Term
| What is a nucleophilic catalysis |
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Definition
| When a nucleophile initiates a chemical reaction |
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Term
| What is the Arrhenius equation? What do the letters stand for? |
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Definition
rate = p.Z.e ^-(Ea/RT)
p is probability factor (orientation of reactants)
Z is collision frequency
Ea is activation energy
R is 8.314X10^-3
T is temperature in Kelvins (273) |
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Term
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Definition
| the fraction of molecules at temp T which possess energy Ea |
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Term
| How do enzymes speed up reactions |
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Definition
lower activation energy
increase probability (eliminate/reduce randomness)
increase collision freqency |
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Term
| How do enzymes reduce randomness? |
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Definition
| hold substrates in the active site long enough for the reaction to take place (proximity effect) |
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Term
| How do enzymes increase probability? |
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Definition
| The substrates are positioned in the active site so that the reactive groups on each are aligned (orientation effect) |
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Term
| How do enzymes decrease activation energy? |
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Definition
| Provide a different chemical pathway for the reaction which involve reactive groups on the enzyme |
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Term
| How would a non-polar prosthetic group found in the active site of an enzyme act on the substrate? |
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Definition
| Would act as an electrophile, accepting extra electrons from the substrate |
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Term
| What is general acid catalysis? |
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Definition
| Is when amino acid donates an H+ to the reaction |
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Term
| What is general base catalysis? |
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Definition
| Is when an amino acid removes H+ from the reation |
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Term
True or False
pH in the surrounding solution will be changed when an enzyme initiates general acid or general base catalysis |
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Definition
False
pH goes unchanged in the surroundings because the reaction is confined to the active site |
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Term
| How do enzymes lower Ea & stabilize the transition state? |
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Definition
| binds the substrate in the ideal shape, so less activation energy is needed for the reaction to occur |
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Term
| Why is a good fit important for enzyme function? |
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Definition
| so the targeted peptide lines up with the catalytic components of the enzyme |
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Term
| Why is peptide hydrolysis by H2O without the help of chymotrypsin ineffective? |
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Definition
-neutral O is not a good nucleophile, makes an unstable transition state
-carboxylate C may give back the excess electrons to the original nucleophilic O
-the H2O forms a good leaving group
-return to original reactants, no net reaction |
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Term
| How does chymotrypsin hydrolyze peptide bonds more easily? |
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Definition
| -breaks the difficult uncatalyzed pathway into two simpler steps with an intermediate formed in between |
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Term
| Summarize the first half of chymotrypsin catalysis |
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Definition
| Nucleophilic group in the enzyme active site targets the carbonyl carbon of the peptide bond, releasing the C terminal half and forming an acyl enzyme intermediate |
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Term
| Summarize the second half of chymotrypsin catalysis |
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Definition
| H2O is brought in, which acts as a nucleophile to release the N terminal half from the acyl enzyme intermediate. The enzyme is restored to its original form |
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Term
| What is the rate of reaction for chymotrypsin vs with H2O? |
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Definition
40/second for chymotrypsin
1/10yrs with H2O |
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Term
| What is the 'better nucleophile' that chymotrypsin has? |
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Definition
A catalytic triad
Asp102, His57, Ser195 |
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Term
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Definition
| has a negative charge so it favours a positively charged partner |
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Term
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Definition
| could be positive if it could capture an H+ |
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Term
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Definition
| could give up an H+ if it shares a lone pair with a suitable atom |
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Term
| What is the combined effect of the 3 components of the catalytic triad? |
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Definition
| Ser195 is made into a better nucleophile |
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Term
| What is the importance of the oxyanion hole? |
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Definition
stabilizes the transition state
(acyl-enzyme intermediate) |
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Term
| What is the oxyanion hole made of? |
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Definition
| the backbone NH groups of Gly193 and Ser195 |
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Term
| If Asp is replaced with Ala, how will the rate of reaction be affected? |
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Definition
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Term
| If His is replaced with Lys how will the rate of reaction be affected? |
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Definition
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Term
| Why does the replacement of His with Lys have such a large effect? |
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Definition
| because Lys has a higher pKa so can act as a base but not an acid |
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