Documents about Nucleophilic Attack

  • 4 Pages

    lec33

    Carnegie Mellon, LEC 03231

    Excerpt: ... Biochemistry I Fall Term, 2004 December 8, 2004 Lecture 33: Catabolism of Fatty Acids Assigned reading in Campbell: Chapter 18.1-18.5 Key Terms: Acyl-carnitine Acyl-CoA -oxidation Links: (I) Review Quiz on Lecture 33 concepts Formation of Acyl-CoA The fatty acids in the cytosol are coupled to Coenzyme A to form acyl-CoA. The activation reaction is catalyzed by acyl-CoA synthetase and involves the following steps (Fig. 18.4): 1. Nucleophilic attack of carboxyl group of fatty acid towards phosphate of ATP 2. Formation of an acyl-AMP intermediate with release of PPi. This reaction is slightly endergonic; however, it is driven by the subsequent hydrolysis of PPi. This is another example of: The hydrolysis of a high energy compound to make a reaction irreversible; and Irreversibility in the first step of a pathway. 3. Nucleophilic attack of the sulfur group of CoA on the carbonyl carbon of the fatty acylAMP intermediate. The resulting high energy thioester bond (G = -31.5 kJ/mol for hydrolysis) preserves the hig ...

  • 9 Pages

    Lecture 18a

    Cornell, BIOBM 3310

    Excerpt: ... LL PRECISELY ALIGNED. THIS PRECISE ALIGNMENT IS BUILT INTO THE ENZYME STRUCTURE. HIS57 ACTS AS BASE; SIMULTANEOUSLY, SER195-O MAKES NUCLEOPHILIC ATTACK ON CARBONYL C OF PEPTIDE BOND THIS STEP IS RATEDETERMINING FOR PEPTIDE HYDROLYSIS i.e. TRANSITION STATE IS HERE! ES OXYANION "HOLE": 1. GOOD STERIC FIT TO O , BUT ONLY IN ITS Asp 194 TETRAHEDRAL ORIENTATION 2. H-BONDS FORM TO PEPTIDE N-H OF GLY193 195 O ATTACK AND SER NOT THE TS, BUT NOT SO STABLE ES' CHYMOTRYPSIN MECHANISM NOW HIS57 ACTS AS AN ACID ELECTRON DENSITY FLOWS OUT OF THE C N PEPTIDE BOND H THE FIRST PRODUCT, A PEPTIDE FRAGMENT, LEAVES THE ENZYME AND DIFFUSES AWAY H ES' NOW INTEMEDIATE IS BOUND WITH SOME STABILITY TO CHYMOTRYPSIN THIS COVALENT INTERMEDIATE HAS BEEN CLEARLY IDENTIFIED: TRAPPED IN CRYSTALS OF CHYMOTRYPSIN AT -55oC, REVEALED BY XRAY DIFFRACTION ES' CHYMOTRYPSIN MECHANISM WATER BINDS IN THE ACTIVE SITE WATER REPLACES FIRST PEPTIDE FRAGMENT IN ACTIVE SITE NOT BULK WATER! A SINGLE H2O, BOU ...

  • 3 Pages

    Lecture 18

    Cornell, BIOBM 3310

    Excerpt: ... are donated/accepted, or an electron pair donated/accepted, but is in contrast to "specific" acid or base catalysis, in which the catalyst is the H+ ion or the OH- ion). The positive charge on this His+ is stabilized by Asp-102. [Note the catalytic triad of His, Ser, Asp] Simultaneous with the transfer of the proton to the His, the Ser-O: makes a nucleophilic attack on the carbonyl C of the peptide bond. This nucleophilic attack leads to the intermediate ES' shown after step 2. This ES' tetrahedral intermediate is not the transition state, but the TS is "something like" ES'. In fact, the actual TS for this overall rxn is indeed believed to occur just prior to formation of ES', and the actual TS is believed to have many of the properties of this tetrahedral intermediate. This tetrahedral intermediate ES' fits into a pocket in the enzyme that fits the oxygen anion only when it is tetrahedral to the peptide carbonyl C. This is the enzymes "oxyanion hole." It makes both a steric and a chemical fit between t ...

  • 3 Pages

    SI05A

    Carnegie Mellon, PSETF 03231

    Excerpt: ... 03-231 Biochemistry SI Thursday, October 13, 2005 Andy Hsieh AMDyMoN@cmu.edu Thursdays 7:30 8:30 PM, OSC 231A Marciella DeGrace mdegrace@andrew.cmu.edu Wednesdays 7 - 8 PM, WeH 5403 Academic Development Office: OSC 212 (412) 268 - 6878 http:/www.cmu.edu/academic-development/ Call, stop by, or check out our website! Services Available: Supplemental Instruction Individual/Walk-In Tutoring Academic Counseling Study Tip Nucleophilic Attack ! (Theme: complementarity) Nucleophile = nucleus loving. Therefore, a nucleophile must be at least partially _ (+ or -) charged, because the nucleus of an atom is _ (+ or -). The atom that the nucleophile attacks (a.k.a electrophile electron loving) is at least partially _ (+ or -) because electrons are _ (+ or -). Define a nucleophile: _ List some functional groups that have the potential to be nucleophiles: List some functional groups that have the potential to be electrophiles: Identify and circle the ...

  • 4 Pages

    Lecture 19

    Cornell, BIOBM 3310

    Excerpt: ... xt intermediate. p. 132 For the family of enzymes known as the Serine proteases, here is the overall reaction equation for the catalyzed reaction: E +S ES ES' ES' P1 ES' EP2E + P2 The rate of enhancement over the uncatalyzed hydrolysis of peptide is about 10 10. What if we mutate either Ser195 or His57? You might imagine that catalysis would be completely ruined. Indeed, the rate enhancement drops to about 10 5. This is a big drop of about 100,000-fold, but there is still impressive catalytic power left! Catalytic power still comes from the binding, hence stabilization, of the tetrahedral transition state. A summary of some key catalytic features of chymotrypsin: Ser195 -O: binds to the peptide carbonyl C ( nucleophilic attack ) Peptide NH of Ser195 and Gly193 H-bond to the O- of the tetrahedral transition state (and tetrahedral intermediates) Enzyme shape fits the tetrahedral intermediate, thereby especially lowering TS free energy. In other words, the enzyme is specialized to fit the TS especi ...

  • 5 Pages

    lec26

    Carnegie Mellon, LEC 03231

    Excerpt: ... ed mechanism of trypsin cleavage: View the chemical structures in the two animations linked above. (Note: Campbell, Fig. 6.13, omits Asp 102 in this mechanism; the hydrogen on the unprotonated His 57 should be on the other nitrogen.) 1. Substrate binds. 2. Nucleophilic attack of the side chain oxygen of Ser 195 on the carbonyl carbon of the scissile bond forming a tetrahedral intermediate. Assist from His 57 (proton transfer from Ser 195). 2 3. Cleavage of the peptide bond with assistance from His 57 (proton transfer to the new amino terminus). 4. Release of the first product. 5. Nucleophilic attack of water on the acyl-enzyme intermediate with assistance of His 57 and formation of the tetrahedral intermediate. 6. Decomposition of acyl intermediate and release of the second product. Nucleophile: group that is electron rich and can form bonds with electron deficient groups. In this case the electronegativity of the oxygen makes the carbonyl carbon electron deficient. Electrophile: group that is electron poor ...

  • 5 Pages

    lec26

    Carnegie Mellon, LEC 03231

    Excerpt: ... echanism of trypsin cleavage: View the chemical structures in the two animations linked above. (Note: Campbell, Fig. 6.13, omits Asp 102 in this mechanism; the hydrogen on the unprotonated His 57 should be on the other nitrogen.) 1. Substrate binds. 2. Nucleophilic attack of the side chain oxygen of Ser 195 on the carbonyl carbon of the scissile bond forming a tetrahedral intermediate. Assist from His 57 (proton transfer from Ser 195). 2 3. Cleavage of the peptide bond with assistance from His 57 (proton transfer to the new amino terminus). 4. Release of the first product. 5. Nucleophilic attack of water on the acyl-enzyme intermediate with assistance of His 57 and formation of the tetrahedral intermediate. 6. Decomposition of acyl intermediate and release of the second product. Nucleophile: group that is electron rich and can form bonds with electron deficient groups. In this case the electronegativity of the oxygen makes the carbonyl carbon electron deficient. Electrophile: group that is electron poor and ...

  • 19 Pages

    lec13

    Arizona, BIOC 460

    Excerpt: ... onverted into an alkoxide ion, a powerful nucleophile, through removal of its hydroxyl proton. This difficult task is accomplished by the charge relay system between Asp 102, His 57, and Ser 195, which comprise the catalytic triad. His 57 can alternately accept or donate protons, while stabilized by Asp 102. (This is a good example of a general base in catalysis.) The charges are stabilized by electrostatic effects. Nucleophilic Attack The carbonyl carbon on the substrate has 3 bonds and so is a trigonal atom. The alkoxide ion attacks the carbonyl carbon, forming a tetrahedral intermediate with 4 bond to that carbon. The former carbonyl oxygen is converted into a negatively charged group, the oxyanion, which is stabilized by by an arrangement of partial positive charges nearby in the oxyanion hole. (an electrostatic effect) Formation of Acyl-enzyme The tetrahedral intermediate breaks down when the histidine donates a proton and creates a new amino group on the terminus of the first product ( PC ), which ...

  • 3 Pages

    Lec16

    Carnegie Mellon, LECF 03231

    Excerpt: ... Biochemistry I, Fall Term Lecture 16: Enzyme Mechanism: Serine Proteases Assigned reading in Lehninger: Chapter 6.4 to pg 218 Key Terms: Substrate specificity Covalent Catalysis Acyl-enzyme intermediate Nucleophile Electrophile Preferential binding of transition state complex Catalytic triad (Ser, His, Asp) Oct 6, 2006 1. Rate enhancement by enzymes small changes in G translate into large rate enhancements 2. Serine proteases: shared mechanisms but divergent substrate specificities. How is specificity determined? 3. Catalytic mechanism: Strategies utilized by serine proteases a. Nucleophilic attack b. Acid/Base chemistry c. Covalent bond formation between enzyme and substrate formation of an acyl enzyme intermediate 4. What are the steps? First half of cycle: i) Substrate binds ii) Deprotonation of Ser 195 by His 57 (with assistance from Asp 102) to generate a potent nucleophile. iii) Nucleophilic attack by Ser 195 on carbonyl carbon of peptide bond to be cleaved; te ...

  • 3 Pages

    Lec16

    Carnegie Mellon, LEC 03231

    Excerpt: ... Biochemistry I, Fall Term Lecture 16: Enzyme Mechanism: Serine Proteases Assigned reading in Lehninger: Chapter 6.4 to pg 218 Key Terms: Transition state theory and rate enhancement Substrate specificity Covalent Catalysis Acyl-enzyme intermediate Nucleophile Electrophile Catalytic triad (Ser, His, Asp) Oct 5, 2007 1. Rate enhancement by enzymes small changes in G translate into large rate enhancements 2. Serine proteases: shared mechanisms but divergent substrate specificities. How is specificity determined? 3. Catalytic mechanism: Strategies utilized by serine proteases a. Nucleophilic attack b. Acid/Base chemistry c. Covalent bond formation between enzyme and substrate formation of an acyl enzyme intermediate 4. What are the steps? First half of cycle: i) Substrate binds ii) Deprotonation of Ser 195 by His 57 (with assistance from Asp 102) to generate a potent nucleophile. iii) Nucleophilic attack by Ser 195 on carbonyl carbon of peptide bond to be cleaved; tetrah ...

  • 26 Pages

    4 proteases

    Utah, BIOLOGY 3515

    Excerpt: ... Introduction to proteases Biology 3515 / Chemistry 3515 Biological Chemistry Lab 1/5/2009 Jean M. Bower, PhD Adapted from slides David P. Goldenberg Stability of the peptide bond Resonance structures give peptide bonds partial double-bond character Reduces susceptibility of carbonyl carbon atom to nucleophilic attack Half-life for hydrolysis of a typical peptide at neutral pH is ~10 - 1000 years Berg, Tymoczko, & Stryer 2002 Proteases catalyze hydrolysis of peptide bonds Some biological functions of proteases Maturation of viral proteins (HIV, other retroviruses) Digestion of food Non-selective Catalyzed by trypsin, chymotrypsin, pepsin, etc. Intracellular protein degradation Highly selective and regulated Often catalyzed by large protein complexes, e.g. the proteasome Regulation of biological activity by proteolytic activation Angiotensin converting enzyme (blood pressure regulation) Blood clotting and clot disruption Complement fixation (an immune response) Apoptosi ...