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How to Read Reaction Mechanisms-A Refresher

Chemical reaction mechanisms, which trace the formation and breakage of covalent bonds, are communicated with dots and curved arrows, a convention known informally as "electron pushing." A covalent bond consists of a shared pair of electrons. Nonbonded electrons important to the reactionmechanism are designated by dots ( OH). Curved arrows ( —)■ ) represent the movement of electron pairs. For movement of a single electron (as in a free radical reaction), a single-headed (fishhook-type) arrow is used ( —( ). Most reaction steps involve an unshared electron pair (as in the chymotrypsin mechanism).

Some atoms are more electronegative than others; that is, they more strongly attract electrons. The relative electronegativities of atoms encountered in this text are F > O > N > C « S > P « H. For example, the two electron pairs making up a C = O (carbonyl) bond are not shared equally; the carbon is relatively electron-deficient as the oxygen draws away the electrons. Many reactions involve an electron-rich atom (a nucleophile) reacting with an electron-deficient atom (an electrophile). Some common nucleophiles and electrophiles in biochemistry are shown at right.

In general, a reaction mechanism is initiated at an unshared electron pair of a nucleophile. In mechanism diagrams, the base of the electron-pushing arrow originates near the electron-pair dots, and the head of the arrow points directly at the electro-philic center being attacked. Where the unshared electron pair confers a formal negative charge on the nucleophile, the negative charge symbol itself can represent the unshared electron pair, and serves as the base of the arrow. In the chymotrypsin mechanism, the nucleophilic electron pair in the ES complex between steps 0 and (2) is provided by the oxygen of the Ser195 hydroxyl group. This electron pair (2 of the 8 valence electrons of the hydroxyl oxygen) provides the base of the curved arrow. The electrophilic center under attack is the carbonyl carbon of the peptide bond to be cleaved. The C, O, and N atoms have a maximum of 8 valence electrons, and H has a maximum of 2. These atoms are occasionally found in unstable states with less than their maximum allotment of electrons, but C, O, and N cannot have more than 8. Thus, when the electron pair from chymo-trypsin's Ser195 attacks the substrate's carbonyl carbon, an electron pair is displaced from the carbon valence shell (you cannot have 5 bonds to carbon!). These electrons move toward the more electronegative carbonyl oxygen. The oxygen has 8 valence electrons both before and after this chemical process, but the number shared with the carbon is reduced from 4 to 2, and the carbonyl oxygen acquires a negative charge. In the next step, the electron pair conferring the negative charge on the oxygen moves back to re-form a bond with carbon and reestablish the carbonyl linkage. Again, an electron pair must be displaced from the carbon, and this time it is the electron pair shared with the amino group of the peptide linkage. This breaks the peptide bond. The remaining steps follow a similar pattern.

Substrate (a polypeptide)

AA»—C—CH—NH— C—CH— NH—AA» » II I , II OR1 O

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