Introduction to Enzyme and Coenzyme Chemistry - E-Library Home

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Enzymes are Wonderful Catalysts 33 be illustrated by intramolecular reactions in organic chemistry, which is where we shall begin the discussion. 3.3 Proximity effects There are many examples of organic reactions that are intramolecular: that is, they involve two or more functional groups within the same molecule, rather than functional groups in diVerent molecules. Intramolecular reactions generally proceed much more rapidly and under much milder reaction conditions than their intermolecular counterparts, which makes sense since the two reacting groups are already ‘in close proximity’ to one another. But how can can we explain these eVects A useful concept in quantitating proximity eVects is that of eVective concentration. In order to deWne the eVective concentration of a participating group (nucleophile, base, etc.), we compare the rate of the intramolecular reaction with the rate of the corresponding intermolecular reaction where the reagent and the participating group are present in separate molecules. The eVective concentration of the participating group is deWned as the concentration of reagent present in the intermolecular reaction required to give the same rate as the intramolecular reaction. I will illustrate this using data for the rates of hydrolysis of a series of phenyl esters in aqueous solution at pH 7, given in Figure 3.5. The reference reaction in this case is the hydrolysis of phenyl acetate catalysed by sodium acetate at the same pH. Introduction of a carboxylate group into the same molecule as the ester leads to an enhancement of the rate of ester hydrolysis, which for phenyl succinate (see Figure 3.5 (3) ) is 23 000-fold faster than phenyl acetate (see Figure 3.5 (1) ). This remarkable rate acceleration is because the neighbouring carboxylate group can attack the ester to form a cyclic anhydride intermediate, shown in Figure 3.6. This intermediate is more reactive than the original ester group and so hydrolyses rapidly. Note that the rate acceleration is largest when a Wve-membered anhydride is formed, since Wve-membered ring formation is kinetically favoured over six-membered ring formation, which in turn is greatly favoured over three-, four- and seven-membered ring formation. The eVective concentration can be worked out by comparing the rates of these intramolecular reactions with the rates of the intermolecular reaction between phenyl acetate and sodium acetate in water. For phenyl succinate an eVective concentration of 4 000 m is found, so the hydrolysis of phenyl succinate proceeds much faster than if phenyl acetate was surrounded completely by acetate ions! Here we start to see the catalytic potential of proximity eVects. In the same series of phenyl esters, if the possible ring size of Wve is maintained, but a cis- double bond is placed in between the reacting groups,
34 Chapter 3 Ester k rel Effective concentration (mol l −1 ) Reference Reaction O (1) (2) − O 2 C OPh O OPh O 1 50 9 O OPh NaOAc H 2 O O O − + PhO − (3) − O 2 C OPh 23,000 4,000 (4) − O 2 C O OPh 150 25 O (5) OPh CO 2 − 1,100,000 2 10 5 O (6) OPh CO 2 − 5 10 10 10 10 O (7) − O 2 C OPh 1 − (8) (9) Me 2 N Me 2 N O O OPh OPh 1,000,000 2,500,000 490 1,300 O OPh Et 3 N H 2 O O O − + PhO − Figure 3.5 Intramolecular catalysis of ester hydrolysis. Et 3 N, triethylamine; NaOAc, sodium acetate. O O O OPh intramolecular nucleophilic attack O OPh O O O O O FAST reactive anhydride intermediate Figure 3.6 Mechanism for intramolecular hydrolysis of phenyl succinate (3). H 2 O O O O O
Page 1 and 2: Introduction to Enzyme and Coenzyme
Page 4 and 5: Introduction to Enzyme and Coenzyme
Page 6 and 7: Contents Preface Representation of
Page 8: Contents vii 8 Enzymatic Addition/E
Page 11 and 12: Representation of Protein Three-Dim
Page 13 and 14: 2 Chapter 1 H 2 N O NH 2 + H 2 O Ja
Page 15 and 16: 4 Chapter 1 Table 1.1 The vitamins.
Page 17 and 18: 6 Chapter 1 has very diVerent biolo
Page 19 and 20: 2 All Enzymes are Proteins 2.1 Intr
Page 21 and 22: 10 Chapter 2 (Gln). There are three
Page 23 and 24: 12 Chapter 2 AAA Lys ACA Thr AGA Ar
Page 25 and 26: 14 Chapter 2 H N O H N O Figure 2.8
Page 27 and 28: 16 Chapter 2 (a) (b) Figure 2.12 St
Page 29 and 30: 18 Chapter 2 Figure 2.14 Structure
Page 31 and 32: 20 Chapter 2 (a) X Y Enzyme + Subst
Page 33 and 34: 22 Chapter 2 maintaining protein te
Page 35 and 36: 24 Chapter 2 surface glycoprotein g
Page 37 and 38: 26 Chapter 2 O-linked glycosylation
Page 39 and 40: 28 Chapter 2 Metalloproteins I. Ber
Page 41 and 42: 30 Chapter 3 O N H R CO 2 H acylase
Page 43: 32 Chapter 3 (a) Free energy uncata
Page 47 and 48: 36 Chapter 3 3.4 The importance of
Page 49 and 50: 38 Chapter 3 pKa Tyrosine CH 2 O H
Page 51 and 52: 40 Chapter 3 glycoside hydrolysis (
Page 53 and 54: 42 Chapter 3 O O Glu 143 O − R H
Page 55 and 56: 44 Chapter 3 the hydroxyl groups of
Page 57 and 58: 46 Chapter 3 E + S E + S ES' ES ‘
Page 59 and 60: 48 Chapter 3 Examination of protein
Page 61 and 62: 50 Chapter 3 (Note: Similar results
Page 63 and 64: 52 Chapter 4 (1) Direct UV (2) Radi
Page 65 and 66: 54 Chapter 4 Figure 4.3 PuriWcation
Page 67 and 68: 56 Chapter 4 The two kinetic consta
Page 69 and 70: 58 Chapter 4 Lineweaver−Burk Plot
Page 71 and 72: 60 Chapter 4 E + S K i EI+ I ES E +
Page 73 and 74: 62 Chapter 4 (2) by treatment with
Page 75 and 76: 64 Chapter 4 In general the stereoc
Page 77 and 78: H D T CO 2 H CO − 2 T HO D H −
Page 79 and 80: 68 Chapter 4 4.5 The existence of i
Page 81 and 82: 70 Chapter 4 18O 18O 18 O O P O −
Page 83 and 84: 72 Chapter 4 If a reaction involves
Page 85 and 86: 74 Chapter 4 O D H ketosteroid isom
Page 87 and 88: 76 Chapter 4 Table 4.3 Group speciW
Page 89 and 90: 78 Chapter 4 [S] (mM) Rate of produ
Page 91 and 92: 80 Chapter 4 Enzyme kinetics I.H. S
Page 93 and 94: 82 Chapter 5 O = C NHR peptidase H
Page 95 and 96:
84 Chapter 5 non-speciWc protease c
Page 97 and 98:
86 Chapter 5 His 57 His 57 Asp 102
Page 99 and 100:
88 Chapter 5 Other serine proteases
Page 101 and 102:
90 Chapter 5 Figure 5.8 Structure o
Page 103 and 104:
92 Chapter 5 now predominate Perhap
Page 105 and 106:
OH R O Zn 2+ O O O Ph Glu 270 H 2 N
Page 107 and 108:
96 Chapter 5 CASE STUDY: HIV-1 prot
Page 109 and 110:
98 Chapter 5 HO Transition state pe
Page 111 and 112:
100 Chapter 5 The aminoacyl group o
Page 113 and 114:
102 Chapter 5 5.5 Enzymatic phospho
Page 115 and 116:
104 Chapter 5 Figure 5.29 Structure
Page 117 and 118:
Page 119 and 120:
108 Chapter 5 Adenosine 5 0 -tripho
Page 121 and 122:
110 Chapter 5 functional group. Gly
Page 123 and 124:
112 Chapter 5 CH 2 OH O RO HO OH O
Page 125 and 126:
114 Chapter 5 to these atoms that t
Page 127 and 128:
116 Chapter 5 Problems (1) Using pa
Page 129 and 130:
118 Chapter 5 (6) Retaining glycosi
Page 131 and 132:
120 Chapter 5 J.R. Knowles (1980) E
Page 133 and 134:
122 Chapter 6 +1.0 Redox potential
Page 135 and 136:
Table 6.1 Classes of redox enzymes.
Page 137 and 138:
126 Chapter 6 An important point is
Page 139 and 140:
128 Chapter 6 O H − OH − O OH H
Page 141 and 142:
130 Chapter 6 one-electron transfer
Page 143 and 144:
132 Chapter 6 (a) R N H + N O R N H
Page 145 and 146:
134 Chapter 6 Inactivation by trany
Page 147 and 148:
Page 149 and 150:
138 Chapter 6 (a) (b) Figure 6.23 S
Page 151 and 152:
140 Chapter 6 glutathione called tr
Page 153 and 154:
142 Chapter 6 neither has a stable
Page 155 and 156:
144 Chapter 6 of the haem cofactor
Page 157 and 158:
146 Chapter 6 Figure 6.33 Active si
Page 159 and 160:
148 Chapter 6 HO H N N O O H N prol
Page 161 and 162:
150 Chapter 6 R R R O 2 , Fe 2+ O O
Page 163 and 164:
152 Chapter 6 CoA. Explain these re
Page 165 and 166:
154 Chapter 6 NADH models O. Almars
Page 167 and 168:
7 Enzymatic Carbon-Carbon Bond Form
Page 169 and 170:
158 Chapter 7 O H − OH O − O H
Page 171 and 172:
Page 173 and 174:
162 Chapter 7 Figure 7.6 Active sit
Page 175 and 176:
164 Chapter 7 7.3 Claisen enzymes I
Page 177 and 178:
166 Chapter 7 CoAS O EnzB − H D T
Page 179 and 180:
168 Chapter 7 onto the acetyl-thioe
Page 181 and 182:
170 Chapter 7 In the case of erythr
Page 183 and 184:
172 Chapter 7 O HO O − O ATP ADP
Page 185 and 186:
174 Chapter 7 CO 2 − vitamin K-de
Page 187 and 188:
176 Chapter 7 7.8 Thiamine pyrophos
Page 189 and 190:
178 Chapter 7 HN N + N H NH S O OPP
Page 191 and 192:
180 Chapter 7 O OH OH camphor geran
Page 193 and 194:
182 Chapter 7 CH 3 * OPP (−)pinen
Page 195 and 196:
Page 197 and 198:
186 Chapter 7 C C C C C O OCH 3 C H
Page 199 and 200:
188 Chapter 7 AcO HO HO NHAc O OH +
Page 201 and 202:
190 Chapter 7 (9) Usnic acid is a n
Page 203 and 204:
192 Chapter 7 Radical couplings W.M
Page 205 and 206:
194 Chapter 8 C-O cleavage H E1 H C
Page 207 and 208:
196 Chapter 8 leads to the formatio
Page 209 and 210:
198 Chapter 8 aconitase citrate cis
Page 211 and 212:
200 Chapter 8 *H R H H CO 2 − NH
Page 213 and 214:
202 Chapter 8 EnzB − 2 H − O 2
Page 215 and 216:
204 Chapter 8 involves no change in
Page 217 and 218:
206 Chapter 8 Glyphosate H H N CO
Page 219 and 220:
208 Chapter 8 (5) Chorismic acid (s
Page 221 and 222:
9 Enzymatic Transformations of Amin
Page 223 and 224:
CO − − 2 CO 2 H H CO 2 − N +
Page 225 and 226:
214 Chapter 9 - BEnz CO − 2 Cl H
Page 227 and 228:
216 Chapter 9 Arg 292 Arg 292 Lys 2
Page 229 and 230:
218 Chapter 9 Arg 292 Asp 292 HN H
Page 231 and 232:
220 Chapter 9 S − B 1 Enz H − C
Page 233 and 234:
222 Chapter 9 9.6 N-Pyruvoyl-depend
Page 235 and 236:
224 Chapter 9 The biosyntheses of n
Page 237 and 238:
226 Chapter 9 Further reading Gener
Page 239 and 240:
228 Chapter 10 B 1 - H + NH 3 CO
Page 241 and 242:
230 Chapter 10 ‘low-barrier’ +
Page 243 and 244:
232 Chapter 10 H S C 6 H 13 HN His
Page 245 and 246:
234 Chapter 10 O H NH 3 CO 2 − CO
Page 247 and 248:
236 Chapter 10 sub-units. Each sub-
Page 249 and 250:
238 Chapter 10 Further reading Gene
Page 251 and 252:
11 Radicals in Enzyme Catalysis 11.
Page 253 and 254:
242 Chapter 11 CH 2 Co III Ad H OH
Page 255 and 256:
244 Chapter 11 − O 2 C − O CO
Page 257 and 258:
246 Chapter 11 H N H O 734 H N H PF
Page 259 and 260:
248 Chapter 11 H H* + H + H 3 N CO
Page 261 and 262:
250 Chapter 11 O HN NH + H 3 N H 3
Page 263 and 264:
252 Chapter 11 cofactor is involved
Page 265 and 266:
254 Chapter 11 Protein Radicals J.
Page 267 and 268:
256 Chapter 12 self-splicing reacti
Page 269 and 270:
258 Chapter 12 Figure 12.2 Structur
Page 271 and 272:
260 Chapter 12 antigen combining si
Page 273 and 274:
262 Chapter 12 R O OR' OH − R O
Page 275 and 276:
264 Chapter 12 CO 2 − − O 2 C O
Page 277 and 278:
266 Chapter 12 (1) Selective substr
Page 279 and 280:
268 Chapter 12 HO O HO OH HO OH O O
Page 281 and 282:
270 Chapter 12 Problems (1) How rev
Page 283 and 284:
Appendix 1: Cahn-Ingold-Prelog Rule
Page 285 and 286:
Appendix 2: Amino Acid Abbreviation
Page 287 and 288:
276 Appendix 3 Preparation of orang
Page 289 and 290:
278 Appendix 4 (2) Intramolecular a
Page 291 and 292:
280 Appendix 4 from water at a-posi
Page 293 and 294:
282 Appendix 4 Chapter 8 (1) Treat
Page 295 and 296:
284 Appendix 4 (b) Formation of rad
Page 297 and 298:
286 Index b-hydroxydecanoyl thioest
Page 299 and 300:
288 Index glycosylation 26-7 glysop
Page 301 and 302:
290 Index phenylalanine ammonia lya
Page 303:
292 Index transition states 31-2 an
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