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Unformatted text preview: BIBC 100 FINAL EXAM WINTER 2008 BIBC 100 FINAL EXAM WINTER 2008 SECTION I CHOOSE ANY 4 OUT OF THE NEXT 5 QUESTIONS TO ANSWER. 5 points each. WRITE OMIT in LARGE LETTERS ON THE PAGE YOU DONT WISH TO ANSWER. 41) Draw a diagram of a three-stranded, antiparallel sheet. Show the exact placement of main chain atoms. Be sure to indicate the pattern of hydrogen-bonding, and indicate where the R groups are situated relative to the main chain. Lehninger Fig. 4-7 R groups alternate above/below the plane of the sheet. 42) What are three similarities between the catalytic activity of chymotrypsin and protein kinases? What are two differences? (It is fine to list Similarities: 1 2.. 3 Differences: 1..2...) NOT ALL POSSIBLE ANSWERS ARE SHOWN BELOW Similarities: 1. both show a preference for certain substrates and not others, through interaction with specific regions of the enzyme (i.e. chymotrypsin specificity pocket, kinase binding on activation loop platform) 2. both use a nucleophilic attack from a hydroxyl group on to a substrate that will be cleaved by the attack (chymotrypsin Ser195, kinase attack from positioned substrate to phosphate of ATP) 3. both must become activated before their catalytic activity functions (chymotrypsin is cleaved into an active form, a protein kinase is activated through phosphorylation or other methods as described in the review article) 4. both use sets of residues to stabilize one another and assist catalysis (chymotrypsin Asp102 and His57, PKA Glu91 and Lys72) 5. both catalyze a reaction involving two different substrates, as opposed to catalyzing intramolecular rearrangements (Id be surprised if anyone says this; chymotrypsin H 2 0 and peptide, in two linked stages, kinase ATP and S/T/Y containing peptide) 6. both catalyze a reaction that uses a polypeptide chain as a substrate 7. both abstract a proton from a hydroxyl group with a catalytic base residue (Id be surprised if anyone says this). Differences: 1. in chymotrypsin, the nucleophilic attacking group comes from Ser195, and later, water; in a protein kinase, the nucleophilic attacking group comes from the hydroxyl that is phosphorylated 2. substrates are different 3. chymotrypsin is transiently covalently bonded to a reaction intermediate, a protein kinase doesnt become covalently linked to a reaction intermediate 4. (similar to 3 above) the chymotrypsin mechanism proceeds in two main stages, while a protein kinase phosphorylates a residue in one reaction step 5. Once activated (by cleavage), the catalytic activity of chymotrypsin is permanently turned on. A protein kinases catalytic activity may be turned on or off through methods described in the book and in the review article. ...
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