
Serine Proteases:
- Serve as digestive enzymes, including trypsin, chymotrypsin, and elastase, that cleave peptide bonds in protein substrates.
- Members of this family share similar sequences and active site residues.
- Are synthesized and stored in the pancreas as inactive zymogens to prevent damage to cellular proteins.
- Zymogens are activated at the appropriate time by selective proteolysis.
- Catalytic mechanism contains elements of both covalent and acid-base catalysis.
Serine Proteases - Substrate Specificities
- Serine proteases have unique specificities that reflect unique substrate binding pockets.
- Thrombin cleaves Arg-Gly bonds
- Trypsin cleaves by Lys and Arg.
- Chymotrypsin cleaves by Phe, Tyr or Met.
- Elastase cleaves by Gly and Ala.
- Papain cuts all peptide bonds.
Serine Protease - Catalytic Triad
- Serine Proteases have a conserved catalytic mechanism based on a catalytic triad of residues (Asp, His, Ser)
- Each residue plays a specific role in the catalytic mechanism
- His acts to accept and donate a proton at each of the two stages of the reaction mechanism (acid base catalysis).
- Asp stabilizes the positively-charged His to facilitate serine ionization.
- Ser attacks the carbonyl group of the peptide bond to be cleaved (covalent catalysis).
Chymotrypsin Mechanism - Overview
Phase I
- Step 1: (Acid/Base) Histidine acts as a base to extract proton from hydroxyl of Ser. This activates the oxygen of the hydroxyl group.
- Step 2: (Covalent) Formation of a covalent linkage from the hydroxyl group of the Ser to the carbonyl carbon of the peptide bond to be cleaved in the substrate.
- Step 3: (Acid/Base) Histidine acts as an acid to donate a proton to the amine group of peptide bond to be cleaved, this cuts the substrate peptide into two pieces.
Phase II
- Step 1: (Acid/Base) Histidine acts as a base to extract a proton from a water molecule, activating the oxygen of this molecule.
- Step 2: (Covalent) Activated water molecule attacks the point of covalent linkage between enzyme and substrate.
- Step 3: (Acid/Base) Histidine acts as an acid to donate a proton to reform the hydroxyl group of Ser.
Regulation of Enzyme Activity - Overview
- The activity of an enzyme can be regulated by controlling the amount of the enzyme (long term), or by adjusting the activity of a constant quantity of the enzyme (short term).
- Regulation of enzyme availability
- location, rates of synthesis and degradation
- Regulation of enzyme activity
- covalent modification -phosphorylation, methylation, glycosylation, etc.
- non-covalent modification (allosteric) -allosteric regulation
Regulation of Enzyme Activity - Points of Regulation
What would be the logical point to regulate a reaction pathway?
- Enzymatic pathways often controlled through negative feedback inhibition by the final product of the pathway.
- The final product often inhibits the enzyme catalyzing the first unique and committed step.
- Regulation at this step conserves material and energy and prevents accumulation of intermediates.
Regulation of Enzyme Activity - Points of Regulation
- Negative feedback in a branched pathway often occurs by the final product of each branch acting to inhibit the enzyme catalyzing the first unique and committed step of the branch.
- Enzyme 7 inhibited by G
- Enzyme 4 inhibited by T
Regulation of Enzyme Activity - Points of Regulation
- Regulation when two pathways cooperate to form a single product.
- The final product can inhibit the first unique step of each branch.
- The molecules preceding the merger can inhibit the first step of their branch as well as activating the first step of the opposing branch.
Allosteric Enzymes - General Properties
Allosteric Enzymes:
- serve as information sensors to coordinate cellular metabolism.
- are regulated by interaction with metabolic intermediates.
- are regulated by allosteric modulators that bind non-covalently at sites other than the active site.
- are usually examples of quaternary structure.
- often catalyze branch-point reactions.
- are often slow, representing the rate limiting step of the pathway.
- do not obey Michaelis-Menten kinetics, instead have sigmoidal curves.
Allosteric Enzymes - General Properties
- Activities of allosteric regulator enzymes are changed by inhibitors and activators (modulators).
- Allosteric modulators bind non-covalently to the enzymes that they regulate.
- Regulatory enzymes often possess quaternary structure.
- There is a rapid transition between the active (R) and inactive (T) conformations.
- Substrates and activators may bind only to the R state while inhibitors may bind only to the T state.
- The binding of the substrate disrupts the R to T equilibrium in favor of R. – This is the basis of the co-operative activation of allosteric enzymes.
Allosteric Enzymes - Physiological Significance of Cooperativity
- Allosteric enzymes transition from a less active state to a more active state within a narrow range of substrate concentration.
- The activity of allosteric enzymes is more sensitive to changes in substrate concentration near the than are Michaelis-Menten enzymes of the same .
- This sensitivity is called a threshold effect: below a certain substrate concentration there is little enzyme activity; after the threshold has been reached the enzyme activity increases rapidly (on/off).
Allosteric Enzymes - Phosphofructokinase 1
- PFK1 catalyzes an early step of glycolysis.
- Phosphoenolpyruvate (PEP), an intermediate near the end of the pathway is an allosteric inhibitor of PFK1.
- ADP is an allosteric activator of PFK1.
- When the ratio [PEP]/[ADP] is high, PFK1 is inhibited; When the ratio of [PEP]/[ADP] is low, PFK-1 is activated and glycolysis produces more ATP from ADP.
- Thus the concentrations of PEP and ADP act allosterically through PFK1 to regulate the activity of the entire pathway.
Allosteric Enzymes - Activation of Phosphofructokinase-1 by ADP
- The activity of PFK1 is responsive to the concentration of the substrate as well as the allosteric activators and inhibitors.
- Even at constant levels of substrate the activity of the enzyme can be modulated through changes in levels of the allosteric modulators.
Enzyme Regulation by Covalent Modification - General
- Many enzymes are regulated through the covalent linkage of a modifying group to changes some aspect of the proteins behavior, such as activity.
- A number of different types of covalent modification have been characterized (methylation, acetylation, etc).
- The most common post-translation covalent modification is through phosphorylation.
- These modifications are usually reversible with one enzyme catalyzing the addition of the group and another enzyme catalyzing its removal.
- Kinases add phosphoryl groups, phosphatases remove them.
Enzyme Regulation by Covalent Modification - Glycogen Metabolism
- Production and utilization of glycogen is controlled by two enzymes:
- glycogen synthase (anabolic) which catalyzes production of glycogen from glucose.
- glycogen phosphorylase (catabolic) which catalyzes the breakdown of glycogen into glucose.
Enzyme Regulation by Covalent Modification - Glycogen Metabolism
- In response to hormones that are released when you are hungry (glucagon) or scared (epinephrine) both enzymes are phosphorylated
- Phosphorylation activates the catabolic enzyme and inactivates the anabolic enzyme.
- This situation favors the breakdown of glycogen into glucose.
Enzyme Regulation by Covalent Modification - Glycogen Metabolism
- In response to hormones released in the fed state (insulin) both enzymes are unphosphorylated.
- When unphosphorylated the anabolic enzyme is active and the catabolic enzyme is inactive.
- This situation favors the storage of glucose within glycogen.