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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 DON’T WISH TO ANSWER. 41) Draw a diagram of a three-stranded, antiparallel β 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 β sheet.
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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 γ 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 (I’d 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 (I’d 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 doesn’t 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. 6. Chymotrypsin cleaves its peptide substrate, a protein kinase doesn’t
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