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Chapter 14 Notes

by: Rachael Couch

Chapter 14 Notes biol 3361

Rachael Couch
GPA 3.9
Biochemistry 1
Dr. Lee

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Here are this weeks notes. They contain lecture information (written and powerpoint) and information from the OWL cengage. Good luck on the upcoming exam! Keep posted, I will be posting note bundle...
Biochemistry 1
Dr. Lee
Class Notes
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This 8 page Class Notes was uploaded by Rachael Couch on Wednesday October 7, 2015. The Class Notes belongs to biol 3361 at University of Texas at Dallas taught by Dr. Lee in Summer 2015. Since its upload, it has received 26 views.


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Date Created: 10/07/15
Chapter 14 Mechanisms of Enzyme Action 0 Enzymes have to bind the transition state of the reaction more tightly than the substrate 0 Must stabilize transition state more than substrate for there to be a decrease in activation energy 0 If ES has too high affinity Km too low there is no benefit of the catalyzed reactlon Destabilization of ES 0 If ES too favorable Ea is higher 0 Raising the energy of ES raises the rate 0 Catalysis Will not occur is ES and transition state X are equally stabilized 0 Can destabilize ES destabilize compared to super stable 0 Entropy loss due to formation of ES Decrease in entropy of overall system and of substrate 0 StrainDistortion in ES 0 Desolvation substrate loses favorable interactions With water 0 Electrostatic destabilization Preferential binding of the transition state 0 2 more H bonds to transition state than substrate large increase in rate 0 Transition state analogs TSAs stable molecules similar to transition state 0 TSAs are great inhibitors 0 K1 Binding affinity to the TSA transition state 0 Enzyme binds better to TS than substrate so most inhibitors resemble the TS Covalent Catalysis 0 Nucleophilic centers in enzymes attacked by electrophilic centers of substrates to make covalent ES complex 0 Covalent intermediate can be attacked in a second step by water or by a second substrate General AcidBase Catalysis 0 Noncovalent bonds 0 Specific acidbase catalysis involves H or OH 0 General acidbase catalysis doesn t directly involve HOH ex basic AA histidine 0 These facilitate the transfer of H in the transition state 0 LP electrons in base attack hydrogen Hydrogen polarizes the bond in water oxygen in water can then attach carbonyl Metal Ion Catalysis 0 13 of enzymes require metal ions for catalysis 0 Some play structural rather than catalytic 0 Bind to substrate to orient it properly for the reaction 0 Mediate redox reactions through reversible changes in metal ion oxidation states 0 By electrostatically stabilizing negative charges 0 Metal ion can polarize to generate OH Proximity and Orientation 0 Bring substrates close to catalytic residues 0 Bind substrate in proper orientation nearattack conformation O NAC Precursors to transition states specific conformationarrangement for reaction to happen Stabilize transition state by electrostatic interation Reduce overall loss of entropy Intramolecular is significantly faster 0 Intermolecular I loss in entropy Protein motions 0 Proteins under constant motion 0 Natural active site conformations can 0 Assist substrate binding 0 Bring catalytic groups into position 0 Induce formation of NACs 0 Assist in bond makingbreaking O Facilitate product formation Readingwriting mechanisms Curved arrow movement of electron pair Full arrowhead electron pair Half arrowhead single electron Consider protonation states to predict whether a residue will act as an acid or a base Active site residues 0 Polar residues engage directly in catalytic effects 0 Act as nucleophiles 0 Facilitate substrate binding 0 Stabilize transition states 0 Catalytic capacities are in uenced by O Raisinglowering pKa values through weak forces 0 Changing orientation 0 Charge stabilization LowB arrier Hydrogen Bonds LBHBs 0 Hydrogen bonds are equally shared between proton donor and acceptor when pKa values are nearly equal 0 Leads to stability of bond 0 Energy released in forming an LBHB can assist catalysis Serine Proteases Class of proteolytic enzymes 0 Each serine protease has binding pockets that bind specificdifferent substrates which means that they cleave after different AA 0 Chyotrypsin Prefers cleaves after Phe Trp or Tyr deep hydrophobic O Trypsin Cleaves after Lys or Arg deep ion pairs 0 Elastase Cleaves after Ala Gly or Val shallowsmall side chains Cleave peptide bond between alpha C and N 0 Active site reactive Ser195 residue Substrate becomes linked in a covalent bond at one or more points in the pathway 0 Ping pong mechanism Serine proteases employ acidbase catalysis as well as covalent catalysis Catalytic triad Ser195 His57 Asp102 O Asp102 works only to orient His57 O His57 acts as a general acidbase depending on the protonation state of His I Side chain pKa 67 so at physiological pH both the acid and base forms are present 0 Ser195 forms a covalent bond with peptide to be cleaved 0 Each catalytic residue is changed and then restored to initial state I Asp102 1 Ser195 His57 Neutral 0 Acylenzyme intermediate pNitrophenylacetate ester instead of amide used as evidence of intermediate 0 Can monitor products pNitrophenolate and acetate 0 Fast step Burst phase 0 Slow step All enzymes are acetylated waiting for water to release them 0 Involves two tetrahedral oxyanion transition states that are stabilized by amide groups 0 oxyanion hole conformation in which Ser195 and G1y193 NH bonds are stabilizing O 0 The preferential binding of TS over ES complex is responsible for much of the catalytic efficiency of serine proteases Aspartic Proteases 0 EX Pepsin HIV1 protease 0 2 Asp residues at the active site work in acidbase catalysis 0 LBHBs between Asp residues


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