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| protein (rarely RNA) catalysts in the cell |
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| substance that speeds up chemical reaction w/out being changed after the reaction |
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| specific heat-stable low MW organic molecules required for enzyme activity |
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| redox reactions with transfer of electrons |
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| transfer of chemical groups b/w molecules |
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| cleave various bonds by means other than hydrolysis and oxidation |
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| transfer of a group w/in a molecule to yield isomeric forms |
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| bond formation coupled to ATP cleavage |
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the energy available to do work
ΔG = ΔH - T ΔS |
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endergonic NOT spontaneous
- must add energy for reaction to occur |
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| formation/breaking of chemical bonds |
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| endothermic (absorbs heat) |
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| exothermic (gives off heat) |
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free energy change for a reaction at standard conditions of 25C, 1M concentration, and pH of 7.0.
-has a constant and unchanging value for a given reaction
- permits direct comparison of free energy changes for different reactions |
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ΔG°' + 2.303 RT log[P]/[S]
The free energy change at non-standard conditions
- determines whether or not a reaction is spontaneous in a cell |
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| region of enzyme that binds substrate and catalyzes the reaction |
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| Key Features of Active Sites |
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1) take up relatively small part of total enzyme volume
2) 3-D site formed by groups that come from different parts of the linear amino acid sequence
3) has catalytic AA sidechains that bind to substrate and position the substrate
4) is a cleft or pocket
5) specificity of binding depends on the precisely defined arrangement of atoms in an active site |
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| Types of Associations b/w Enzyme and Substrate |
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| H-bonds, hydrophobic interactions, salt bridges, and dipole-dipole interactions |
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(flexible active site)
formation of enzyme substrate complex is accompanied by conformational changes in enzyme |
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enzyme binds substrate at the active site and brings them together
- increases the concentration and, in turn, increases the rate of reaction |
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| reactants must collide with correct orientation for reaction to occur. -Enzymes orient substrates at the active site |
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| Substrate Strain and Distortion |
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binding of substrate to enzyme can strain specific bonds
- enzyme active site is designed to apply strain and push the substrate towards the transition state |
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| amino acid side chains in the active site can donate or accept H+ to promote transition state formation and to promote conversion of the transition state to product |
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| involves formation of a transient covalent bond b/w the enzyme and substrate to promote formation of the transition state |
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| Transition-State Stabilization |
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- enzyme active site is complementary to the transition sate substrate
- enzyme active site stabilizes those features of S which appear in transition state substrate
- enzyme binds more tightly to the transition state substrate |
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| experimental proof for transition state stabilization by enzymes |
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| disappearance of substrate with time |
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| appearance of product with time |
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| International Unit of Enzyme Activity (U) |
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| quantity of enzyme required to convert 1 µmole/min at optimum assay conditions |
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(µmole/min)/mg protein
- As an enzyme is purified, the specific activity increases until, in the pure preparation, it reaches a maximum |
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| Michaelis-Menten Equation |
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V_o = V_max ([S])/([S]+ k_M )
-relates the rate of catalysis to [S] and [E] and also the rates of the individual steps |
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[S] which gives 1/2 Vmax
- enzyme landmark to explain enzyme behavior and identify different enzymes
- typically range from 10^-1 to 10^-7 M
- reflects the affinity of enzyme for its substrate (the smaller, the higher the affinity) |
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number of substrate molecules converted into product by an enzyme molecule in a unit time when the enzyme is fully saturated with substrate
- is equal to the rate constant k_2
- for most enzymes, falls in range of 1 to 10,000 per second |
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Kcat/Km
- typically b/w .1 and 1
- used to rank enzymes according to how well they utilize different substrates (catalytic efficiency)
- upper limit of 10^8 to 10^9 M^-1sec^-1 (represents enzyme perfection) |
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very slow dissociation from enzyme
ex: DIPF and Iodoacetamide |
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| Diisopropylfluorophosphate |
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group specific irreversible inhibitor
- covalently reacts with serine sidechains
- inactivates chymotrypsin and acetlycholinesterase |
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group-specific irreversible inhibitor
- covalently reacts with -SH groups |
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| reversibly and rapidly binds to/dissociates from the enzyme - many drugs are examples - concentration required to inhibit the enzyme depends on how tightly the inhibitor binds to the enzyme |
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Ki = [E][I]/[EI]
- equilibrium dissociation constant of enzyme-inhibitor complex
- if Ki is small, less inhibitor is required to inhibit the enzyme |
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| Forces involved in binding of reversible inhibitors to enzyme |
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1) complementarity
2) H-bonds, salt bridges, dipole-dipole, and hydrophobic interactions |
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1/v vs. 1/[S]
- y-intercept = 1/Vmax
- slope = Km/Vmax
- x-intercept = -1/Km |
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| Reversible Inhibitor Effects on Lineweaver-Burk plot |
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competitive: slope effect
noncompetitive: slope and y-intercept effect
uncompetitive: y-intercept effect |
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- bind only with enzyme
- resemble substrate structurally
- can be overcome by adding substrate
- Km increases |
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| Two Examples of Competitive Inhibitors |
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| succinate dehdrogenase and bisphosphoglycerate mutase |
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- binds only to ES complex
- Vmax decreases and Km decreases |
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| Noncompetitive Inhibitors |
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- binds to both E and ES
- Vmax is decreased (when Ki=Ki') |
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| Potential Uses of Reversible Inhibitors |
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1) therapeutic agents
2) experimental techniques
3) Information about structure of enzyme and its active site |
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