Understanding Enzyme Mechanism and Structure

Question 1

delta G

Answer 1

• g products minus G reactants
• can predict whether a reaction can occur spontaneously
• neg=spon
• 0=equil
• pos=not spon
• related to overall change in entropy and enthalpy of a system
• deltaG=deltaH-TdeltaS
• DOESNT PREDICT rate of reaction-independent of mechanism

Question 2

prediction of reaction rate

Answer 2

• activation energy

- catalysts lower Ea

Question 3

enzymes

Answer 3

• lower the activation energy
• can’t change deltaG
• direct stabilization of TS or creation of new reaction pathways

Question 4

enzyme catalysis must lower Ea

Answer 4

• need to reduce energy at the transition state by”
  1. directly stabilizing the transition state complex with the enzyme
  2. creating a new pathway for the reaction
  3. or combination of both!

Question 5

enzyme active sites

Answer 5

• used to think it was lock and key

- probably more likely to be induced fit

Question 6

common features of an active site

Answer 6

• occupy a small part of total volume of most enzymes
• 3D structure
• bind substrates through multiple weak, non covalent interactions
• water is excluded unless it is a reagent-active sites are in the clefts of proteins
• highly specific binding of substrate
• can include non-protein prosthetic groups and cofactors-increase repertoires

Question 7

prosthetic groups

Answer 7

-tightly and stably integrated into enzymes, often covalently bound

Question 8

co factors

Answer 8

loosely bound, generally come on and off the enzyme

Question 9

chemical strategies in enzymatic catalysis

Answer 9

• direct stabilization of TS-preferential binding of the TS, proximity and orientation effects
• chemical assistance-acid/base catalysis, covalent catalysis, metal ion catalysis, electrostatic catalysis

Question 10

preferential binding of the TS

Answer 10

• direct stabilization, lowers Ea
• enzyme binds TS structure with greater affinity than substrate or products (does it’s work on TS, not on substrate)
• usually implies that enzyme fits the TS state better than the substrate and can form additional bonds to TS
• important factor in catalytic activity of almost all enzymes

Question 11

proximity and orientation effects

Answer 11

• reactants must come together with the proper spatial orientation for reaction to occur
• enzymes immobilize substrates by binding, and the active site is designed to orient them for optimal reactivity

Question 12

acid base catalysis

Answer 12

• general acid-enzyme is weak acid and gives proton
• general base-enzyme is weak base and accepts proton
• concerted-both acid and base groups on enzyme participate
• his

Question 13

covalent catalysis

Answer 13

• transient formation of covalent bond between enzyme and substrate (new intermediate)
• groups are usually cys, ser, lys, his, prosthetic groups

Question 14

meal ion catalysis

Answer 14

-metal ions participate

Question 15

electrostatic catalysis

Answer 15

• charge distribution in active site helps stabilize the TS

- asp, glu, arg, his, lys, metal ion cofactos

Question 16

proteolysis

Answer 16

• cleavage of a peptide bond by addition of water across bond
• specificity is critical
• breakage of peptide bond is spontaneous
• Ea very high

Question 17

classes of proteases

Answer 17

• serine
• aspartyl
• thiol
• Zn2+
• each class uses a different set of catalytic strategies
• members of the same class use the same strategy but have different substrate specificity

Question 18

serine proteases

Answer 18

• catalytic triad-serine, his, asp
• serine does covalent catalysis-forms a TS that decomposes to acyl enzyme intermediate
• his does acid/base
• asp stabilizes acceptance of H+
• two steps
  1. nucleophilic attack, TS, covalent catalysis (acyl intermediate), general base catalysis, electrostatic catalysis, and enzyme binding to TS are utilized
  2. general base catalysis, general acid catalysis used. amino group half of peptide leaves and water comes in to nucleophilic attack, forms second TS. His donates H+, c terminus formed and released

Question 19

preferential stabilization by serine protease

Answer 19

• TS of substrate makes new bonds to serine and glycine of enzyme (not in acitve site)
• not available to substrate
• makes E-TS more favorable

Question 20

rate determining step

Answer 20

• formation of intermediate in this reaction

- E thru TS 1 and intermediate is bigger than TS2 and product

Question 21

chymotrypsin

Answer 21

• cleaves after large non polar side chain, large non polar pocket on enzyme
• Phe, Try

Question 22

trypsin

Answer 22

-cleaves after basic (+) aa, neg charged asp in pocket of enzyme

Question 23

elastase

Answer 23

• cleaves after small uncharged side chain
• bulky aa on enzyme block pocket
• val, thr

Question 24

suicide inhibitors

Answer 24

• irreversible
• bind to enzyme because of resemblance to the substrate and are converted to an irreversible inhibitor by the initial steps of the enzymes reaction mechanism

Question 25

penicillin

Answer 25

- inhibitor of glycopeptide transpeptidase-needed for cell wall - mechanism of transpeptidase is similar to serine protease - penicillin looks like substrate, but has a 4 membered ring including the peptide bone - initial step=cleavage, transpeptidase forms intermediate, but N terminus can't leave

Question 26

acetylcholinesterase

Answer 26

- breaks down ach in synapses - similar mech to chymotrypsin - nerve gases are irreversible inhibs-inactivate active site- can't breakdown ach-pulm spasms and loss of neuromuscular and cardiac function and death - reversible inhibitors are AD drugs-aricept and cognex-improve cog function- can't stop but slow down. competitive or non competitive- boost ach to improve memory and cognition